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Sample records for monopyrrolide map complexes

  1. On Complex Maps with Delay Memory

    NASA Astrophysics Data System (ADS)

    Alonso-Sanz, Ramón

    2015-06-01

    An exploratory study is made on the dynamics of complex maps endowed with delay type memory of past states. Particular attention is paid to the quadratic map. Other maps, i.e. the cubic map, the map induced by the Newton-Raphson numerical method, and the purely real logistic map are also scrutinized.

  2. Physical mapping of complex genomes

    DOEpatents

    Evans, Glen A.

    1993-01-01

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

  3. Physical mapping of complex genomes

    DOEpatents

    Evans, G.A.

    1993-06-15

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

  4. Grammatical complexity for two-dimensional maps

    NASA Astrophysics Data System (ADS)

    Hagiwara, Ryouichi; Shudo, Akira

    2004-11-01

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

  5. Structural investigations into microtubule-MAP complexes.

    PubMed

    Hoenger, Andreas; Gross, Heinz

    2008-01-01

    Microtubules interact with a large variety of factors commonly referred to as either molecular motors (kinesins, dyneins) or structural microtubule-associated proteins (MAPs). MAPs do not exhibit motor activity, but regulate microtubule dynamics and their interactions with molecular motors, and organelles such as kinetochores or centrosomes. Structural investigations into microtubule-kinesin motor complexes are quite advanced today and by helical three-dimensional (3-D) analysis reveal a resolution of the motor-tubulin interface at <1.0 nm. However, due to their flexible structure MAPs like tau or MAP2C cannot be visualized in the same straightforward manner. Helical averaging usually reveals only the location of strong binding sites while the overall structure of the MAP remains unsolved. Other MAPs such as EB1 bind very selectively only to some parts of the microtubule lattice such as the lattice seam. Thus, they do not reveal a stoichiometric tubulin:MAP-binding ratio that would allow for a quantitative helical 3-D analysis. Therefore, to get a better view on the structure of microtubule-MAP complexes we often used a strategy that combined cryo-electron microscopy and helical or tomographic 3-D analysis with freeze-drying and high-resolution unidirectional surface shadowing. 3-D analysis of ice-embedded specimens reveals their full 3-D volume. This relies either on a repetitive structure following a helical symmetry that can be used for averaging or suffers from the limited resolution that is currently achievable with cryotomography. Surface metal shadowing exclusively images surface-exposed features at very high contrast, adding highly valuable information to 2-D or 3-D data of vitrified structures.

  6. 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.

  7. Is Mapping of Complex Fractionated Electrograms Obsolete?

    PubMed Central

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

    2015-01-01

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

  8. 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

  9. Approaches to mapping genetically correlated complex traits

    PubMed Central

    George, Andrew W; Basu, Saonli; Li, Na; Rothstein, Joseph H; Sieberts, Solveig K; Stewart, William; Wijsman, Ellen M; Thompson, Elizabeth A

    2003-01-01

    Our Markov chain Monte Carlo (MCMC) methods were used in linkage analyses of the Framingham Heart Study data using all available pedigrees. Our goal was to detect and map loci associated with covariate-adjusted traits log triglyceride (lnTG) and high-density lipoprotein cholesterol (HDL) using multipoint LOD score analysis, Bayesian oligogenic linkage analysis and identity-by-descent (IBD) scoring methods. Each method used all marker data for all markers on a chromosome. Bayesian linkage analysis detected a linkage signal on chromosome 7 for lnTG and HDL, corroborating previously published results. However, these results were not replicated in a classical linkage analysis of the data or by using IBD scoring methods. We conclude that Bayesian linkage analysis provides a powerful paradigm for mapping trait loci but interpretation of the Bayesian linkage signals is subjective. In the absence of a LOD score method accommodating genetically complex traits and linkage heterogeneity, validation of these signals remains elusive. PMID:14975139

  10. 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.

  11. Mapping complex traits as a dynamic system.

    PubMed

    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. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. Mapping complex traits as a dynamic system

    PubMed Central

    Sun, Lidan; Wu, Rongling

    2017-01-01

    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. PMID:25772476

  13. 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.

  14. 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…

  15. 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…

  16. A fast algorithm for functional mapping of complex traits.

    PubMed Central

    Zhao, Wei; Wu, Rongling; Ma, Chang-Xing; Casella, George

    2004-01-01

    By integrating the underlying developmental mechanisms for the phenotypic formation of traits into a mapping framework, functional mapping has emerged as an important statistical approach for mapping complex traits. In this note, we explore the feasibility of using the simplex algorithm as an alternative to solve the mixture-based likelihood for functional mapping of complex traits. The results from the simplex algorithm are consistent with those from the traditional EM algorithm, but the simplex algorithm has considerably reduced computational times. Moreover, because of its nonderivative nature and easy implementation with current software, the simplex algorithm enjoys an advantage over the EM algorithm in the dynamic modeling and analysis of complex traits. PMID:15342547

  17. Mapping mechanical force propagation through biomolecular complexes

    SciTech Connect

    Schoeler, Constantin; Bernardi, Rafael C.; Malinowska, Klara H.; Durner, Ellis; Ott, Wolfgang; Bayer, Edward A.; Schulten, Klaus; Nash, Michael A.; Gaub, Hermann E.

    2015-08-11

    In this paper, we employ single-molecule force spectroscopy with an atomic force microscope (AFM) and steered molecular dynamics (SMD) simulations to reveal force propagation pathways through a mechanically ultrastable multidomain cellulosome protein complex. We demonstrate a new combination of network-based correlation analysis supported by AFM directional pulling experiments, which allowed us to visualize stiff paths through the protein complex along which force is transmitted. Finally, the results implicate specific force-propagation routes nonparallel to the pulling axis that are advantageous for achieving high dissociation forces.

  18. Nomenclature for physical mapping of complex genomes

    SciTech Connect

    Not Available

    1989-08-01

    Among these issues, that of establishing nomenclature conventions, was seen to be fundamental to the development of useful data management systems and essential for the orderly and efficient development of such systems. Therefore, the present workshop was convened, as the first in the recommended series, to identify the issues involved in establishing nomenclature standards and to develop a set of recommendations for such standards. This report summarizes the proceedings of the workshop and lays out specific proposals for naming DNA entities for physical mapping. The scientific community should discuss and develop these proposals so that naming conventions can be established. The proposals apply specifically to human DNA entities; however, the relevance to nomenclature in other systems should be part of the broader discussion. 13 refs.

  19. Quantifying the complexity of the delayed logistic map.

    PubMed

    Masoller, Cristina; Rosso, Osvaldo A

    2011-01-28

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

  20. A 'transient' automated mapping procedure for complex geometries

    NASA Technical Reports Server (NTRS)

    Raad, Peter E.; White, James W.

    1988-01-01

    A numerical procedure is presented which is applicable to the general curvilinear mappings of complex geometries and is unrestricted by slow convergence or strong dependence on the initial conditions of physical space. The scheme, employing a time-dependent factored-implicit scheme, is shown to be general and robust. In the illustrative applications presented, complex, closed geometries are routinely mapped even when they begin with unreasonable initial conditions created through the analytical and computer graphics inputs. Due to the natural damping introduced into the governing equations, fast convergence is achieved and high stability is observed.

  1. Composite linkage map and enhanced genome map for Culex pipiens complex mosquitoes.

    PubMed

    Hickner, Paul V; Mori, Akio; Chadee, Dave D; Severson, David W

    2013-01-01

    We report here the development of 65 novel microsatellite loci and construction of a composite genetic linkage map for Culex pipiens complex mosquitoes. Microsatellites were identified by in silico screening of the Culex quinquefasciatus genome assembly. Cross-species utility of 73 microsatellites for population studies in C. pipiens sensu stricto and C. quinquefasciatus was evaluated by genotyping a subset of samples collected in Indiana, United States, and Point Fortin, Trinidad. Allele frequencies of 67 microsatellites were within Hardy-Weinberg expectations in both population subsets. A composite linkage map was constructed based on restriction fragment length polymorphism and microsatellite polymorphisms in 12 independent F1 intercross mapping populations. The composite map consists of 61 marker loci totaling 183.9 cM distributed across the 3 linkage groups. These loci cover 29.5, 88.8, and 65.6 cM on chromosomes I-III, respectively, and allow for assignment of 10.4% of the genome assembly and 13.5% of the protein coding genes to chromosome position. Our results suggest that these microsatellites will be useful for mapping and population studies of 2 pervasive species in the C. pipiens complex. Moreover, the composite map presented here will serve as a basis for the construction of high-resolution genetic and physical maps, as well as detection of quantitative trait loci to aid in the investigation of complex genetic traits influencing phenotypes of interest.

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

    NASA Astrophysics Data System (ADS)

    Pagon, Dušan

    2008-11-01

    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.

  3. 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.

  4. 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

  5. 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

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

    PubMed

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

    2016-01-01

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

  7. 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

  8. 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.

  9. Mapping rare and common causal alleles for complex human diseases

    PubMed Central

    Raychaudhuri, Soumya

    2011-01-01

    Advances in genotyping and sequencing technologies have revolutionized the genetics of complex disease by locating rare and common variants that influence an individual’s risk for diseases, such as diabetes, cancers, and psychiatric disorders. However, to capitalize on this data for prevention and therapies requires the identification of causal alleles and a mechanistic understanding for how these variants contribute to the disease. After discussing the strategies currently used to map variants for complex diseases, this Primer explores how variants may be prioritized for follow-up functional studies and the challenges and approaches for assessing the contributions of rare and common variants to disease phenotypes. PMID:21962507

  10. 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.

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

    PubMed

    Kaneko, Kunihiko

    2015-09-01

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

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

    PubMed

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

    2015-11-03

    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 (H(2) = 0.61) and seedling greening in response to salt (H(2) = 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.

  13. Molecular mapping within the mouse albino-deletion complex.

    PubMed

    Johnson, D K; Hand, R E; Rinchik, E M

    1989-11-01

    Induced germ-line deletion mutations in the mouse provide a malleable experimental system for in-depth molecular and functional analysis of large segments of the mammalian genome. To obtain an initial bank of molecular probes for the region of mouse chromosome 7 associated with the albino-deletion complex, random anonymous DNA clones, derived from a library constructed from flow-sorted chromosomes, were screened on DNAs from Mus musculus-Mus spretus F1 hybrids carrying large, multilocus, lethal albino deletions. Clones falling within a given deletion interval can easily be recognized because hybridization bands that represent restriction fragment length polymorphisms specific for the mutant (deleted) chromosome inherited from the M. musculus parent will be absent. Among 72 informative clones used as probes, one, which defines the locus D7OR1, mapped within two deletions that are 6-11 centimorgans in length. Submapping of this anonymous clone across a panel of 27 smaller deletions localized D7OR1 distal to a chromosomal subregion important for survival of the preimplantation embryo, proximal to globin [beta-chain (Hbb)], and near the shaker-1 (sh-1) locus. The results of these deletion-mapping experiments were also confirmed by standard three-point linkage analysis. This strategy for selection and rapid mapping of anonymous DNA probes to chromosomal segments corresponding to germ-line deletion mutations should contribute to the generation of more detailed physical and functional maps of genomic regions associated with mutant developmental phenotypes.

  14. 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. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. 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.

  16. 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.

  17. Interval mapping of quantitative trait loci employing correlated trait complexes

    SciTech Connect

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

    1995-07-01

    An approach to increase the resolution power of interval mapping of quantitative trait (QT) loci is proposed, based on analysis of correlated trait complexes. For a given set of QTs, the broad sense heritablity attributed to a QT locus (QTL) (say, A/a) is an increasing function of the number of traits. Thus, for some traits x and y are correlated within the groups AA, Aa and aa due to nongenetic factors and segregation of genes from other chromosomes. A simple relationship connects H{sup 2} (both in single trait and two-trait analysis) with the expected LOD value, ELOD = -1/2Nlog(1-H{sup 2}). Thus, situations could exist that from the inequality H{sup 2}{sub xy}(A/a) {ge} H{sup 2}{sub x} (A/a) a higher resolution is provided by the two-trait analysis, in spite of the increased number of parameters. Employing LOD-score procedure to simulated backcross data, we showed that the resolution power of the QTL mapping model can be elevated if correlation between QTs is taken into account. The method allows us to test numerous biologically important hypotheses concerning manifold effects of genomic segments on the defined trait complex (means, variances and correlations). 33 refs., 2 figs., 5 tabs.

  18. Complexity analysis of pipeline mapping problems in distributed heterogeneous networks

    SciTech Connect

    Lin, Ying; Wu, Qishi; Zhu, Mengxia; Rao, Nageswara S

    2009-04-01

    Largescale scientific applications require using various system resources to execute complex computing pipelines in distributed networks to support collaborative research. System resources are typically shared in the Internet or over dedicated connections based on their location, availability, capability, and capacity. Optimizing the network performance of computing pipelines in such distributed environments is critical to the success of these applications. We consider two types of largescale distributed applications: (1) interactive applications where a single dataset is sequentially processed along a pipeline; and (2) streaming applications where a series of datasets continuously flow through a pipeline. The computing pipelines of these applications consist of a number of modules executed in a linear order in network environments with heterogeneous resources under different constraints. Our goal is to find an efficient mapping scheme that allocates the modules of a pipeline to network nodes for minimum endtoend delay or maximum frame rate. We formulate the pipeline mappings in distributed environments as optimization problems and categorize them into six classes with different optimization goals and mapping constraints: (1) Minimum Endtoend Delay with No Node Reuse (MEDNNR), (2) Minimum Endtoend Delay with Contiguous Node Reuse (MEDCNR), (3) Minimum Endtoend Delay with Arbitrary Node Reuse (MEDANR), (4) Maximum Frame Rate with No Node Reuse or Share (MFRNNRS), (5) Maximum Frame Rate with Contiguous Node Reuse and Share (MFRCNRS), and (6) Maximum Frame Rate with Arbitrary Node Reuse and Share (MFRANRS). Here, 'contiguous node reuse' means that multiple contiguous modules along the pipeline may run on the same node and 'arbitrary node reuse' imposes no restriction on node reuse. Note that in interactive applications, a node can be reused but its resource is not shared. We prove that MEDANR is polynomially solvable and the rest are NP-complete. MEDANR, where either

  19. 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

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

    ERIC Educational Resources Information Center

    Gold, John R.; Coaffee, Jon

    1998-01-01

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

  1. On the mapping associated with the complex representation of functions and processes.

    NASA Technical Reports Server (NTRS)

    Harger, R. O.

    1972-01-01

    The mapping between function spaces that is implied by the representation of a real 'bandpass' function by a complex 'low-pass' function is explicitly accepted. The discussion is extended to the representation of stationary random processes where the mapping is between spaces of random processes. This approach clarifies the nature of the complex representation, especially in the case of random processes and, in addition, derives the properties of the complex representation.-

  2. Complexity and properties of a multidimensional Cat-Hadamard map for pseudo random number generation

    NASA Astrophysics Data System (ADS)

    Kim Hue, Ta Thi; Hoang, Thang Manh

    2017-01-01

    This paper presents a novel method to extend the Cat map from 2-dimension to higher dimension using the fast pseudo Hadamard Transform, and the resulted maps are called Cat-Hadamard maps. The complexity and properties of Cat-Hadamard maps are investigated under the point of view for cryptographic applications. In addition, we propose a method for constructing a pseudo random number generator using a novel design concept of the high dimensional Cat map. The simulation results show that the proposed generator fulfilled all the statistic tests of the NIST SP 800-90 A.

  3. Complexity and properties of a multidimensional Cat-Hadamard map for pseudo random number generation

    NASA Astrophysics Data System (ADS)

    Kim Hue, Ta Thi; Hoang, Thang Manh

    2017-07-01

    This paper presents a novel method to extend the Cat map from 2-dimension to higher dimension using the fast pseudo Hadamard Transform, and the resulted maps are called Cat-Hadamard maps. The complexity and properties of Cat-Hadamard maps are investigated under the point of view for cryptographic applications. In addition, we propose a method for constructing a pseudo random number generator using a novel design concept of the high dimensional Cat map. The simulation results show that the proposed generator fulfilled all the statistic tests of the NIST SP 800-90 A.

  4. Systems mapping: how to improve the genetic mapping of complex traits through design principles of biological systems.

    PubMed

    Wu, Rongling; Cao, Jiguo; Huang, Zhongwen; Wang, Zhong; Gai, Junyi; Vallejos, Eduardo

    2011-05-27

    Every phenotypic trait can be viewed as a "system" in which a group of interconnected components function synergistically to yield a unified whole. Once a system's components and their interactions have been delineated according to biological principles, we can manipulate and engineer functionally relevant components to produce a desirable system phenotype. We describe a conceptual framework for mapping quantitative trait loci (QTLs) that control complex traits by treating trait formation as a dynamic system. This framework, called systems mapping, incorporates a system of differential equations that quantifies how alterations of different components lead to the global change of trait development and function through genes, and provides a quantitative and testable platform for assessing the interplay between gene action and development. We applied systems mapping to analyze biomass growth data in a mapping population of soybeans and identified specific loci that are responsible for the dynamics of biomass partitioning to leaves, stem, and roots. We show that systems mapping implemented by design principles of biological systems is quite versatile for deciphering the genetic machineries for size-shape, structural-functional, sink-source and pleiotropic relationships underlying plant physiology and development. Systems mapping should enable geneticists to shed light on the genetic complexity of any biological system in plants and other organisms and predict its physiological and pathological states.

  5. Maps of random walks on complex networks reveal community structure.

    PubMed

    Rosvall, Martin; Bergstrom, Carl T

    2008-01-29

    To comprehend the multipartite organization of large-scale biological and social systems, we introduce an information theoretic approach that reveals community structure in weighted and directed networks. We use the probability flow of random walks on a network as a proxy for information flows in the real system and decompose the network into modules by compressing a description of the probability flow. The result is a map that both simplifies and highlights the regularities in the structure and their relationships. We illustrate the method by making a map of scientific communication as captured in the citation patterns of >6,000 journals. We discover a multicentric organization with fields that vary dramatically in size and degree of integration into the network of science. Along the backbone of the network-including physics, chemistry, molecular biology, and medicine-information flows bidirectionally, but the map reveals a directional pattern of citation from the applied fields to the basic sciences.

  6. 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

  7. 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. © 2015 J. E. Dowd et al. CBE—Life Sciences Education © 2015 The American Society for Cell Biology. This article is distributed by The American Society for Cell Biology under license from the author(s). It is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0).

  8. 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. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  9. 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

  10. Pattern transitions and complexity for a nonlocal logistic map

    NASA Astrophysics Data System (ADS)

    Barbosa, Fernando V.; Penna, André A. L.; Ferreira, Rogelma M. S.; Novais, Keila L. V.; da Cunha, Jefferson A. R.; Oliveira, Fernando A.

    2017-05-01

    We examine the pattern solutions in a generalized nonlocal logistic map that includes spatial kernels in both growth and competition terms. We show that this map includes as a particular case the nonlocal Fisher-Kolmogorov equation, and we demonstrate the existence of three kinds of stationary nonlinear solutions: one uniform, one cosine type that we refer to as wavelike solution, and another in the form of Gaussian. We also obtain analytical expressions that describe the nonlinear pattern behavior in the system, and we establish the stability criterion. We define thermodynamics quantities such as entropy and the order parameter. Based on this, the pattern-no-pattern and pattern-pattern transitions are properly analyzed. We show that these pattern solutions may be related to the recently observed peak adding phenomenon in nonlinear optics.

  11. Battlespace Awareness: Heterogeneous Sensor Maps of Large Scale, Complex Environments

    DTIC Science & Technology

    2017-06-13

    intelligence, machine learning , mapping, autonomous vehicles, optimization 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF a. REPORT b. ABSTRACT c. THIS...regulariser creates reconstructions with median errors between 5.64 cm and 9.24 cm. Finally, we present a machine- learning pipeline that learns , in an...132 Contents xi 6 Towards (Deep) Learning Where Dense Reconstructions GoWrong133 6.1 System Pipeline

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

    PubMed

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

    2012-04-26

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

  13. 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…

  14. 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…

  15. Complex graph matrix representations and characterizations of proteomic maps and chemically induced changes to proteomes.

    PubMed

    Balasubramanian, Krishnan; Khokhani, Kanan; Basak, Subhash C

    2006-05-01

    We have presented a complex graph matrix representation to characterize proteomics maps obtained from 2D-gel electrophoresis. In this method, each bubble in a 2D-gel proteomics map is represented by a complex number with components which are charge and mass. Then, a graph with complex weights is constructed by connecting the vertices in the relative order of abundance. This yields adjacency matrices and distance matrices of the proteomics graph with complex weights. We have computed the spectra, eigenvectors, and other properties of complex graphs and the Euclidian/graph distance obtained from the complex graphs. The leading eigenvalues and eigenvectors and, likewise, the smallest eigenvalues and eigenvectors, and the entire graph spectral patterns of the complex matrices derived from them yield novel weighted biodescriptors that characterize proteomics maps with information of charge and masses of proteins. We have also applied these eigenvector and eigenvalue maps to contrast the normal cells and cells exposed to four peroxisome proliferators, namely, clofibrate, diethylhexyl phthalate (DEHP), perfluorodecanoic acid (PFDA), and perfluoroctanoic acid (PFOA). Our complex eigenspectra show that the proteomic response induced by DEHP differs from the corresponding responses of other three chemicals consistent with their chemical structures and properties.

  16. Complex multi-enhancer contacts captured by genome architecture mapping.

    PubMed

    Beagrie, Robert A; Scialdone, Antonio; Schueler, Markus; Kraemer, Dorothee C A; Chotalia, Mita; Xie, Sheila Q; Barbieri, Mariano; de Santiago, Inês; Lavitas, Liron-Mark; Branco, Miguel R; Fraser, James; Dostie, Josée; Game, Laurence; Dillon, Niall; Edwards, Paul A W; Nicodemi, Mario; Pombo, Ana

    2017-03-23

    The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. Here we report a genome-wide method, genome architecture mapping (GAM), for measuring chromatin contacts and other features of three-dimensional chromatin topology on the basis of sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify enrichment for specific interactions between active genes and enhancers across very large genomic distances using a mathematical model termed SLICE (statistical inference of co-segregation). GAM also reveals an abundance of three-way contacts across the genome, especially between regions that are highly transcribed or contain super-enhancers, providing a level of insight into genome architecture that, owing to the technical limitations of current technologies, has previously remained unattainable. Furthermore, GAM highlights a role for gene-expression-specific contacts in organizing the genome in mammalian nuclei.

  17. 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.

  18. 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

  19. Epigenetic map and genetic map basis of complex traits in cassava population

    PubMed Central

    Zou, Meiling; Lu, Cheng; Zhang, Shengkui; Chen, Qing; Sun, Xianglai; Ma, Pingan; Hu, Meizhen; Peng, Ming; Ma, Zilong; Chen, Xin; Zhou, Xincheng; Wang, Haiyan; Feng, Subin; Fang, Kaixin; Xie, Hairong; Li, Zaiyun; Liu, Kede; Qin, Qiongyao; Pei, Jinli; Wang, Shujuan; Pan, Kun; Hu, Wenbin; Feng, Binxiao; Fan, Dayong; Zhou, Bin; Wu, Chunling; Su, Ming; Xia, Zhiqiang; Li, Kaimian; Wang, Wenquan

    2017-01-01

    Cassava (Manihot esculenta Crantz) is an important tropical starchy root crop that is adapted to drought but extremely cold sensitive. A cold-tolerant, high-quality, and robust supply of cassava is urgently needed. Here, we clarify genome-wide distribution and classification of CCGG hemi-methylation and full-methylation, and detected 77 much candidate QTLsepi for cold stress and 103 much candidate QTLsepi for storage root quality and yield in 186 cassava population, generated by crossing two non-inbred lines with female parent KU50 and male parent SC124 (KS population). We developed amplified-fragment single nucleotide polymorphism and methylation (AFSM) genetic map in this population. We also constructed the AFSM QTL map, identified 260 much candidate QTL genes for cold stress and 301 much candidate QTL genes for storage root quality and yield, based on the years greenhouse and field trials. This may accounted for a significant amount of the variation in the key traits controlling cold tolerance and the high quality and yield of cassava. PMID:28120898

  20. Development of Maps of Simple and Complex Cells in the Primary Visual Cortex

    PubMed Central

    Antolík, Ján; Bednar, James A.

    2011-01-01

    Hubel and Wiesel (1962) classified primary visual cortex (V1) neurons as either simple, with responses modulated by the spatial phase of a sine grating, or complex, i.e., largely phase invariant. Much progress has been made in understanding how simple-cells develop, and there are now detailed computational models establishing how they can form topographic maps ordered by orientation preference. There are also models of how complex cells can develop using outputs from simple cells with different phase preferences, but no model of how a topographic orientation map of complex cells could be formed based on the actual connectivity patterns found in V1. Addressing this question is important, because the majority of existing developmental models of simple-cell maps group neurons selective to similar spatial phases together, which is contrary to experimental evidence, and makes it difficult to construct complex cells. Overcoming this limitation is not trivial, because mechanisms responsible for map development drive receptive fields (RF) of nearby neurons to be highly correlated, while co-oriented RFs of opposite phases are anti-correlated. In this work, we model V1 as two topographically organized sheets representing cortical layer 4 and 2/3. Only layer 4 receives direct thalamic input. Both sheets are connected with narrow feed-forward and feedback connectivity. Only layer 2/3 contains strong long-range lateral connectivity, in line with current anatomical findings. Initially all weights in the model are random, and each is modified via a Hebbian learning rule. The model develops smooth, matching, orientation preference maps in both sheets. Layer 4 units become simple cells, with phase preference arranged randomly, while those in layer 2/3 are primarily complex cells. To our knowledge this model is the first explaining how simple cells can develop with random phase preference, and how maps of complex cells can develop, using only realistic patterns of connectivity. PMID

  1. Feature level fusion for enhanced geological mapping of ophiolile complex using ASTER and Landsat TM data

    NASA Astrophysics Data System (ADS)

    Pournamdari, M.; Hashim, M.

    2014-02-01

    Chromite ore deposit occurrence is related to ophiolite complexes as a part of the oceanic crust and provides a good opportunity for lithological mapping using remote sensing data. The main contribution of this paper is a novel approaches to discriminate different rock units associated with ophiolite complex using the Feature Level Fusion technique on ASTER and Landsat TM satellite data at regional scale. In addition this study has applied spectral transform approaches, consisting of Spectral Angle Mapper (SAM) to distinguish the concentration of high-potential areas of chromite and also for determining the boundary between different rock units. Results indicated both approaches show superior outputs compared to other methods and can produce a geological map for ophiolite complex rock units in the arid and the semi-arid region. The novel technique including feature level fusion and Spectral Angle Mapper (SAM) discriminated ophiolitic rock units and produced detailed geological maps of the study area. As a case study, Sikhoran ophiolite complex located in SE, Iran has been selected for image processing techniques. In conclusion, a suitable approach for lithological mapping of ophiolite complexes is demonstrated, this technique contributes meaningfully towards economic geology in terms of identifying new prospects.

  2. An integrated map of HIV-human protein complexes that facilitate viral infection.

    PubMed

    Emig-Agius, Dorothea; Olivieri, Kevin; Pache, Lars; Shih, Hsin Ling; Pustovalova, Olga; Bessarabova, Marina; Young, John A T; Chanda, Sumit K; Ideker, Trey

    2014-01-01

    Recent proteomic and genetic studies have aimed to identify a complete network of interactions between HIV and human proteins and genes. This HIV-human interaction network provides invaluable information as to how HIV exploits the host machinery and can be used as a starting point for further functional analyses. We integrated this network with complementary datasets of protein function and interaction to nominate human protein complexes with likely roles in viral infection. Based on our approach we identified a global map of 40 HIV-human protein complexes with putative roles in HIV infection, some of which are involved in DNA replication and repair, transcription, translation, and cytoskeletal regulation. Targeted RNAi screens were used to validate several proteins and complexes for functional impact on viral infection. Thus, our HIV-human protein complex map provides a significant resource of potential HIV-host interactions for further study.

  3. 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

  4. New conformal mapping for adaptive resolving of the complex singularities of Stokes wave

    NASA Astrophysics Data System (ADS)

    Lushnikov, Pavel M.; Dyachenko, Sergey A.; Silantyev, Denis A.

    2017-06-01

    A new highly efficient method is developed for computation of travelling periodic waves (Stokes waves) on the free surface of deep water. A convergence of numerical approximation is determined by the complex singularities above the free surface for the analytical continuation of the travelling wave into the complex plane. An auxiliary conformal mapping is introduced which moves singularities away from the free surface thus dramatically speeding up numerical convergence by adapting the numerical grid for resolving singularities while being consistent with the fluid dynamics. The efficiency of that conformal mapping is demonstrated for the Stokes wave approaching the limiting Stokes wave (the wave of the greatest height) which significantly expands the family of numerically accessible solutions. It allows us to provide a detailed study of the oscillatory approach of these solutions to the limiting wave. Generalizations of the conformal mapping to resolve multiple singularities are also introduced.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

    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.

  6. 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)

  7. Nested association mapping for dissecting complex traits using Peanut 58K SNP array

    USDA-ARS?s Scientific Manuscript database

    Genome-wide association studies (GWAS) and linkage mapping have been the two most predominant strategies to dissect complex traits, but are limited by the occurrence of false positives reported for GWAS, and low resolution in the case of linkage analysis. This has led to the development of a joint a...

  8. 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.

  9. 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.

  10. Application of Intervention Mapping to the Development of a Complex Physical Therapist Intervention.

    PubMed

    Jones, Taryn M; Dear, Blake F; Hush, Julia M; Titov, Nickolai; Dean, Catherine M

    2016-12-01

    Physical therapist interventions, such as those designed to change physical activity behavior, are often complex and multifaceted. In order to facilitate rigorous evaluation and implementation of these complex interventions into clinical practice, the development process must be comprehensive, systematic, and transparent, with a sound theoretical basis. Intervention Mapping is designed to guide an iterative and problem-focused approach to the development of complex interventions. The purpose of this case report is to demonstrate the application of an Intervention Mapping approach to the development of a complex physical therapist intervention, a remote self-management program aimed at increasing physical activity after acquired brain injury. Intervention Mapping consists of 6 steps to guide the development of complex interventions: (1) needs assessment; (2) identification of outcomes, performance objectives, and change objectives; (3) selection of theory-based intervention methods and practical applications; (4) organization of methods and applications into an intervention program; (5) creation of an implementation plan; and (6) generation of an evaluation plan. The rationale and detailed description of this process are presented using an example of the development of a novel and complex physical therapist intervention, myMoves-a program designed to help individuals with an acquired brain injury to change their physical activity behavior. The Intervention Mapping framework may be useful in the development of complex physical therapist interventions, ensuring the development is comprehensive, systematic, and thorough, with a sound theoretical basis. This process facilitates translation into clinical practice and allows for greater confidence and transparency when the program efficacy is investigated. © 2016 American Physical Therapy Association.

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

    PubMed

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

    2015-07-07

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

  12. 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.

  13. Next-Generation Mapping of Complex Traits with Phenotype-Based Selection and Introgression

    PubMed Central

    Earley, Eric J.; Jones, Corbin D.

    2011-01-01

    Finding the genes underlying complex traits is difficult. We show that new sequencing technology combined with traditional genetic techniques can efficiently identify genetic regions underlying a complex and quantitative behavioral trait. As a proof of concept we used phenotype-based introgression to backcross loci that control innate food preference in Drosophila simulans into the genomic background of D. sechellia, which expresses the opposite preference. We successfully mapped D. simulans introgression regions in a small mapping population (30 flies) with whole-genome resequencing using light coverage (∼1×). We found six loci contributing to D. simulans food preference, one of which overlaps a previously discovered allele. This approach is applicable to many systems, does not rely on laborious marker development or genotyping, does not require existing high quality reference genomes, and needs only small mapping populations. Because introgression is used, researchers can scale mapping population size, replication, and number of backcross generations to their needs. Finally, in contrast to more widely used mapping techniques like F2 bulk-segregant analysis, our method produces near-isogenic lines that can be kept and reused indefinitely. PMID:21940681

  14. 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

  15. 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

  16. 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

    2007-09-04

    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.

  17. 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.

  18. 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.

  19. 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

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

    PubMed

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

    2016-03-11

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

  1. 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

  2. Megabase-scale mapping of the HLA gene complex by pulsed field gel electrophoresis

    SciTech Connect

    Lawrance, S.K.; Smith, C.L.; Srivastava, R.; Cantor, C.R.; Weissman, S.M.

    1987-03-13

    In the study of the genetic structure of mammalian chromosomes, there exists a resolution gap between molecular cloning experiments and meiotic linkage analyses. This gap has discouraged attempts to construct full-scale genetic maps of mammalian chromosomes. The organization of the human major histocompatibility complex was examined within this range by pulsed field gel electrophoresis. The data obtained indicate that the complex spans over 3000 kilobases and enable the construction of a megabase-scale molecular map. These results indicate that the techniques employed in DNA extraction, enzymatic digestion, electrophoresis, and hybridization are suitable for the efficient analysis of megabase regions of mammalian chromosomes and effectively bridge the resolution gap between molecular cloning and classical genetics.

  3. Mapping of a molecular complex in a northern spiral arm of M 31

    NASA Astrophysics Data System (ADS)

    Casoli, F.; Combes, F.; Stark, A. A.

    1987-02-01

    A restricted CO map at high resolution (22arcsec) has been obtained with the IRAM 30 m telescope towards a North-East spiral arm of M31. The authors have detected 12CO emission in 17 positions out of 41 observed. All the detected lines appear at the same LSR velocity, which implies that they come from a well-defined entity: a giant molecular complex. It has an H2 mass of about 1.3×106M_sun; and extends over roughly 160 pc. This complex is gravitationally bound; its structure is elongated and inhomogeneous on the 35 pc scale. The authors have also obtained a 13CO spectrum towards one point of the map, and confirmed an earlier determination of the ratio of 12CO to 13CO integrated emissivities around 10.

  4. 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).

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

    NASA Astrophysics Data System (ADS)

    Rebich-Hespanha, S.; Gautier, C.

