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Sample records for ancestral state reconstruction

  1. Optimized ancestral state reconstruction using Sankoff parsimony

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    Valiente Gabriel

    2009-02-01

    Full Text Available Abstract Background Parsimony methods are widely used in molecular evolution to estimate the most plausible phylogeny for a set of characters. Sankoff parsimony determines the minimum number of changes required in a given phylogeny when a cost is associated to transitions between character states. Although optimizations exist to reduce the computations in the number of taxa, the original algorithm takes time O(n2 in the number of states, making it impractical for large values of n. Results In this study we introduce an optimization of Sankoff parsimony for the reconstruction of ancestral states when ultrametric or additive cost matrices are used. We analyzed its performance for randomly generated matrices, Jukes-Cantor and Kimura's two-parameter models of DNA evolution, and in the reconstruction of elongation factor-1α and ancestral metabolic states of a group of eukaryotes, showing that in all cases the execution time is significantly less than with the original implementation. Conclusion The algorithms here presented provide a fast computation of Sankoff parsimony for a given phylogeny. Problems where the number of states is large, such as reconstruction of ancestral metabolism, are particularly adequate for this optimization. Since we are reducing the computations required to calculate the parsimony cost of a single tree, our method can be combined with optimizations in the number of taxa that aim at finding the most parsimonious tree.

  2. Global Alignment of Molecular Sequences via Ancestral State Reconstruction

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    Andoni, Alexandr; Hassidim, Avinatan; Roch, Sebastien

    2009-01-01

    Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on substitution-only models of sequence evolution. In practice these methods are extended beyond this simplified setting with the use of heuristics that produce global alignments of the input sequences--an important problem which has no rigorous model-based solution. In this paper we consider a new version of the multiple sequence alignment in the context of stochastic indel models. More precisely, we introduce the following {\\em trace reconstruction problem on a tree} (TRPT): a binary sequence is broadcast through a tree channel where we allow substitutions, deletions, and insertions; we seek to reconstruct the original sequence from the sequences received at the leaves of the tree. We give a recursive procedure for this problem with strong reconstruction guarantees at low mut...

  3. Which came first: The lizard or the egg? Robustness in phylogenetic reconstruction of ancestral states.

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    Wright, April M; Lyons, Kathleen M; Brandley, Matthew C; Hillis, David M

    2015-09-01

    Changes in parity mode between egg-laying (oviparity) and live-bearing (viviparity) have occurred repeatedly throughout vertebrate evolution. Oviparity is the ancestral amniote state, and viviparity has evolved many times independently within amniotes (especially in lizards and snakes), with possibly a few reversions to oviparity. In amniotes, the shelled egg is considered a complex structure that is unlikely to re-evolve if lost (i.e., it is an example of Dollo's Principle). However, a recent ancestral state reconstruction analysis concluded that viviparity was the ancestral state of squamate reptiles (lizards and snakes), and that oviparity re-evolved from viviparity many times throughout the evolutionary history of squamates. Here, we re-evaluate support for this provocative conclusion by testing the sensitivity of the analysis to model assumptions and estimates of squamate phylogeny. We found that the models and methods used for parity mode reconstruction are highly sensitive to the specific estimate of phylogeny used, and that the point estimate of phylogeny used to suggest that viviparity is the root state of the squamate tree is far from an optimal phylogenetic solution. The ancestral state reconstructions are also highly sensitive to model choice and specific values of model parameters. A method that is designed to account for biases in taxon sampling actually accentuates, rather than lessens, those biases with respect to ancestral state reconstructions. In contrast to recent conclusions from the same data set, we find that ancestral state reconstruction analyses provide highly equivocal support for the number and direction of transitions between oviparity and viviparity in squamates. Moreover, the reconstructions of ancestral parity state are highly dependent on the assumptions of each model. We conclude that the common ancestor of squamates was oviparous, and subsequent evolutionary transitions to viviparity were common, but reversals to oviparity were

  4. Ancestral state reconstruction, rate heterogeneity, and the evolution of reptile viviparity.

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    King, Benedict; Lee, Michael S Y

    2015-05-01

    Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. However, this assumption is unlikely to hold in many situations, particularly as ancestral state reconstructions are being performed on increasingly large phylogenies. Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. The random local clock method, implemented in BEAST, estimates the position and magnitude of rate changes on the tree; split BiSSE estimates separate rate parameters for pre-specified clades; and the hidden rates model partitions each character state into a number of rate categories. Simulations show the inadequacy of traditional models when characters evolve with both asymmetry (different rates of change between states within a character) and heterotachy (different rates of character evolution across different clades). The importance of accounting for rate heterogeneity in ancestral state reconstruction is highlighted empirically with a new analysis of the evolution of viviparity in squamate reptiles, which reveal a predominance of forward (oviparous-viviparous) transitions and very few reversals.

  5. Analysis on the reconstruction accuracy of the Fitch method for inferring ancestral states

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    Grünewald Stefan

    2011-01-01

    Full Text Available Abstract Background As one of the most widely used parsimony methods for ancestral reconstruction, the Fitch method minimizes the total number of hypothetical substitutions along all branches of a tree to explain the evolution of a character. Due to the extensive usage of this method, it has become a scientific endeavor in recent years to study the reconstruction accuracies of the Fitch method. However, most studies are restricted to 2-state evolutionary models and a study for higher-state models is needed since DNA sequences take the format of 4-state series and protein sequences even have 20 states. Results In this paper, the ambiguous and unambiguous reconstruction accuracy of the Fitch method are studied for N-state evolutionary models. Given an arbitrary phylogenetic tree, a recurrence system is first presented to calculate iteratively the two accuracies. As complete binary tree and comb-shaped tree are the two extremal evolutionary tree topologies according to balance, we focus on the reconstruction accuracies on these two topologies and analyze their asymptotic properties. Then, 1000 Yule trees with 1024 leaves are generated and analyzed to simulate real evolutionary scenarios. It is known that more taxa not necessarily increase the reconstruction accuracies under 2-state models. The result under N-state models is also tested. Conclusions In a large tree with many leaves, the reconstruction accuracies of using all taxa are sometimes less than those of using a leaf subset under N-state models. For complete binary trees, there always exists an equilibrium interval [a, b] of conservation probability, in which the limiting ambiguous reconstruction accuracy equals to the probability of randomly picking a state. The value b decreases with the increase of the number of states, and it seems to converge. When the conservation probability is greater than b, the reconstruction accuracies of the Fitch method increase rapidly. The reconstruction

  6. Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple.

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    Ismail, Siti Izera; Batzer, Jean Carlson; Harrington, Thomas C; Crous, Pedro W; Lavrov, Dennis V; Li, Huanyu; Gleason, Mark L

    2016-01-01

    Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi.

  7. Evolutionary history of assassin bugs (insecta: hemiptera: Reduviidae: insights from divergence dating and ancestral state reconstruction.

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    Wei Song Hwang

    Full Text Available Assassin bugs are one of the most successful clades of predatory animals based on their species numbers (∼6,800 spp. and wide distribution in terrestrial ecosystems. Various novel prey capture strategies and remarkable prey specializations contribute to their appeal as a model to study evolutionary pathways involved in predation. Here, we reconstruct the most comprehensive reduviid phylogeny (178 taxa, 18 subfamilies to date based on molecular data (5 markers. This phylogeny tests current hypotheses on reduviid relationships emphasizing the polyphyletic Reduviinae and the blood-feeding, disease-vectoring Triatominae, and allows us, for the first time in assassin bugs, to reconstruct ancestral states of prey associations and microhabitats. Using a fossil-calibrated molecular tree, we estimated divergence times for key events in the evolutionary history of Reduviidae. Our results indicate that the polyphyletic Reduviinae fall into 11-14 separate clades. Triatominae are paraphyletic with respect to the reduviine genus Opisthacidius in the maximum likelihood analyses; this result is in contrast to prior hypotheses that found Triatominae to be monophyletic or polyphyletic and may be due to the more comprehensive taxon and character sampling in this study. The evolution of blood-feeding may thus have occurred once or twice independently among predatory assassin bugs. All prey specialists evolved from generalist ancestors, with multiple evolutionary origins of termite and ant specializations. A bark-associated life style on tree trunks is ancestral for most of the lineages of Higher Reduviidae; living on foliage has evolved at least six times independently. Reduviidae originated in the Middle Jurassic (178 Ma, but significant lineage diversification only began in the Late Cretaceous (97 Ma. The integration of molecular phylogenetics with fossil and life history data as presented in this paper provides insights into the evolutionary history of

  8. Ancestral state reconstruction by comparative analysis of a GRN kernel operating in echinoderms.

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    Erkenbrack, Eric M; Ako-Asare, Kayla; Miller, Emily; Tekelenburg, Saira; Thompson, Jeffrey R; Romano, Laura

    2016-01-01

    Diverse sampling of organisms across the five major classes in the phylum Echinodermata is beginning to reveal much about the structure and function of gene regulatory networks (GRNs) in development and evolution. Sea urchins are the most studied clade within this phylum, and recent work suggests there has been dramatic rewiring at the top of the skeletogenic GRN along the lineage leading to extant members of the euechinoid sea urchins. Such rewiring likely accounts for some of the observed developmental differences between the two major subclasses of sea urchins-cidaroids and euechinoids. To address effects of topmost rewiring on downstream GRN events, we cloned four downstream regulatory genes within the skeletogenic GRN and surveyed their spatiotemporal expression patterns in the cidaroid Eucidaris tribuloides. We performed phylogenetic analyses with homologs from other non-vertebrate deuterostomes and characterized their spatiotemporal expression by quantitative polymerase chain reaction (qPCR) and whole-mount in situ hybridization (WMISH). Our data suggest the erg-hex-tgif subcircuit, a putative GRN kernel, exhibits a mesoderm-specific expression pattern early in Eucidaris development that is directly downstream of the initial mesodermal GRN circuitry. Comparative analysis of the expression of this subcircuit in four echinoderm taxa allowed robust ancestral state reconstruction, supporting hypotheses that its ancestral function was to stabilize the mesodermal regulatory state and that it has been co-opted and deployed as a unit in mesodermal subdomains in distantly diverged echinoderms. Importantly, our study supports the notion that GRN kernels exhibit structural and functional modularity, locking down and stabilizing clade-specific, embryonic regulatory states.

  9. Muscle fiber-type variation in lizards (Squamata) and phylogenetic reconstruction of hypothesized ancestral states.

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    Bonine, Kevin E; Gleeson, Todd T; Garland, Theodore

    2005-12-01

    . Reconstruction of ancestral trait values by use of phylogenetically based statistical methods indicates especially large changes in fiber-type composition during the evolution of horned lizards.

  10. Reconstructing ancestral ranges in historical biogeography: properties and prospects

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    Kristin S. LAMM; Benjamin D. REDELINGS

    2009-01-01

    Recent years have witnessed a proliferation of quantitative methods for biogeographic inference. In particular, novel parametric approaches represent exciting new opportunities for the study of range evolution. Here, we review a selection of current methods for biogeographic analysis and discuss their respective properties. These methods include generalized parsimony approaches, weighted ancestral area analysis, dispersal-vicariance analysis, the dispersal-extinction-cladogenesis model and other maximum likelihood approaches, and Bayesian stochastic mapping of ancestral ranges, including a novel approach to inferring range evolution in the context of island biogeography. Some of these methods were developed specifically for problems of ancestral range reconstruction, whereas others were designed for more general problems of character state reconstruction and subsequently applied to the study of ancestral ranges. Methods for reconstructing ancestral history on a phylogenetic tree differ not only in the types of ancestral range states that are allowed, but also in the various historical events that may change the ancestral ranges. We explore how the form of allowed ancestral ranges and allowed transitions can both affect the outcome of ancestral range estimation. Finally, we mention some promising avenues for future work in the development of model-based approaches to biogeographic analysis.

  11. Ancestral state reconstructions require biological evidence to test evolutionary hypotheses: A case study examining the evolution of reproductive mode in squamate reptiles.

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    Griffith, Oliver W; Blackburn, Daniel G; Brandley, Matthew C; Van Dyke, James U; Whittington, Camilla M; Thompson, Michael B

    2015-09-01

    To understand evolutionary transformations it is necessary to identify the character states of extinct ancestors. Ancestral character state reconstruction is inherently difficult because it requires an accurate phylogeny, character state data, and a statistical model of transition rates and is fundamentally constrained by missing data such as extinct taxa. We argue that model based ancestral character state reconstruction should be used to generate hypotheses but should not be considered an analytical endpoint. Using the evolution of viviparity and reversals to oviparity in squamates as a case study, we show how anatomical, physiological, and ecological data can be used to evaluate hypotheses about evolutionary transitions. The evolution of squamate viviparity requires changes to the timing of reproductive events and the successive loss of features responsible for building an eggshell. A reversal to oviparity requires that those lost traits re-evolve. We argue that the re-evolution of oviparity is inherently more difficult than the reverse. We outline how the inviability of intermediate phenotypes might present physiological barriers to reversals from viviparity to oviparity. Finally, we show that ecological data supports an oviparous ancestral state for squamates and multiple transitions to viviparity. In summary, we conclude that the first squamates were oviparous, that frequent transitions to viviparity have occurred, and that reversals to oviparity in viviparous lineages either have not occurred or are exceedingly rare. As this evidence supports conclusions that differ from previous ancestral state reconstructions, our paper highlights the importance of incorporating biological evidence to evaluate model-generated hypotheses.

  12. Bayesian phylogeography of influenza A/H3N2 for the 2014-15 season in the United States using three frameworks of ancestral state reconstruction

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    Suchard, Marc A.

    2017-01-01

    Ancestral state reconstructions in Bayesian phylogeography of virus pandemics have been improved by utilizing a Bayesian stochastic search variable selection (BSSVS) framework. Recently, this framework has been extended to model the transition rate matrix between discrete states as a generalized linear model (GLM) of genetic, geographic, demographic, and environmental predictors of interest to the virus and incorporating BSSVS to estimate the posterior inclusion probabilities of each predictor. Although the latter appears to enhance the biological validity of ancestral state reconstruction, there has yet to be a comparison of phylogenies created by the two methods. In this paper, we compare these two methods, while also using a primitive method without BSSVS, and highlight the differences in phylogenies created by each. We test six coalescent priors and six random sequence samples of H3N2 influenza during the 2014–15 flu season in the U.S. We show that the GLMs yield significantly greater root state posterior probabilities than the two alternative methods under five of the six priors, and significantly greater Kullback-Leibler divergence values than the two alternative methods under all priors. Furthermore, the GLMs strongly implicate temperature and precipitation as driving forces of this flu season and nearly unanimously identified a single root state, which exhibits the most tropical climate during a typical flu season in the U.S. The GLM, however, appears to be highly susceptible to sampling bias compared with the other methods, which casts doubt on whether its reconstructions should be favored over those created by alternate methods. We report that a BSSVS approach with a Poisson prior demonstrates less bias toward sample size under certain conditions than the GLMs or primitive models, and believe that the connection between reconstruction method and sampling bias warrants further investigation. PMID:28170397

  13. Musculature in sipunculan worms: ontogeny and ancestral states.

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    Schulze, Anja; Rice, Mary E

    2009-01-01

    Molecular phylogenetics suggests that the Sipuncula fall into the Annelida, although they are morphologically very distinct and lack segmentation. To understand the evolutionary transformations from the annelid to the sipunculan body plan, it is important to reconstruct the ancestral states within the respective clades at all life history stages. Here we reconstruct the ancestral states for the head/introvert retractor muscles and the body wall musculature in the Sipuncula using Bayesian statistics. In addition, we describe the ontogenetic transformations of the two muscle systems in four sipunculan species with different developmental modes, using F-actin staining with fluorescent-labeled phalloidin in conjunction with confocal laser scanning microscopy. All four species, which have smooth body wall musculature and less than the full set of four introvert retractor muscles as adults, go through developmental stages with four retractor muscles that are eventually reduced to a lower number in the adult. The circular and sometimes the longitudinal body wall musculature are split into bands that later transform into a smooth sheath. Our ancestral state reconstructions suggest with nearly 100% probability that the ancestral sipunculan had four introvert retractor muscles, longitudinal body wall musculature in bands and circular body wall musculature arranged as a smooth sheath. Species with crawling larvae have more strongly developed body wall musculature than those with swimming larvae. To interpret our findings in the context of annelid evolution, a more solid phylogenetic framework is needed for the entire group and more data on ontogenetic transformations of annelid musculature are desirable.

  14. Ancestral gene synteny reconstruction improves extant species scaffolding.

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    Anselmetti, Yoann; Berry, Vincent; Chauve, Cedric; Chateau, Annie; Tannier, Eric; Bérard, Sèverine

    2015-01-01

    We exploit the methodological similarity between ancestral genome reconstruction and extant genome scaffolding. We present a method, called ARt-DeCo that constructs neighborhood relationships between genes or contigs, in both ancestral and extant genomes, in a phylogenetic context. It is able to handle dozens of complete genomes, including genes with complex histories, by using gene phylogenies reconciled with a species tree, that is, annotated with speciation, duplication and loss events. Reconstructed ancestral or extant synteny comes with a support computed from an exhaustive exploration of the solution space. We compare our method with a previously published one that follows the same goal on a small number of genomes with universal unicopy genes. Then we test it on the whole Ensembl database, by proposing partial ancestral genome structures, as well as a more complete scaffolding for many partially assembled genomes on 69 eukaryote species. We carefully analyze a couple of extant adjacencies proposed by our method, and show that they are indeed real links in the extant genomes, that were missing in the current assembly. On a reduced data set of 39 eutherian mammals, we estimate the precision and sensitivity of ARt-DeCo by simulating a fragmentation in some well assembled genomes, and measure how many adjacencies are recovered. We find a very high precision, while the sensitivity depends on the quality of the data and on the proximity of closely related genomes.

  15. Fast phylogeny reconstruction through learning of ancestral sequences

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    Mihaescu, Radu; Rao, Satish

    2008-01-01

    Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial but reliable information about the tree (\\cite{Mo07, DMR08,DHJ06,GMS08}), and reaching "deeper" in the tree through reconstruction of ancestral sequences. In the latter category, \\cite{DMR06} settled an important conjecture of M.Steel, showing that, under the CFN model of evolution, all trees on $n$ leaves with edge lengths bounded by the Ising model phase transition can be recovered with high probability from genomes of length $O(\\log n)$ with a polynomial time algorithm. Their methods had a running time of $O(n^{10})$. Here we enhance our methods from \\cite{DHJ06} with the learning of ancestral sequences and provide an algorithm for reconstructing a sub-forest of the tree which is reliable given available data, without requiring a-priori known bounds on the edge lengths o...

  16. Reconstructing the ancestral butterfly eye: focus on the opsins.

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    Briscoe, Adriana D

    2008-06-01

    The eyes of butterflies are remarkable, because they are nearly as diverse as the colors of wings. Much of eye diversity can be traced to alterations in the number, spectral properties and spatial distribution of the visual pigments. Visual pigments are light-sensitive molecules composed of an opsin protein and a chromophore. Most butterflies have eyes that contain visual pigments with a wavelength of peak absorbance, lambda(max), in the ultraviolet (UV, 300-400 nm), blue (B, 400-500 nm) and long wavelength (LW, 500-600 nm) part of the visible light spectrum, respectively, encoded by distinct UV, B and LW opsin genes. In the compound eye of butterflies, each individual ommatidium is composed of nine photoreceptor cells (R1-9) that generally express only one opsin mRNA per cell, although in some butterfly eyes there are ommatidial subtypes in which two opsins are co-expressed in the same photoreceptor cell. Based on a phylogenetic analysis of opsin cDNAs from the five butterfly families, Papilionidae, Pieridae, Nymphalidae, Lycaenidae and Riodinidae, and comparative analysis of opsin gene expression patterns from four of the five families, I propose a model for the patterning of the ancestral butterfly eye that is most closely aligned with the nymphalid eye. The R1 and R2 cells of the main retina expressed UV-UV-, UV-B- or B-B-absorbing visual pigments while the R3-9 cells expressed a LW-absorbing visual pigment. Visual systems of existing butterflies then underwent an adaptive expansion based on lineage-specific B and LW opsin gene multiplications and on alterations in the spatial expression of opsins within the eye. Understanding the molecular sophistication of butterfly eye complexity is a challenge that, if met, has broad biological implications.

  17. On the Potential Origins of the High Stability of Reconstructed Ancestral Proteins.

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    Trudeau, Devin L; Kaltenbach, Miriam; Tawfik, Dan S

    2016-10-01

    Ancestral reconstruction provides instrumental insights regarding the biochemical and biophysical characteristics of past proteins. A striking observation relates to the remarkably high thermostability of reconstructed ancestors. The latter has been linked to high environmental temperatures in the Precambrian era, the era relating to most reconstructed proteins. We found that inferred ancestors of the serum paraoxonase (PON) enzyme family, including the mammalian ancestor, exhibit dramatically increased thermostabilities compared with the extant, human enzyme (up to 30 °C higher melting temperature). However, the environmental temperature at the time of emergence of mammals is presumed to be similar to the present one. Additionally, the mammalian PON ancestor has superior folding properties (kinetic stability)-unlike the extant mammalian PONs, it expresses in E. coli in a soluble and functional form, and at a high yield. We discuss two potential origins of this unexpectedly high stability. First, ancestral stability may be overestimated by a "consensus effect," whereby replacing amino acids that are rare in contemporary sequences with the amino acid most common in the family increases protein stability. Comparison to other reconstructed ancestors indicates that the consensus effect may bias some but not all reconstructions. Second, we note that high stability may relate to factors other than high environmental temperature such as oxidative stress or high radiation levels. Foremost, intrinsic factors such as high rates of genetic mutations and/or of transcriptional and translational errors, and less efficient protein quality control systems, may underlie the high kinetic and thermodynamic stability of past proteins.

  18. Assessing the prediction fidelity of ancestral reconstruction by a library approach.

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    Bar-Rogovsky, Hagit; Stern, Adi; Penn, Osnat; Kobl, Iris; Pupko, Tal; Tawfik, Dan S

    2015-11-01

    Ancestral reconstruction is a powerful tool for studying protein evolution as well as for protein design and engineering. However, in many positions alternative predictions with relatively high marginal probabilities exist, and thus the prediction comprises an ensemble of near-ancestor sequences that relate to the historical ancestor. The ancestral phenotype should therefore be explored for the entire ensemble, rather than for the sequence comprising the most probable amino acid at all positions [the most probable ancestor (mpa)]. To this end, we constructed libraries that sample ensembles of near-ancestor sequences. Specifically, we identified positions where alternatively predicted amino acids are likely to affect the ancestor's structure and/or function. Using the serum paraoxonases (PONs) enzyme family as a test case, we constructed libraries that combinatorially sample these alternatives. We next characterized these libraries, reflecting the vertebrate and mammalian PON ancestors. We found that the mpa of vertebrate PONs represented only one out of many different enzymatic phenotypes displayed by its ensemble. The mammalian ancestral library, however, exhibited a homogeneous phenotype that was well represented by the mpa. Our library design strategy that samples near-ancestor ensembles at potentially critical positions therefore provides a systematic way of examining the robustness of inferred ancestral phenotypes.

  19. Ancestral Protein Reconstruction Yields Insights into Adaptive Evolution of Binding Specificity in Solute-Binding Proteins.

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    Clifton, Ben E; Jackson, Colin J

    2016-02-18

    The promiscuous functions of proteins are an important reservoir of functional novelty in protein evolution, but the molecular basis for binding promiscuity remains elusive. We used ancestral protein reconstruction to experimentally characterize evolutionary intermediates in the functional expansion of the polar amino acid-binding protein family, which has evolved to bind a variety of amino acids with high affinity and specificity. High-resolution crystal structures of an ancestral arginine-binding protein in complex with l-arginine and l-glutamine show that the promiscuous binding of l-glutamine is enabled by multi-scale conformational plasticity, water-mediated interactions, and selection of an alternative conformational substate productive for l-glutamine binding. Evolution of specialized glutamine-binding proteins from this ancestral protein was achieved by displacement of water molecules from the protein-ligand interface, reducing the entropic penalty associated with the promiscuous interaction. These results provide a structural and thermodynamic basis for the co-option of a promiscuous interaction in the evolution of binding specificity.

  20. Ancestral Protein Reconstruction and Circular Permutation for Improving the Stability and Dynamic Range of FRET Sensors.

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    Clifton, Ben E; Whitfield, Jason H; Sanchez-Romero, Inmaculada; Herde, Michel K; Henneberger, Christian; Janovjak, Harald; Jackson, Colin J

    2017-01-01

    Small molecule biosensors based on Förster resonance energy transfer (FRET) enable small molecule signaling to be monitored with high spatial and temporal resolution in complex cellular environments. FRET sensors can be constructed by fusing a pair of fluorescent proteins to a suitable recognition domain, such as a member of the solute-binding protein (SBP) superfamily. However, naturally occurring SBPs may be unsuitable for incorporation into FRET sensors due to their low thermostability, which may preclude imaging under physiological conditions, or because the positions of their N- and C-termini may be suboptimal for fusion of fluorescent proteins, which may limit the dynamic range of the resulting sensors. Here, we show how these problems can be overcome using ancestral protein reconstruction and circular permutation. Ancestral protein reconstruction, used as a protein engineering strategy, leverages phylogenetic information to improve the thermostability of proteins, while circular permutation enables the termini of an SBP to be repositioned to maximize the dynamic range of the resulting FRET sensor. We also provide a protocol for cloning the engineered SBPs into FRET sensor constructs using Golden Gate assembly and discuss considerations for in situ characterization of the FRET sensors.

  1. EREM: Parameter Estimation and Ancestral Reconstruction by Expectation-Maximization Algorithm for a Probabilistic Model of Genomic Binary Characters Evolution

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    Liran Carmel

    2010-01-01

    Full Text Available Evolutionary binary characters are features of species or genes, indicating the absence (value zero or presence (value one of some property. Examples include eukaryotic gene architecture (the presence or absence of an intron in a particular locus, gene content, and morphological characters. In many studies, the acquisition of such binary characters is assumed to represent a rare evolutionary event, and consequently, their evolution is analyzed using various flavors of parsimony. However, when gain and loss of the character are not rare enough, a probabilistic analysis becomes essential. Here, we present a comprehensive probabilistic model to describe the evolution of binary characters on a bifurcating phylogenetic tree. A fast software tool, EREM, is provided, using maximum likelihood to estimate the parameters of the model and to reconstruct ancestral states (presence and absence in internal nodes and events (gain and loss events along branches.

  2. Permutationally invariant state reconstruction

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    Moroder, Tobias; Toth, Geza; Schwemmer, Christian; Niggebaum, Alexander; Gaile, Stefanie; Gühne, Otfried; Weinfurter, Harald

    2012-01-01

    Feasible tomography schemes for large particle numbers must possess, besides an appropriate data acquisition protocol, also an efficient way to reconstruct the density operator from the observed finite data set. Since state reconstruction typically requires the solution of a non-linear large-scale optimization problem, this is a major challenge in the design of scalable tomography schemes. Here we present an efficient state reconstruction scheme for permutationally invariant quantum state tomography. It works for all common state-of-the-art reconstruction principles, including, in particular, maximum likelihood and least squares methods, which are the preferred choices in today's experiments. This high efficiency is achieved by greatly reducing the dimensionality of the problem employing a particular representation of permutationally invariant states known from spin coupling combined with convex optimization, which has clear advantages regarding speed, control and accuracy in comparison to commonly employed n...

  3. Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees.

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    Groussin, Mathieu; Hobbs, Joanne K; Szöllősi, Gergely J; Gribaldo, Simonetta; Arcus, Vickery L; Gouy, Manolo

    2015-01-01

    The resurrection of ancestral proteins provides direct insight into how natural selection has shaped proteins found in nature. By tracing substitutions along a gene phylogeny, ancestral proteins can be reconstructed in silico and subsequently synthesized in vitro. This elegant strategy reveals the complex mechanisms responsible for the evolution of protein functions and structures. However, to date, all protein resurrection studies have used simplistic approaches for ancestral sequence reconstruction (ASR), including the assumption that a single sequence alignment alone is sufficient to accurately reconstruct the history of the gene family. The impact of such shortcuts on conclusions about ancestral functions has not been investigated. Here, we show with simulations that utilizing information on species history using a model that accounts for the duplication, horizontal transfer, and loss (DTL) of genes statistically increases ASR accuracy. This underscores the importance of the tree topology in the inference of putative ancestors. We validate our in silico predictions using in vitro resurrection of the LeuB enzyme for the ancestor of the Firmicutes, a major and ancient bacterial phylum. With this particular protein, our experimental results demonstrate that information on the species phylogeny results in a biochemically more realistic and kinetically more stable ancestral protein. Additional resurrection experiments with different proteins are necessary to statistically quantify the impact of using species tree-aware gene trees on ancestral protein phenotypes. Nonetheless, our results suggest the need for incorporating both sequence and DTL information in future studies of protein resurrections to accurately define the genotype-phenotype space in which proteins diversify.

  4. Comparative genome-scale reconstruction of gapless metabolic networks for present and ancestral species.

    Directory of Open Access Journals (Sweden)

    Esa Pitkänen

    2014-02-01

    Full Text Available We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/.

  5. Comparative Genome-Scale Reconstruction of Gapless Metabolic Networks for Present and Ancestral Species

    Science.gov (United States)

    Pitkänen, Esa; Jouhten, Paula; Hou, Jian; Syed, Muhammad Fahad; Blomberg, Peter; Kludas, Jana; Oja, Merja; Holm, Liisa; Penttilä, Merja; Rousu, Juho; Arvas, Mikko

    2014-01-01

    We introduce a novel computational approach, CoReCo, for comparative metabolic reconstruction and provide genome-scale metabolic network models for 49 important fungal species. Leveraging on the exponential growth in sequenced genome availability, our method reconstructs genome-scale gapless metabolic networks simultaneously for a large number of species by integrating sequence data in a probabilistic framework. High reconstruction accuracy is demonstrated by comparisons to the well-curated Saccharomyces cerevisiae consensus model and large-scale knock-out experiments. Our comparative approach is particularly useful in scenarios where the quality of available sequence data is lacking, and when reconstructing evolutionary distant species. Moreover, the reconstructed networks are fully carbon mapped, allowing their use in 13C flux analysis. We demonstrate the functionality and usability of the reconstructed fungal models with computational steady-state biomass production experiment, as these fungi include some of the most important production organisms in industrial biotechnology. In contrast to many existing reconstruction techniques, only minimal manual effort is required before the reconstructed models are usable in flux balance experiments. CoReCo is available at http://esaskar.github.io/CoReCo/. PMID:24516375

  6. Elongation Factor-Tu (EF-Tu) proteins structural stability and bioinformatics in ancestral gene reconstruction

    Science.gov (United States)

    Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Schneider, P.; Lieberman, D.; Holden, T.; Cheung, T.

    2013-09-01

    A paleo-experimental evolution report on elongation factor EF-Tu structural stability results has provided an opportunity to rewind the tape of life using the ancestral protein sequence reconstruction modeling approach; consistent with the book of life dogma in current biology and being an important component in the astrobiology community. Fractal dimension via the Higuchi fractal method and Shannon entropy of the DNA sequence classification could be used in a diagram that serves as a simple summary. Results from biomedical gene research provide examples on the diagram methodology. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, DLG1 in cognitive skill, and HLA-C in mosquito bite immunology with EF Tu DNA sequences have accounted for the reported circular dichroism thermo-stability data systematically; the results also infer a relatively less volatility geologic time period from 2 to 3 Gyr from adaptation viewpoint. Comparison to Thermotoga maritima MSB8 and Psychrobacter shows that Thermus thermophilus HB8 EF-Tu calibration sequence could be an outlier, consistent with free energy calculation by NUPACK. Diagram methodology allows computer simulation studies and HAR1 shows about 0.5% probability from chimp to human in terms of diagram location, and SNP simulation results such as amoebic meningoencephalitis NAF1 suggest correlation. Extensions to the studies of the translation and transcription elongation factor sequences in Megavirus Chiliensis, Megavirus Lba and Pandoravirus show that the studied Pandoravirus sequence could be an outlier with the highest fractal dimension and lowest entropy, as compared to chicken as a deviant in the DNMT3A DNA methylation gene sequences from zebrafish to human and to the less than one percent probability in computer simulation using the HAR1 0.5% probability as reference. The diagram methodology would be useful in ancestral gene

  7. Permutationally invariant state reconstruction

    DEFF Research Database (Denmark)

    Moroder, Tobias; Hyllus, Philipp; Tóth, Géza;

    2012-01-01

    Feasible tomography schemes for large particle numbers must possess, besides an appropriate data acquisition protocol, an efficient way to reconstruct the density operator from the observed finite data set. Since state reconstruction typically requires the solution of a nonlinear large-scale opti......Feasible tomography schemes for large particle numbers must possess, besides an appropriate data acquisition protocol, an efficient way to reconstruct the density operator from the observed finite data set. Since state reconstruction typically requires the solution of a nonlinear large...... likelihood and least squares methods, which are the preferred choices in today's experiments. This high efficiency is achieved by greatly reducing the dimensionality of the problem employing a particular representation of permutationally invariant states known from spin coupling combined with convex...

  8. Ancestral feeding state of ruminants reconsidered: earliest grazing adaptation claims a mixed condition for Cervidae

    Directory of Open Access Journals (Sweden)

    Azanza Beatriz

    2008-01-01

    Full Text Available Abstract Background Specialised leaf-eating is almost universally regarded as the ancestral state of all ruminants, yet little evidence can be cited in support of this assumption, apart from the fact that all early ruminants had low crowned cheek teeth. Instead, recent years have seen the emergence evidence contradicting the conventional view that low tooth crowns always indicate leaf-eating and high tooth crowns grass-eating. Results Here we report the results of two independent palaeodietary reconstructions for one of the earliest deer, Procervulus ginsburgi from the Early Miocene of Spain, suggesting that despite having lower tooth crowns than any living ruminant, this species included a significant proportion of grass in its diet. Conclusion The phylogenetic distribution of feeding styles strongly supports that leaf-grass mixed feeding was the original feeding style of deer, and that later dietary specialization on leaves or grass occurred independently in several lineages. Evidence for other ruminant clades suggests that facultative mixed feeding may in fact have been the primitive dietary state of the Ruminantia, which would have been morphologically expressed only under specific environmental factors.

  9. Reconstruction of ancestral chromosome architecture and gene repertoire reveals principles of genome evolution in a model yeast genus.

    Science.gov (United States)

    Vakirlis, Nikolaos; Sarilar, Véronique; Drillon, Guénola; Fleiss, Aubin; Agier, Nicolas; Meyniel, Jean-Philippe; Blanpain, Lou; Carbone, Alessandra; Devillers, Hugo; Dubois, Kenny; Gillet-Markowska, Alexandre; Graziani, Stéphane; Huu-Vang, Nguyen; Poirel, Marion; Reisser, Cyrielle; Schott, Jonathan; Schacherer, Joseph; Lafontaine, Ingrid; Llorente, Bertrand; Neuvéglise, Cécile; Fischer, Gilles

    2016-07-01

    Reconstructing genome history is complex but necessary to reveal quantitative principles governing genome evolution. Such reconstruction requires recapitulating into a single evolutionary framework the evolution of genome architecture and gene repertoire. Here, we reconstructed the genome history of the genus Lachancea that appeared to cover a continuous evolutionary range from closely related to more diverged yeast species. Our approach integrated the generation of a high-quality genome data set; the development of AnChro, a new algorithm for reconstructing ancestral genome architecture; and a comprehensive analysis of gene repertoire evolution. We found that the ancestral genome of the genus Lachancea contained eight chromosomes and about 5173 protein-coding genes. Moreover, we characterized 24 horizontal gene transfers and 159 putative gene creation events that punctuated species diversification. We retraced all chromosomal rearrangements, including gene losses, gene duplications, chromosomal inversions and translocations at single gene resolution. Gene duplications outnumbered losses and balanced rearrangements with 1503, 929, and 423 events, respectively. Gene content variations between extant species are mainly driven by differential gene losses, while gene duplications remained globally constant in all lineages. Remarkably, we discovered that balanced chromosomal rearrangements could be responsible for up to 14% of all gene losses by disrupting genes at their breakpoints. Finally, we found that nonsynonymous substitutions reached fixation at a coordinated pace with chromosomal inversions, translocations, and duplications, but not deletions. Overall, we provide a granular view of genome evolution within an entire eukaryotic genus, linking gene content, chromosome rearrangements, and protein divergence into a single evolutionary framework.

  10. Reconstructed ancestral Myo-inositol-3-phosphate synthases indicate that ancestors of the Thermococcales and Thermotoga species were more thermophilic than their descendants.

    Directory of Open Access Journals (Sweden)

    Nicholas C Butzin

    Full Text Available The bacterial genomes of Thermotoga species show evidence of significant interdomain horizontal gene transfer from the Archaea. Members of this genus acquired many genes from the Thermococcales, which grow at higher temperatures than Thermotoga species. In order to study the functional history of an interdomain horizontally acquired gene we used ancestral sequence reconstruction to examine the thermal characteristics of reconstructed ancestral proteins of the Thermotoga lineage and its archaeal donors. Several ancestral sequence reconstruction methods were used to determine the possible sequences of the ancestral Thermotoga and Archaea myo-inositol-3-phosphate synthase (MIPS. These sequences were predicted to be more thermostable than the extant proteins using an established sequence composition method. We verified these computational predictions by measuring the activities and thermostabilities of purified proteins from the Thermotoga and the Thermococcales species, and eight ancestral reconstructed proteins. We found that the ancestral proteins from both the archaeal donor and the Thermotoga most recent common ancestor recipient were more thermostable than their descendants. We show that there is a correlation between the thermostability of MIPS protein and the optimal growth temperature (OGT of its host, which suggests that the OGT of the ancestors of these species of Archaea and the Thermotoga grew at higher OGTs than their descendants.

  11. PhyloBot: A Web Portal for Automated Phylogenetics, Ancestral Sequence Reconstruction, and Exploration of Mutational Trajectories.

    Science.gov (United States)

    Hanson-Smith, Victor; Johnson, Alexander

    2016-07-01

    The method of phylogenetic ancestral sequence reconstruction is a powerful approach for studying evolutionary relationships among protein sequence, structure, and function. In particular, this approach allows investigators to (1) reconstruct and "resurrect" (that is, synthesize in vivo or in vitro) extinct proteins to study how they differ from modern proteins, (2) identify key amino acid changes that, over evolutionary timescales, have altered the function of the protein, and (3) order historical events in the evolution of protein function. Widespread use of this approach has been slow among molecular biologists, in part because the methods require significant computational expertise. Here we present PhyloBot, a web-based software tool that makes ancestral sequence reconstruction easy. Designed for non-experts, it integrates all the necessary software into a single user interface. Additionally, PhyloBot provides interactive tools to explore evolutionary trajectories between ancestors, enabling the rapid generation of hypotheses that can be tested using genetic or biochemical approaches. Early versions of this software were used in previous studies to discover genetic mechanisms underlying the functions of diverse protein families, including V-ATPase ion pumps, DNA-binding transcription regulators, and serine/threonine protein kinases. PhyloBot runs in a web browser, and is available at the following URL: http://www.phylobot.com. The software is implemented in Python using the Django web framework, and runs on elastic cloud computing resources from Amazon Web Services. Users can create and submit jobs on our free server (at the URL listed above), or use our open-source code to launch their own PhyloBot server.

  12. Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex.

    Directory of Open Access Journals (Sweden)

    Katherine Belov

    2006-03-01

    Full Text Available The first sequenced marsupial genome promises to reveal unparalleled insights into mammalian evolution. We have used the Monodelphis domestica (gray short-tailed opossum sequence to construct the first map of a marsupial major histocompatibility complex (MHC. The MHC is the most gene-dense region of the mammalian genome and is critical to immunity and reproductive success. The marsupial MHC bridges the phylogenetic gap between the complex MHC of eutherian mammals and the minimal essential MHC of birds. Here we show that the opossum MHC is gene dense and complex, as in humans, but shares more organizational features with non-mammals. The Class I genes have amplified within the Class II region, resulting in a unique Class I/II region. We present a model of the organization of the MHC in ancestral mammals and its elaboration during mammalian evolution. The opossum genome, together with other extant genomes, reveals the existence of an ancestral "immune supercomplex" that contained genes of both types of natural killer receptors together with antigen processing genes and MHC genes.

  13. Creation of Functional Viruses from Non-Functional cDNA Clones Obtained from an RNA Virus Population by the Use of Ancestral Reconstruction

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Dräger, Carolin;

    2015-01-01

    the reconstructed cDNAs were tested in cell culture and pigs. Both reconstructed ancestral genomes proved functional, and displayed distinct phenotypes in vitro and in vivo. We suggest that reconstruction of ancestral viruses is a useful tool for experimental and computational investigations of virulence and viral......RNA viruses have the highest known mutation rates. Consequently it is likely that a high proportion of individual RNA virus genomes, isolated from an infected host, will contain lethal mutations and be non-functional. This is problematic if the aim is to clone and investigate high...... a moderately virulent isolate. In addition to here being used as a model for RNA viruses generally, CSFV has high socioeconomic importance and remains a threat to animal welfare and pig production. We find that the majority of the investigated genomes are non-functional and only 12% produced infectious RNA...

  14. Reconstructing quantum states efficiently

    OpenAIRE

    Cramer, M; Plenio, M. B.

    2010-01-01

    Quantum state tomography, the ability to deduce the density matrix of a quantum system from measured data, is of fundamental importance for the verification of present and future quantum devices. It has been realized in systems with few components but for larger systems it becomes rapidly infeasible because the number of quantum measurements and computational resources required to process them grow exponentially in the system size. Here we show that we can gain an exponential advantage over d...