    2010-12-01

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

  6. Plenoptic mapping for imaging and retrieval of the complex field amplitude of a laser beam.

    PubMed

    Wu, Chensheng; Ko, Jonathan; Davis, Christopher C

    2016-12-26

    The plenoptic sensor has been developed to sample complicated beam distortions produced by turbulence in the low atmosphere (deep turbulence or strong turbulence) with high density data samples. In contrast with the conventional Shack-Hartmann wavefront sensor, which utilizes all the pixels under each lenslet of a micro-lens array (MLA) to obtain one data sample indicating sub-aperture phase gradient and photon intensity, the plenoptic sensor uses each illuminated pixel (with significant pixel value) under each MLA lenslet as a data point for local phase gradient and intensity. To characterize the working principle of a plenoptic sensor, we propose the concept of plenoptic mapping and its inverse mapping to describe the imaging and reconstruction process respectively. As a result, we show that the plenoptic mapping is an efficient method to image and reconstruct the complex field amplitude of an incident beam with just one image. With a proof of concept experiment, we show that adaptive optics (AO) phase correction can be instantaneously achieved without going through a phase reconstruction process under the concept of plenoptic mapping. The plenoptic mapping technology has high potential for applications in imaging, free space optical (FSO) communication and directed energy (DE) where atmospheric turbulence distortion needs to be compensated.

  7. Visualizing complex processes using a cognitive-mapping tool to support the learning of clinical reasoning.

    PubMed

    Wu, Bian; Wang, Minhong; Grotzer, Tina A; Liu, Jun; Johnson, Janice M

    2016-08-22

    Practical experience with clinical cases has played an important role in supporting the learning of clinical reasoning. However, learning through practical experience involves complex processes difficult to be captured by students. This study aimed to examine the effects of a computer-based cognitive-mapping approach that helps students to externalize the reasoning process and the knowledge underlying the reasoning process when they work with clinical cases. A comparison between the cognitive-mapping approach and the verbal-text approach was made by analyzing their effects on learning outcomes. Fifty-two third-year or higher students from two medical schools participated in the study. Students in the experimental group used the computer-base cognitive-mapping approach, while the control group used the verbal-text approach, to make sense of their thinking and actions when they worked with four simulated cases over 4 weeks. For each case, students in both groups reported their reasoning process (involving data capture, hypotheses formulation, and reasoning with justifications) and the underlying knowledge (involving identified concepts and the relationships between the concepts) using the given approach. The learning products (cognitive maps or verbal text) revealed that students in the cognitive-mapping group outperformed those in the verbal-text group in the reasoning process, but not in making sense of the knowledge underlying the reasoning process. No significant differences were found in a knowledge posttest between the two groups. The computer-based cognitive-mapping approach has shown a promising advantage over the verbal-text approach in improving students' reasoning performance. Further studies are needed to examine the effects of the cognitive-mapping approach in improving the construction of subject-matter knowledge on the basis of practical experience.

  8. 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

  9. 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)

  10. 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.

  11. Functional dissection of protein complexes involved in yeast chromosome biology using a genetic interaction map.

    PubMed

    Collins, Sean R; Miller, Kyle M; Maas, Nancy L; Roguev, Assen; Fillingham, Jeffrey; Chu, Clement S; Schuldiner, Maya; Gebbia, Marinella; Recht, Judith; Shales, Michael; Ding, Huiming; Xu, Hong; Han, Junhong; Ingvarsdottir, Kristin; Cheng, Benjamin; Andrews, Brenda; Boone, Charles; Berger, Shelley L; Hieter, Phil; Zhang, Zhiguo; Brown, Grant W; Ingles, C James; Emili, Andrew; Allis, C David; Toczyski, David P; Weissman, Jonathan S; Greenblatt, Jack F; Krogan, Nevan J

    2007-04-12

    Defining the functional relationships between proteins is critical for understanding virtually all aspects of cell biology. Large-scale identification of protein complexes has provided one important step towards this goal; however, even knowledge of the stoichiometry, affinity and lifetime of every protein-protein interaction would not reveal the functional relationships between and within such complexes. Genetic interactions can provide functional information that is largely invisible to protein-protein interaction data sets. Here we present an epistatic miniarray profile (E-MAP) consisting of quantitative pairwise measurements of the genetic interactions between 743 Saccharomyces cerevisiae genes involved in various aspects of chromosome biology (including DNA replication/repair, chromatid segregation and transcriptional regulation). This E-MAP reveals that physical interactions fall into two well-represented classes distinguished by whether or not the individual proteins act coherently to carry out a common function. Thus, genetic interaction data make it possible to dissect functionally multi-protein complexes, including Mediator, and to organize distinct protein complexes into pathways. In one pathway defined here, we show that Rtt109 is the founding member of a novel class of histone acetyltransferases responsible for Asf1-dependent acetylation of histone H3 on lysine 56. This modification, in turn, enables a ubiquitin ligase complex containing the cullin Rtt101 to ensure genomic integrity during DNA replication.

  12. Interactome mapping for analysis of complex phenotypes: insights from benchmarking binary interaction assays.

    PubMed

    Braun, Pascal

    2012-05-01

    Protein interactions mediate essentially all biological processes and analysis of protein-protein interactions using both large-scale and small-scale approaches has contributed fundamental insights to the understanding of biological systems. In recent years, interactome network maps have emerged as an important tool for analyzing and interpreting genetic data of complex phenotypes. Complementary experimental approaches to test for binary, direct interactions, and for membership in protein complexes are used to explore the interactome. The two approaches are not redundant but yield orthogonal perspectives onto the complex network of physical interactions by which proteins mediate biological processes. In recent years, several publications have demonstrated that interactions from high-throughput experiments can be equally reliable as the high quality subset of interactions identified in small-scale studies. Critical for this insight was the introduction of standardized experimental benchmarking of interaction and validation assays using reference sets. The data obtained in these benchmarking experiments have resulted in greater appreciation of the limitations and the complementary strengths of different assays. Moreover, benchmarking is a central element of a conceptual framework to estimate interactome sizes and thereby measure progress toward near complete network maps. These estimates have revealed that current large-scale data sets, although often of high quality, cover only a small fraction of a given interactome. Here, I review the findings of assay benchmarking and discuss implications for quality control, and for strategies toward obtaining a near-complete map of the interactome of an organism.

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

    NASA Astrophysics Data System (ADS)

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

    2016-08-01

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

  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

    Aitken, Karen S; McNeil, Meredith D; Berkman, Paul J; Hermann, Scott; Kilian, Andrzej; Bundock, Peter C; Li, Jingchuan

    2014-07-26

    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. 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. 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 events seen in both species.

  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 "mélange". 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. 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.

  19. 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.

  20. A random model approach to mapping quantitative trait loci for complex binary traits in outbred populations.

    PubMed Central

    Yi, N; Xu, S

    1999-01-01

    Mapping quantitative trait loci (QTL) for complex binary traits is more challenging than for normally distributed traits due to the nonlinear relationship between the observed phenotype and unobservable genetic effects, especially when the mapping population contains multiple outbred families. Because the number of alleles of a QTL depends on the number of founders in an outbred population, it is more appropriate to treat the effect of each allele as a random variable so that a single variance rather than individual allelic effects is estimated and tested. Such a method is called the random model approach. In this study, we develop the random model approach of QTL mapping for binary traits in outbred populations. An EM-algorithm with a Fisher-scoring algorithm embedded in each E-step is adopted here to estimate the genetic variances. A simple Monte Carlo integration technique is used here to calculate the likelihood-ratio test statistic. For the first time we show that QTL of complex binary traits in an outbred population can be scanned along a chromosome for their positions, estimated for their explained variances, and tested for their statistical significance. Application of the method is illustrated using a set of simulated data. PMID:10511576

  1. 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.

  2. 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. Copyright © 2012 Elsevier Inc. All rights reserved.

  3. Mapping of drug-like chemical universe with reduced complexity molecular frameworks.

    PubMed

    Kontijevskis, Aleksejs

    2017-03-28

    The emergence of DNA-encoded chemical libraries (DEL) field in past decade has attracted attention of pharmaceutical industry as a powerful mechanism for the discovery of novel drug-like hits for various biological targets. Nuevolution Chemetics technology enables DNA encoded synthesis of billions of chemically diverse drug-like small molecule compounds, and the efficient screening and optimization of these, facilitating effective identification of drug candidates at an unprecedented speed and scale. Although many approaches have been developed by the cheminformatics community for the analysis and visualization of drug-like chemical space, most of them are restricted to the analysis of maximum few millions of compounds and cannot handle collections of 10(8)-10(12) compounds typical for DELs. To address this big chemical data challenge, we developed Reduced Complexity Molecular (RCM) frameworks methodology as an abstract and very general way of representing chemical structures. By further introducing RCM framework descriptors we constructed a global framework map of drug-like chemical space and demonstrate how chemical space occupied by multi-million-member drug-like Chemetics DNA-encoded libraries and virtual combinatorial libraries with >10(12) members could be analysed and mapped without a need for library enumeration. We further validate the approach by performing RCM framework-based searches in drug-like chemical universe and mapping Chemetics library selection outputs for LSD1 target on a global framework chemical space map.

  4. Citizen-Scientist Digitization of a Complex Geologic Map of the McDowell Mountains (Scottsdale, Arizona).

    NASA Astrophysics Data System (ADS)

    Gruber, D.; Skotnicki, S.; Gootee, B.

    2016-12-01

    The work of citizen scientists has become very important to researchers doing field work and internet-based projects but has not been widely utilized in digital mapping. The McDowell Mountains - located in Scottsdale, Arizona, at the edge of the basin-and-range province and protected as part of the McDowell Sonoran Preserve - are geologically complex. Until recently, no comprehensive geologic survey of the entire range had been done. Over the last 9 years geologist Steven Skotnicki spent 2000 hours mapping the complex geology of the range. His work, born of personal interest and partially supported by the McDowell Sonoran Conservancy, resulted in highly detailed hand-drawn survey maps. Dr. Skotnicki's work provides important new information and raises interesting research questions about the geology of this range. Citizen scientists of the McDowell Sonoran Conservancy Field Institute digitized Dr. Skotnicki's maps. A team of 10 volunteers, trained in ArcMap digitization techniques and led by volunteer project leader Daniel Gruber, performed the digitization work. Technical oversight of mapping using ArcMap, including provision of USGS-based mapping toolbars, was provided by Arizona Geological Survey (AZGS) research geologist Brian Gootee. The map digitization process identified and helped resolve a number of mapping questions. The citizen-scientist team spent 900 hours on training, digitization, quality checking, and project coordination with support and review by Skotnicki and Gootee. The resulting digital map has approximately 3000 polygons, 3000 points, and 86 map units with complete metadata and unit descriptions. The finished map is available online through AZGS and can be accessed in the field on mobile devices. User location is shown on the map and metadata can be viewed with a tap. The citizen scientist map digitization team has made this important geologic information available to the public and accessible to other researchers quickly and efficiently.

  5. 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

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

    PubMed Central

    2011-01-01

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

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

    PubMed

    Dedukh, Dmitry; Mazepa, Glib; Shabanov, Dmitry; Rosanov, Juriy; Litvinchuk, Spartak; Borkin, Leo; Saifitdinova, Alsu; Krasikova, Alla

    2013-04-16

    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. 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. The constructed cytological maps of lampbrush chromosomes of P. ridibundus and P. lessonae provide

  8. Statistical Power of Expression Quantitative Trait Loci for Mapping of Complex Trait Loci in Natural Populations

    PubMed Central

    Schliekelman, Paul

    2008-01-01

    A number of recent genomewide surveys have found numerous QTL for gene expression, often with intermediate to high heritability values. As a result, there is currently a great deal of interest in genetical genomics—that is, the combination of genomewide expression data and molecular marker data to elucidate the genetics of complex traits. To date, most genetical genomics studies have focused on generating candidate genes for previously known trait loci or have otherwise leveraged existing knowledge about trait-related genes. The purpose of this study is to explore the potential for genetical genomics approaches in the context of genomewide scans for complex trait loci. I explore the expected strength of association between expression-level traits and a clinical trait, as a function of the underlying genetic model in natural populations. I give calculations of statistical power for detecting differential expression between affected and unaffected individuals. I model both reactive and causative expression-level traits with both additive and multiplicative multilocus models for the relationship between phenotype and genotype and explore a variety of assumptions about dominance, number of segregating loci, and other parameters. There are two key results. If a transcript is causative for the disease (in the sense that disease risk depends directly on transcript level), then the power to detect association between transcript and disease is quite good. Sample sizes on the order of 100 are sufficient for 80% power. On the other hand, if the transcript is reactive to a disease locus, then the correlation between expression-level traits and disease is low unless the expression-level trait shares several causative loci with the disease—that is, the expression-level trait itself is a complex trait. Thus, there is a trade-off between the power to show association between a reactive expression-level trait and the clinical trait of interest and the power to map expression

  9. Evolution of genetic redundancy: the relevance of complexity in genotype-phenotype mapping

    NASA Astrophysics Data System (ADS)

    Saito, Nen; Ishihara, Shuji; Kaneko, Kunihiko

    2014-06-01

    Despite its ubiquity among organisms, genetic redundancy is presumed to reduce total population fitness and is therefore unlikely to evolve. This study evaluates an evolutionary model with high-dimensional genotype-phenotype mapping (GPM) by applying a replica method to deal with quenched randomness. From the method, the dependence of fitness on genetic redundancy is analytically calculated. The results demonstrate that genetic redundancy can have higher population fitness under complex GPM, which tends to favor gene duplication in selection processes, further enhancing the potential for evolutionary innovations.

  10. Mapping of West Siberian taiga wetland complexes using Landsat imagery: Implications for methane emissions

    NASA Astrophysics Data System (ADS)

    Terentieva, Irina; Sabrekov, Alexander; Glagolev, Mikhail; Maksyutov, Shamil

    2017-04-01

    Boreal wetlands are important for understanding climate change risks because these environments sink carbon dioxide and emit methane. The West Siberia Lowland (WSL) is the biggest peatland area in Eurasia and is situated in the high latitudes experiencing enhanced rate of climate change. However, fine-scale heterogeneity of wetland landscapes poses a serious challenge when generating regional-scale estimates of greenhouse gas fluxes from point observations. A number of peatland maps of the West Siberia was developed in 1970s, but their accuracy is limited. In order to reduce uncertainties at the regional scale, we mapped wetlands and water bodies in the WSL on a scene-by-scene basis using a supervised classification of Landsat imagery. Training data consisted of high-resolution images and extensive field data collected at 41 test areas. The classification scheme aimed at supporting methane inventory applications and included 7 wetland ecosystem types comprising 9 wetland complexes distinguishable at the Landsat resolution. To merge typologies, mean relative areas of wetland ecosystems within each wetland complex type were estimated using high-resolution images. Accuracy assessment based on 1082 validation polygons of 10×10 pixels indicated an overall map accuracy of 79%. The total area of the WSL wetlands and water bodies was estimated to be 70.78 Mha or 5-17% of the global wetland area. Various oligotrophic environments are dominant among wetland ecosystems, while different fens cover only 14% of the area. Taiga zone contains 75% of WSL's wetlands; their distribution was described in detail by Terentieva et al. (2016). Concerning methane emission, taiga contributes 85% to regional methane flux and tundra only 8%, however ebullition in tundra lakes was not directly measured. Elevated environments as forested bogs and ridges emit at the lowest rates of methane emission. They account for only 2% of the regional total emissions occupying almost 40% of the wetland

  11. 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

  12. 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.

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

    PubMed

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

    2016-02-27

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

  14. 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

  15. 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.

  16. MAPS

    Atmospheric Science Data Center

    2014-07-03

    ... Measurement of Air Pollution from Satellites (MAPS) data were collected during Space Shuttle flights in 1981, ... Facts Correlative Data  - CDIAC - Spring & Fall 1994 - Field and Aircraft Campaigns SCAR-B Block:  ...

  17. 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

  18. Three-Dimensional Mapping of mRNA Export through the Nuclear Pore Complex.

    PubMed

    Schnell, Steven J; Ma, Jiong; Yang, Weidong

    2014-11-11

    The locations of transcription and translation of mRNA in eukaryotic cells are spatially separated by the nuclear envelope (NE). Plenty of nuclear pore complexes (NPCs) embedded in the NE function as the major gateway for the export of transcribed mRNAs from the nucleus to the cytoplasm. Whereas the NPC, perhaps one of the largest protein complexes, provides a relatively large channel for macromolecules to selectively pass through it in inherently three-dimensional (3D) movements, this channel is nonetheless below the diffraction limit of conventional light microscopy. A full understanding of the mRNA export mechanism urgently requires real-time mapping of the 3D dynamics of mRNA in the NPC of live cells with innovative imaging techniques breaking the diffraction limit of conventional light microscopy. Recently, super-resolution fluorescence microscopy and single-particle tracking (SPT) techniques have been applied to the study of nuclear export of mRNA in live cells. In this review, we emphasize the necessity of 3D mapping techniques in the study of mRNA export, briefly summarize the feasibility of current 3D imaging approaches, and highlight the new features of mRNA nuclear export elucidated with a newly developed 3D imaging approach combining SPT-based super-resolution imaging and 2D-to-3D deconvolution algorithms.

  19. Three-Dimensional Mapping of mRNA Export through the Nuclear Pore Complex

    PubMed Central

    Schnell, Steven J.; Ma, Jiong; Yang, Weidong

    2014-01-01

    The locations of transcription and translation of mRNA in eukaryotic cells are spatially separated by the nuclear envelope (NE). Plenty of nuclear pore complexes (NPCs) embedded in the NE function as the major gateway for the export of transcribed mRNAs from the nucleus to the cytoplasm. Whereas the NPC, perhaps one of the largest protein complexes, provides a relatively large channel for macromolecules to selectively pass through it in inherently three-dimensional (3D) movements, this channel is nonetheless below the diffraction limit of conventional light microscopy. A full understanding of the mRNA export mechanism urgently requires real-time mapping of the 3D dynamics of mRNA in the NPC of live cells with innovative imaging techniques breaking the diffraction limit of conventional light microscopy. Recently, super-resolution fluorescence microscopy and single-particle tracking (SPT) techniques have been applied to the study of nuclear export of mRNA in live cells. In this review, we emphasize the necessity of 3D mapping techniques in the study of mRNA export, briefly summarize the feasibility of current 3D imaging approaches, and highlight the new features of mRNA nuclear export elucidated with a newly developed 3D imaging approach combining SPT-based super-resolution imaging and 2D-to-3D deconvolution algorithms. PMID:25393401

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

    NASA Astrophysics Data System (ADS)

    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

    2013-12-01

    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.

  1. 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

  2. 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.

  3. 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.

  4. An assessment of the Irish population for large-scale genetic mapping studies involving epilepsy and other complex diseases.

    PubMed

    O'Dushlaine, Colm T; Dolan, Ciara; Weale, Michael E; Stanton, Alice; Croke, David T; Kalviainen, Reetta; Eriksson, Kai; Kantanen, Anne-Mari; Gibson, Rachel A; Hosford, David; Sisodiya, Sanjay M; Gill, Michael; Corvin, Aiden P; Morris, Derek W; Delanty, Norman; Cavalleri, Gianpiero L

    2008-02-01

    The recent completion of the International HapMap Project has rapidly advanced our understanding of linkage disequilibrium (LD) in the human genome. Today, tagging SNPs (tSNPs) can be quickly and easily selected and consequently HapMap data are regularly applied to both small- and large-scale genetic mapping studies. However, to correctly interpret the application of HapMap-derived tSNPs in a genetic mapping study, an understanding of how well HapMap data represents LD in the study population is critical. The Irish population had not previously been characterised in this way. Here, we do so using a set of 4424 SNPs selected from 279 candidate genes for epilepsy genotyped across 1118 healthy individuals from the Irish, British, Finnish and Australian populations. By considering the Irish population alongside surrounding European populations, our results confirm that the HapMap European-derived population accurately estimates patterning of LD in European descent populations. The Irish population appears notably well matched to the European HapMap population, and is markedly similar to the neighbouring British population. Although we were unable to detect significant substructure within the Irish population (a favourable result for genetic mapping), methods for controlling stratification should always be incorporated. This analysis therefore confirms that the genetic architecture of the Irish population is well suited to the study of complex traits and that tSNPs selected using the HapMap data can be confidently applied to the Irish population.

  5. A complete DNA sequence map of the ovine Major Histocompatibility Complex

    PubMed Central

    2010-01-01

    Background The ovine Major Histocompatibility Complex (MHC) harbors clusters of genes involved in overall resistance/susceptibility of an animal to infectious pathogens. However, only a limited number of ovine MHC genes have been identified and no adequate sequence information is available, as compared to those of swine and bovine. We previously constructed a BAC clone-based physical map that covers entire class I, class II and class III region of ovine MHC. Here we describe the assembling of a complete DNA sequence map for the ovine MHC by shotgun sequencing of 26 overlapping BAC clones. Results DNA shotgun sequencing generated approximately 8-fold genome equivalent data that were successfully assembled into a finished sequence map of the ovine MHC. The sequence map spans approximately 2,434,000 nucleotides in length, covering almost all of the MHC loci currently known in the sheep and cattle. Gene annotation resulted in the identification of 177 protein-coding genes/ORFs, among which 145 were not previously reported in the sheep, and 10 were ovine species specific, absent in cattle or other mammals. A comparative sequence analyses among human, sheep and cattle revealed a high conservation in the MHC structure and loci order except for the class II, which were divided into IIa and IIb subregions in the sheep and cattle, separated by a large piece of non-MHC autosome of approximately 18.5 Mb. In addition, a total of 18 non-protein-coding microRNAs were predicted in the ovine MHC region for the first time. Conclusion An ovine MHC DNA sequence map was successfully assembled by shotgun sequencing of 26 overlapping BAC clone. This makes the sheep the second ruminant species for which the complete MHC sequence information is available for evolution and functional studies, following that of the bovine. The results of the comparative analysis support a hypothesis that an inversion of the ancestral chromosome containing the MHC has shaped the MHC structures of ruminants

  6. Evaluation of services for children with complex needs: mapping service provision in one NHS Trust.

    PubMed

    Brooks, Fiona; Bloomfield, Linda; Offredy, Maxine; Shaughnessy, Philomena

    2013-01-01

    The aim of this paper is to identify and descriptively map the key characteristics of the model of service delivery in operation, and to explore the user, carer and professional experience of service provision. This included an exploration of congruity and mismatch between the different stakeholder groups. In the United Kingdom (UK), 15% of the children under five years of age and 20% of the 5 to 15-year age group are reported to have a complex long-term condition, with the likelihood of having a condition increasing according to socio-economic circumstances. An increasing number of young people with complex needs are now surviving into late adolescence and early adulthood. However, service provision for children with complex needs is an area that, nationally, has been underdeveloped. An exploratory single-site case study was undertaken across one Primary Care Trust in the UK. Documentary and policy review were undertaken along with in-depth qualitative exploration. Eighteen in-depth interviews were undertaken with relevant stakeholders and professionals across the multidisciplinary teams. Families with children between 12 months and 16 years of age who have continuing complex care needs were invited to take part in an interview to give their views about the care they receive. Interviews focused on the family experience and understanding of the child's condition, transition between secondary and primary care, effectiveness of admission and discharge planning and the overall contribution of different professionals. Professionals were also asked about their experiences of delivering care. Findings This study highlighted issues of communication between professionals and with parents and children as a major factor in determining the quality of service provision. Key aspects relating to the model of service provision, namely, paucity of communication, interagency collaboration and the parent as health worker, are highlighted. Parents experienced both health and social

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

    NASA Astrophysics Data System (ADS)

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

    2012-04-01

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

  8. Super-resolution mapping of scaffold nucleoporins in the nuclear pore complex.

    PubMed

    Ma, Jiong; Kelich, Joseph M; Junod, Samuel L; Yang, Weidong

    2017-02-15

    The nuclear pore complex (NPC), composed of ∼30 different nucleoporins (Nups), is one of the largest supramolecular structures in eukaryotic cells. Its octagonal ring-scaffold perforates the nuclear envelope and features a unique molecular machinery that regulates nucleocytoplasmic transport. However, the precise copy number and the spatial location of each Nup in the native NPC remain obscure due to the inherent difficulty of counting and localizing proteins inside the sub-micrometer supramolecular complex. Here we combined super-resolution SPEED microscopy and nanobody specific labeling to reveal the spatial distribution of scaffold Nups within three separate layers in the native NPC with a precision of ∼3 nm. Our data reveals both the radial and axial spatial distributions for Pom121, Nup37 and Nup35 and provides evidence for their copy numbers of 8, 32, and 16 respectively per NPC. This approach can help pave the path for mapping the entirety of Nups in native NPCs and also other structural components of macromolecular complexes.

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

    PubMed

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

    2010-05-01

    The understanding and engineering of complex phenotypes is a critical issue in biotechnology. Conventional approaches for engineering such phenotypes are often resource intensive, marginally effective, and unable to generate the level of biological understanding desired. Here, we report a new approach for rapidly dissecting a complex phenotype that is based upon the combination of genome-scale growth phenotype data, precisely targeted growth selections, and informatic strategies for abstracting and summarizing data onto coherent biological processes. We measured at high resolution (125 NT) and for the entire genome the effect of increased gene copy number on overall biological fitness corresponding to the expression of a complex phenotype (tolerance to 3-hydroxypropionic acid (3-HP) in Escherichia coli). Genetic level fitness data were then mapped according to various definitions of gene-gene interaction in order to generate network-level fitness data. When metabolic pathways were used to define interactions, we observed that genes within the chorismate and threonine super-pathways were disproportionately enriched throughout selections for 3-HP tolerance. Biochemical and genetic studies demonstrated that alleviation of inhibition of either of these super-pathways was sufficient to mitigate 3-HP toxicity. These data enabled the design of combinatorial modifications that almost completely offset 3-HP toxicity in minimal medium resulting in a 20 g/L and 25-fold increase in tolerance and specific growth, respectively. 2009 Elsevier Inc. All rights reserved.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Mapping the complex morphology of cell interactions with nanowire substrates using FIB-SEM.

    PubMed

    Wierzbicki, Rafał; Købler, Carsten; Jensen, Mikkel R B; Lopacińska, 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.

  15. Semi-automatic mapping for identifying complex geobodies in seismic images

    NASA Astrophysics Data System (ADS)

    Domínguez-C, Raymundo; Romero-Salcedo, Manuel; Velasquillo-Martínez, Luis G.; Shemeretov, Leonid

    2017-03-01

    Seismic images are composed of positive and negative seismic wave traces with different amplitudes (Robein 2010 Seismic Imaging: A Review of the Techniques, their Principles, Merits and Limitations (Houten: EAGE)). The association of these amplitudes together with a color palette forms complex visual patterns. The color intensity of such patterns is directly related to impedance contrasts: the higher the contrast, the higher the color intensity. Generally speaking, low impedance contrasts are depicted with low tone colors, creating zones with different patterns whose features are not evident for a 3D automated mapping option available on commercial software. In this work, a workflow for a semi-automatic mapping of seismic images focused on those areas with low-intensity colored zones that may be associated with geobodies of petroleum interest is proposed. The CIE L*A*B* color space was used to perform the seismic image processing, which helped find small but significant differences between pixel tones. This process generated binary masks that bound color regions to low-intensity colors. The three-dimensional-mask projection allowed the construction of 3D structures for such zones (geobodies). The proposed method was applied to a set of digital images from a seismic cube and tested on four representative study cases. The obtained results are encouraging because interesting geobodies are obtained with a minimum of information.

  16. Irreversible denaturation mapping of a pyrimidine-rich domain of a complex satellite DNA

    SciTech Connect

    LaMarca, M.E.; Allison, D.P.; Skinner, D.M.

    1981-06-25

    The highly complex G + C-rich satellite DNA of the Bermuda land crab Gecarcinus lateralis has been studied by denaturation mapping. Following digestion of the satellite with EndoR.Eco RI, the major 2.07-kilo-base pair (kbp) basic repeating unit and a minor 4.14-kbp fragment were exposed to 254 nm light in the presence of silver ions, conditions which resulted in essentially irreversible denaturation of regions rich in adjacent pyrimidines by the formation of pyrimidine dimers. The positions and sizes of the denatured regions were determined in electron micrographs of partially denatured 2.07-kbp and 4.14-kbp fragments spread in the presence of formamide. The positions of the denaturation bubbles in the 4.14-kbp fragments support restriction enzyme mapping evidence that it is a dimer of the 2.07-kbp fragment arranged head to tail. Sequencing data show that the predominant sequence of a 0.29-kbp region centered aroung 0.64 kbp in the basic repeat unit is 49% A + T and that 42% of the bases are adjacent TTs and CTs capable of dimerization under the conditions used.

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

    PubMed

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

    2011-12-09

    Family studies for Crohn disease (CD) report extensive linkage on chromosome 16q and pinpoint NOD2 as a possible causative locus. However, linkage is also observed in families that do not bear the most frequent NOD2 causative mutations, but no other signals on 16q have been found so far in published genome-wide association studies. Our aim is to identify this missing genetic contribution. We apply a powerful genetic mapping approach to the Wellcome Trust Case-Control Consortium and the National Institute of Diabetes and Digestive and Kidney Diseases genome-wide association data on CD. This method takes into account the underlying structure of linkage disequilibrium (LD) by using genetic distances from LD maps and provides a location for the causal agent. We find genetic heterogeneity within the NOD2 locus and also show an independent and unsuspected involvement of the neighboring gene, CYLD. We find associations with the IRF8 region and the region containing CDH1 and CDH3, as well as substantial phenotypic and genetic heterogeneity for CD itself. The genes are known to be involved in inflammation and immune dysregulation. These findings provide insight into the genetics of CD and suggest promising directions for understanding disease heterogeneity. The application of this method thus paves the way for understanding complex inheritance in general, leading to the dissection of different pathways and ultimately, personalized treatment. Copyright © 2011 The American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

  18. Dissecting the Genetics of Complex Inheritance: Linkage Disequilibrium Mapping Provides Insight into Crohn Disease

    PubMed Central

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

    2011-01-01

    Family studies for Crohn disease (CD) report extensive linkage on chromosome 16q and pinpoint NOD2 as a possible causative locus. However, linkage is also observed in families that do not bear the most frequent NOD2 causative mutations, but no other signals on 16q have been found so far in published genome-wide association studies. Our aim is to identify this missing genetic contribution. We apply a powerful genetic mapping approach to the Wellcome Trust Case-Control Consortium and the National Institute of Diabetes and Digestive and Kidney Diseases genome-wide association data on CD. This method takes into account the underlying structure of linkage disequilibrium (LD) by using genetic distances from LD maps and provides a location for the causal agent. We find genetic heterogeneity within the NOD2 locus and also show an independent and unsuspected involvement of the neighboring gene, CYLD. We find associations with the IRF8 region and the region containing CDH1 and CDH3, as well as substantial phenotypic and genetic heterogeneity for CD itself. The genes are known to be involved in inflammation and immune dysregulation. These findings provide insight into the genetics of CD and suggest promising directions for understanding disease heterogeneity. The application of this method thus paves the way for understanding complex inheritance in general, leading to the dissection of different pathways and ultimately, personalized treatment. PMID:22152681

  19. Linkage mapping and physical localization of the major histocompatibility complex region of the marsupial Monodelphis domestica.

    PubMed

    Gouin, N; Deakin, J E; Miska, K B; Miller, R D; Kammerer, C M; Graves, J A M; VandeBerg, J L; Samollow, P B

    2006-01-01

    We used genetic linkage mapping and fluorescence in situ hybridization (FISH) to conduct the first analysis of genic organization and chromosome localization of the major histocompatibility complex (MHC) of a marsupial, the gray, short-tailed opossum Monodelphis domestica. Family based linkage analyses of two M. domestica MHC Class I genes (UA1, UG) and three MHC Class II genes (DAB, DMA, and DMB) revealed that these genes were tightly linked and positioned in the central region of linkage group 3 (LG3). This cluster of MHC genes was physically mapped to the centromeric region of chromosome 2q by FISH using a BAC clone containing the UA1 gene. An interesting finding from the linkage analyses is that sex-specific recombination rates were virtually identical within the MHC region. This stands in stark contrast to the genome-wide situation, wherein males exhibit approximately twice as much recombination as females, and could have evolutionary implications for maintaining equality between males and females in the ability to generate haplotype diversity in this region. These analyses also showed that three non-MHC genes that flank the MHC region on human chromosome 6, myelin oligodendrocyte glycoprotein (MOG), bone morphogenetic protein 6 (BMP6), and prolactin (PRL), are split among two separate linkage groups (chromosomes) in M. domestica. Comparative analysis with eight other vertebrate species suggests strong conservation of the BMP6-PRL synteny among birds and mammals, although the BMP6-PRL-MHC-ME1 synteny is not conserved.

  20. 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.

  1. 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.

  2. 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

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

    PubMed Central

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

    2011-01-01

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

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

    PubMed

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

    2011-09-13

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

  5. Complex multi-enhancer contacts captured by Genome Architecture Mapping (GAM)

    PubMed Central

    Beagrie, Robert A.; Scialdone, Antonio; Schueler, Markus; Kraemer, Dorothee C.A.; Chotalia, Mita; Xie, Sheila Q.; Barbieri, Mariano; de Santiago, Inês; Lavitas, Liron-Mark; Branco, Miguel R.; Fraser, James; Dostie, Josée; Game, Laurence; Dillon, Niall; Edwards, Paul A.W.; Nicodemi, Mario; Pombo, Ana

    2017-01-01

    Summary The organization of the genome in the nucleus and the interactions of genes with their regulatory elements are key features of transcriptional control and their disruption can cause disease. We developed a novel genome-wide method, Genome Architecture Mapping (GAM), for measuring chromatin contacts, and other features of three-dimensional chromatin topology, based on sequencing DNA from a large collection of thin nuclear sections. We apply GAM to mouse embryonic stem cells and identify an enrichment for specific interactions between active genes and enhancers across very large genomic distances, using a mathematical model ‘SLICE’ (Statistical Inference of Co-segregation). GAM also reveals an abundance of three-way contacts genome-wide, especially between regions that are highly transcribed or contain super-enhancers, highlighting a previously inaccessible complexity in genome architecture and a major role for gene-expression specific contacts in organizing the genome in mammalian nuclei. PMID:28273065

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

    PubMed

    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

    2015-01-22

    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.

  7. Integrating aeromagnetic and Landsat™ 8 data into subsurface structural mapping of Precambrian basement complex

    NASA Astrophysics Data System (ADS)

    Kayode, John Stephen; Nawawi, M. N. M.; Abdullah, Khiruddin B.; Khalil, Amin E.