  15. Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals

    Directory of Open Access Journals (Sweden)

    Keightley Peter D

    2008-09-01

    Full Text Available Abstract Background Molecular evolutionary studies in mammals often estimate nucleotide substitution rates within and outside CpG dinucleotides separately. Frequently, in alignments of two sequences, the division of sites into CpG and non-CpG classes is based simply on the presence or absence of a CpG dinucleotide in either sequence, a procedure that we refer to as CpG/non-CpG assignment. Although it likely that this procedure is biased, it is generally assumed that the bias is negligible if species are very closely related. Results Using simulations of DNA sequence evolution we show that assignment of the ancestral CpG state based on the simple presence/absence of the CpG dinucleotide can seriously bias estimates of the substitution rate, because many true non-CpG changes are misassigned as CpG. Paradoxically, this bias is most severe between closely related species, because a minimum of two substitutions are required to misassign a true ancestral CpG site as non-CpG whereas only a single substitution is required to misassign a true ancestral non-CpG site as CpG in a two branch tree. We also show that CpG misassignment bias differentially affects fourfold degenerate and noncoding sites due to differences in base composition such that fourfold degenerate sites can appear to be evolving more slowly than noncoding sites. We demonstrate that the effects predicted by our simulations occur in a real evolutionary setting by comparing substitution rates estimated from human-chimp coding and intronic sequence using CpG/non-CpG assignment with estimates derived from a method that is largely free from bias. Conclusion Our study demonstrates that a common method of assigning sites into CpG and non CpG classes in pairwise alignments is seriously biased and recommends against the adoption of ad hoc methods of ancestral state assignment.

  16. The impact of ancestral heath management on soils and landscapes. A reconstruction based on paleoecological analyses of soil records in the middle and southeast Netherlands.

    Science.gov (United States)

    van Mourik, Jan; Doorenbosch, Marieke

    2016-04-01

    The evolution of heath lands during the Holocene has been registered in various soil records . Paleoecological analyses of these records enable to reconstruct the changing economic and cultural management of heaths and the consequences for landscape and soils. Heaths are characteristic components of cultural landscape mosaics on sandy soils in the Netherlands. The natural habitat of heather species was moorland. At first, natural events like forest fires and storms caused small-scale forest degradation, in addition on the forest degradation accelerated due to cultural activities like forest grazing, wood cutting and shifting cultivation. Heather plants invaded on degraded forest soils and heaths developed. People learned to use the heaths for economic and cultural purposes. The impact of the heath management on landscape and soils was registered in soil records of barrows, drift sand sequences and plaggic Anthrosols. Based on pollen diagrams of such records we could reconstruct that heaths were developed and used for cattle grazing before the Bronze Age. During the Late Neolithic, the Bronze Age and Iron Age, people created the barrow landscape on the ancestral heaths. After the Iron Age people probably continued with cattle grazing on the heaths and plaggic agriculture until the Early Middle Ages. After 1000 AD two events affected the heaths. At first deforestation for the sale of wood resulted in the first regional extension of sand drifting and heath degradation. After that the introduction of the deep stable economy and heath sods digging resulted in acceleration of the rise of plaggic horizons, severe heath degradation and the second extension of sand drifting. At the end of the 19th century the heath lost its economic value due to the introduction of chemical fertilizers. The heaths were transformed into 'new' arable fields and forests and due to deep ploughing most soil archives were destroyed. Since 1980 AD, the remaining relicts of the ancestral heaths are

  17. Classical and Quantum-Mechanical State Reconstruction

    Science.gov (United States)

    Khanna, F. C.; Mello, P. A.; Revzen, M.

    2012-01-01

    The aim of this paper is to present the subject of state reconstruction in classical and in quantum physics, a subject that deals with the experimentally acquired information that allows the determination of the physical state of a system. Our first purpose is to explain a method for retrieving a classical state in phase space, similar to that…

  18. The impact of ancestral heath management on soils and landscapes: a reconstruction based on paleoecological analyses of soil records in the central and southeastern Netherlands

    Science.gov (United States)

    Doorenbosch, Marieke; van Mourik, Jan M.

    2016-07-01

    The evolution of heathlands during the Holocene has been registered in various soil records. Paleoecological analyses of these records enable reconstruction of the changing economic and cultural management of heaths and the consequences for landscape and soils. Heaths are characteristic components of cultural landscape mosaics on sandy soils in the Netherlands. The natural habitat of heather species was moorland. At first, natural events like forest fires and storms caused small-scale forest degradation; in addition on that, the forest degradation accelerated due to cultural activities like forest grazing, wood cutting, and shifting cultivation. Heather plants invaded degraded forest soils, and heaths developed. People learned to use the heaths for economic and cultural purposes. The impact of the heath management on landscape and soils was registered in soil records of barrows, drift sand sequences, and plaggic Anthrosols. Based on pollen diagrams of such records we could reconstruct that heaths were developed and used for cattle grazing before the Bronze Age. During the late Neolithic, the Bronze Age, and Iron Age, people created the barrow landscape on the ancestral heaths. After the Iron Age, people probably continued with cattle grazing on the heaths and plaggic agriculture until the early Middle Ages. Severe forest degradation by the production of charcoal for melting iron during the Iron Age till the 6th-7th century and during the 11th-13th century for the trade of wood resulted in extensive sand drifting, a threat to the valuable heaths. The introduction of the deep, stable economy and heath sods digging in the course of the 18th century resulted in acceleration of the rise of plaggic horizons, severe heath degradation, and again extension of sand drifting. At the end of the 19th century heath lost its economic value due to the introduction of chemical fertilizers. The heaths were transformed into "new" arable fields and forests, and due to deep ploughing

  19. Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple

    NARCIS (Netherlands)

    Ismail, Siti Izera; Batzer, Jean Carlson; Harrington, Thomas C.; Crous, Pedro W.; Lavrov, Dennis V.; Li, Huanyu; Gleason, Mark L.

    2016-01-01

    Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we

  20. Ancestral state reconstruction infers phytopathogenic origins of sooty blotch and flyspeck fungi on apple

    NARCIS (Netherlands)

    Ismail, Siti Izera; Batzer, Jean Carlson; Harrington, Thomas C.; Crous, Pedro W.; Lavrov, Dennis V.; Li, Huanyu; Gleason, Mark L.

    2016-01-01

    Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so

  1. Optimal Frames for Polarisation State Reconstruction

    CERN Document Server

    Foreman, Matthew R; Aiello, Andrea

    2015-01-01

    Complete determination of the polarisation state of light requires projection of the associated Stokes vector onto a basis of at least four distinct analysis states by means of suitable polarisation state analysers. Stability of state reconstruction in such measurements, however, hinges on the condition number, $\\kappa$, of the corresponding instrument matrix. Optimisation of redundant measurement frames with an arbitrary finite number of analysis states, $m$, is considered in this Letter in the sense of minimisation of $\\kappa$. The minimum achievable $\\kappa$ is analytically found and shown to be independent of $m$, except for $m=5$ where this minimum is unachievable. Formal equivalence between minimisation of $\\kappa$, maximisation of the determinant of the associated Gram matrix and minimisation of the equally weighted variance is established. Distribution of the optimal analysis states over the Poincar\\'e sphere is furthermore found to be described by spherical 2-designs, including those defined by the P...

  2. State reconstruction of molecular spatial rotation

    Institute of Scientific and Technical Information of China (English)

    Qin Xiao; Gao Jun-Yi

    2012-01-01

    We establish a reconstruction approach for the rotational quantum state of linear molecules possessing a magnetic manifold.Our approximate method contains an iteration with generalized matrix inverses,processing the tomographic integral of the time-dependent molecular-axis distribution in a polar angle.As shown in a simulated example for an alignment state,the density matrix is determined in a high fidelity.An analytic tomographic formula is also derived for the symmetric top rotation.The state coherent in the quantun space of both the angular momentum and its magnetic projection can be approximately retrieved from the observable time-resolved solid-angle distribution of the molecular.

  3. Are palaeoscolecids ancestral ecdysozoans?

    Science.gov (United States)

    Harvey, Thomas H P; Dong, Xiping; Donoghue, Philip C J

    2010-01-01

    The reconstruction of ancestors is a central aim of comparative anatomy and evolutionary developmental biology, not least in attempts to understand the relationship between developmental and organismal evolution. Inferences based on living taxa can and should be tested against the fossil record, which provides an independent and direct view onto historical character combinations. Here, we consider the nature of the last common ancestor of living ecdysozoans through a detailed analysis of palaeoscolecids, an early and extinct group of introvert-bearing worms that have been proposed to be ancestral ecdysozoans. In a review of palaeoscolecid anatomy, including newly resolved details of the internal and external cuticle structure, we identify specific characters shared with various living nematoid and scalidophoran worms, but not with panarthropods. Considered within a formal cladistic context, these characters provide most overall support for a stem-priapulid affinity, meaning that palaeoscolecids are far-removed from the ecdysozoan ancestor. We conclude that previous interpretations in which palaeoscolecids occupy a deeper position in the ecdysozoan tree lack particular morphological support and rely instead on a paucity of preserved characters. This bears out a more general point that fossil taxa may appear plesiomorphic merely because they preserve only plesiomorphies, rather than the mélange of primitive and derived characters anticipated of organisms properly allocated to a position deep within animal phylogeny.

  4. Reconstructing complex networks with binary-state dynamics

    CERN Document Server

    Li, Jingwen; Lai, Ying-Cheng; Grebogi, Celso

    2015-01-01

    The prerequisite for our understanding of many complex networked systems lies in the reconstruction of network structure from measurable data. Although binary-state dynamics occurring in a broad class of complex networked systems in nature and society and has been intensively investigated, a general framework for reconstructing complex networks from binary states, the inverse problem, is lacking. Here we offer a general solution to the reconstruction problem by developing a data-based linearization approach for binary-state dynamics with linear, nonlinear, discrete and stochastic switching functions. The linearization allows us to convert the network reconstruction problem into a sparse signal reconstruction problem that can be resolved efficiently and credibly by convex optimization based on compressed sensing. The completely data-based linearization method and the sparse signal reconstruction constitutes a general framework for reconstructing complex networks without any knowledge of the binary-state dynami...

  5. Mandibular Reconstruction, State of the Art

    Directory of Open Access Journals (Sweden)

    Julio ACERO

    2011-08-01

    Full Text Available SUMMARY: Mandibular bone loss can result in severe aesthetic and functional consequences for the patient, posing a challenge to the reconstructive maxillo-facial surgeon. Advent of microvascular surgery revolutionized mandible reconstruction introducing the possibility to transfer vascularized bone and soft tissues with high success rate. Major donor sites are the fibula, iliac crest and scapula. Planning of the reconstruction and advantages and disadvantages of the different reconstructive methods are discussed. The iliac crest provides an excellent bone for mandibular reconstruction but has some limits concerning length and versatility of soft tissues. The fibula permits the repair of large mandibular defects due to its length while the scapular osteocutaneous flap allows for the reconstruction of limited bone defects associated with large soft tissue defects. Nonvascularized reconstructive methods are associated with higher failure rates but can be considered in selected cases.

  6. Perianth evolution in Ranunculaceae: are petals ancestral in the family?

    Directory of Open Access Journals (Sweden)

    Sophie Nadot

    2016-04-01

    Full Text Available Progress has been made recently towards the elucidation of phylogenetic relationships among subfamilies and tribes of the Ranunculaceae – the most recent hypothesis was published in 2016 by our team. Although relationships among the 10 tribes of the subfamily Ranunculoideae remain incompletely supported, this hypothesis provides an interesting framework to address the key issue of the ancestral vs. derived nature of a differentiated perianth within the family, and at the level of Ranunculales as a whole. Here, we present ancestral state reconstructions for several perianth characters, such as differentiation into sepals and petals, shape of petals, presence/absence of nectaries, and petaloid or sepaloid aspect of sepals. Characters were scored using the PROTEUS database and optimized on the most recent phylogeny of Ranunculaceae using parsimony and maximum likelihood methods. The results are discussed with regard to recent evo-devo studies focused on identifying genes involved in floral organs identity (the so-called ABC model in Ranunculales.

  7. Ancestral Relationships Using Metafounders

    DEFF Research Database (Denmark)

    Legarra, Andres; Christensen, Ole Fredslund; Vitezica, Zulma G

    2015-01-01

    due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships....... We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view where each population is considered as an infinite, unrelated pool. Several ancestral populations may......Recent use of genomic (marker-based) relationships shows that relationships exist within and across base population (breeds or lines). However, current treatment of pedigree relationships is unable to consider relationships within or across base populations, although such relationships must exist...

  8. Comparative genomic analysis of the arthropod muscle myosin heavy chain genes allows ancestral gene reconstruction and reveals a new type of 'partially' processed pseudogene

    Directory of Open Access Journals (Sweden)

    Kollmar Martin

    2008-02-01

    Full Text Available Abstract Background Alternative splicing of mutually exclusive exons is an important mechanism for increasing protein diversity in eukaryotes. The insect Mhc (myosin heavy chain gene produces all different muscle myosins as a result of alternative splicing in contrast to most other organisms of the Metazoa lineage, that have a family of muscle genes with each gene coding for a protein specialized for a functional niche. Results The muscle myosin heavy chain genes of 22 species of the Arthropoda ranging from the waterflea to wasp and Drosophila have been annotated. The analysis of the gene structures allowed the reconstruction of an ancient muscle myosin heavy chain gene and showed that during evolution of the arthropods introns have mainly been lost in these genes although intron gain might have happened in a few cases. Surprisingly, the genome of Aedes aegypti contains another and that of Culex pipiens quinquefasciatus two further muscle myosin heavy chain genes, called Mhc3 and Mhc4, that contain only one variant of the corresponding alternative exons of the Mhc1 gene. Mhc3 transcription in Aedes aegypti is documented by EST data. Mhc3 and Mhc4 inserted in the Aedes and Culex genomes either by gene duplication followed by the loss of all but one variant of the alternative exons, or by incorporation of a transcript of which all other variants have been spliced out retaining the exon-intron structure. The second and more likely possibility represents a new type of a 'partially' processed pseudogene. Conclusion Based on the comparative genomic analysis of the alternatively spliced arthropod muscle myosin heavy chain genes we propose that the splicing process operates sequentially on the transcript. The process consists of the splicing of the mutually exclusive exons until one exon out of the cluster remains while retaining surrounding intronic sequence. In a second step splicing of introns takes place. A related mechanism could be responsible for

  9. Highly efficient solid state catalysis by reconstructed (001) Ceria surface

    Energy Technology Data Exchange (ETDEWEB)

    Solovyov, VF; Ozaki, T; Atrei, A; Wu, LJ; Al-Mahboob, A; Sadowski, JT; Tong, X; Nykypanchuk, D; Li, Q

    2014-04-10

    Substrate engineering is a key factor in the synthesis of new complex materials. The substrate surface has to be conditioned in order to minimize the energy threshold for the formation of the desired phase or to enhance the catalytic activity of the substrate. The mechanism of the substrate activity, especially of technologically relevant oxide surfaces, is poorly understood. Here we design and synthesize several distinct and stable CeO2 (001) surface reconstructions which are used to grow epitaxial films of the high-temperature superconductor YBa2Cu3O7. The film grown on the substrate having the longest, fourfold period, reconstruction exhibits a twofold increase in performance over surfaces with shorter period reconstructions. This is explained by the crossover between the nucleation site dimensions and the period of the surface reconstruction. This result opens a new avenue for catalysis mediated solid state synthesis.

  10. State Space Reduction of Linear Processes Using Control Flow Reconstruction

    NARCIS (Netherlands)

    Pol, van de Jaco; Timmer, Mark; Liu, Z.; Ravn, A.P.

    2009-01-01

    We present a new method for fighting the state space explosion of process algebraic specifications, by performing static analysis on an intermediate format: linear process equations (LPEs). Our method consists of two steps: (1) we reconstruct the LPE's control flow, detecting control flow parameters

  11. State Space Reduction of Linear Processes using Control Flow Reconstruction

    NARCIS (Netherlands)

    Pol, van de Jaco; Timmer, Mark

    2009-01-01

    We present a new method for fighting the state space explosion of process algebraic specifications, by performing static analysis on an intermediate format: linear process equations (LPEs). Our method consists of two steps: (1) we reconstruct the LPE's control flow, detecting control flow parameters

  12. Reconstructing the dark energy equation of state with varying couplings

    CERN Document Server

    Pina-Avelino, P; Nunes, N J; Olive, Keith A

    2006-01-01

    We revisit the idea of using varying couplings to probe the nature of dark energy, in particular by reconstructing its equation of state. We show that this method can be far superior to the standard methods (using type Ia supernovae or weak lensing). We also show that the simultaneous use of measurements of the fine-structure constant $\\alpha$ and the electron-to-proton mass ratio $\\mu$ allows a direct probe of grand unification scenarios. We present forecasts for the sensitivity of this method, both for the near future and for the next generation of spectrographs -- for the latter we focus on the planned CODEX instrument for ESO's Extremely Large Telescope (formerly known as OWL). A high-accuracy reconstruction of the equation of state may be possible all the way up to redshift $z\\sim4$.

  13. State of bream populations in reconstructed water bodies of Moldova

    Directory of Open Access Journals (Sweden)

    Adrian USATYI

    2010-11-01

    Full Text Available Bream, Abramis brama L., is a key species in fish communities of Moldovian Rivers and a main component of bottom food chains of river and lake ecosystems. With the reconstruction of water bodies, mainly for hydroelectric power stations needs, the ecological conditions changed substantially, which results in modifications in population state of biota. The negative effects of water bodies’ reconstruction upon population status of bream in several Moldovian Rivers and reservoirs were studied. These effects manifest in detrimental changes in bream growth, age composition and reproductive success. The conclusion is made that the economical gain after the regulation of large and middle-size rivers is opposed by the negative impact upon fish community as a whole, as well as upon the ecology of individual species as applied to the indicator species Abramis brama.

  14. Direct state reconstruction with coupling-deformed pointer observables

    Science.gov (United States)

    Zhu, Xuanmin; Zhang, Yu-Xiang; Wu, Shengjun

    2016-06-01

    Direct state tomography (DST) using weak measurements has received wide attention. Based on the concept of coupling-deformed pointer observables presented by Zhang et al. [Y.-X. Zhang, S. Wu, and Z.-B. Chen, Phys. Rev. A 93, 032128 (2016), 10.1103/PhysRevA.93.032128], a modified direct state tomography (MDST) is proposed, examined, and compared with other typical state tomography schemes. MDST has exact validity for measurements of any strength. We identify the strength needed to attain the highest efficiency level of MDST by using statistical theory. MDST is much more efficient than DST in the sense that far fewer samples are needed to reach DST's level of reconstruction accuracy. Moreover, MDST has no inherent bias when compared to DST.

  15. Optimal reconstruction of a pure qubit state with local measurements

    CERN Document Server

    Bagán, E; Monras, A; Muñoz-Tàpia, R

    2003-01-01

    We analyse the reconstruction of an unknown pure qubit state. We derive the optimal guess that can be inferred from any set of measurements on N identical copies of the system with the fidelity as a figure of merit. We study in detail the estimation process with individual von Neumann measurements and demonstrate that they are very competitive as compared to (complicated) collective measurements. We compute the expressions of the fidelity for large $N$ and show that individual measurement schemes can perform optimally in the asymptotic regime.

  16. Full reconstruction of a 14-qubit state within four hours

    Science.gov (United States)

    Hou, Zhibo; Zhong, Han-Sen; Tian, Ye; Dong, Daoyi; Qi, Bo; Li, Li; Wang, Yuanlong; Nori, Franco; Xiang, Guo-Yong; Li, Chuan-Feng; Guo, Guang-Can

    2016-08-01

    Full quantum state tomography (FQST) plays a unique role in the estimation of the state of a quantum system without a priori knowledge or assumptions. Unfortunately, since FQST requires informationally (over)complete measurements, both the number of measurement bases and the computational complexity of data processing suffer an exponential growth with the size of the quantum system. A 14-qubit entangled state has already been experimentally prepared in an ion trap, and the data processing capability for FQST of a 14-qubit state seems to be far away from practical applications. In this paper, the computational capability of FQST is pushed forward to reconstruct a 14-qubit state with a run time of only 3.35 hours using the linear regression estimation (LRE) algorithm, even when informationally overcomplete Pauli measurements are employed. The computational complexity of the LRE algorithm is first reduced from ∼1019 to ∼1015 for a 14-qubit state, by dropping all the zero elements, and its computational efficiency is further sped up by fully exploiting the parallelism of the LRE algorithm with parallel Graphic Processing Unit (GPU) programming. Our result demonstrates the effectiveness of using parallel computation to speed up the postprocessing for FQST, and can play an important role in quantum information technologies with large quantum systems.

  17. Multiproxy Reconstruction of Tropical Pacific Holocene Mean State Variability

    Science.gov (United States)

    Arbuszewski, J. A.; Oppo, D.; Huang, K. F.; Galy, V.; Dubois, N.; Mohtadi, M.; Herbert, T.; Rosenthal, Y.; Linsley, B. K.; Lynch-Stieglitz, J.; Koutavas, A.; Rustic, G. T.

    2014-12-01

    The El Niño-Southern Oscillation (ENSO) is the most prominent mode of tropical Pacific climate variability, significantly impacting both regional and global climate. In the past, the mean state of the Pacific Ocean has differed from today as evidenced by variability in the zonal water column structure. Recent paleoproxy based studies of tropical Pacific hydrology and surface temperature variability have hypothesized that observed climatological changes over the Holocene are directly linked to ENSO and/or mean state variability, complementing studies that dynamically relate centennial scale ENSO variability to mean state changes. These studies have suggested that mid Holocene ENSO variability was low and the mean state was more "La Niña" like. In the late Holocene, data have been interpreted as indicating an increase in ENSO variability with a more moderate mean state. Here, we test the hypothesis that observed climatological changes in the eastern tropical Pacific are related to mean state or ENSO variability during the Holocene. We focus our study on three sediment core locations from the equatorial Pacific: the Indo-Pacific Warm Pool (BJ803-119 GGC, 117MC), the Line Islands in the central Pacific (ML1208-18GC) and the Galapagos Islands in the Eastern Cold Tongue (KNR195-5 43 GGC, 42MC). These sites lie in regions poised to provide evidence of basin-wide equatorial water column structure changes in response to mean state and/or long-term ENSO variability. We use a multiproxy approach with data from both organic (sterol abundances) and inorganic proxies (Mg/Ca and δ18O of 4 planktonic foraminiferal species, % G. bulloides) to reconstruct zonal tropical Pacific (sub)surface temperature and stratification gradients over the Holocene. This approach enables us to combine the strengths of each individual proxy to derive more robust records. To put our data in the context of the broader Pacific and Indo-Pacific regions, we compare our new data to published records.

  18. Ancestral process and diffusion model with selection

    CERN Document Server

    Mano, Shuhei

    2008-01-01

    The ancestral selection graph in population genetics introduced by Krone and Neuhauser (1997) is an analogue to the coalescent genealogy. The number of ancestral particles, backward in time, of a sample of genes is an ancestral process, which is a birth and death process with quadratic death and linear birth rate. In this paper an explicit form of the number of ancestral particle is obtained, by using the density of the allele frequency in the corresponding diffusion model obtained by Kimura (1955). It is shown that fixation is convergence of the ancestral process to the stationary measure. The time to fixation of an allele is studied in terms of the ancestral process.

  19. Conditional large Fock state preparation and field state reconstruction in cavity QED.

    Science.gov (United States)

    Santos, M F; Solano, E; de Matos Filho, R L

    2001-08-27

    We propose a scheme for producing large Fock states in cavity QED via the implementation of a highly selective atom-field interaction. It is based on Raman excitation of a three-level atom by a classical field and a quantized field mode. Selectivity appears when one tunes to resonance a specific transition inside a chosen atom-field subspace, while other transitions remain dispersive, as a consequence of the field dependent electronic energy shifts. We show that this scheme can be also employed for reconstructing, in a new and efficient way, the Wigner function of the cavity field state.

  20. Evolutionary site-number changes of ribosomal DNA loci during speciation: complex scenarios of ancestral and more recent polyploid events.

    Science.gov (United States)

    Rosato, Marcela; Moreno-Saiz, Juan C; Galián, José A; Rosselló, Josep A

    2015-11-16

    Several genome duplications have been identified in the evolution of seed plants, providing unique systems for studying karyological processes promoting diversification and speciation. Knowledge about the number of ribosomal DNA (rDNA) loci, together with their chromosomal distribution and structure, provides clues about organismal and molecular evolution at various phylogenetic levels. In this work, we aim to elucidate the evolutionary dynamics of karyological and rDNA site-number variation in all known taxa of subtribe Vellinae, showing a complex scenario of ancestral and more recent polyploid events. Specifically, we aim to infer the ancestral chromosome numbers and patterns of chromosome number variation, assess patterns of variation of both 45S and 5S rDNA families, trends in site-number change of rDNA loci within homoploid and polyploid series, and reconstruct the evolutionary history of rDNA site number using a phylogenetic hypothesis as a framework. The best-fitting model of chromosome number evolution with a high likelihood score suggests that the Vellinae core showing x = 17 chromosomes arose by duplication events from a recent x = 8 ancestor. Our survey suggests more complex patterns of polyploid evolution than previously noted for Vellinae. High polyploidization events (6x, 8x) arose independently in the basal clade Vella castrilensis-V. lucentina, where extant diploid species are unknown. Reconstruction of ancestral rDNA states in Vellinae supports the inference that the ancestral number of loci in the subtribe was two for each multigene family, suggesting that an overall tendency towards a net loss of 5S rDNA loci occurred during the splitting of Vellinae ancestors from the remaining Brassiceae lineages. A contrasting pattern for rDNA site change in both paleopolyploid and neopolyploid species was linked to diversification of Vellinae lineages. This suggests dynamic and independent changes in rDNA site number during speciation processes and a

  1. Reconstruction

    Directory of Open Access Journals (Sweden)

    Stefano Zurrida

    2011-01-01

    Full Text Available Breast cancer is the most common cancer in women. Primary treatment is surgery, with mastectomy as the main treatment for most of the twentieth century. However, over that time, the extent of the procedure varied, and less extensive mastectomies are employed today compared to those used in the past, as excessively mutilating procedures did not improve survival. Today, many women receive breast-conserving surgery, usually with radiotherapy to the residual breast, instead of mastectomy, as it has been shown to be as effective as mastectomy in early disease. The relatively new skin-sparing mastectomy, often with immediate breast reconstruction, improves aesthetic outcomes and is oncologically safe. Nipple-sparing mastectomy is newer and used increasingly, with better acceptance by patients, and again appears to be oncologically safe. Breast reconstruction is an important adjunct to mastectomy, as it has a positive psychological impact on the patient, contributing to improved quality of life.

  2. Quantum reconstruction of an intense polarization squeezed optical state

    DEFF Research Database (Denmark)

    Marquardt, Ch.; Heersink, J.; Dong, R.;

    2007-01-01

    We perform a reconstruction of the polarization sector of the density matrix of an intense polarization squeezed beam starting from a complete set of Stokes measurements. By using an appropriate quasidistribution, we map this onto the Poincare space, providing a full quantum mechanical characteri...

  3. A theory of state space reconstruction in the presence of noise

    Energy Technology Data Exchange (ETDEWEB)

    Casdagli, M.; Eubank, S.; Farmer, J.D.; Gibson, J. (Los Alamos National Lab., NM (USA) Santa Fe Inst., NM (USA))

    1990-01-01

    Takens' theorem demonstrates that in the absence of noise a multidimensional state space can be reconstructed from a single time series. This theorem does not treat the effect of noise, however, and so gives no guidance about practical considerations for reconstructing a good state space. We study the problem of reconstructing a state space with observational noise, examining the likelihood for a particular state given a series of noisy observations. We define a quantity called distortion, which is proportional to the covariance of the likelihood function in a reconstructed state space. This is related to the noise amplification, which corresponds to the root-mean-square errors for time series prediction with an ideal model. We prove that in the low noise limit minimizing the distortion is equivalent to minimizing the noise amplification. We derive several asymptotic scaling laws for distortion and noise amplification. They depend on properties of the state space reconstruction, such as the sampling time and the reconstruction dimension, and properties of the dynamical system, such as the dimension and Lyapunov exponents. When the dimension and Lyapunov exponents are sufficiently large these scaling laws show that, no matter how the state space is reconstructed, there is an explosion in the noise amplification -- from a practical point of view all determinism is lost, even for short times, so that the time series is effectively a random process. In the low noise, large data limit we show that the technique of local principal value decomposition (PVD) is an optimal method of state space reconstruction, in the sense that it achieves the minimum distortion in a state space of the lowest possible dimension. 20 refs., 12 figs.

  4. State exact reconstruction for switched linear systems via a super-twisting algorithm

    Science.gov (United States)

    Bejarano, Francisco J.; Fridman, Leonid

    2011-05-01

    This article discusses the problem of state reconstruction synthesis for switched linear systems. Based only on the continuous output information, an observer is proposed ensuring the reconstruction of the entire state (continuous and discrete) in finite time. For the observer design an exact sliding mode differentiator is used, which allows the finite time convergence of the observer trajectories to the actual trajectories. The design scheme includes both cases: zero control input and nonzero control input. Simulations illustrate the effectiveness of the proposed observer.

  5. Reconstruction of the joint state of a two-mode Bose-Einstein condensate

    CERN Document Server

    Bolda, E L; Walls, D F; Bolda, Eric L.; Tan, Sze M.; Walls, Dan F.

    1997-01-01

    We propose a scheme to reconstruct the state of a two-mode Bose-Einstein condensate, with a given total number of atoms, using an atom interferometer that requires beam splitter, phase shift and non-ideal atom counting operations. The density matrix in the number-state basis can be computed directly from the probabilities of different counts for various phase shifts between the original modes, unless the beamsplitter is exactly balanced. Simulated noisy data from a two-mode coherent state is produced and the state is reconstructed, for 49 atoms. The error can be estimated from the singular values of the transformation matrix between state and probability data.

  6. Universal data-based method for reconstructing complex networks with binary-state dynamics

    Science.gov (United States)

    Li, Jingwen; Shen, Zhesi; Wang, Wen-Xu; Grebogi, Celso; Lai, Ying-Cheng

    2017-03-01

    To understand, predict, and control complex networked systems, a prerequisite is to reconstruct the network structure from observable data. Despite recent progress in network reconstruction, binary-state dynamics that are ubiquitous in nature, technology, and society still present an outstanding challenge in this field. Here we offer a framework for reconstructing complex networks with binary-state dynamics by developing a universal data-based linearization approach that is applicable to systems with linear, nonlinear, discontinuous, or stochastic dynamics governed by monotonic functions. The linearization procedure enables us to convert the network reconstruction into a sparse signal reconstruction problem that can be resolved through convex optimization. We demonstrate generally high reconstruction accuracy for a number of complex networks associated with distinct binary-state dynamics from using binary data contaminated by noise and missing data. Our framework is completely data driven, efficient, and robust, and does not require any a priori knowledge about the detailed dynamical process on the network. The framework represents a general paradigm for reconstructing, understanding, and exploiting complex networked systems with binary-state dynamics.

  7. Ancestral facial morphology of Old World higher primates.

    Science.gov (United States)

    Benefit, B R; McCrossin, M L

    1991-06-15

    Fossil remains of the cercopithecoid Victoria-pithecus recently recovered from middle Miocene deposits of Maboko Island (Kenya) provide evidence of the cranial anatomy of Old World monkeys prior to the evolutionary divergence of the extant subfamilies Colobinae and Cercopithecinae. Victoria-pithecus shares a suite of craniofacial features with the Oligocene catarrhine Aegyptopithecus and early Miocene hominoid Afropithecus. All three genera manifest supraorbital costae, anteriorly convergent temporal lines, the absence of a postglabellar fossa, a moderate to long snout, great facial height below the orbits, a deep cheek region, and anteriorly tapering premaxilla. The shared presence of these features in a catarrhine generally ancestral to apes and Old World monkeys, an early ape, and an early Old World monkey indicates that they are primitive characteristics that typified the last common ancestor of Hominoidea and Cercopithecoidea. These results contradict prevailing cranial morphotype reconstructions for ancestral catarrhines as Colobus- or Hylobates-like, characterized by a globular anterior braincase and orthognathy. By resolving several equivocal craniofacial morphocline polarities, these discoveries lay the foundation for a revised interpretation of the ancestral cranial morphology of Catarrhini more consistent with neontological and existing paleontological evidence.

  8. Statistical Reconstruction of arbitrary spin states of particles: root approach

    OpenAIRE

    Bogdanov, Yu. I.

    2005-01-01

    A method of quantum tomography of arbitrary spin particle states is developed on the basis of the root approach. It is shown that the set of mutually complementary distributions of angular momentum projections can be naturally described by a set of basis functions based on the Kravchuk polynomials. The set of Kravchuk basis functions leads to a multi-parametric statistical distribution that generalizes the binomial distribution. In order to analyze a statistical inverse problem of quantum mec...

  9. On the ancestral recruitment of metalloproteinases into the venom of snakes.

    Science.gov (United States)

    Casewell, Nicholas R

    2012-09-15

    Tracing the evolutionary history of proteins can reveal insights into gene alterations responsible for changes in structure and function. Here, the origin of snake venom metalloproteinases was rigorously reassessed using phylogenetics and the reconstruction of ancestral sequences. Basal SVMPs are most closely related to ADAM 7, 28 and decysin-1 proteins. Reconstructing the evolutionary history of these proteins and their hypothetical ancestors reveals progressive alterations in the amino acid composition and structural characteristics of ADAMs/SVMPs through evolutionary time.

  10. Statistical Reconstruction of arbitrary spin states of particles: root approach

    CERN Document Server

    Bogdanov, Y I

    2005-01-01

    A method of quantum tomography of arbitrary spin particle states is developed on the basis of the root approach. It is shown that the set of mutually complementary distributions of angular momentum projections can be naturally described by a set of basis functions based on the Kravchuk polynomials. The set of Kravchuk basis functions leads to a multi-parametric statistical distribution that generalizes the binomial distribution. In order to analyze a statistical inverse problem of quantum mechanics, we investigated the likelihood equation and the statistical properties of the obtained estimates. The conclusions of the analytical researches are approved by the results of numerical calculations.

  11. Homogenization of steady-state creep of porous metals using three-dimensional microstructural reconstructions

    DEFF Research Database (Denmark)

    Kwok, Kawai; Boccaccini, Dino; Persson, Åsa Helen;

    2016-01-01

    The effective steady-state creep response of porous metals is studied by numerical homogenization and analytical modeling in this paper. The numerical homogenization is based on finite element models of three-dimensional microstructures directly reconstructed from tomographic images. The effects ...... model, and closely matched by the Gibson-Ashby compression and the Ramakrishnan-Arunchalam creep models. [All rights reserved Elsevier]....

  12. Reconstructing high-dimensional two-photon entangled states via compressive sensing.

    Science.gov (United States)

    Tonolini, Francesco; Chan, Susan; Agnew, Megan; Lindsay, Alan; Leach, Jonathan

    2014-10-13

    Accurately establishing the state of large-scale quantum systems is an important tool in quantum information science; however, the large number of unknown parameters hinders the rapid characterisation of such states, and reconstruction procedures can become prohibitively time-consuming. Compressive sensing, a procedure for solving inverse problems by incorporating prior knowledge about the form of the solution, provides an attractive alternative to the problem of high-dimensional quantum state characterisation. Using a modified version of compressive sensing that incorporates the principles of singular value thresholding, we reconstruct the density matrix of a high-dimensional two-photon entangled system. The dimension of each photon is equal to d = 17, corresponding to a system of 83521 unknown real parameters. Accurate reconstruction is achieved with approximately 2500 measurements, only 3% of the total number of unknown parameters in the state. The algorithm we develop is fast, computationally inexpensive, and applicable to a wide range of quantum states, thus demonstrating compressive sensing as an effective technique for measuring the state of large-scale quantum systems.

  13. Conference Report: Quo Vadis Reconstructive Social Work Research? Traditions—State of the Art—Perspectives

    Directory of Open Access Journals (Sweden)

    Ulrike Loch

    2008-01-01

    Full Text Available This conference report gives an overview of the 3rd annual conference of the "Network for Reconstructive Research and Biography" held at the Alice-Salomon-University of Applied Science, Berlin, Germany, on 23rd and 24th March, 2007. The aim of this year's conference was to report on the state of the art of research on social work, the current research situations at various universities in Germany, and the discourse on reconstructive social work within the discipline. This was to serve as a basis for the planned next step regarding the further development of the Network, i.e. intensive exchange, promotion of networking with colleagues and concrete forms of co-operation and strategies designed to further consolidate reconstructive social work in the Federal Republic of Germany. The keynote speakers gave further particulars about the state of the art of social work research, the workshops explored this situation in the areas of international social work practice and research, the teaching of research, junior researchers, research funding and new bachelor and master degree programs in the reconstructive social work. Approximately 40 participants met and provided new trend-setting ideas for qualitative research in social work and for the work and structure of the Network. URN: urn:nbn:de:0114-fqs0801338

  14. Quantum state engineering and reconstruction in cavity QED. An analytical approach

    Energy Technology Data Exchange (ETDEWEB)

    Lougovski, P.

    2004-09-25

    The models of a strongly-driven micromaser and a one-atom laser are developed. Their analytical solutions are obtained by means of phase space techniques. It is shown how to exploit the model of a one-atom laser for simultaneous generation and monitoring of the decoherence of the atom-field ''Schroedinger cat'' states. The similar machinery applied to the problem of the generation of the maximally-entangled states of two atoms placed inside an optical cavity permits its analytical solution. The steady-state solution of the problem exhibits a structure in which the two-atom maximally-entangled state correlates with the vacuum state of the cavity. As a consequence, it is demonstrated that the atomic maximally-entangled state, depending on a coupling regime, can be produced via a single or a sequence of no-photon measurements. The question of the implementation of a quantum memory device using a dispersive interaction between the collective internal ground state of an atomic ensemble and two orthogonal modes of a cavity is addressed. The problem of quantum state reconstruction in the context of cavity quantum electrodynamics is considered. The optimal operational definition of the Wigner function of a cavity field is worked out. It is based on the Fresnel transform of the atomic inversion of a probe atom. The general integral transformation for the Wigner function reconstruction of a particle in an arbitrary symmetric potential is derived.

  15. Quantum state reconstruction of an oscillator network in an optomechanical setting

    Science.gov (United States)

    Moore, Darren W.; Tufarelli, Tommaso; Paternostro, Mauro; Ferraro, Alessandro

    2016-11-01

    We introduce a scheme to reconstruct an arbitrary quantum state of a mechanical oscillator network. We assume that a single element of the network is coupled to a cavity field via a linearized optomechanical interaction, the time dependence of which is controlled by a classical driving field. By designing a suitable interaction profile, we show how the statistics of an arbitrary mechanical quadrature can be encoded in the cavity field, which can then be measured. We discuss the important special case of Gaussian state reconstruction and study numerically the effectiveness of our scheme for a finite number of measurements. Finally, we speculate on possible routes to extend our ideas to the regime of single-photon optomechanics.

  16. Genes Suggest Ancestral Colour Polymorphisms Are Shared across Morphologically Cryptic Species in Arctic Bumblebees.

    Directory of Open Access Journals (Sweden)

    Paul H Williams

    Full Text Available Our grasp of biodiversity is fine-tuned through the process of revisionary taxonomy. If species do exist in nature and can be discovered with available techniques, then we expect these revisions to converge on broadly shared interpretations of species. But for the primarily arctic bumblebees of the subgenus Alpinobombus of the genus Bombus, revisions by some of the most experienced specialists are unusual for bumblebees in that they have all reached different conclusions on the number of species present. Recent revisions based on skeletal morphology have concluded that there are from four to six species, while variation in colour pattern of the hair raised questions as to whether at least seven species might be present. Even more species are supported if we accept the recent move away from viewing species as morphotypes to viewing them instead as evolutionarily independent lineages (EILs using data from genes. EILs are recognised here in practice from the gene coalescents that provide direct evidence for their evolutionary independence. We show from fitting both general mixed Yule/coalescent (GMYC models and Poisson-tree-process (PTP models to data for the mitochondrial COI gene that there is support for nine species in the subgenus Alpinobombus. Examination of the more slowly evolving nuclear PEPCK gene shows further support for a previously unrecognised taxon as a new species in northwestern North America. The three pairs of the most morphologically similar sister species are separated allopatrically and prevented from interbreeding by oceans. We also find that most of the species show multiple shared colour patterns, giving the appearance of mimicry among parts of the different species. However, reconstructing ancestral colour-pattern states shows that speciation is likely to have cut across widespread ancestral polymorphisms, without or largely without convergence. In the particular case of Alpinobombus, morphological, colour-pattern, and

  17. Special Inspector General for Iraq Reconstruction. Quaterly and Semiannual Report to the United States Congress

    Science.gov (United States)

    2007-07-30

    Electricity Sector engineers, who provided day-to-day technical supervision and implementation management of GRD’s plan to bring Units 5 and 6 online ...telephone, mail, fax, and online contacts from people in Iraq, the United States, and throughout the world. Second quarter Reporting As of June 30, 2007...Investigative Task Force for Iraq Reconstruction SPOC Sector Project and Contracting Office Contractor TAMU Texas A&M University TBI Trade Bank of Iraq

  18. Special Inspector General for Iraq Reconstruction: Quarterly Report and Semiannual Report to the United States Congress

    Science.gov (United States)

    2007-07-30

    Sector engineers, who provided day-to-day technical supervision and implementation management of GRD’s plan to bring Units 5 and 6 online . GRD...fax, and online contacts from people in Iraq, the United States, and throughout the world. Second quarter Reporting As of June 30, 2007, SIGIR...Task Force for Iraq Reconstruction SPOC Sector Project and Contracting Office Contractor TAMU Texas A&M University TBI Trade Bank of Iraq TF-BSO

  19. The ancestral gene repertoire of animal stem cells.

    Science.gov (United States)

    Alié, Alexandre; Hayashi, Tetsutaro; Sugimura, Itsuro; Manuel, Michaël; Sugano, Wakana; Mano, Akira; Satoh, Nori; Agata, Kiyokazu; Funayama, Noriko

    2015-12-22

    Stem cells are pivotal for development and tissue homeostasis of multicellular animals, and the quest for a gene toolkit associated with the emergence of stem cells in a common ancestor of all metazoans remains a major challenge for evolutionary biology. We reconstructed the conserved gene repertoire of animal stem cells by transcriptomic profiling of totipotent archeocytes in the demosponge Ephydatia fluviatilis and by tracing shared molecular signatures with flatworm and Hydra stem cells. Phylostratigraphy analyses indicated that most of these stem-cell genes predate animal origin, with only few metazoan innovations, notably including several partners of the Piwi machinery known to promote genome stability. The ancestral stem-cell transcriptome is strikingly poor in transcription factors. Instead, it is rich in RNA regulatory actors, including components of the "germ-line multipotency program" and many RNA-binding proteins known as critical regulators of mammalian embryonic stem cells.

  20. Reconstruction of Optical Schr\\"odinger Kitten States Solely with Continuous Variable Field Measurements

    CERN Document Server

    Chrzanowski, H M; Sparkes, B M; Hage, B; Lund, A P; Ralph, T C; Lam, P K; Symul, T

    2011-01-01

    The Schr\\"odinger Cat gedankenexperiment, which considers the quantum superposition of the dead and alive states of a household pet, is a quintessential example of the enigmatic nature of quantum physics. Optical Schr\\"odinger cats, commonly defined as the quantum super- position of two classically distinguishable coherent states, have applications in quantum communications, metrology and quantum computing. To deterministically generate such states requires extreme nonlinearity with negligible losses. An alternative to this experimental difficulty is to introduce non- Gaussian post-selective measurements. For example, photon-counting can be exploited to conditionally herald non-Gaussian states, while field measurements are subsequently used to characterise them. These `hybrid' experiments face the challenges arising from simultaneously measuring both the wave and particle proper- ties of light. In this letter, we demonstrate a method to reconstruct non-Gaussian states solely with continuous variable field mea...

  1. Measurement of the B^0 and B^+ meson lifetimes with fully reconstructed hadronic final states

    CERN Document Server

    Aubert, Bernard

    2001-01-01

    The B0 and B+ meson lifetimes have been measured in e+e- annihilation data collected in 1999 and 2000 with the BABAR detector at center-of-mass energies near the Upsilon(4S) resonance. Events are selected in which one B meson is fully reconstructed in a hadronic final state while the second B meson is reconstructed inclusively. A combined fit to the B0 and the B+ decay time difference distributions yields tau_{B0} = 1.546 +/- 0.032 (stat) +/- 0.022(syst) ps, tau_{B+} = 1.673 +/- 0.032 (stat) +/- 0.023 (syst) ps and tau_{B+} / tau_{B0} = 1.082 +/- 0.026 (stat) +/- 0.012 (syst).

  2. Measurement of the B(0) and B(+) meson lifetimes with fully reconstructed hadronic final states.

    Science.gov (United States)

    Aubert, B; Boutigny, D; Gaillard, J M; Hicheur, A; Karyotakis, Y; Lees, J P; Robbe, P; Tisserand, V; Palano, A; Chen, G P; Chen, J C; Qi, N D; Rong, G; Wang, P; Zhu, Y S; Eigen, G; Reinertsen, P L; Stugu, B; Abbott, B; Abrams, G S; Borgland, A W; Breon, A B; Brown, D N; Button-Shafer, J; Cahn, R N; Clark, A R; Gill, M S; Gritsan, A; Groysman, Y; Jacobsen, R G; Kadel, R W; Kadyk, J; Kerth, L T; Kluth, S; Kolomensky, Y G; Kral, J F; LeClerc, C; Levi, M E; Liu, T; Lynch, G; Meyer, A B; Momayezi, M; Oddone, P J; Perazzo, A; Pripstein, M; Roe, N A; Romosan, A; Ronan, M T; Shelkov, V G; Telnov, A V; Wenzel, W A; Bright-Thomas, P G; Harrison, T J; Hawkes, C M; Knowles, D J; O'Neale, S W; Penny, R C; Watson, A T; Watson, N K; Deppermann, T; Goetzen, K; Koch, H; Krug, J; Kunze, M; Lewandowski, B; Peters, K; Schmuecker, H; Steinke, M; Andress, J C; Barlow, N R; Bhimji, W; Chevalier, N; Clark, P J; Cottingham, W N; De Groot, N; Dyce, N; Foster, B; McFall, J D; Wallom, D; Wilson, F F; Abe, K; Hearty, C; Mattison, T S; McKenna, J A; Thiessen, D; Jolly, S; McKemey, A K; Tinslay, J; Blinov, V E; Bukin, A D; Bukin, D A; Buzykaev, A R; Golubev, V B; Ivanchenko, V N; Korol, A A; Kravchenko, E A; Onuchin, A P; Salnikov, A A; Serednyakov, S I; Skovpen, Y I; Telnov, V I; Yushkov, A N; Best, D; Lankford, A J; Mandelkern, M; McMahon, S; Stoker, D P; Ahsan, A; Arisaka, K; Buchanan, C; Chun, S; Branson, J G; MacFarlane, D B; Prell, S; Rahatlou, S; Raven, G; Sharma, V; Campagnari, C; Dahmes, B; Hart, P A; Kuznetsova, N; Levy, S L; Long, O; Lu, A; Richman, J D; Verkerke, W; Witherell, M; Yellin, S; Beringer, J; Dorfan, D E; Eisner, A M; Frey, A; Grillo, A A; Grothe, M; Heusch, C A; Johnson, R P; Kroeger, W; Lockman, W S; Pulliam, T; Sadrozinski, H; Schalk, T; Schmitz, R E; Schumm, B A; Seiden, A; Turri, M; Walkowiak, W; Williams, D C; Wilson, M G; Chen, E; Dubois-Felsmann, G P; Dvoretskii, A; Hitlin, D G; Metzler, S; Oyang, J; Porter, F C; Ryd, A; Samuel, A; Weaver, M; Yang, S; Zhu, R Y; Devmal, S; Geld, T L; Jayatilleke, S; Mancinelli, G; Meadows, B T; Sokoloff, M D; Barillari, T; Bloom, P; Dima, M O; Fahey, S; Ford, W T; Johnson, D R; Nauenberg, U; Olivas, A; Park, H; Rankin, P; Roy, J; Sen, S; Smith, J G; van Hoek, W C; Wagner, D L; Blouw, J; Harton, J L; Krishnamurthy, M; Soffer, A; Toki, W H; Wilson, R J; Zhang, J; Brandt, T; Brose, J; Colberg, T; Dahlinger, G; Dickopp, M; Dubitzky, R S; Maly, E; Müller-Pfefferkorn, R; Otto, S; Schubert, K R; Schwierz, R; Spaan, B; Wilden, L; Behr, L; Bernard, D; Bonneaud, G R; Brochard, F; Cohen-Tanugi, J; Ferrag, S; Roussot, E; T'Jampens, S; Thiebaux, C; Vasileiadis, G; Verderi, M; Anjomshoaa, A; Bernet, R; Khan, A; Muheim, F; Playfer, S; Swain, J E; Falbo, M; Borean, C; Bozzi, C; Dittongo, S; Folegani, M; Piemontese, L; Treadwell, E; Anulli, F; Baldini-Ferroli, R; Calcaterra, A; de Sangro, R; Falciai, D; Finocchiaro, G; Patteri, P; Peruzzi, I M; Piccolo, M; Xie, Y; Zallo, A; Bagnasco, S; Buzzo, A; Contri, R; Crosetti, G; Fabbricatore, P; Farinon, S; Lo Vetere, M; Macri, M; Monge, M R; Musenich, R; Pallavicini, M; Parodi, R; Passaggio, S; Pastore, F C; Patrignani, C; Pia, M G; Priano, C; Robutti, E; Santroni, A; Morii, M; Bartoldus, R; Dignan, T; Hamilton, R; Mallik, U; Cochran, J; Crawley, H B; Fischer, P A; Lamsa, J; Meyer, W T; Rosenberg, E I; Benkebil, M; Grosdidier, G; Hast, C; Höcker, A; Lacker, H M; LePeltier, V; Lutz, A M; Plaszczynski, S; Schune, M H; Trincaz-Duvoid, S; Valassi, A; Wormser, G; Bionta, R M; Brigljević, V; Lange, D J; Mugge, M; Shi, X; van Bibber, K; Wenaus, T J; Wright, D M; Wuest, C R; Carroll, M; Fry, J R; Gabathuler, E; Gamet, R; George, M; Kay, M; Payne, D J; Sloane, R J; Touramanis, C; Aspinwall, M L; Bowerman, D A; Dauncey, P D; Egede, U; Eschrich, I; Gunawardane, N J; Nash, J A; Sanders, P; Smith, D; Azzopardi, D E; Back, J J; Dixon, P; Harrison, P F; Potter, R J; Shorthouse, H W; Strother, P; Vidal, P B; Williams, M I; Cowan, G; George, S; Green, M G; Kurup, A; Marker, C E; McGrath, P; McMahon, T R; Ricciardi, S; Salvatore, F; Scott, I; Vaitsas, G; Brown, D; Davis, C L; Allison, J; Barlow, R J; Boyd, J T; Forti, A C; Fullwood, J; Jackson, F; Lafferty, G D; Savvas, N; Simopoulos, E T; Weatherall, J H; Farbin, A; Jawahery, A; Lillard, V; Olsen, J; Roberts, D A; Schieck, J R; Blaylock, G; Dallapiccola, C; Flood, K T; Hertzbach, S S; Kofler, R; Moore, T B; Staengle, H; Willocq, S; Brau, B; Cowan, R; Sciolla, G; Taylor, F; Yamamoto, R K; Milek, M; Patel, P M; Trischuk, J; Lanni, F; Palombo, F; Bauer, J M; Booke, M; Cremaldi, L; Eschenburg, V; Kroeger, R; Reidy, J; Sanders, D A; Summers, D J; Martin, J P; Nief, J Y; Seitz, R; Taras, P; Zacek, V; Nicholson, H; Sutton, C S; Cartaro, C; Cavallo, N; De Nardo, G; Fabozzi, F; Gatto, C; Lista, L; Paolucci, P; Piccolo, D; Sciacca, C; LoSecco, J M; Alsmiller, J R; Gabriel, T A; Handler, T; Brau, J; Frey, R; Iwasaki, M; Sinev, N B; Strom, D; Colecchia, F; Dal Corso, F; Dorigo, A; Galeazzi, F; Margoni, M; Michelon, G; Morandin, M; Posocco, M; Rotondo, M; Simonetto, F; Stroili, R; Torassa, E; Voci, C; Benayoun, M; Briand, H; Chauveau, J; David, P; De la Vaissière, C; Del Buono, L; Hamon, O; Le Diberder, F; Leruste, P; Lory, J; Roos, L; Stark, J; Versillé, S; Manfredi, P F; Re, V; Speziali, V; Frank, E D; Gladney, L; Guo, Q H; Panetta, J H; Angelini, C; Batignani, G; Bettarini, S; Bondioli, M; Carpinelli, M; Forti, F; Giorgi, M A; Lusiani, A; Martinez-Vidal, F; Morganti, M; Neri, N; Paoloni, E; Rama, M; Rizzo, G; Sandrelli, F; Simi, G; Triggiani, G; Walsh, J; Haire, M; Judd, D; Paick, K; Turnbull, L; Wagoner, D E; Albert, J; Bula, C; Elmer, P; Lu, C; McDonald, K T; Miftakov, V; Schaffner, S F; Smith, A J; Tumanov, A; Varnes, E W; Cavoto, G; del Re, D; Faccini, R; Ferrarotto, F; Ferroni, F; Fratini, K; Lamanna, E; Leonardi, E; Mazzoni, M A; Morganti, S; Piredda, G; Safai Tehrani, F; Serra, M; Voena, C; Christ, S; Waldi, R; Adye, T; Franek, B; Geddes, N I; Gopal, G P; Xella, S M; Aleksan, R; De Domenico, G; Emery, S; Gaidot, A; Ganzhur, S F; Hamel de Monchenault, G; Kozanecki, W; Langer, M; London, G W; Mayer, B; Serfass, B; Vasseur, G; Yeche, C; Zito, M; Copty, N; Purohit, M V; Singh, H; Yumiceva, F X; Adam, I; Anthony, P L; Aston, D; Baird, K; Bloom, E; Boyarski, A M; Bulos, F; Calderini, G; Claus, R; Convery, M R; Coupal, D P; Coward, D H; Dorfan, J; Doser, M; Dunwoodie, W; Field, R C; Glanzman, T; Godfrey, G L; Gowdy, S J; Grosso, P; Himel, T; Huffer, M E; Innes, W R; Jessop, C P; Kelsey, M H; Kim, P; Kocian, M L; Langenegger, U; Leith, D W; Luitz, S; Luth, V; Lynch, H L; Marsiske, H; Menke, S; Messner, R; Moffeit, K C; Mount, R; Muller, D R; O'Grady, C P; Perl, M; Petrak, S; Quinn, H; Ratcliff, B N; Robertson S H; Rochester, L S; Roodman, A; Schietinger, T; Schindler, R H; Schwiening, J; Serbo, V V; Snyder, A; Soha, A; Spanier, S M; Stelzer, J; Su, D; Sullivan, M K; Tanaka, H A; Va'vra, J; Wagner, S R; Weinstein, A J; Wisniewski, W J; Wright, D W; Young, C C; Burchat, P R; Cheng, C H; Kirkby, D; Meyer, T I; Roat, C; Henderson, R; Bugg, W; Cohn, H; Weideman, A W; Izen, J M; Kitayama, L; Lou, X C; Turcotte, M; Bona, M; Di Girolamo, B; Gamba, D; Smol, A; Zanin, D; Lanceri, L; Pompili, A; Vaugnin, G; Panvini, R S; Brown, C M; De Silva, A; Kowalewski, R; Roney, J M; Band, H R; Charles, E; Dasu, S; Di Lodovico, F; Eichenbaum, A M; Hu, H; Johnson, J R; Liu, R; Nielsen, J; Pan, Y; Prepost, R; Scott, I J; Sekula, S J; von Wimmersperg-Toeller, J H; Wu, S L; Yu, Z; Zobernig, H; Kordich, T M; Neal, H

    2001-11-12

    The B(0) and B(+) meson lifetimes have been measured in e(+)e(-) annihilation data collected in 1999 and 2000 with the BABAR detector at center-of-mass energies near the Upsilon(4S) resonance. Events are selected in which one B meson is fully reconstructed in a hadronic final state while the second B meson is reconstructed inclusively. A combined fit to the B(0) and the B(+) decay time difference distributions yields tau(B(0)) = 1.546+/-0.032(stat)+/-0.022(syst) ps, tau(B(+)) = 1.673+/-0.032(stat)+/-0.023(syst) ps, and tau(B(+))/tau(B(0)) = 1.082+/-0.026(stat)+/-0.012(syst).

  3. LICORS: Light Cone Reconstruction of States for Non-parametric Forecasting of Spatio-Temporal Systems

    CERN Document Server

    Goerg, Georg M

    2012-01-01

    We present a new, non-parametric forecasting method for data where continuous values are observed discretely in space and time. Our method, "light-cone reconstruction of states" (LICORS), uses physical principles to identify predictive states which are local properties of the system, both in space and time. LICORS discovers the number of predictive states and their predictive distributions automatically, and consistently, under mild assumptions on the data source. We provide an algorithm to implement our method, along with a cross-validation scheme to pick control settings. Simulations show that CV-tuned LICORS outperforms standard methods in forecasting challenging spatio-temporal dynamics. Our work provides applied researchers with a new, highly automatic method to analyze and forecast spatio-temporal data.

  4. Pre-mesozoic palinspastic reconstruction of the eastern great basin (Western United States).

    Science.gov (United States)

    Levy, M; Christie-Blick, N

    1989-09-29

    The Great Basin of the western United States has proven important for studies of Proterozoic and Paleozoic geology [2500 to 245 million years ago (Ma)] and has been central to the development of ideas about the mechanics of crustal shortening and extension. An understanding of the deformational history of this region during Mesozoic and Cenozoic time (245 Ma to the present) is required for palinspastic reconstruction of now isolated exposures of older geology in order to place these in an appropriate regional geographic context. Considerable advances in unraveling both the crustal shortening that took place during Mesozoic to early Cenozoic time (especially from about 150 to 50 Ma) and the extension of the past 37 million years have shown that earlier reconstructions need to be revised significantly. A new reconstruction is developed for rocks of middle Proterozoic to Early Cambrian age based on evidence that total shortening by generally east-vergent thrusts and folds was at least 104 to 135 kilometers and that the Great Basin as a whole accommodated approximately 250 kilometers of extension in the direction 287 degrees +/- 12 degrees between the Colorado Plateau and the Sierra Nevada. Extension is assumed to be equivalent at all latitudes because available paleomagnetic evidence suggests that the Sierra Nevada experienced little or no rotation with respect to the extension direction since the late Mesozoic. An estimate of the uncertainty in the amount of extension obtained from geological and paleomagnetic uncertainties increases northward from +/-56 kilometers at 36 degrees 30N to (-87)(+108) kilometers at 40 degrees N. On the basis of the reconstruction, the original width of the preserved part of the late Proterozoic and Early Cambrian basin was about 150 to 300 kilometers, about 60 percent of the present width, and the basin was oriented slightly more north-south with respect to present-day coordinates.

  5. Inference of Ancestral Recombination Graphs through Topological Data Analysis.

    Science.gov (United States)

    Cámara, Pablo G; Levine, Arnold J; Rabadán, Raúl

    2016-08-01

    The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands.

  6. Electronic states of zigzag graphene nanoribbons with edges reconstructed with topological defects

    Energy Technology Data Exchange (ETDEWEB)

    Pincak, R., E-mail: pincak@saske.sk [Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 043 53 Kosice (Slovakia); Bogoliubov Laboratory of Theoretical Physics, Joint Institute for Nuclear Research, 141980 Dubna, Moscow Region (Russian Federation); Smotlacha, J., E-mail: smota@centrum.cz [Bogoliubov Laboratory of Theoretical Physics, Joint Institute for Nuclear Research, 141980 Dubna, Moscow Region (Russian Federation); Faculty of Nuclear Sciences and Physical Engineering, Czech Technical University, Brehova 7, 110 00 Prague (Czech Republic); Osipov, V.A., E-mail: osipov@theor.jinr.ru [Bogoliubov Laboratory of Theoretical Physics, Joint Institute for Nuclear Research, 141980 Dubna, Moscow Region (Russian Federation)

    2015-10-15

    The energy spectrum and electronic density of states (DOS) of zigzag graphene nanoribbons with edges reconstructed with topological defects are investigated within the tight-binding method. In case of the Stone–Wales zz(57) edge the low-energy spectrum is markedly changed in comparison to the pristine zz edge. We found that the electronic DOS at the Fermi level is different from zero at any width of graphene nanoribbons. In contrast, for ribbons with heptagons only at one side and pentagons at another one the energy gap at the Fermi level is open and the DOS is equal to zero. The reason is the influence of uncompensated topological charges on the localized edge states, which are topological in nature. This behavior is similar to that found for the structured external electric potentials along the edges.

  7. Testing for causality in reconstructed state spaces by an optimized mixed prediction method

    Science.gov (United States)

    Krakovská, Anna; Hanzely, Filip

    2016-11-01

    In this study, a method of causality detection was designed to reveal coupling between dynamical systems represented by time series. The method is based on the predictions in reconstructed state spaces. The results of the proposed method were compared with outcomes of two other methods, the Granger VAR test of causality and the convergent cross-mapping. We used two types of test data. The first test example is a unidirectional connection of chaotic systems of Rössler and Lorenz type. The second one, the fishery model, is an example of two correlated observables without a causal relationship. The results showed that the proposed method of optimized mixed prediction was able to reveal the presence and the direction of coupling and distinguish causality from mere correlation as well.

  8. Reconstructing and analysing cellular states, space and time from gene expression profiles of many cells and single cells.

    Science.gov (United States)

    Francesconi, Mirko; Lehner, Ben

    2015-10-01

    Genome-wide gene expression profiling is a fast, cheap and standardised analysis that provides a high dimensional measurement of the state of a biological sample. In this review we describe computational methods that can be applied to identify and interpret sources of variance in gene expression in whole organisms, organs, tissues or single cells. This allows the identification of constituent cell types and states in complex mixtures, the reconstruction of temporal trajectories of development, differentiation and progression, and the reconstruction of spatial patterning. When applied to genetically variable samples, these methods allow the efficient investigation of how genetic variation influences gene expression and biological processes in space and time.

  9. Petrologic, tectonic, and metallogenic evolution of the Ancestral Cascades magmatic arc, Washington, Oregon, and northern California

    Science.gov (United States)

    du Bray, Edward A.; John, David A.

    2011-01-01

    Present-day High Cascades arc magmatism was preceded by ~40 m.y. of nearly cospatial magmatism represented by the ancestral Cascades arc in Washington, Oregon, and northernmost California (United States). Time-space-composition relations for the ancestral Cascades arc have been synthesized from a recent compilation of more than 4000 geochemical analyses and associated age data. Neither the composition nor distribution of ancestral Cascades magmatism was uniform along the length of the ancestral arc through time. Initial (>40 to 36 Ma) ancestral Cascades magmatism (mostly basalt and basaltic andesite) was focused at the north end of the arc between the present-day locations of Mount Rainier and the Columbia River. From 35 to 18 Ma, initial basaltic andesite and andesite magmatism evolved to include dacite and rhyolite; magmatic activity became more voluminous and extended along most of the arc. Between 17 and 8 Ma, magmatism was focused along the part of the arc coincident with the northern two-thirds of Oregon and returned to more mafic compositions. Subsequent ancestral Cascades magmatism was dominated by basaltic andesite to basalt prior to the post–4 Ma onset of High Cascades magmatism. Transitional tholeiitic to calc-alkaline compositions dominated early (before 40 to ca. 25 Ma) ancestral Cascades eruptive products, whereas the majority of the younger arc rocks have a calc-alkaline affinity. Tholeiitic compositions characteristic of the oldest ancestral arc magmas suggest development associated with thin, immature crust and slab window processes, whereas the younger, calc-alkaline magmas suggest interaction with thicker, more evolved crust and more conventional subduction-related magmatic processes. Presumed changes in subducted slab dip through time also correlate with fundamental magma composition variation. The predominance of mafic compositions during latest ancestral arc magmatism and throughout the history of modern High Cascades magmatism probably

  10. Reconstructions of the dark-energy equation of state and the inflationary potential

    CERN Document Server

    Barrow, John D

    2016-01-01

    We use a new mathematical approach to reconstruct the equation of state and the inflationary potential for the inflaton field from the spectral indices for the density perturbations $n_{s}$ and the tensor to scalar ratio $r$. According to the astronomical data, the measured values of these two indices lie on a two-dimensional surface. We express these indices in terms of the Hubble slow-roll parameters and we assume that $n_{s}-1=h\\left( r\\right) $. For the function $h\\left( r\\right) $, we consider three cases, where $h\\left( r\\right) $ is constant, linear and quadratic, respectively. From this, we derive second-order equations whose solutions provide us with the explicit forms for the expansion scale-factor, the scalar-field potential, and the effective equation of state for the scalar field. Finally, we show that for there exist mappings which transform one cosmological solution to another and allow new solutions to be generated from existing ones.

  11. Ancestral Area Analysis of the Genus Caragara (Leguminosae)

    Institute of Scientific and Technical Information of China (English)

    ZHANGMing-Li

    2004-01-01

    Caragana has a temperate Asian distribution. Based on the phylogeny and 13 distributionalareas of this genus, its ancestral area was studied via the ancestral area analysis suggested by Bremer(1992), Ronquist (1994) and Hausdorf (1997). The results indicate that three areas, Far East-NortheastChina, Altai-Sayan and North China-Qinling Mountains (Mts) are likely the ancestral areas. Linking to theviewpoints of the Holarctic origin for north temperate flora, Far East-Northeast China seems more likely tobe the ancestral area. According to the three ancestral areas isolated geographically and the analysis inthe present study, as well as former biogeographical analysis of this genus, it is suggested that Caraganaspeciation is mainly in the mode of vicariance rather than dispersal, and dispersed is often in shortdistance.

  12. Reconstructing Equation of State for Dark Energy in Double Complex Symmetric Gravitational Theory

    Institute of Scientific and Technical Information of China (English)

    SHAO Ying; GUI Yuan-Xing; WANG Wei

    2007-01-01

    We propose to study the accelerating expansion of the universe in the double complex symmetric gravitational theory (DCSGT). The universe we live in is taken as the real part of the whole spacetime M4C(J), which is double complex. By introducing the spatially flat FRW metric, not only the double Friedmann equations but also the two constraint conditions pJ = 0 and J2 = 1 are obtained. Furthermore, using parametric DL(z) ansatz, we reconstruct the ω′(z) and V(φ) for dark energy from real observational data. We find that in the two cases of J = i, pJ = 0, and J = ε, pJ ≠ 0, the corresponding equations of state ω′(z) remain close to -1 at present (z = 0) and change from below -1 to above -1. The results illustrate that the whole spacetime, i.e. the double complex spacetime M4C(J), may be either ordinary complex (J = i, pJ = 0) or hyperbolic complex (J = ε, pJ ≠ 0). And the fate of the universe would be Big Rip in the future.

  13. Stoichiometric network reconstruction and analysis of yeast sphingolipid metabolism incorporating different states of hydroxylation.

    Science.gov (United States)

    Kavun Ozbayraktar, Fatma Betul; Ulgen, Kutlu O

    2011-04-01

    The first elaborate metabolic model of Saccharomyces cerevisiae sphingolipid metabolism was reconstructed in silico. The model considers five different states of sphingolipid hydroxylation, rendering it unique among other models. It is aimed to clarify the significance of hydroxylation on sphingolipids and hence to interpret the preferences of the cell between different metabolic pathway branches under different stress conditions. The newly constructed model was validated by single, double and triple gene deletions with experimentally verified phenotypes. Calcium sensitivity and deletion mutations that may suppress calcium sensitivity were examined by CSG1 and CSG2 related deletions. The model enabled the analysis of complex sphingolipid content of the plasma membrane coupled with diacylglycerol and phosphatidic acid biosynthesis and ATP consumption in in silico cell. The flux data belonging to these critically important key metabolites are integrated with the fact of phytoceramide induced cell death to propose novel potential drug targets for cancer therapeutics. In conclusion, we propose that IPT1, GDA1, CSG and AUR1 gene deletions may be novel candidates of drug targets for cancer therapy according to the results of flux balance and variability analyses coupled with robustness analysis.

  14. Optimal quasifree approximation: Reconstructing the spectrum from ground-state energies

    Science.gov (United States)

    Campos Venuti, Lorenzo

    2011-07-01

    The sequence of ground-state energy density at finite size, eL, provides much more information than usually believed. Having at our disposal eL for short lattice sizes, we show how to reconstruct an approximate quasiparticle dispersion for any interacting model. The accuracy of this method relies on the best possible quasifree approximation to the model, consistent with the observed values of the energy eL. We also provide a simple criterion to assess whether such a quasifree approximation is valid. As a side effect, our method is able to assess whether the nature of the quasiparticles is fermionic or bosonic together with the effective boundary conditions of the model. When applied to the spin-1/2 Heisenberg model, the method produces a band of Fermi quasiparticles very close to the exact one of des Cloizeaux and Pearson. The method is further tested on a spin-1/2 Heisenberg model with explicit dimerization and on a spin-1 chain with single-ion anisotropy. A connection with the Riemann hypothesis is also pointed out.

  15. Chromium isotopes in carbonates — A tracer for climate change and for reconstructing the redox state of ancient seawater

    DEFF Research Database (Denmark)

    Frei, Robert; Gaucher, Claudio; Døssing, Lasse Nørbye

    2011-01-01

    Strontium and carbon isotopes of marine carbonates are routinely applied for chemostratigraphic cross correlations of time-equivalent sedimentary sequences and for calibration of the compositional evolution of seawater throughout Earth's history, mainly for the purpose of reconstructing ancient.......708, and lower 147Sm/144Nd values of ~0.11, a source which is strongly affected by continentally derived input. Chromium isotopes provide a powerful tool for reconstructing the redox state of ancient seawater since positive values indicate that, at least locally, Neoproterozoic shallow ocean waters were......, glaciation acts as an amplifier of d53Cr signals. These signals in marine carbonates are a sensitive tracer for redox processes in the ocean and/or on land and have the potential to contribute significantly, in combination with the other commonly used isotopic tracers, to the reconstruction of climatic...

  16. Quantum Oscillations in the Parent pnictide BaFe2As2 : Itinerant Electrons in the Reconstructed State

    Energy Technology Data Exchange (ETDEWEB)

    Analytis, J.G.

    2010-05-26

    We report quantum oscillation measurements that enable the direct observation of the Fermi surface of the low temperature ground state of BaFe{sub 2}As{sub 2}. From these measurements we characterize the low energy excitations, revealing that the Fermi surface is reconstructed in the antiferromagnetic state, but leaving itinerant electrons in its wake. The present measurements are consistent with a conventional band folding picture of the antiferromagnetic ground state, placing important limits on the topology and size of the Fermi surface.

  17. Long-term dust climatology in the western United States reconstructed from routine aerosol ground monitoring

    Directory of Open Access Journals (Sweden)

    D. Q. Tong

    2012-06-01

    Full Text Available This study introduces an observation-based dust identification approach and applies it to reconstruct long-term dust climatology in the western United States. Long-term dust climatology is important for quantifying the effects of atmospheric aerosols on regional and global climate. Although many routine aerosol monitoring networks exist, it is often difficult to obtain dust records from these networks, because these monitors are either deployed far away from dust active regions (most likely collocated with dense population or contaminated by anthropogenic sources and other natural sources, such as wildfires and vegetation detritus. Here we propose an approach to identify local dust events relying solely on aerosol mass and composition from general-purpose aerosol measurements. Through analyzing the chemical and physical characteristics of aerosol observations during satellite-detected dust episodes, we select five indicators to be used to identify local dust records: (1 high PM10 concentrations; (2 low PM2.5/PM10 ratio; (3 higher concentrations and percentage of crustal elements; (4 lower percentage of anthropogenic pollutants; and (5 low enrichment factors of anthropogenic elements. After establishing these identification criteria, we conduct hierarchical cluster analysis for all validated aerosol measurement data over 68 IMPROVE sites in the western United States. A total of 182 local dust events were identified over 30 of the 68 locations from 2000 to 2007. These locations are either close to the four US Deserts, namely the Great Basin Desert, the Mojave Desert, the Sonoran Desert, and the Chihuahuan Desert, or in the high wind power region (Colorado. During the eight-year study period, the total number of dust events displays an interesting four-year activity cycle (one in 2000–2003 and the other in 2004–2007. The years of 2003, 2002 and 2007 are the three most active dust periods, with 46, 31 and 24

  18. Description of Colponema vietnamica sp.n. and Acavomonas peruviana n. gen. n. sp., two new alveolate phyla (Colponemidia nom. nov. and Acavomonidia nom. nov. and their contributions to reconstructing the ancestral state of alveolates and eukaryotes.

    Directory of Open Access Journals (Sweden)

    Denis V Tikhonenkov

    Full Text Available The evolutionary and ecological importance of predatory flagellates are too often overlooked. This is not only a gap in our understanding of microbial diversity, but also impacts how we interpret their better-studied relatives. A prime example of these problems is found in the alveolates. All well-studied species belong to three large clades (apicomplexans, dinoflagellates, and ciliates, but the predatory colponemid flagellates are also alveolates that are rare in nature and seldom cultured, but potentially important to our understanding of alveolate evolution. Recently we reported the first cultivation and molecular analysis of several colponemid-like organisms representing two novel clades in molecular trees. Here we provide ultrastructural analysis and formal species descriptions for both new species, Colponema vietnamica n. sp. and Acavomonas peruviana n. gen. n. sp. Morphological and feeding characteristics concur with molecular data that both species are distinct members of alveolates, with Acavomonas lacking the longitudinal phagocytotic groove, a defining feature of Colponema. Based on ultrastructure and molecular phylogenies, which both provide concrete rationale for a taxonomic reclassification of Alveolata, we establish the new phyla Colponemidia nom. nov. for the genus Colponema and its close relatives, and Acavomonidia nom. nov. for the genus Acavomonas and its close relatives. The morphological data presented here suggests that colponemids are central to our understanding of early alveolate evolution, and suggest they also retain features of the common ancestor of all eukaryotes.

  19. Why Meillassoux’s Speculative Materialism Struggles with Ancestrality

    Directory of Open Access Journals (Sweden)

    Ciprian Jeler

    2014-12-01

    Full Text Available This paper shows that Quentin Meillassoux’s speculative materialism doesn’t offer us the means to account for the ancestral statements that the modern sciences produce, i.e. for the scientific statements about events preceding all forms of life. An analysis of the reasons why Meillassoux thinks that the problem of ancestrality problematizes the contemporary self-evidence of correlationism is first offered. The results of this analysis are then applied to speculative materialism itself and the consequences are not very promising: very much like correlationism, speculative materialism explicitly denies what I call the “generalized version of the realistic assumption of science” and, in so doing, renders scientific ancestral statements de jure unverifiable. Therefore, if correlationism is rendered suspicious by the issue of ancestrality, the same can be said of speculative materialism.

  20. Reconstruction of the solar spectral UV irradiance for nowcasting of the middle atmosphere state on the basis of LYRA measurements

    Directory of Open Access Journals (Sweden)

    T. Egorova

    2008-02-01

    Full Text Available The LYRA instrument onboard ESA PROBA2 satellite will provide 6-hourly solar irradiance at the Lyman-alpha (121.6 nm and the Herzberg continuum (~200–220 nm wavelength range. Because the nowcasting of the neutral and ionic state of the middle atmosphere requires the solar irradiance for the wide spectral area (120–680 nm we have developed the statistical tool for the reconstruction of the full spectrum from the LYRA measurements. The accuracy of the reconstructed irradiance has been evaluated with 1-D transient radiative-convective model with neutral and ion chemistry using the daily solar spectral irradiance measured with SUSIM and SOLSTICE instruments onboard UARS satellite. We compared the results of transient 1-yr long model simulations for 2000 driven by the observed and reconstructed solar irradiance and showed that the reconstruction of the full spectrum using linear regression equation based on the solar irradiance in two LYRA channels can be successfully used for nowcasting of the middle atmosphere. We have also defined some conditions when the proposed approach does not provide reasonable accuracy.

  1. Special Inspector General for Iraq Reconstruction Quarterly Report to the United States Congress

    Science.gov (United States)

    2009-10-30

    and to introduce salt-tolerant Bermuda grass into Iraq674 Th e PRT also met with German investors in- terested in establishing car dealerships in... Triangle Institute International SET Security Escort Team SIGAR Special Inspector General for Afghanistan Reconstruction SIGIR Special Inspector

  2. Evaluation of state-of-the-art hardware architectures for fast cone-beam CT reconstruction

    CERN Document Server

    Scherl, Holger

    2011-01-01

    Holger Scherl introduces the reader to the reconstruction problem in computed tomography and its major scientific challenges that range from computational efficiency to the fulfillment of Tuy's sufficiency condition. The assessed hardware architectures include multi- and many-core systems, cell broadband engine architecture, graphics processing units, and field programmable gate arrays.

  3. Community incidence of pathogen-specific gastroenteritis: reconstructing the surveillance pyramid for seven pathogens in seven European Union member states.

    Science.gov (United States)

    Haagsma, J A; Geenen, P L; Ethelberg, S; Fetsch, A; Hansdotter, F; Jansen, A; Korsgaard, H; O'Brien, S J; Scavia, G; Spitznagel, H; Stefanoff, P; Tam, C C; Havelaar, A H

    2013-08-01

    By building reconstruction models for a case of gastroenteritis in the general population moving through different steps of the surveillance pyramid we estimated that millions of illnesses occur annually in the European population, leading to thousands of hospitalizations. We used data on the healthcare system in seven European Union member states in relation to pathogen characteristics that influence healthcare seeking. Data on healthcare usage were obtained by harmonized cross-sectional surveys. The degree of under-diagnosis and underreporting varied by pathogen and country. Overall, underreporting and under-diagnosis were estimated to be lowest for Germany and Sweden, followed by Denmark, The Netherlands, UK, Italy and Poland. Across all countries, the incidence rate was highest for Campylobacter spp. and Salmonella spp. Incidence estimates resulting from the pyramid reconstruction approach are adjusted for biases due to different surveillance systems and are therefore a better basis for international comparisons than reported data.

  4. The reconstructed final state of Pb + Pb 158 AGeV reactions from spectra and correlation data of NA49, NA44 and WA98

    CERN Document Server

    Ster, A; Lörstad, B; Ster, Andras; Csorgo, Tamas; Lorstad, Bengt

    1999-01-01

    The final state of Pb + Pb reactions at CERN SPS has been reconstructed with the Buda-Lund hydro model, by performing a simultaneous fit to NA49, NA44 and WA98 data on particle correlations and spectra.

  5. Cost of Outpatient Arthroscopic Anterior Cruciate Ligament Reconstruction Among Commercially Insured Patients in the United States, 2005-2013

    Science.gov (United States)

    Herzog, Mackenzie M.; Marshall, Stephen W.; Lund, Jennifer L.; Pate, Virginia; Spang, Jeffrey T.

    2017-01-01

    Background: Despite the significance of anterior cruciate ligament (ACL) injuries, these conditions have been under-researched from a population-level perspective. It is important to determine the economic effect of these injuries in order to document the public health burden in the United States. Purpose: To describe the cost of outpatient arthroscopic ACL reconstruction and health care utilization among commercially insured beneficiaries in the United States. Study Design: Economic and decision analysis; Level of evidence, 3. Methods: The study used the Truven Health Analytics MarketScan Commercial Claims and Encounters database, an administrative claims database that contains a large sample (approximately 148 million) of privately insured individuals aged <65 years and enrolled in employer-sponsored plans. All claims with Current Procedural Terminology (CPT) code 29888 (arthroscopically aided ACL reconstruction or augmentation) from 2005 to 2013 were included. “Immediate procedure” cost was computed assuming a 3-day window of care centered on date of surgery. “Total health care utilization” cost was computed using a 9-month window of care (3 months preoperative and 6 months postoperative). Results: There were 229,446 outpatient arthroscopic ACL reconstructions performed over the 9-year study period. Median immediate procedure cost was $9399.49. Median total health care utilization cost was $13,403.38. Patients who underwent concomitant collateral ligament (medial [MCL], lateral [LCL]) repair or reconstruction had the highest costs for both immediate procedure ($12,473.24) and health care utilization ($17,006.34). For patients who had more than 1 reconstruction captured in the database, total health care utilization costs were higher for the second procedure than the first procedure ($16,238.43 vs $15,000.36), despite the fact that immediate procedure costs were lower for second procedures ($8685.73 vs $9445.26). Conclusion: These results provide a

  6. Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states

    DEFF Research Database (Denmark)

    Cho, Byung-Kwan; Kim, Donghyuk; Knight, Eric M.

    2014-01-01

    to transcription units (TUs), representing an increase of more than 300% over what has been previously reported. The reconstructed network was used to investigate competition between alternative sigma-factors (the sigma(70) and sigma(38) regulons), confirming the competition model of sigma substitution......Background: At the beginning of the transcription process, the RNA polymerase (RNAP) core enzyme requires a sigma-factor to recognize the genomic location at which the process initiates. Although the crucial role of sigma-factors has long been appreciated and characterized for many individual...... promoters, we do not yet have a genome-scale assessment of their function. Results: Using multiple genome-scale measurements, we elucidated the network of s-factor and promoter interactions in Escherichia coli. The reconstructed network includes 4,724 sigma-factor-specific promoters corresponding...

  7. OSSEOINTEGRATION IN RECONSTRUCTIVE SURGERY: CONTEMPORARY STATE AND PERSPECTIVES OF FURHTHER DEVELOPMENT (REVIEW

    Directory of Open Access Journals (Sweden)

    M. A. Shevtsov

    2012-01-01

    Full Text Available Method of intraosseous prosthesis based on the principle of osseointegration that was introduced by Prof. Per-Ingvar Branemark is one of the most perspective approaches in contemporary reconstructive surgery This method helps to achieve increased functional activity and to improve patients quality of life in comparison to conventional treatment. In presented article the results of prosthetic treatment of amputees of different localizations, application of this technology in cranio-fascial surgery, finger joint prostheses are discussed.

  8. Photon-number discrimination without a photon counter and its application to reconstructing non-Gaussian states

    Energy Technology Data Exchange (ETDEWEB)

    Chrzanowski, H. M.; Bernu, J.; Sparkes, B. M.; Hage, B.; Lam, P. K.; Symul, T. [Centre for Quantum Computation and Communication Technology, Quantum Optics group, Department of Quantum Science, Research School of Physics and Engineering, Australian National University, Canberra ACT 0200 (Australia); Lund, A. P. [Centre for Quantum Computation and Communication Technology, Centre for Quantum Dynamics, Griffith University, Nathan QLD 4111 (Australia); Ralph, T. C. [Centre for Quantum Computation and Communication Technology, Department of Physics, University of Queensland, St. Lucia QLD 4072 (Australia)

    2011-11-15

    The nonlinearity of a conditional photon-counting measurement can be used to ''de-Gaussify'' a Gaussian state of light. Here we present and experimentally demonstrate a technique for photon-number resolution using only homodyne detection. We then apply this technique to inform a conditional measurement, unambiguously reconstructing the statistics of the non-Gaussian one- and two-photon-subtracted squeezed vacuum states. Although our photon-number measurement relies on ensemble averages and cannot be used to prepare non-Gaussian states of light, its high efficiency, photon-number-resolving capabilities, and compatibility with the telecommunications band make it suitable for quantum-information tasks relying on the outcomes of mean values.