    2017-01-01

    The integration of Aeromagnetic data and remotely sensed imagery with the intents of mapping the subsurface geological structures in part of the South-western basement complex of Nigeria was developed using the PCI Geomatica Software. 2013. The data obtained from the Nigerian Geological Survey Agency; was corrected using Regional Residual Separation of the Total Magnetic field anomalies enhanced, and International Geomagnetic Reference Field removed. The principal objective of this study is, therefore, to introduce a rapid and efficient method of subsurface structural depth estimate and structural index evaluation through the incorporation of the Euler Deconvolution technique into PCI Geomatica 2013 to prospect for subsurface geological structures. The shape and depth of burial helped to define these structures from the regional aeromagnetic map. The method enabled various structural indices to be automatically delineated for an index of between 0.5 SI and 3.0 SI at a maximum depth of 1.1 km that clearly showed the best depths estimate for all the structural indices. The results delineate two major magnetic belts in the area; the first belt shows an elongated ridge-like structure trending mostly along the NorthNortheast-SouthSouthwest and the other anomalies trends primarily in the Northeast, Northwest, Northeast-Southwest parts of the study area that could be attributed to basement complex granitic intrusions from the tectonic history of the area. The majority of the second structures showed various linear structures different from the first structure. Basically, a significant offset was delineated at the core segment of the study area, suggesting a major subsurface geological feature that controls mineralisation in this area.

  8. 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.

  9. A velocity map ion imaging study of difluorobenzene-water complexes: binding energies and recoil distributions.

    PubMed

    Bellm, Susan M; Moulds, Rebecca J; van Leeuwen, Matthew P; Lawrance, Warren D

    2008-03-21

    The binding energies of the p-, m-, and o-difluorobenzene-H(2)O complexes have been measured by velocity map ion imaging to be 922+/-10, 945+/-10, and 891+/-4 cm(-1), respectively. The lack of variation provides circumstantial evidence for water binding to the three isomers via the same interaction, viz. an in-plane O-H...F hydrogen bond to one of the fluorine atoms on the ring, with a second, weaker interaction of the water O atom with an ortho hydrogen, as determined previously for the p-difluorobenzene-H(2)O complex [Kang et al., J. Phys. Chem. A 109, 767 (2005)]. The ground state binding energies for the difluorobenzene-H(2)O complexes are approximately 5%-11% larger than that for benzene-H(2)O, where binding occurs to the pi electrons out-of-plane. However, in the S(1) state the binding energies of the o- and p-difluorobenzene-H(2)O complexes are smaller than the benzene-H(2)O value, raising an interesting question about whether the geometry at the global energy minimum remains in-plane in the excited electronic states of these two complexes. Recoil energy distributions for dissociation of p-difluorobenzene-H(2)O have been measured from the 3(1), 5(2), and 3(1)5(1) levels of the excited electronic state. These levels are 490, 880, and 1304 cm(-1), respectively, above the dissociation threshold. Within the experimental uncertainty, the recoil energy distributions are the same for dissociation from these three states, with average recoil energies of approximately 100 cm(-1). These recoil energies are 60% larger than was observed for the dissociation of p-difluorobenzene-Ar, which is a substantially smaller increase than the 400% seen in a comparable study of dissociation within the triplet state for pyrazine-Ar, -H(2)O complexes. The majority of the available energy is partitioned into vibration and rotation of the fragments.

  10. Venous drainage map of the liver for complex hepatobiliary surgery and liver transplantation.

    PubMed

    Tani, Keigo; Shindoh, Junichi; Akamatsu, Nobuhisa; Arita, Junichi; Kaneko, Junichi; Sakamoto, Yoshihiro; Hasegawa, Kiyoshi; Kokudo, Norihiro

    2016-12-01

    Inflow and outflow patency of the liver parenchyma is required to maximize the metabolic function of the liver. However, the definition and distribution of hepatic venous drainage regions has yet to be reported. The aim of this study was to define major hepatic venous tributaries and investigate the mean drainage volume of each territory. Three-dimensional (3D) simulations from the livers of 100 healthy donors were reviewed for living donor liver transplantation to determine the distribution of the significant hepatic venous tributaries and the drainage patterns of each segment. The left hepatic vein (LHV), middle hepatic vein (MHV), and right hepatic vein (RHV) contributed a mean drainage of 20.7%, 32.7%, and 39.6% of the entire liver, respectively. Accessory hepatic veins accounted for remaining 7.0%. The middle right hepatic vein (MRHV) and inferior right hepatic vein (IRHV) accounted for a mean total drainage of 8.0% and 10.6%, respectively, when they present. In addition, major tributaries of hepatic veins were clearly detected, and their typical distributions were described. Knowledge of hepatic venous territories is necessary for complex hepatobiliary surgery. This "venous drainage map" may provide useful information for complex liver surgery and transplantation. Copyright © 2016 International Hepato-Pancreato-Biliary Association Inc. Published by Elsevier Ltd. All rights reserved.

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

    PubMed

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

    2001-12-01

    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.

  12. 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

  13. Automated algorithm for mapping regions of cold-air pooling in complex terrain

    NASA Astrophysics Data System (ADS)

    Lundquist, Jessica D.; Pepin, Nicholas; Rochford, Caitlin

    2008-11-01

    In complex terrain, air in contact with the ground becomes cooled from radiative energy loss on a calm clear night and, being denser than the free atmosphere at the same elevation, sinks to valley bottoms. Cold-air pooling (CAP) occurs where this cooled air collects on the landscape. This article focuses on identifying locations on a landscape subject to considerably lower minimum temperatures than the regional average during conditions of clear skies and weak synoptic-scale winds, providing a simple automated method to map locations where cold air is likely to pool. Digital elevation models of regions of complex terrain were used to derive surfaces of local slope, curvature, and percentile elevation relative to surrounding terrain. Each pixel was classified as prone to CAP, not prone to CAP, or exhibiting no signal, based on the criterion that CAP occurs in regions with flat slopes in local depressions or valleys (negative curvature and low percentile). Along-valley changes in the topographic amplification factor (TAF) were then calculated to determine whether the cold air in the valley was likely to drain or pool. Results were checked against distributed temperature measurements in Loch Vale, Rocky Mountain National Park, Colorado; in the Eastern Pyrenees, France; and in Yosemite National Park, Sierra Nevada, California. Using CAP classification to interpolate temperatures across complex terrain resulted in improvements in root-mean-square errors compared to more basic interpolation techniques at most sites within the three areas examined, with average error reductions of up to 3°C at individual sites and about 1°C averaged over all sites in the study areas.

  14. 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

  15. 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.

  16. Multi-area visuotopic map complexes in macaque striate and extra-striate cortex

    PubMed Central

    Polimeni, J.R.; Balasubramanian, M.; Schwartz, E.L.

    2007-01-01

    We propose that a simple, closed-form mathematical expression—the Wedge–Dipole mapping—provides a concise approximation to the full-field, two-dimensional topographic structure of macaque V1, V2, and V3. A single map function, which we term a map complex, acts as a simultaneous descriptor of all three areas. Quantitative estimation of the Wedge–Dipole parameters is provided via 2DG data of central-field V1 topography and a publicly available data set of full-field macaque V1 and V2 topography. Good quantitative agreement is obtained between the data and the model presented here. The increasing importance of fMRI-based brain imaging motivates the development of more sophisticated two-dimensional models of cortical visuotopy, in contrast to the one-dimensional approximations that have been in common use. One reason is that topography has traditionally supplied an important aspect of “ground truth,” or validation, for brain imaging, suggesting that further development of high-resolution fMRI will be facilitated by this data analysis. In addition, several important insights into the nature of cortical topography follow from this work. The presence of anisotropy in cortical magnification factor is shown to follow mathematically from the shared boundary conditions at the V1–V2 and V2–V3 borders, and therefore may not causally follow from the existence of columnar systems in these areas, as is widely assumed. An application of the Wedge–Dipole model to localizing aspects of visual processing to specific cortical areas—extending previous work in correlating V1 cortical magnification factor to retinal anatomy or visual psychophysics data—is briefly discussed. PMID:16831455

  17. 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.

  18. 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.

  19. 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

  20. Mapping Vesta South Polar Quadrangle V-15SP: A Complex Geological Structure Dominates Vesta

    NASA Astrophysics Data System (ADS)

    Jaumann, R.; Yingst, R.; Schenk, P.; Schmedemann, N.; Williams, D. A.; Pieters, C. M.; Buczkowski, D.; Stephan, K.; Roatsch, T.; Preusker, F.; Scholten, F.; Neukum, G.; O'Brien, D. P.; Mest, S. C.; Krohn, K.; Marchi, S.; Filacchione, G.; Russell, C. T.; Raymond, C. A.; De Sanctis, M. C.

    2011-12-01

    Images of the asteroid and protoplanet 4Vesta by the Hubble Space Telescope in 1994 and 1996 revealed a ~460 km diameter feature at its south pole that was interpreted to be a large impact structure. NASA's Dawn spacecraft arrived at the asteroid Vesta on July 15, 2011 and collected science data during the approach to Vesta, a circular polar orbit at an altitude of 2700 km providing ~ 230 m/pix camera resolution and a lower main mapping orbit, at 700 km altitude with a camera resolution of ~ 65 m/pixel. As part of the geological analysis of Vesta's surface, a series of 15 quadrangle maps are being produced. We present the results of the geological mapping achieved for quadrangle V-15SP. Unit boundaries and feature characteristics were determined primarily using morphologic data. Color and spectral data was utilized to refine unit contacts and to separate compositional or mineralogical distinctions. Those units that could be discerned both in morphology and in the color data were interpreted as geologically derived units. The south polar feature is a semi-circular structure with a central hill that is characterized by a white-grey color and smoother texture distinctive from the surrounding terrain. Some images show patches of bright, smooth terrain on the central hill, perhaps indicative of impact melt or ponded volcanic flows. A complex network of deep grooves and ridges is the primary characteristic on the feature floor; these grooves appear radial to the central mound or trend along a north-south line. The structure also has a distinctive color from both the central hill and surrounding terrain, consistent with a different composition or texture. A steep semi-arcuate scarp bounds part of the outer perimeter of the south polar feature. Although asymmetric in general form, these characteristics do not contradict an impact origin but may also allow endogenic processes like convective downwelling or hybrid modification of an impact. Rapid rotation of Vesta during

  1. Subsurface mapping of Rustenburg Layered Suite (RLS), Bushveld Complex, South Africa: Inferred structural features using borehole data and spatial analysis

    NASA Astrophysics Data System (ADS)

    Bamisaiye, O. A.; Eriksson, P. G.; Van Rooy, J. L.; Brynard, H. M.; Foya, S.; Billay, A. Y.; Nxumalo, V.

    2017-08-01

    Faults and other structural features within the mafic-ultramafic layers of the Bushveld Complex have been a major issue mainly for exploration and mine planning. This study employed a new approach in detecting faults with both regional and meter scale offsets, which was not possible with the usually applied structure contour mapping. Interpretations of faults from structural and isopach maps were previously based on geological experience, while meter-scale faults were virtually impossible to detect from such maps. Spatial analysis was performed using borehole data primarily. This resulted in the identification of previously known structures and other hitherto unsuspected structural features. Consequently, the location, trends, and geometry of faults and some regional features within the Rustenburg Layered Suite (RLS) that might not be easy to detect through field mapping are adequately described in this study.

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

    USDA-ARS?s Scientific Manuscript database

    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 ...

  3. 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…

  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. Using continuous underway isotope measurements to map water residence time in hydrodynamically complex tidal environments

    USGS Publications Warehouse

    Downing, Bryan D.; Bergamaschi, Brian; Kendall, Carol; Kraus, Tamara; Dennis, Kate J.; Carter, Jeffery A.; von Dessonneck, Travis

    2016-01-01

    Stable isotopes present in water (δ2H, δ18O) have been used extensively to evaluate hydrological processes on the basis of parameters such as evaporation, precipitation, mixing, and residence time. In estuarine aquatic habitats, residence time (τ) is a major driver of biogeochemical processes, affecting trophic subsidies and conditions in fish-spawning habitats. But τ is highly variable in estuaries, owing to constant changes in river inflows, tides, wind, and water height, all of which combine to affect τ in unpredictable ways. It recently became feasible to measure δ2H and δ18O continuously, at a high sampling frequency (1 Hz), using diffusion sample introduction into a cavity ring-down spectrometer. To better understand the relationship of τ to biogeochemical processes in a dynamic estuarine system, we continuously measured δ2H and δ18O, nitrate and water quality parameters, on board a small, high-speed boat (5 to >10 m s–1) fitted with a hull-mounted underwater intake. We then calculated τ as is classically done using the isotopic signals of evaporation. The result was high-resolution (∼10 m) maps of residence time, nitrate, and other parameters that showed strong spatial gradients corresponding to geomorphic attributes of the different channels in the area. The mean measured value of τ was 30.5 d, with a range of 0–50 d. We used the measured spatial gradients in both τ and nitrate to calculate whole-ecosystem uptake rates, and the values ranged from 0.006 to 0.039 d–1. The capability to measure residence time over single tidal cycles in estuaries will be useful for evaluating and further understanding drivers of phytoplankton abundance, resolving differences attributable to mixing and water sources, explicitly calculating biogeochemical rates, and exploring the complex linkages among time-dependent biogeochemical processes in hydrodynamically complex environments such as estuaries.

  6. Using Continuous Underway Isotope Measurements To Map Water Residence Time in Hydrodynamically Complex Tidal Environments.

    PubMed

    Downing, Bryan D; Bergamaschi, Brian A; Kendall, Carol; Kraus, Tamara E C; Dennis, Kate J; Carter, Jeffery A; Von Dessonneck, Travis S

    2016-12-20

    Stable isotopes present in water (δ(2)H, δ(18)O) have been used extensively to evaluate hydrological processes on the basis of parameters such as evaporation, precipitation, mixing, and residence time. In estuarine aquatic habitats, residence time (τ) is a major driver of biogeochemical processes, affecting trophic subsidies and conditions in fish-spawning habitats. But τ is highly variable in estuaries, owing to constant changes in river inflows, tides, wind, and water height, all of which combine to affect τ in unpredictable ways. It recently became feasible to measure δ(2)H and δ(18)O continuously, at a high sampling frequency (1 Hz), using diffusion sample introduction into a cavity ring-down spectrometer. To better understand the relationship of τ to biogeochemical processes in a dynamic estuarine system, we continuously measured δ(2)H and δ(18)O, nitrate and water quality parameters, on board a small, high-speed boat (5 to >10 m s(-1)) fitted with a hull-mounted underwater intake. We then calculated τ as is classically done using the isotopic signals of evaporation. The result was high-resolution (∼10 m) maps of residence time, nitrate, and other parameters that showed strong spatial gradients corresponding to geomorphic attributes of the different channels in the area. The mean measured value of τ was 30.5 d, with a range of 0-50 d. We used the measured spatial gradients in both τ and nitrate to calculate whole-ecosystem uptake rates, and the values ranged from 0.006 to 0.039 d(-1). The capability to measure residence time over single tidal cycles in estuaries will be useful for evaluating and further understanding drivers of phytoplankton abundance, resolving differences attributable to mixing and water sources, explicitly calculating biogeochemical rates, and exploring the complex linkages among time-dependent biogeochemical processes in hydrodynamically complex environments such as estuaries.

  7. Mapping Complexity: the Wavy Edges of the Encke and Keeler Gaps in Saturn's Rings

    NASA Astrophysics Data System (ADS)

    Torrey, Paul A.; Tiscareno, M. S.; Burns, J. A.; Porco, C. C.

    2008-05-01

    The edges of the Keeler and Encke gaps of Saturn's A Ring are significantly disturbed as the embedded moons (Daphnis and Pan, respectively) interact with the adjacent dense rings. Cassini images of these edges reveal the structure to be much more complex than predicted by analytical perturbation theory (Tiscareno et al 2005, DPS). In the Encke Gap, we see both amplitude and frequency modulations of the expected monochromatic sinusoid, as well as some sharper "glitches” in the pattern. In the Keeler Gap, the expected 32-lobed pattern in the inner edge due to a resonance with Prometheus is "lumpy” and asymmetric, while the outer edge features sharp-edged asymmetric "wisps". Much of the unexpected structure may be due to the superposition of multiple patterns, each moving with its own frequency. Determination of these pattern speeds will help us to identify the source of the perturbations, and may help us better appreciate the transfer of angular momentum between dense particle disks and embedded moons. We will present high-resolution maps of these edges covering all longitudes and at many points in time.

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

    NASA Astrophysics Data System (ADS)

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

    2014-08-01

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

  9. Numerical model for mapping of complex hydrogeological conditions: the Chmielnik area (South Poland) case study

    NASA Astrophysics Data System (ADS)

    Buszta, Kamila; Szklarczyk, Tadeusz; Malina, Grzegorz

    2017-04-01

    Detailed analysis of hydrogeological conditions at a study area is the basis for characterising adjacent groundwater circulation systems. It is also an essential element during executing hydrogeological documentations. The goal of this work was to reconstruct on a numerical model natural groundwater circulation systems of the studied area located within the municipality of Chmielnik in the region of Kielce (South Poland). The area is characterized by a complex geological structure, which along with the existing hydrographic network, makes the scheme of groundwater circulation complicated and difficult to map on a numerical model. The studied area is situated at the border of three geological units: on the North - the extended portion of the Palaeozoic Swietokrzyskie Mountains (mainly Devonian and Permian), in the center - the S-W part of the Mesozoic Margin of the Swietokrzyskie Mountains, and on the South - a marginal zone of the Carpathian Foredeep. The whole area belongs to the Vistula river basin, and it includes catchments of its left tributaries: the Nida and Czarna Staszowska rivers. Based on the collected field and archival hydrogeological, hydrological and sozological data a conceptual model was built, under which a numerical model of groundwater flow was developed using the specialized software - Visual MODFLOW. The numerical model maps the five-layer groundwater circulation system in conjunction with surface watercourses. Such division reflects appropriately the variability of hydrogeological parameters within the geological structures. Two principal and exploited aquifers comprise: a fractured-porous Neogene and fractured Upper Jurassic formations. The external model borders are based primarily on surface watercourses and locally on watersheds. The modelled area of 130 km2 was divided into square grids of 50 m. The model consists of 275 rows and 277 columns. Each of five layers was simulated with the same number of active blocks. In the construction of

  10. 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.

  11. Structure of the PSD-95/MAP1A complex reveals a unique target recognition mode of the MAGUK GK domain.

    PubMed

    Xia, Yitian; Shang, Yuan; Zhang, Rongguang; Zhu, Jinwei

    2017-08-10

    The PSD-95 family of membrane-associated guanylate kinases (MAGUKs) are major synaptic scaffold proteins and play crucial roles in the dynamic regulation of dendritic remodelling, which is understood to be the foundation of synaptogenesis and synaptic plasticity. The guanylate kinase (GK) domain of MAGUK family proteins functions as a phosphor-peptide binding module. However, the GK domain of PSD-95 has been found to directly bind to a peptide sequence within the C-terminal region of neuronal-specific microtubule-associated protein 1A (MAP1A), although the detailed molecular mechanism governing this phosphorylation-independent interaction at the atomic level is missing. In the present study, we determine the crystal structure of PSD-95 GK in complex with the MAP1A peptide at 2.6-Å resolution. The complex structure reveals that, unlike a linear and elongated conformation in the phosphor-peptide/GK complexes, the MAP1A peptide adopts a unique conformation with a stretch of hydrophobic residues far from each other in the primary sequence clustering and interacting with the 'hydrophobic site' of PSD-95 GK and a highly conserved aspartic acid of MAP1A (D2117) mimicking the phosphor-serine/threonine in binding to the 'phosphor-site' of PSD-95 GK. We demonstrate that the MAP1A peptide may undergo a conformational transition upon binding to PSD-95 GK. Further structural comparison of known DLG GK-mediated complexes reveals the target recognition specificity and versatility of DLG GKs. © 2017 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  12. Adhesion Regulates MAP Kinase-Ternary Complex Factor Exchange to Control a Proliferative Transcriptional Switch

    PubMed Central

    Wozniak, Michele A.; Cheng, Catherine Q.; Shen, Colette J.; Gao, Lin; Olarerin-George, Anthony O.; Won, Kyoung-Jae; Hogenesch, John B.; Chen, Christopher S.

    2013-01-01

    Background The ternary complex factors (TCFs; Elk1, Net, and Sap-1) are growth factor-responsive transcription co-factors of serum response factor (SRF) and are activated by map kinase (MAPK) phosphorylation to regulate immediate early gene transcription. Although cell adhesion also can regulate immediate early genes and proliferation, the mechanism for this effect has remained unexplored. Results Restricting adhesion and spreading of G0-synchronized cells on substrates with decreasing size of micropatterned islands of fibronectin suppressed serum-induced immediate early gene expression and S-phase entry. Knockdown of Sap-1 decreased expression of the immediate early genes egr1 and fos and subsequent proliferation normally present with high adhesion, whereas knockdown of Net rescued egr1 and fos expression and proliferation normally suppressed by low adhesion. ChIP studies showed increased occupancy of egr1 and fos promoters by Sap-1 with high adhesion, while low adhesion increased Net occupancy. This switch in TCF promoter binding was regulated by an adhesion-mediated switch in MAPK activity. Increasing adhesion enhanced serum-induced JNK activity while suppressing p38 activity, leading to increased Sap-1 phosphorylation and Net dephosphorylation, and switching Net with Sap-1 at egr1 and fos promoters to support proliferation. Microarray studies confirmed this switch in TCF regulation of proliferative genes and uncovered novel gene targets and functions co-regulated by Sap-1 and Net. Conclusions These data demonstrate a key role for the TCFs in adhesion-induced transcription and proliferation, and reveals a novel MAPK/TCF transcriptional switch that controls this process. PMID:23063436

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

    PubMed Central

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

    2015-01-01

    We use computer simulations to investigate the amount of genetic variation for complex traits that can be revealed by single-SNP genome-wide association studies (GWAS) or regional heritability mapping (RHM) analyses based on full genome sequence data or SNP chips. We model a large population subject to mutation, recombination, selection, and drift, assuming a pleiotropic model of mutations sampled from a bivariate distribution of effects of mutations on a quantitative trait and fitness. The pleiotropic model investigated, in contrast to previous models, implies that common mutations of large effect are responsible for most of the genetic variation for quantitative traits, except when the trait is fitness itself. We show that GWAS applied to the full sequence increases the number of QTL detected by as much as 50% compared to the number found with SNP chips but only modestly increases the amount of additive genetic variance explained. Even with full sequence data, the total amount of additive variance explained is generally below 50%. Using RHM on the full sequence data, a slightly larger number of QTL are detected than by GWAS if the same probability threshold is assumed, but these QTL explain a slightly smaller amount of genetic variance. Our results also suggest that most of the missing heritability is due to the inability to detect variants of moderate effect (∼0.03–0.3 phenotypic SDs) segregating at substantial frequencies. Very rare variants, which are more difficult to detect by GWAS, are expected to contribute little genetic variation, so their eventual detection is less relevant for resolving the missing heritability problem. PMID:26482794

  14. Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize

    PubMed Central

    Riedelsheimer, Christian; Lisec, Jan; Czedik-Eysenberg, Angelika; Sulpice, Ronan; Flis, Anna; Grieder, Christoph; Altmann, Thomas; Stitt, Mark; Willmitzer, Lothar; Melchinger, Albrecht E.

    2012-01-01

    The diversity of metabolites found in plants is by far greater than in most other organisms. Metabolic profiling techniques, which measure many of these compounds simultaneously, enabled investigating the regulation of metabolic networks and proved to be useful for predicting important agronomic traits. However, little is known about the genetic basis of metabolites in crops such as maize. Here, a set of 289 diverse maize inbred lines was genotyped with 56,110 SNPs and assayed for 118 biochemical compounds in the leaves of young plants, as well as for agronomic traits of mature plants in field trials. Metabolite concentrations had on average a repeatability of 0.73 and showed a correlation pattern that largely reflected their functional grouping. Genome-wide association mapping with correction for population structure and cryptic relatedness identified for 26 distinct metabolites strong associations with SNPs, explaining up to 32.0% of the observed genetic variance. On nine chromosomes, we detected 15 distinct SNP–metabolite associations, each of which explained more then 15% of the genetic variance. For lignin precursors, including p-coumaric acid and caffeic acid, we found strong associations (P values to ) with a region on chromosome 9 harboring cinnamoyl-CoA reductase, a key enzyme in monolignol synthesis and a target for improving the quality of lignocellulosic biomass by genetic engineering approaches. Moreover, lignin precursors correlated significantly with lignin content, plant height, and dry matter yield, suggesting that metabolites represent promising connecting links for narrowing the genotype–phenotype gap of complex agronomic traits. PMID:22615396

  15. 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.

  16. 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…

  17. MDcons: Intermolecular contact maps as a tool to analyze the interface of protein complexes from molecular dynamics trajectories.

    PubMed

    Abdel-Azeim, Safwat; Chermak, Edrisse; Vangone, Anna; Oliva, Romina; Cavallo, Luigi

    2014-01-01

    Molecular Dynamics (MD) simulations of protein complexes suffer from the lack of specific tools in the analysis step. Analyses of MD trajectories of protein complexes indeed generally rely on classical measures, such as the RMSD, RMSF and gyration radius, conceived and developed for single macromolecules. As a matter of fact, instead, researchers engaged in simulating the dynamics of a protein complex are mainly interested in characterizing the conservation/variation of its biological interface. On these bases, herein we propose a novel approach to the analysis of MD trajectories or other conformational ensembles of protein complexes, MDcons, which uses the conservation of inter-residue contacts at the interface as a measure of the similarity between different snapshots. A "consensus contact map" is also provided, where the conservation of the different contacts is drawn in a grey scale. Finally, the interface area of the complex is monitored during the simulations. To show its utility, we used this novel approach to study two protein-protein complexes with interfaces of comparable size and both dominated by hydrophilic interactions, but having binding affinities at the extremes of the experimental range. MDcons is demonstrated to be extremely useful to analyse the MD trajectories of the investigated complexes, adding important insight into the dynamic behavior of their biological interface. MDcons specifically allows the user to highlight and characterize the dynamics of the interface in protein complexes and can thus be used as a complementary tool for the analysis of MD simulations of both experimental and predicted structures of protein complexes.

  18. 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.

  19. 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

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-05-01

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

  3. Documentation & Condition Mapping for Restoration & Revitalisation of Historic Sheesh Mahal & Char Bagh Complex in Patiala (punjab), India

    NASA Astrophysics Data System (ADS)

    Dasgupta, S.

    2017-08-01

    Located in the Northern State of Punjab, the historic city of Patiala has always been a centre of culture in north India, and has seen the evolution of its own distinct style of architecture with Rajput and Mughal influences. The city is renowned for its rich architectural heritage, Music, Craft, Sports and Cuisine. The fourth Maharaja Narinder Singh was a great patron of art, architecture and music and it was during his time that several palaces like the Moti Bagh Palace, Sheesh Mahal and Banasur Bagh were designed followed by Baradari Palace. Later it was Maharaja Bhupinder Singh (1900-1938) who made Patiala State famous with his lavish lifestyle.This paper describes the process followed for Documentation and condition assessment of the historic Sheesh Mahal & Char Bagh Complex in order to restore and revitalise the palace building and the Mughal garden. The exercise included Archival research, Field surveys, Condition Mapping, inventories using traditional methods as well as GIS and preparation of restoration & conservation solutions along with post conservation management manual. The Major challenges encountered were identifying the correct documentation methodology for mapping as well as managing the large database generated on site. The Documentation and Mapping was used as a significant tool to guide towards the conservation and Management strategy of the complex.

  4. 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.

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

    PubMed

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

    2011-10-17

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

  6. 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

  7. 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.

  8. High spatial resolution spectral unmixing for mapping ash species across a complex urban environment

    Treesearch

    Jennifer Pontius; Ryan P. Hanavan; Richard A. Hallett; Bruce D. Cook; Lawrence A. Corp

    2017-01-01

    Ash (Fraxinus L.) species are currently threatened by the emerald ash borer (EAB; Agrilus planipennis Fairmaire) across a growing area in the eastern US. Accurate mapping of ash species is required to monitor the host resource, predict EAB spread and better understand the short- and long-term effects of EAB on the ash resource...

  9. Extensive recombination rate variation in the house mouse species complex inferred from genetic linkage maps.

    PubMed

    Dumont, Beth L; White, Michael A; Steffy, Brian; Wiltshire, Tim; Payseur, Bret A

    2011-01-01

    The rate of recombination is a key genomic parameter that displays considerable variation among taxa. Species comparisons have demonstrated that the rate of evolution in recombination rate is strongly dependent on the physical scale of measurement. Individual recombination hotspots are poorly conserved among closely related taxa, whereas genomic-scale recombination rate variation bears a strong signature of phylogenetic history. In contrast, the mode and tempo of evolution in recombination rates measured on intermediate physical scales is poorly understood. Here, we conduct a detailed statistical comparison between two whole-genome F₂ genetic linkage maps constructed from experimental intercrosses between closely related house mouse subspecies (Mus musculus). Our two maps profile a common wild-derived inbred strain of M. m. domesticus crossed to distinct wild-derived inbred strains representative of two other house mouse subspecies, M. m. castaneus and M. m. musculus. We identify numerous orthologous genomic regions with significant map length differences between these two crosses. Because the genomes of these recently diverged house mice are highly collinear, observed differences in map length (centimorgans) are suggestive of variation in broadscale recombination rate (centimorgans per megabase) within M. musculus. Collectively, these divergent intervals span 19% of the house mouse genome, disproportionately aggregating on the X chromosome. In addition, we uncover strong statistical evidence for a large effect, sex-linked, site-specific modifier of recombination rate segregating within M. musculus. Our findings reveal considerable variation in the megabase-scale recombination landscape among recently diverged taxa and underscore the continued importance of genetic linkage maps in the post-genome era.

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

    PubMed

    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.

  11. 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.

  12. Heritability and Demographic Analyses in the Large Isolated Population of Val Borbera Suggest Advantages in Mapping Complex Traits Genes

    PubMed Central

    Masciullo, Corrado; Cverhova, Valeria; Lori, Francesca; Pistis, Giorgio; Bione, Silvia; Gasparini, Paolo; Ulivi, Sheila; Ciullo, Marina; Nutile, Teresa; Bosi, Emanuele; Sirtori, Marcella; Mignogna, Giovanna; Rubinacci, Alessandro; Buetti, Iwan; Camaschella, Clara; Petretto, Enrico; Toniolo, Daniela

    2009-01-01

    Background Isolated populations are a useful resource for mapping complex traits due to shared stable environment, reduced genetic complexity and extended Linkage Disequilibrium (LD) compared to the general population. Here we describe a large genetic isolate from the North West Apennines, the mountain range that runs through Italy from the North West Alps to the South. Methodology/Principal Findings The study involved 1,803 people living in 7 villages of the upper Borbera Valley. For this large population cohort, data from genealogy reconstruction, medical questionnaires, blood, anthropometric and bone status QUS parameters were evaluated. Demographic and epidemiological analyses indicated a substantial genetic component contributing to each trait variation as well as overlapping genetic determinants and family clustering for some traits. Conclusions/Significance The data provide evidence for significant heritability of medical relevant traits that will be important in mapping quantitative traits. We suggest that this population isolate is suitable to identify rare variants associated with complex phenotypes that may be difficult to study in larger but more heterogeneous populations. PMID:19847309

  13. 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…

  14. "But there are no snakes in the wood": risk mapping as an outcome measure in evaluating complex interventions.

    PubMed

    Power, Robert; Langhaug, Lisa; Cowan, Frances

    2007-06-01

    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. 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. 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. 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.

  15. “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

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

    USDA-ARS?s Scientific Manuscript database

    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...

  17. Archival, demographic and genetic studies define a Sardinian sub-isolate as a suitable model for mapping complex traits.

    PubMed

    Angius, A; Melis, P M; Morelli, L; Petretto, E; Casu, G; Maestrale, G B; Fraumene, C; Bebbere, D; Forabosco, P; Pirastu, M

    2001-08-01

    Genetic isolates represent exceptional resources for the mapping of complex traits but not all isolates are similar. We have selected a genetic and cultural isolate, the village of Talana from an isolated area of Sardinia, and propose that this population is suitable for the mapping of complex traits. A wealth of historical and archive data allowed the reconstruction of the demographic and genealogical history of the village. Key features of the population, which has grown slowly with no significant immigration, were defined by using a combination of historical, demographic and genetic studies. The genealogy of each Talana inhabitant was reconstructed and the main maternal and paternal lineages of the village were defined. Haplotype and phylogenetic analyses of the Y chromosome and characterisation of mitochondrial DNA haplogroups were used to determine the number of ancestral village founders. The extent of linkage disequilibrium (LD) was evaluated by the analysis of several microsatellites in chromosomal region Xq13.3, which was previously used to asses the extension of LD. Genealogical reconstructions were confirmed and reinforced by the genetic analyses, since some lineages were found to have merged prior to the beginning of the archival records, suggesting an even smaller number of founders than initially predicted. About 80% of the present-day population appears to derive from eight paternal and eleven maternal ancestral lineages. LD was found to span, on average, a 5-Mb region in Xq13.3. This suggests the possibility of identifying identical-by-descent regions associated with complex traits in a genome-wide search by using a low-density marker map. The present study emphasises the importance of combining genetic studies with genealogical and historical information.

  18. Automatic Generation of Issue Maps: Structured, Interactive Outputs for Complex Information Needs

    DTIC Science & Technology

    2012-09-01

    keys fell into the river during rafting), and for being a great friend (with a perfect sense of timing); Ali Kemal Sinop, for spring carnivals...ship president , Clinton, water portauprince, building, body Silsby, abduct, jail Figure 4.4: Map about the earthquake in Haiti, before interaction...structure. Instead, articles are sorted chronologically and displayed in a fashion similar to Google News. We recruited participants in the study via Amazon

  19. keep your models up-to-date: connecting community mapping data to complex urban flood modelling

    NASA Astrophysics Data System (ADS)

    Winsemius, Hessel; Eilander, Dirk; Ward, Philip; Diaz Loaiza, Andres; Iliffe, Mark; Mawanda, Shaban; Luo, Tianyi; Kimacha, Nyambiri; Chen, Jorik

    2017-04-01

    The world is urbanizing rapidly. According to the United Nation's World Urbanization Prospect, 50% of the global population already lives in urban areas today. This number is expected to grow to 66% by 2050. The rapid changes in these urban environments go hand in hand with rapid changes in natural hazard risks, in particular in informal unplanned neighbourhoods. In Dar Es Salaam - Tanzania, flood risk dominates and given the rapid changes in the city, continuous updates of detailed street level hazard and risk mapping are needed to adequately support decision making for urban planning, infrastructure design and disaster response. Over the past years, the Ramani Huria and Zuia Mafuriko projects have mapped the most flood prone neighbourhoods, including roads, buildings, drainage and land use and contributed data to the open-source OpenStreetMap database. In this contribution, we will demonstrate how we mobilize these contributed data to establish dynamic flood models for Dar Es Salaam and keep these up-to-date by making a direct link between the data, and model schematization. The tools automatically establish a sound 1D drainage network as well as a high resolution terrain dataset, by fusing the OpenStreetMap data with existing lower resolution terrain data such as the globally available satellite based SRTM 30. It then translates these fully automatically into the inputs required for the D-HYDRO modeling suite. Our tools are built such that community and stakeholder knowledge can be included in the model details through workshops with the tools so that missing essential information about the city's details can be augmented on-the-fly. This process creates a continuous dialogue between members of the community that collect data, and stakeholders requiring data for flood models. Moreover, used taxonomy and data filtering can be configured to conditions in other cities, making the tools generic and scalable. The tools are made available open-source.

  20. Dynamic semiparametric Bayesian models for genetic mapping of complex trait with irregular longitudinal data.

    PubMed

    Das, Kiranmoy; Li, Jiahan; Fu, Guifang; Wang, Zhong; Li, Runze; Wu, Rongling

    2013-02-10

    Many phenomena of fundamental importance to biology and biomedicine arise as a dynamic curve, such as organ growth and HIV dynamics. The genetic mapping of these traits is challenged by longitudinal variables measured at irregular and possibly subject-specific time points, in which case nonnegative definiteness of the estimated covariance matrix needs to be guaranteed. We present a semiparametric approach for genetic mapping within the mixture-model setting by jointly modeling mean and covariance structures for irregular longitudinal data. Penalized spline is used to model the mean functions of individual quantitative trait locus (QTL) genotypes as latent variables, whereas an extended generalized linear model is used to approximate the covariance matrix. The parameters for modeling the mean-covariances are estimated by MCMC, using the Gibbs sampler and the Metropolis-Hastings algorithm. We derive the full conditional distributions for the mean and covariance parameters and compute Bayes factors to test the hypothesis about the existence of significant QTLs. We used the model to screen the existence of specific QTLs for age-specific change of body mass index with a sparse longitudinal data set. The new model provides powerful means for broadening the application of genetic mapping to reveal the genetic control of dynamic traits.

  1. From the Cover: Simplifying the representation of complex free-energy landscapes using sketch-map.

    PubMed

    Ceriotti, Michele; Tribello, Gareth A; Parrinello, Michele

    2011-08-09

    A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.

  2. Feasibility of DINSAR for mapping complex motion fields of alpine ice- and rock-glaciers

    NASA Astrophysics Data System (ADS)

    Nagler, Thomas; Mayer, Christoph; Rott, Helmut

    2002-01-01

    Possibilities and methods of differential SAR interferometry (DINSAR) for mapping the motion of alpine ice and rock glaciers of small spatial extent were investigated. Test sites for these studies were the glacier Hintereisferner (covering 8 km2 in area) and several of its small side glaciers, and the rock glaciers Inner and Outer Hochebenkar, located in the Ötztaler mountains, Austria. For mapping the motion of the ice glaciers only one-day repeat pass SAR images from the ERS Tandem Mission, acquired during winter, were useful. 35-day repeat pass interferometric images did not show sufficient coherence. On the rock glaciers the coherence is preserved over longer periods. 35-day ERS SAR repeat pass interferograms from summer were used for motion analysis. The topographic phase was derived by differential methods using several one-day tandem pairs and applying the multi-baseline technique. The surface-parallel flow assumption was used for estimating the velocity vectors. The accuracy of the interferometric motion is assessed by comparison with field measurements and aerial photogrammetric analysis. The detail of the interferometric maps, but spaceborne DINSAR is a very cost-effective tool for comprehensive regional surveys and monitoring of ice and rock glaciers with good accuracy.

  3. Mapping the UV Photophysics of Platinum Metal Complexes Bound to Nucleobases

    NASA Astrophysics Data System (ADS)

    Sen, Ananya; Dessent, Caroline

    2015-03-01

    We report the first UV laser spectroscopic study of isolated gas-phase complexes of Platinum metal complex anions bound to a nucleobase as model systems for exploring at the molecular level the key photophysical processes involved in photodynamic therapy. Spectra of the PtIV CN 6 2 - • Uracil and PtII CN 4 2 - • Uracil complexes were acquired across the 220 -320 nm range using mass-selective photodepletion and photofragment action spectroscopy. The spectra of both complexes reveal prominent UV absorption bands that we assign primarily to excitation of the Uracil π - π * localized chromophore. Distinctive UV photofragments are observed for the complexes, with PtIV CN 6 2 - • Uracil photoexcitation resulting in complex fission, while PtII CN 4 2 - • Uracil photoexcitation initiates a nucleobase proton-transfer reaction across 4.4 -5.2 eV and electron detachment above 5.2 eV. The observed photofragments are consistent with ultrafast decay of a Uracil localized excited state back to the electronic ground state followed by intramolecular vibrational relaxation and ergodic complex fragmentation. In addition, we present recent results to explore how the photophysics of the Platinum complex-nucleobase clusters evolves as a function of nucleobase. Results are presented for PtII CN 4 2 - • Uracil complexed to Cytosine, Thymine and Adenine, reveal distinctive decay dynamics which we attribute to the intrinsic decay dynamics of the nucleobase. JPC. Lett. 2014, 5, 3281 to 3285 and PCCP 2014, 16, 15490 to 15500.

  4. Intracortical Microstimulation Maps of Motor, Somatosensory, and Posterior Parietal Cortex in Tree Shrews (Tupaia belangeri) Reveal Complex Movement Representations.

    PubMed

    Baldwin, Mary K L; Cooke, Dylan F; Krubitzer, Leah

    2017-02-01

    Long-train intracortical microstimulation (LT-ICMS) is a popular method for studying the organization of motor and posterior parietal cortex (PPC) in mammals. In primates, LT-ICMS evokes both multijoint and multiple-body-part movements in primary motor, premotor, and PPC. In rodents, LT-ICMS evokes complex movements of a single limb in motor cortex. Unfortunately, very little is known about motor/PPC organization in other mammals. Tree shrews are closely related to both primates and rodents and could provide insights into the evolution of complex movement domains in primates. The present study investigated the extent of cortex in which movements could be evoked with ICMS and the characteristics of movements elicited using both short train (ST) and LT-ICMS in tree shrews. We demonstrate that LT-ICMS and ST-ICMS maps are similar, with the movements elicited with ST-ICMS being truncated versions of those elicited with LT-ICMS. In addition, LT-ICMS-evoked complex movements within motor cortex similar to those in rodents. More complex movements involving multiple body parts such as the hand and mouth were also elicited in motor cortex and PPC, as in primates. Our results suggest that complex movement networks present in PPC and motor cortex were present in mammals prior to the emergence of primates.

  5. 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

  6. 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

  7. Studying Spectral Variability of an Igneous Stratified Complex as a Tool to Map Lunar Highlands

    NASA Astrophysics Data System (ADS)

    Carli, C.; Sgavetti, M.; Capaccioni, F.; Serventi, G.

    2012-07-01

    Moon Mineralogy Mapper data have revealed different portion of magmatic chambers or separate plutons. We analysed Stillwater Complex (SWC) rock suite. Spectral signatures and spectral parameters could help to interpret the new spectral lunar data.

  8. 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. Copyright © 2016 Elsevier B.V. All rights reserved.

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

    PubMed Central

    Benn, J; Schneider, R J

    1994-01-01

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

  10. Near-real-time mapping of GNSS products from an area of complex topography for operational meteorology

    NASA Astrophysics Data System (ADS)

    Terradellas, E.; Téllez, B.; Valdés, M.

    2009-04-01

    Triggering of severe convection is often focalized in areas of moisture convergence. On the other hand, the inflow of wet air usually plays an important role in the fog onset, even in typical events of radiation fog. Therefore, knowledge of the spatial distribution of atmospheric humidity is crucial to the operational forecaster, especially in the weather nowcasting at regions of complex topography. Radiosonde measurements are very sparse and present a limited time resolution of 6 or 12 hours. Near-real-time mapping of the vertically-integrated water vapour (IWV) retrieved from ground-based GNSS observations is an alternative way to present information on the horizontal distribution of humidity with a high time resolution. On average, nearly half the total atmospheric water is between sea level and a 1.5-km height. Therefore, the horizontal distribution of water vapour is strongly modulated by the topography. In the Iberian Peninsula, an area of complex topography, the penetration of shallow air masses of maritime origin through passes underneath mountain ranges is a common mechanism of moistening the air of inland regions. This fact makes difficult to build a realistic map of IWV without a high-resolution network of GNSS receivers. A method to smooth the dependence on height of the magnitude to be interpolated is presented here. The method is based on the decomposition of any IWV value into a constant statistical average and a variable part. The mean geographical distribution of IWV is computed from the dataset of daily averages at the different stations. Since this dataset usually presents some gaps, the estimation of the mean values and covariance matrix is performed together with the imputation of the missing values using an iterative method based on a regularized maximization-expectation algorithm. A linear regression yields a model accounting for the statistical dependence of the mean values on latitude, longitude and altitude. The model residuals are then

  11. 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

  12. Processing Connectives with a Complex Form-Function Mapping in L2: The Case of French “En Effet”

    PubMed Central

    Zufferey, Sandrine; Gygax, Pascal M.

    2017-01-01

    Discourse connectives are often reported to be difficult for second language learners, yet the causes of these difficulties are still not fully understood. In this paper, we test the ability of German-speaking learners to process and understand a connective with a complex form-function mapping in their L2-French, namely “en effet,” a connective that does not have an exact translation equivalent in their L1-German. We assess learners' competence both in an on-line processing experiment and an off-line judgment task. We argue that one of the interesting specificities of “en effet” is that the two coherence relations that it conveys cannot equally be conveyed implicitly. This case study therefore provides some information about advanced learners' sensitivity to the necessity of explicitly marking a coherence relation by the use of a connective. Our results indicate that advanced learners do not perceive the difference between relations that need and need not be marked by a discourse connective and have not acquired the complex form-function mapping of “en effet.” We argue that these difficulties cannot be attributed to negative transfer effects, but reflect general limitations in proficiency. PMID:28769842

  13. Regional heritability mapping and genome-wide association identify loci for complex growth, wood and disease resistance traits in Eucalyptus.

    PubMed

    Resende, Rafael Tassinari; Resende, Marcos Deon Vilela; Silva, Fabyano Fonseca; Azevedo, Camila Ferreira; Takahashi, Elizabete Keiko; Silva-Junior, Orzenil Bonfim; Grattapaglia, Dario

    2017-02-01

    Although genome-wide association studies (GWAS) have provided valuable insights into the decoding of the relationships between sequence variation and complex phenotypes, they have explained little heritability. Regional heritability mapping (RHM) provides heritability estimates for genomic segments containing both common and rare allelic effects that individually contribute too little variance to be detected by GWAS. We carried out GWAS and RHM for seven growth, wood and disease resistance traits in a breeding population of 768 Eucalyptus hybrid trees using EuCHIP60K. Total genomic heritabilities accounted for large proportions (64-89%) of pedigree-based trait heritabilities, providing additional evidence that complex traits in eucalypts are controlled by many sequence variants across the frequency spectrum, each with small contributions to the phenotypic variance. RHM detected 26 quantitative trait loci (QTLs) encompassing 2191 single nucleotide polymorphisms (SNPs), whereas GWAS detected 13 single SNP-trait associations. RHM and GWAS QTLs individually explained 5-15% and 4-6% of the genomic heritability, respectively. RHM was superior to GWAS in capturing larger proportions of genomic heritability. Equated to previously mapped QTLs, our results highlighted genomic regions for further examination towards gene discovery. RHM-QTLs bearing a combination of common and rare variants could be useful enhancements to incorporate prior knowledge of the underlying genetic architecture in genomic prediction models.

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

    PubMed Central

    Weber, Allison L.; Briggs, William H.; Rucker, Jesse; Baltazar, Baltazar M.; de Jesús Sánchez-Gonzalez, José; Feng, Ping; Buckler, Edward S.; Doebley, John

    2008-01-01

    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 association with 31 traits in a population of 817 individuals. Thirty-three significant associations for markers from 15 candidate genes and 10 traits survive correction for multiple testing. Our analyses suggest several new putative causative relationships between specific genes and trait variation in teosinte. For example, two ramosa genes (ra1 and ra2) associate with ear structure, and the MADS-box gene, zagl1, associates with ear shattering. Since zagl1 was previously shown to be a target of selection during maize domestication, we suggest that this gene was under selection for its effect on the loss of ear shattering, a key domestication trait. All observed effects were relatively small in terms of the percentage of phenotypic variation explained (<10%). We also detected several epistatic interactions between markers in the same gene that associate with the same trait. Candidate-gene-based association mapping appears to be a promising method for investigating the inheritance of complex traits in teosinte. PMID:18791250

  15. Making sense of complex data: a mapping process for analyzing findings of a realist review on guideline implementability.

    PubMed

    Kastner, Monika; Makarski, Julie; Hayden, Leigh; Durocher, Lisa; Chatterjee, Ananda; Brouwers, Melissa; Bhattacharyya, Onil

    2013-09-12

    Realist reviews offer a rigorous method to analyze heterogeneous data emerging from multiple disciplines as a means to develop new concepts, understand the relationships between them, and identify the evidentiary base underpinning them. However, emerging synthesis methods such as the Realist Review are not well operationalized and may be difficult for the novice researcher to grasp. The objective of this paper is to describe the development of an analytic process to organize and synthesize data from a realist review. Clinical practice guidelines have had an inconsistent and modest impact on clinical practice, which may in part be due to limitations in their design. This study illustrates the development of a transparent method for organizing and analyzing a complex data set informed by a Realist Review on guideline implementability to better understand the characteristics of guidelines that affect their uptake in practice (e.g., clarity, format). The data organization method consisted of 4 levels of refinement: 1) extraction and 2) organization of data; 3) creation of a conceptual map of guideline implementability; and 4) the development of a codebook of definitions. This new method is comprised of four steps: data extraction, data organization, development of a conceptual map, and operationalization vis-a-vis a codebook. Applying this method, we extracted 1736 guideline attributes from 278 articles into a consensus-based set of categories, and collapsed them into 5 core conceptual domains for our guideline implementability map: Language, Format, Rigor of development, Feasibility, Decision-making. This study advances analysis methods by offering a systematic approach to analyzing complex data sets where the goals are to condense, organize and identify relationships.

  16. Complex Structure in Class 0 Protostellar Envelopes. II. Kinematic Structure from Single-dish and Interferometric Molecular Line Mapping

    NASA Astrophysics Data System (ADS)

    Tobin, John J.; Hartmann, Lee; Chiang, Hsin-Fang; Looney, Leslie W.; Bergin, Edwin A.; Chandler, Claire J.; Masqué, Josep M.; Maret, Sébastien; Heitsch, Fabian

    2011-10-01

    We present a study of dense molecular gas kinematics in 17 nearby protostellar systems using single-dish and interferometric molecular line observations. The non-axisymmetric envelopes around a sample of Class 0/I protostars were mapped in the N2H+ (J = 1 → 0) tracer with the IRAM 30 m, CARMA, and Plateau de Bure Interferometer, as well as NH3 (1,1) with the Very Large Array. The molecular line emission is used to construct line-center velocity and linewidth maps for all sources to examine the kinematic structure in the envelopes on spatial scales from 0.1 pc to ~1000 AU. The direction of the large-scale velocity gradients from single-dish mapping is within 45° of normal to the outflow axis in more than half the sample. Furthermore, the velocity gradients are often quite substantial, the average being ~2.3 km s-1 pc-1. The interferometric data often reveal small-scale velocity structure, departing from the more gradual large-scale velocity gradients. In some cases, this likely indicates accelerating infall and/or rotational spin-up in the inner envelope; the median velocity gradient from the interferometric data is ~10.7 km s-1 pc-1. In two systems, we detect high-velocity HCO+ (J = 1 → 0) emission inside the highest-velocity N2H+ emission. This enables us to study the infall and rotation close to the disk and estimate the central object masses. The velocity fields observed on large and small scales are more complex than would be expected from rotation alone, suggesting that complex envelope structure enables other dynamical processes (i.e., infall) to affect the velocity field. Based on observations carried out with the IRAM 30 m Telescope and IRAM Plateau de Bure Interferometer. IRAM is supported by INSU/CNRS (France), MPG (Germany), and IGN (Spain).

  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. 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

  19. Mapping of the epitopes of poliovirus type 2 in complex with antibodies.

    PubMed

    Bannwarth, Ludovic; Girerd-Chambaz, Yves; Arteni, Ana; Guigner, Jean-Michel; Ronzon, Frederic; Manin, Catherine; Vénien-Bryan, Catherine

    2015-10-01

    The inactivated polio vaccine (IPV) contains poliovirus (PV) samples that belong to serotypes 1, 2 and 3. All three serotypes contain the D-antigen, which induces protective antibodies. The antigenic structure of PVs consists of at least four different antigenic sites and the D-antigen content represents the combined activity of multiple epitopes (Ferguson et al., 1993; Minor, 1990; Minor et al., 1986). The potency of IPV vaccines is determined by measuring the D-antigen content. Several ELISA methods have been developed using polyclonal or monoclonal antibodies (Mabs) in order to quantify the D-antigen content. Characterization of the epitopes recognized by the different Mabs is crucial to map the entire virus surface and ensure the presence of epitopes able to induce neutralizing antibodies. Using a new approach that we developed to study the interaction between monoclonal antibodies and poliovirus type 2, which combines cryo-electron microscopy, image analysis and X-ray crystallography along with identification of exposed amino acids, we have mapped in 3D the epitope sites recognized by three specific Fabs at the surface of poliovirus type 2 (PV2) and characterized precisely the antigenic sites for these Fabs.

  20. 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

  1. A jumbo problem: mapping the structure and functions of the nuclear pore complex

    PubMed Central

    Fernandez-Martinez, Javier; Rout, Michael P

    2012-01-01

    Macromolecular assemblies can be intrinsically refractive to classical structural analysis, due to their size, complexity, plasticity and dynamic nature. One such assembly is the nuclear pore complex (NPC). The NPC is formed from ~450 copies of 30 different proteins, called nucleoporins, and is the sole mediator of exchange between the nucleus and the cytoplasm in eukaryotic cells. Despite significant progress, it has become increasingly clear that new approaches, integrating different sources of structural and functional data, will be needed to understand the functional biology of the NPC. Here, we discuss the latest approaches trying to address this challenge. PMID:22321828

  2. What lies beneath: geophysical mapping of a concealed Precambrian intrusive complex along the Iowa–Minnesota border

    USGS Publications Warehouse

    Drenth, Benjamin J.; Anderson, Raymond R.; Schulz, Klaus J.; Feinberg, Joshua M.; Chandler, Val W.; Cannon, William F.

    2015-01-01

    Large-amplitude gravity and magnetic highs over northeast Iowa are interpreted to reflect a buried intrusive complex composed of mafic–ultramafic rocks, the northeast Iowa intrusive complex (NEIIC), intruding Yavapai province (1.8–1.72 Ga) rocks. The age of the complex is unproven, although it has been considered to be Keweenawan (∼1.1 Ga). Because only four boreholes reach the complex, which is covered by 200–700 m of Paleozoic sedimentary rocks, geophysical methods are critical to developing a better understanding of the nature and mineral resource potential of the NEIIC. Lithologic and cross-cutting relations interpreted from high-resolution aeromagnetic and airborne gravity gradient data are presented in the form of a preliminary geologic map of the basement Precambrian rocks. Numerous magnetic anomalies are coincident with airborne gravity gradient (AGG) highs, indicating widespread strongly magnetized and dense rocks of likely mafic–ultramafic composition. A Yavapai-age metagabbro unit is interpreted to be part of a layered intrusion with subvertical dip. Another presumed Yavapai unit has low density and weak magnetization, observations consistent with felsic plutons. Northeast-trending, linear magnetic lows are interpreted to reflect reversely magnetized diabase dikes and have properties consistent with Keweenawan rocks. The interpreted dikes are cut in places by normally magnetized mafic–ultramafic rocks, suggesting that the latter represent younger Keweenawan rocks. Distinctive horseshoe-shaped magnetic and AGG highs correspond with a known gabbro, and surround rocks with weaker magnetization and lower density. Here, informally called the Decorah complex, the source body has notable geophysical similarities to Keweenawan alkaline ring complexes, such as the Coldwell and Killala Lake complexes, and Mesoproterozoic anorogenic complexes, such as the Kiglapait, Hettasch, and Voisey’s Bay intrusions in Labrador. Results presented here suggest that

  3. The high molecular weight insulin-like growth factor-binding protein complex: epitope mapping, immunoassay, and preliminary clinical evaluation.

    PubMed

    Khosravi, J; Diamandi, A; Mistry, J; Krischna, R G

    1999-08-01

    Measurements of insulin-like growth factor I(IGF-I), IGF-binding protein-3 (IGFBP-3), and the acid-labile subunit (ALS) are important in assessing the GH-IGF axis. As nearly all IGF-I, IGFBP-3, and ALS circulate in a GH-dependent ternary protein complex, direct determination of the complex may be of significant analytical and clinical importance. We evaluated a panel of monoclonal antibodies (mAb) to human IGFBP-3 and classified them into four groups (G-1 to G-4). G-1 antibodies recognized epitopes that mapped at or near IGFBP-3 ligand (IGF)-binding site. This region overlapped with the G-2 defined region, which, in turn, overlapped with G-3 epitopes defined by one antibody (mAb 3). Only G-1 and G-3 antibodies paired without interference. mAb 9 recognized a conformational epitope (G-4), and mAb 10 was nonreactive. In pairwise mixed antibody evaluation, mAbs in G-2 and G-3 showed simultaneous binding to serum IGFBP-3 complexes in combination with an anti-IGF-I or an anti-ALS antibody. On this basis, two novel enzyme-linked immunosorbent assays (ELISAs) involving IGFBP-3/IGF-I (ELISA-1) and IGFBP-3/ALS (ELISA-2) recognition partners were developed, both demonstrating acceptable analytical performance characteristics. IGFBP-3 complexes measured by ELISA-1 and -2 in samples from normal individuals and subjects with GH deficiency, acromegaly, and GH receptor deficiency more tightly correlated with IGF-I, IGFBP-3, and ALS than IGF-II. ELISA-1 determinations were comparatively more age dependent and, in comparison to ELISA-2, showed better discriminations among the various sample groups, particularly among GH receptor deficiency, normal, and GH deficiency subjects. The development of IGFBP-3 complex ELISAs may simplify diagnostic applications and facilitate investigations of the physiological relevance of the ternary complex formation.

  4. 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…

  5. 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…

  6. Mapping fusiform rust resistance genes within a complex mating design of loblolly pine

    Treesearch

    Tania Quesada; Marcio F.R. Resende Jr.; Patricio Munoz; Jill L. Wegrzyn; David B. Neale; Matias Kirst; Gary F. Peter; Salvador A. Gezan; C.Dana Nelson; John M. Davis

    2014-01-01

    Fusiform rust resistance can involve gene-for-gene interactions where resistance (Fr) genes in the host interact with corresponding avirulence genes in the pathogen, Cronartium quercuum f.sp. fusiforme (Cqf). Here, we identify trees with Fr genes in a loblolly pine population derived from a complex mating design challenged with two Cqf inocula (one gall and 10 gall...

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

    PubMed Central

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  9. 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.

  10. 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.

  11. Mixed Linear Model Approaches of Association Mapping for Complex Traits Based on Omics Variants.

    PubMed

    Zhang, Fu-Tao; Zhu, Zhi-Hong; Tong, Xiao-Ran; Zhu, Zhi-Xiang; Qi, Ting; Zhu, Jun

    2015-07-30

    Precise prediction for genetic architecture of complex traits is impeded by the limited understanding on genetic effects of complex traits, especially on gene-by-gene (GxG) and gene-by-environment (GxE) interaction. In the past decades, an explosion of high throughput technologies enables omics studies at multiple levels (such as genomics, transcriptomics, proteomics, and metabolomics). The analyses of large omics data, especially two-loci interaction analysis, are very time intensive. Integrating the diverse omics data and environmental effects in the analyses also remain challenges. We proposed mixed linear model approaches using GPU (Graphic Processing Unit) computation to simultaneously dissect various genetic effects. Analyses can be performed for estimating genetic main effects, GxG epistasis effects, and GxE environment interaction effects on large-scale omics data for complex traits, and for estimating heritability of specific genetic effects. Both mouse data analyses and Monte Carlo simulations demonstrated that genetic effects and environment interaction effects could be unbiasedly estimated with high statistical power by using the proposed approaches.

  12. 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

  13. 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.

  14. 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

  15. Genetic architecture of the F7 gene in a Spanish population: implication for mapping complex diseases and for functional assays.

    PubMed

    Sabater-Lleal, M; Almasy, L; Martínez-Marchán, E; Martínez-Sánchez, E; Souto, R; Blangero, J; Souto, Jc; Fontcuberta, J; Soria, J M

    2006-05-01

    Delineating the genetic variability of loci coding for complex diseases helps to understand the individual variation in disease susceptibility and drug response. We present the allelic architecture of the F7 gene. This gene is the major determinant of FVII plasma levels, and these plasma levels constitute an important intermediate risk factor for cardiovascular disease. As part of the Genetic Analysis of Idiopathic Thrombophila Project, we completely re-sequenced the F7 locus (promoter, exons, introns, and 3'-untranslated region) in 40 unrelated individuals. We found 49 polymorphisms with only two amino acid changes suggesting that regulatory non-coding and intronic variants are responsible for the FVII variability. These results are important for mapping susceptibility alleles of complex diseases, because differences in pair-wise linkage disequilibrium patterns between DNA variants and haplotype frequency distributions may help to detect disease-associated alleles. In addition, we present the results of an in silico search that established genomic comparisons among different species. In conclusion, our study of the F7 DNA sequence variations is an example of a strategy for analyzing the genetic architecture of a quantitative trait locus. Furthermore, it provides a model for future analyses of genetic factors that contribute to the susceptibility of complex diseases in humans.

  16. Large-Scale In Silico Mapping of Complex Quantitative Traits in Inbred Mice

    PubMed Central

    Liu, Pengyuan; Vikis, Haris; Lu, Yan; Wang, Daolong; You, Ming

    2007-01-01

    Understanding the genetic basis of common disease and disease-related quantitative traits will aid in the development of diagnostics and therapeutics. The processs of gene discovery can be sped up by rapid and effective integration of well-defined mouse genome and phenome data resources. We describe here an in silico gene-discovery strategy through genome-wide association (GWA) scans in inbred mice with a wide range of genetic variation. We identified 937 quantitative trait loci (QTLs) from a survey of 173 mouse phenotypes, which include models of human disease (atherosclerosis, cardiovascular disease, cancer and obesity) as well as behavioral, hematological, immunological, metabolic, and neurological traits. 67% of QTLs were refined into genomic regions <0.5 Mb with ∼40-fold increase in mapping precision as compared with classical linkage analysis. This makes for more efficient identification of the genes that underlie disease. We have identified two QTL genes, Adam12 and Cdh2, as causal genetic variants for atherogenic diet-induced obesity. Our findings demonstrate that GWA analysis in mice has the potential to resolve multiple tightly linked QTLs and achieve single-gene resolution. These high-resolution QTL data can serve as a primary resource for positional cloning and gene identification in the research community. PMID:17653278

  17. Mapping the HLA-DO/HLA-DM complex by FRET and mutagenesis

    PubMed Central

    Yoon, Taejin; Macmillan, Henriette; Mortimer, Sarah E.; Jiang, Wei; Rinderknecht, Cornelia H.; Stern, Lawrence J.; Mellins, Elizabeth D.

    2012-01-01

    HLA-DO (DO) is a nonclassic class II heterodimer that inhibits the action of the class II peptide exchange catalyst, HLA-DM (DM), and influences DM localization within late endosomes and exosomes. In addition, DM acts as a chaperone for DO and is required for its egress from the endoplasmic reticulum (ER). These reciprocal functions are based on direct DO/DM binding, but the topology of DO/DM complexes is not known, in part, because of technical limitations stemming from DO instability. We generated two variants of recombinant soluble DO with increased stability [zippered DOαP11A (szDOv) and chimeric sDO-Fc] and confirmed their conformational integrity and ability to inhibit DM. Notably, we found that our constructs, as well as wild-type sDO, are inhibitory in the full pH range where DM is active (4.7 to ∼6.0). To probe the nature of DO/DM complexes, we used intermolecular fluorescence resonance energy transfer (FRET) and mutagenesis and identified a lateral surface spanning the α1 and α2 domains of szDO as the apparent binding site for sDM. We also analyzed several sDM mutants for binding to szDOv and susceptibility to DO inhibition. Results of these assays identified a region of DM important for interaction with DO. Collectively, our data define a putative binding surface and an overall orientation of the szDOv/sDM complex and have implications for the mechanism of DO inhibition of DM. PMID:22733780

  18. Mapping the spatial overlap of excitons in a photosynthetic complex via coherent nonlinear frequency generation.

    PubMed

    Dawlaty, Jahan M; Bennett, Doran I G; Huxter, Vanessa M; Fleming, Graham R

    2011-07-28

    We experimentally demonstrate a nonlinear spectroscopic method that is sensitive to exciton-exciton interactions in a Frenkel exciton system. Spatial overlap of one-exciton wavefunctions leads to coupling between them, resulting in two-exciton eigenstates that have the character of many single-exciton pairs. The mixed character of the two-exciton wavefunctions gives rise to a four-wave-mixing nonlinear frequency generation signal. When only part of the linear excitation spectrum of the complex is excited with three spectrally tailored pulses with separate spatial directions, a frequency-shifted third-order nonlinear signal emerges in the phase-matched direction. We employ the nonlinear response function formalism to show that the emergence of the signal is mediated by and carries information about the two-exciton eigenstates of the system. We report experimental results for nonlinear frequency generation in the Fenna-Matthews-Olson (FMO) photosynthetic pigment-protein complex. Our theoretical analysis of the signal from FMO confirms that the emergence of the frequency-shifted signal is due to the interaction of spatially overlapped excitons. In this method, the signal intensity is directly measured in the frequency domain and does not require scanning of pulse delays or signal phase retrieval. The wavefunctions of the two-exciton states contain information about the spatial overlap of excitons and can be helpful in identifying coupling strengths and relaxation pathways. We propose this method as a facile experimental means of studying exciton correlations in systems with complicated electronic structures.

  19. Genomic mapping of binding regions for the Ecdysone receptor protein complex

    PubMed Central

    Gauhar, Zareen; Sun, Ling V.; Hua, Sujun; Mason, Christopher E.; Fuchs, Florian; Li, Tong-Ruei; Boutros, Michael; White, Kevin P.

    2009-01-01

    We determined the physical locations of the heterodimeric Ecdysone receptor/Ultraspiracle (ECR/USP) nuclear hormone receptor complex throughout the entire nonrepetitive genome of Drosophila melanogaster using a cell line (Kc167) that differentiates in response to 20-hydroxyecdysone (20-HE). 20-HE, the natural ligand of this complex, controls major aspects of insect development, including molting, metamorphosis, and reproduction. Direct gene targets of 20-HE signaling were identified by combining this physical binding-site profiling with gene expression profiling after treatment with 20-HE. We found 502 significant regions of ECR/USP binding throughout the genome. Only 42% of these regions are nearby genes that are 20-HE responsive in these cells. However, at least three quarters of the remaining ECR/USP regions are near 20-HE-regulated genes in other tissue and cell types during metamorphosis, suggesting that binding at many regulatory elements in the genome is largely noncell-type specific. The majority (21/26) of the early targets of 20-HE encode transcriptional regulatory factors. To determine whether any of these targets are required for the morphological differentiation of these cells, we used RNAi to reduce the expression of each of the 26 early genes. Accordingly, we found that three direct targets of ECR/USP—hairy, vrille, and Hr4—are required for cellular differentiation in response to the hormone. Initial mutational analysis of vrille in vivo reveals that it is required for metamorphosis. PMID:19237466

  20. Approach of automatic 3D geological mapping: the case of the Kovdor phoscorite-carbonatite complex, NW Russia.

    PubMed

    Kalashnikov, A O; Ivanyuk, G Yu; Mikhailova, J A; Sokharev, V A

    2017-07-31

    We have developed an approach for automatic 3D geological mapping based on conversion of chemical composition of rocks to mineral composition by logical computation. It allows to calculate mineral composition based on bulk rock chemistry, interpolate the mineral composition in the same way as chemical composition, and, finally, build a 3D geological model. The approach was developed for the Kovdor phoscorite-carbonatite complex containing the Kovdor baddeleyite-apatite-magnetite deposit. We used 4 bulk rock chemistry analyses - Femagn, P2O5, CO2 and SiO2. We used four techniques for prediction of rock types - calculation of normative mineral compositions (norms), multiple regression, artificial neural network and developed by logical evaluation. The two latter became the best. As a result, we distinguished 14 types of phoscorites (forsterite-apatite-magnetite-carbonate rock), carbonatite and host rocks. The results show good convergence with our petrographical studies of the deposit, and recent manually built maps. The proposed approach can be used as a tool of a deposit genesis reconstruction and preliminary geometallurgical modelling.