  9. On the historical biogeography of global Galliformes: ancestral range and diversification patterns

    Institute of Scientific and Technical Information of China (English)

    Youhua; Chen

    2014-01-01

    Background: In this study, the ancestral distributional ranges and the tempo of diversification patterns of global Galliformes were investigated.Methods: Different diversification models characterizing possible tempo patterns were fitted and compared onto the phylogenetic tree for the 197 Galliforme species, consisting of a constant-speciation and constant-extinction model(CONSTANT), a decreasing-speciation and constant-extinction model(SPVAR), a constant-speciation and increasing-extinction model(EXVAR) and a decreasing-speciation and increasing-extinction model(BOTHVAR).Ancestral range reconstruction was conducted using the dispersal-extinction-cladogenesis model.Results: A constant-diversification-rate(CONSTANT) model best quantified the historical speciation patterns of this avian assemblage through model selection. Clade age and species richness are significantly and positively correlated. The most recent common ancestor for Galliformes species was originally found in the disjunctive regions between Southeast Asia and North America. High-frequency dispersal events were identified across the whole evolutionary time.Conclusions: The constant diversification rate for global Galliforme species implied that there were no diversification rate-shifting trends for Galliformes species. The present study may contribute to the understanding of the ecology and diversity patterns of Galliformes from the perspective of historical biogeography, although some limitations existed.

  10. Cambrian cinctan echinoderms shed light on feeding in the ancestral deuterostome.

    Science.gov (United States)

    Rahman, Imran A; Zamora, Samuel; Falkingham, Peter L; Phillips, Jeremy C

    2015-11-07

    Reconstructing the feeding mode of the latest common ancestor of deuterostomes is key to elucidating the early evolution of feeding in chordates and allied phyla; however, it is debated whether the ancestral deuterostome was a tentaculate feeder or a pharyngeal filter feeder. To address this, we evaluated the hydrodynamics of feeding in a group of fossil stem-group echinoderms (cinctans) using computational fluid dynamics. We simulated water flow past three-dimensional digital models of a Cambrian fossil cinctan in a range of possible life positions, adopting both passive tentacular feeding and active pharyngeal filter feeding. The results demonstrate that an orientation with the mouth facing downstream of the current was optimal for drag and lift reduction. Moreover, they show that there was almost no flow to the mouth and associated marginal groove under simulations of passive feeding, whereas considerable flow towards the animal was observed for active feeding, which would have enhanced the transport of suspended particles to the mouth. This strongly suggests that cinctans were active pharyngeal filter feeders, like modern enteropneust hemichordates and urochordates, indicating that the ancestral deuterostome employed a similar feeding strategy.

  11. On the historical biogeography of global Galliformes:ancestral range and diversification patterns

    Institute of Scientific and Technical Information of China (English)

    Youhua Chen

    2014-01-01

    Background:In this study, the ancestral distributional ranges and the tempo of diversification patterns of global Galliformes were investigated. Methods:Different diversification models characterizing possible tempo patterns were fitted and compared onto the phylogenetic tree for the 197 Galliforme species, consisting of a constant-speciation and constant-extinction model (CONSTANT), a decreasing-speciation and constant-extinction model (SPVAR), a constant-speciation and increasing-extinction model (EXVAR) and a decreasing-speciation and increasing-extinction model (BOTHVAR). Ancestral range reconstruction was conducted using the dispersal-extinction-cladogenesis model. Results:A constant-diversification-rate (CONSTANT) model best quantified the historical speciation patterns of this avian assemblage through model selection. Clade age and species richness are significantly and positively correlated. The most recent common ancestor for Galliformes species was originally found in the disjunctive regions between Southeast Asia and North America. High-frequency dispersal events were identified across the whole evolutionary time. Conclusions:The constant diversification rate for global Gal iforme species implied that there were no diversification rate-shifting trends for Galliformes species. The present study may contribute to the understanding of the ecology and diversity patterns of Galliformes from the perspective of historical biogeography, although some limitations existed.

  12. The Road to Success: Importance of Construction on Reconstruction in Conflict-Affected States

    Science.gov (United States)

    2011-12-01

    state exhibits high capacity and control when it can collect income taxes from the population (Weller & Ziegler , 2008, p. 16). 4. Sustainable...have left” (DOA, 2008, p. C-2). Another benefit of the CDD approach tackles the difficult challenge of absorptive capacity of the state. The... absorptive capacity of the state by stimulating the demand through small manageable projects. This is done by creating jobs, growing state administrative

  13. Conceptual design of the PANDA luminosity monitor and reconstruction strategy to measure the width of the X(3872) state

    Energy Technology Data Exchange (ETDEWEB)

    Randriamalala, Tsitohaina

    2012-04-19

    The PANDA experiment has a great potential to test with high precision QCD in the low momentum transfer region using an antiproton beam of unprecedented quality. The resonance scan method will be used to determine the lineshape of specific hadronic states. It requires a precise knowledge of the luminosity. This thesis develops the conceptual design of the PANDA luminosity monitor and a scan simulation to determine the width resolution of the X(3872) state. The luminosity monitor concept is based on the reconstruction of elastically scattered antiprotons from the interaction region. Monte Carlo performance studies of the detector were carried out. The implementation test was done using a detector prototype instrumented at the COSY accelerator and testing it with proton beam. The studies show that a precision of better than 3% on the luminosity and a width resolution for the X(3872) of about 2% can be achieved.

  14. State space parsimonious reconstruction of attractor produced by an electronic oscillator

    Science.gov (United States)

    Aguirre, Luis A.; Freitas, Ubiratan S.; Letellier, Christophe; Sceller, Lois Le; Maquet, Jean

    2000-02-01

    This work discusses the reconstruction, from a set of real data, of a chaotic attractor produced by a well-known electronic oscillator, Chua's circuit. The mathematical representation used is a nonlinear differential equation of the polynomial type. One of the contributions of the present study is that structure selection techniques have been applied to help determine the regressors in the model. Models of the chaotic attractor obtained with and without structure selection were compared. The main differences between structure-selected models and complete structure models are: i) the former are more parsimonious that the latter, ii) fixed-point symmetry is guaranteed for the former, iii) for structure-selected models a trivial fixed point is also guaranteed, and iv) the former set of models produce attractors that are topologically closer to the original attractor than those produced by the complete structure models.

  15. 75 FR 52797 - State-68, Office of the Coordinator for Reconstruction and Stabilization Records

    Science.gov (United States)

    2010-08-27

    ... has the capability of printing audit trails of access from the computer media, thereby permitting regular and ad hoc monitoring of computer usage. When it is determined that a user no longer needs access... granted access to Department of State computer systems. Remote access to the Department of State...

  16. Special Inspector General for Afghanistan Reconstruction Quarterly Report to the United States Congress

    Science.gov (United States)

    2014-10-30

    terminated the contract for convenience . State also funded three capital-improvement projects—a potable-water tower, a commercial power upgrade, and...Million 37 SIGAR OVERSIGHT ACTIVITIES REPORT TO THE UNITED STATES CONGRESS I OCTOBER 30, 2014 convenience . INL paid AWCC $18.5 million of the $20.2...Abduzaziz, the owner of Aziz Restaurant and a bazaar, who was allegedly engaging in various criminal schemes on BAF, including vehicle thefts. The TCN

  17. Magmatism and Epithermal Gold-Silver Deposits of the Southern Ancestral Cascade Arc, Western Nevada and Eastern California

    Science.gov (United States)

    John, David A.; du Bray, Edward A.; Henry, Christopher D.; Vikre, Peter

    2015-01-01

    Many epithermal gold-silver deposits are temporally and spatially associated with late Oligocene to Pliocene magmatism of the southern ancestral Cascade arc in western Nevada and eastern California. These deposits, which include both quartz-adularia (low- and intermediate-sulfidation; Comstock Lode, Tonopah, Bodie) and quartz-alunite (high-sulfidation; Goldfield, Paradise Peak) types, were major producers of gold and silver. Ancestral Cascade arc magmatism preceded that of the modern High Cascades arc and reflects subduction of the Farallon plate beneath North America. Ancestral arc magmatism began about 45 Ma, continued until about 3 Ma, and extended from near the Canada-United States border in Washington southward to about 250 km southeast of Reno, Nevada. The ancestral arc was split into northern and southern segments across an inferred tear in the subducting slab between Mount Shasta and Lassen Peak in northern California. The southern segment extends between 42°N in northern California and 37°N in western Nevada and was active from about 30 to 3 Ma. It is bounded on the east by the northeast edge of the Walker Lane. Ancestral arc volcanism represents an abrupt change in composition and style of magmatism relative to that in central Nevada. Large volume, caldera-forming, silicic ignimbrites associated with the 37 to 19 Ma ignimbrite flareup are dominant in central Nevada, whereas volcanic centers of the ancestral arc in western Nevada consist of andesitic stratovolcanoes and dacitic to rhyolitic lava domes that mostly formed between 25 and 4 Ma. Both ancestral arc and ignimbrite flareup magmatism resulted from rollback of the shallowly dipping slab that began about 45 Ma in northeast Nevada and migrated south-southwest with time. Most southern segment ancestral arc rocks have oxidized, high potassium, calc-alkaline compositions with silica contents ranging continuously from about 55 to 77 wt%. Most lavas are porphyritic and contain coarse plagioclase

  18. Local observability of state variables and parameters in nonlinear modeling quantified by delay reconstruction

    CERN Document Server

    Parlitz, Ulrich; Luther, Stefan

    2015-01-01

    Features of the Jacobian matrix of the delay coordinates map are exploited for quantifying the robustness and reliability of state and parameter estimations for a given dynamical model using an observed time series. Relevant concepts of this approach are introduced and illustrated for discrete and continuous time systems employing a filtered H\\'enon map and a R\\"ossler system.

  19. Multi-Species Temperature and Proxy Reconstructions of the Tropical Pacific Mean State across Marine Isotope Stage 3

    Science.gov (United States)

    Hertzberg, J. E.; Schmidt, M. W.

    2015-12-01

    The current climatic mean state of the Pacific is characterized by trade wind induced upwelling of cold water in the east and accumulation of warm surface waters in the west, resulting in a strong E-W sea surface temperature (SST) gradient. The initiation and propagation of ENSO events are due to perturbations in this system. Changes in the mean state have the potential to alter ENSO-related processes, feedbacks, and properties. However, it remains unclear how ENSO feedbacks interact as the mean state changes - an increasingly important question as current climate warms, potentially altering the mean state. Here, we use the abrupt climate warming events of Marine Isotope Stage 3 from 32-64 kyr as a natural experiment for understanding how the tropical Pacific mean state varied across past periods of rapid climate warming. We measured Mg/Ca ratios in the thermocline dwelling planktonic foraminifera N. dutertrei as a proxy for thermocline temperature variability from Eastern Pacific sediment core MV1014-17JC (0°10.8'S, 85°52.0'W). Reconstructing subsurface temperatures removes the seasonal cycle imprint on SSTs, and instead, thermocline temperatures vary with ENSO conditions. Our record reveals that interstadial warming events are characterized by a more El Niño-like mean state, characterized by increased thermocline temperatures up to 6°C. Thermocline warming events are more pronounced from 64-44 kyr when overall global climate was in a warmer state. Moving from 44-32 kyr, our record shows cooler thermocline temperatures, suggesting a shift to a more La Niña-like mean state, as climate began transitioning into the Glacial Maximum. We also measured Mg/Ca ratios in the surface dwelling planktonic foraminifera G. ruber. Our G. ruber SST record displays the same cooling trend as the N. dutertrei record from 64-32 kyr. SSTs cool 1-1.5°C while thermocline temperatures cool 2.5-3°C. Preliminary comparison with a SST record from the Western Pacific suggests a

  20. Effects of different states of sheep fetal fibroblasts as donor cells on the early development in vitro of reconstructed sheep embryos

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    To investigate the effects of different states of donor cells on the development of reconstructed sheep embryos, we designed five treatments of donor cells, including cell passage, cell size, serum starvation, colchicine treatment and gene transfection. Results are as follows: (Ⅰ) Compared with 16-18 passage cells, the morula/blastocyst rate of 5-7 passage cells as donor nuclei was significantly higher (17.3% vs. 4.9%, P<0.05), suggesting the advantage of short-time cultured cells in supporting the development of reconstructed embryos. (Ⅱ) The morula/blastocyst rate of reconstructed embryos derived from medium cells (15-25μm) as donor nuclei was higher than that from large cells (25-33μm) and small cells (8-15μm)( 20.0% vs. 8.0%, 9.7%), indicating that reconstructed embryos from medium cells had a greater potentiality to develop into morula/blastocysts than those from small or large ones. (Ⅲ) The morula/blastocyst rate of reconstructed embryos from donor cells of SS (serum starvation) was lower than that from donor cells of NSS (non-serum starvation), but no significant difference was detected between SS and NSS(11.8% vs. 18.6%, P>0.05). (Ⅳ) Fetal fibroblasts treated with 0.05μmol/L colchicine exhibited a higher morula/blastocyst rate of reconstructed embryos than those treated with 0.10 μmol/L colchicine and untreated ones (27.5% vs. 12.1%, 17.1%), however, no significant difference among the three treatments was detected (P>0.05). (Ⅴ) The morula/blastocyst rate of reconstructed embryos from fetal fibroblasts transfected with GFP gene only was 3.1%, significantly lower than that from non-transgenic cells (3.1% vs. 20.4%, P<0.05). In conclusion, our results demonstrated that fetal fibroblasts of fewer passages, medium size could ensure a higher morula/blastocyst rate of reconstructed embryos. Serum starvation of donor cells might be unnecessary to the development of reconstructed embryos. Donor cells treated with 0.05μmol/L colchicine could

  1. Effects of different states of sheep fetal fibroblasts as donor cells on the early development in vitro of reconstructed sheep embryos

    Institute of Scientific and Technical Information of China (English)

    WANG Hai; AO Hong; PAN QiuZhen; LI RongQi; ZHAO MengBin; LIAN ZhengXing; LI Ning; WU ChangXin

    2007-01-01

    To investigate the effects of different states of donor cells on the development of reconstructed sheep embryos, we designed five treatments of donor cells, including cell passage, cell size, serum starvation,colchicine treatment and gene transfection. Results are as follows: ( Ⅰ ) Compared with 16-18 passage cells, the morula/blastocyst rate of 5-7 passage cells as donor nuclei was significantly higher (17.3%vs. 4.9%, P<0.05), suggesting the advantage of short-time cultured cells in supporting the development of reconstructed embryos. (Ⅱ) The morula/blastocyst rate of reconstructed embryos derived from medium cells (15-25 μm) as donor nuclei was higher than that from large cells (25-33 μm) and small cells (8-15 μm)( 20.0% vs. 8.0%, 9.7%), indicating that reconstructed embryos from medium cells had a greater potentiality to develop into morula/blastocysts than those from small or large ones. (Ⅲ) The morula/blastocyst rate of reconstructed embryos from donor cells of SS (serum starvation) was lower than that from donor cells of NSS (non-serum starvation), but no significant difference was detected between SS and NSS( 11.8% vs. 18.6%, P>0.05). (Ⅳ) Fetal fibroblasts treated with 0.05 μmol/L colchicine exhibited a higher morula/blastocyst rate of reconstructed embryos than those treated with 0.10 μmol/L colchicine and untreated ones (27.5% vs. 12.1%, 17.1%), however, no significant difference among the three treatments was detected (P>0.05). (Ⅴ) The morula/blastocyst rate of reconstructed embryos from fetal fibroblasts transfected with GFP gene only was 3.1%, significantly lower than that from non-transgenic cells (3.1% vs. 20.4%, P<0.05). In conclusion, our results demonstrated that fetal fibroblasts of fewer passages, medium size could ensure a higher morula/blastocyst rate of reconstructed embryos. Serum starvation of donor cells might be unnecessary to the development of reconstructed embryos. Donor cells treated with 0.05 μmol/L colchicine

  2. Bilingualism (Ancestral Language Maintenance) among Native American, Vietnamese American, and Hispanic American College Students.

    Science.gov (United States)

    Wharry, Cheryl

    1993-01-01

    A survey of 21 Hispanic, 22 Native American, and 10 Vietnamese American college students found that adoption or maintenance of ancestral language was related to attitudes toward ancestral language, beliefs about parental attitudes, and integrative motivation (toward family and ancestral ethnic group). There were significant differences by gender…

  3. The ancestral eutherian karyotype is present in Xenarthra.

    Directory of Open Access Journals (Sweden)

    Marta Svartman

    2006-07-01

    Full Text Available Molecular studies have led recently to the proposal of a new super-ordinal arrangement of the 18 extant Eutherian orders. From the four proposed super-orders, Afrotheria and Xenarthra were considered the most basal. Chromosome-painting studies with human probes in these two mammalian groups are thus key in the quest to establish the ancestral Eutherian karyotype. Although a reasonable amount of chromosome-painting data with human probes have already been obtained for Afrotheria, no Xenarthra species has been thoroughly analyzed with this approach. We hybridized human chromosome probes to metaphases of species (Dasypus novemcinctus, Tamandua tetradactyla, and Choloepus hoffmanii representing three of the four Xenarthra families. Our data allowed us to review the current hypotheses for the ancestral Eutherian karyotype, which range from 2n = 44 to 2n = 48. One of the species studied, the two-toed sloth C. hoffmanii (2n = 50, showed a chromosome complement strikingly similar to the proposed 2n = 48 ancestral Eutherian karyotype, strongly reinforcing it.

  4. The ancestral eutherian karyotype is present in Xenarthra.

    Science.gov (United States)

    Svartman, Marta; Stone, Gary; Stanyon, Roscoe

    2006-07-01

    Molecular studies have led recently to the proposal of a new super-ordinal arrangement of the 18 extant Eutherian orders. From the four proposed super-orders, Afrotheria and Xenarthra were considered the most basal. Chromosome-painting studies with human probes in these two mammalian groups are thus key in the quest to establish the ancestral Eutherian karyotype. Although a reasonable amount of chromosome-painting data with human probes have already been obtained for Afrotheria, no Xenarthra species has been thoroughly analyzed with this approach. We hybridized human chromosome probes to metaphases of species (Dasypus novemcinctus, Tamandua tetradactyla, and Choloepus hoffmanii) representing three of the four Xenarthra families. Our data allowed us to review the current hypotheses for the ancestral Eutherian karyotype, which range from 2n = 44 to 2n = 48. One of the species studied, the two-toed sloth C. hoffmanii (2n = 50), showed a chromosome complement strikingly similar to the proposed 2n = 48 ancestral Eutherian karyotype, strongly reinforcing it.

  5. Special Inspector General for Iraq Reconstruction: Quarterly Report and Semiannual Report to the United States Congress

    Science.gov (United States)

    2012-07-30

    residents. Although DoS officials have stated that Camp Hurriya has Internet connectivity, a mosque, and a gym , several humanitarian chal- lenges...remains uncertain.376 DoS also found that Iraq remains a source and destination country for men, women, and children subjected to sex trafficking...shelters that provided protective services to sex - trafficking victims. DoS granted Iraq a waiver from Tier 3 status based on its assessment that the

  6. Special Inspector General for Iraq Reconstruction Quarterly Report to the United States Congress

    Science.gov (United States)

    2010-04-30

    stated in its comments that SIGIR is correct that 2 Broadband Global Area Network ( BGAN ) systems are “unlocated” and the other 16 are not being used...USF-I reiterated its earlier point that the recurring cost of commercial satel- lite usage to operate the BGAN is beyond the fiscal capability of...Broadcasting Board of Governors BCT Brigade Combat Team BEZ Baghdad International Airport Economic Zone BGAN Broadband Global Area Network BGC Basrah Gas

  7. Reconstructing the hidden states in time course data of stochastic models.

    Science.gov (United States)

    Zimmer, Christoph

    2015-11-01

    Parameter estimation is central for analyzing models in Systems Biology. The relevance of stochastic modeling in the field is increasing. Therefore, the need for tailored parameter estimation techniques is increasing as well. Challenges for parameter estimation are partial observability, measurement noise, and the computational complexity arising from the dimension of the parameter space. This article extends the multiple shooting for stochastic systems' method, developed for inference in intrinsic stochastic systems. The treatment of extrinsic noise and the estimation of the unobserved states is improved, by taking into account the correlation between unobserved and observed species. This article demonstrates the power of the method on different scenarios of a Lotka-Volterra model, including cases in which the prey population dies out or explodes, and a Calcium oscillation system. Besides showing how the new extension improves the accuracy of the parameter estimates, this article analyzes the accuracy of the state estimates. In contrast to previous approaches, the new approach is well able to estimate states and parameters for all the scenarios. As it does not need stochastic simulations, it is of the same order of speed as conventional least squares parameter estimation methods with respect to computational time.

  8. Reconstruction of active regular motion in amoeba extract: dynamic cooperation between sol and gel states.

    Science.gov (United States)

    Nishigami, Yukinori; Ichikawa, Masatoshi; Kazama, Toshiya; Kobayashi, Ryo; Shimmen, Teruo; Yoshikawa, Kenichi; Sonobe, Seiji

    2013-01-01

    Amoeboid locomotion is one of the typical modes of biological cell migration. Cytoplasmic sol-gel conversion of an actomyosin system is thought to play an important role in locomotion. However, the mechanisms underlying sol-gel conversion, including trigger, signal, and regulating factors, remain unclear. We developed a novel model system in which an actomyosin fraction moves like an amoeba in a cytoplasmic extract. Rheological study of this model system revealed that the actomyosin fraction exhibits shear banding: the sol-gel state of actomyosin can be regulated by shear rate or mechanical force. Furthermore, study of the living cell indicated that the shear-banding property also causes sol-gel conversion with the same order of magnitude as that of shear rate. Our results suggest that the inherent sol-gel transition property plays an essential role in the self-regulation of autonomous translational motion in amoeba.

  9. Reconstruction of active regular motion in amoeba extract: dynamic cooperation between sol and gel states.

    Directory of Open Access Journals (Sweden)

    Yukinori Nishigami

    Full Text Available Amoeboid locomotion is one of the typical modes of biological cell migration. Cytoplasmic sol-gel conversion of an actomyosin system is thought to play an important role in locomotion. However, the mechanisms underlying sol-gel conversion, including trigger, signal, and regulating factors, remain unclear. We developed a novel model system in which an actomyosin fraction moves like an amoeba in a cytoplasmic extract. Rheological study of this model system revealed that the actomyosin fraction exhibits shear banding: the sol-gel state of actomyosin can be regulated by shear rate or mechanical force. Furthermore, study of the living cell indicated that the shear-banding property also causes sol-gel conversion with the same order of magnitude as that of shear rate. Our results suggest that the inherent sol-gel transition property plays an essential role in the self-regulation of autonomous translational motion in amoeba.

  10. Reconstructing the Freeze-out State in Pb + Pb Collisions at 158 AGeV/c

    CERN Document Server

    Tomasik, Boris; Heinz, Ulrich W; Tomasik, Boris; Wiedemann, Urs Achim; Heinz, Ulrich

    2003-01-01

    For a class of analytical parametrizations of the freeze-out state of relativistic heavy ion collisions, we perform a simultaneous analysis of the single-particle m_t-spectra and two-particle Bose-Einstein correlations measured in central Pb+Pb collisions at the CERN SPS. The analysis includes a full model parameter scan with chi^2 confidence levels. A comparison of different transverse density profiles for the particle emission region allows for a quantitative discussion of possible model dependencies of the results. Our fit results suggest a low thermal freeze-out temperature T approximately 95 +- 15 MeV and a large average transverse flow velocity of about 0.55c +- 0.07c. Moreover, the fit favours a box-shaped transverse density profile over a Gaussian one. We discuss the origins and the consequences of these results in detail. In order to reproduce the measured pion multiplicity our model requires a positive pion chemical potential. A study of the pion phase-space density indicates \\mu_\\pi approximately 6...

  11. The Impact of Reconstruction Methods, Phylogenetic Uncertainty and Branch Lengths on Inference of Chromosome Number Evolution in American Daisies (Melampodium, Asteraceae)

    Science.gov (United States)

    McCann, Jamie; Stuessy, Tod F.; Villaseñor, Jose L.; Weiss-Schneeweiss, Hanna

    2016-01-01

    Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (maximum parsimony, maximum likelihood, Bayesian methods), branch length model (phylograms versus chronograms) and phylogenetic uncertainty (topological and branch length uncertainty) on the inference of chromosome number evolution. We also address the suitability of the maximum clade credibility (MCC) tree as single representative topology for chromosome number reconstruction. Each of the listed factors causes considerable incongruence among chromosome number reconstructions. Discrepancies between inferences on the MCC tree from those made by integrating over a set of trees are moderate for ancestral chromosome numbers, but severe for the difference of chromosome gains and losses, a measure of the directionality of dysploidy. Therefore, reliance on single trees, such as the MCC tree, is strongly discouraged and model averaging, taking both phylogenetic and model uncertainty into account, is recommended. For studying chromosome number evolution, dedicated models implemented in the program ChromEvol and ordered maximum parsimony may be most appropriate. Chromosome number evolution in Melampodium follows a pattern of bidirectional dysploidy (starting from x = 11 to x = 9 and x = 14, respectively) with no prevailing direction. PMID:27611687

  12. Reconstructing the climate states of the Late Pleistocene with the MIROC climate model

    Science.gov (United States)

    Chan, Wing-Le; Abe-Ouchi, Ayako; O'ishi, Ryouta; Takahashi, Kunio

    2014-05-01

    The Late Pleistocene was a period which lasted from the Eemian interglacial period to the start of the warm Holocene and was characterized mostly by widespread glacial ice. It was also a period which saw modern humans spread throughout the world and other species of the same genus, like the Neanderthals, become extinct. Various hypotheses have been put forward to explain the extinction of Neanderthals, about 30,000 years ago. Among these is one which involves changes in past climate and the inability of Neanderthals to adapt to such changes. The last traces of Neanderthals coincide with the end of Marine Isotope Stage 3 (MIS3) which was marked by large fluctuations in temperature and so-called Heinrich events, as suggested by geochemical records from ice cores. It is thought that melting sea ice or icebergs originating from the Laurentide ice sheet led to a large discharge of freshwater into the North Atlantic Ocean during the Heinrich events and severely weakened the Atlantic meridional overturning circulation, with important environmental ramifications across parts of Europe such as sharp decreases in temperature and reduction in forest cover. In order to assess the effects of past climate change on past hominin migration and on the extinction of certain species, it is first important to have a good understanding of the past climate itself. In this study, we have used three variants of MIROC (The Model for Interdisciplinary Research on Climate), a global climate model, for a time slice experiment within the Late Pleistocene: two mid-resolution models (an atmosphere model and a coupled atmosphere-ocean model) and a high-resolution atmosphere model. To obtain a fuller picture, we also look at a cool stadial state as obtained from a 'freshwater hosing' coupled-model experiment, designed to mimic the effects of freshwater discharge in the North Atlantic. We next use the sea surface temperature response from this experiment to drive the atmosphere models. We discuss

  13. Visual system evolution and the nature of the ancestral snake.

    Science.gov (United States)

    Simões, B F; Sampaio, F L; Jared, C; Antoniazzi, M M; Loew, E R; Bowmaker, J K; Rodriguez, A; Hart, N S; Hunt, D M; Partridge, J C; Gower, D J

    2015-07-01

    The dominant hypothesis for the evolutionary origin of snakes from 'lizards' (non-snake squamates) is that stem snakes acquired many snake features while passing through a profound burrowing (fossorial) phase. To investigate this, we examined the visual pigments and their encoding opsin genes in a range of squamate reptiles, focusing on fossorial lizards and snakes. We sequenced opsin transcripts isolated from retinal cDNA and used microspectrophotometry to measure directly the spectral absorbance of the photoreceptor visual pigments in a subset of samples. In snakes, but not lizards, dedicated fossoriality (as in Scolecophidia and the alethinophidian Anilius scytale) corresponds with loss of all visual opsins other than RH1 (λmax 490-497 nm); all other snakes (including less dedicated burrowers) also have functional sws1 and lws opsin genes. In contrast, the retinas of all lizards sampled, even highly fossorial amphisbaenians with reduced eyes, express functional lws, sws1, sws2 and rh1 genes, and most also express rh2 (i.e. they express all five of the visual opsin genes present in the ancestral vertebrate). Our evidence of visual pigment complements suggests that the visual system of stem snakes was partly reduced, with two (RH2 and SWS2) of the ancestral vertebrate visual pigments being eliminated, but that this did not extend to the extreme additional loss of SWS1 and LWS that subsequently occurred (probably independently) in highly fossorial extant scolecophidians and A. scytale. We therefore consider it unlikely that the ancestral snake was as fossorial as extant scolecophidians, whether or not the latter are para- or monophyletic.

  14. Comparative analysis of iterative reconstruction algorithms with resolution recovery and new solid state cameras dedicated to myocardial perfusion imaging.

    Science.gov (United States)

    Brambilla, Marco; Lecchi, Michela; Matheoud, Roberta; Leva, Lucia; Lucignani, Giovanni; Marcassa, Claudio; Zoccarato, Orazio

    2017-03-23

    New technologies are available in myocardial perfusion imaging. They include new software that recovers image resolution and limits image noise, multifocal collimators and dedicated cardiac cameras in which solid-state detectors are used and all available detectors are constrained to imaging just the cardiac field of view. These innovations resulted in shortened study times or reduced administered activity to patients, while preserving image quality. Many single center and some multicenter studies have been published during the introduction of these innovations in the clinical practice. Most of these studies were lead in the framework of "agreement studies" between different methods of clinical measurement. They aimed to demonstrate that these new software/hardware solutions allow the acquisition of images with reduced acquisition time or administered activity with comparable results (as for image quality, image interpretation, perfusion defect quantification, left ventricular volumes and ejection fraction) to the standard-time or standard-dose SPECT acquired with a conventional gamma camera and reconstructed with the traditional FBP method, considered as the gold standard. The purpose of this review is to provide the reader with a comprehensive understanding of the pro and cons of the different approaches summarizing the achievements reached so far and the issues that need further investigations.

  15. Evaluation of Origin Ensemble algorithm for image reconstruction for pixelated solid-state detectors with large number of channels

    Science.gov (United States)

    Kolstein, M.; De Lorenzo, G.; Mikhaylova, E.; Chmeissani, M.; Ariño, G.; Calderón, Y.; Ozsahin, I.; Uzun, D.

    2013-04-01

    The Voxel Imaging PET (VIP) Pathfinder project intends to show the advantages of using pixelated solid-state technology for nuclear medicine applications. It proposes designs for Positron Emission Tomography (PET), Positron Emission Mammography (PEM) and Compton gamma camera detectors with a large number of signal channels (of the order of 106). For PET scanners, conventional algorithms like Filtered Back-Projection (FBP) and Ordered Subset Expectation Maximization (OSEM) are straightforward to use and give good results. However, FBP presents difficulties for detectors with limited angular coverage like PEM and Compton gamma cameras, whereas OSEM has an impractically large time and memory consumption for a Compton gamma camera with a large number of channels. In this article, the Origin Ensemble (OE) algorithm is evaluated as an alternative algorithm for image reconstruction. Monte Carlo simulations of the PET design are used to compare the performance of OE, FBP and OSEM in terms of the bias, variance and average mean squared error (MSE) image quality metrics. For the PEM and Compton camera designs, results obtained with OE are presented.

  16. Water balance-based actual evapotranspiration reconstruction from ground and satellite observations over the conterminous United States

    Science.gov (United States)

    Wan, Zhanming; Zhang, Ke; Xue, Xianwu; Hong, Zhen; Hong, Yang; Gourley, Jonathan J.

    2015-08-01

    The objective of this study is to produce an observationally based monthly evapotranspiration (ET) product using the simple water balance equation across the conterminous United States (CONUS). We adopted the best quality ground and satellite-based observations of the water budget components, i.e., precipitation, runoff, and water storage change, while ET is computed as the residual. Precipitation data are provided by the bias-corrected PRISM observation-based precipitation data set, while runoff comes from observed monthly streamflow values at 592 USGS stream gauging stations that have been screened by strict quality controls. We developed a land surface model-based downscaling approach to disaggregate the monthly GRACE equivalent water thickness data to daily, 0.125° values. The derived ET computed as the residual from the water balance equation is evaluated against three sets of existing ET products. The similar spatial patterns and small differences between the reconstructed ET in this study and the other three products show the reliability of the observationally based approach. The new ET product and the disaggregated GRACE data provide a unique, important hydro-meteorological data set that can be used to evaluate the other ET products as a benchmark data set, assess recent hydrological and climatological changes, and terrestrial water and energy cycle dynamics across the CONUS. These products will also be valuable for studies and applications in drought assessment, water resources management, and climate change evaluation.

  17. Tay-Sachs disease preconception screening in Australia: self-knowledge of being an Ashkenazi Jew predicts carrier state better than does ancestral origin, although there is an increased risk for c.1421 + 1G > C mutation in individuals with South African heritage.

    Science.gov (United States)

    Lew, Raelia; Burnett, Leslie; Proos, Anné

    2011-12-01

    The Australasian Community Genetics Program provided a preconception screening for Tay-Sachs disease (TSD) to 4,105 Jewish high school students in Sydney and Melbourne over the 12-year period 1995-2007. By correlating the frequencies of mutant HEXA, MIM *606869 (gene map locus 15q23-q24) alleles with subjects' nominated ethnicity (Ashkenazi/Sephardi/Mixed) and grandparental birthplaces, we established that Ashkenazi ethnicity is a better predictor of TSD carrier status than grandparental ancestral origins. Screening self-identified Ashkenazi subjects detected 95% of TSD carriers (carrier frequency 1:25). Having mixed Ashkenazi and non-Ashkenazi heritage reduced the carrier frequency (1:97). South African heritage conveyed a fourfold risk of c.1421 + 1G > C mutation compared with other AJ subjects (odds ratio (OR), 4.19; 95% confidence interval (CI), 1.83-9.62, p = 0.001), but this was the only specific case of ancestral origin improving diagnostic sensitivity over that based on determining Ashkenazi ethnicity. Carriers of c.1278insTATC mutations were more likely to have heritage from Western Europe (OR, 1.65 (95% CI, 1.04-2.60), p = 0.032) and South Eastern Europe (OR, 1.77 (95% CI, 1.14-2.73), p = 0.010). However, heritage from specific European countries investigated did not significantly alter the overall odds of TSD carrier status.

  18. Estimating ancestral geographical distributions: a Gondwanan origin for aphid parasitoids?

    Science.gov (United States)

    Belshaw, R; Dowton, M; Quicke, D L; Austin, A D

    2000-01-01

    We tested the published hypothesis of a Gondwanan origin for the overwhelmingly northern hemisphere aphid parasitoids (Aphidiinae) as follows: (i) finding their sister group by a phylogenetic analysis of the entire Braconidae (Insecta: Hymenopterai using sequence data from approximately 500 bp fragments of both the nuclear 28S (D2 region) and mitochondrial 16S rDNA genes, (ii) using this sister-group relationship and the more informative 28S D2 gene to estimate the phylogeny of the Aphidiinae and (iii) estimating the ancestral distribution for the Aphidiinae using maximum-likelihood and maximum-parsimony methods. Both methods indicated a Gondwanan origin. PMID:10737407

  19. ACL reconstruction

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/007208.htm ACL reconstruction To use the sharing features on this page, please enable JavaScript. ACL reconstruction is surgery to reconstruct the ligament in ...

  20. Ancestral heaths : reconstructing the barrow landscape in the Central and Southern Netherlands

    NARCIS (Netherlands)

    Doorenbosch, Marieke

    2013-01-01

    Barrows, i.e. burial mounds, are amongst the most important of Europe’s prehistoric monuments. Across Europe, barrows still figure as a prominent element in the landscape. Many barrows in Europe have been excavated, revealing much about what was buried inside these monuments. Little is known, howeve

  1. Ancestral reconstruction of the ligand-binding pocket of Family C G protein-coupled receptors

    OpenAIRE

    Kuang, Donghui; Yao, Yi; MacLean, David; Wang, Minghua; Hampson, David R.; Chang, Belinda S. W.

    2006-01-01

    The metabotropic glutamate receptors (mGluRs) within the Family C subclass of G protein-coupled receptors are crucial modulators of synaptic transmission. However, their closest relatives include a diverse group of sensory receptors whose biological functions are not associated with neurotransmission, raising the question of the evolutionary origin of amino acid-binding Family C receptors. A common feature of most, if not all, functional Family C receptors is the presence of an amino acid-bin...

  2. The ancestral process of long term seed bank models

    CERN Document Server

    Blath, Jochen; Kurt, Noemi; Spanò, Dario

    2012-01-01

    We present a new model for the evolution of genetic types in the presence of so-called seed banks, i.e., where individuals may obtain their genetic type from ancestors which have lived in the near as well as the very far past. The classical Wright-Fisher model, as well as a seed bank model with bounded age distribution considered by Kaj, Krone and Lascoux (2001) are special cases of our model. We discern three parameter regimes of the seed bank age distribution, which lead to substantially different behaviour in terms of genetic variability, in particular with respect to fixation of types and time to the most recent common ancestor. We prove that for age distributions with finite mean, the rescaled ancestral process converges to a time-changed Kingman coalescent, while in the case of infinite mean, ancestral lineages might not merge at all with positive probability. Further, we present a construction of the forward in time process in equilibrium. The mathematical methods are based on renewal theory, the urn p...

  3. Phase Transition in Distance-Based Phylogeny Reconstruction

    CERN Document Server

    Roch, Sebastien

    2011-01-01

    We introduce a new distance-based phylogeny reconstruction technique which provably achieves, at sufficiently short branch lengths, a logarithmic sequence-length requirement---improving significantly over previous polynomial bounds for distance-based methods and matching existing results for general methods. The technique is based on an averaging procedure that implicitly reconstructs ancestral sequences. In the same token, we extend previous results on phase transitions in phylogeny reconstruction to general time-reversible models. More precisely, we show that in the so-called Kesten-Stigum zone (roughly, a region of the parameter space where ancestral sequences are well approximated by "linear combinations" of the observed sequences) sequences of length $O(\\log n)$ suffice for reconstruction when branch lengths are discretized. Here $n$ is the number of extant species. Our results challenge, to some extent, the conventional wisdom that estimates of evolutionary distances alone carry significantly less infor...

  4. Assessing the significance of fidelity as a figure of merit in quantum state reconstruction of discrete and continuous-variable systems

    Science.gov (United States)

    Mandarino, Antonio; Bina, Matteo; Porto, Carmen; Cialdi, Simone; Olivares, Stefano; Paris, Matteo G. A.

    2016-06-01

    We experimentally address the significance of fidelity as a figure of merit in quantum state reconstruction of discrete (DV) and continuous-variable (CV) quantum optical systems. In particular, we analyze the use of fidelity in quantum homodyne tomography of CV states and maximum-likelihood polarization tomography of DV ones, focusing attention on nonclassicality, entanglement, and quantum discord as a function of fidelity to a target state. Our findings show that high values of fidelity, despite well quantifying geometrical proximity in the Hilbert space, may be obtained for states displaying opposite physical properties, e.g., quantum or semiclassical features. In particular, we analyze in detail the quantum-to-classical transition for squeezed thermal states of a single-mode optical system and for Werner states of a two-photon polarization qubit system.

  5. Extensive Chromosomal Reorganization in the Evolution of New World Muroid Rodents (Cricetidae, Sigmodontinae): Searching for Ancestral Phylogenetic Traits

    Science.gov (United States)

    Pereira, Adenilson Leão; Malcher, Stella Miranda; Nagamachi, Cleusa Yoshiko; O’Brien, Patricia Caroline Mary; Ferguson-Smith, Malcolm Andrew; Mendes-Oliveira, Ana Cristina; Pieczarka, Julio Cesar

    2016-01-01

    Sigmodontinae rodents show great diversity and complexity in morphology and ecology. This diversity is accompanied by extensive chromosome variation challenging attempts to reconstruct their ancestral genome. The species Hylaeamys megacephalus–HME (Oryzomyini, 2n = 54), Necromys lasiurus—NLA (Akodontini, 2n = 34) and Akodon sp.–ASP (Akodontini, 2n = 10) have extreme diploid numbers that make it difficult to understand the rearrangements that are responsible for such differences. In this study we analyzed these changes using whole chromosome probes of HME in cross-species painting of NLA and ASP to construct chromosome homology maps that reveal the rearrangements between species. We include data from the literature for other Sigmodontinae previously studied with probes from HME and Mus musculus (MMU) probes. We also use the HME probes on MMU chromosomes for the comparative analysis of NLA with other species already mapped by MMU probes. Our results show that NLA and ASP have highly rearranged karyotypes when compared to HME. Eleven HME syntenic blocks are shared among the species studied here. Four syntenies may be ancestral to Akodontini (HME2/18, 3/25, 18/25 and 4/11/16) and eight to Sigmodontinae (HME26, 1/12, 6/21, 7/9, 5/17, 11/16, 20/13 and 19/14/19). Using MMU data we identified six associations shared among rodents from seven subfamilies, where MMU3/18 and MMU8/13 are phylogenetic signatures of Sigmodontinae. We suggest that the associations MMU2entire, MMU6proximal/12entire, MMU3/18, MMU8/13, MMU1/17, MMU10/17, MMU12/17, MMU5/16, MMU5/6 and MMU7/19 are part of the ancestral Sigmodontinae genome. PMID:26800516

  6. Mouthparts of the Burgess Shale fossils Odontogriphus and Wiwaxia: implications for the ancestral molluscan radula.

    Science.gov (United States)

    Smith, Martin R

    2012-10-22

    The Middle Cambrian lophotrochozoans Odontogriphus omalus and Wiwaxia corrugata have been interpreted as stem-group members of either the Mollusca, the Annelida, or a group containing Mollusca + Annelida. The case for each classification rests on the organisms' unusual mouthparts, whose two to three tooth-rows resemble both the molluscan radula and the jaws of certain annelid worms. Despite their potential significance, these mouthparts have not previously been described in detail. This study examined the feeding apparatuses of over 300 specimens from the 505-million-year-old Burgess Shale, many of which were studied for the first time. Rather than denticulate plates, each tooth row comprises a single axial tooth that is flanked on each side by eight to 16 separate shoehorn-shaped teeth. Tooth rows sat on a grooved basal tongue, and two large lobes flanked the apparatus. New observations--the shape, distribution and articulation of the individual teeth, and the mouthparts' mode of growth--are incompatible with an annelid interpretation, instead supporting a classification in Mollusca. The ancestral molluscan radula is best reconstructed as unipartite with a symmetrical medial tooth, and Odontogriphus and Wiwaxia as grazing deposit-feeders.