  1. The genotype-phenotype map of yeast complex traits: basic parameters and the role of natural selection.

    PubMed

    Ho, Wei-Chin; Zhang, Jianzhi

    2014-06-01

    Most phenotypic traits are controlled by many genes, but a global picture of the genotype-phenotype map (GPM) is lacking. For example, in no species do we know generally how many genes affect a trait and how large these effects are. It is also unclear to what extent GPMs are shaped by natural selection. Here we address these fundamental questions using the reverse genetic data of 220 morphological traits in 4,718 budding yeast strains, each of which lacks a nonessential gene. We show that 1) the proportion of genes affecting a trait varies from <1% to >30%, averaging 6%, 2) most traits are impacted by many more small-effect genes than large-effect genes, and 3) the mean effect of all nonessential genes on a trait decreases precipitously as the estimated importance of the trait to fitness increases. An analysis of 3,116 yeast gene expression traits in 754 gene-deletion strains reveals a similar pattern. These findings illustrate the power of genome-wide reverse genetics in genotype-phenotype mapping, uncover an enormous range of genetic complexity of phenotypic traits, and suggest that the GPM of cellular organisms has been shaped by natural selection for mutational robustness.

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

    PubMed

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

    2013-11-01

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

  3. 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.

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

    SciTech Connect

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

    1992-01-01

    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.

  5. Dynamics of thermochemical plumes: 2. Complexity of plume structures and its implications for mapping mantle plumes

    NASA Astrophysics Data System (ADS)

    Lin, Shu-Chuan; van Keken, Peter E.

    2006-03-01

    The mantle plume hypothesis provides explanations for several major observations of surface volcanism. The dynamics of plumes with purely thermal origin has been well established, but our understanding of the role of compositional variations in the Earth's mantle on plume formation is still incomplete. In this study we explore the structures of plumes originating from a thermochemical boundary layer at the base of the mantle in an attempt to complement fluid dynamical studies of purely thermal plumes. Our numerical experiments reveal diverse characteristics of thermochemical plumes that frequently deviate from the classic features of plumes. In addition, owing to the interplay between the thermal and compositional buoyancy forces, the morphology, temperature, and flow fields in both the plume head and plume conduit are strongly time-dependent. The entrainment of the dense layer and secondary instabilities developed in the boundary layer contribute to lateral heterogeneities and enhance stirring processes in the plume head. Our models show that substantial topography of the compositional layer can develop simultaneously with the plumes. In addition, plumes may be present in the lower mantle for more than 70 million years. These features may contribute to the large low seismic velocity provinces beneath the south central Pacific, the southern Atlantic Ocean, and Africa. Our model results support the idea that the dynamics of mantle plumes is much more complicated than conventional thinking based on studies of purely thermal plumes. The widely used criteria for mapping mantle plumes, such as a vertically continuous low seismic velocity signature and strong surface topography swell, may not be universally applicable. We propose that the intrinsic density contrast of the distinct composition may reduce the associated topography of some large igneous provinces such as Ontong Java.

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

    NASA Astrophysics Data System (ADS)

    van Eeuwijk, Fred

    2015-06-01

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

  7. 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.

  8. Immunohistochemical Mapping of Sensory Nerve Endings in the Human Triangular Fibrocartilage Complex.

    PubMed

    Rein, Susanne; Semisch, Manuel; Garcia-Elias, Marc; Lluch, Alex; Zwipp, Hans; Hagert, Elisabet

    2015-10-01

    The triangular fibrocartilage complex is the main stabilizer of the distal radioulnar joint. While static joint stability is constituted by osseous and ligamentous integrity, the dynamic aspects of joint stability chiefly concern proprioceptive control of the compressive and directional muscular forces acting on the joint. Therefore, an investigation of the pattern and types of sensory nerve endings gives more insight in dynamic distal radioulnar joint stability. We aimed to (1) analyze the general distribution of sensory nerve endings and blood vessels; (2) examine interstructural distribution of sensory nerve endings and blood vessels; (3) compare the number and types of mechanoreceptors in each part; and (4) analyze intrastructural distribution of nerve endings at different tissue depth. The subsheath of the extensor carpi ulnaris tendon sheath, the ulnocarpal meniscoid, the articular disc, the dorsal and volar radioulnar ligaments, and the ulnolunate and ulnotriquetral ligaments were dissected from 11 human cadaver wrists. Sensory nerve endings were counted in five levels per specimen as total cell amount/cm(2) after staining with low-affinity neurotrophin receptor p75, protein gene product 9.5, and S-100 protein and thereafter classified according to Freeman and Wyke. All types of sensory corpuscles were found in the various structures of the triangular fibrocartilage complex with the exception of the ulnolunate ligament, which contained only Golgi-like endings, free nerve endings, and unclassifiable corpuscles. The articular disc had only free nerve endings. Furthermore, free nerve endings were the predominant sensory nerve ending (median, 72.6/cm(2); range, 0-469.4/cm(2)) and more prevalent than all other types of mechanoreceptors: Ruffini (median, 0; range, 0-5.6/cm(2); difference of medians, 72.6; p < 0.001), Pacini (median, 0; range, 0-3.8/cm(2); difference of medians, 72.6; p < 0.001), Golgi-like (median, 0; range, 0-2.1/cm(2); difference of medians, 72

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  11. Geological Mapping of Impact Melt Deposits at Lunar Complex Craters: New Insights into Morphological Diversity, Distribution and the Cratering Process

    NASA Astrophysics Data System (ADS)

    Dhingra, D.; Head, J. W., III; Pieters, C. M.

    2014-12-01

    We have completed high resolution geological mapping of impact melt deposits at the young lunar complex craters (<1 billion years) Copernicus, Jackson and Tycho using data from recent missions. Crater floors being the largest repository of impact melt, we have mapped their morphological diversity expressed in terms of varied surface texture, albedo, character and occurrence of boulder units as well as relative differences in floor elevation. Examples of wall and rim impact melt units and their relation to floor units have also been mapped. Among the distinctive features of these impact melt deposits are: 1) Impact Melt Wave Fronts: These are extensive (sometimes several kilometers in length) and we have documented their occurrence and distribution in different parts of the crater floor at Jackson and Tycho. These features emphasize melt mobility and style of emplacement during the modification stage of the craters. 2) Variations in Floor Elevations: Spatially extensive and coherent sections of crater floors have different elevations at all the three craters. The observed elevation differences could be caused by subsidence due to cooling of melt and/or structural failure, together with a contribution from regional slope. 3) Melt-Covered Megablocks: We also observe large blocks/rock-fragments (megablocks) covered in impact melt, which could be sections of collapsed wall or in some cases, subdued sections of central peaks. 4) Melt-Covered Central Peaks: Impact melt has also been mapped on the central peaks but varies in spatial extent among the craters. The presence of melt on peaks must be taken into account when interpreting peak mineralogy as exposures of deeper crust. 5) Boulder Distribution: Interesting trends are observed in the distribution of boulder units of various sizes; some impact melt units have spatially extensive boulders, while boulder distribution is very scarce in other units on the floor. We interpret these distributions to be influenced by a) the

  12. High Resolution Stratigraphic Mapping in Complex Terrain: A Comparison of Traditional Remote Sensing Techniques with Unmanned Aerial Vehicle - Structure from Motion Photogrammetry

    NASA Astrophysics Data System (ADS)

    Nesbit, P. R.; Hugenholtz, C.; Durkin, P.; Hubbard, S. M.; Kucharczyk, M.; Barchyn, T.

    2016-12-01

    Remote sensing and digital mapping have started to revolutionize geologic mapping in recent years as a result of their realized potential to provide high resolution 3D models of outcrops to assist with interpretation, visualization, and obtaining accurate measurements of inaccessible areas. However, in stratigraphic mapping applications in complex terrain, it is difficult to acquire information with sufficient detail at a wide spatial coverage with conventional techniques. We demonstrate the potential of a UAV and Structure from Motion (SfM) photogrammetric approach for improving 3D stratigraphic mapping applications within a complex badland topography. Our case study is performed in Dinosaur Provincial Park (Alberta, Canada), mapping late Cretaceous fluvial meander belt deposits of the Dinosaur Park formation amidst a succession of steeply sloping hills and abundant drainages - creating a challenge for stratigraphic mapping. The UAV-SfM dataset (2 cm spatial resolution) is compared directly with a combined satellite and aerial LiDAR dataset (30 cm spatial resolution) to reveal advantages and limitations of each dataset before presenting a unique workflow that utilizes the dense point cloud from the UAV-SfM dataset for analysis. The UAV-SfM dense point cloud minimizes distortion, preserves 3D structure, and records an RGB attribute - adding potential value in future studies. The proposed UAV-SfM workflow allows for high spatial resolution remote sensing of stratigraphy in complex topographic environments. This extended capability can add value to field observations and has the potential to be integrated with subsurface petroleum models.

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

    PubMed

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

    2016-08-01

    Previously we extended the utility of mapping-by-sequencing by combining it with sequence capture and mapping sequence data to pseudo-chromosomes that were organized using wheat-Brachypodium synteny. This, with a bespoke haplotyping algorithm, enabled us to map the flowering time locus in the diploid wheat Triticum monococcum L. identifying a set of deleted genes (Gardiner et al., 2014). Here, we develop this combination of gene enrichment and sliding window mapping-by-synteny analysis to map the Yr6 locus for yellow stripe rust resistance in hexaploid wheat. A 110 MB NimbleGen capture probe set was used to enrich and sequence a doubled haploid mapping population of hexaploid wheat derived from an Avalon and Cadenza cross. The Yr6 locus was identified by mapping to the POPSEQ chromosomal pseudomolecules using a bespoke pipeline and algorithm (Chapman et al., 2015). Furthermore the same locus was identified using newly developed pseudo-chromosome sequences as a mapping reference that are based on the genic sequence used for sequence enrichment. The pseudo-chromosomes allow us to demonstrate the application of mapping-by-sequencing to even poorly defined polyploidy genomes where chromosomes are incomplete and sub-genome assemblies are collapsed. This analysis uniquely enabled us to: compare wheat genome annotations; identify the Yr6 locus - defining a smaller genic region than was previously possible; associate the interval with one wheat sub-genome and increase the density of SNP markers associated. Finally, we built the pipeline in iPlant, making it a user-friendly community resource for phenotype mapping. © 2016 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.

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

    SciTech Connect

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

    1996-04-01

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

  15. 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.

  16. 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

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

    NASA Technical Reports Server (NTRS)

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

    1973-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-02-01

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

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

    PubMed Central

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

    2012-01-01

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

  20. Selection between multiple periodic regimes in a biochemical system: complex dynamic behaviour resolved by use of one-dimensional maps.

    PubMed

    Decroly, O; Goldbeter, A

    1985-04-21

    We analyse a model biochemical system in which two autocatalytic enzyme reactions are coupled in series, in conditions where multiple stable periodic regimes coexist for the same set of parameter values. We determine how the periodic regimes are reached from different initial conditions. The structure of the attraction basins is generally simple in the case of two coexisting limit cycles (birhythmicity). This structure and the associated behaviour may, however, become highly complex. In particular, the system exhibits enhanced sensitivity to initial conditions when the boundaries of the attraction basins are fractal. In the latter case, it becomes difficult to predict the evolution towards either one of two limit cycles, a phenomenon known as final state sensitivity. We show how these complex phenomena can be explained in a unified and simple manner by means of one-dimensional return maps derived from the time evolution of the model and from fifth degree polynomial equations. We suggest experimental tests of the sensitivity to initial conditions in chemical systems presenting birhythmicity. The physiological significance of the results is discussed with respect to the sensitivity of regulatory systems admitting multiple stable biological rhythms.

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

    PubMed

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

    2014-01-01

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

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

    PubMed

    Kumar, Ajay; Seetan, Raed; Mergoum, Mohamed; Tiwari, Vijay K; Iqbal, Muhammad J; Wang, Yi; Al-Azzam, Omar; Šimková, Hana; Luo, Ming-Cheng; Dvorak, Jan; Gu, Yong Q; Denton, Anne; Kilian, Andrzej; Lazo, Gerard R; Kianian, Shahryar F

    2015-10-16

    The large and complex genome of bread wheat (Triticum aestivum L., ~17 Gb) requires high resolution genome maps with saturated marker scaffolds to anchor and orient BAC contigs/ sequence scaffolds for whole genome assembly. Radiation hybrid (RH) mapping has proven to be an excellent tool for the development of such maps for it offers much higher and more uniform marker resolution across the length of the chromosome compared to genetic mapping and does not require marker polymorphism per se, as it is based on presence (retention) vs. absence (deletion) marker assay. In this study, a 178 line RH panel was genotyped with SSRs and DArT markers to develop the first high resolution RH maps of the entire D-genome of Ae. tauschii accession AL8/78. To confirm map order accuracy, the AL8/78-RH maps were compared with:1) a DArT consensus genetic map constructed using more than 100 bi-parental populations, 2) a RH map of the D-genome of reference hexaploid wheat 'Chinese Spring', and 3) two SNP-based genetic maps, one with anchored D-genome BAC contigs and another with anchored D-genome sequence scaffolds. Using marker sequences, the RH maps were also anchored with a BAC contig based physical map and draft sequence of the D-genome of Ae. tauschii. A total of 609 markers were mapped to 503 unique positions on the seven D-genome chromosomes, with a total map length of 14,706.7 cR. The average distance between any two marker loci was 29.2 cR which corresponds to 2.1 cM or 9.8 Mb. The average mapping resolution across the D-genome was estimated to be 0.34 Mb (Mb/cR) or 0.07 cM (cM/cR). The RH maps showed almost perfect agreement with several published maps with regard to chromosome assignments of markers. The mean rank correlations between the position of markers on AL8/78 maps and the four published maps, ranged from 0.75 to 0.92, suggesting a good agreement in marker order. With 609 mapped markers, a total of 2481 deletions for the whole D-genome were detected with an average

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

    NASA Astrophysics Data System (ADS)

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

    2015-04-01

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

  4. Vegetation map for the Hakalau Forest Unit of the Big Island National Wildlife Refuge Complex on the island of Hawai‘i

    USGS Publications Warehouse

    Jacobi, James D.

    2017-01-01

    This vegetation map was produced to serve as an updated habitat base for management of natural resources of the Hakalau Forest Unit (HFU) of the Big Island National Wildlife Refuge Complex (Refuge) on the island of Hawai‘i. The map is based on a vegetation map originally produced as part of the U.S. Fish and Wildlife Service’s Hawai‘i Forest Bird Survey to depict the distribution, structure, and composition of plant communities on the island of Hawai‘i as they existed in 1977. The current map has been updated to represent current conditions of plant communities in the HFU, based on WorldView 2 imagery taken in 2012 and very-high-resolution imagery collected by Pictometry International from 2010 to 2014. Thirty-one detailed plant communities are identified on this map, and fourteen of these units are found within the boundaries of HFU. Additionally, the mapped units can be displayed as five tree canopy cover units, three moisture zones units, eight dominant tree species units, and four habitat status units by choosing the various fields to group the units from the map attribute table. This updated map will provide a foundation for the refinement and tracking of management actions on the Refuge for the near future, particularly as the habitats in this area are subject to projected climate change.

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

    USGS Publications Warehouse

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

    2002-01-01

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

  6. Biochemical mapping of interactions within the intraflagellar transport (IFT) B core complex: IFT52 binds directly to four other IFT-B subunits.

    PubMed

    Taschner, Michael; Bhogaraju, Sagar; Vetter, Melanie; Morawetz, Michaela; Lorentzen, Esben

    2011-07-29

    Cilia and flagella are complex structures emanating from the surface of most eukaroytic cells and serve important functions including motility, signaling, and sensory reception. A process called intraflagellar transport (IFT) is of central importance to ciliary assembly and maintenance. The IFT complex is required for this transport and consists of two distinct multisubunit subcomplexes, IFT-A and IFT-B. Despite the importance of the IFT complex, little is known about its overall architecture. This paper presents a biochemical dissection of the molecular interactions within the IFT-B core complex. Two stable subcomplexes consisting of IFT88/70/52/46 and IFT81/74/27/25 were recombinantly co-expressed and purified. We identify a novel interaction between IFT70/52 and map the interaction domains between IFT52 and the other subunits within the IFT88/70/52/46 complex. Additionally, we show that IFT52 binds directly to the IFT81/74/27/25 complex, indicating that it could mediate the interaction between the two subcomplexes. Our data lead to an improved architectural map for the IFT-B core complex with new interactions as well as domain resolution mapping for several subunits.

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

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  8. 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."

  9. 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.

  10. 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

  11. Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce

    PubMed Central

    Pavy, Nathalie; Pelgas, Betty; Beauseigle, Stéphanie; Blais, Sylvie; Gagnon, France; Gosselin, Isabelle; Lamothe, Manuel; Isabel, Nathalie; Bousquet, Jean

    2008-01-01

    Background To explore the potential value of high-throughput genotyping assays in the analysis of large and complex genomes, we designed two highly multiplexed Illumina bead arrays using the GoldenGate SNP assay for gene mapping in white spruce (Picea glauca [Moench] Voss) and black spruce (Picea mariana [Mill.] B.S.P.). Results Each array included 768 SNPs, identified by resequencing genomic DNA from parents of each mapping population. For white spruce and black spruce, respectively, 69.2% and 77.1% of genotyped SNPs had valid GoldenGate assay scores and segregated in the mapping populations. For each of these successful SNPs, on average, valid genotyping scores were obtained for over 99% of progeny. SNP data were integrated to pre-existing ALFP, ESTP, and SSR markers to construct two individual linkage maps and a composite map for white spruce and black spruce genomes. The white spruce composite map contained 821 markers including 348 gene loci. Also, 835 markers including 328 gene loci were positioned on the black spruce composite map. In total, 215 anchor markers (mostly gene markers) were shared between the two species. Considering lineage divergence at least 10 Myr ago between the two spruces, interspecific comparison of homoeologous linkage groups revealed remarkable synteny and marker colinearity. Conclusion The design of customized highly multiplexed Illumina SNP arrays appears as an efficient procedure to enhance the mapping of expressed genes and make linkage maps more informative and powerful in such species with poorly known genomes. This genotyping approach will open new avenues for co-localizing candidate genes and QTLs, partial genome sequencing, and comparative mapping across conifers. PMID:18205909

  12. Mapping the human translation elongation factor eEF1H complex using the yeast two-hybrid system.

    PubMed Central

    Mansilla, Francisco; Friis, Irene; Jadidi, Mandana; Nielsen, Karen M; Clark, Brian F C; Knudsen, Charlotte R

    2002-01-01

    In eukaryotes, the eukaryotic translation elongation factor eEF1A responsible for transporting amino-acylated tRNA to the ribosome forms a higher-order complex, eEF1H, with its guanine-nucleotide-exchange factor eEF1B. In metazoans, eEF1B consists of three subunits: eEF1B alpha, eEF1B eta and eEF1B gamma. The first two subunits possess the nucleotide-exchange activity, whereas the role of the last remains poorly defined. In mammals, two active tissue-specific isoforms of eEF1A have been identified. The reason for this pattern of differential expression is unknown. Several models on the basis of in vitro experiments have been proposed for the macromolecular organization of the eEF1H complex. However, these models differ in various aspects. This might be due to the difficulties of handling, particularly the eEF1B beta and eEF1B gamma subunits in vitro. Here, the human eEF1H complex is for the first time mapped using the yeast two-hybrid system, which is a powerful in vivo technique for analysing protein-protein interactions. The following complexes were observed: eEF1A1:eEF1B alpha, eEF1A1:eEF1B beta, eEF1B beta:eEF1B beta, eEF1B alpha:eEF1B gamma, eEF1B beta:eEF1B gamma and eEF1B alpha:eEF1B gamma:eEF1B beta, where the last was observed using a three-hybrid approach. Surprisingly, eEF1A2 showed no or only little affinity for the guanine-nucleotide-exchange factors. Truncated versions of the subunits of eEF1B were used to orientate these subunits within the resulting model. The model unit is a pentamer composed of two molecules of eEF1A, each interacting with either eEF1B alpha or eEF1B beta held together by eEF1B gamma. These units can dimerize via eEF1B beta. Our model is compared with other models, and structural as well as functional aspects of the model are discussed. PMID:11985494

  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. 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

  15. Complexity.

    PubMed

    Gómez-Hernández, J Jaime

    2006-01-01

    It is difficult to define complexity in modeling. Complexity is often associated with uncertainty since modeling uncertainty is an intrinsically difficult task. However, modeling uncertainty does not require, necessarily, complex models, in the sense of a model requiring an unmanageable number of degrees of freedom to characterize the aquifer. The relationship between complexity, uncertainty, heterogeneity, and stochastic modeling is not simple. Aquifer models should be able to quantify the uncertainty of their predictions, which can be done using stochastic models that produce heterogeneous realizations of aquifer parameters. This is the type of complexity addressed in this article.

  16. Molecular cloning and mapping of the ecotropic leukemia provirus Emv-23 provides molecular access to the albino-deletion complex in mouse chromosome 7.

    PubMed

    Rinchik, E M; Machanoff, R; Cummings, C C; Johnson, D K

    1989-04-01

    Genetic analysis of radiation-induced deletion mutations involving the chromosome 7 albino (c) locus has expanded the functional map of this 6 to 11-cM region of the mouse genome. To generate one of many points of molecular access necessary for intensifying the analysis of the genes and phenotypes associated with this particular complex of deletions, we have cloned an endogenous ecotropic leukemia provirus (Emv-23), known to be closely linked to c, along with its flanking chromosome 7 sequences. A unique-sequence probe (23.3), derived from a region immediately 5' to the proviral integration site, was found to map less than 0.5 cM from c in a standard backcross analysis. Southern blot analysis of DNAs from animals carrying homozygous or overlapping albino deletions demonstrated that the 23.3 probe was deleted in several relatively small c-region deletions. The deletion mapping of the 23.3 probe places the Emv-23 locus between c and Mod-2, just proximal to a region important for male fertility and juvenile fitness. Mapping of this locus also provides a refinement of the genetic/deletion map for several mutations within this deletion complex.

  17. Complex B1 mapping and electrical properties imaging of the human brain using a 16-channel transceiver coil at 7T.

    PubMed

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

    2013-05-01

    The electric properties of biological tissue provide important diagnostic information within radio and microwave frequencies, and also play an important role in specific absorption rate calculation which is a major safety concern at ultrahigh field. The recently proposed electrical properties tomography (EPT) technique aims to reconstruct electric properties in biological tissues based on B1 measurement. However, for individual coil element in multichannel transceiver coil which is increasingly utilized at ultrahigh field, current B1-mapping techniques could not provide adequate information (magnitude and absolute phase) of complex transmit and receive B1 which are essential for electrical properties tomography, electric field, and quantitative specific absorption rate 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 electric properties 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 electric properties reconstruction method.

  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. Fine Mapping of Murine Antibody Responses to Immunization with a Novel Soluble Form of Hepatitis C Virus Envelope Glycoprotein Complex

    PubMed Central

    Ruwona, Tinashe B.; Giang, Erick; Nieusma, Travis

    2014-01-01

    ABSTRACT The hepatitis C virus (HCV) envelope glycoprotein E1E2 complex is a candidate vaccine antigen. Previous immunization studies of E1E2 have yielded various results on its ability to induce virus-neutralizing antibodies in animal models and humans. The murine model has become a vital tool for HCV research owing to the development of humanized mice susceptible to HCV infection. In this study, we investigated the antibody responses of mice immunized with E1E2 and a novel soluble form of E1E2 (sE1E2) by a DNA prime and protein boost strategy. The results showed that sE1E2 elicited higher antibody titers and a greater breadth of reactivity than the wild-type cell-associated E1E2. However, immune sera elicited by either immunogen were only weakly neutralizing. In order to understand the contrasting results of binding and serum neutralizing activities, epitopes targeted by the polyclonal antibody responses were mapped and monoclonal antibodies (MAbs) were generated. The results showed that the majority of serum antibodies were directed to the E1 region 211 to 250 and the E2 regions 421 to 469, 512 to 539, 568 to 609, and 638 to 651, instead of the well-known immunodominant E2 hypervariable region 1 (HVR1). Unexpectedly, in MAb analysis, ∼12% of MAbs isolated were specific to the conserved E2 antigenic site 412 to 423, and 85% of them cross-neutralized multiple HCV isolates. The epitopes recognized by these MAbs are similar but distinct from the previously reported HCV1 and AP33 broadly neutralizing epitopes. In conclusion, E1E2 can prime B cells specific to conserved neutralizing epitopes, but the levels of serum neutralizing antibodies elicited are insufficient for effective virus neutralization. The sE1E2 constructs described in this study can be a useful template for rational antigen engineering. IMPORTANCE Hepatitis C virus infects 2 to 3% of the world's population and is a leading cause of liver failures and the need for liver transplantation. The virus

  20. Predictive analysis and mapping of indoor radon concentrations in a complex environment using kernel estimation: an application to Switzerland.

    PubMed

    Kropat, Georg; Bochud, Francois; Jaboyedoff, Michel; Laedermann, Jean-Pascal; Murith, Christophe; Palacios Gruson, Martha; Baechler, Sébastien

    2015-02-01

    The aim of this study was to develop models based on kernel regression and probability estimation in order to predict and map IRC in Switzerland by taking into account all of the following: architectural factors, spatial relationships between the measurements, as well as geological information. We looked at about 240,000 IRC measurements carried out in about 150,000 houses. As predictor variables we included: building type, foundation type, year of construction, detector type, geographical coordinates, altitude, temperature and lithology into the kernel estimation models. We developed predictive maps as well as a map of the local probability to exceed 300 Bq/m(3). Additionally, we developed a map of a confidence index in order to estimate the reliability of the probability map. Our models were able to explain 28% of the variations of IRC data. All variables added information to the model. The model estimation revealed a bandwidth for each variable, making it possible to characterize the influence of each variable on the IRC estimation. Furthermore, we assessed the mapping characteristics of kernel estimation overall as well as by municipality. Overall, our model reproduces spatial IRC patterns which were already obtained earlier. On the municipal level, we could show that our model accounts well for IRC trends within municipal boundaries. Finally, we found that different building characteristics result in different IRC maps. Maps corresponding to detached houses with concrete foundations indicate systematically smaller IRC than maps corresponding to farms with earth foundation. IRC mapping based on kernel estimation is a powerful tool to predict and analyze IRC on a large-scale as well as on a local level. This approach enables to develop tailor-made maps for different architectural elements and measurement conditions and to account at the same time for geological information and spatial relations between IRC measurements. Copyright © 2014 Elsevier B.V. All rights

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

    PubMed

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

    2015-05-07

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

  2. 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

  3. 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.

  4. Isolation and characterization of human and mouse ZIRTL, a member of the IRT1 family of transporters, mapping within the epidermal differentiation complex.

    PubMed

    Lioumi, M; Ferguson, C A; Sharpe, P T; Freeman, T; Marenholz, I; Mischke, D; Heizmann, C; Ragoussis, J

    1999-12-01

    We report the precise mapping and characterization of ZIRTL (zinc-iron regulated transporter-like) gene, the first mammalian member of an extensive family of divalent metal ion transporters, comprising IRT1 and ZIP1, ZIP2, ZIP3, and ZIP4 in plants and ZRT1 and ZRT2 in yeast. The human gene maps at the telomeric end of the epidermal differentiation complex (EDC), within chromosomal band 1q21, while the mouse gene maps within the mouse EDC, on mouse chromosome 3, between S100A9 and S100A13. The structure of the human gene has been determined, and message was detected in most adult and fetal tissues including the epidermis. The mouse gene is developmentally regulated and found expressed in fetal and adult suprabasal epidermis, osteoblasts, small intestine, and salivary gland.

  5. Comparison of gene-based rare variant association mapping methods for quantitative traits in a bovine population with complex familial relationships.

    PubMed

    Zhang, Qianqian; Guldbrandtsen, Bernt; Calus, Mario P L; Lund, Mogens Sandø; Sahana, Goutam

    2016-08-17

    There is growing interest in the role of rare variants in the variation of complex traits due to increasing evidence that rare variants are associated with quantitative traits. However, association methods that are commonly used for mapping common variants are not effective to map rare variants. Besides, livestock populations have large half-sib families and the occurrence of rare variants may be confounded with family structure, which makes it difficult to disentangle their effects from family mean effects. We compared the power of methods that are commonly applied in human genetics to map rare variants in cattle using whole-genome sequence data and simulated phenotypes. We also studied the power of mapping rare variants using linear mixed models (LMM), which are the method of choice to account for both family relationships and population structure in cattle. We observed that the power of the LMM approach was low for mapping a rare variant (defined as those that have frequencies lower than 0.01) with a moderate effect (5 to 8 % of phenotypic variance explained by multiple rare variants that vary from 5 to 21 in number) contributing to a QTL with a sample size of 1000. In contrast, across the scenarios studied, statistical methods that are specialized for mapping rare variants increased power regardless of whether multiple rare variants or a single rare variant underlie a QTL. Different methods for combining rare variants in the test single nucleotide polymorphism set resulted in similar power irrespective of the proportion of total genetic variance explained by the QTL. However, when the QTL variance is very small (only 0.1 % of the total genetic variance), these specialized methods for mapping rare variants and LMM generally had no power to map the variants within a gene with sample sizes of 1000 or 5000. We observed that the methods that combine multiple rare variants within a gene into a meta-variant generally had greater power to map rare variants compared

  6. MAP kinase signaling specificity mediated by the LIN-1 Ets/LIN-31 WH transcription factor complex during C. elegans vulval induction.

    PubMed

    Tan, P B; Lackner, M R; Kim, S K

    1998-05-15

    The let-23 receptor/mpk-1 MAP kinase signaling pathway induces the vulva in C. elegans. We show that MPK-1 directly regulates both the LIN-31 winged-helix and the LIN-1 Ets transcription factors to specify the vulval cell fate. lin-31 and lin-1 act genetically downstream of mpk-1, and both proteins can be directly phosphorylated by MAP kinase. LIN-31 binds to LIN-1, and the LIN-1/LIN-31 complex inhibits vulval induction. Phosphorylation of LIN-31 by MPK-1 disrupts the LIN-1/LIN-31 complex, relieving vulval inhibition. Phosphorylated LIN-31 may also act as a transcriptional activator, promoting vulval cell fates. LIN-31 is a vulval-specific effector of MPK-1, while LIN-1 acts as a general effector. The partnership of tissue-specific and general effectors may confer specificity onto commonly used signaling pathways, creating distinct tissue-specific outcomes.

  7. 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.

  8. Lz-0 × Berkeley: a new Arabidopsis recombinant inbred line population for the mapping of complex traits.

    PubMed

    Capron, Arnaud; Chang, Xue Feng; Shi, Chun; Beatson, Rodger; Berleth, Thomas

    2014-06-01

    This study describes the generation and test of a genetic resource suited to identify determinants of cell biological traits in plants. The use of quantitative trait loci (QTL) mapping for a better genetic understanding of cell biological traits is still at an early stage, even for biotechnologically important cell properties, such as the dimensions of fiber cells. A common strategy, the mapping of QTLs in recombinant inbred line (RIL) populations, is limited by the fact that the existing RIL populations exploit only a small fraction of the existing natural variation. Here, we report the mapping of QTLs impacting on the length of fiber cells in Arabidopsis inflorescence stems in a newly generated RIL population derived from a cross between the accessions Berkeley and the little known Lz-0. Through inbreeding of individual F(2) plants, a total of 159 new F8 lines were produced and genotyped with a set of 49 single nucleotide polymorphism markers. The population was successfully used not only for the mapping of three QTLs controlling fiber length, but also to map five QTL controlling flowering time under short and long-day conditions. Our study demonstrates the usefulness of this new genetic resource by mapping in it QTLs underlying a poorly explored cellular trait as well as an already better explored regulatory pathway. The new RIL population and an online platform for the continuous supplementation of genetic markers will be generally available to substantially broaden the genetic diversity through which loci with impact on plant quantitative traits can be identified.

  9. 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 Central

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

    2015-01-01

    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

  10. 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. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. C. elegans RBX-2-CUL-5- and RBX-1-CUL-2-based complexes are redundant for oogenesis and activation of the MAP kinase MPK-1.

    PubMed

    Sasagawa, Yohei; Sato, Shusei; Ogura, Teru; Higashitani, Atsushi

    2007-01-09

    Cul5-based complex is a member of ECS (Elongin B/C-Cul2/Cul5-SOCS-box protein) ubiquitin ligase family. The cellular function of the Cul5-based complex is poorly understood. In this study, we found that oocyte septum formation and egg production did not occur in either cul-5- or rbx-2-depleted cul-2 homozygotes, although control cul-2 homozygotes laid approximately 50 eggs. These phenotypes are reminiscent of those caused by the MAP kinase mpk-1 depletion. In fact, activation of MPK-1 was significantly inhibited in cul-5-depleted cul-2 mutant and cul-2-depleted cul-5 mutant. Yeast two-hybrid analysis and RNAi-knockdown experiments suggest that oocyte maturation from pachytene exit and MPK-1 activation are redundantly controlled by the RBX-2-CUL-5- and RBX-1-CUL-2-based complexes.

  12. 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.

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

    PubMed

    Evrendilek, Fatih

    2007-12-12

    This study aims at quantifying spatio-temporal dynamics of monthly mean dailyincident photosynthetically active radiation (PAR) over a vast and complex terrain such asTurkey. The spatial interpolation method of universal kriging, and the combination ofmultiple linear regression (MLR) models and map algebra techniques were implemented togenerate surface maps of PAR with a grid resolution of 500 x 500 m as a function of fivegeographical and 14 climatic variables. Performance of the geostatistical and MLR modelswas compared using mean prediction error (MPE), root-mean-square prediction error(RMSPE), average standard prediction error (ASE), mean standardized prediction error(MSPE), root-mean-square standardized prediction error (RMSSPE), and adjustedcoefficient of determination (R²adj.). The best-fit MLR- and universal kriging-generatedmodels of monthly mean daily PAR were validated against an independent 37-year observeddataset of 35 climate stations derived from 160 stations across Turkey by the Jackknifingmethod. The spatial variability patterns of monthly mean daily incident PAR were moreaccurately reflected in the surface maps created by the MLR-based models than in thosecreated by the universal kriging method, in particular, for spring (May) and autumn(November). The MLR-based spatial interpolation algorithms of PAR described in thisstudy indicated the significance of the multifactor approach to understanding and mappingspatio-temporal dynamics of PAR for a complex terrain over meso-scales.

  14. 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.

  15. Complexing of the CD-3 subunit by a monoclonal antibody activates a microtubule-associated protein 2 (MAP-2) serine kinase in Jurkat cells.

    PubMed Central

    Hanekom, C; Nel, A; Gittinger, C; Rheeder, A; Landreth, G

    1989-01-01

    Treatment of Jurkat T-cells with anti-CD-3 monoclonal antibodies resulted in the rapid and transient activation of a serine kinase which utilized the microtubule-associated protein, MAP-2, as a substrate in vitro. The kinase was also activated on treatment of Jurkat cells with phytohaemagglutinin, but with a different time course. The activation of the MAP-2 kinase by anti-CD-3 antibodies was dose-dependent, with maximal activity observed at concentrations of greater than 500 ng/ml. Normal human E-rosette-positive T-cells also exhibited induction of MAP-2 kinase activity during anti-CD-3 treatment. The enzyme was optimally active in the presence of 2 mM-Mn2+; lower levels of activity were observed with Mg2+, even at concentrations up to 20 mM. The kinase was partially purified by passage over DE-52 Sephacel with the activity eluting as a single peak at 0.25 M-NaCl. The molecular mass was estimated to be 45 kDa by gel filtration. The activation of the MAP-2 kinase was probably due to phosphorylation of this enzyme as treatment with alkaline phosphatase diminished its activity. These data demonstrate that the stimulation of T-cells through the CD-3 complex results in the activation of a novel serine kinase which may be critically involved in signal transduction in these cells. Images Fig. 1. Fig. 7. Fig. 8. PMID:2552997

  16. Quantitative trait locus mapping reveals complex genetic architecture of quantitative virulence in the wheat pathogen Zymoseptoria tritici.

    PubMed

    Stewart, Ethan L; Croll, Daniel; Lendenmann, Mark H; Sanchez-Vallet, Andrea; Hartmann, Fanny E; Palma-Guerrero, Javier; Ma, Xin; McDonald, Bruce A

    2016-11-21

    We conducted a comprehensive analysis of virulence in the fungal wheat pathogen Zymoseptoria tritici using quantitative trait locus (QTL) mapping. High-throughput phenotyping based on automated image analysis allowed the measurement of pathogen virulence on a scale and with a precision that was not previously possible. Across two mapping populations encompassing more than 520 progeny, 540 710 pycnidia were counted and their sizes and grey values were measured. A significant correlation was found between pycnidia size and both spore size and number. Precise measurements of percentage leaf area covered by lesions provided a quantitative measure of host damage. Combining these large and accurate phenotypic datasets with a dense panel of restriction site-associated DNA sequencing (RADseq) genetic markers enabled us to genetically dissect pathogen virulence into components related to host damage and those related to pathogen reproduction. We showed that different components of virulence can be under separate genetic control. Large- and small-effect QTLs were identified for all traits, with some QTLs specific to mapping populations, cultivars and traits and other QTLs shared among traits within the same mapping population. We associated the presence of four accessory chromosomes with small, but significant, increases in several virulence traits, providing the first evidence for a meaningful function associated with accessory chromosomes in this organism. A large-effect QTL involved in host specialization was identified on chromosome 7, leading to the identification of candidate genes having a large effect on virulence.

  17. Complex early rifting in Valles Marineris: Results from preliminary geologic mapping of the Ophir Planum Region of Mars

    NASA Technical Reports Server (NTRS)

    Schultz, Richard A.

    1990-01-01

    Photogeologic mapping of the Ophir Planum quadrangle was undertaken to solve two main problems: (1) what controlled the location, orientation, and growth of Ophir Planum grabens; and (2) how are the grabens and trough faulting related. The rich geological history of the Ophir Planum quadrangle underscores the fundamental importance of faulting in the early growth of Valles Marineris.

  18. Transcription map of the tuberous sclerosis complex I candidate region in human chromosome segment 9q34

    SciTech Connect

    Murrell, J.; Trofatter, J.; Rutter, M.

    1994-09-01

    A high resolution and transcription map of the tuberous sclerosis (TSCI) region on human chromosome 9 has been constructed between the polymorphic dinucleotide markers DBH and D9S114. This 600 kb region was originally thought to be 2 Mb which is much less than expected given a genetic distance of 4 cM. A minimum of three YACs from the flow-sorted human chromosome 9 library and two cosmids span this distance. Each YAC was used to identify cosmids from the flow-sorted human chromosome 9 cosmid libraries from Los Alamos National Laboratories and Lawrence Livermore National Laboratories. All cosmids were then subjected to exon amplification, and the resulting exons mapped back to the cosmids and YACs. Fifty exons, 25 sequence tagged sites which include YAC ends and four simple sequence repeats were used to order the map creating a marker every 5-10 Kb. Exons were also used to obtain cDNAs. Two genes with interesting similarity to known sequences were mapped in this region. One 2.7 Kb cDNA that detected a 5.5 Kb transcript on a Northern has homology to a tumor suppressor gene. The other 2.3 Kb cDNA detected a 7 Kb transcript with Northern analysis. This previously unmapped cDNA has sequence similarity to a homeobox gene. Both transcripts are excellent candidate genes for TSCI.

  19. A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits.

    PubMed

    Decker, Jared E; Vasco, Daniel A; McKay, Stephanie D; McClure, Matthew C; Rolf, Megan M; Kim, JaeWoo; Northcutt, Sally L; Bauck, Stewart; Woodward, Brent W; Schnabel, Robert D; Taylor, Jeremy F

    2012-11-09

    Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on complex traits. We examine the effects of multi-trait selection on the genome of a population of US registered Angus beef cattle born over a 50-year period representing approximately 10 generations of selection. We present results from the application of a quantitative genetic model, called Birth Date Selection Mapping, to identify signatures of recent ongoing selection. We show that US Angus cattle have been systematically selected to alter their mean additive genetic merit for most of the 16 production traits routinely recorded by breeders. Using Birth Date Selection Mapping, we estimate the time-dependency of allele frequency for 44,817 SNP loci using genomic best linear unbiased prediction, generalized least squares, and BayesCπ analyses. Finally, we reconstruct the primary phenotypes that have historically been exposed to selection from a genome-wide analysis of the 16 production traits and gene ontology enrichment analysis. We demonstrate that Birth Date Selection Mapping utilizing mixed models corrects for time-dependent pedigree sampling effects that lead to spurious SNP associations and reveals genomic signatures of ongoing selection on complex traits. Because multiple traits have historically been selected in concert and most quantitative trait loci have small effects, selection has incrementally altered allele frequencies throughout the genome. Two quantitative trait loci of large effect were not the most strongly selected of the loci due to their antagonistic pleiotropic effects on strongly selected phenotypes. Birth Date Selection Mapping may readily be extended to temporally-stratified human or model organism populations.

  20. A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.

    PubMed

    Wilmes, Gwendolyn M; Bergkessel, Megan; Bandyopadhyay, Sourav; Shales, Michael; Braberg, Hannes; Cagney, Gerard; Collins, Sean R; Whitworth, Gregg B; Kress, Tracy L; Weissman, Jonathan S; Ideker, Trey; Guthrie, Christine; Krogan, Nevan J

    2008-12-05

    We used a quantitative, high-density genetic interaction map, or E-MAP (Epistatic MiniArray Profile), to interrogate the relationships within and between RNA-processing pathways. Due to their complexity and the essential roles of many of the components, these pathways have been difficult to functionally dissect. Here, we report the results for 107,155 individual interactions involving 552 mutations, 166 of which are hypomorphic alleles of essential genes. Our data enabled the discovery of links between components of the mRNA export and splicing machineries and Sem1/Dss1, a component of the 19S proteasome. In particular, we demonstrate that Sem1 has a proteasome-independent role in mRNA export as a functional component of the Sac3-Thp1 complex. Sem1 also interacts with Csn12, a component of the COP9 signalosome. Finally, we show that Csn12 plays a role in pre-mRNA splicing, which is independent of other signalosome components. Thus, Sem1 is involved in three separate and functionally distinct complexes.

  1. 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.

  2. Assessing the value of phenotypic information from non-genotyped animals for QTL mapping of complex traits in real and simulated populations.

    PubMed

    Melo, Thaise P; Takada, Luciana; Baldi, Fernando; Oliveira, Henrique N; Dias, Marina M; Neves, Haroldo H R; Schenkel, Flavio S; Albuquerque, Lucia G; Carvalheiro, Roberto

    2016-06-21

    QTL mapping through genome-wide association studies (GWAS) is challenging, especially in the case of low heritability complex traits and when few animals possess genotypic and phenotypic information. When most of the phenotypic information is from non-genotyped animals, GWAS can be performed using the weighted single-step GBLUP (WssGBLUP) method, which permits to combine all available information, even that of non-genotyped animals. However, it is not clear to what extent phenotypic information from non-genotyped animals increases the power of QTL detection, and whether factors such as the extent of linkage disequilibrium (LD) in the population and weighting SNPs in WssGBLUP affect the importance of using information from non-genotyped animals in GWAS. These questions were investigated in this study using real and simulated data. Analysis of real data showed that the use of phenotypes of non-genotyped animals affected SNP effect estimates and, consequently, QTL mapping. Despite some coincidence, the most important genomic regions identified by the analyses, either using or ignoring phenotypes of non-genotyped animals, were not the same. The simulation results indicated that the inclusion of all available phenotypic information, even that of non-genotyped animals, tends to improve QTL detection for low heritability complex traits. For populations with low levels of LD, this trend of improvement was less pronounced. Stronger shrinkage on SNPs explaining lower variance was not necessarily associated with better QTL mapping. The use of phenotypic information from non-genotyped animals in GWAS may improve the ability to detect QTL for low heritability complex traits, especially in populations in which the level of LD is high.

  3. Low-Cost Optical Mapping Systems for Panoramic Imaging of Complex Arrhythmias and Drug-Action in Translational Heart Models.

    PubMed

    Lee, Peter; Calvo, Conrado J; Alfonso-Almazán, José M; Quintanilla, Jorge G; Chorro, Francisco J; Yan, Ping; Loew, Leslie M; Filgueiras-Rama, David; Millet, José

    2017-02-27

    Panoramic optical mapping is the primary method for imaging electrophysiological activity from the entire outer surface of Langendorff-perfused hearts. To date, it is the only method of simultaneously measuring multiple key electrophysiological parameters, such as transmembrane voltage and intracellular free calcium, at high spatial and temporal resolution. Despite the impact it has already had on the fields of cardiac arrhythmias and whole-heart computational modeling, present-day system designs precludes its adoption by the broader cardiovascular research community because of their high costs. Taking advantage of recent technological advances, we developed and validated low-cost optical mapping systems for panoramic imaging using Langendorff-perfused pig hearts, a clinically-relevant model in basic research and bioengineering. By significantly lowering financial thresholds, this powerful cardiac electrophysiology imaging modality may gain wider use in research and, even, teaching laboratories, which we substantiated using the lower-cost Langendorff-perfused rabbit heart model.

  4. Low-Cost Optical Mapping Systems for Panoramic Imaging of Complex Arrhythmias and Drug-Action in Translational Heart Models

    NASA Astrophysics Data System (ADS)

    Lee, Peter; Calvo, Conrado J.; Alfonso-Almazán, José M.; Quintanilla, Jorge G.; Chorro, Francisco J.; Yan, Ping; Loew, Leslie M.; Filgueiras-Rama, David; Millet, José

    2017-02-01

    Panoramic optical mapping is the primary method for imaging electrophysiological activity from the entire outer surface of Langendorff-perfused hearts. To date, it is the only method of simultaneously measuring multiple key electrophysiological parameters, such as transmembrane voltage and intracellular free calcium, at high spatial and temporal resolution. Despite the impact it has already had on the fields of cardiac arrhythmias and whole-heart computational modeling, present-day system designs precludes its adoption by the broader cardiovascular research community because of their high costs. Taking advantage of recent technological advances, we developed and validated low-cost optical mapping systems for panoramic imaging using Langendorff-perfused pig hearts, a clinically-relevant model in basic research and bioengineering. By significantly lowering financial thresholds, this powerful cardiac electrophysiology imaging modality may gain wider use in research and, even, teaching laboratories, which we substantiated using the lower-cost Langendorff-perfused rabbit heart model.

  5. Low-Cost Optical Mapping Systems for Panoramic Imaging of Complex Arrhythmias and Drug-Action in Translational Heart Models

    PubMed Central

    Lee, Peter; Calvo, Conrado J.; Alfonso-Almazán, José M.; Quintanilla, Jorge G.; Chorro, Francisco J.; Yan, Ping; Loew, Leslie M.; Filgueiras-Rama, David; Millet, José

    2017-01-01

    Panoramic optical mapping is the primary method for imaging electrophysiological activity from the entire outer surface of Langendorff-perfused hearts. To date, it is the only method of simultaneously measuring multiple key electrophysiological parameters, such as transmembrane voltage and intracellular free calcium, at high spatial and temporal resolution. Despite the impact it has already had on the fields of cardiac arrhythmias and whole-heart computational modeling, present-day system designs precludes its adoption by the broader cardiovascular research community because of their high costs. Taking advantage of recent technological advances, we developed and validated low-cost optical mapping systems for panoramic imaging using Langendorff-perfused pig hearts, a clinically-relevant model in basic research and bioengineering. By significantly lowering financial thresholds, this powerful cardiac electrophysiology imaging modality may gain wider use in research and, even, teaching laboratories, which we substantiated using the lower-cost Langendorff-perfused rabbit heart model. PMID:28240274

  6. A novel approach to land-cover maps updating in complex scenarios based on multitemporal remote sensing images

    NASA Astrophysics Data System (ADS)

    Bahirat, K.; Bovolo, F.; Bruzzone, L.; Chaudhuri, S.

    2010-10-01

    Nowadays, an ever increasing number of multi-temporal images is available, giving the possibility of having with high temporal frequency information about the land-cover evolution on the ground. In general, the production of accurate land-cover maps requires the availability of reliable ground truth information on the considered area for each image to be classified. Unfortunately the rate of ground truth information collection will never equal the remote sensing image acquisition rate, making supervised classification unfeasible for land-cover maps updating. This problem has been faced according to domain adaptation methods that update land-cover maps under the assumption that: i) training data are available for one of the considered multi-temporal acquisitions while they are not for the others and ii) set of land-cover classes is same for all considered acquisitions. In real applications, the latter assumption represents a constraint which is often not satisfied due to possible changes occurred on the ground and associated with the presence of new classes or the absence of old classes in the new images. In this work, we propose an approach that removes this constraint by automatically identifying whether there exist differences between classes in multi-temporal images and properly handling these differences in the updating process. Experimental results on a real multi-temporal remote sensing data set confirm the effectiveness and the reliability of the proposed approach.

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

    PubMed

    Frenkel, Zeev; Paux, Etienne; Mester, David; Feuillet, Catherine; Korol, Abraham

    2010-11-30

    Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC) software, which often results in short contig lengths (of 3-5 clones before merging) as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs). To address these problems, we propose a novel approach that: (i) reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii) obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii) explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv) performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v) uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC) were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize. The results show that compared to other methods, LTC enables the construction of highly reliable and longer contigs (5-12 clones before

  8. Geological mapping of impact melt deposits at lunar complex craters Jackson and Tycho: Morphologic and topographic diversity and relation to the cratering process

    NASA Astrophysics Data System (ADS)

    Dhingra, Deepak; Head, James W.; Pieters, Carle M.

    2017-02-01

    High resolution geological mapping, aided by imagery and elevation data from the lunar reconnaissance orbiter (LRO) and Kaguya missions, has revealed the scientifically rich character of impact melt deposits at two young complex craters: Jackson (71 km) and Tycho (85 km). The morphology and distribution of mapped impact melt units provide several insights into the cratering process. We report elevation differences (>200 m) among large, coherent floor sections within a single crater and interpret them to be caused by crater wall collapse and/or large scale structural failure of the floor region. Clast-poor, smooth melt deposits are correlated with floor sections at lower elevations and likely represent ponded deposits sourced from higher elevation regions (viz. crater walls). In addition, these deposits are also located in the inferred downrange direction of the impact. Melt-coated large blocks spanning several kilometers are common on the crater floors and may represent collapsed wall sections or in some cases, subdued sections of the central peaks. Spatial trends in the mapped impact melt units at the two craters provide clues to decipher the conditions during each impact event and subsequent evolution of the crater floor.

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

    PubMed Central

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

    2012-01-01

    Telomerase, the enzyme that extends single-stranded telomeric DNA, consists of an RNA subunit (TER) including a short template sequence, a catalytic protein (TERT) and accessory proteins. We used site-specific UV cross-linking to map the binding sites for DNA primers in TER within active Tetrahymena telomerase holoenzyme complexes. The mapping was performed at single-nucleotide resolution by a novel technique based on RNase H digestion of RNA–DNA hybrids made with overlapping complementary oligodeoxynucleotides. These data allowed tracing of the DNA path through the telomerase complexes from the template to the TERT binding element (TBE) region of TER. TBE is known to bind TERT and to be involved in the template 5′-boundary definition. Based on these findings, we propose that upstream sequences of each growing telomeric DNA chain are involved in regulation of its growth arrest at the 5′-end of the RNA template. The upstream DNA–TBE interaction may also function as an anchor for the subsequent realignment of the 3′-end of the DNA with the 3′-end of the template to enable initiation of synthesis of a new telomeric repeat. PMID:22584626

  10. Extending systems thinking in planning and evaluation using group concept mapping and system dynamics to tackle complex problems.

    PubMed

    Hassmiller Lich, Kristen; Urban, Jennifer Brown; Frerichs, Leah; Dave, Gaurav

    2017-02-01

    Group concept mapping (GCM) has been successfully employed in program planning and evaluation for over 25 years. The broader set of systems thinking methodologies (of which GCM is one), have only recently found their way into the field. We present an overview of systems thinking emerging from a system dynamics (SD) perspective, and illustrate the potential synergy between GCM and SD. As with GCM, participatory processes are frequently employed when building SD models; however, it can be challenging to engage a large and diverse group of stakeholders in the iterative cycles of divergent thinking and consensus building required, while maintaining a broad perspective on the issue being studied. GCM provides a compelling resource for overcoming this challenge, by richly engaging a diverse set of stakeholders in broad exploration, structuring, and prioritization. SD provides an opportunity to extend GCM findings by embedding constructs in a testable hypothesis (SD model) describing how system structure and changes in constructs affect outcomes over time. SD can be used to simulate the hypothesized dynamics inherent in GCM concept maps. We illustrate the potential of the marriage of these methodologies in a case study of BECOMING, a federally-funded program aimed at strengthening the cross-sector system of care for youth with severe emotional disturbances. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. A Flexible Computational Framework Using R and Map-Reduce for Permutation Tests of Massive Genetic Analysis of Complex Traits.

    PubMed

    Mahjani, Behrang; Toor, Salman; Nettelblad, Carl; Holmgren, Sverker

    2017-01-01

    In quantitative trait locus (QTL) mapping significance of putative QTL is often determined using permutation testing. The computational needs to calculate the significance level are immense, 10(4) up to 10(8) or even more permutations can be needed. We have previously introduced the PruneDIRECT algorithm for multiple QTL scan with epistatic interactions. This algorithm has specific strengths for permutation testing. Here, we present a flexible, parallel computing framework for identifying multiple interacting QTL using the PruneDIRECT algorithm which uses the map-reduce model as implemented in Hadoop. The framework is implemented in R, a widely used software tool among geneticists. This enables users to rearrange algorithmic steps to adapt genetic models, search algorithms, and parallelization steps to their needs in a flexible way. Our work underlines the maturity of accessing distributed parallel computing for computationally demanding bioinformatics applications through building workflows within existing scientific environments. We investigate the PruneDIRECT algorithm, comparing its performance to exhaustive search and DIRECT algorithm using our framework on a public cloud resource. We find that PruneDIRECT is vastly superior for permutation testing, and perform 2 ×10(5) permutations for a 2D QTL problem in 15 hours, using 100 cloud processes. We show that our framework scales out almost linearly for a 3D QTL search.

  12. Neurog1 Genetic Inducible Fate Mapping (GIFM) Reveals the Existence of Complex Spatiotemporal Cyto-Architectures in the Developing Cerebellum.

    PubMed

    Obana, Edwin A; Lundell, Travis G; Yi, Kevin J; Radomski, Kryslaine L; Zhou, Qiong; Doughty, Martin L

    2015-06-01

    Neurog1 is a pro-neural basic helix-loop-helix (bHLH) transcription factor expressed in progenitor cells located in the ventricular zone and subsequently the presumptive white matter tracts of the developing mouse cerebellum. We used genetic inducible fate mapping (GIFM) with a transgenic Neurog1-CreER allele to characterize the contributions of Neurog1 lineages to cerebellar circuit formation in mice. GIFM reveals Neurog1-expressing progenitors are fate-mapped to become Purkinje cells and all GABAergic interneuron cell types of the cerebellar cortex but not glia. The spatiotemporal sequence of GIFM is unique to each neuronal cell type. GIFM on embryonic days (E) 10.5 to E12.5 labels Purkinje cells with different medial-lateral settling patterns depending on the day of tamoxifen delivery. GIFM on E11.5 to P7 labels interneurons and the timing of tamoxifen administration correlates with the final inside-to-outside resting position of GABAergic interneurons in the cerebellar cortex. Proliferative status and long-term BrdU retention of GIFM lineages reveals Purkinje cells express Neurog1 around the time they become post-mitotic. In contrast, GIFM labels mitotic and post-mitotic interneurons. Neurog1-CreER GIFM reveals a correlation between the timing of Neurog1 expression and the spatial organization of GABAergic neurons in the cerebellar cortex with possible implications for cerebellar circuit assembly.

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

    PubMed Central

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

    2013-01-01

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

  14. 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…

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

    PubMed Central

    Nelson, William; Luo, Meizhong; Ma, Jianxin; Estep, Matt; Estill, James; He, Ruifeng; Talag, Jayson; Sisneros, Nicholas; Kudrna, David; Kim, HyeRan; Ammiraju, Jetty SS; Collura, Kristi; Bharti, Arvind K; Messing, Joachim; Wing, Rod A; SanMiguel, Phillip; Bennetzen, Jeffrey L; Soderlund, Carol

    2008-01-01

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

  16. 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. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  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. CREB, AP‐1, ternary complex factors and MAP kinases connect transient receptor potential melastatin‐3 (TRPM3) channel stimulation with increased c‐Fos expression

    PubMed Central

    Rubil, Sandra; Rössler, Oliver G.

    2016-01-01

    Background and Purpose The rise in intracellular Ca2+ stimulates the expression of the transcription factor c‐Fos. Depending on the mode of entry of Ca2+ into the cytosol, distinct signal transducers and transcription factors are required. Here, we have analysed the signalling pathway connecting a Ca2+ influx via activation of transient receptor potential melastatin‐3 (TRPM3) channels with enhanced c‐Fos expression. Experimental Approach Transcription of c‐Fos promoter/reporter genes that were integrated into the chromatin via lentiviral gene transfer was analysed in HEK293 cells overexpressing TRPM3. The transcriptional activation potential of c‐Fos was measured using a GAL4‐c‐Fos fusion protein. Key Results The signalling pathway connecting TRPM3 stimulation with enhanced c‐Fos expression requires the activation of MAP kinases. On the transcriptional level, three Ca2+‐responsive elements, the cAMP‐response element and the binding sites for the serum response factor (SRF) and AP‐1, are essential for the TRPM3‐mediated stimulation of the c‐Fos promoter. Ternary complex factors are additionally involved in connecting TRPM3 stimulation with the up‐regulation of c‐Fos expression. Stimulation of TRPM3 channels also increases the transcriptional activation potential of c‐Fos. Conclusions and Implications Signalling molecules involved in connecting TRPM3 with the c‐Fos gene are MAP kinases and the transcription factors CREB, SRF, AP‐1 and ternary complex factors. As c‐Fos constitutes, together with other basic region leucine zipper transcription factors, the AP‐1 transcription factor complex, the results of this study explain TRPM3‐induced activation of AP‐1 and connects TRPM3 with the biological functions regulated by AP‐1. © 2015 The British Pharmacological Society PMID:26493679

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-01

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

  1. 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

  2. Interactions between avian myeloblastosis reverse transcriptase and tRNATrp. Mapping of complexed tRNA with chemicals and nucleases.

    PubMed

    Garret, M; Romby, P; Giegé, R; Litvak, S

    1984-03-12

    The interactions between beef tRNATrp with avian myeloblastosis reverse transcriptase have been studied by statistical chemical modifications of phosphate (ethylnitrosourea) and cytidine (dimethyl sulfate) residues, as well as by digestion of complexed tRNA by Cobra venom nuclease and Neurospora crassa endonuclease. Results with nucleases and chemicals show that reverse transcriptase interacts preferentially with the D arm, the anticodon stem and the T psi stem. All these regions are located in the outside of the L-shaped structure of tRNA. This domain of interaction is different to that reported previously in the complex of beef tRNA with the cognate aminoacyl-tRNA synthetase (M. Garret et al.; Eur. J. Biochem. In press). Avian reverse transcriptase destabilizes the region of tRNA where most of the tertiary interactions maintaining the structure of tRNA are located.

  3. Interactions between avian myeloblastosis reverse transcriptase and tRNATrp. Mapping of complexed tRNA with chemicals and nucleases.

    PubMed Central

    Garret, M; Romby, P; Giegé, R; Litvak, S

    1984-01-01

    The interactions between beef tRNATrp with avian myeloblastosis reverse transcriptase have been studied by statistical chemical modifications of phosphate (ethylnitrosourea) and cytidine (dimethyl sulfate) residues, as well as by digestion of complexed tRNA by Cobra venom nuclease and Neurospora crassa endonuclease. Results with nucleases and chemicals show that reverse transcriptase interacts preferentially with the D arm, the anticodon stem and the T psi stem. All these regions are located in the outside of the L-shaped structure of tRNA. This domain of interaction is different to that reported previously in the complex of beef tRNA with the cognate aminoacyl-tRNA synthetase (M. Garret et al.; Eur. J. Biochem. In press). Avian reverse transcriptase destabilizes the region of tRNA where most of the tertiary interactions maintaining the structure of tRNA are located. Images PMID:6200830

  4. Fluorescence mapping of mitochondrial TIM23 complex reveals a water-facing, substrate-interacting helix surface.

    PubMed

    Alder, Nathan N; Jensen, Robert E; Johnson, Arthur E

    2008-08-08

    Protein translocation across the mitochondrial inner membrane is mediated by the TIM23 complex. While its central component, Tim23, is believed to form a protein-conducting channel, the regions of this subunit that face the imported protein are unknown. To examine Tim23 structure and environment in intact membranes at high resolution, various derivatives, each with a single, environment-sensitive fluorescent probe positioned at a specific site, were assembled into functional TIM23 complexes in active mitochondria and analyzed by multiple spectral techniques. Probes placed sequentially throughout a transmembrane region that was identified by crosslinking as part of the protein-conducting channel revealed an alpha helix in an amphipathic environment. Probes on the aqueous-facing helical surface specifically underwent spectral changes during protein import, and their accessibility to hydrophilic quenching agents is considered in terms of channel gating. This approach has therefore provided an unprecedented view of a translocon channel structure in an intact, fully operational, membrane-embedded complex.

  5. Structural and Biochemical Analyses of Swine Major Histocompatibility Complex Class I Complexes and Prediction of the Epitope Map of Important Influenza A Virus Strains

    PubMed Central

    Fan, Shuhua; Wu, Yanan; Wang, Song; Wang, Zhenbao; Jiang, Bo; Liu, Yanjie; Liang, Ruiying; Zhou, Wenzhong

    2016-01-01

    ABSTRACT The lack of a peptide-swine leukocyte antigen class I (pSLA I) complex structure presents difficulties for the study of swine cytotoxic T lymphocyte (CTL) immunity and molecule vaccine development to eliminate important swine viral diseases, such as influenza A virus (IAV). Here, after cloning and comparing 28 SLA I allelic genes from Chinese Heishan pigs, pSLA-3*hs0202 was crystalized and solved. SLA-3*hs0202 binding with sβ2m and a KMNTQFTAV (hemagglutinin [HA]-KMN9) peptide from the 2009 pandemic swine H1N1 strain clearly displayed two distinct conformations with HA-KMN9 peptides in the structures, which are believed to be beneficial to stimulate a broad spectrum of CTL immune responses. Notably, we found that different HA-KMN9 conformations are caused, not only by the flexibility of the side chains of residues in the peptide-binding groove (PBG), but also by the skewing of α1 and α2 helixes forming the PBG. In addition, alanine scanning and circular-dichroism (CD) spectra confirmed that the B, D, and F pockets play critical biochemical roles in determining the peptide-binding motif of SLA-3*hs0202. Based on biochemical parameters and comparisons to similar pockets in other known major histocompatibility complex class I (MHC-I) structures, the fundamental motif for SLA-3*hs0202 was determined to be X-(M/A/R)-(N/Q/R/F)-X-X-X-X-X-(V/I) by refolding in vitro and multiple mutant peptides. Finally, 28 SLA-3*hs0202-restricted epitope candidates were identified from important IAV strains, and two of them have been found in humans as HLA-A*0201-specific IAV epitopes. Structural and biochemical illumination of pSLA-3*hs0202 can benefit vaccine development to control IAV in swine. IMPORTANCE We crystalized and solved the first SLA-3 structure, SLA-3*hs0202, and found that it could present the same IAV peptide with two distinct conformations. Unlike previous findings showing that variable peptide conformations are caused only by the flexibility of the side

  6. Mapping the ligand binding site at protein side-chains in protein-ligand complexes through NOE difference spectroscopy.

    PubMed

    Eichmüller, C; Tollinger, M; Kräutler, B; Konrat, R

    2001-07-01

    This report describes a novel NMR approach for mapping the interaction surface between an unlabeled ligand and a 13C,15N-labeled protein. The method relies on the spin inversion properties of the dipolar relaxation pathways and records the differential relaxation of two spin modes, where ligand and protein 1H magnetizations are aligned either in a parallel or anti-parallel manner. Selective inversion of protein protons is achieved in a straightforward manner by exploiting the one-bond heteronuclear scalar couplings (1J(CH), 1J(NH)). Suppression of indirect relaxation pathways mediated by bulk water or rapidly exchanging protons is achieved by selective inversion of the water signal in the middle of the NOESY mixing period. The method does not require deuteration of the protein or well separated spectral regions for the protein and the ligand, respectively. Additionally, in contrast to previous methods, the new experiment identifies side-chain enzyme ligand interactions along the intermolecular binding interface. The method is demonstrated with an application to the B12-binding subunit of glutamate mutase from Clostridium tetanomorphum for which NMR chemical shift changes upon B12-nucleotide loop binding and a high-resolution solution structure are available.

  7. 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.

  8. 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.

  9. Mapping the Ultrafast Changes of Continuous Shape Measures in Photoexcited Spin Crossover Complexes without Long-Range Order

    SciTech Connect

    Canton, S. E.; Zhang, X.; Lawson Daku, M. L.; Liu, Y.; Zhang, J.; Alvarez, S.

    2015-02-12

    Establishing a tractable yet complete reaction coordinate for the spin-state interconversion in d(4)-d(7) transition metal complexes is an integral aspect of controlling the dynamics that govern their functionality. For spin crossover phenomena, the limitations of a single-mode approximation that solely accounts for an isotropic increase in the metal-ligand bond length have long been recognized for all but the simple octahedral monodentate FeII compounds. However, identifying the coupled deformations that also impact on the unimolecular rate constants remains experimentally and theoretically challenging, especially for samples that do not display long-range order or when crystallization profoundly alters the dynamics. Owing to the rapid progress in ultrafast X-ray absorption spectroscopy (XAS), it is now possible to obtain transient structural information in any physical phase with unprecedented details. Using picosecond XAS and DFT modeling, the structure adopted by the photoinduced high-spin state of solvated [Fe(terpy)(2)](2+) (terpy: 2,2':6',2 ''-terpyridine) has been recently established. Based on these results, the methodology of the continuous shape measure is applied to classify and quantify the short-lived distortion of the first coordination shell. The reaction coordinate of the spin-state interconversion is clearly identified as a double axial bending. This finding sets a benchmark for gauging the influence of first-sphere and second-sphere interactions in the family of FeII complexes that incorporate terpy derivatives. Some implications for the optimization of related photoactive FeII complexes are also outlined.

  10. Tetramer-guided epitope mapping: rapid identification and characterization of immunodominant CD4+ T cell epitopes from complex antigens.

    PubMed

    Novak, E J; Liu, A W; Gebe, J A; Falk, B A; Nepom, G T; Koelle, D M; Kwok, W W

    2001-06-01

    T cell responses to Ags involve recognition of selected peptide epitopes contained within the antigenic protein. In this report, we describe a new approach for direct identification of CD4+ T cell epitopes of complex Ags that uses human class II tetramers to identify reactive cells. With a panel of 60 overlapping peptides covering the entire sequence of the VP16 protein, a major Ag for HSV-2, we generated a panel of class II MHC tetramers loaded with peptide pools that were used to stain peripheral lymphocytes of an HSV-2 infected individual. With this approach, we identified four new DRA1*0101/DRB1*0401- and two DRA1*0101/DRB1*0404-restricted, VP16-specific epitopes. By using tetramers to sort individual cells, we easily obtained a large number of clones specific to these epitopes. Although DRA1*0101/DRB1*0401 and DRA1*0101/DRB1*0404 are structurally very similar, nonoverlapping VP16 epitopes were identified, illustrating high selectivity of individual allele polymorphisms within common MHC variants. This rapid approach to detecting CD4+ T cell epitopes from complex Ags can be applied to any known Ag that gives a T cell response.

  11. Physical map of human 6p21.2-6p21.3: region flanking the centromeric end of the major histocompatibility complex.

    PubMed

    Tripodis, N; Mason, R; Humphray, S J; Davies, A F; Herberg, J A; Trowsdale, J; Nizetic, D; Senger, G; Ragoussis, J

    1998-06-01

    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.

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

    PubMed

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

    2015-01-01

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

  13. 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

  14. A long way to Tipperary? Young people with complex health conditions living in residential aged care: a metaphorical map for understanding the call for change.