  7. Genotype-based ancestral background consistently predicts efficacy and side effects across treatments in CATIE and STAR*D.

    Directory of Open Access Journals (Sweden)

    Daniel E Adkins

    Full Text Available Only a subset of patients will typically respond to any given prescribed drug. The time it takes clinicians to declare a treatment ineffective leaves the patient in an impaired state and at unnecessary risk for adverse drug effects. Thus, diagnostic tests robustly predicting the most effective and safe medication for each patient prior to starting pharmacotherapy would have tremendous clinical value. In this article, we evaluated the use of genetic markers to estimate ancestry as a predictive component of such diagnostic tests. We first estimated each patient's unique mosaic of ancestral backgrounds using genome-wide SNP data collected in the Clinical Antipsychotic Trials of Intervention Effectiveness (CATIE (n = 765 and the Sequenced Treatment Alternatives to Relieve Depression (STAR*D (n = 1892. Next, we performed multiple regression analyses to estimate the predictive power of these ancestral dimensions. For 136/89 treatment-outcome combinations tested in CATIE/STAR*D, results indicated 1.67/1.84 times higher median test statistics than expected under the null hypothesis assuming no predictive power (p<0.01, both samples. Thus, ancestry showed robust and pervasive correlations with drug efficacy and side effects in both CATIE and STAR*D. Comparison of the marginal predictive power of MDS ancestral dimensions and self-reported race indicated significant improvements to model fit with the inclusion of MDS dimensions, but mixed evidence for self-reported race. Knowledge of each patient's unique mosaic of ancestral backgrounds provides a potent immediate starting point for developing algorithms identifying the most effective and safe medication for a wide variety of drug-treatment response combinations. As relatively few new psychiatric drugs are currently under development, such personalized medicine offers a promising approach toward optimizing pharmacotherapy for psychiatric conditions.

  8. The mechanistic basis of hemoglobin adaptation in the high-flying barheaded goose: insights from ancestral protein resurrection

    DEFF Research Database (Denmark)

    Natarajan, Chandrasekhar; Kumar, Amit; Moriyama, Hideaki

    2016-01-01

    of this text-book example of biochemical adaptation. Previous hypotheses about the molecular basis of the evolved increase in Hb-O2 affinity were tested by engineering BHGspecific mutations into recombinant human Hb. This approach can provide important insights, but one problem with such ‘horizontal......’ comparisons – swapping residues between proteins of contemporary species – is that the focal mutations are introduced into a sequence context that may not be evolutionarily relevant. If mutations have context-dependent effects, then introducing BHG-specific substitutions into human Hb may not recapitulate...... the functional effects of causative mutations on the genetic background in which they actually occurred during evolution (i.e., in the BHG ancestor). An alternative ‘vertical’ approach is to reconstruct and resurrect ancestral proteins to test the effects of historical mutations on the genetic background...

  9. Community incidence of pathogen-specific gastroenteritis: reconstructing the surveillance pyramid for seven pathogens in seven European Union member states

    DEFF Research Database (Denmark)

    Haagsma, J. A.; Geenen, P. L.; Ethelberg, S.

    2013-01-01

    , underreporting and under-diagnosis were estimated to be lowest for Germany and Sweden, followed by Denmark, The Netherlands, UK, Italy and Poland. Across all countries, the incidence rate was highest for Campylobacter spp. and Salmonella spp. Incidence estimates resulting from the pyramid reconstruction approach...

  10. Meeting the Challenge of Reconstruction and Development in Fragile States: Lessons from Aceh, Haiti, and South Sudan

    OpenAIRE

    Leitmann, Josef

    2014-01-01

    Reconstruction and development in poor, fragile countries present a double challenge: tackling the issues of poverty and underdevelopment as well as the constraints posed by instability, poor governance, and weak capacity. This context generates a range of problems that include: insecurity, insufficient planning, inadequate implementation capacity, poor financial management, misprocurement, corruption, a volatile fiscal environment, ineffective donor coordination, and negative environmental a...

  11. Applying the Israeli Practice of Reconstruction Following a Terrorist Attack as a Model for Cities in the United States

    Science.gov (United States)

    2013-03-01

    A 13. ABSTRACT (maximum 200 words) A component of the Israeli counter-terrorism policy includes a strategic choreographed response to restore and...includes a strategic choreographed response to restore and reconstruct physical damage caused by a terrorist attack with the goal of removing all markings

  12. Estimation of the ancestral effective population sizes of African great apes under different selection regimes.

    Science.gov (United States)

    Schrago, Carlos G

    2014-08-01

    Reliable estimates of ancestral effective population sizes are necessary to unveil the population-level phenomena that shaped the phylogeny and molecular evolution of the African great apes. Although several methods have previously been applied to infer ancestral effective population sizes, an analysis of the influence of the selective regime on the estimates of ancestral demography has not been thoroughly conducted. In this study, three independent data sets under different selective regimes were used were composed to tackle this issue. The results showed that selection had a significant impact on the estimates of ancestral effective population sizes of the African great apes. The inference of the ancestral demography of African great apes was affected by the selection regime. The effects, however, were not homogeneous along the ancestral populations of great apes. The effective population size of the ancestor of humans and chimpanzees was more impacted by the selection regime when compared to the same parameter in the ancestor of humans, chimpanzees and gorillas. Because the selection regime influenced the estimates of ancestral effective population size, it is reasonable to assume that a portion of the discrepancy found in previous studies that inferred the ancestral effective population size may be attributable to the differential action of selection on the genes sampled.

  13. Allatotropin: An Ancestral Myotropic Neuropeptide Involved in Feeding

    Science.gov (United States)

    Alzugaray, María Eugenia; Adami, Mariana Laura; Diambra, Luis Anibal; Hernandez-Martinez, Salvador; Damborenea, Cristina; Noriega, Fernando Gabriel; Ronderos, Jorge Rafael

    2013-01-01

    Background Cell-cell interactions are a basic principle for the organization of tissues and organs allowing them to perform integrated functions and to organize themselves spatially and temporally. Peptidic molecules secreted by neurons and epithelial cells play fundamental roles in cell-cell interactions, acting as local neuromodulators, neurohormones, as well as endocrine and paracrine messengers. Allatotropin (AT) is a neuropeptide originally described as a regulator of Juvenile Hormone synthesis, which plays multiple neural, endocrine and myoactive roles in insects and other organisms. Methods A combination of immunohistochemistry using AT-antibodies and AT-Qdot nanocrystal conjugates was used to identify immunoreactive nerve cells containing the peptide and epithelial-muscular cells targeted by AT in Hydra plagiodesmica. Physiological assays using AT and AT- antibodies revealed that while AT stimulated the extrusion of the hypostome in a dose-response fashion in starved hydroids, the activity of hypostome in hydroids challenged with food was blocked by treatments with different doses of AT-antibodies. Conclusions AT antibodies immunolabeled nerve cells in the stalk, pedal disc, tentacles and hypostome. AT-Qdot conjugates recognized epithelial-muscular cell in the same tissues, suggesting the existence of anatomical and functional relationships between these two cell populations. Physiological assays indicated that the AT-like peptide is facilitating food ingestion. Significance Immunochemical, physiological and bioinformatics evidence advocates that AT is an ancestral neuropeptide involved in myoregulatory activities associated with meal ingestion and digestion. PMID:24143240

  14. Deep phylogeny, ancestral groups and the four ages of life.

    Science.gov (United States)

    Cavalier-Smith, Thomas

    2010-01-12

    Organismal phylogeny depends on cell division, stasis, mutational divergence, cell mergers (by sex or symbiogenesis), lateral gene transfer and death. The tree of life is a useful metaphor for organismal genealogical history provided we recognize that branches sometimes fuse. Hennigian cladistics emphasizes only lineage splitting, ignoring most other major phylogenetic processes. Though methodologically useful it has been conceptually confusing and harmed taxonomy, especially in mistakenly opposing ancestral (paraphyletic) taxa. The history of life involved about 10 really major innovations in cell structure. In membrane topology, there were five successive kinds of cell: (i) negibacteria, with two bounding membranes, (ii) unibacteria, with one bounding and no internal membranes, (iii) eukaryotes with endomembranes and mitochondria, (iv) plants with chloroplasts and (v) finally, chromists with plastids inside the rough endoplasmic reticulum. Membrane chemistry divides negibacteria into the more advanced Glycobacteria (e.g. Cyanobacteria and Proteobacteria) with outer membrane lipolysaccharide and primitive Eobacteria without lipopolysaccharide (deserving intenser study). It also divides unibacteria into posibacteria, ancestors of eukaryotes, and archaebacteria-the sisters (not ancestors) of eukaryotes and the youngest bacterial phylum. Anaerobic eobacteria, oxygenic cyanobacteria, desiccation-resistant posibacteria and finally neomura (eukaryotes plus archaebacteria) successively transformed Earth. Accidents and organizational constraints are as important as adaptiveness in body plan evolution.

  15. Ancestral TSH mechanism signals summer in a photoperiodic mammal.

    Science.gov (United States)

    Hanon, Elodie A; Lincoln, Gerald A; Fustin, Jean-Michel; Dardente, Hugues; Masson-Pévet, Mireille; Morgan, Peter J; Hazlerigg, David G

    2008-08-05

    In mammals, day-length-sensitive (photoperiodic) seasonal breeding cycles depend on the pineal hormone melatonin, which modulates secretion of reproductive hormones by the anterior pituitary gland [1]. It is thought that melatonin acts in the hypothalamus to control reproduction through the release of neurosecretory signals into the pituitary portal blood supply, where they act on pituitary endocrine cells [2]. Contrastingly, we show here that during the reproductive response of Soay sheep exposed to summer day lengths, the reverse applies: Melatonin acts directly on anterior-pituitary cells, and these then relay the photoperiodic message back into the hypothalamus to control neuroendocrine output. The switch to long days causes melatonin-responsive cells in the pars tuberalis (PT) of the anterior pituitary to increase production of thyrotrophin (TSH). This acts locally on TSH-receptor-expressing cells in the adjacent mediobasal hypothalamus, leading to increased expression of type II thyroid hormone deiodinase (DIO2). DIO2 initiates the summer response by increasing hypothalamic tri-iodothyronine (T3) levels. These data and recent findings in quail [3] indicate that the TSH-expressing cells of the PT play an ancestral role in seasonal reproductive control in vertebrates. In mammals this provides the missing link between the pineal melatonin signal and thyroid-dependent seasonal biology.

  16. Electronic structures of bare and terephthalic acid adsorbed TiO2(110)-(1 × 2) reconstructed surfaces: origin and reactivity of the band gap states.

    Science.gov (United States)

    Zhang, Wenhua; Liu, Liming; Wan, Li; Liu, Lingyun; Cao, Liang; Xu, Faqiang; Zhao, Jin; Wu, Ziyu

    2015-08-21

    Combined core level spectroscopy, valence spectroscopy and density functional theory studies have probed the terephthalic acid (TPA) adsorption behavior and the electronic structure of the rutile TiO2(110)-(1 × 2) reconstructed surface at room temperature. The TiO2(110)-(1 × 2) reconstructed surface exhibits an electron rich nature owing to the unsaturated coordination of the surface terminated Ti2O3 rows. Deprotonation of TPA molecules upon adsorption produces both surface bridging hydroxyl (ObH) and bidentate terephthalate species with a saturation coverage of nearly 0.5 monolayers (ML). In contrast to the TiO2(110)-(1 × 1) surface, the band gap states (BGSs) on the bare (1 × 2) surface exhibit an asymmetric spectral feature, which is originated from integrated contributions of the Ti2O3 termination and the defects in the near-surface region. The Ti2O3 originated BGSs are found to be highly sensitive to the TPA adsorption, a phenomenon well reproduced by the density functional theory (DFT) calculations. Theoretical simulations of the adsorption process also suggest that the redistribution of the electronic density on the (1 × 2) reconstructed surface accompanying the hydroxyl formation promotes the disappearance of the Ti2O3-row derived BGS.

  17. Simulating deforestation and carbon loss in Amazonia: impacts in Brazil's Roraima state from reconstructing Highway BR-319 (Manaus-Porto Velho).

    Science.gov (United States)

    Barni, Paulo Eduardo; Fearnside, Philip Martin; Graça, Paulo Maurício Lima de Alencastro

    2015-02-01

    Reconstruction of Highway BR-319 (Manaus-Porto Velho) would allow for access from the "arc of deforestation" in the southern part of Brazil's Amazon region to vast blocks of forests in central and northern Amazonia. Building roads is known to be a major driver of deforestation, allowing entry of squatters, and other actors. Rather than deforestation along the highway route, here we consider the road's potential for stimulating deforestation in a separate location, approximately 550 km north of BR-319's endpoint in Manaus. Reconstructing BR-319 has great potential impact to start a new wave of migration to this remote region. The southern portion of the state of Roraima, the focus of our study, is already connected to Manaus by Highway BR-174. We modeled deforestation in southern Roraima and simulated carbon emissions between 2007 and 2030 under four scenarios. Simulations used the AGROECO model in DINAMICA-EGO © software. Two scenarios were considered with reconstruction of BR-319 and two without this road connection. For each of the two possibilities regarding BR-319, simulations were developed for (1) a "conservation" (CONSERV) scenario that assumes the creation of a series of protected areas, and (2) a "business-as-usual" (BAU) scenario that assumes no additional protected areas. Results show that by 2030, with BR-319 rebuilt, deforestation carbon emissions would increase between 19% (CONSERV) and 42% (BAU) over and above those corresponding to no-road scenarios.

  18. Complete forelimb myology of the basal theropod dinosaur Tawa hallae based on a novel robust muscle reconstruction method.

    Science.gov (United States)

    Burch, Sara H

    2014-09-01

    The forelimbs of nonavian theropod dinosaurs have been the subject of considerable study and speculation due to their varied morphology and role in the evolution of flight. Although many studies on the functional morphology of a limb require an understanding of its musculature, comparatively little is known about the forelimb myology of theropods and other bipedal dinosaurs. Previous phylogenetically based myological reconstructions have been limited to the shoulder, restricting their utility in analyses of whole-limb function. The antebrachial and manual musculature in particular have remained largely unstudied due to uncertain muscular homologies in archosaurs. Through analysis of the musculature of extant taxa in a robust statistical framework, this study presents new hypotheses of homology for the distal limb musculature of archosaurs and provides the first complete reconstruction of dinosaurian forelimb musculature, including the antebrachial and intrinsic manual muscles. Data on the forelimb myology of a broad sample of extant birds, crocodylians, lizards, and turtles were analyzed using maximum likelihood ancestral state reconstruction and examined together with the osteology of the early theropod Tawa hallae from the Late Triassic of New Mexico to formulate a complete plesiomorphic myology for the theropod forelimb. Comparisons with previous reconstructions show that the shoulder musculature of basal theropods is more similar to that of basal ornithischians and sauropodomorphs than to that of dromaeosaurids. Greater development of the supracoracoideus and deltoideus musculature in theropods over other bipedal dinosaurs correlates with stronger movements of the forelimb at the shoulder and an emphasis on apprehension of relatively large prey. This emphasis is further supported by the morphology of the antebrachium and the intrinsic manual musculature, which exhibit a high degree of excursion and a robust morphology well-suited for powerful digital flexion

  19. Reconstructing Step by Step

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    On May 22,10 days after the Wenchuan earthquake in Sichuan Province,the State Council formed the Post-earthquake Reconstruction Planning Group,deciding to work out a general recon- struction plan within a period of three months. Sichuan was the worst-hit area of China,so reconstruction work there will have a direct influence on how plans proceed in other areas.On July 18,Beijing Review reporter Feng Jianhua interviewed Wang Guangsi,Vice Director of the Sichuan Development and Reform Commission,about Sichuan’s reconstruction plan.

  20. Paraphyly of organelle DNAs in Cycas Sect. Asiorientales due to ancient ancestral polymorphisms

    Directory of Open Access Journals (Sweden)

    Hsu Tsai-Wen

    2009-07-01

    Full Text Available Abstract Background This study addresses the apportionment of genetic diversity between Cycas revoluta and C. taitungensis, species that constitute the section Asiorientales and represent a unique, basal lineage of the Laurasian genus Cycas. Fossil evidence indicates divergence of the section from the rest of Cycas at least 30 million years ago. Geographically, C. taitungensis is limited to Taiwan whereas C. revoluta is found in the Ryukyu Archipelago and on mainland China. Results The phylogenies of ribosomal ITS region of mtDNA and the intergenic spacer between atpB and rbcL genes of cpDNA were reconstructed. Phylogenetic analyses revealed paraphyly of both loci in the two species and also in the section Asiorientales. The lack of reciprocal monophyly between these long isolated sections is likely due to persistent shared ancestral polymorphisms. Molecular dating estimated that mt- and cp DNA lineages coalesced to the most recent common ancestors (TMRCA about 327 (mt and 204 MYA (cp, corresponding with the divergence of cycad sections in the Mesozoic. Conclusion Fates of newly derived mutations of cycads follow Klopfstein et al.'s surfing model where the majority of new mutations do not spread geographically and remain at low frequencies or are eventually lost by genetic drift. Only successful 'surfing mutations' reach very high frequencies and occupy a large portion of a species range. These mutations exist as dominant cytotypes across populations and species. Geographical subdivision is lacking in both species, even though recurrent gene flow by both pollen and seed is severely limited. In total, the contrasting levels between historical and ongoing gene flow, large population sizes, a long lifespan, and slow mutation rates in both organelle DNAs have all likely contributed to the unusually long duration of paraphyly in cycads.

  1. The microcephalin ancestral allele in a Neanderthal individual.

    Directory of Open Access Journals (Sweden)

    Martina Lari

    Full Text Available BACKGROUND: The high frequency (around 0.70 worldwide and the relatively young age (between 14,000 and 62,000 years of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1 locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. METHODOLOGY/PRINCIPAL FINDINGS: Here we report the first PCR amplification and high-throughput sequencing of nuclear DNA at the microcephalin (MCPH1 locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy. We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. CONCLUSIONS/SIGNIFICANCE: The MCPH1 genotype of the Monti Lessini (MLS Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA.

  2. The Korarchaeota: Archaeal orphans representing an ancestral lineage of life

    Energy Technology Data Exchange (ETDEWEB)

    Elkins, James G.; Kunin, Victor; Anderson, Iain; Barry, Kerrie; Goltsman, Eugene; Lapidus, Alla; Hedlund, Brian; Hugenholtz, Phil; Kyrpides, Nikos; Graham, David; Keller, Martin; Wanner, Gerhard; Richardson, Paul; Stetter, Karl O.

    2007-05-01

    Based on conserved cellular properties, all life on Earth can be grouped into different phyla which belong to the primary domains Bacteria, Archaea, and Eukarya. However, tracing back their evolutionary relationships has been impeded by horizontal gene transfer and gene loss. Within the Archaea, the kingdoms Crenarchaeota and Euryarchaeota exhibit a profound divergence. In order to elucidate the evolution of these two major kingdoms, representatives of more deeply diverged lineages would be required. Based on their environmental small subunit ribosomal (ss RNA) sequences, the Korarchaeota had been originally suggested to have an ancestral relationship to all known Archaea although this assessment has been refuted. Here we describe the cultivation and initial characterization of the first member of the Korarchaeota, highly unusual, ultrathin filamentous cells about 0.16 {micro}m in diameter. A complete genome sequence obtained from enrichment cultures revealed an unprecedented combination of signature genes which were thought to be characteristic of either the Crenarchaeota, Euryarchaeota, or Eukarya. Cell division appears to be mediated through a FtsZ-dependent mechanism which is highly conserved throughout the Bacteria and Euryarchaeota. An rpb8 subunit of the DNA-dependent RNA polymerase was identified which is absent from other Archaea and has been described as a eukaryotic signature gene. In addition, the representative organism possesses a ribosome structure typical for members of the Crenarchaeota. Based on its gene complement, this lineage likely diverged near the separation of the two major kingdoms of Archaea. Further investigations of these unique organisms may shed additional light onto the evolution of extant life.

  3. New measurements from fully reconstructed hadronic final states of the $B^0_2$ meson at CDF II experiment

    Energy Technology Data Exchange (ETDEWEB)

    Da Ronco, Saverio [Univ. of Padua (Italy)

    2006-01-01

    This thesis reports the reconstruction and lifetime measurement of B+, B$0/atop{d}$ and B$0/atop{s}$ mesons, performed using fully reconstructed hadronic decays collected by a dedicated trigger at CDF II experiment. This dedicated trigger selects significantly displaced tracks from primary vertex of p$\\bar{p}$ collisions generated at Tevatron collider, obtaining, in this way, huge data samples enriched of long-lived particles, and is therefore suitable for reconstruction of B meson in hadronic decay modes. Due to the trigger track impact parameter selections, the proper decay time distributions of the B mesons no longer follow a simply exponential decay law. This complicates the lifetime measurement and requires a correct understanding and treatment of all the involved effects to keep systematic uncertainties under control. This thesis presents a method to extract the lifetime of B mesons in “ct- biased” samples, based on a Monte Carlo approach, to correct for the effects of the trigger and analysis selections. We present the results of this method when applied on fully re- constructed decays of B collected by CDF II in the data taking runs up to August 2004, corresponding to an integrated luminosity of about 360 pb-1. The lifetimes are extracted using the decay modes B+ → $\\bar{D}$0π+,B$0\\atop{d}$ → D-π+, B$0\\atop{d}$ → D-π+π-π+, B$0\\atop{s}$ → D$-\\atop{s}$π+ and B$0\\atop{s}$ → D$-\\atop{s}$ π+π-π+(and c.c.) and performing combined mass-lifetime unbinned maximum likelihood fits.

  4. An ancestral role for the mitochondrial pyruvate carrier in glucose-stimulated insulin secretion

    Directory of Open Access Journals (Sweden)

    Kyle S. McCommis

    2016-08-01

    Conclusions: Altogether, these studies suggest that the MPC plays an important and ancestral role in insulin-secreting cells in mediating glucose sensing, regulating insulin secretion, and controlling systemic glycemia.

  5. Analysis of the stone ancestral hall of Guo’s tomb on Xiaotang mountainin Han dynasty architectural features

    Institute of Scientific and Technical Information of China (English)

    刘国庆

    2014-01-01

    The stone ancestral hall of Guo’s tomb in Xiaotang mountain is the earliest existing buildings on the ground in China. It has a very high historical, cultural and artistic value, and it was described by the ancient and modern scholars and experts in their books and articles. But the study of architectural of ancestral hall was emphasized from 1930s, and became a brilliant star in the Chinese historic buildings. In this article, the architectural characteristics of the stone ancestral hall are discussed through fieldworks, in order to clarify the real architecture appearance of the ancestral hall and refer more informations for comprehensive study of Xiaotang stone ancestral hall.

  6. Widely divergent transcriptional patterns between SLE patients of different ancestral backgrounds in sorted immune cell populations.

    Science.gov (United States)

    Sharma, Shruti; Jin, Zhongbo; Rosenzweig, Elizabeth; Rao, Swapna; Ko, Kichul; Niewold, Timothy B

    2015-06-01

    Systemic lupus erythematosus (SLE) is a complex autoimmune disease of uncertain etiology. Patients from different ancestral backgrounds demonstrate differences in clinical manifestations and autoantibody profiles. We examined genome-wide transcriptional patterns in major immune cell subsets across different ancestral backgrounds. Peripheral blood was collected from African-American (AA) and European-American (EA) SLE patients and controls. CD4 T-cells, CD8 T-cells, monocytes, and B cells were purified by flow sorting, and each cell subset from each subject was run on a genome-wide expression array. Cases were compared to controls of the same ancestral background. The overlap in differentially expressed gene (DEG) lists between different cell types from the same ancestral background was modest (type between different ancestral backgrounds. IFN-stimulated gene (ISG) expression was not up-regulated synchronously in all cell types from a given patient, for example a given subject could have high ISG expression in T and B cells, but not in monocytes. AA subjects demonstrated more concordance in ISG expression between cell types from the same individual, and AA patients demonstrated significant down-regulation of metabolic gene expression which was not observed in EA patients. ISG expression was significantly decreased in B cells in patients taking immunosuppressants, while ISGs in other cell types did not differ with medication use. In conclusion, gene expression was strikingly different between immune cell subsets and between ancestral backgrounds in SLE patients. These findings emphasize the critical importance of studying multiple ancestral backgrounds and multiple cell types in gene expression studies. Ancestral backgrounds which are not studied will not benefit from personalized medicine strategies in SLE.

  7. Penile reconstruction

    Institute of Scientific and Technical Information of China (English)

    Giulio Garaffa; Salvatore Sansalone; David J Ralph

    2013-01-01

    During the most recent years,a variety of new techniques of penile reconstruction have been described in the literature.This paper focuses on the most recent advances in male genital reconstruction after trauma,excision of benign and malignant disease,in gender reassignment surgery and aphallia with emphasis on surgical technique,cosmetic and functional outcome.

  8. The survival effect in memory: does it hold into old age and non-ancestral scenarios?

    Science.gov (United States)

    Yang, Lixia; Lau, Karen P L; Truong, Linda

    2014-01-01

    The survival effect in memory refers to the memory enhancement for materials encoded in reference to a survival scenario compared to those encoded in reference to a control scenario or with other encoding strategies. The current study examined whether this effect is well maintained in old age by testing young (ages 18-29) and older adults (ages 65-87) on the survival effect in memory for words encoded in ancestral and/or non-ancestral modern survival scenarios relative to a non-survival control scenario. A pilot study was conducted to select the best matched comparison scenarios based on potential confounding variables, such as valence and arousal. Experiment 1 assessed the survival effect with a well-matched negative control scenario in both young and older adults. The results showed an age-equivalent survival effect across an ancestral and a non-ancestral modern survival scenario. Experiment 2 replicated the survival effect in both age groups with a positive control scenario. Taken together, the data suggest a robust survival effect that is well preserved in old age across ancestral and non-ancestral survival scenarios.

  9. Evaluation of list-mode ordered subset expectation maximization image reconstruction for pixelated solid-state compton gamma camera with large number of channels

    Science.gov (United States)

    Kolstein, M.; De Lorenzo, G.; Chmeissani, M.

    2014-04-01

    The Voxel Imaging PET (VIP) Pathfinder project intends to show the advantages of using pixelated solid-state technology for nuclear medicine applications. It proposes designs for Positron Emission Tomography (PET), Positron Emission Mammography (PEM) and Compton gamma camera detectors with a large number of signal channels (of the order of 106). For Compton camera, especially with a large number of readout channels, image reconstruction presents a big challenge. In this work, results are presented for the List-Mode Ordered Subset Expectation Maximization (LM-OSEM) image reconstruction algorithm on simulated data with the VIP Compton camera design. For the simulation, all realistic contributions to the spatial resolution are taken into account, including the Doppler broadening effect. The results show that even with a straightforward implementation of LM-OSEM, good images can be obtained for the proposed Compton camera design. Results are shown for various phantoms, including extended sources and with a distance between the field of view and the first detector plane equal to 100 mm which corresponds to a realistic nuclear medicine environment.

  10. Stable isotopic analysis of fossil chironomids as an approach to environmental reconstruction: state of development and future challenges

    Directory of Open Access Journals (Sweden)

    Oliver Heiri

    2012-10-01

    Full Text Available Remains of chironomid larvae, especially their strongly sclerotized head capsules, can be found abundantly and well preserved in most lake sediment records. These remains mainly consist of chitin and proteins and, since their chemical composition does not seem to be strongly affected by decompositional processes, they can be used to develop palaeoenvironmental reconstructions based on their stable isotopic composition. Here we review available stable isotope studies based on fossil chironomids and indicate future research necessary to further develop this still relatively new research approach. Efforts to produce stable isotope records based on fossil chironomids have mainly examined the elements H, N, C, and O. They have focussed on (1 developing the methodology for preparing samples for isotopic analysis, (2 laboratory studies cultivating chironomid larvae under controlled conditions to determine the factors affecting their stable isotopic composition, (3 ecosystem-scale studies relating stable isotopic measurements of fossil chironomid assemblages to environmental conditions, and (4 developing first down-core records describing past changes in the stable isotopic composition of chironomid assemblages. These studies have shown that chemical sample pretreatment may affect the isotopic composition for some elements. Laboratory runs suggest that the diet of the larvae influences their stable isotopic composition for H, N, C and O, whereas stable isotopes in the ambient water also strongly influence their oxygen and to a lesser extent hydrogen isotopic composition. These experiments also indicate only minor offsets between the nitrogen and carbon isotopic composition of chironomid soft tissue and the fossilizing head capsules, whereas for hydrogen and oxygen this offset remains to be explored. Though few datasets have been published, the available ecosystem studies and developed down-core sediment records indicate that stable isotopes in

  11. Ligament reconstruction.

    Science.gov (United States)

    Glickel, Steven Z; Gupta, Salil

    2006-05-01

    Volar ligament reconstruction is an effective technique for treating symptomatic laxity of the CMC joint of the thumb. The laxity may bea manifestation of generalized ligament laxity,post-traumatic, or metabolic (Ehler-Danlos). There construction reduces the shear forces on the joint that contribute to the development and persistence of inflammation. Although there have been only a few reports of the results of volar ligament reconstruction, the use of the procedure to treat Stage I and Stage II disease gives good to excellent results consistently. More advanced stages of disease are best treated by trapeziectomy, with or without ligament reconstruction.

  12. The Paradox of Religion: The (reConstruction of Hindu and Muslim Identities amongst South Asian Diasporas in the United States

    Directory of Open Access Journals (Sweden)

    Aminah Mohammad-Arif

    2007-10-01

    Full Text Available In the process of (reconstructing their identities in an alien society, South Asians have tended to give to religion a significant importance. This salience of religion owes as much to the dislocation and the stigmatization engendered by the migration experience as to the local context, the United States, who, while promoting a policy of multiculturalism, sees religion as an ‘acceptable’ identity marker. Drawing on this process, this article examines the implications on the inter-ethnic relationships, in particular between Hindus and Muslims (both Indian and Pakistani, as two opposite and competing trends are underway: on the one hand, separate, if not confrontational, Hindu and Muslim identities are arising, while on the other hand, a South Asian identity, ignoring the borders of Partition, is shaping up.

  13. Rapid fat-suppressed isotropic steady-state free precession imaging using true 3D multiple-half-echo projection reconstruction.

    Science.gov (United States)

    Lu, Aiming; Brodsky, Ethan; Grist, Thomas M; Block, Walter F

    2005-03-01

    Three-dimensional projection reconstruction (3D PR)-based techniques are advantageous for steady-state free precession (SSFP) imaging for several reasons, including the capability to achieve short repetition times (TRs). In this paper, a multi-half-echo technique is presented that dramatically improves the data-sampling efficiency of 3D PR sequences while it retains this short-TR capability. The k-space trajectory deviations are measured quickly and corrected on a per-sample point basis. A two-pass RF cycling technique is then applied to the dual-half-echo implementation to generate fat/water-separated images. The resultant improvement in the signal-to-noise ratio (SNR) and contrast-to-noise ratio (CNR) was demonstrated in volunteer studies. Volumetric images with excellent spatial resolution, coverage, and contrast were obtained with high speed. The non-contrast-enhanced SSFP studies show that this technique has promising potential for MR angiography (MRA).

  14. Detailed reconstruction of the functional state of the Central Yamal khasyrey as a response to local conditions and regional climate changes in the late Holocene

    Science.gov (United States)

    Preis, Yu I.; Simonova, G. V.; Slagoda, E. A.

    2016-11-01

    In this article, data of reconstruction of the dynamics of plant communities, water regimes, geocryological conditions, and peat accumulation of the khasyrey of Central Yamal Peninsula located in the tundra of Western Siberia by traditional paleoecological methods on the basis of detailed studies of the botanical composition, degree of decomposition, density, ash content and δ13C in the cellulose of peat cut pulp age about 1300 cal. BP are considered. It has been shown that the khasyrey has a sensitive response on century and decadal scales to climate change and the lake regime level. Moreover, the stages of khasyrey functional state are in a good agreement with similar data on mires of the forest zone of Western Siberia and the solar activity periods.

  15. Climate Reconstructions

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The NOAA Paleoclimatology Program archives reconstructions of past climatic conditions derived from paleoclimate proxies, in addition to the Program's large holdings...

  16. Breast Reconstruction

    Science.gov (United States)

    ... senos Preguntas Para el Médico Datos Para la Vida Komen El cuidado de sus senos:Consejos útiles ... that can help . Federal law requires most insurance plans cover the cost of breast reconstruction. Learn more ...

  17. Twentieth century ENSO-related precipitation mean states in twentieth century reanalysis, reconstructed precipitation and CMIP5 models

    Science.gov (United States)

    Dai, Ni; Arkin, Phillip A.

    2016-07-01

    El Niño-Southern Oscillation (ENSO)-related precipitation during the entire twentieth century is compared among the twentieth century reanalysis (20CR), a statistically reconstructed precipitation dataset (REC) and 30 Coupled Model Intercomparison Project Phase 5 (CMIP5) models. Empirical orthogonal functions, ENSO-related precipitation composites based on sea surface temperature (SST)-constructed ENSO index and singular value decomposition (SVD) are employed to extract ENSO-related precipitation/SST signals in each dataset. With the background trend being removed in all of the data, our results show that the REC and the 20CR resemble both in their precipitation climatology and ENSO-related precipitation results. The biases in the CMIP5 models precipitation climatology such as dry equator over the Pacific Ocean, "double-intertropical convergence zones (ITCZs)" and overly zonal Southern Pacific convergence zone (SPCZ) are major reasons for lowering spatial correlations with the REC and the 20CR precipitation climatology. Two groups of CMIP5 models are built based on severity of these biases in their precipitation background and the spatial correlations of ENSO-related precipitation with the observations. Compared with the group with more severe biases in its precipitation climatology, the group with smaller biases tends to produce more ENSO-like precipitation patterns, simulate more realistic mean magnitude and seasonal variability of ENSO precipitation signals, as well as generating better ENSO-related SST/precipitation correlation patterns produced in its SVD analysis. The ENSO-related precipitation biases in the CMIP5 models over the western Pacific and Indian Ocean, as well as the equatorial Pacific, are strongly related with their precipitation climatology biases over these regions. The ENSO-related precipitation biases over the off-equator eastern Pacific Ocean are associated with both the "double-ITCZs" biases in the precipitation climatology and the ENSO

  18. Sequence-Length Requirement of Distance-Based Phylogeny Reconstruction: Breaking the Polynomial Barrier

    CERN Document Server

    Roch, Sebastien

    2009-01-01

    We introduce a new distance-based phylogeny reconstruction technique which provably achieves, at sufficiently short branch lengths, a polylogarithmic sequence-length requirement -- improving significantly over previous polynomial bounds for distance-based methods. The technique is based on an averaging procedure that implicitly reconstructs ancestral sequences. In the same token, we extend previous results on phase transitions in phylogeny reconstruction to general time-reversible models. More precisely, we show that in the so-called Kesten-Stigum zone (roughly, a region of the parameter space where ancestral sequences are well approximated by ``linear combinations'' of the observed sequences) sequences of length $\\poly(\\log n)$ suffice for reconstruction when branch lengths are discretized. Here $n$ is the number of extant species. Our results challenge, to some extent, the conventional wisdom that estimates of evolutionary distances alone carry significantly less information about phylogenies than full sequ...

  19. Reconstructing Large-Scale Brain Resting-State Networks from High-Resolution EEG: Spatial and Temporal Comparisons with fMRI.

    Science.gov (United States)

    Yuan, Han; Ding, Lei; Zhu, Min; Zotev, Vadim; Phillips, Raquel; Bodurka, Jerzy

    2016-03-01

    Functional magnetic resonance imaging (fMRI) studies utilizing measures of hemodynamic signal, such as the blood oxygenation level-dependent (BOLD) signal, have discovered that resting-state brain activities are organized into multiple large-scale functional networks, coined as resting-state networks (RSNs). However, an important limitation of the available fMRI studies is that hemodynamic signals only provide an indirect measure of the neuronal activity. In contrast, electroencephalography (EEG) directly measures electrophysiological activity of the brain. However, little is known about the brain-wide organization of such spontaneous neuronal population signals at the resting state. It is not entirely clear if or how the network structure built upon slowly fluctuating hemodynamic signals is represented in terms of fast, dynamic, and spontaneous neuronal activity. In this study, we investigated the electrophysiological representation of RSNs from simultaneously acquired EEG and fMRI data in the resting human brain. We developed a data-driven analysis approach that reconstructed multiple large-scale electrophysiological networks from high-resolution EEG data alone. The networks derived from EEG were then compared with RSNs independently derived from simultaneously acquired fMRI in their spatial structures as well as temporal dynamics. Results reveal spatially and temporally specific electrophysiological correlates for the fMRI-RSNs. Findings suggest that the spontaneous activity of various large-scale cortical networks is reflected in macroscopic EEG potentials.

  20. Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs.

    Science.gov (United States)

    Green, Richard E; Braun, Edward L; Armstrong, Joel; Earl, Dent; Nguyen, Ngan; Hickey, Glenn; Vandewege, Michael W; St John, John A; Capella-Gutiérrez, Salvador; Castoe, Todd A; Kern, Colin; Fujita, Matthew K; Opazo, Juan C; Jurka, Jerzy; Kojima, Kenji K; Caballero, Juan; Hubley, Robert M; Smit, Arian F; Platt, Roy N; Lavoie, Christine A; Ramakodi, Meganathan P; Finger, John W; Suh, Alexander; Isberg, Sally R; Miles, Lee; Chong, Amanda Y; Jaratlerdsiri, Weerachai; Gongora, Jaime; Moran, Christopher; Iriarte, Andrés; McCormack, John; Burgess, Shane C; Edwards, Scott V; Lyons, Eric; Williams, Christina; Breen, Matthew; Howard, Jason T; Gresham, Cathy R; Peterson, Daniel G; Schmitz, Jürgen; Pollock, David D; Haussler, David; Triplett, Eric W; Zhang, Guojie; Irie, Naoki; Jarvis, Erich D; Brochu, Christopher A; Schmidt, Carl J; McCarthy, Fiona M; Faircloth, Brant C; Hoffmann, Federico G; Glenn, Travis C; Gabaldón, Toni; Paten, Benedict; Ray, David A

    2014-12-12

    To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes of three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus (the saltwater crocodile), and Gavialis gangeticus (the Indian gharial). We observed an exceptionally slow rate of genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content and movement, gene family evolution, and chromosomal synteny. When placed within the context of related taxa including birds and turtles, this suggests that the common ancestor of all of these taxa also exhibited slow genome evolution and that the comparatively rapid evolution is derived in birds. The data also provided the opportunity to analyze heterozygosity in crocodilians, which indicates a likely reduction in population size for all three taxa through the Pleistocene. Finally, these data combined with newly published bird genomes allowed us to reconstruct the partial genome of the common ancestor of archosaurs, thereby providing a tool to investigate the genetic starting material of crocodilians, birds, and dinosaurs.

  1. Comprehensive phylogenetic analysis of all species of swordtails and platies (Pisces: Genus Xiphophorus uncovers a hybrid origin of a swordtail fish, Xiphophorus monticolus, and demonstrates that the sexually selected sword originated in the ancestral lineage of the genus, but was lost again secondarily

    Directory of Open Access Journals (Sweden)

    Kang Ji Hyoun

    2013-01-01

    Full Text Available Abstract Background Males in some species of the genus Xiphophorus, small freshwater fishes from Meso-America, have an extended caudal fin, or sword – hence their common name “swordtails”. Longer swords are preferred by females from both sworded and – surprisingly also, non-sworded (platyfish species that belong to the same genus. Swordtails have been studied widely as models in research on sexual selection. Specifically, the pre-existing bias hypothesis was interpreted to best explain the observed bias of females in presumed ancestral lineages of swordless species that show a preference for assumed derived males with swords over their conspecific swordless males. However, many of the phylogenetic relationships within this genus still remained unresolved. Here we construct a comprehensive molecular phylogeny of all 26 known Xiphophorus species, including the four recently described species (X. kallmani, X. mayae, X. mixei and X. monticolus. We use two mitochondrial and six new nuclear markers in an effort to increase the understanding of the evolutionary relationships among the species in this genus. Based on the phylogeny, the evolutionary history and character state evolution of the sword was reconstructed and found to have originated in the common ancestral lineage of the genus Xiphophorus and that it was lost again secondarily. Results We estimated the evolutionary relationships among all known species of the genus Xiphophorus based on the largest set of DNA markers so far. The phylogeny indicates that one of the newly described swordtail species, Xiphophorus monticolus, is likely to have arisen through hybridization since it is placed with the southern platyfish in the mitochondrial phylogeny, but with the southern swordtails in the nuclear phylogeny. Such discordance between these two types of markers is a strong indication for a hybrid origin. Additionally, by using a maximum likelihood approach the possession of the sexually

  2. Vertex Reconstruction in CMS

    CERN Document Server

    Chabanat, E; D'Hondt, J; Vanlaer, P; Prokofiev, K; Speer, T; Frühwirth, R; Waltenberger, W

    2005-01-01

    Because of the high track multiplicity in the final states expected in proton collisions at the LHC experiments, novel vertex reconstruction algorithms are required. The vertex reconstruction problem can be decomposed into a pattern recognition problem ("vertex finding") and an estimation problem ("vertex fitting"). Starting from least-square methods, ways to render the classical algorithms more robust are discussed and the statistical properties of the novel methods are shown. A whole set of different approaches for the vertex finding problem is presented and compared in relevant physics channels.