    PubMed

    Muenchberger, Heidi; Sunderland, Naomi; Kendall, Elizabeth; Quinn, Hayley

    2011-01-01

    There is ongoing public and private concern regarding the appropriateness of young people with complex health needs residing in nursing homes and the search for alternative living environments. Despite the demand for change, there is only tacit understanding of the key motivations behind this call for change and even less in the way of coherent arguments underlying the need for alternative solutions. The study aimed to explore the assumed truths that have formed around this topic in recent years and to reposition ambitious but ambiguous arguments regarding the need to relocate younger people from aged care facilities. By applying the method of systematic metaphor analysis, the authors conducted a review of social discourse (i.e. media corpus of 904 published articles dated 2001-2009). A conceptual media map was developed to document the process of social change around this topic. Additionally, the narrative described five metaphors that outlined the experience of aged care residential homes for young people with complex health conditions, namely 'captivity', 'commodity', 'battlelines', 'fragmentation' and 'a contemporary life'. These metaphors reflected the fears and hopes held by young people and their families. Results indicate that young people at risk of nursing home placement are confronted with a range of distinct and complex personal dilemmas which ought to be resolved through initiatives purported to offer 'more appropriate' residential options. We conclude that principles of good quality care are in danger of becoming misplaced within over-simplified interpretations of the needs of young people with complex conditions. Alignment of disability and rehabilitation policy with residential care practice will allow for more informed decisions about long-term care needs of young people, leading to quality outcomes.

  15. Mapping of second-nearest-neighbor fluoride ions of orthorhombic Gd 3+-Ag + complexes in CaF 2

    NASA Astrophysics Data System (ADS)

    Nakata, R.; Den Hartog, H. W.

    The ENDOR technique is applied to determine the positions of 24 second-nearest-neighbor F - ions around an orthorhombic Gd 3+-Ag + complex in CaF 2 crystals. Experimental ENDOR data of the second-nearest-neighbor F - ions are analyzed by using the usual spin Hamiltonian and a least-squares fitting method. The best fits of the experimental results give superhyperfine (shf) constants and the F - directions ( K, L, M) with respect to the Gd 3+ ion, from which the distance between the second-nearest-neighbor F - ion and the Gd 3+ ion is determined by assuming that the hyperfine interaction is due to the classical dipole-dipole interaction. The displacements of the F - ions are estimated and compared with the theoretical values calculated by Bijvank and den Hartog on the basis of a polarizable point charge model.

  16. The stress-induced MAP kinase p38 regulates endocytic trafficking via the GDI:Rab5 complex.

    PubMed

    Cavalli, V; Vilbois, F; Corti, M; Marcote, M J; Tamura, K; Karin, M; Arkinstall, S; Gruenberg, J

    2001-02-01

    Early endocytic membrane traffic is regulated by the small GTPase Rab5, which cycles between GTP- and GDP-bound states as well as between membrane and cytosol. The latter cycle depends on GDI, which functions as a Rab vehicle in the aqueous environment of the cytosol. Here, we report that formation of the GDI:Rab5 complex is stimulated by a cytosolic factor that we purified and then identified as p38 MAPK. We find that p38 regulates GDI in the cytosolic cycle of Rab5 and modulates endocytosis in vivo. Our observations reveal the existence of a cross-talk between endocytosis and the p38-dependent stress response, thus providing molecular evidence that endocytosis can be regulated by the environment.

  17. Selection, characterisation and mapping of complex electrochemical processes at individual single-walled carbon nanotubes: the case of serotonin oxidation.

    PubMed

    Güell, Aleix G; Meadows, Katherine E; Dudin, Petr V; Ebejer, Neil; Byers, Joshua C; Macpherson, Julie V; Unwin, Patrick R

    2014-01-01

    The electrochemical (EC) oxidation of the neurotransmitter, serotonin, at individual single-walled carbon nanotubes (SWNTs) is investigated at high resolution using a novel platform that combines flow-aligned SWNTs with atomic force microscopy, Raman microscopy, electronic conductance measurements, individual SWNT electrochemistry and high-resolution scanning electrochemical cell microscopy (SECCM). SECCM has been used to visualise the EC activity along side-wall sections of metallic SWNTs to assess the extent to which side-walls promote the electrochemistry of this complex multi-step process. Uniform and high EC activity is observed that is consistent with significant reaction at the side-wall, rather than electrochemistry being driven by defects alone. By scanning forward and reverse (trace and retrace) over the same region of a SWNT, it is also possible to assess any blocking of EC activity by serotonin oxidation reaction products. At a physiologically relevant concentration (5 μM), there is no detectable blocking of SWNTs, which can be attributed, at least in part, to the high diffusion rate to an individual, isolated SWNT in the SECCM format. At higher serotonin concentration (2 mM), oligomer formation from oxidation products is much more significant and major blocking of the EC process is observed from line profiles recorded as the SECCM meniscus moves over an SWNT. The SECCM line profile morphology is shown to be highly diagnostic of whether blocking occurs during EC processes. The studies herein add to a growing body of evidence that various EC processes at SWNTs, from simple outer sphere redox reactions to complex multi-step processes, occur readily at pristine SWNTs. The platform described is of general applicability to various types of nanostructures and nanowires.

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

    PubMed

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

    2014-02-01

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

  19. Mapping of Genetic Factors That Elicit Intermale Aggressive Behavior on Mouse Chromosome 15: Intruder Effects and the Complex Genetic Basis

    PubMed Central

    Takahashi, Aki; Sugimoto, Hiroki; Kato, Shogo; Shiroishi, Toshihiko; Koide, Tsuyoshi

    2015-01-01

    Despite high estimates of the heritability of aggressiveness, the genetic basis for individual differences in aggression remains unclear. Previously, we showed that the wild-derived mouse strain MSM/Ms (MSM) exhibits highly aggressive behaviors, and identified chromosome 15 (Chr 15) as the location of one of the genetic factors behind this escalated aggression by using a panel of consomic strains of MSM in a C57BL/6J (B6) background. To understand the genetic effect of Chr 15 derived from MSM in detail, this study examined the aggressive behavior of a Chr 15 consomic strain towards different types of opponent. Our results showed that both resident and intruder animals had to have the same MSM Chr 15 genotype in order for attack bites to increase and attack latency to be reduced, whereas there was an intruder effect of MSM Chr 15 on tail rattle behavior. To narrow down the region that contains the genetic loci involved in the aggression-eliciting effects on Chr 15, we established a panel of subconsomic strains of MSM Chr 15. Analysis of these strains suggested the existence of multiple genes that enhance and suppress aggressive behavior on Chr 15, and these loci interact in a complex way. Regression analysis successfully identified four genetic loci on Chr 15 that influence attack latency, and one genetic locus that partially elicits aggressive behaviors was narrowed down to a 4.1-Mbp region (from 68.40 Mb to 72.50 Mb) on Chr 15. PMID:26389588

  20. Brain imaging genetics in ADHD and beyond - mapping pathways from gene to disorder at different levels of complexity.

    PubMed

    Klein, Marieke; Onnink, Marten; van Donkelaar, Marjolein; Wolfers, Thomas; Harich, Benjamin; Shi, Yan; Dammers, Janneke; Arias-Va Squez, Alejandro; Hoogman, Martine; Franke, Barbara

    2017-01-31

    Attention-deficit/hyperactivity disorder (ADHD) is a common and often persistent neurodevelopmental disorder. Beyond gene-finding, neurobiological parameters, such as brain structure, connectivity, and function, have been used to link genetic variation to ADHD symptomatology. We performed a systematic review of brain imaging genetics studies involving 62 ADHD candidate genes in childhood and adult ADHD cohorts. Fifty-one eligible research articles described studies of 13 ADHD candidate genes. Almost exclusively, single genetic variants were studied, mostly focussing on dopamine-related genes. While promising results have been reported, imaging genetics studies are thus far hampered by methodological differences in study design and analysis methodology, as well as limited sample sizes. Beyond reviewing imaging genetics studies, we also discuss the need for complementary approaches at multiple levels of biological complexity and emphasize the importance of combining and integrating findings across levels for a better understanding of biological pathways from gene to disease. These may include multi-modal imaging genetics studies, bioinformatic analyses, and functional analyses of cell and animal models.

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

    PubMed

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

    2012-12-01

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

  2. Geological mapping and spectral based classification of basement rocks using remote sensing data analysis: The Korbiai-Gerf nappe complex, South Eastern Desert, Egypt

    NASA Astrophysics Data System (ADS)

    Hassan, Safaa M.; Sadek, Mohamed F.

    2017-10-01

    The Pan-African Neoproterozoic Korbiai-Gerf nappe complex in the extreme South Eastern Desert of Egypt comprises dismembered ophiolite assemblages tectonically thrusted over pelite-psammopelite, quartzo-feldspathic gneiss and island-arc schistose metavolcanics. The whole sequence is intruded by syn-late to post tectonic mafic and felsic intrusions. The enhanced Landsat-8 band ratio (bands 6/2, 6/7 and 6/5 × 4/5) and Advanced Spaceborne Thermal Emission and Reflection Radiometer (ASTER) Principal Component (PC2, PC6, and PC5) successfully discriminated most of the exposed lithological units and produced a detailed geological map. Granitoids, psammopelite-pelite, gneiss and serpentinite-talc carbonate rocks have been discriminated using ASTER kaolinite, clay, sericite-muscovite and calcite-carbonate indices respectively. Three spectral based classification algorithms have been compared using Landsat-8 and the Advanced Space-borne Thermal Emission and Reflection Radiometer (ASTER) datasets to obtain the best lithological classification for the exposed basement rock units. Results from the present study revealed that, Support Vector Machine (SVM) classifier algorithm provided the best lithological classification accuracy (97.72%) using the combination of 9 ASTER bands and 20 ASTER derivative images. The results of the present study concluded that, the integrated data of ASTER and Landsat-8 enhanced images are effective in the discrimination and classification of the basement rock units exposed at Korbiai-Gerf nappe complex and can be applied in similar areas in the Arabian-Nubian Shield.

  3. Genotype-based association mapping of complex diseases: gene-environment interactions with multiple genetic markers and measurement error in environmental exposures.

    PubMed

    Lobach, Iryna; Fan, Ruzong; Carroll, Raymond J

    2010-12-01

    With the advent of dense single nucleotide polymorphism genotyping, population-based association studies have become the major tools for identifying human disease genes and for fine gene mapping of complex traits. We develop a genotype-based approach for association analysis of case-control studies of gene-environment interactions in the case when environmental factors are measured with error and genotype data are available on multiple genetic markers. To directly use the observed genotype data, we propose two genotype-based models: genotype effect and additive effect models. Our approach offers several advantages. First, the proposed risk functions can directly incorporate the observed genotype data while modeling the linkage disequilibrium information in the regression coefficients, thus eliminating the need to infer haplotype phase. Compared with the haplotype-based approach, an estimating procedure based on the proposed methods can be much simpler and significantly faster. In addition, there is no potential risk due to haplotype phase estimation. Further, by fitting the proposed models, it is possible to analyze the risk alleles/variants of complex diseases, including their dominant or additive effects. To model measurement error, we adopt the pseudo-likelihood method by Lobach et al. [2008]. Performance of the proposed method is examined using simulation experiments. An application of our method is illustrated using a population-based case-control study of association between calcium intake with the risk of colorectal adenoma development.

  4. Genotype-Based Association Mapping of Complex Diseases: Gene-Environment Interactions with Multiple Genetic Markers and Measurement Error in Environmental Exposures

    PubMed Central

    Lobach, Irvna; Fan, Ruzone; Carroll, Raymond T.

    2011-01-01

    With the advent of dense single nucleotide polymorphism genotyping, population-based association studies have become the major tools for identifying human disease genes and for fine gene mapping of complex traits. We develop a genotype-based approach for association analysis of case-control studies of gene-environment interactions in the case when environmental factors are measured with error and genotype data are available on multiple genetic markers. To directly use the observed genotype data, we propose two genotype-based models: genotype effect and additive effect models. Our approach offers several advantages. First, the proposed risk functions can directly incorporate the observed genotype data while modeling the linkage disequihbrium information in the regression coefficients, thus eliminating the need to infer haplotype phase. Compared with the haplotype-based approach, an estimating procedure based on the proposed methods can be much simpler and significantly faster. In addition, there is no potential risk due to haplotype phase estimation. Further, by fitting the proposed models, it is possible to analyze the risk alleles/variants of complex diseases, including their dominant or additive effects. To model measurement error, we adopt the pseudo-likelihood method by Lobach et al. [2008]. Performance of the proposed method is examined using simulation experiments. An application of our method is illustrated using a population-based case-control study of association between calcium intake with the risk of colorectal adenoma development. PMID:21031455

  5. 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.

  6. 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.

  7. 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

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

    PubMed Central

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

    2011-01-01

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

  9. 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

  10. 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

  11. Using intervention mapping to develop a theory-driven, group-based complex intervention to support self-management of osteoarthritis and low back pain (SOLAS).

    PubMed

    Hurley, Deirdre A; Murphy, Laura Currie; Hayes, David; Hall, Amanda M; Toomey, Elaine; McDonough, Suzanne M; Lonsdale, Chris; Walsh, Nicola E; Guerin, Suzanne; Matthews, James

    2016-04-26

    The Medical Research Council framework provides a useful general approach to designing and evaluating complex interventions, but does not provide detailed guidance on how to do this and there is little evidence of how this framework is applied in practice. This study describes the use of intervention mapping (IM) in the design of a theory-driven, group-based complex intervention to support self-management (SM) of patients with osteoarthritis (OA) and chronic low back pain (CLBP) in Ireland's primary care health system. The six steps of the IM protocol were systematically applied to develop the self-management of osteoarthritis and low back pain through activity and skills (SOLAS) intervention through adaptation of the Facilitating Activity and Self-management in Arthritis (FASA) intervention. A needs assessment including literature reviews, interviews with patients and physiotherapists and resource evaluation was completed to identify the programme goals, determinants of SM behaviour, consolidated definition of SM and required adaptations to FASA to meet health service and patient needs and the evidence. The resultant SOLAS intervention behavioural outcomes, performance and change objectives were specified and practical application methods selected, followed by organised programme, adoption, implementation and evaluation plans underpinned by behaviour change theory. The SOLAS intervention consists of six weekly sessions of 90-min education and exercise designed to increase participants' physical activity level and use of evidence-based SM strategies (i.e. pain self-management, pain coping, healthy eating for weight management and specific exercise) through targeting of individual determinants of SM behaviour (knowledge, skills, self-efficacy, fear, catastrophizing, motivation, behavioural regulation), delivered by a trained physiotherapist to groups of up to eight individuals using a needs supportive interpersonal style based on self-determination theory

  12. 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.

  13. 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

  14. 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.

  15. 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.

  16. An autosomal dominant locus, Nka, mapping to the Ly-49 region of a rat natural killer (NK) gene complex, controls NK cell lysis of allogeneic lymphocytes

    PubMed Central

    1996-01-01

    Natural Killer (NK) cells can recognize and kill MHC-incompatible normal bone marrow-derived cells. Presently characterized MHC-binding receptors on NK cells, including the Ly-49 family in the mouse, transmit inhibitory signals upon binding to cognate class I MHC ligands. Here we study in vivo NK-mediated lysis of normal allogeneic lymphocytes in crosses between alloreactivity-competent PVG rats and alloreactivity-deficient DA rats. NK cells from both strains are able to lyse standard tumor targets. We identify an autosomal dominant locus, Nka, that controls NK-mediated alloreactivity. Individuals carrying the dominant PVG allele in single dose were fully competent in eliminating allogeneic target cells, suggesting that Nka encodes or regulates a gene product inducing or activating alloreactivity. By linkage analysis and pulsed field gel electrophoresis, a natural killer gene complex (NKC) on rat chromosome 4 is described that contains the rat NKR-P1 and Ly-49 multigene families plus a rat NKG2D homologue. Nka maps within the NKC, together with the most telomeric Ly-49 family members, but separate from NKG2D and the NKR-P1 family. The Nka-encoded response, moreover, correlates with the expression of transcripts for Ly-49 receptors in NK cell populations, as Northern blot analysis demonstrated low expression of Ly-49 genes in DA NK cells, in contrast to high expression in alloreactivity-competent PVG, (DA X PVG)F1, and PVG.1AVI NK cells. The low Ly-49 expression in DA is not induced by MHC haplotype, as demonstrated by high expression of Ly-49 in the DA MHC- congenic PVG.1AVI strain. Finally, we have cloned and characterized the first four members of the rat Ly-49 gene family. Their cytoplasmic domains demonstrate substantial heterogeneity, consistent with the hypothesis that different Ly-49 family members may subserve different signaling functions. PMID:8642329

  17. Somatotopic mapping of chordotonal organ neurons in a primitive ensiferan, the New Zealand tree weta Hemideina femorata: II. complex tibial organ.

    PubMed

    Nishino, Hiroshi; Field, Laurence H

    2003-09-22

    Most ensiferan insects possess sets of highly specialized chordotonal organs in the proximal tibiae to detect conspecific auditory/vibratory signals or approach of predators. To date, most auditory/vibratory afferents have been classified according to their physiological properties and axonal projection morphology, but not to somatotopic origins. Hence, the functional specialization of identified receptor cells in the tibial organs remains uncertain. To address this question from an anatomical aspect, we investigated the structure of the weta, Hemideina femorata, tibial organs (the most elaborated tibial chordotonal organs among ensiferans) and their central projections by staining small numbers of receptor afferents from identified tibial organs. These organs comprise the "complex tibial organ," including the subgenual organ (primary vibration detector) and its posterior complement, the accessory organ, and the crista acustica (primary auditory organ) and its proximal complement, the intermediate organ. Unlike reports of a membranous organ structure for homologs in other ensiferans, weta tibial organs contain receptor cells embedded in thick solid masses. Primary afferents project ipsilaterally to the medial ventral association center of thoracic ganglia, where axon terminals are arrayed topographically in different areas specific to each organ, except for almost complete overlap of afferents originating from the distal part of the crista acustica and from the intermediate organ. In contrast to somatotopic reflection of sensilla position on limbs, as known for mechanoreceptor hairs, the somatotopic projection map of the insect ear reveals topographic association with acoustic tracheae or tibial cuticular attachment sites, which in turn must reflect determinants of response sensitivity (e.g., frequency or threshold).

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

    USDA-ARS?s Scientific Manuscript database

    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...

  19. 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

  20. Planetary maps

    USGS Publications Warehouse

    ,

    1992-01-01

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

  1. 1-Quasiconformal Mappings and CR Mappings on Goursat Groups

    PubMed Central

    Wu, Qing Yan; Fu, Zun Wei

    2014-01-01

    We show that 1-quasiconformal mappings on Goursat groups are CR or anti-CR mappings. This can reduce the determination of 1-quasiconformal mappings to the determination of CR automorphisms of CR manifolds, which is a fundamental problem in the theory of several complex variables. PMID:24895673

  2. 1-Quasiconformal mappings and CR mappings on Goursat groups.

    PubMed

    Wu, Qing Yan; Fu, Zun Wei

    2014-01-01

    We show that 1-quasiconformal mappings on Goursat groups are CR or anti-CR mappings. This can reduce the determination of 1-quasiconformal mappings to the determination of CR automorphisms of CR manifolds, which is a fundamental problem in the theory of several complex variables.

  3. Factorized Diffusion Map Approximation

    PubMed Central

    Amizadeh, Saeed; Valizadegan, Hamed; Hauskrecht, Milos

    2013-01-01

    Diffusion maps are among the most powerful Machine Learning tools to analyze and work with complex high-dimensional datasets. Unfortunately, the estimation of these maps from a finite sample is known to suffer from the curse of dimensionality. Motivated by other machine learning models for which the existence of structure in the underlying distribution of data can reduce the complexity of estimation, we study and show how the factorization of the underlying distribution into independent subspaces can help us to estimate diffusion maps more accurately. Building upon this result, we propose and develop an algorithm that can automatically factorize a high dimensional data space in order to minimize the error of estimation of its diffusion map, even in the case when the underlying distribution is not decomposable. Experiments on both the synthetic and real-world datasets demonstrate improved estimation performance of our method over the standard diffusion-map framework. PMID:25309676

  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 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

  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

    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.

  6. 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

  7. Mapping snow depth in complex alpine terrain with close range aerial imagery - estimating the spatial uncertainties of repeat autonomous aerial surveys over an active rock glacier

    NASA Astrophysics Data System (ADS)

    Goetz, Jason; Marcer, Marco; Bodin, Xavier; Brenning, Alexander

    2017-04-01

    Snow depth mapping in open areas using close range aerial imagery is just one of the many cases where developments in structure-from-motion and multi-view-stereo (SfM-MVS) 3D reconstruction techniques have been applied for geosciences - and with good reason. Our ability to increase the spatial resolution and frequency of observations may allow us to improve our understanding of how snow depth distribution varies through space and time. However, to ensure accurate snow depth observations from close range sensing we must adequately characterize the uncertainty related to our measurement techniques. In this study, we explore the spatial uncertainties of snow elevation models for estimation of snow depth in a complex alpine terrain from close range aerial imagery. We accomplish this by conducting repeat autonomous aerial surveys over a snow-covered active-rock glacier located in the French Alps. The imagery obtained from each flight of an unmanned aerial vehicle (UAV) is used to create an individual digital elevation model (DEM) of the snow surface. As result, we obtain multiple DEMs of the snow surface for the same site. These DEMs are obtained from processing the imagery with the photogrammetry software Agisoft Photoscan. The elevation models are also georeferenced within Photoscan using the geotagged imagery from an onboard GNSS in combination with ground targets placed around the rock glacier, which have been surveyed with highly accurate RTK-GNSS equipment. The random error associated with multi-temporal DEMs of the snow surface is estimated from the repeat aerial survey data. The multiple flights are designed to follow the same flight path and altitude above the ground to simulate the optimal conditions of repeat survey of the site, and thus try to estimate the maximum precision associated with our snow-elevation measurement technique. The bias of the DEMs is assessed with RTK-GNSS survey observations of the snow surface elevation of the area on and surrounding

  8. 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

  9. FIGO stage IIIC endometrial cancer identification among patients with complex atypical hyperplasia, grade 1 and 2 endometrioid endometrial cancer: laparoscopic indocyanine green sentinel lymph node mapping versus frozen section of the uterus, why get around the problem?

    PubMed

    Papadia, Andrea; Gasparri, Maria Luisa; Siegenthaler, Franziska; Imboden, Sara; Mohr, Stefan; Mueller, Michael D

    2017-03-01

    To compare two surgical strategies used to identify lymph node metastases in patients with preoperative diagnosis of complex atypical hyperplasia (CAH), grade 1 and 2 endometrial cancer (EC). Data on patients with preoperative diagnosis of CAH, grade 1 and 2 EC undergoing laparoscopic indocyanine green (ICG) sentinel lymph node (SLN) mapping followed by frozen section of the uterus were collected. When risk factors were identified at frozen section, patients were subjected to a systematic lymphadenectomy. False negative (FN) rates, negative predictive values (NPV), positive predictive values (PPV) and correlation with stage IIIC EC were calculated for the systematic lymphadenectomy based on frozen section of the uterus and for the SLN mapping. Six (9.5%) out of 63 patients had lymph nodal metastases. Based on frozen section of the uterus, 22 (34.9%) and 15 (22.2%) patients underwent a pelvic and a pelvic and paraaortic lymphadenectomy, respectively. Five patients with stage IIIC disease were identified with a FN rate of 16.7% and a NPV and PPV of 97.6 and 27.3%, respectively. Overall and bilateral detection rates of ICG SLN mapping were 100 and 97.6%, respectively; no FN were recorded. The identification of patients with stage IIIC disease with ICG SLN mapping showed a NPV and PPV of 100%. Correlation between indication to lymphadenectomy and stage IIIC disease was poor (κ = 0.244) when based on frozen section of the uterus and excellent (κ = 1) when based on SLN mapping. ICG SLN mapping reduces the number of unnecessary systematic lymphadenectomies and the risk of underdiagnosing patients with metastatic lymph nodes.

  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. Exploring maps

    USGS Publications Warehouse

    ,

    1993-01-01

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

  12. 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.

  13. Numerical Conformal Mapping and Applications

    DTIC Science & Technology

    1990-02-26

    complex analysis in scientific computing , 13 6.1...Technical results: applications of complex analysis in scientific computing 6.1. Matrix iterative algorithms based on complex approximation Since the 1950s...polygons - Review of "Schwarz-Christoffel Mapping in the 1980’s" * Release of second edition of SCPACK User’s Guide Applications of complex analysis

  14. 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.

  15. Digital field mapping and the interpretation of the complex geomorphologcal setting of the Flims and Tamins Landslides ((Rhein River valley Switzerland)

    NASA Astrophysics Data System (ADS)

    Giardino, Marco; Masera, Diego; Perotti, Luigi; Poschinger, Andreas; Clague, John; Calhoun, Nancy

    2015-04-01

    We analyze landforms and deposits related to the Flims and Tamins landslides (Rhein Valley, Switzerland) using an integrated geomorphologic-geomatic approach that includes literature analysis, field mapping and remote sensing. These huge landslides (estimated volumes of 9.3 km3 for Flims and 1.6 km3 for Tamins) occurred at a time of large slope instabilities in the Rhein valley around 9000 years ago. Our focus is peculiar landforms called "Tomas" that occur as a series of distributed hills in the vicinity of and downstream of the Vorderrhein-Hinterrhein confluence. Their origin has been debated for more than one and one-half centuries, but current thinking is that they are, depending on the area, intact rootless masses of Flims or Tamins landslide debris rafted downvalley in a thick layer of liquefied valley fill ("Bonaduz gravel" for the ones upstram) during the Flims landslide event. Our analysis of the features involved: 1) analysis of a LiDAR-derived DTM (Swissmap) and base maps produced from the DTM for field work (hillshade and 1 m spacing contour maps); and 2) field data collection and digital GIS mapping of deposits and landforms with a pocket PC and GPS. We created a geo-database that includes morphometric, structural and sedimentological data on the Tomas. We produced a digital map from the DTM and field data, along with a comprehensive legend linked to our kinematic and dynamic interpretations. We recognize and describe four groups of Tomas, which provide new insights into the genesis of these peculiar features. Remote sensing and field data also allow us to precisely map the eastern boundary of the Flims landslide deposit and to interpret the spatial relation between the Tomas and the Bonaduz gravel.

  16. Historical Topographic Map Collection bookmark

    USGS Publications Warehouse

    Fishburn, Kristin A.; Allord, Gregory J.

    2017-06-29

    The U.S. Geological Survey (USGS) National Geospatial Program is scanning published USGS 1:250,000-scale and larger topographic maps printed between 1884, the inception of the topographic mapping program, and 2006. The goal of this project, which began publishing the historical scanned maps in 2011, is to provide a digital repository of USGS topographic maps, available to the public at no cost. For more than 125 years, USGS topographic maps have accurately portrayed the complex geography of the Nation. The USGS is the Nation’s largest producer of printed topographic maps, and prior to 2006, USGS topographic maps were created using traditional cartographic methods and printed using a lithographic printing process. As the USGS continues the release of a new generation of topographic maps (US Topo) in electronic form, the topographic map remains an indispensable tool for government, science, industry, land management planning, and leisure.

  17. USGS maps

    USGS Publications Warehouse

    ,

    2005-01-01

    Discover a small sample of the millions of maps produced by the U.S. Geological Survey (USGS) in its mission to map the Nation and survey its resources. This booklet gives a brief overview of the types of maps sold and distributed by the USGS through its Earth Science Information Centers (ESIC) and also available from business partners located in most States. The USGS provides a wide variety of maps, from topographic maps showing the geographic relief and thematic maps displaying the geology and water resources of the United States, to special studies of the moon and planets.

  18. 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

  19. 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...

  20. 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...

  1. Historical Mapping

    USGS Publications Warehouse

    ,

    1999-01-01

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

  2. Image processing for optical mapping.

    PubMed

    Ravindran, Prabu; Gupta, Aditya

    2015-01-01

    Optical Mapping is an established single-molecule, whole-genome analysis system, which has been used to gain a comprehensive understanding of genomic structure and to study structural variation of complex genomes. A critical component of Optical Mapping system is the image processing module, which extracts single molecule restriction maps from image datasets of immobilized, restriction digested and fluorescently stained large DNA molecules. In this review, we describe robust and efficient image processing techniques to process these massive datasets and extract accurate restriction maps in the presence of noise, ambiguity and confounding artifacts. We also highlight a few applications of the Optical Mapping system.

  3. 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

  4. Topographic mapping

    USGS Publications Warehouse

    ,

    2008-01-01

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

  5. An integrated pipeline for the development of novel panels of mapped microsatellite markers for Leishmania donovani complex, Leishmania braziliensis and Leishmania major.

    PubMed

    Fakhar, M; Motazedian, M H; Daly, D; Lowe, C D; Kemp, S J; Noyes, H A

    2008-04-01

    A panel of microsatellites mapped to the Leishmania genome might make it possible to find associations between specific loci and phenotypic traits. To identify such loci, a Perl programme was written that scans the sequence of a genome and writes all loci containing microsatellites to a MySQL database. The programme was applied to the sequences of the L. braziliensis, L. infantum and L. major genomes. The database is publicly available over the internet: http://www.genomics.liv.ac.uk/tryps/resources.html 'Microsatellite Locus Extractor', and allows the selection of mapped microsatellites that meet user-defined criteria from a specified region of the selected genome. The website also incorporates a primer design pipeline that will design primers to amplify the selected loci. Using this pipeline 12 out of 17 primer sets designed against the L. infantum genome generated polymorphic PCR products. A tailed primer protocol was used to label all microsatellite primers with a single set of labelled primers. To avoid the culture of parasites prior to genotyping, sets of nested PCR primers were developed to amplify parasite DNA eluted from microscope slides. The limit of detection was approximately 1.6 parasite equivalents. However, only 6/56 DNA from slides stored at ambient temperature for over 6 months gave positive PCR results.

  6. Vitiligo road map.

    PubMed

    Lee, Brian W; Schwartz, Robert A; Hercogová, Jana; Valle, Yan; Lotti, Torello M

    2012-01-01

    Vitiligo is a depigmenting disorder stemming from melanocyte loss or dysfunction. It has a complex, multifaceted etiology. We constructed a "vitiligo road map," consisting of basic science, clinical, and treatment components, in order to better portray our current understanding of vitiligo pathogenesis and reflect upon novel biomarkers and therapeutic targets for future research. The melanocyte map elaborates on the molecular processes and intracellular signaling pathways initiated by various external autocrine/paracrine factors in representing normal melanocyte homeostatic functions modulating its viability, proliferation, differentiation, dendricity, migration, and melanogenic processes. This vitiligo map identifies known inducers/triggers of vitiligo onset and progression that cultivate a microenvironment for melanocyte disappearance, real or functional. This map describes the molecular mechanisms of currently utilized clinical and experimental treatments of vitiligo that facilitate repigmentation.

  7. Building maps from maps in primary visual cortex.

    PubMed

    Nauhaus, Ian; Nielsen, Kristina J

    2014-02-01

    Neurons in the visual system respond to more complex and holistic features at each new stage of processing. Often, these features are organized into continuous maps. Could there be a fundamental link between continuous maps and functional hierarchies? Here, we review recent studies regarding V1 maps providing some of the most noteworthy advances in our understanding of how and why maps exist. In particular, we focus on the common theme that some maps are inherited from the input of parallel pathways, which are then intimately linked to the emergence of new functional properties and their corresponding maps. These results on V1 maps may prove to be a unifying framework for hierarchical representations in the visual cortex. Copyright © 2013 Elsevier Ltd. All rights reserved.

  8. Native Top‐Down Mass Spectrometry of TAR RNA in Complexes with a Wild‐Type tat Peptide for Binding Site Mapping

    PubMed Central

    Schneeberger, Eva‐Maria

    2016-01-01

    Abstract Ribonucleic acids (RNA) frequently associate with proteins in many biological processes to form more or less stable complex structures. The characterization of RNA–protein complex structures and binding interfaces by nuclear magnetic resonance (NMR) spectroscopy, X‐ray crystallography, or strategies based on chemical crosslinking, however, can be quite challenging. Herein, we have explored the use of an alternative method, native top‐down mass spectrometry (MS), for probing of complex stoichiometry and protein binding sites at the single‐residue level of RNA. Our data show that the electrostatic interactions between HIV‐1 TAR RNA and a peptide comprising the arginine‐rich binding region of tat protein are sufficiently strong in the gas phase to survive phosphodiester backbone cleavage of RNA by collisionally activated dissociation (CAD), thus allowing its use for probing tat binding sites in TAR RNA by top‐down MS. Moreover, the MS data reveal time‐dependent 1:2 and 1:1 stoichiometries of the TAR–tat complexes and suggest structural rearrangements of TAR RNA induced by binding of tat peptide. PMID:28000363

  9. 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....

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

    USDA-ARS?s Scientific Manuscript database

    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...

  11. 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....

  12. Bedrock geologic map of Vermont

    USGS Publications Warehouse

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

    2011-01-01

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

  13. Mapping of a region of the paramyxovirus L protein required for the formation of a stable complex with the viral phosphoprotein P.

    PubMed

    Parks, G D

    1994-08-01

    The paramyxovirus large protein (L) and phosphoprotein (P) are both required for viral RNA-dependent RNA polymerase activity. Previous biochemical experiments have shown that L and P can form a complex when expressed from cDNA plasmids in vivo. In this report, L and P proteins of the paramyxovirus simian virus 5 (SV5) were coexpressed in HeLa T4 cells from cDNA plasmids, and L-P complexes were examined. To identify regions of the SV5 L protein that are required for L-P complex formation, 16 deletion mutants were constructed by mutagenesis of an SV5 L cDNA. Following coexpression of these L mutants with cDNA-derived P and radiolabeling with 35S-amino acids, cell lysates were analyzed for stable L-P complexes by a coimmunoprecipitation assay and by sedimentation on 5 to 20% glycerol gradients. Mutant forms of L containing deletions that removed as much as 1,008 residues from the C-terminal half of the full-length 2,255-residue L protein were detected in complexes with P by these two assays. In contrast, large deletions in the N-terminal half of L resulted in proteins that were defective in the formation of stable L-P complexes. Likewise, L mutants containing smaller deletions that individually removed N-terminal regions which are conserved among paramyxovirus and rhabdovirus L proteins (domain I, II, or III) were also defective in stable interactions with P. These results suggest that the N-terminal half of the L protein contains sequences important for stable L-P complex formation and that the C-terminal half of L is not directly involved in these interactions. SV5-infected HeLa T4 cells were pulse-labeled with 35S-amino acids, and cell extracts were examined by gradient sedimentation. Solubilized L protein was detected as an approximately 8 to 10S species, while the P protein was found as both a approximately 4S form (approximately 85%) and a species that cosedimented with L (approximately 15%). These data provide the first biochemical evidence in support of a

  14. 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

  15. 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.