  3. Common 5' beta-globin RFLP haplotypes harbour a surprising level of ancestral sequence mosaicism.

    Science.gov (United States)

    Webster, Matthew T; Clegg, John B; Harding, Rosalind M

    2003-07-01

    Blocks of linkage disequilibrium (LD) in the human genome represent segments of ancestral chromosomes. To investigate the relationship between LD and genealogy, we analysed diversity associated with restriction fragment length polymorphism (RFLP) haplotypes of the 5' beta-globin gene complex. Genealogical analyses were based on sequence alleles that spanned a 12.2-kb interval, covering 3.1 kb around the psibeta gene and 6.2 kb of the delta-globin gene and its 5' flanking sequence known as the R/T region. Diversity was sampled from a Kenyan Luo population where recent malarial selection has contributed to substantial LD. A single common sequence allele spanning the 12.2-kb interval exclusively identified the ancestral chromosome bearing the "Bantu" beta(s) (sickle-cell) RFLP haplotype. Other common 5' RFLP haplotypes comprised interspersed segments from multiple ancestral chromosomes. Nucleotide diversity was similar between psibeta and R/T-delta-globin but was non-uniformly distributed within the R/T-delta-globin region. High diversity associated with the 5' R/T identified two ancestral lineages that probably date back more than 2 million years. Within this genealogy, variation has been introduced into the 3' R/T by gene conversion from other ancestral chromosomes. Diversity in delta-globin was found to lead through parts of the main genealogy but to coalesce in a more recent ancestor. The well-known recombination hotspot is clearly restricted to the region 3' of delta-globin. Our analyses show that, whereas one common haplotype in a block of high LD represents a long segment from a single ancestral chromosome, others are mosaics of short segments from multiple ancestors related in genealogies of unsuspected complexity.

  4. Evolution of echinoderms may not have required modification of the ancestral deuterostome HOX gene cluster: first report of PG4 and PG5 Hox orthologues in echinoderms.

    Science.gov (United States)

    Long, Suzanne; Martinez, Pedro; Chen, Wei-Chung; Thorndyke, Michael; Byrne, Maria

    2003-11-01

    Is the extreme derivation of the echinoderm body plan reflected in a derived echinoderm Hox genotype? Building on previous work, we exploited the sequence conservation of the homeobox to isolate putative orthologues of several Hox genes from two asteroid echinoderms. The 5-peptide motif (LPNTK) diagnostic of PG4 Hox genes was identified immediately downstream of one of the partial homeodomains from Patiriella exigua. This constitutes the first unequivocal report of a PG4 Hox gene orthologue from an echinoderm. Subsequent screenings identified genes of both PG4 and PG4/5 in Asterias rubens. Although in echinoids only a single gene (PG4/5) occupies these two contiguous cluster positions, we conclude that the ancestral echinoderm must have had the complete deuterostome suite of medial Hox genes, including orthologues of both PG4 and PG4/5 (=PG5). The reported absence of PG4 in the HOX cluster of echinoids is therefore a derived state, and the ancestral echinoderm probably had a HOX cluster not dissimilar to that of other deuterostomes. Modification of the ancestral deuterostome Hox genotype may not have been required for evolution of the highly derived echinoderm body plan.

  5. Testing the museum versus cradle tropical biological diversity hypothesis: phylogeny, diversification, and ancestral biogeographic range evolution of the ants.

    Science.gov (United States)

    Moreau, Corrie S; Bell, Charles D

    2013-08-01

    Ants are one of the most ecologically and numerically dominant group of terrestrial organisms with most species diversity currently found in tropical climates. Several explanations for the disparity of biological diversity in the tropics compared to temperate regions have been proposed including that the tropics may act as a "museum" where older lineages persist through evolutionary time or as a "cradle" where new species continue to be generated. We infer the molecular phylogenetic relationships of 295 ant specimens including members of all 21 extant subfamilies to explore the evolutionary diversification and biogeography of the ants. By constraining the topology and age of the root node while using 45 fossils as minimum constraints, we converge on an age of 139-158 Mya for the modern ants. Further diversification analyses identified 10 periods with a significant change in the tempo of diversification of the ants, although these shifts did not appear to correspond to ancestral biogeographic range shifts. Likelihood-based historical biogeographic reconstructions suggest that the Neotropics were important in early ant diversification (e.g., Cretaceous). This finding coupled with the extremely high-current species diversity suggests that the Neotropics have acted as both a museum and cradle for ant diversity.

  6. Nonlinear Reconstruction

    CERN Document Server

    Zhu, Hong-Ming; Pen, Ue-Li; Chen, Xuelei; Yu, Hao-Ran

    2016-01-01

    We present a direct approach to non-parametrically reconstruct the linear density field from an observed non-linear map. We solve for the unique displacement potential consistent with the non-linear density and positive definite coordinate transformation using a multigrid algorithm. We show that we recover the linear initial conditions up to $k\\sim 1\\ h/\\mathrm{Mpc}$ with minimal computational cost. This reconstruction approach generalizes the linear displacement theory to fully non-linear fields, potentially substantially expanding the BAO and RSD information content of dense large scale structure surveys, including for example SDSS main sample and 21cm intensity mapping.

  7. Between participation and resistance: reconstruction of the social fabric from below, beyond the logic of the state

    Directory of Open Access Journals (Sweden)

    Juan David Villa Gómez

    2016-07-01

    Full Text Available The findings around the meanings and social constructions of the participants of the municipality of San Carlos, Antioquia around the State repairs for the victims of the armed conflict in Colombia (Law 1448 are related. It was found that reparative processes, are not being fully developed. On the other hand, in some cases, re-victimizing actions were evident, which, according to our perception, could imply barriers in the transition from war to peace national reconciliation, and the recovery ofthe victims (Villa Gómez & Insuasty Rodríguez, 2015 & (Villa Gómez & Insuasty Rodríguez, 2016 in Colombia, which are key to be taken into account in the current Negotiation process and transition of the armed conflict between the insurgency of the FARC-EP and the national Government, and the possible process with the ELN insurgency.

  8. ACL reconstruction - discharge

    Science.gov (United States)

    Anterior cruciate ligament reconstruction - discharge; ACL reconstruction - discharge ... had surgery to reconstruct your anterior cruciate ligament (ACL). The surgeon drilled holes in the bones of ...

  9. Inheritance of the 8.1 ancestral haplotype in recurrent pregnancy loss

    DEFF Research Database (Denmark)

    Kolte, Astrid M; Nielsen, Henriette S; Steffensen, Rudi;

    2015-01-01

    BACKGROUND AND OBJECTIVES: The 8.1 ancestral haplotype (AH) (HLA-A1, C7, B8, C4AQ0, C4B1, DR3, DQ2) is a remarkably long and conserved haplotype in the human major histocompatibility complex. It has been associated with both beneficial and detrimental effects, consistent with antagonistic pleiotr...

  10. Language Shift and Maintenance in Multilingual Mauritius: The Case of Indian Ancestral Languages

    Science.gov (United States)

    Bissoonauth, Anu

    2011-01-01

    This paper reports on a research study conducted in Mauritius between June and July 2009. The aim of this research was to investigate the use of Indian ancestral languages in the domestic domain by the younger generations. The data were collected in the field by means of a questionnaire and interviews from a quota sample of secondary school…

  11. Ancestral TCDD exposure promotes epigenetic transgenerational inheritance of imprinted gene Igf2: Methylation status and DNMTs.

    Science.gov (United States)

    Ma, Jing; Chen, Xi; Liu, Yanan; Xie, Qunhui; Sun, Yawen; Chen, Jingshan; Leng, Ling; Yan, Huan; Zhao, Bin; Tang, Naijun

    2015-12-01

    Ancestral TCDD exposure could induce epigenetic transgenerational phenotypes, which may be mediated in part by imprinted gene inheritance. The aim of our study was to evaluate the transgenerational effects of ancestral TCDD exposure on the imprinted gene insulin-like growth factor-2 (Igf2) in rat somatic tissue. TCDD was administered daily by oral gavage to groups of F0 pregnant SD rats at dose levels of 0 (control), 200 or 800 ng/kg bw during gestation day 8-14. Animal transgenerational model of ancestral exposure to TCDD was carefully built, avoiding sibling inbreeding. Hepatic Igf2 expression of the TCDD male progeny was decreased concomitantly with hepatic damage and increased activities of serum hepatic enzymes both in the F1 and F3 generation. Imprinted Control Region (ICR) of Igf2 manifested a hypermethylated pattern, whereas methylation status in the Differentially Methylated Region 2 (DMR2) showed a hypomethylated manner in the F1 generation. These epigenetic alterations in these two regions maintained similar trends in the F3 generation. Meanwhile, the expressions of DNA methyltransferases (DNMT1, DNMT3A and DNMT3B) changed in a non-monotonic manner both in the F1 and F3 generation. This study provides evidence that ancestral TCDD exposure may promote epigenetic transgenerational alterations of imprinted gene Igf2 in adult somatic tissue.

  12. Reconstruction of the Palaeo-environment of the Alluvial Deposits in the Eastern Free State, South Africa

    Science.gov (United States)

    Evans, M. Y.

    2009-04-01

    Small alluvial fan systems have formed off the hillslopes of the remnant Karoo koppies at Heelbo in the Eastern Free State, South Africa. The landform geometry is a result of complex relationships between climate, lithology, structure and vegetation. This research area, which includes a large mammal mass death site, potentially contains a wealth of palaeo-environmental and specifically palaeoclimatic information. Palaeo-environmental information and proxy records on past climates in southern Africa has traditionally been obtained from a variety of techniques including stable isotope analysis of speleothems, pollen , faunal analyses at archeological sites, animal remains and crater-lake sediments (see references below). However, little information exists in the scientific literature on the use of palaeosols for defining the depositional palaeoenvironments in southern Africa. The aim of this research is to attempt to address the lack of palaeo-environmental information by extracting palaeoclimatic information from the sedimentary processes and the palaeosols at the Heelbo farm that have been extensively exposed through gullying. The sedimentary fans in the area have experienced climatically controlled histories of erosion, sedimentation and pedogenesis. Extreme sedimentation is assumed to have occurred during relatively arid climatic intervals, when decreased vegetation cover provided little surface protection. In contrast pedogenesis occurs during humid intervals when vegetation cover is restored, the land stabilizes and the uppermost gravely sands weather to form soils. A combined approach of both radiocarbon- and luminescence -dating may provide a detailed chronology of these successive hillslope events in order to relate hillslope instability to climatic forcing factors. Preliminary results indicate that at least 3 depositional events are recorded within the large mammal mass death site, which have been confirmed by the radiocarbon dates of 3,610 ±110 in the top

  13. Breast Reconstruction Alternatives

    Science.gov (United States)

    ... Breast Reconstruction Surgery Breast Cancer Breast Reconstruction Surgery Breast Reconstruction Alternatives Some women who have had a ... chest. What if I choose not to get breast reconstruction? Some women decide not to have any ...

  14. Smooth Reconstruction

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Eighty percent of the reconstruction projects in Sichuan Province will be completed by the end of the year Despite ruins still seen everywhere in the earthquake-hit areas in Sichuan (Province, new buildings have been completed, and many people have moved into new houses. Through cameras of the media, the faces, once painful and melancholy after last year’s earthquake, now look confident and firm, gratifying people all over the

  15. Maxillary reconstruction

    Directory of Open Access Journals (Sweden)

    Brown James

    2007-12-01

    Full Text Available This article aims to discuss the various defects that occur with maxillectomy with a full review of the literature and discussion of the advantages and disadvantages of the various techniques described. Reconstruction of the maxilla can be relatively simple for the standard low maxillectomy that does not involve the orbital floor (Class 2. In this situation the structure of the face is less damaged and the there are multiple reconstructive options for the restoration of the maxilla and dental alveolus. If the maxillectomy includes the orbit (Class 4 then problems involving the eye (enopthalmos, orbital dystopia, ectropion and diplopia are avoided which simplifies the reconstruction. Most controversy is associated with the maxillectomy that involves the orbital floor and dental alveolus (Class 3. A case is made for the use of the iliac crest with internal oblique as an ideal option but there are other methods, which may provide a similar result. A multidisciplinary approach to these patients is emphasised which should include a prosthodontist with a special expertise for these defects.

  16. Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life

    Directory of Open Access Journals (Sweden)

    Richard Egel

    2012-01-01

    Full Text Available This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii an inherently complex communal system at the common root of present life forms; (iii a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial super-cells; (iv a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v multiple rounds of micro-cellular escape with streamlined reductive evolution—leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.

  17. Primal Eukaryogenesis: On the Communal Nature of Precellular States, Ancestral to Modern Life

    OpenAIRE

    Richard Egel

    2012-01-01

    This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) sup...

  18. Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life.

    Science.gov (United States)

    Egel, Richard

    2012-01-23

    This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.

  19. Afghanistan Reconstruction

    Institute of Scientific and Technical Information of China (English)

    Fu Xiaoqiang

    2006-01-01

    @@ The Karzai regime has made some progress over the past four years and a half in the post-war reconstruction.However, Taliban's destruction and drug economy are still having serious impacts on the security and stability of Afghanistan.Hence the settlement of the two problems has become a crux of affecting the country' s future.Moreover, the Karzai regime is yet to handle a series of hot potatoes in the fields of central government' s authority, military and police building-up and foreign relations as well.

  20. Ancestral genes can control the ability of horizontally acquired loci to confer new traits.

    Directory of Open Access Journals (Sweden)

    H Deborah Chen

    2011-07-01

    Full Text Available Horizontally acquired genes typically function as autonomous units conferring new abilities when introduced into different species. However, we reasoned that proteins preexisting in an organism might constrain the functionality of a horizontally acquired gene product if it operates on an ancestral pathway. Here, we determine how the horizontally acquired pmrD gene product activates the ancestral PmrA/PmrB two-component system in Salmonella enterica but not in the closely related bacterium Escherichia coli. The Salmonella PmrD protein binds to the phosphorylated PmrA protein (PmrA-P, protecting it from dephosphorylation by the PmrB protein. This results in transcription of PmrA-dependent genes, including those conferring polymyxin B resistance. We now report that the E. coli PmrD protein can activate the PmrA/PmrB system in Salmonella even though it cannot do it in E. coli, suggesting that these two species differ in an additional component controlling PmrA-P levels. We establish that the E. coli PmrB displays higher phosphatase activity towards PmrA-P than the Salmonella PmrB, and we identified a PmrB subdomain responsible for this property. Replacement of the E. coli pmrB gene with the Salmonella homolog was sufficient to render E. coli resistant to polymyxin B under PmrD-inducing conditions. Our findings provide a singular example whereby quantitative differences in the biochemical activities of orthologous ancestral proteins dictate the ability of a horizontally acquired gene product to confer species-specific traits. And they suggest that horizontally acquired genes can potentiate selection at ancestral loci.

  1. The ancestral karyotype of Carnivora: comparison with that of platyrrhine monkeys.

    Science.gov (United States)

    Dutrillaux, B; Couturier, J

    1983-01-01

    The karyotypes of six species of Carnivora (Mungos mungo, Paradoxurus hermaphroditus, Potos flavus, Mustela furo, Felis serval, and Halichoerus grypus), representative of five different families, were studied and compared. Correspondence between almost all chromosome segments was found, and a presumed ancestral karyotype of Carnivora is proposed. Analogies to human chromosomes are also given, and the results obtained are in excellent agreement with previously published gene mapping data on man and the domestic cat.

  2. Diverse adaptations of an ancestral gill: a common evolutionary origin for wings, breathing organs, and spinnerets.

    Science.gov (United States)

    Damen, Wim G M; Saridaki, Theodora; Averof, Michalis

    2002-10-01

    Changing conditions of life impose new requirements on the morphology and physiology of an organism. One of these changes is the evolutionary transition from aquatic to terrestrial life, leading to adaptations in locomotion, breathing, reproduction, and mechanisms for food capture. We have shown previously that insects' wings most likely originated from one of the gills of ancestral aquatic arthropods during their transition to life on land. Here we investigate the fate of these ancestral gills during the evolution of another major arthropod group, the chelicerates. We examine the expression of two developmental genes, pdm/nubbin and apterous, that participate in the specification of insects' wings and are expressed in particular crustacean epipods/gills. In the horseshoe crab, a primitively aquatic chelicerate, pdm/nubbin is specifically expressed in opisthosomal appendages that give rise to respiratory organs called book gills. In spiders (terrestrial chelicerates), pdm/nubbin and apterous are expressed in successive segmental primordia that give rise to book lungs, lateral tubular tracheae, and spinnerets, novel structures that are used by spiders to breathe on land and to spin their webs. Combined with morphological and palaeontological evidence, these observations suggest that fundamentally different new organs (wings, air-breathing organs, and spinnerets) evolved from the same ancestral structure (gills) in parallel instances of terrestrialization.

  3. Ancestral informative marker selection and population structure visualization using sparse Laplacian eigenfunctions.

    Directory of Open Access Journals (Sweden)

    Jun Zhang

    Full Text Available Identification of a small panel of population structure informative markers can reduce genotyping cost and is useful in various applications, such as ancestry inference in association mapping, forensics and evolutionary theory in population genetics. Traditional methods to ascertain ancestral informative markers usually require the prior knowledge of individual ancestry and have difficulty for admixed populations. Recently Principal Components Analysis (PCA has been employed with success to select SNPs which are highly correlated with top significant principal components (PCs without use of individual ancestral information. The approach is also applicable to admixed populations. Here we propose a novel approach based on our recent result on summarizing population structure by graph laplacian eigenfunctions, which differs from PCA in that it is geometric and robust to outliers. Our approach also takes advantage of the priori sparseness of informative markers in the genome. Through simulation of a ring population and the real global population sample HGDP of 650K SNPs genotyped in 940 unrelated individuals, we validate the proposed algorithm at selecting most informative markers, a small fraction of which can recover the similar underlying population structure efficiently. Employing a standard Support Vector Machine (SVM to predict individuals' continental memberships on HGDP dataset of seven continents, we demonstrate that the selected SNPs by our method are more informative but less redundant than those selected by PCA. Our algorithm is a promising tool in genome-wide association studies and population genetics, facilitating the selection of structure informative markers, efficient detection of population substructure and ancestral inference.

  4. What was the ancestral sex-determining mechanism in amniote vertebrates?

    Science.gov (United States)

    Johnson Pokorná, Martina; Kratochvíl, Lukáš

    2016-02-01

    Amniote vertebrates, the group consisting of mammals and reptiles including birds, possess various mechanisms of sex determination. Under environmental sex determination (ESD), the sex of individuals depends on the environmental conditions occurring during their development and therefore there are no sexual differences present in their genotypes. Alternatively, through the mode of genotypic sex determination (GSD), sex is determined by a sex-specific genotype, i.e. by the combination of sex chromosomes at various stages of differentiation at conception. As well as influencing sex determination, sex-specific parts of genomes may, and often do, develop specific reproductive or ecological roles in their bearers. Accordingly, an individual with a mismatch between phenotypic (gonadal) and genotypic sex, for example an individual sex-reversed by environmental effects, should have a lower fitness due to the lack of specialized, sex-specific parts of their genome. In this case, evolutionary transitions from GSD to ESD should be less likely than transitions in the opposite direction. This prediction contrasts with the view that GSD was the ancestral sex-determining mechanism for amniote vertebrates. Ancestral GSD would require several transitions from GSD to ESD associated with an independent dedifferentiation of sex chromosomes, at least in the ancestors of crocodiles, turtles, and lepidosaurs (tuataras and squamate reptiles). In this review, we argue that the alternative theory postulating ESD as ancestral in amniotes is more parsimonious and is largely concordant with the theoretical expectations and current knowledge of the phylogenetic distribution and homology of sex-determining mechanisms.

  5. Ancestral sleep.

    Science.gov (United States)

    de la Iglesia, Horacio O; Moreno, Claudia; Lowden, Arne; Louzada, Fernando; Marqueze, Elaine; Levandovski, Rosa; Pilz, Luisa K; Valeggia, Claudia; Fernandez-Duque, Eduardo; Golombek, Diego A; Czeisler, Charles A; Skene, Debra J; Duffy, Jeanne F; Roenneberg, Till

    2016-04-01

    While we do not yet understand all the functions of sleep, its critical role for normal physiology and behaviour is evident. Its amount and temporal pattern depend on species and condition. Humans sleep about a third of the day with the longest, consolidated episode during the night. The change in lifestyle from hunter-gatherers via agricultural communities to densely populated industrialized centres has certainly affected sleep, and a major concern in the medical community is the impact of insufficient sleep on health [1,2]. One of the causal mechanisms leading to insufficient sleep is altered exposure to the natural light-dark cycle. This includes the wide availability of electric light, attenuated exposure to daylight within buildings, and evening use of light-emitting devices, all of which decrease the strength of natural light-dark signals that entrain circadian systems [3].

  6. 3D Reconstruction Technique for Tomographic PIV

    Institute of Scientific and Technical Information of China (English)

    姜楠; 包全; 杨绍琼

    2015-01-01

    Tomographic particle image velocimetry(Tomo-PIV) is a state-of-the-art experimental technique based on a method of optical tomography to achieve the three-dimensional(3D) reconstruction for three-dimensional three-component(3D-3C) flow velocity measurements. 3D reconstruction for Tomo-PIV is carried out herein. Meanwhile, a 3D simplified tomographic reconstruction model reduced from a 3D volume light inten-sity field with 2D projection images into a 2D Tomo-slice plane with 1D projecting lines, i.e., simplifying this 3D reconstruction into a problem of 2D Tomo-slice plane reconstruction, is applied thereafter. Two kinds of the most well-known algebraic reconstruction techniques, algebraic reconstruction technique(ART) and multiple algebraic reconstruction technique(MART), are compared as well. The principles of the two reconstruction algorithms are discussed in detail, which has been performed by a series of simulation images, yielding the corresponding recon-struction images that show different features between the ART and MART algorithm, and then their advantages and disadvantages are discussed. Further discussions are made for the standard particle image reconstruction when the background noise of the pre-initial particle image has been removed. Results show that the particle image recon-struction has been greatly improved. The MART algorithm is much better than the ART. Furthermore, the computa-tional analyses of two parameters(the particle density and the number of cameras), are performed to study their effects on the reconstruction. Lastly, the 3D volume particle field is reconstructed by using the improved algorithm based on the simplified 3D tomographic reconstruction model, which proves that the algorithm simplification is feasible and it can be applied to the reconstruction of 3D volume particle field in a Tomo-PIV system.

  7. Reconstruction of China’s Tax System under Modern State Governance%现代国家治理下我国税制体系的重构

    Institute of Scientific and Technical Information of China (English)

    朱为群; 曾军平

    2015-01-01

    现代国家治理下的税制体系重构,应该将增强税收筹资能力和税制的正当性建设作为基本目标,用公平正义统领税制体系架构,并基于公共品筹资、社会保障和特定政策调控等不同的征税目的来重构我国实体税制、基于法定原则来构建税收程序制度和基于公众同意原则来构建税收决策机制,坚持将社会精英主导的顶层设计与普通公众推动的探索实践相结合、长期目标与短期目标相协调和整体推进与重点突破相促进来推动我国税制体系的重构。%In the reconstruction China's tax system under modern state governance,the fundamental goal should be set to both increase the fund-raising ability of tax and construct the legitimacy of tax system.Fairness and justice should first be the leading force that gov-erns the structure of the tax system.China's substantive tax system should then be restructured on the basis of various taxation purposes such as financing of public goods,social security,and specific policy control.Also,the tax procedural system should be built on the principles of legality and the public consent rule should be the foundation of the mechanism of tax decision-making.Finally,to a-chieve the goal,persistent efforts should be made to combine the top level design initiated by social elites with the experiments and practice by ordinary people,to coordinate long-term goals with short-term goals,and to impel the mutual promotion of overall pro-gress and key breakthrough.

  8. Reconstructive Urology

    Directory of Open Access Journals (Sweden)

    Fikret Fatih Önol

    2014-11-01

    Full Text Available In the treatment of urethral stricture, Buccal Mucosa Graft (BMG and reconstruction is applied with different patch techniques. Recently often prefered, this approach is, in bulber urethra strictures of BMG’s; by “ventral onley”, in pendulous urethra because of thinner spingiosis body, which provides support and nutrition of graft; by means of “dorsal inley” being anastomosis. In the research that Cordon et al. did, they compared conventional BMJ “onley” urethroplast and “pseudo-spongioplasty” which base on periurethral vascular tissues to be nourished by closing onto graft. In repairment of front urethras that spongiosis supportive tissue is insufficient, this method is defined as peripheral dartos [çevre dartos?] and buck’s fascia being mobilized and being combined on BMG patch. Between the years 2007 and 2012, assessment of 56 patients with conventional “ventral onley” BMG urethroplast and 46 patients with “pseudo-spongioplasty” were reported to have similar success rates (80% to 84% in 3.5 year follow-up on average. While 74% of the patients that were applied pseudo-spongioplasty had disease present at distal urethra (pendulous, bulbopendulous, 82% of the patients which were applied conventional onley urethroplast had stricture at proximal (bulber urethra yet. Also lenght of the stricture at the pseudo-spongioplasty group was longer in a statistically significant way (5.8 cm to 4.7 cm on average, p=0.028. This study which Cordon et al. did, shows that conditions in which conventional sponjiyoplasti is not possible, periurethral vascular tissues are adequate to nourish BMG. Even it is an important technique in terms of bringing a new point of view to today’s practice, data especially about complications that may show up after pseudo-spongioplasty usage on long distal strictures (e.g. appearance of urethral diverticulum is not reported. Along with this we think that, providing an oppurtinity to patch directly

  9. Evidence that the ancestral haplotype in Australian hemochromatosis patients may be associated with a common mutation in the gene

    Energy Technology Data Exchange (ETDEWEB)

    Crawford, D.H.G.; Powell, L.W.; Leggett, B.A. [Univ. of Queensland (Australia)] [and others

    1995-08-01

    Hemochromatosis (HC) is a common inherited disorder of iron metabolism for which neither the gene nor biochemical defect have yet been identified. The aim of this study was to look for clinical evidence that the predominant ancestral haplotype in Australian patients is associated with a common mutation in the gene. We compared indices of iron metabolism and storage in three groups of HC patients categorized according to the presence of the ancestral haplotype (i.e., patients with two copies, one copy, and no copies of the ancestral haplotype). We also examined iron indices in two groups of HC heterozygotes (those with the ancestral haplotype and those without) and in age-matched controls. These analyses indicate that (i) HC patients with two copies of the ancestral haplotype show significantly more severe expression of the disorder than those with one copy or those without, (ii) HC heterozygotes have partial clinical expression, which may be influenced by the presence of the ancestral haplotype in females but not in males, and (iii) the high population frequency of the HC gene may be the result of the selective advantage conferred by protecting heterozygotes against iron deficiency. 18 refs., 3 tabs.

  10. Cochlear gene therapy with ancestral AAV in adult mice: complete transduction of inner hair cells without cochlear dysfunction

    Science.gov (United States)

    Suzuki, Jun; Hashimoto, Ken; Xiao, Ru; Vandenberghe, Luk H.; Liberman, M. Charles

    2017-01-01

    The use of viral vectors for inner ear gene therapy is receiving increased attention for treatment of genetic hearing disorders. Most animal studies to date have injected viral suspensions into neonatal ears, via the round window membrane. Achieving transduction of hair cells, or sensory neurons, throughout the cochlea has proven difficult, and no studies have been able to efficiently transduce sensory cells in adult ears while maintaining normal cochlear function. Here, we show, for the first time, successful transduction of all inner hair cells and the majority of outer hair cells in an adult cochlea via virus injection into the posterior semicircular canal. We used a “designer” AAV, AAV2/Anc80L65, in which the main capsid proteins approximate the ancestral sequence state of AAV1, 2, 8, and 9. Our injections also transduced ~10% of spiral ganglion cells and a much larger fraction of their satellite cells. In the vestibular sensory epithelia, the virus transduced large numbers of hair cells and virtually all the supporting cells, along with close to half of the vestibular ganglion cells. We conclude that this viral vector and this delivery route hold great promise for gene therapy applications in both cochlear and vestibular sense organs. PMID:28367981

  11. Neanderthal and Denisova genetic affinities with contemporary humans: introgression versus common ancestral polymorphisms.

    Science.gov (United States)

    Lowery, Robert K; Uribe, Gabriel; Jimenez, Eric B; Weiss, Mark A; Herrera, Kristian J; Regueiro, Maria; Herrera, Rene J

    2013-11-01

    Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1-4% of the non-Sub-Saharan African gene pool may be Neanderthal derived, while 6-8% of the Melanesian gene pool may be the product of admixture between the Denisovans and the direct ancestors of Melanesians. In the present study, we analyzed single nucleotide polymorphism (SNP) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee). We partitioned SNPs into subsets, including those that are derived in both archaic lineages, those that are ancestral in both archaic lineages and those that are only derived in one archaic lineage. By doing this, we have conducted separate examinations of subsets of mutations with higher probabilities of divergent phylogenetic origins. While previous investigations have excluded SNPs from common ancestors in principal component analyses, we included common ancestral SNPs in our analyses to visualize the relative placement of the Neanderthal and Denisova among human populations. To assess the genetic similarities among the various hominin lineages, we performed genetic structure analyses to provide a comparison of genetic patterns found within contemporary human genomes that may have archaic or common ancestral roots. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Our results suggest that Neanderthal genetic associations with contemporary non-Sub-Saharan African populations, as well as the genetic affinities observed between Denisovans and Melanesians most likely result from the retention of ancient mutations in these populations.

  12. Chromosome painting in three-toed sloths: a cytogenetic signature and ancestral karyotype for Xenarthra

    Directory of Open Access Journals (Sweden)

    Azevedo Nathália F

    2012-03-01

    Full Text Available Abstract Background Xenarthra (sloths, armadillos and anteaters represent one of four currently recognized Eutherian mammal supraorders. Some phylogenomic studies point to the possibility of Xenarthra being at the base of the Eutherian tree, together or not with the supraorder Afrotheria. We performed painting with human autosomes and X-chromosome specific probes on metaphases of two three-toed sloths: Bradypus torquatus and B. variegatus. These species represent the fourth of the five extant Xenarthra families to be studied with this approach. Results Eleven human chromosomes were conserved as one block in both B. torquatus and B. variegatus: (HSA 5, 6, 9, 11, 13, 14, 15, 17, 18, 20, 21 and the X chromosome. B. torquatus, three additional human chromosomes were conserved intact (HSA 1, 3 and 4. The remaining human chromosomes were represented by two or three segments on each sloth. Seven associations between human chromosomes were detected in the karyotypes of both B. torquatus and B. variegatus: HSA 3/21, 4/8, 7/10, 7/16, 12/22, 14/15 and 17/19. The ancestral Eutherian association 16/19 was not detected in the Bradypus species. Conclusions Our results together with previous reports enabled us to propose a hypothetical ancestral Xenarthran karyotype with 48 chromosomes that would differ from the proposed ancestral Eutherian karyotype by the presence of the association HSA 7/10 and by the split of HSA 8 into three blocks, instead of the two found in the Eutherian ancestor. These same chromosome features point to the monophyly of Xenarthra, making this the second supraorder of placental mammals to have a chromosome signature supporting its monophyly.

  13. Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data.

    Directory of Open Access Journals (Sweden)

    Art F Y Poon

    Full Text Available At the early stage of infection, human immunodeficiency virus (HIV-1 predominantly uses the CCR5 coreceptor for host cell entry. The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progression to AIDS. The presence of a 'fitness valley' separating CCR5- and CXCR4-using genotypes is postulated to be a biological determinant of whether the HIV coreceptor switch occurs. Using phylogenetic methods to reconstruct the evolutionary dynamics of HIV within hosts enables us to discriminate between competing models of this process. We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data. These data were generated by next-generation sequencing of HIV RNA extracted from longitudinal serum samples (median 7 time points from 8 untreated subjects with chronic HIV infections (Amsterdam Cohort Studies on HIV-1 infection and AIDS. We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days. HIV coreceptor usage was predicted from reconstructed ancestral sequences using the geno2pheno algorithm. We determined that the first mutations contributing to CXCR4 use emerged about 16 (per subject range 4 to 30 months before the earliest predicted CXCR4-using ancestor, which preceded the first positive cell-based assay of CXCR4 usage by 10 (range 5 to 25 months. CXCR4 usage arose in multiple lineages within 5 of 8 subjects, and ancestral lineages following alternate mutational pathways before going extinct were common. We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant.

  14. Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data.

    Science.gov (United States)

    Poon, Art F Y; Swenson, Luke C; Bunnik, Evelien M; Edo-Matas, Diana; Schuitemaker, Hanneke; van 't Wout, Angélique B; Harrigan, P Richard

    2012-01-01

    At the early stage of infection, human immunodeficiency virus (HIV)-1 predominantly uses the CCR5 coreceptor for host cell entry. The subsequent emergence of HIV variants that use the CXCR4 coreceptor in roughly half of all infections is associated with an accelerated decline of CD4+ T-cells and rate of progression to AIDS. The presence of a 'fitness valley' separating CCR5- and CXCR4-using genotypes is postulated to be a biological determinant of whether the HIV coreceptor switch occurs. Using phylogenetic methods to reconstruct the evolutionary dynamics of HIV within hosts enables us to discriminate between competing models of this process. We have developed a phylogenetic pipeline for the molecular clock analysis, ancestral reconstruction, and visualization of deep sequence data. These data were generated by next-generation sequencing of HIV RNA extracted from longitudinal serum samples (median 7 time points) from 8 untreated subjects with chronic HIV infections (Amsterdam Cohort Studies on HIV-1 infection and AIDS). We used the known dates of sampling to directly estimate rates of evolution and to map ancestral mutations to a reconstructed timeline in units of days. HIV coreceptor usage was predicted from reconstructed ancestral sequences using the geno2pheno algorithm. We determined that the first mutations contributing to CXCR4 use emerged about 16 (per subject range 4 to 30) months before the earliest predicted CXCR4-using ancestor, which preceded the first positive cell-based assay of CXCR4 usage by 10 (range 5 to 25) months. CXCR4 usage arose in multiple lineages within 5 of 8 subjects, and ancestral lineages following alternate mutational pathways before going extinct were common. We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant.

  15. Sustainability of ancestral methods of agricultural production in Perú: ¿keep or replace?

    Directory of Open Access Journals (Sweden)

    Dani Eduardo Vargas Huanca

    2016-09-01

    Full Text Available Based on the success of some Andean products such as quinoa, potatoes or maca in international food trade and the growing environmental degradation facing developing countries, resulting from intensive exploitation activities; Our research seeks to show the trend that is assumed from the academic / scientific community and public officials in the food sector in Peru, against the need to maintain sustainable various ancestral modes of agricultural production (case quinoa, for it analyze quantitative and qualitative obtained from public institutions and Peruvian universities.

  16. Sandals as Icons: Representations in Ancestral Pueblo Rock Art and Effigies in Stone and Wood

    OpenAIRE

    Polly Schaafsma

    2016-01-01

    Dating the late 1000s to the mid-1200s CE, petroglyphs of sandal images are among others that distinguish ancient Pueblo rock art in the San Juan and Little Colorado River drainages on the Colorado Plateau from Ancestral Pueblo rock art elsewhere across the Southwest. The sandal “track” also has counterparts  as effigies in stone and wood often found in ceremonial contexts in Pueblo sites. These representations reflect the sandal styles of the times, both plain in contour and the jog-toed var...

  17. Consistency and inconsistency of consensus methods for inferring species trees from gene trees in the presence of ancestral population structure.

    Science.gov (United States)

    DeGiorgio, Michael; Rosenberg, Noah A

    2016-08-01

    In the last few years, several statistically consistent consensus methods for species tree inference have been devised that are robust to the gene tree discordance caused by incomplete lineage sorting in unstructured ancestral populations. One source of gene tree discordance that has only recently been identified as a potential obstacle for phylogenetic inference is ancestral population structure. In this article, we describe a general model of ancestral population structure, and by relying on a single carefully constructed example scenario, we show that the consensus methods Democratic Vote, STEAC, STAR, R(∗) Consensus, Rooted Triple Consensus, Minimize Deep Coalescences, and Majority-Rule Consensus are statistically inconsistent under the model. We find that among the consensus methods evaluated, the only method that is statistically consistent in the presence of ancestral population structure is GLASS/Maximum Tree. We use simulations to evaluate the behavior of the various consensus methods in a model with ancestral population structure, showing that as the number of gene trees increases, estimates on the basis of GLASS/Maximum Tree approach the true species tree topology irrespective of the level of population structure, whereas estimates based on the remaining methods only approach the true species tree topology if the level of structure is low. However, through simulations using species trees both with and without ancestral population structure, we show that GLASS/Maximum Tree performs unusually poorly on gene trees inferred from alignments with little information. This practical limitation of GLASS/Maximum Tree together with the inconsistency of other methods prompts the need for both further testing of additional existing methods and development of novel methods under conditions that incorporate ancestral population structure.

  18. Bearing the unbearable: ancestral transmission through dreams and moving metaphors in the analtyic field.

    Science.gov (United States)

    Pickering, Judith

    2012-11-01

    This paper explores how untold and unresolved intergenerational trauma may be transmitted through unconscious channels of communication, manifesting in the dreams of descendants. Unwitting carriers for that which was too horrific for their ancestors to bear, descendants may enter analysis through an unconscious need to uncover past secrets, piece together ancestral histories before the keys to comprehending their terrible inheritance die with their forebears. They seek the relational containment of the analytic relationship to provide psychological conditions to bear the unbearable, know the unknowable, speak the unspeakable and redeem the unredeemable. In the case of 'Rachael', initial dreams gave rise to what Hobson (1984) called 'moving metaphors of self' in the analytic field. Dream imagery, projective and introjective processes in the transference-countertransference dynamics gradually revealed an unknown ancestral history. I clarify the back and forth process from dream to waking dream thoughts to moving metaphors and differentiate the moving metaphor from a living symbol. I argue that the containment of the analytic relationship nested within the security of the analytic space is a necessary precondition for such healing processes to occur.

  19. Ancestral origin of the ATTCT repeat expansion in spinocerebellar ataxia type 10 (SCA10.

    Directory of Open Access Journals (Sweden)

    Teresa Almeida

    Full Text Available Spinocerebellar ataxia type 10 (SCA10 is an autosomal dominant neurodegenerative disease characterized by cerebellar ataxia and seizures. The disease is caused by a large ATTCT repeat expansion in the ATXN10 gene. The first families reported with SCA10 were of Mexican origin, but the disease was soon after described in Brazilian families of mixed Portuguese and Amerindian ancestry. The origin of the SCA10 expansion and a possible founder effect that would account for its geographical distribution have been the source of speculation over the last years. To unravel the mutational origin and spread of the SCA10 expansion, we performed an extensive haplotype study, using closely linked STR markers and intragenic SNPs, in families from Brazil and Mexico. Our results showed (1 a shared disease haplotype for all Brazilian and one of the Mexican families, and (2 closely-related haplotypes for the additional SCA10 Mexican families; (3 little or null genetic distance in small normal alleles of different repeat sizes, from the same SNP lineage, indicating that they are being originated by a single step mechanism; and (4 a shared haplotype for pure and interrupted expanded alleles, pointing to a gene conversion model for its generation. In conclusion, we show evidence for an ancestral common origin for SCA10 in Latin America, which might have arisen in an ancestral Amerindian population and later have been spread into the mixed populations of Mexico and Brazil.

  20. The mosaic of ancestral karyotype blocks in the Sinapis alba L. genome.

    Science.gov (United States)

    Nelson, Matthew N; Parkin, Isobel A P; Lydiate, Derek J

    2011-01-01

    The organisation of the Sinapis alba genome, comprising 12 linkage groups (n = 12), was compared with the Brassicaceae ancestral karyotype (AK) genomic blocks previously described in other crucifer species. Most of the S. alba genome falls into conserved triplicated genomic blocks that closely match the AK-defined genomic blocks found in other crucifer species including the A, B, and C genomes of closely related Brassica species. In one instance, an S. alba linkage group (S05) was completely collinear with one AK chromosome (AK1), the first time this has been observed in a member of the Brassiceae tribe. However, as observed for other members of the Brassiceae tribe, ancestral genomic blocks were fragmented in the S. alba genome, supporting previously reported comparative chromosome painting describing rearrangements of the AK karyotype prior to the divergence of the Brassiceae from other crucifers. The presented data also refute previous phylogenetic reports that suggest S. alba was more closely related to Brassica nigra (B genome) than to B. rapa (A genome) and B. oleracea (C genome). A comparison of the S. alba and Arabidopsis thaliana genomes revealed many regions of conserved gene order, which will facilitate access to the rich genomic resources available in the model species A. thaliana for genetic research in the less well-resourced crop species S. alba.

  1. Internal structural variations in a debris-avalanche deposit from ancestral Mount Shasta, California, USA

    Science.gov (United States)

    Ui, T.; Glicken, H.

    1986-01-01

    Various parameters of the internal structure of a debris-avalanche deposit from ancestral Mount Shasta (size and percentage of block facies in each exposure, number and width of jigsaw cracks, and number of rounded clasts in matrix facies) were measured in order to study flow and emplacement mechanisms. Three types of coherent blocks were identified: blocks of massive or brecciated lava flows or domes, blocks of layered volcaniclastic deposits, and blocks of accidental material, typically from sedimentary units underlying Shasta Valley. The mean maximum dimension of the three largest blocks of layered volcaniclastic material is 220 m, and that of the lava blocks, 110 m. This difference may reflect plastic deformation of blocks of layered volcaniclastic material; blocks of massive or brecciated volcanic rock deformated brittly and may have split into several smaller blocks. The blocks in the deposit are one order of magnitude larger, and the height of collapse 1100 m higher, than the Pungarehu debris-avalanche deposit at Mount Egmont, New Zealand, although the degree of fracturing is about the same.This suggests either that the Shasta source material was less broken, or that the intensity of any accompanying explosion was smaller at ancestral Mount Shasta. The Shasta debris-avalanche deposit covered the floor of a closed basin; the flanks of the basin may have retarded the opening of jigsaw cracks and the formation of stretched and deformed blocks such as those of the Pungarehu debris-avalanche deposit. ?? 1986 Springer-Verlag.