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

    PubMed Central

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

    2014-01-01

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

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

    SciTech Connect

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

    2014-08-19

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

  18. Collection Mapping.

    ERIC Educational Resources Information Center

    Harbour, Denise

    2002-01-01

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

  19. Concept Mapping

    ERIC Educational Resources Information Center

    Technology & Learning, 2005

    2005-01-01

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

  20. 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)

  1. 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…

  2. Concept Mapping

    ERIC Educational Resources Information Center

    Technology & Learning, 2005

    2005-01-01

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

  3. 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…

  4. 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…

  5. Collection Mapping.

    ERIC Educational Resources Information Center

    Harbour, Denise

    2002-01-01

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

  6. 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)

  7. Genome mapping

    USDA-ARS?s Scientific Manuscript database

    Genome maps can be thought of much like road maps except that, instead of traversing across land, they traverse across the chromosomes of an organism. Genetic markers serve as landmarks along the chromosome and provide researchers information as to how close they may be to a gene or region of inter...

  8. From complex B(1) mapping to local SAR estimation for human brain MR imaging using multi-channel transceiver coil at 7T.

    PubMed

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

    2013-06-01

    Elevated specific absorption rate (SAR) associated with increased main magnetic field strength remains 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 radio-frequency (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.

  9. 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

  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. The Effects of Theta Precession on Spatial Learning and Simplicial Complex Dynamics in a Topological Model of the Hippocampal Spatial Map

    PubMed Central

    Arai, Mamiko; Brandt, Vicky; Dabaghian, Yuri

    2014-01-01

    Learning arises through the activity of large ensembles of cells, yet most of the data neuroscientists accumulate is at the level of individual neurons; we need models that can bridge this gap. We have taken spatial learning as our starting point, computationally modeling the activity of place cells using methods derived from algebraic topology, especially persistent homology. We previously showed that ensembles of hundreds of place cells could accurately encode topological information about different environments (“learn” the space) within certain values of place cell firing rate, place field size, and cell population; we called this parameter space the learning region. Here we advance the model both technically and conceptually. To make the model more physiological, we explored the effects of theta precession on spatial learning in our virtual ensembles. Theta precession, which is believed to influence learning and memory, did in fact enhance learning in our model, increasing both speed and the size of the learning region. Interestingly, theta precession also increased the number of spurious loops during simplicial complex formation. We next explored how downstream readout neurons might define co-firing by grouping together cells within different windows of time and thereby capturing different degrees of temporal overlap between spike trains. Our model's optimum coactivity window correlates well with experimental data, ranging from ∼150–200 msec. We further studied the relationship between learning time, window width, and theta precession. Our results validate our topological model for spatial learning and open new avenues for connecting data at the level of individual neurons to behavioral outcomes at the neuronal ensemble level. Finally, we analyzed the dynamics of simplicial complex formation and loop transience to propose that the simplicial complex provides a useful working description of the spatial learning process. PMID:24945927

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

    PubMed

    Wollesen, T; Loesel, R; Wanninger, A

    2009-04-30

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

  13. Mapping the contact surfaces in the Lamin A:AIMP3 complex by hydrogen/deuterium exchange FT-ICR mass spectrometry

    PubMed Central

    Tao, Yeqing; Fang, Pengfei; Kim, Sunghoon; Guo, Min; Young, Nicolas L.; Marshall, Alan G.

    2017-01-01

    Aminoacyl-tRNA synthetases-interacting multifunctional protein3 (AIMP3/p18) is involved in the macromolecular tRNA synthetase complex via its interaction with several aminoacyl-tRNA synthetases. Recent reports reveal a novel function of AIMP3 as a tumor suppressor by accelerating cellular senescence and causing defects in nuclear morphology. AIMP3 specifically mediates degradation of mature Lamin A (LmnA), a major component of the nuclear envelope matrix; however, the mechanism of how AIMP3 interacts with LmnA is unclear. Here we report solution-phase hydrogen/deuterium exchange (HDX) for AIMP3, LmnA, and AIMP3 in association with the LmnA C-terminus. Reversed-phase LC coupled with LTQ 14.5 T Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) results in high mass accuracy and resolving power for comparing the D-uptake profiles for AIMP3, LmnA, and their complex. The results show that the AIMP3-LmnA interaction involves one of the two putative binding sites and an adjacent novel interface on AIMP3. LmnA binds AIMP3 via its extreme C-terminus. Together these findings provide a structural insight for understanding the interaction between AIMP3 and LmnA in AIMP3 degradation. PMID:28797100

  14. 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.

  15. 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.

  16. Large-scale Spectroscopic Mapping of the ρ Ophiuchi Molecular Cloud Complex. I. The C2H-to-N2H+ Ratio as a Signpost of Cloud Characteristics

    NASA Astrophysics Data System (ADS)

    Pan, Zhichen; Li, Di; Chang, Qiang; Qian, Lei; Bergin, Edwin A.; Wang, Junzhi

    2017-02-01

    We present 2.5-square-degree C2H N = 1-0 and N2H+ J = 1-0 maps of the ρ Ophiuchi molecular cloud complex. These are the first large-scale maps of the ρ Ophiuchi molecular cloud complex with these two tracers. The C2H emission is spatially more extended than the N2H+ emission. One faint N2H+ clump, Oph-M, and one C2H ring, Oph-RingSW, are identified for the first time. The observed C2H-to-N2H+ abundance ratio ([C2H]/[N2H+]) varies between 5 and 110. We modeled the C2H and N2H+ abundances with 1D chemical models, which show a clear decline of [C2H]/[N2H+] with chemical age. Such an evolutionary trend is little affected by temperatures when they are below 40 K. At high density (n H > 105 cm-3), however, the time it takes for the abundance ratio to drop at least one order of magnitude becomes less than the dynamical time (e.g., turbulence crossing time of ˜105 yr). The observed [C2H]/[N2H+] difference between L1688 and L1689 can be explained by L1688 having chemically younger gas in relatively less dense regions. The observed [C2H]/[N2H+] values are the results of time evolution, accelerated at higher densities. For the relatively low density regions in L1688 where only C2H emission was detected, the gas should be chemically younger.

  17. Seismic scattering and absorption mapping from intermediate-depth earthquakes reveals complex tectonic interactions acting in the Vrancea region and surroundings (Romania)

    NASA Astrophysics Data System (ADS)

    Borleanu, F.; De Siena, L.; Thomas, C.; Popa, M.; Radulian, M.

    2017-06-01

    The Vrancea region, located at the southeastern edge of the Carpathians arc bend, is a region of intense seismicity, whose major earthquakes produce hazard in southeastern Europe. Despite the consequent focus of the geophysical and geological community on providing accurate structural and dynamical models of Vrancea, these are still subject to numerous controversies and debates. In the present study, we use intermediate-depth seismicity recorded by the broadband stations of the Romanian Seismic Network between 2009 and 2011 to measure S-wave peak delay times and late-time coda quality factors. After mapping these two quantities in space, a cluster analysis provides a quantitative structural interpretation of the region in terms of different attenuation mechanisms affecting the seismic wave field, i.e. seismic scattering and seismic absorption. The results show that scattering is higher west and northwest of Vrancea, while absorption dominates in the Focsani Basin, located in the forearc region. In general, we obtain higher absorption in stable regions, with patterns emphasized at high-frequency affected by the presence of hydrocarbons and natural gas reservoirs in the upper crustal layers. Regions characterized by active seismicity and structural heterogeneity show higher scattering, spatially correlated with the highest velocity contrasts and the lowest density. The high-frequency scattering/absorption contrasts obtained using the cluster analysis depict a southwest-to-northeast lithospheric contrast, following the epicentral trend of Vrancea earthquakes, and characteristic of either lithospheric subduction or delamination. Low-frequency cluster analysis results, sampling deeper Earth layers, mark a unique high-absorption trend perpendicular to the epicentral trend, feasibly linked to Neogene volcanism, and induced by the back-arc mantle upwelling. Its most recent expression is Ciomadul volcano, located at the northwestern limit of the absorption trend.

  18. Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping.

    PubMed

    Misceo, Doriana; Capozzi, Oronzo; Roberto, Roberta; Dell'oglio, Maria P; Rocchi, Mariano; Stanyon, Roscoe; Archidiacono, Nicoletta

    2008-09-01

    In this study we characterized the extension, reciprocal arrangement, and orientation of syntenic chromosomal segments in the lar gibbon (Hylobates lar, HLA) by hybridization of a panel of approximately 1000 human BAC clones. Each lar gibbon rearrangement was defined by a splitting BAC clone or by two overlapping clones flanking the breakpoint. A reconstruction of the synteny arrangement of the last common ancestor of all living lesser apes was made by combining these data with previous results in Nomascus leucogenys, Hoolock hoolock, and Symphalangus syndactylus. The definition of the ancestral synteny organization facilitated tracking the cascade of chromosomal changes from the Hominoidea ancestor to the present day karyotype of Hylobates and Nomascus. Each chromosomal rearrangement could be placed within an approximate phylogenetic and temporal framework. We identified 12 lar-specific rearrangements and five previously undescribed rearrangements that occurred in the Hylobatidae ancestor. The majority of the chromosomal differences between lar gibbons and humans are due to rearrangements that occurred in the Hylobatidae ancestor (38 events), consistent with the hypothesis that the genus Hylobates is the most recently evolved lesser ape genus. The rates of rearrangements in gibbons are 10 to 20 times higher than the mammalian default rate. Segmental duplication may be a driving force in gibbon chromosome evolution, because a consistent number of rearrangements involves pericentromeric regions (10 events) and centromere inactivation (seven events). Both phenomena can be reasonably supposed to have strongly contributed to the euchromatic dispersal of segmental duplications typical of pericentromeric regions. This hypothesis can be more fully tested when the sequence of this gibbon species becomes available. The detailed synteny map provided here will, in turn, substantially facilitate sequence assembly efforts.

  19. Tracking the complex flow of chromosome rearrangements from the Hominoidea Ancestor to extant Hylobates and Nomascus Gibbons by high-resolution synteny mapping

    PubMed Central

    Misceo, Doriana; Capozzi, Oronzo; Roberto, Roberta; Dell’Oglio, Maria P.; Rocchi, Mariano; Stanyon, Roscoe; Archidiacono, Nicoletta

    2008-01-01

    In this study we characterized the extension, reciprocal arrangement, and orientation of syntenic chromosomal segments in the lar gibbon (Hylobates lar, HLA) by hybridization of a panel of ∼1000 human BAC clones. Each lar gibbon rearrangement was defined by a splitting BAC clone or by two overlapping clones flanking the breakpoint. A reconstruction of the synteny arrangement of the last common ancestor of all living lesser apes was made by combining these data with previous results in Nomascus leucogenys, Hoolock hoolock, and Symphalangus syndactylus. The definition of the ancestral synteny organization facilitated tracking the cascade of chromosomal changes from the Hominoidea ancestor to the present day karyotype of Hylobates and Nomascus. Each chromosomal rearrangement could be placed within an approximate phylogenetic and temporal framework. We identified 12 lar-specific rearrangements and five previously undescribed rearrangements that occurred in the Hylobatidae ancestor. The majority of the chromosomal differences between lar gibbons and humans are due to rearrangements that occurred in the Hylobatidae ancestor (38 events), consistent with the hypothesis that the genus Hylobates is the most recently evolved lesser ape genus. The rates of rearrangements in gibbons are 10 to 20 times higher than the mammalian default rate. Segmental duplication may be a driving force in gibbon chromosome evolution, because a consistent number of rearrangements involves pericentromeric regions (10 events) and centromere inactivation (seven events). Both phenomena can be reasonably supposed to have strongly contributed to the euchromatic dispersal of segmental duplications typical of pericentromeric regions. This hypothesis can be more fully tested when the sequence of this gibbon species becomes available. The detailed synteny map provided here will, in turn, substantially facilitate sequence assembly efforts. PMID:18552313

  20. 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.

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

    PubMed

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

    2004-05-01

    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.

  2. Mapping Children--Mapping Space.

    ERIC Educational Resources Information Center

    Pick, Herbert L., Jr.

    Research is underway concerning the way the perception, conception, and representation of spatial layout develops. Three concepts are important here--space itself, frame of reference, and cognitive map. Cognitive map refers to a form of representation of the behavioral space, not paired associate or serial response learning. Other criteria…

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

    NASA Astrophysics Data System (ADS)

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

    2014-03-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2013-10-01

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

  5. Radiation hybrid mapping in crop plants

    USDA-ARS?s Scientific Manuscript database

    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 ...

  6. 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

  7. 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)

  8. Planetary Mapping

    NASA Astrophysics Data System (ADS)

    Greeley, Ronald; Batson, Raymond M.

    2007-02-01

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

  9. Genome-Wide Mapping of Uncapped and Cleaved Transcripts Reveals a Role for the Nuclear mRNA Cap-Binding Complex in Cotranslational RNA Decay in Arabidopsis[OPEN

    PubMed Central

    Willmann, Matthew R.

    2016-01-01

    RNA turnover is necessary for controlling proper mRNA levels posttranscriptionally. In general, RNA degradation is via exoribonucleases that degrade RNA either from the 5′ end to the 3′ end, such as XRN4, or in the opposite direction by the multisubunit exosome complex. Here, we use genome-wide mapping of uncapped and cleaved transcripts to reveal the global landscape of cotranslational mRNA decay in the Arabidopsis thaliana transcriptome. We found that this process leaves a clear three nucleotide periodicity in open reading frames. This pattern of cotranslational degradation is especially evident near the ends of open reading frames, where we observe accumulation of cleavage events focused 16 to 17 nucleotides upstream of the stop codon because of ribosomal pausing during translation termination. Following treatment of Arabidopsis plants with the translation inhibitor cycloheximide, cleavage events accumulate 13 to 14 nucleotides upstream of the start codon where initiating ribosomes have been stalled with these sequences in their P site. Further analysis in xrn4 mutant plants indicates that cotranslational RNA decay is XRN4 dependent. Additionally, studies in plants lacking CAP BINDING PROTEIN80/ABA HYPERSENSITIVE1, the largest subunit of the nuclear mRNA cap binding complex, reveal a role for this protein in cotranslational decay. In total, our results demonstrate the global prevalence and features of cotranslational RNA decay in a plant transcriptome. PMID:27758893

  10. Map Separates

    USGS Publications Warehouse

    ,

    2001-01-01

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

  11. 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.

  12. 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

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

    DOE PAGES

    Aggarwal, Mayank; Kovalevsky, Andrey Y.; Velazquez, Hector; ...

    2016-07-22

    Carbonic anhydrases (CAs; EC 4.2.1.1) catalyze the interconversion of CO2 and HCO3–, and their inhibitors have long been used as diuretics and as a therapeutic treatment for many disorders such as glaucoma and epilepsy. Acetazolamide (AZM) and methazolamide (MZM, a methyl derivative of AZM) are two of the classical CA inhibitory drugs that have been used clinically for decades. The jointly refined X-ray/neutron structure of MZM in complex with human CA isoform II (hCA II) has been determined to a resolution of 2.2 Å with an Rcryst of ~16.0%. Presented in this article, along with only the second neutron structuremore » of a clinical drug-bound hCA, is an in-depth structural comparison and analyses of differences in hydrogen-bonding network, water-molecule orientation and solvent displacement that take place upon the binding of AZM and MZM in the active site of hCA II. Even though MZM is slightly more hydrophobic and displaces more waters than AZM, the overall binding affinity (Ki) for both of the drugs against hCA II is similar (~10 nM). The plausible reasons behind this finding have also been discussed using molecular dynamics and X-ray crystal structures of hCA II–MZM determined at cryotemperature and room temperature. Furthermore, this study not only allows a direct comparison of the hydrogen bonding, protonation states and solvent orientation/displacement of AZM and MZM, but also shows the significant effect that the methyl derivative has on the solvent organization in the hCA II active site.« less

  14. Preliminary geologic mapping of Arsia Mons, Mars

    NASA Technical Reports Server (NTRS)

    Zimbelman, James R.

    1991-01-01

    Geologic mapping of the Tharsis Montes at a scale of 1:500,000 was recently initiated as part of the Mars Geologic Mapping Program of NASA. Detailed mapping of the three large shield volcanoes and their surroundings will help to clarify the sequence of events which led to the formation of these features, as well as provide a basis for comparing the complex histories of the three related yet distinctive volcanic centers. Preliminary mapping of Arsia Mons at a scale of 1:2 M was carried out in preparation for detailed mapping. A map is presented along with a discussion of its contents.

  15. Automated geologic mapping using rock reflectances.

    NASA Technical Reports Server (NTRS)

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

    1971-01-01

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

  16. Mapping Potassium

    NASA Image and Video Library

    2015-04-16

    During the first year of NASA MESSENGER orbital mission, the spacecraft GRS instrument measured the elemental composition of Mercury surface materials. mong the most important discoveries from the GRS was the observation of higher abundances of the moderately volatile elements potassium, sodium, and chlorine than expected from previous scientific models and theories. Particularly high concentrations of these elements were observed at high northern latitudes, as illustrated in this potassium abundance map, which provides a view of the surface centered at 60° N latitude and 120° E longitude. This map was the first elemental map ever made of Mercury's surface and is to-date the only map to report absolute elemental concentrations, in comparison to element ratios. Prior to MESSENGER's arrival at Mercury, scientists expected that the planet would be depleted in moderately volatile elements, as is the case for our Moon. The unexpectedly high abundances observed with the GRS have forced a reevaluation of our understanding of the formation and evolution of Mercury. In addition, the K map provided the first evidence for distinct geochemical terranes on Mercury, as the high-potassium region was later found to also be distinct in its low Mg/Si, Ca/Si, S/Si, and high Na/Si and Cl/Si abundances. Instrument: Gamma-Ray Spectrometer (GRS) http://photojournal.jpl.nasa.gov/catalog/PIA19414

  17. 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

  18. 2 n -rational maps

    NASA Astrophysics Data System (ADS)

    Kassotakis, Pavlos; Nieszporski, Maciej

    2017-05-01

    We present a natural extension of the notion of nondegenerate rational maps (quadrirational maps) to arbitrary dimensions. We refer to these maps as 2 n -rational maps. In this note we construct a rich family of 2 n -rational maps. These maps by construction are involutions and highly symmetric in the sense that the maps and their companion maps have the same functional form.

  19. Map projections and the Internet: Chapter 4

    USGS Publications Warehouse

    Kessler, Fritz; Battersby, Sarah E.; Finn, Michael P.; Clarke, Keith

    2017-01-01

    The field of map projections can be described as mathematical, static, and challenging. However, this description is evolving in concert with the development of the Internet. The Internet has enabled new outlets for software applications, learning, and interaction with and about map projections . This chapter examines specific ways in which the Internet has moved map projections from a relatively obscure paper-based setting to a more engaging and accessible online environment. After a brief overview of map projections, this chapter discusses four perspectives on how map projections have been integrated into the Internet. First, map projections and their role in web maps and mapping services is examined. Second, an overview of online atlases and the map projections chosen for their maps is presented. Third, new programming languages and code libraries that enable map projections to be included in mapping applications are reviewed. Fourth, the Internet has facilitated map projection education and research especially with the map reader’s comprehension and understanding of complex topics like map projection distortion is discussed.

  20. Generating Multi-destination Maps.

    PubMed

    Zhang, Junsong; Fan, Jiepeng; Luo, Zhenshan

    2016-08-03

    Multi-destination maps are a kind of navigation maps aimed to guide visitors to multiple destinations within a region, which can be of great help to urban visitors. However, they have not been developed in the current online map service. To address this issue, we introduce a novel layout model designed especially for generating multi-destination maps, which considers the global and local layout of a multi-destination map. We model the layout problem as a graph drawing that satisfies a set of hard and soft constraints. In the global layout phase, we balance the scale factor between ROIs. In the local layout phase, we make all edges have good visibility and optimize the map layout to preserve the relative length and angle of roads. We also propose a perturbation-based optimization method to find an optimal layout in the complex solution space. The multi-destination maps generated by our system are potential feasible on the modern mobile devices and our result can show an overview and a detail view of the whole map at the same time. In addition, we perform a user study to evaluate the effectiveness of our method, and the results prove that the multi-destination maps achieve our goals well.

  1. 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.

  2. 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.

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

    USDA-ARS?s Scientific Manuscript database

    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...

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

    USDA-ARS?s Scientific Manuscript database

    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...

  5. Genetic Analysis Workshop 15: simulation of a complex genetic model for rheumatoid arthritis in nuclear families including a dense SNP map with linkage disequilibrium between marker loci and trait loci

    PubMed Central

    Miller, Michael B; Lind, Gregg R; Li, Na; Jang, Soon-Young

    2007-01-01

    Data for Problem 3 of the Genetic Analysis Workshop 15 were generated by computer simulation in an attempt to mimic some of the genetic and epidemiological features of rheumatoid arthritis (RA) such as its population prevalence, sex ratio, risk to siblings of affected individuals, association with cigarette smoking, the strong effect of genotype in the HLA region and other genetic effects. A complex genetic model including epistasis and genotype-by-environment interaction was applied to a population of 1.9 million nuclear families of size four from which we selected 1500 families with both offspring affected and 2000 unrelated, unaffected individuals all of whose first-degree relatives were unaffected. This process was repeated to produce 100 replicate data sets. In addition, we generated marker data for 22 autosomes consisting of a genome-wide set of 730 simulated STRP markers, 9187 SNP markers and an additional 17,820 SNP markers on chromosome 6. Appropriate linkage disequilibrium between markers and between trait loci and markers was modelled using HapMap Phase 1 data . The code base for this project was written primarily in the Octave programming language, but it is being ported to the R language and developed into a larger project for general genetic simulation called GenetSim . All of the source code that was used to generate the GAW 15 Problem 3 data is freely available for download at . PMID:18466538

  6. Quantification of cyclin B1 and p34(cdc2) in bovine cumulus-oocyte complexes and expression mapping of genes involved in the cell cycle by complementary DNA macroarrays.

    PubMed

    Robert, Claude; Hue, Isabelle; McGraw, Serge; Gagné, Dominic; Sirard, Marc-André

    2002-11-01

    Although high amounts of cyclin B1 mRNA are present in bovine oocytes arrested at the germinal vesicle (GV) stage, the protein is not detectable. Furthermore, there is a depletion of the stored cyclin B1 mRNA in the oocyte as follicular growth progresses. To assess the effect of follicular growth on the accumulation of M-phase promoting factor (MPF) components, mRNA and protein levels of cyclin B1 and p34(cdc2) were measured in GV oocytes collected from diverse follicle size groups (<2 mm, 3-5 mm, and >6 mm). Because oocytes collected from very small follicles have high levels of cyclin B1 mRNA, the onset of its accumulation in the oocytes was evaluated by in situ hybridization of fetal ovaries. Also, a comparative expression map of cell cycle-related genes expressed in the oocyte and cumulus cells was established using nylon-based cDNA arrays, which allowed the detection of 35 different genes transcribed mostly in oocytes. Both components of the pre-MPF complex were expressed at the mRNA level in GV oocytes, whereas p34(cdc2) was the only pre-MPF protein detected at that stage, thus indicating that meiosis resumption in bovine oocytes is differentially regulated as compared with other mammals, and meiosis resumption seems to be regulated by the translation of cyclin B1 mRNA.

  7. Mapping of the Saccharomyces cerevisiae Oxa1-mitochondrial ribosome interface and identification of MrpL40, a ribosomal protein in close proximity to Oxa1 and critical for oxidative phosphorylation complex assembly.

    PubMed

    Jia, Lixia; Kaur, Jasvinder; Stuart, Rosemary A

    2009-11-01

    The Oxa1 protein plays a central role in facilitating the cotranslational insertion of the nascent polypeptide chains into the mitochondrial inner membrane. Mitochondrially encoded proteins are synthesized on matrix-localized ribosomes which are tethered to the inner membrane and in physical association with the Oxa1 protein. In the present study we used a chemical cross-linking approach to map the Saccharomyces cerevisiae Oxa1-ribosome interface, and we demonstrate here a close association of Oxa1 and the large ribosomal subunit protein, MrpL40. Evidence to indicate that a close physical and functional relationship exists between MrpL40 and another large ribosomal protein, the Mrp20/L23 protein, is also provided. MrpL40 shares sequence features with the bacterial ribosomal protein L24, which like Mrp20/L23 is known to be located adjacent to the ribosomal polypeptide exit site. We propose therefore that MrpL40 represents the Saccharomyces cerevisiae L24 homolog. MrpL40, like many mitochondrial ribosomal proteins, contains a C-terminal extension region that bears no similarity to the bacterial counterpart. We show that this C-terminal mitochondria-specific region is important for MrpL40's ability to support the synthesis of the correct complement of mitochondrially encoded proteins and their subsequent assembly into oxidative phosphorylation complexes.

  8. Geological mapping in West Virginia

    SciTech Connect

    Dean, S.L. . Dept. of Geology); Kulander, B.R. . Dept. of Geological Sciences); Lessing, P. )

    1992-01-01

    Geological mapping at 1:24,000 scale in the Valley and Ridge province of West Virginia is an ongoing program to up-date 75-year old 1:62,500 scale county geological maps. Large-scale topographic maps, remote-sensing imagery, geophysical data, well-log data, and advances in structural concepts provide information leading to thin-skinned tectonic interpretations. The five maps displayed (22 7.5-minute quadrangles) illustrate the complex deformational styles in the Paleozoic section of the Massanutten/Blue Ridge, Waynesboro, and Martinsburg sheets. Detailed field mapping reveals that many previously mapped anticlines, such as Great North Mountain and Adams run, are complex anticlinoria and that large expanses of Lower Mississippian clastics were overlooked in the Sector and Lost River State Park quadrangles. Furthermore, prevalent thrust and strike-slip faulting in the Cambrian-Ordovician carbonates of the Great Valley and extensive folding, faulting, and pre-fold layer-parallel shortening have occurred in the upper sheet to an extent not previously reported. Finally, imbrication of the underlying Waynesboro sheet forms a duplex that defines major anticlinoria and synclinoria in the Valley and Ridge. Complete maps have proven beneficial to government and the public. Examples are the siting of high-yield water wells, delineation of wellheat protection areas, and providing maps suitable for GIS systems. The maps have also been used to organize regional and local field trips and have served as the basis for the further structural and stratigraphic investigations. The West Virginia Geological Survey places high priority on detailed geological mapping. However, continuation of the program is dependent upon adequate funding.

  9. Mining Concept Maps to Understand University Students' Learning

    ERIC Educational Resources Information Center

    Yoo, Jin Soung; Cho, Moon-Heum

    2012-01-01

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

  10. Discrete Conformal Approximation of Complex Earthquake Maps

    DTIC Science & Technology

    2005-08-01

    Distribution Unlimited Edward . Allen Accepted John Borrelli Dean of the Graduate School AUGUST, 2005 20050802 092 __ rUt2 7_205 REPORT DOCUMENTATION PAGE Form...TEXAS TECH UNIVERSITY AT LUBBOCK REPORT NUMBER CI04-1143 9. SPONSORING/MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSORING/MONITORING THE DEPARTMENT...corner on the first day of Math 5320 laughing to yourself as we wondered, "Where is the professor?" Thank you, sir . To the United States Air Force, the

  11. Map projections

    USGS Publications Warehouse

    ,

    1993-01-01

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

  12. 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

  13. A prospective, multicenter evaluation of ablating complex fractionated electrograms (CFEs) during atrial fibrillation (AF) identified by an automated mapping algorithm: acute effects on AF and efficacy as an adjuvant strategy.

    PubMed

    Verma, Atul; Novak, Paul; Macle, Laurent; Whaley, Bonnie; Beardsall, Marianne; Wulffhart, Zaev; Khaykin, Yaariv

    2008-02-01

    Complex fractionated electrograms (CFEs) are continuous electrograms (EGMs) of very short cycle length (CL) representing substrate for atrial fibrillation (AF) perpetuation. Ablation of CFEs may result in AF slowing, termination, and prevention, but identifying them can be subjective. The purpose of this study was to prospectively assess (1) whether an automated algorithm can identify CFE regions, (2) the acute effects of ablating these regions on AF, and (3) the long-term efficacy as an adjuvant strategy to pulmonary vein antrum isolation (PVAI). Thirty-five patients (three centers, 61 +/- 9 years, left atrium [LA] 43 +/- 9 mm, ejection fraction 53% +/- 7%) with symptomatic paroxysmal (n = 21) or persistent (n = 14) AF were studied. A decapolar lasso (2-mm spacing) was used for mapping. A three-dimensional shell of the LA and pulmonary veins (PVs) was created. If not already in AF, AF was induced by burst pacing (with or without isoproterenol). Atrial EGMs during AF were mapped/analyzed using an automated CFE algorithm. The algorithm measures the time between discrete deflections in a local EGM over 5 seconds (based on selectable width and peak-to-peak [>0.03 mV] criteria). The mean CL of the local EGM is projected onto the LA shell as a color-coded display. Regions of CL <120 ms (published criteria) were targeted for ablation/elimination. Atrial fibrillation cycle length (AFCL) and regularity were measured from the CS. After CFE ablation, further ablation was done to achieve complete PVAI. AF was spontaneous (n = 20) or induced (n = 15) in all patients. CFEs were most commonly found along the septum (97%), anterior LA (97%), PV antra (83%), base of appendage (83%), and annulus (71%). CFE ablation alone prolonged the AFCL (171 +/- 27 vs. 304 +/- 41 ms; P = .03) and regularized AF to left/right flutter (AFL) in 74% of patients. CFE ablation terminated AF/AFL in 19 patients (54%)-the other 16 were cardioverted-and AF became noninducible in 77%. CFE ablation alone

  14. 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.

  15. Mapping Pluto Broken Heart

    NASA Image and Video Library

    2015-10-29

    In addition to transmitting new high-resolution images and other data on the familiar close-approach hemispheres of Pluto and Charon, NASA's New Horizons spacecraft is also returning images -- such as this one -- to improve maps of other regions. This image was taken by the New Horizons Long Range Reconnaissance Imager (LORRI) on the morning of July 13, 2015, from a range of 1.03 million miles (1.7 million kilometers) and has a resolution of 5.1 miles (8.3 kilometers) per pixel. It provides fascinating new details to help the science team map the informally named Krun Macula (the prominent dark spot at the bottom of the image) and the complex terrain east and northeast of Pluto's "heart" (Tombaugh Regio). Pluto's north pole is on the planet's disk at the 12 o'clock position of this image. http://photojournal.jpl.nasa.gov/catalog/PIA20037

  16. 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

  17. 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

  18. 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.

  19. 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.

  20. Evaluation of Techniques Used to Estimate Cortical Feature Maps

    PubMed Central

    Katta, Nalin; Chen, Thomas L.; Watkins, Paul V.; Barbour, Dennis L.

    2011-01-01

    Functional properties of neurons are often distributed nonrandomly within a cortical area and form topographic maps that reveal insights into neuronal organization and interconnection. Some functional maps, such as in visual cortex, are fairly straightforward to discern with a variety of techniques, while other maps, such as in auditory cortex, have resisted easy characterization. In order to determine appropriate protocols for establishing accurate functional maps in auditory cortex, artificial topographic maps were probed under various conditions, and the accuracy of estimates formed from the actual maps was quantified. Under these conditions, low-complexity maps such as sound frequency can be estimated accurately with as few as 25 total samples (e.g., electrode penetrations or imaging pixels) if neural responses are averaged together. More samples are required to achieve the highest estimation accuracy for higher complexity maps, and averaging improves map estimate accuracy even more than increasing sampling density. Undersampling without averaging can result in misleading map estimates, while undersampling with averaging can lead to the false conclusion of no map when one actually exists. Uniform sample spacing only slightly improves map estimation over nonuniform sample spacing typical of serial electrode penetrations. Tessellation plots commonly used to visualize maps estimated using nonuniform sampling are always inferior to linearly interpolated estimates, although differences are slight at higher sampling densities. Within primary auditory cortex, then, multiunit sampling with at least 100 samples would likely result in reasonable feature map estimates for all but the highest complexity maps and the highest variability that might be expected. PMID:21889537

  1. 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.

  2. Mapping the Natchez Trace Parkway

    USGS Publications Warehouse

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

    2011-01-01

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

  3. Development and evaluation of a specialized task taxonomy for spatial planning - A map literacy experiment with topographic maps

    NASA Astrophysics Data System (ADS)

    Rautenbach, Victoria; Coetzee, Serena; Çöltekin, Arzu

    2017-05-01

    Topographic maps are among the most commonly used map types, however, their complex and information-rich designs depicting natural, human-made and cultural features make them difficult to read. Regardless of their complexity, spatial planners make extensive use of topographic maps in their work. On the other hand, various studies suggest that map literacy among the development planning professionals in South Africa is not very high. The widespread use of topographic maps combined with the low levels of map literacy presents challenges for effective development planning. In this paper we address some of these challenges by developing a specialized task taxonomy based on systematically assessed map literacy levels; and conducting an empirical experiment with topographic maps to evaluate our task taxonomy. In such empirical studies if non-realistic tasks are used, the results of map literacy tests may be skewed. Furthermore, experience and familiarity with the studied map type play a role in map literacy. There is thus a need to develop map literacy tests aimed at planners specifically. We developed a taxonomy of realistic map reading tasks typically executed during the planning process. The taxonomy defines six levels tasks of increasing difficulty and complexity, ranging from recognising symbols to extracting knowledge. We hypothesized that competence in the first four levels indicates functional map literacy. In this paper, we present results from an empirical experiment with 49 map literate participants solving a subset of tasks from the first four levels of the taxonomy with a topographic map. Our findings suggest that the proposed taxonomy is a good reference for evaluating topographic map literacy. Participants solved the tasks on all four levels as expected and we therefore conclude that the experiment based on the first four levels of the taxonomy successfully determined the functional map literacy of the participants. We plan to continue the study for the

  4. 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…

  5. The National Map: from geography to mapping and back again

    USGS Publications Warehouse

    Kelmelis, John A.; DeMulder, Mark L.; Ogrosky, Charles E.; Van Driel, J. Nicholas; Ryan, Barbara J.

    2003-01-01

    When the means of production for national base mapping were capital intensive, required large production facilities, and had ill-defined markets, Federal Government mapping agencies were the primary providers of the spatial data needed for economic development, environmental management, and national defense. With desktop geographic information systems now ubiquitous, source data available as a commodit