  2. Evolution of steroid receptors from an estrogen-sensitive ancestral receptor.

    Science.gov (United States)

    Eick, Geeta N; Thornton, Joseph W

    2011-03-01

    Members of the steroid hormone receptor (SR) family activate transcription from different DNA response elements and are regulated by distinct hormonal ligands. Understanding the evolutionary process by which this diversity arose can provide insight into how and why SRs function as they do. Here we review the characteristics of the ancient receptor protein from which the SR family descends by a process of gene duplication and divergence. Several orthogonal lines of evidence - bioinformatic, phylogenetic, and experimental - indicate that this ancient SR had the capacity to activate transcription from DNA estrogen response elements in response to estrogens. Duplication and divergence of the ancestral SR gene subsequently generated new receptors that were activated by other steroid hormones, including progestagens, androgens, and corticosteroids. The androgen and progesterone receptors recruited as their ligands steroids that were previously present as biochemical intermediates in the synthesis of estrogens. This process is an example of molecular exploitation--the evolution of new molecular interactions when an older molecule, which previously had a different function, is co-opted as a binding partner by a newly evolved molecule. The primordial interaction between the ancestral steroid receptor and estrogens may itself have evolved due to an early molecular exploitation event.

  3. QTL linkage analysis of connected populations using ancestral marker and pedigree information.

    Science.gov (United States)

    Bink, Marco C A M; Totir, L Radu; ter Braak, Cajo J F; Winkler, Christopher R; Boer, Martin P; Smith, Oscar S

    2012-04-01

    The common assumption in quantitative trait locus (QTL) linkage mapping studies that parents of multiple connected populations are unrelated is unrealistic for many plant breeding programs. We remove this assumption and propose a Bayesian approach that clusters the alleles of the parents of the current mapping populations from locus-specific identity by descent (IBD) matrices that capture ancestral marker and pedigree information. Moreover, we demonstrate how the parental IBD data can be incorporated into a QTL linkage analysis framework by using two approaches: a Threshold IBD model (TIBD) and a Latent Ancestral Allele Model (LAAM). The TIBD and LAAM models are empirically tested via numerical simulation based on the structure of a commercial maize breeding program. The simulations included a pilot dataset with closely linked QTL on a single linkage group and 100 replicated datasets with five linkage groups harboring four unlinked QTL. The simulation results show that including parental IBD data (similarly for TIBD and LAAM) significantly improves the power and particularly accuracy of QTL mapping, e.g., position, effect size and individuals' genotype probability without significantly increasing computational demand.

  4. A FORTRAN subroutine to compute inbreeding and kinship coefficients according to the number of ancestral generations.

    Science.gov (United States)

    Vu Tien Khang, J

    1989-07-01

    This paper presents a FORTRAN IV subroutine to calculate inbreeding and kinship coefficients from pedigree information in a diploid population without self-fertilization. The user can specify the number of ancestral generations to be taken into account. It is thus possible to determine contributions of succeeding ancestral generations to the inbreeding and kinship coefficients under consideration. The subroutine is based on a recursive procedure that generates systematically all paths connecting two individuals. NP and NM, whose kinship coefficient is to be calculated (or between the father NP and the mother NM of the individual whose inbreeding coefficient is to be calculated). These paths obey the following conditions: (i) a given path does not contain the same parent-offspring link more than once; (ii) the vertex of a path is an ancestor common to individuals NP and NM, with a rank lower or equal to the parameter specified in input. Constraints regarding the size of the corpus of genealogical data and the storage method are discussed, as well as the interest of this subroutine compared to the existing ones. An example of application is given.

  5. Neuromagnetic source reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Lewis, P.S.; Mosher, J.C. [Los Alamos National Lab., NM (United States); Leahy, R.M. [University of Southern California, Los Angeles, CA (United States)

    1994-12-31

    In neuromagnetic source reconstruction, a functional map of neural activity is constructed from noninvasive magnetoencephalographic (MEG) measurements. The overall reconstruction problem is under-determined, so some form of source modeling must be applied. We review the two main classes of reconstruction techniques-parametric current dipole models and nonparametric distributed source reconstructions. Current dipole reconstructions use a physically plausible source model, but are limited to cases in which the neural currents are expected to be highly sparse and localized. Distributed source reconstructions can be applied to a wider variety of cases, but must incorporate an implicit source, model in order to arrive at a single reconstruction. We examine distributed source reconstruction in a Bayesian framework to highlight the implicit nonphysical Gaussian assumptions of minimum norm based reconstruction algorithms. We conclude with a brief discussion of alternative non-Gaussian approachs.

  6. Reconstrucción craneal con biomateriales: Revisión histórica y estado actual Cranial reconstruction with biomaterials: Historical revision and current state

    Directory of Open Access Journals (Sweden)

    I. Zubillaga Rodríguez

    2007-04-01

    Full Text Available La reconstrucción de defectos craneofaciales es todavía hoy día un proceso desafiante. Se define craneoplastia como la reparación de un defecto o deformidad craneal. La persistencia de traumatismos craneofaciales y procedimientos neuroquirúrgicos aporta un número importante de casos que permiten un fascinante progreso y desarrollo de nuevos materiales. El objetivo de este artículo es la revisión histórica de los distintos métodos reconstructivos craneales empleados, comentando sus ventajas e inconvenientes según el tamaño y forma del defecto a reparar. Se presentan casos clínicos recientes reconstruidos con diversos biomateriales.Craniofacial defect reconstruction is still a challenging procedure. A cranioplasty is the treatment of a cranial defect or a deformity. Cranial injuries and neurosurgical procedures provide an important group of cases that allow the development of new materials and fascinating progress. The aim of this article is a historic review of the different cranial reconstructive techniques used, describing advantages and drawbacks. The biomaterials applied in recent cases are presented.

  7. Migration of the Pee Dee River system inferred from ancestral paleochannels underlying the South Carolina Grand Strand and Long Bay inner shelf

    Science.gov (United States)

    Baldwin, W.E.; Morton, R.A.; Putney, T.R.; Katuna, M.P.; Harris, M.S.; Gayes, P.T.; Driscoll, N.W.; Denny, J.F.; Schwab, W.C.

    2006-01-01

    Several generations of the ancestral Pee Dee River system have been mapped beneath the South Carolina Grand Strand coastline and adjacent Long Bay inner shelf. Deep boreholes onshore and high-resolution seismic-reflection data offshore allow for reconstruction of these paleochannels, which formed during glacial lowstands, when the Pee Dee River system incised subaerially exposed coastal-plain and continental-shelf strata. Paleochannel groups, representing different generations of the system, decrease in age to the southwest, where the modern Pee Dee River merges with several coastal-plain tributaries at Winyah Bay, the southern terminus of Long Bay. Positions of the successive generational groups record a regional, southwestward migration of the river system that may have initiated during the late Pliocene. The migration was primarily driven by barrier-island deposition, resulting from the interaction of fluvial and shoreline processes during eustatic highstands. Structurally driven, subsurface paleotopography associated with the Mid-Carolina Platform High has also indirectly assisted in forcing this migration. These results provide a better understanding of the evolution of the region and help explain the lack of mobile sediment on the Long Bay inner shelf. Migration of the river system caused a profound change in sediment supply during the late Pleistocene. The abundant fluvial source that once fed sand-rich barrier islands was cut off and replaced with a limited source, supplied by erosion and reworking of former coastal deposits exposed at the shore and on the inner shelf.

  8. Transcriptome Profiling of the Green Alga Spirogyra pratensis (Charophyta) Suggests an Ancestral Role for Ethylene in Cell Wall Metabolism, Photosynthesis, and Abiotic Stress Responses1[OPEN

    Science.gov (United States)

    2016-01-01

    It is well known that ethylene regulates a diverse set of developmental and stress-related processes in angiosperms, yet its roles in early-diverging embryophytes and algae are poorly understood. Recently, it was shown that ethylene functions as a hormone in the charophyte green alga Spirogyra pratensis. Since land plants evolved from charophytes, this implies conservation of ethylene as a hormone in green plants for at least 450 million years. However, the physiological role of ethylene in charophyte algae has remained unknown. To gain insight into ethylene responses in Spirogyra, we used mRNA sequencing to measure changes in gene expression over time in Spirogyra filaments in response to an ethylene treatment. Our analyses show that at the transcriptional level, ethylene predominantly regulates three processes in Spirogyra: (1) modification of the cell wall matrix by expansins and xyloglucan endotransglucosylases/hydrolases, (2) down-regulation of chlorophyll biosynthesis and photosynthesis, and (3) activation of abiotic stress responses. We confirmed that the photosynthetic capacity and chlorophyll content were reduced by an ethylene treatment and that several abiotic stress conditions could stimulate cell elongation in an ethylene-dependent manner. We also found that the Spirogyra transcriptome harbors only 10 ethylene-responsive transcription factor (ERF) homologs, several of which are regulated by ethylene. These results provide an initial understanding of the hormonal responses induced by ethylene in Spirogyra and help to reconstruct the role of ethylene in ancestral charophytes prior to the origin of land plants. PMID:27489312

  9. Where did the chili get its spice? Biogeography of capsaicinoid production in ancestral wild chili species.

    Science.gov (United States)

    Tewksbury, Joshua J; Manchego, Carlos; Haak, David C; Levey, Douglas J

    2006-03-01

    The biogeography of pungency in three species of wild chili in the chaco and surrounding highland habitats of southeastern Bolivia is described. We report that Capsicum chacoense, C. baccatum, and C. eximium are polymorphic for production of capsaicin and its analogs, such that completely pungent and completely nonpungent individuals co-occur in some populations. In C. chacoense, the density of plants and the proportion of pungent plants increased with elevation. Above 900 m, all individuals in all populations except two were pungent; nonpungent individuals in at least one of the two polymorphic populations were likely a result of spreading by humans. The occurrence of pungent and nonpungent individuals in three species of ancestral Capsicum and the geographic variation of pungency within species suggest that production of capsaicin and its analogs entails both costs and benefits, which shift from one locality to another. Determining the selection pressures behind such shifts is necessary to understand the evolution of pungency in chilies.

  10. A phenol-enriched cuticle is ancestral to lignin evolution in land plants

    Science.gov (United States)

    Renault, Hugues; Alber, Annette; Horst, Nelly A.; Basilio Lopes, Alexandra; Fich, Eric A.; Kriegshauser, Lucie; Wiedemann, Gertrud; Ullmann, Pascaline; Herrgott, Laurence; Erhardt, Mathieu; Pineau, Emmanuelle; Ehlting, Jürgen; Schmitt, Martine; Rose, Jocelyn K. C.; Reski, Ralf; Werck-Reichhart, Danièle

    2017-01-01

    Lignin, one of the most abundant biopolymers on Earth, derives from the plant phenolic metabolism. It appeared upon terrestrialization and is thought critical for plant colonization of land. Early diverging land plants do not form lignin, but already have elements of its biosynthetic machinery. Here we delete in a moss the P450 oxygenase that defines the entry point in angiosperm lignin metabolism, and find that its pre-lignin pathway is essential for development. This pathway does not involve biochemical regulation via shikimate coupling, but instead is coupled with ascorbate catabolism, and controls the synthesis of the moss cuticle, which prevents desiccation and organ fusion. These cuticles share common features with lignin, cutin and suberin, and may represent the extant representative of a common ancestor. Our results demonstrate a critical role for the ancestral phenolic metabolism in moss erect growth and cuticle permeability, consistent with importance in plant adaptation to terrestrial conditions. PMID:28270693

  11. Novel ancestral Dysferlin splicing mutation which migrated from the Iberian peninsula to South America.

    Science.gov (United States)

    Vernengo, Luis; Oliveira, Jorge; Krahn, Martin; Vieira, Emilia; Santos, Rosário; Carrasco, Luisa; Negrão, Luís; Panuncio, Ana; Leturcq, France; Labelle, Veronique; Bronze-da-Rocha, Elsa; Mesa, Rosario; Pizzarossa, Carlos; Lévy, Nicolas; Rodriguez, Maria-Mirta

    2011-05-01

    Primary dysferlinopathies are a group of recessive heterogeneous muscular dystrophies. The most common clinical presentations are Miyoshi myopathy and LGMD2B. Additional presentations range from isolated hyperCKemia to severe functional disability. Symptomatology begins in the posterior muscle compartment of the calf and its clinical course progresses slowly in Miyoshi myopathy whereas LGMD2B involves predominantly the proximal muscles of the lower limbs. The age of onset ranges from 13 to 60years in Caucasians. We present five patients that carry a novel mutation in the exon12/intron12 boundary: c.1180_1180+7delAGTGCGTG (r.1054_1284del). We provide evidence of a founder effect due to a common ancestral origin of this mutation, detected in heterozygosity in four patients and in homozygosity in one patient.

  12. On the ancestral compatibility of two phylogenetic trees with nested taxa.

    Science.gov (United States)

    Llabrés, Mercè; Rocha, Jairo; Rosselló, Francesc; Valiente, Gabriel

    2006-09-01

    Compatibility of phylogenetic trees is the most important concept underlying widely-used methods for assessing the agreement of different phylogenetic trees with overlapping taxa and combining them into common supertrees to reveal the tree of life. The notion of ancestral compatibility of phylogenetic trees with nested taxa was recently introduced. In this paper we analyze in detail the meaning of this compatibility from the points of view of the local structure of the trees, of the existence of embeddings into a common supertree, and of the joint properties of their cluster representations. Our analysis leads to a very simple polynomial-time algorithm for testing this compatibility, which we have implemented and is freely available for download from the BioPerl collection of Perl modules for computational biology.

  13. Inferring genome-wide patterns of admixture in Qataris using fifty-five ancestral populations

    Directory of Open Access Journals (Sweden)

    Omberg Larsson

    2012-06-01

    Full Text Available Abstract Background Populations of the Arabian Peninsula have a complex genetic structure that reflects waves of migrations including the earliest human migrations from Africa and eastern Asia, migrations along ancient civilization trading routes and colonization history of recent centuries. Results Here, we present a study of genome-wide admixture in this region, using 156 genotyped individuals from Qatar, a country located at the crossroads of these migration patterns. Since haplotypes of these individuals could have originated from many different populations across the world, we have developed a machine learning method "SupportMix" to infer loci-specific genomic ancestry when simultaneously analyzing many possible ancestral populations. Simulations show that SupportMix is not only more accurate than other popular admixture discovery tools but is the first admixture inference method that can efficiently scale for simultaneous analysis of 50-100 putative ancestral populations while being independent of prior demographic information. Conclusions By simultaneously using the 55 world populations from the Human Genome Diversity Panel, SupportMix was able to extract the fine-scale ancestry of the Qatar population, providing many new observations concerning the ancestry of the region. For example, as well as recapitulating the three major sub-populations in Qatar, composed of mainly Arabic, Persian, and African ancestry, SupportMix additionally identifies the specific ancestry of the Persian group to populations sampled in Greater Persia rather than from China and the ancestry of the African group to sub-Saharan origin and not Southern African Bantu origin as previously thought.

  14. Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle.

    Science.gov (United States)

    Huson, Heather J; Kim, Eui-Soo; Godfrey, Robert W; Olson, Timothy A; McClure, Matthew C; Chase, Chad C; Rizzi, Rita; O'Brien, Ana M P; Van Tassell, Curt P; Garcia, José F; Sonstegard, Tad S

    2014-01-01

    The slick hair coat (SLICK) is a dominantly inherited trait typically associated with tropically adapted cattle that are from Criollo descent through Spanish colonization of cattle into the New World. The trait is of interest relative to climate change, due to its association with improved thermo-tolerance and subsequent increased productivity. Previous studies localized the SLICK locus to a 4 cM region on chromosome (BTA) 20 and identified signatures of selection in this region derived from Senepol cattle. The current study compares three slick-haired Criollo-derived breeds including Senepol, Carora, and Romosinuano and three additional slick-haired cross-bred lineages to non-slick ancestral breeds. Genome-wide association (GWA), haplotype analysis, signatures of selection, runs of homozygosity (ROH), and identity by state (IBS) calculations were used to identify a 0.8 Mb (37.7-38.5 Mb) consensus region for the SLICK locus on BTA20 in which contains SKP2 and SPEF2 as possible candidate genes. Three specific haplotype patterns are identified in slick individuals, all with zero frequency in non-slick individuals. Admixture analysis identified common genetic patterns between the three slick breeds at the SLICK locus. Principal component analysis (PCA) and admixture results show Senepol and Romosinuano sharing a higher degree of genetic similarity to one another with a much lesser degree of similarity to Carora. Variation in GWA, haplotype analysis, and IBS calculations with accompanying population structure information supports potentially two mutations, one common to Senepol and Romosinuano and another in Carora, effecting genes contained within our refined location for the SLICK locus.

  15. Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle

    Directory of Open Access Journals (Sweden)

    Heather Jay Huson

    2014-04-01

    Full Text Available The slick hair coat (SLICK is a dominantly inherited trait typically associated with tropically adapted cattle that are from Criollo descent through Spanish colonization of cattle into the New World. The trait is of interest relative to climate change, due to its association with improved thermo-tolerance and subsequent increased productivity. Previous studies localized the SLICK locus to a 4 cM region on chromosome (Chr 20 and identified signatures of selection in this region derived from Senepol cattle. The current study compares three slick-haired Criollo-derived breeds including Senepol, Carora, and Romosinuano and three additional slick-haired cross-bred lineages to non-slick ancestral breeds. Genome-wide association (GWA, haplotype analysis, signatures of selection, runs of homozygosity, and identity by state (IBS calculations were used to identify a 0.8Mb (37.7-38.5Mb consensus region for the SLICK locus on Chr 20 in which contains SKP2 and SPEF2 as possible candidate genes. Three specific haplotype patterns are identified in slick individuals, all with zero frequency in non-slick individuals. Admixture analysis identified common genetic patterns between the three slick breeds at the SLICK locus. Principle component analysis and admixture results show Senepol and Romosinuano sharing a higher degree of genetic similarity to one another with a much lesser degree of similarity to Carora. Variation in GWA, haplotype analysis, and IBS calculations with accompanying population structure information supports potentially two mutations, one common to Senepol and Romosinuano and another in Carora, effecting genes contained within our refined location for the SLICK locus.

  16. Breast reconstruction after mastectomy

    Directory of Open Access Journals (Sweden)

    Daniel eSchmauss

    2016-01-01

    Full Text Available Breast cancer is the leading cause of cancer death in women worldwide. Its surgical approach has become less and less mutilating in the last decades. However, the overall number of breast reconstructions has significantly increased lately. Nowadays breast reconstruction should be individualized at its best, first of all taking into consideration oncological aspects of the tumor, neo-/adjuvant treatment and genetic predisposition, but also its timing (immediate versus delayed breast reconstruction, as well as the patient’s condition and wish. This article gives an overview over the various possibilities of breast reconstruction, including implant- and expander-based reconstruction, flap-based reconstruction (vascularized autologous tissue, the combination of implant and flap, reconstruction using non-vascularized autologous fat, as well as refinement surgery after breast reconstruction.

  17. Reoperative midface reconstruction.

    Science.gov (United States)

    Acero, Julio; García, Eloy

    2011-02-01

    Reoperative reconstruction of the midface is a challenging issue because of the complexity of this region and the severity of the aesthetic and functional sequela related to the absence or failure of a primary reconstruction. The different situations that can lead to the indication of a reoperative reconstructive procedure after previous oncologic ablative procedures in the midface are reviewed. Surgical techniques, anatomic problems, and limitations affecting the reoperative reconstruction in this region of the head and neck are discussed.

  18. Reconstructability analysis of epistasis.

    Science.gov (United States)

    Zwick, Martin

    2011-01-01

    The literature on epistasis describes various methods to detect epistatic interactions and to classify different types of epistasis. Reconstructability analysis (RA) has recently been used to detect epistasis in genomic data. This paper shows that RA offers a classification of types of epistasis at three levels of resolution (variable-based models without loops, variable-based models with loops, state-based models). These types can be defined by the simplest RA structures that model the data without information loss; a more detailed classification can be defined by the information content of multiple candidate structures. The RA classification can be augmented with structures from related graphical modeling approaches. RA can analyze epistatic interactions involving an arbitrary number of genes or SNPs and constitutes a flexible and effective methodology for genomic analysis.

  19. Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification.

    Science.gov (United States)

    Baker, Christopher R; Booth, Lauren N; Sorrells, Trevor R; Johnson, Alexander D

    2012-09-28

    We examine how different transcriptional network structures can evolve from an ancestral network. By characterizing how the ancestral mode of gene regulation for genes specific to a-type cells in yeast species evolved from an activating paradigm to a repressing one, we show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel regulatory mode. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species.

  20. Surfaces, Digitisations and Reconstructions

    DEFF Research Database (Denmark)

    2015-01-01

    We present a new digital reconstruction of r-regular sets in three-dimensional Euclidean space. We introduce a vector field and analyse the relation between the topologies of the boundaries of the r-regular set and its reconstruction. This reconstruction can be carried out faster than prior models...

  1. Efficient algorithms for reconstructing gene content by co-evolution

    Directory of Open Access Journals (Sweden)

    Tuller Tamir

    2011-10-01

    Full Text Available Abstract Background In a previous study we demonstrated that co-evolutionary information can be utilized for improving the accuracy of ancestral gene content reconstruction. To this end, we defined a new computational problem, the Ancestral Co-Evolutionary (ACE problem, and developed algorithms for solving it. Results In the current paper we generalize our previous study in various ways. First, we describe new efficient computational approaches for solving the ACE problem. The new approaches are based on reductions to classical methods such as linear programming relaxation, quadratic programming, and min-cut. Second, we report new computational hardness results related to the ACE, including practical cases where it can be solved in polynomial time. Third, we generalize the ACE problem and demonstrate how our approach can be used for inferring parts of the genomes of non-ancestral organisms. To this end, we describe a heuristic for finding the portion of the genome ('dominant set’ that can be used to reconstruct the rest of the genome with the lowest error rate. This heuristic utilizes both evolutionary information and co-evolutionary information. We implemented these algorithms on a large input of the ACE problem (95 unicellular organisms, 4,873 protein families, and 10, 576 of co-evolutionary relations, demonstrating that some of these algorithms can outperform the algorithm used in our previous study. In addition, we show that based on our approach a ’dominant set’ cab be used reconstruct a major fraction of a genome (up to 79% with relatively low error-rate (e.g. 0.11. We find that the ’dominant set’ tends to include metabolic and regulatory genes, with high evolutionary rate, and low protein abundance and number of protein-protein interactions. Conclusions The ACE problem can be efficiently extended for inferring the genomes of organisms that exist today. In addition, it may be solved in polynomial time in many practical cases

  2. Should I Have Breast Reconstruction?

    Science.gov (United States)

    ... Reconstruction Surgery Breast Cancer Breast Reconstruction Surgery Should I Get Breast Reconstruction Surgery? Women who have surgery ... It usually responds well to treatment. What if I choose not to have breast reconstruction? Many women ...

  3. Voicing-State Identification Based on Speech Observation Sequence and Non-reconstruction in Compressing Sensing%基于语音压缩感知观测序列非重构的清浊音判别法

    Institute of Scientific and Technical Information of China (English)

    王文娟; 杨震

    2013-01-01

    针对语音产生的数字模型来分析清音和浊音的特点,研究了清音和浊音的压缩感知观测序列的特性,从而推出清音的压缩感知观测序列具有近似高斯信号的特性,而浊音的压缩感知观测序列具有非高斯信号的特性.基于这种特性来设计一种直接针对压缩感知观测序列、非重构的清浊音判别方法,并给出了它与重构信号清浊音判别在准确性和计算量两个方面的比较结果,解决了基于语音压缩感知观测序列重构情况下判别清浊音的高计算量问题.%Based on the theory of compressed sensing,the observation sequence after compressing sensing is different from the Nyquist sequence,so the voicing-state identification can be achieved only by reconstructing the original speech signal with high complexity.The voicingstate characteristics are analyzed based on the speech digital model,and a conclusion can be drawn that the unvoiced observation sequence has the characteristics of Gaussian signal while the voiced observation sequence has the characteristics of non-Gaussian signal.According to the characteristic,a voicing-state identification algorithm of third-order accumulation is designed based on observation sequence,and is compared with the energy discrimination method of the reconstructing speech signal in accuracy and computing.Therefore,the problem of high complexity in voicing-state identification can be solved after reconstructing the original speech signal.

  4. Intersection of opposing pedagogical frameworks: Native Hawaiian ancestral stories and scientific inquiry in a high school science class

    Science.gov (United States)

    Kanahele-Mossman, Huihui

    Inquiry is defined as "an examination into facts and principles." In science education science inquiry is a process through which important discoveries are made by students through scientific methodology. The most important step in this process is forming the right question. The questions formed by students are usually the wrong questions which deem the remainder of the inquiry process impotent. This research will look at the pedagogy of ancestral stories for a solution. For the researcher, ancestral stories were a source of wonderment and learning not only from the lessons the stories revealed but mainly from the questions that still remained after the stories were told. Questions such as "why does the eel only swim near that part?", or "why does the story only talk about the uhu?" are examples of questions that remained after experiencing an ancestral narrative. The research questions were composed for the purpose of finding compatibility between the two pedagogies. The first research question which reads "how can Native Hawaiian ancestral stories encourage an increased level of student driven interactions at all levels of feedback from Native Hawaiian students in science classroom" focuses the research on the level of student feedback that initiate questions. Question two which reads "how can teachers of Native Hawaiian students facilitate the construction of science inquiry projects from ancestral stories" addresses the skill of the teacher and imbeds the concept of pedagogical knowledge into the literature. The last research question "how do analysis and discussion of the stories connect Native Hawaiian students to their ancestral intelligence" examines the role of identity and identity to ancestral intelligence. The method intended for this research was Grounded theory which allows the researcher to develop principles, concepts and theories based on the data presented. Another method utilized in this research is an undocumented but culturally imbedded method

  5. Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences

    Directory of Open Access Journals (Sweden)

    Baele Guy

    2010-08-01

    Full Text Available Abstract Background Recent approaches for context-dependent evolutionary modelling assume that the evolution of a given site depends upon its ancestor and that ancestor's immediate flanking sites. Because such dependency pattern cannot be imposed on the root sequence, we consider the use of different orders of Markov chains to model dependence at the ancestral root sequence. Root distributions which are coupled to the context-dependent model across the underlying phylogenetic tree are deemed more realistic than decoupled Markov chains models, as the evolutionary process is responsible for shaping the composition of the ancestral root sequence. Results We find strong support, in terms of Bayes Factors, for using a second-order Markov chain at the ancestral root sequence along with a context-dependent model throughout the remainder of the phylogenetic tree in an ancestral repeats dataset, and for using a first-order Markov chain at the ancestral root sequence in a pseudogene dataset. Relaxing the assumption of a single context-independent set of independent model frequencies as presented in previous work, yields a further drastic increase in model fit. We show that the substitution rates associated with the CpG-methylation-deamination process can be modelled through context-dependent model frequencies and that their accuracy depends on the (order of the Markov chain imposed at the ancestral root sequence. In addition, we provide evidence that this approach (which assumes that root distribution and evolutionary model are decoupled outperforms an approach inspired by the work of Arndt et al., where the root distribution is coupled to the evolutionary model. We show that the continuous-time approximation of Hwang and Green has stronger support in terms of Bayes Factors, but the parameter estimates show minimal differences. Conclusions We show that the combination of a dependency scheme at the ancestral root sequence and a context

  6. [Breast reconstruction after mastectomy].

    Science.gov (United States)

    Ho Quoc, C; Delay, E

    2013-02-01

    The mutilating surgery for breast cancer causes deep somatic and psychological sequelae. Breast reconstruction can mitigate these effects and permit the patient to help rebuild their lives. The purpose of this paper is to focus on breast reconstruction techniques and on factors involved in breast reconstruction. The methods of breast reconstruction are presented: objectives, indications, different techniques, operative risks, and long-term monitoring. Many different techniques can now allow breast reconstruction in most patients. Clinical cases are also presented in order to understand the results we expect from a breast reconstruction. Breast reconstruction provides many benefits for patients in terms of rehabilitation, wellness, and quality of life. In our mind, breast reconstruction should be considered more as an opportunity and a positive choice (the patient can decide to do it), than as an obligation (that the patient would suffer). The consultation with the surgeon who will perform the reconstruction is an important step to give all necessary informations. It is really important that the patient could speak again with him before undergoing reconstruction, if she has any doubt. The quality of information given by medical doctors is essential to the success of psychological intervention. This article was written in a simple, and understandable way to help gynecologists giving the best information to their patients. It is maybe also possible to let them a copy of this article, which would enable them to have a written support and would facilitate future consultation with the surgeon who will perform the reconstruction.

  7. Exploring the topology of dynamical reconstructions

    Science.gov (United States)

    Garland, Joshua; Bradley, Elizabeth; Meiss, James D.

    2016-11-01

    Computing the state-space topology of a dynamical system from scalar data requires accurate reconstruction of those dynamics and construction of an appropriate simplicial complex from the results. The reconstruction process involves a number of free parameters and the computation of homology for a large number of simplices can be expensive. This paper is a study of how to compute the homology efficiently and effectively without a full (diffeomorphic) reconstruction. Using trajectories from the classic Lorenz system, we reconstruct the dynamics using the method of delays, then build a simplicial complex whose vertices are a small subset of the data: the "witness complex". Surprisingly, we find that the witness complex correctly resolves the homology of the underlying invariant set from noisy samples of that set even if the reconstruction dimension is well below the thresholds for assuring topological conjugacy between the true and reconstructed dynamics that are specified in the embedding theorems. We conjecture that this is because the requirements for reconstructing homology are less stringent: a homeomorphism is sufficient-as opposed to a diffeomorphism, as is necessary for the full dynamics. We provide preliminary evidence that a homeomorphism, in the form of a delay-coordinate reconstruction map, may exist at a lower dimension than that required to achieve an embedding.

  8. Acoustic imaging for temperature distribution reconstruction

    Science.gov (United States)

    Jia, Ruixi; Xiong, Qingyu; Liang, Shan

    2016-12-01

    For several industrial processes, such as burning and drying, temperature distribution is important because it can reflect the internal running state of industrial equipment and assist to develop control strategy and ensure safety in operation of industrial equipment. The principle of this technique is mainly based on the relationship between acoustic velocity and temperature. In this paper, an algorithm for temperature distribution reconstruction is considered. Compared with reconstruction results of simulation experiments with the least square algorithm and the proposed one, the latter indicates a better information reflection of temperature distribution and relatively higher reconstruction accuracy.

  9. Acoustic imaging for temperature distribution reconstruction

    Directory of Open Access Journals (Sweden)

    Ruixi Jia

    2016-12-01

    Full Text Available For several industrial processes, such as burning and drying, temperature distribution is important because it can reflect the internal running state of industrial equipment and assist to develop control strategy and ensure safety in operation of industrial equipment. The principle of this technique is mainly based on the relationship between acoustic velocity and temperature. In this paper, an algorithm for temperature distribution reconstruction is considered. Compared with reconstruction results of simulation experiments with the least square algorithm and the proposed one, the latter indicates a better information reflection of temperature distribution and relatively higher reconstruction accuracy.

  10. Developments on jet reconstruction by DELPHI

    CERN Document Server

    Kiskinen, A

    2002-01-01

    The most relevant techniques used by DELPHI to identify jets in multihadronic final states are reviewed. The performance of jet reconstruction algorithms is analysed together with the additional use of energy and momentum conservation in order to allow for a precise reconstruction of the event kinematics. Also jet flavour tagging methods are summarised. Applications in some analyses like searches for new particles such as Higgs bosons, W mass physics and QCD studies are presented. (9 refs).

  11. A PCA-based method for ancestral informative markers selection in structured populations

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Identification of population structure can help trace population histories and identify disease genes. Structured association (SA) is a commonly used approach for population structure identification and association mapping. A major issue with SA is that its performance greatly depends on the informa-tiveness and the numbers of ancestral informative markers (AIMs). Present major AIM selection meth-ods mostly require prior individual ancestry information, which is usually not available or uncertain in practice. To address this potential weakness, we herein develop a novel approach for AIM selection based on principle component analysis (PCA), which does not require prior ancestry information of study subjects. Our simulation and real genetic data analysis results suggest that, with equivalent AIMs, PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs. Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure, which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.

  12. Anomalously high variation in postnatal development is ancestral for dinosaurs but lost in birds.

    Science.gov (United States)

    Griffin, Christopher T; Nesbitt, Sterling J

    2016-12-20

    Compared with all other living reptiles, birds grow extremely fast and possess unusually low levels of intraspecific variation during postnatal development. It is now clear that birds inherited their high rates of growth from their dinosaurian ancestors, but the origin of the avian condition of low variation during development is poorly constrained. The most well-understood growth trajectories of later Mesozoic theropods (e.g., Tyrannosaurus, Allosaurus) show similarly low variation to birds, contrasting with higher variation in extant crocodylians. Here, we show that deep within Dinosauria, among the earliest-diverging dinosaurs, anomalously high intraspecific variation is widespread but then is lost in more derived theropods. This style of development is ancestral for dinosaurs and their closest relatives, and, surprisingly, this level of variation is far higher than in living crocodylians. Among early dinosaurs, this variation is widespread across Pangaea in the Triassic and Early Jurassic, and among early-diverging theropods (ceratosaurs), this variation is maintained for 165 million years to the end of the Cretaceous. Because the Late Triassic environment across Pangaea was volatile and heterogeneous, this variation may have contributed to the rise of dinosaurian dominance through the end of the Triassic Period.

  13. Bacterial community composition and diversity in an ancestral ant fungus symbiosis.

    Science.gov (United States)

    Kellner, Katrin; Ishak, Heather D; Linksvayer, Timothy A; Mueller, Ulrich G

    2015-07-01

    Fungus-farming ants (Hymenoptera: Formicidae, Attini) exhibit some of the most complex microbial symbioses because both macroscopic partners (ants and fungus) are associated with a rich community of microorganisms. The ant and fungal microbiomes are thought to serve important beneficial nutritional and defensive roles in these symbioses. While most recent research has investigated the bacterial communities in the higher attines (e.g. the leaf-cutter ant genera Atta and Acromyrmex), which are often associated with antibiotic-producing Actinobacteria, very little is known about the microbial communities in basal lineages, labeled as 'lower attines', which retain the ancestral traits of smaller and more simple societies. In this study, we used 16S amplicon pyrosequencing to characterize bacterial communities of the lower attine ant Mycocepurus smithii among seven sampling sites in central Panama. We discovered that ant and fungus garden-associated microbiota were distinct from surrounding soil, but unlike the situation in the derived fungus-gardening ants, which show distinct ant and fungal microbiomes, microbial community structure of the ants and their fungi were similar. Another surprising finding was that the abundance of actinomycete bacteria was low and instead, these symbioses were characterized by an abundance of Lactobacillus and Pantoea bacteria. Furthermore, our data indicate that Lactobacillus strains are acquired from the environment rather than acquired vertically.

  14. DNA replication fidelity in Mycobacterium tuberculosis is mediated by an ancestral prokaryotic proofreader.

    Science.gov (United States)

    Rock, Jeremy M; Lang, Ulla F; Chase, Michael R; Ford, Christopher B; Gerrick, Elias R; Gawande, Richa; Coscolla, Mireia; Gagneux, Sebastien; Fortune, Sarah M; Lamers, Meindert H

    2015-06-01

    The DNA replication machinery is an important target for antibiotic development in increasingly drug-resistant bacteria, including Mycobacterium tuberculosis. Although blocking DNA replication leads to cell death, disrupting the processes used to ensure replication fidelity can accelerate mutation and the evolution of drug resistance. In Escherichia coli, the proofreading subunit of the replisome, the ɛ exonuclease, is essential for high-fidelity DNA replication; however, we find that the corresponding subunit is completely dispensable in M. tuberculosis. Rather, the mycobacterial replicative polymerase DnaE1 itself encodes an editing function that proofreads DNA replication, mediated by an intrinsic 3'-5' exonuclease activity within its PHP domain. Inactivation of the DnaE1 PHP domain increases the mutation rate by more than 3,000-fold. Moreover, phylogenetic analysis of DNA replication proofreading in the bacterial kingdom suggests that E. coli is a phylogenetic outlier and that PHP domain-mediated proofreading is widely conserved and indeed may be the ancestral prokaryotic proofreader.

  15. The tendency to recreate ancestral CG dinucleotides in the human genome

    Directory of Open Access Journals (Sweden)

    Li Mingkun

    2011-01-01

    Full Text Available Abstract Background The CG dinucleotides are known to be deficient in the human genome, due to a high mutation rate from 5-methylated CG to TG and its complementary pair CA. Meanwhile, many cellular functions rely on these CG dinucleotides, such as gene expression controlled by cytosine methylation status. Thus, CG dinucleotides that provide essential functional substrates should be retained in genomes. How these two conflicting processes regarding the fate of CG dinucleotides - i.e., high mutation rate destroying CG dinucleotides, vs. functional processes that require their preservation remains an unsolved question. Results By analyzing the mutation and frequency spectrum of newly derived alleles in the human genome, a tendency towards generating more CGs was observed, which was mainly contributed by an excess number of mutations from CA/TG to CG. Simultaneously, we found a fixation preference for CGs derived from TG/CA rather than CGs generated by other dinucleotides. These tendencies were observed both in intergenic and genic regions. An analysis of Integrated Extended Haplotype Homozygosity provided no evidence of selection for newly derived CGs. Conclusions Ancestral CG dinucleotides that were subsequently lost by mutation tend to be recreated in the human genome, as indicated by a biased mutation and fixation pattern favoring new CGs that derived from TG/CA.

  16. Sandals as Icons: Representations in Ancestral Pueblo Rock Art and Effigies in Stone and Wood

    Directory of Open Access Journals (Sweden)

    Polly Schaafsma

    2016-10-01

    Full Text Available Dating the late 1000s to the mid-1200s CE, petroglyphs of sandal images are among others that distinguish ancient Pueblo rock art in the San Juan and Little Colorado River drainages on the Colorado Plateau from Ancestral Pueblo rock art elsewhere across the Southwest. The sandal “track” also has counterparts  as effigies in stone and wood often found in ceremonial contexts in Pueblo sites. These representations reflect the sandal styles of the times, both plain in contour and the jog-toed variety, the latter characterized by a projection where the little toe is positioned. These representations are both plain and patterned,  as are their material sandal counterparts. Their significance  as symbolic icons is their dominant aspect, and a ritual meaning is implicit.  As a component of a symbol system that was radically altered after 1300 CE, however, there is no ethnographic information that provides clues as to the sandal icon’s meaning. While there is no significant pattern of its associations with other symbolic content in the petroglyph panels, in some western San Juan sites cases a relationship to the hunt can be inferred. It is suggested that the track itself could refer to a deity, a mythological hero, or the carver ’s social identity. In conclusion, however, no clear meaning of the images themselves is forthcoming, and further research beckons.

  17. Ancestral gene duplication enabled the evolution of multifunctional cellulases in stick insects (Phasmatodea).

    Science.gov (United States)

    Shelomi, Matan; Heckel, David G; Pauchet, Yannick

    2016-04-01

    The Phasmatodea (stick insects) have multiple, endogenous, highly expressed copies of glycoside hydrolase family 9 (GH9) genes. The purpose for retaining so many was unknown. We cloned and expressed the enzymes in transfected insect cell lines, and tested the individual proteins against different plant cell wall component poly- and oligosaccharides. Nearly all isolated enzymes were active against carboxymethylcellulose, however most could also degrade glucomannan, and some also either xylan or xyloglucan. The latter two enzyme groups were each monophyletic, suggesting the evolution of these novel substrate specificities in an early ancestor of the order. Such enzymes are highly unusual for Metazoa, for which no xyloglucanases had been reported. Phasmatodea gut extracts could degrade multiple plant cell wall components fully into sugar monomers, suggesting that enzymatic breakdown of plant cell walls by the entire Phasmatodea digestome may contribute to the Phasmatodea nutritional budget. The duplication and neofunctionalization of GH9s in the ancestral Phasmatodea may have enabled them to specialize as folivores and diverge from their omnivorous ancestors. The structural changes enabling these unprecedented activities in the cellulases require further study.

  18. Multiple chromosomal rearrangements structured the ancestral vertebrate Hox-bearing protochromosomes.

    Directory of Open Access Journals (Sweden)

    Vincent J Lynch

    2009-01-01

    Full Text Available While the proposal that large-scale genome expansions occurred early in vertebrate evolution is widely accepted, the exact mechanisms of the expansion--such as a single or multiple rounds of whole genome duplication, bloc chromosome duplications, large-scale individual gene duplications, or some combination of these--is unclear. Gene families with a single invertebrate member but four vertebrate members, such as the Hox clusters, provided early support for Ohno's hypothesis that two rounds of genome duplication (the 2R-model occurred in the stem lineage of extant vertebrates. However, despite extensive study, the duplication history of the Hox clusters has remained unclear, calling into question its usefulness in resolving the role of large-scale gene or genome duplications in early vertebrates. Here, we present a phylogenetic analysis of the vertebrate Hox clusters and several linked genes (the Hox "paralogon" and show that different phylogenies are obtained for Dlx and Col genes than for Hox and ErbB genes. We show that these results are robust to errors in phylogenetic inference and suggest that these competing phylogenies can be resolved if two chromosomal crossover events occurred in the ancestral vertebrate. These results resolve conflicting data on the order of Hox gene duplications and the role of genome duplication in vertebrate evolution and suggest that a period of genome reorganization occurred after genome duplications in early vertebrates.

  19. Ancestral origins of the prion protein gene D178N mutation in the Basque Country.

    Science.gov (United States)

    Rodríguez-Martínez, Ana B; Barreau, Christian; Coupry, Isabelle; Yagüe, Jordi; Sánchez-Valle, Raquel; Galdós-Alcelay, Luis; Ibáñez, Agustín; Digón, Antón; Fernández-Manchola, Ignacio; Goizet, Cyril; Castro, Azucena; Cuevas, Nerea; Alvarez-Alvarez, Maite; de Pancorbo, Marian M; Arveiler, Benoît; Zarranz, Juan J

    2005-06-01

    Fatal familial insomnia (FFI) and familial Creutzfeldt-Jakob disease (fCJD) are familial prion diseases with autosomal dominant inheritance of the D178N mutation. FFI has been reported in at least 27 pedigrees around the world. Twelve apparently unrelated FFI and fCJD pedigrees with the characteristic D178N mutation have been reported in the Prion Diseases Registry of the Basque Country since 1993. The high incidence of familial prion diseases in this region may reflect a unique ancestral origin of the chromosome carrying this mutation. In order to investigate this putative founder effect, we developed "happy typing", a new approach to the happy mapping method, which consists of the physical isolation of large haploid genomic DNA fragments and their analysis by the Polymerase Chain Reaction in order to perform haplotypic analysis instead of pedigree analysis. Six novel microsatellite markers, located in a 150-kb genomic segment flanking the PRNP gene were characterized for typing haploid DNA fragments of 285 kb in size. A common haplotype was found in patients from the Basque region, strongly suggesting a founder effect. We propose that "happy typing" constitutes an efficient method for determining disease-associated haplotypes, since the analysis of a single affected individual per pedigree should provide sufficient evidence.

  20. Nondecarboxylating and decarboxylating isocitrate dehydrogenases: oxalosuccinate reductase as an ancestral form of isocitrate dehydrogenase.

    Science.gov (United States)

    Aoshima, Miho; Igarashi, Yasuo

    2008-03-01

    Isocitrate dehydrogenase (ICDH) from Hydrogenobacter thermophilus catalyzes the reduction of oxalosuccinate, which corresponds to the second step of the reductive carboxylation of 2-oxoglutarate in the reductive tricarboxylic acid cycle. In this study, the oxidation reaction catalyzed by H. thermophilus ICDH was kinetically analyzed. As a result, a rapid equilibrium random-order mechanism was suggested. The affinities of both substrates (isocitrate and NAD+) toward the enzyme were extremely low compared to other known ICDHs. The binding activities of isocitrate and NAD+ were not independent; rather, the binding of one substrate considerably promoted the binding of the other. A product inhibition assay demonstrated that NADH is a potent inhibitor, although 2-oxoglutarate did not exhibit an inhibitory effect. Further chromatographic analysis demonstrated that oxalosuccinate, rather than 2-oxoglutarate, is the reaction product. Thus, it was shown that H. thermophilus ICDH is a nondecarboxylating ICDH that catalyzes the conversion between isocitrate and oxalosuccinate by oxidation and reduction. This nondecarboxylating ICDH is distinct from well-known decarboxylating ICDHs and should be categorized as a new enzyme. Oxalosuccinate-reducing enzyme may be the ancestral form of ICDH, which evolved to the extant isocitrate oxidative decarboxylating enzyme by acquiring higher substrate affinities.

  1. Anomalously high variation in postnatal development is ancestral for dinosaurs but lost in birds

    Science.gov (United States)

    Griffin, Christopher T.; Nesbitt, Sterling J.

    2016-12-01

    Compared with all other living reptiles, birds grow extremely fast and possess unusually low levels of intraspecific variation during postnatal development. It is now clear that birds inherited their high rates of growth from their dinosaurian ancestors, but the origin of the avian condition of low variation during development is poorly constrained. The most well-understood growth trajectories of later Mesozoic theropods (e.g., Tyrannosaurus, Allosaurus) show similarly low variation to birds, contrasting with higher variation in extant crocodylians. Here, we show that deep within Dinosauria, among the earliest-diverging dinosaurs, anomalously high intraspecific variation is widespread but then is lost in more derived theropods. This style of development is ancestral for dinosaurs and their closest relatives, and, surprisingly, this level of variation is far higher than in living crocodylians. Among early dinosaurs, this variation is widespread across Pangaea in the Triassic and Early Jurassic, and among early-diverging theropods (ceratosaurs), this variation is maintained for 165 million years to the end of the Cretaceous. Because the Late Triassic environment across Pangaea was volatile and heterogeneous, this variation may have contributed to the rise of dinosaurian dominance through the end of the Triassic Period.

  2. Major Chromosomal Rearrangements Distinguish Willow and Poplar After the Ancestral "Salicoid" Genome Duplication.

    Science.gov (United States)

    Hou, Jing; Ye, Ning; Dong, Zhongyuan; Lu, Mengzhu; Li, Laigeng; Yin, Tongming

    2016-06-27

    Populus (poplar) and Salix (willow) are sister genera in the Salicaceae family. In both lineages extant species are predominantly diploid. Genome analysis previously revealed that the two lineages originated from a common tetraploid ancestor. In this study, we conducted a syntenic comparison of the corresponding 19 chromosome members of the poplar and willow genomes. Our observations revealed that almost every chromosomal segment had a parallel paralogous segment elsewhere in the genomes, and the two lineages shared a similar syntenic pinwheel pattern for most of the chromosomes, which indicated that the two lineages diverged after the genome reorganization in the common progenitor. The pinwheel patterns showed distinct differences for two chromosome pairs in each lineage. Further analysis detected two major interchromosomal rearrangements that distinguished the karyotypes of willow and poplar. Chromosome I of willow was a conjunction of poplar chromosome XVI and the lower portion of poplar chromosome I, whereas willow chromosome XVI corresponded to the upper portion of poplar chromosome I. Scientists have suggested that Populus is evolutionarily more primitive than Salix. Therefore, we propose that, after the "salicoid" duplication event, fission and fusion of the ancestral chromosomes first give rise to the diploid progenitor of extant Populus species. During the evolutionary process, fission and fusion of poplar chromosomes I and XVI subsequently give rise to the progenitor of extant Salix species. This study contributes to an improved understanding of genome divergence after ancient genome duplication in closely related lineages of higher plants.

  3. Convergent evolution of caffeine in plants by co-option of exapted ancestral enzymes.

    Science.gov (United States)

    Huang, Ruiqi; O'Donnell, Andrew J; Barboline, Jessica J; Barkman, Todd J

    2016-09-20

    Convergent evolution is a process that has occurred throughout the tree of life, but the historical genetic and biochemical context promoting the repeated independent origins of a trait is rarely understood. The well-known stimulant caffeine, and its xanthine alkaloid precursors, has evolved multiple times in flowering plant history for various roles in plant defense and pollination. We have shown that convergent caffeine production, surprisingly, has evolved by two previously unknown biochemical pathways in chocolate, citrus, and guaraná plants using either caffeine synthase- or xanthine methyltransferase-like enzymes. However, the pathway and enzyme lineage used by any given plant species is not predictable from phylogenetic relatedness alone. Ancestral sequence resurrection reveals that this convergence was facilitated by co-option of genes maintained over 100 million y for alternative biochemical roles. The ancient enzymes of the Citrus lineage were exapted for reactions currently used for various steps of caffeine biosynthesis and required very few mutations to acquire modern-day enzymatic characteristics, allowing for the evolution of a complete pathway. Future studies aimed at manipulating caffeine content of plants will require the use of different approaches given the metabolic and genetic diversity revealed by this study.

  4. Evolution of outer membrane beta-barrels from an ancestral beta beta hairpin.

    Science.gov (United States)

    Remmert, M; Biegert, A; Linke, D; Lupas, A N; Söding, J

    2010-06-01

    Outer membrane beta-barrels (OMBBs) are the major class of outer membrane proteins from Gram-negative bacteria, mitochondria, and plastids. Their transmembrane domains consist of 8-24 beta-strands forming a closed, barrel-shaped beta-sheet around a central pore. Despite their obvious structural regularity, evidence for an origin by duplication or for a common ancestry has not been found. We use three complementary approaches to show that all OMBBs from Gram-negative bacteria evolved from a single, ancestral beta beta hairpin. First, we link almost all families of known single-chain bacterial OMBBs with each other through transitive profile searches. Second, we identify a clear repeat signature in the sequences of many OMBBs in which the repeating sequence unit coincides with the structural beta beta hairpin repeat. Third, we show that the observed sequence similarity between OMBB hairpins cannot be explained by structural or membrane constraints on their sequences. The third approach addresses a longstanding problem in protein evolution: how to distinguish between a very remotely homologous relationship and the opposing scenario of "sequence convergence." The origin of a diverse group of proteins from a single hairpin module supports the hypothesis that, around the time of transition from the RNA to the protein world, proteins arose by amplification and recombination of short peptide modules that had previously evolved as cofactors of RNAs.

  5. Transgenerational actions of environmental compounds on reproductive disease and identification of epigenetic biomarkers of ancestral exposures.

    Directory of Open Access Journals (Sweden)

    Mohan Manikkam

    Full Text Available Environmental factors during fetal development can induce a permanent epigenetic change in the germ line (sperm that then transmits epigenetic transgenerational inheritance of adult-onset disease in the absence of any subsequent exposure. The epigenetic transgenerational actions of various environmental compounds and relevant mixtures were investigated with the use of a pesticide mixture (permethrin and insect repellant DEET, a plastic mixture (bisphenol A and phthalates, dioxin (TCDD and a hydrocarbon mixture (jet fuel, JP8. After transient exposure of F0 gestating female rats during the period of embryonic gonadal sex determination, the subsequent F1-F3 generations were obtained in the absence of any environmental exposure. The effects on the F1, F2 and F3 generations pubertal onset and gonadal function were assessed. The plastics, dioxin and jet fuel were found to promote early-onset female puberty transgenerationally (F3 generation. Spermatogenic cell apoptosis was affected transgenerationally. Ovarian primordial follicle pool size was significantly decreased with all treatments transgenerationally. Differential DNA methylation of the F3 generation sperm promoter epigenome was examined. Differential DNA methylation regions (DMR were identified in the sperm of all exposure lineage males and found to be consistent within a specific exposure lineage, but different between the exposures. Several genomic features of the DMR, such as low density CpG content, were identified. Exposure-specific epigenetic biomarkers were identified that may allow for the assessment of ancestral environmental exposures associated with adult onset disease.

  6. Detection of Weakly Conserved Ancestral Mammalian RegulatorySequences by Primate Comparisons

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Qian-fei; Prabhakar, Shyam; Chanan, Sumita; Cheng,Jan-Fang; Rubin, Edward M.; Boffelli, Dario

    2006-06-01

    Genomic comparisons between human and distant, non-primatemammals are commonly used to identify cis-regulatory elements based onconstrained sequence evolution. However, these methods fail to detectcryptic functional elements, which are too weakly conserved among mammalsto distinguish from nonfunctional DNA. To address this problem, weexplored the potential of deep intra-primate sequence comparisons. Wesequenced the orthologs of 558 kb of human genomic sequence, coveringmultiple loci involved in cholesterol homeostasis, in 6 nonhumanprimates. Our analysis identified 6 noncoding DNA elements displayingsignificant conservation among primates, but undetectable in more distantcomparisons. In vitro and in vivo tests revealed that at least three ofthese 6 elements have regulatory function. Notably, the mouse orthologsof these three functional human sequences had regulatory activity despitetheir lack of significant sequence conservation, indicating that they arecryptic ancestral cis-regulatory elements. These regulatory elementscould still be detected in a smaller set of three primate speciesincluding human, rhesus and marmoset. Since the human and rhesus genomesequences are already available, and the marmoset genome is activelybeing sequenced, the primate-specific conservation analysis describedhere can be applied in the near future on a whole-genome scale, tocomplement the annotation provided by more distant speciescomparisons.

  7. Evolutionary Psychology: How Psychological Mechanisms Shaped by Natural Selection for Ancestral Environments Produce Current Behaviours

    Institute of Scientific and Technical Information of China (English)

    Charles Crawford

    2009-01-01

    The central purpose of this paper is to explain how Darwin's theory of evolution by natural selection can be used in understanding current human behaviour. First, Darwin's logic is briefly described. Development is an important issue when applying evolutionary theory to human behaviour. The notion of innate developmental orga-nization of psychological mechanisms is introduced. The possible social and political outcomes produced when differ-ent levels of innate developmental organization are paired with different beliefs about it are considered. The notion of psychological mechanisms as evolved adaptations is considered in some detail. Then I discuss different ways evo-htionists think about how genes are involved in the development of adaptations. The paper concludes with a frame-work for considering how ancestral adaptations function in current environments and outlines some ways of studying them. In China and many other parts of the world people desire a more harmonious society. Ⅰ hope that this paper will be of some small help in achieving this great task.

  8. A PCA-based method for ancestral informative markers selection in structured populations

    Institute of Scientific and Technical Information of China (English)

    ZHANG Feng; ZHANG Lei; DENG Hong-Wen

    2009-01-01

    Identification of population structure can help trace population histories and identify disease genes.Structured association (SA) is a commonly used approach for population structure identification and association mapping. A major issue with SA is that its performance greatly depends on the informativeness and the numbers of ancestral informative markers (AIMs). Present major AIM selection methods mostly require prior individual ancestry information, which is usually not available or uncertain in practice. To address this potential weakness, we herein develop a novel approach for AIM selection based on principle component analysis (PCA), which does not require prior ancestry information of study subjects. Our simulation and real genetic data analysis results suggest that, with equivalent AIMs,PCA-based selected AIMs can significantly increase the accuracy of inferred individual ancestries compared with traditionally randomly selected AIMs. Our method can easily be applied to whole genome data to select a set of highly informative AIMs in population structure, which can then be used to identify potential population structure and correct possible statistical biases caused by population stratification.

  9. The Spectrum of the Molecular Eigenstates of Pyrazine and the Reconstruction of Decays of Rotational States of the 1B3u (0-0) Transition of Pyrazine

    NARCIS (Netherlands)

    Meer, Barend J. van der; Jonkman, Harry Th.; Kommandeur, Jan

    1983-01-01

    The spectrum of the molecular eigenstates (ME) belonging to the various rotational members of the 1B3u (0-0) transition of pyrazine was measured with a very narrow band laser in a molecular beam with a Doppler width of 30 MHz. It is shown that, when the ME’s belonging to a single rotational state ar

  10. Cosmic Tidal Reconstruction

    CERN Document Server

    Zhu, Hong-Ming; Yu, Yu; Er, Xinzhong; Chen, Xuelei

    2015-01-01

    The gravitational coupling of a long wavelength tidal field with small scale density fluctuations leads to anisotropic distortions of the locally measured small scale matter correlation function. Since the local correlation function is statistically isotropic in the absence of such tidal interactions, the tidal distortions can be used to reconstruct the long wavelength tidal field and large scale density field in analogy with the cosmic microwave background lensing reconstruction. In this paper we present in detail a formalism for the cosmic tidal reconstruction and test the reconstruction in numerical simulations. We find that the density field on large scales can be reconstructed with good accuracy and the cross correlation coefficient between the reconstructed density field and the original density field is greater than 0.9 on large scales ($k\\lesssim0.1h/\\mathrm{Mpc}$). This is useful in the 21cm intensity mapping survey, where the long wavelength radial modes are lost due to foreground subtraction proces...

  11. Ptychographic ultrafast pulse reconstruction

    CERN Document Server

    Spangenberg, D; Brügmann, M H; Feurer, T

    2014-01-01

    We demonstrate a new ultrafast pulse reconstruction modality which is somewhat reminiscent of frequency resolved optical gating but uses a modified setup and a conceptually different reconstruction algorithm that is derived from ptychography. Even though it is a second order correlation scheme it shows no time ambiguity. Moreover, the number of spectra to record is considerably smaller than in most other related schemes which, together with a robust algorithm, leads to extremely fast convergence of the reconstruction.

  12. 客家祠堂的文化内涵研究--以三明客家祠堂为例%Study on the Culture Connotation of Hakka Ancestral Hall---Taking Sanming Hakka Ancestral Hall as an Example

    Institute of Scientific and Technical Information of China (English)

    黄晓珍

    2014-01-01

    Hakka ancestral hall is the most important place of Hakka clan ancestors,and it is an emotion carrier of Hakka as well, which contains rich cultural connotation. Sanming,as an important part of Fujian,Guangdong and Jiangxi Hakka stronghold,has a large number of Hakka ancestral halls. The name、couplets and architectural pattern of Hakka ancestral hall reflect how deeply the con-cept of ancestor worship of Hakka is;The pedigree of a clan、temple monument and ancestral hall couplets reflect how difficult Hakka' s migration path is;Its ancestor's instruction and function reflect how strong Hakka's concept of farming-reading is;Its site selection and layout reflect how prosperous Feng Shui Culture in Hakka is. They are the windows through which we can know Hakka history and Hak-ka culture.%客家祠堂是客家宗族祭祖的首要重地,也是客家人的情感载体,蕴含着丰富的文化内涵。三明作为闽粤赣边客家大本营的重要地区,拥有大量的客家祠堂,其堂号、楹联、建筑格局反映了客家人崇祖观念之深;其族谱、祠碑、楹联反映了客家人移民道路之艰;其祖训、功能反映出客家人耕读思想之重;其选址、布局反映出客家人风水文化之盛。客家祠堂是研究与理解客家历史文化的重要窗口。

  13. Analysis of two separate Higgs boson production processes which decay to two W bosons: vector boson fusion production with a fully leptonic final state and only one reconstructed jet; and WH production with the final state signature WWW*->lvlvqq

    CERN Document Server

    Gormsen, Helle

    2016-01-01

    The possible separation of signal and background for two Higgs boson processes is investigated comparing the significance achieved from an analysis fully based on binary selection criteria with an event selection applying a boosted decision tree as a multivariate method. The two examined channels are: vector boson fusion production of the Higgs particle with the decay H -> WW* -> lvlv, with only one of the two tag jets reconstructed; and the Higgs-strahlung process from a W boson with the signature WH -> WWW* -> lvlvqq. The results for the VBF and WH analysis are obtained from data samples corresponding to an integrated luminosity of 3.2 fb^-1 and 5.8 fb^-1 respectively and a center-of-mass energy of sqrt(s)=13 TeV.

  14. Thermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses

    DEFF Research Database (Denmark)

    Caspeta, Luis; Nielsen, Jens

    2015-01-01

    . Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3°C, whereas they showed a growth trade-off at temperatures below 34°C. Computational analysis of the physical properties...... in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures....... In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance...

  15. Identification of a new Newcastle disease virus isolate from Indonesia represents an ancestral lineage of class II genotype XIII.

    Science.gov (United States)

    Forrester, Naomi L; Widen, Steve G; Wood, Thomas G; Travassos da Rosa, Amelia P; Ksiazek, Thomas G; Vasilakis, Nikos; Tesh, Robert B

    2013-08-01

    An unknown virus was isolated from a mosquito pool collected in Jakarta during routine surveillance in 1979. Analysis of the sample using the Illumina platform resulted in the identification of a Newcastle disease virus (NDV) isolate. The sequence of the isolate indicated that it is an ancestral lineage of class II, genotype XIII. The source of the isolate is unusual, as newcastle disease virus is not believed to be vector-borne, although this mosquito pool was processed in a laboratory also handling samples for avian influenza surveillance and it is possible that this resulted in cross-contamination. This NDV isolate is still ancestral to most extant genotype XIII strains and provides a useful insight into historic NDV evolution.

  16. The Ancestral Carnivore Karyotype As Substantiated by Comparative Chromosome Painting of Three Pinnipeds, the Walrus, the Steller Sea Lion and the Baikal Seal (Pinnipedia, Carnivora.

    Directory of Open Access Journals (Sweden)

    Violetta R Beklemisheva

    Full Text Available Karyotype evolution in Carnivora is thoroughly studied by classical and molecular cytogenetics and supplemented by reconstructions of Ancestral Carnivora Karyotype (ACK. However chromosome painting information from two pinniped families (Odobenidae and Otariidae is noticeably missing. We report on the construction of the comparative chromosome map for species from each of the three pinniped families: the walrus (Odobenus rosmarus, Odobenidae-monotypic family, near threatened Steller sea lion (Eumetopias jubatus, Otariidae and the endemic Baikal seal (Pusa sibirica, Phocidae using combination of human, domestic dog and stone marten whole-chromosome painting probes. The earliest karyological studies of Pinnipedia showed that pinnipeds were characterized by a pronounced karyological conservatism that is confirmed here with species from Phocidae, Otariidae and Odobenidae sharing same low number of conserved human autosomal segments (32. Chromosome painting in Pinnipedia and comparison with non-pinniped carnivore karyotypes provide strong support for refined structure of ACK with 2n = 38. Constructed comparative chromosome maps show that pinniped karyotype evolution was characterized by few tandem fusions, seemingly absent inversions and slow rate of genome rearrangements (less then one rearrangement per 10 million years. Integrative comparative analyses with published chromosome painting of Phoca vitulina revealed common cytogenetic signature for Phoca/Pusa branch and supports Phocidae and Otaroidea (Otariidae/Odobenidae as sister groups. We revealed rearrangements specific for walrus karyotype and found the chromosomal signature linking together families Otariidae and Odobenidae. The Steller sea lion karyotype is the most conserved among three studied species and differs from the ACK by single fusion. The study underlined the strikingly slow karyotype evolution of the Pinnipedia in general and the Otariidae in particular.

  17. [Evolutionary history of Metazoa, ancestral status of the bilateria clonal reproduction, and semicolonial origin of the mollusca].

    Science.gov (United States)

    Martynov, A V

    2013-01-01

    Evolutionary history of any metazoan group is a history of the entire ontogenetic cycles instead of separate stages and genes only. Ontogeny in the most objective way links two key components of the biological systematics: historically-independent characters attribution and phylogeny itself. A general theory encompassing "static" traditional taxonomy and dynamic evolutionary process, based on the ontogenetic transformation of the organisms' shape is suggested here to term as ontogenetic systematics. As an important practical implication of the ontogenetic systematics, a new model of the bilaterian metazoans evolution is suggested. The new model considers asexual clonal reproduction as a central feature of the ancestral ontogenetic cycles of basal Bilateria. The new scenario resolves several notable contradictions, e.g. morphological, ontogenetic and molecular similarities of Pogonophora, Vestimentifera, Phoronida simultaneously to protostomian Spiralia (Lophotrochozoa) and Deuterostomia. The suggested model implies individuation (possibly multiple) of ancestral semicolonial sedentary group as a major factor of the basal Bilateria diversification. In the late Ediacaran and early Cambrian thus existed ancestral bilaterian group that shared characters of both Spiralia and Deuterostomia and possessed polyp-shape body and cephalic secretory shield (like in modern Pterobranchia and Vestimentifera), that later on reduced in various lines. This ancestral taxon in rank of supraphylum is suggested to term as Carmaphora (shield-bearers). Presence of the enigmatic sedentary fossil of the genus Cloudina with vestimentiferan-like tubes and evident clonal reproduction already in the late Ediacaran, and most recent found of an unquestionable pterobranch already in the early Cambrian support the new model of Bilateria evolution.

  18. Estimating ancestral proportions in a multi-ethnic US sample: implications for studies of admixed populations

    Directory of Open Access Journals (Sweden)

    Levran Orna

    2012-07-01

    Full Text Available Abstract This study was designed to determine the ancestral composition of a multi-ethnic sample collected for studies of drug addictions in New York City and Las Vegas, and to examine the reliability of self-identified ethnicity and three-generation family history data. Ancestry biographical scores for seven clusters corresponding to world major geographical regions were obtained using STRUCTURE, based on genotypes of 168 ancestry informative markers (AIMs, for a sample of 1,291 African Americans (AA, European Americans (EA, and Hispanic Americans (HA along with data from 1,051 HGDP-CEPH ‘diversity panel’ as a reference. Self-identified ethnicity and family history data, obtained in an interview, were accurate in identifying the individual major ancestry in the AA and the EA samples (approximately 99% and 95%, respectively but were not useful for the HA sample and could not predict the extent of admixture in any group. The mean proportions of the combined clusters corresponding to European and Middle Eastern populations in the AA sample, revealed by AIMs analysis, were 0.13. The HA subjects, predominantly Puerto Ricans, showed a highly variable hybrid contribution pattern of clusters corresponding to Europe (0.27, Middle East (0.27, Africa (0.20, and Central Asia (0.14. The effect of admixture on allele frequencies is demonstrated for two single-nucleotide polymorphisms (118A > G, 17 C > T of the mu opioid receptor gene (OPRM1. This study reiterates the importance of AIMs in defining ancestry, especially in admixed populations.

  19. Does body posture influence hand preference in an ancestral primate model?

    Directory of Open Access Journals (Sweden)

    Leliveld Lisette

    2011-02-01

    Full Text Available Abstract Background The origin of human handedness and its evolution in primates is presently under debate. Current hypotheses suggest that body posture (postural origin hypothesis and bipedalism hypothesis have an important impact on the evolution of handedness in primates. To gain insight into the origin of manual lateralization in primates, we studied gray mouse lemurs, suggested to represent the most ancestral primate condition. First, we investigated hand preference in a simple food grasping task to explore the importance of hand usage in a natural foraging situation. Second, we explored the influence of body posture by applying a forced food grasping task with varying postural demands (sit, biped, cling, triped. Results The tested mouse lemur population did not prefer to use their hands alone to grasp for food items. Instead, they preferred to pick them up using a mouth-hand combination or the mouth alone. If mouth usage was inhibited, they showed an individual but no population level handedness for all four postural forced food grasping tasks. Additionally, we found no influence of body posture on hand preference in gray mouse lemurs. Conclusion Our results do not support the current theories of primate handedness. Rather, they propose that ecological adaptation indicated by postural habit and body size of a given species has an important impact on hand preference in primates. Our findings suggest that small-bodied, quadrupedal primates, adapted to the fine branch niche of dense forests, prefer mouth retrieval of food and are less manually lateralized than large-bodied species which consume food in a more upright, and less stable body posture.

  20. Identification of the ancestral killer immunoglobulin-like receptor gene in primates

    Directory of Open Access Journals (Sweden)

    Coggill Penny

    2006-08-01

    Full Text Available Abstract Background Killer Immunoglobulin-like Receptors (KIR are essential immuno-surveillance molecules. They are expressed on natural killer and T cells, and interact with human leukocyte antigens. KIR genes are highly polymorphic and contribute vital variability to our immune system. Numerous KIR genes, belonging to five distinct lineages, have been identified in all primates examined thus far and shown to be rapidly evolving. Since few KIR remain orthologous between species, with only one of them, KIR2DL4, shown to be common to human, apes and monkeys, the evolution of the KIR gene family in primates remains unclear. Results Using comparative analyses, we have identified the ancestral KIR lineage (provisionally named KIR3DL0 in primates. We show KIR3DL0 to be highly conserved with the identification of orthologues in human (Homo sapiens, common chimpanzee (Pan troglodytes, gorilla (Gorilla gorilla, rhesus monkey (Macaca mulatta and common marmoset (Callithrix jacchus. We predict KIR3DL0 to encode a functional molecule in all primates by demonstrating expression in human, chimpanzee and rhesus monkey. Using the rhesus monkey as a model, we further show the expression profile to be typical of KIR by quantitative measurement of KIR3DL0 from an enriched population of natural killer cells. Conclusion One reason why KIR3DL0 may have escaped discovery for so long is that, in human, it maps in between two related leukocyte immunoglobulin-like receptor clusters outside the known KIR gene cluster on Chromosome 19. Based on genomic, cDNA, expression and phylogenetic data, we report a novel lineage of immunoglobulin receptors belonging to the KIR family, which is highly conserved throughout 50 million years of primate evolution.

  1. Regionalization of the shark hindbrain: a survey of an ancestral organization

    Directory of Open Access Journals (Sweden)

    Isabel eRodríguez-Moldes

    2011-03-01

    Full Text Available Cartilaginous fishes (chondrichthyans represent an ancient radiation of vertebrates currently considered the sister group of the group of gnathostomes with a bony skeleton that gave rise to land vertebrates. This out-group position makes chondrichthyans essential in assessing the ancestral organization of the brain of jawed vertebrates. To gain knowledge about hindbrain evolution we have studied its development in a shark, the lesser spotted dogfish Scyliorhinus canicula by analyzing the expression of some developmental genes and the origin and distribution of specific neuronal populations, which may help to identify hindbrain subdivisions and boundaries and the topology of specific cell groups. We have characterized three developmental periods that will serve as a framework to compare the development of different neuronal systems and may represent a suitable tool for comparing the absolute chronology of development among vertebrates. The expression patterns of Pax6, Wnt8 and Hoxa2 genes in early embryos of S. canicula showed close correspondence to what has been described in other vertebrates and helped to identify the anterior rhombomeres. Also in these early embryos, the combination of Pax6 with protein markers of migrating neuroblasts (DCX and early differentiating neurons (general: HuC/D; neuron type specific: GAD, the GABA synthesizing enzyme revealed the organization of S. canicula hindbrain in both transverse segmental units corresponding to visible rhombomeres and longitudinal columns. Later in development, when the interrhombomeric boundaries fade away, accurate information about S. canicula hindbrain subdivisions was achieved by comparing the expression patterns of Pax6 and GAD, serotonin (serotoninergic neurons, tyrosine hydroxylase (catecholaminergic neurons, choline acetyltransferase (cholinergic neurons and calretinin (a calcium-binding protein. The patterns observed revealed many topological correspondences with other vertebrates

  2. Streptococcus thermophilus Biofilm Formation: A Remnant Trait of Ancestral Commensal Life?

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    Benoit Couvigny

    Full Text Available Microorganisms have a long history of use in food production and preservation. Their adaptation to food environments has profoundly modified their features, mainly through genomic flux. Streptococcus thermophilus, one of the most frequent starter culture organisms consumed daily by humans emerged recently from a commensal ancestor. As such, it is a useful model for genomic studies of bacterial domestication processes. Many streptococcal species form biofilms, a key feature of the major lifestyle of these bacteria in nature. However, few descriptions of S. thermophilus biofilms have been reported. An analysis of the ability of a representative collection of natural isolates to form biofilms revealed that S. thermophilus was a poor biofilm producer and that this characteristic was associated with an inability to attach firmly to surfaces. The identification of three biofilm-associated genes in the strain producing the most biofilms shed light on the reasons for the rarity of this trait in this species. These genes encode proteins involved in crucial stages of biofilm formation and are heterogeneously distributed between strains. One of the biofilm genes appears to have been acquired by horizontal transfer. The other two are located in loci presenting features of reductive evolution, and are absent from most of the strains analyzed. Their orthologs in commensal bacteria are involved in adhesion to host cells, suggesting that they are remnants of ancestral functions. The biofilm phenotype appears to be a commensal trait that has been lost during the genetic domestication of S. thermophilus, consistent with its adaptation to the milk environment and the selection of starter strains for dairy fermentations.

  3. Streptococcus thermophilus Biofilm Formation: A Remnant Trait of Ancestral Commensal Life?

    Science.gov (United States)

    Couvigny, Benoit; Thérial, Claire; Gautier, Céline; Renault, Pierre; Briandet, Romain; Guédon, Eric

    2015-01-01

    Microorganisms have a long history of use in food production and preservation. Their adaptation to food environments has profoundly modified their features, mainly through genomic flux. Streptococcus thermophilus, one of the most frequent starter culture organisms consumed daily by humans emerged recently from a commensal ancestor. As such, it is a useful model for genomic studies of bacterial domestication processes. Many streptococcal species form biofilms, a key feature of the major lifestyle of these bacteria in nature. However, few descriptions of S. thermophilus biofilms have been reported. An analysis of the ability of a representative collection of natural isolates to form biofilms revealed that S. thermophilus was a poor biofilm producer and that this characteristic was associated with an inability to attach firmly to surfaces. The identification of three biofilm-associated genes in the strain producing the most biofilms shed light on the reasons for the rarity of this trait in this species. These genes encode proteins involved in crucial stages of biofilm formation and are heterogeneously distributed between strains. One of the biofilm genes appears to have been acquired by horizontal transfer. The other two are located in loci presenting features of reductive evolution, and are absent from most of the strains analyzed. Their orthologs in commensal bacteria are involved in adhesion to host cells, suggesting that they are remnants of ancestral functions. The biofilm phenotype appears to be a commensal trait that has been lost during the genetic domestication of S. thermophilus, consistent with its adaptation to the milk environment and the selection of starter strains for dairy fermentations.

  4. The ancestral activation promiscuity of ADP-glucose pyrophosphorylases from oxygenic photosynthetic organisms

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    Kuhn Misty L

    2013-02-01

    Full Text Available Abstract Background ADP-glucose pyrophosphorylase (ADP-Glc PPase catalyzes the first committed step in the synthesis of glycogen in bacteria and starch in algae and plants. In oxygenic photosynthetic organisms, ADP-Glc PPase is mainly activated by 3-phosphoglycerate (3-PGA and to a lesser extent by other metabolites. In this work, we analyzed the activation promiscuity of ADP-Glc PPase subunits from the cyanobacterium Anabaena PCC 7120, the green alga Ostreococcus tauri, and potato (Solanum tuberosum tuber by comparing a specificity constant for 3-PGA, fructose-1,6-bisphosphate (FBP, fructose-6-phosphate, and glucose-6-phosphate. Results The 3-PGA specificity constant for the enzymes from Anabaena (homotetramer, O. tauri, and potato tuber was considerably higher than for other activators. O. tauri and potato tuber enzymes were heterotetramers comprising homologous small and large subunits. Conversely, the O. tauri small subunit (OtaS homotetramer was more promiscuous because its FBP specificity constant was similar to that for 3-PGA. To explore the role of both OtaS and OtaL (O. tauri large subunit in determining the specificity of the heterotetramer, we knocked out the catalytic activity of each subunit individually by site-directed mutagenesis. Interestingly, the mutants OtaSD148A/OtaL and OtaS/OtaLD171A had higher specificity constants for 3-PGA than for FBP. Conclusions After gene duplication, OtaS seemed to have lost specificity for 3-PGA compared to FBP. This was physiologically and evolutionarily feasible because co-expression of both subunits restored the specificity for 3-PGA of the resulting heterotetrameric wild type enzyme. This widespread promiscuity seems to be ancestral and intrinsic to the enzyme family. Its presence could constitute an efficient evolutionary mechanism to accommodate the ADP-Glc PPase regulation to different metabolic needs.

  5. Evolution of neural crest and placodes: amphioxus as a model for the ancestral vertebrate?

    Science.gov (United States)

    Holland, L. Z.; Holland, N. D.

    2001-01-01

    Recent studies of protochordates (ascidian tunicates and amphioxus) have given insights into possible ancestors of 2 of the characteristic features of the vertebrate head: neural crest and placodes. The neural crest probably evolved from cells on either side of the neural plate-epidermis boundary in a protochordate ancestral to the vertebrates. In amphioxus, homologues of several vertebrate neural crest marker genes (BMP2/4, Pax3/7, Msx, Dll and Snail) are expressed at the edges of the neural plate and/or adjacent nonneural ectoderm. Some of these markers are also similarly expressed in tunicates. In protochordates, however, these cells, unlike vertebrate neural crest, neither migrate as individuals through embryonic tissues nor differentiate into a wide spectrum of cell types. Therefore, while the protochordate ancestor of the vertebrates probably had the beginnings of a genetic programme for neural crest formation, this programme was augmented in the earliest vertebrates to attain definitive neural crest. Clear homologues of vertebrate placodes are lacking in protochordates. However, both amphioxus and tunicates have ectodermal sensory cells. In tunicates these are all primary neurons, sending axons to the central nervous system, while in amphioxus, the ectodermal sensory cells include both primary neurons and secondary neurons lacking axons. Comparisons of developmental gene expression suggest that the anterior ectoderm in amphioxus may be homologous to the vertebrate olfactory placode, the only vertebrate placode with primary, not secondary, neurons. Similarly, biochemical, morphological and gene expression data suggest that amphioxus and tunicates also have homologues of the adenohypophysis, one of the few vertebrate structures derived from nonneurogenic placodes. In contrast, the origin of the other vertebrate placodes is very uncertain.

  6. Evidence-based green algal genomics reveals marine diversity and ancestral characteristics of land plants

    Energy Technology Data Exchange (ETDEWEB)

    van Baren, Marijke J.; Bachy, Charles; Reistetter, Emily Nahas; Purvine, Samuel O.; Grimwood, Jane; Sudek, Sebastian; Yu, Hang; Poirier, Camille; Deerinck, Thomas J.; Kuo, Alan; Grigoriev, Igor V.; Wong, Chee-Hong; Smith, Richard D.; Callister, Stephen J.; Wei, Chia-Lin; Schmutz, Jeremy; Worden, Alexandra Z.

    2016-03-31

    Prasinophytes are widespread marine green algae that are related to plants. Abundance of the genus Micromonas has reportedly increased in the Arctic due to climate-induced changes. Thus, studies of these organisms are important for marine ecology and understanding Virdiplantae evolution and diversification. We generated evidence-based Micromonas gene models using proteomics and RNA-Seq to improve prasinophyte genomic resources. First, sequences of four chromosomes in the 22 Mb Micromonas pusilla (CCMP1545) genome were finished. Comparison with the finished 21 Mb Micromonas commoda (RCC299) shows they share less than 8,142of ~10,000 protein-encoding genes, depending on the analysis method. Unlike RCC299 and other sequenced eukaryotes, CCMP1545 has two abundant repetitive intron types and a high percent (26%) GC splice donors. Micromonas has more genus-specific protein families (19%) than other genome sequenced prasinophytes (11%). Comparative analyses using predicted proteomes from other prasinophytes reveal proteins likely related to scale formation and ancestral photosynthesis. Our studies also indicate that peptidoglycan (PG) biosynthesis enzymes have been lost in multiple independent events in select prasinophytes and most plants. However, CCMP1545, polar Micromonas CCMP2099 and prasinophytes from other claasses retain the entire PG pathway, like moss and glaucophyte algae. Multiple vascular plants that share a unique bi-domain protein also have the pathway, except the Penicillin-Binding-Protein. Alongside Micromonas experiments using antibiotics that halt bacterial PG biosynthesis, the findings highlight unrecognized phylogenetic complexity in the PG-pathway retention and implicate a role in chloroplast structure of division in several extant Vridiplantae lineages. Extensive differences in gene loss and architecture between related prasinophytes underscore their extensive divergence. PG biosynthesis genes from the cyanobacterial endosymbiont that became the

  7. BAC libraries construction from the ancestral diploid genomes of the allotetraploid cultivated peanut

    Directory of Open Access Journals (Sweden)

    Chaine Christian

    2008-01-01

    Full Text Available Abstract Background Cultivated peanut, Arachis hypogaea is an allotetraploid of recent origin, with an AABB genome. In common with many other polyploids, it seems that a severe genetic bottle-neck was imposed at the species origin, via hybridisation of two wild species and spontaneous chromosome duplication. Therefore, the study of the genome of peanut is hampered both by the crop's low genetic diversity and its polyploidy. In contrast to cultivated peanut, most wild Arachis species are diploid with high genetic diversity. The study of diploid Arachis genomes is therefore attractive, both to simplify the construction of genetic and physical maps, and for the isolation and characterization of wild alleles. The most probable wild ancestors of cultivated peanut are A. duranensis and A. ipaënsis with genome types AA and BB respectively. Results We constructed and characterized two large-insert libraries in Bacterial Artificial Chromosome (BAC vector, one for each of the diploid ancestral species. The libraries (AA and BB are respectively c. 7.4 and c. 5.3 genome equivalents with low organelle contamination and average insert sizes of 110 and 100 kb. Both libraries were used for the isolation of clones containing genetically mapped legume anchor markers (single copy genes, and resistance gene analogues. Conclusion These diploid BAC libraries are important tools for the isolation of wild alleles conferring resistances to biotic stresses, comparisons of orthologous regions of the AA and BB genomes with each other and with other legume species, and will facilitate the construction of a physical map.

  8. Allelic lineages of the ficolin genes (FCNs are passed from ancestral to descendant primates.

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    Tina Hummelshøj

    Full Text Available The ficolins recognize carbohydrates and acetylated compounds on microorganisms and dying host cells and are able to activate the lectin pathway of the complement system. In humans, three ficolin genes have been identified: FCN1, FCN2 and FCN3, which encode ficolin-1, ficolin-2 and ficolin-3, respectively. Rodents have only two ficolins designated ficolin-A and ficolin-B that are closely related to human ficolin-1, while the rodent FCN3 orthologue is a pseudogene. Ficolin-2 and ficolin-3 have so far only been observed in humans. Thus, we performed a systematic investigation of the FCN genes in non-human primates. The exons and intron-exon boundaries of the FCN1-3 genes were sequenced in the following primate species: chimpanzee, gorilla, orangutan, rhesus macaque, cynomolgus macaque, baboon and common marmoset. We found that the exon organisation of the FCN genes was very similar between all the non-human primates and the human FCN genes. Several variations in the FCN genes were found in more than one primate specie suggesting that they were carried from one species to another including humans. The amino acid diversity of the ficolins among human and non-human primate species was estimated by calculating the Shannon entropy revealing that all three proteins are generally highly conserved. Ficolin-1 and ficolin-2 showed the highest diversity, whereas ficolin-3 was more conserved. Ficolin-2 and ficolin-3 were present in non-human primate sera with the same characteristic oligomeric structures as seen in human serum. Taken together all the FCN genes show the same characteristics in lower and higher primates. The existence of trans-species polymorphisms suggests that different FCN allelic lineages may be passed from ancestral to descendant species.

  9. CHAAJ (JUEGO DE PELOTA MESOAMERICANO: UN jUEGO ANCESTRAL ENTRE EMERGENCIAS CULTURALES

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    Jairzinho Francisco Panqueba Cifuentes

    2012-06-01

    Full Text Available Los juegos de pelota mesoamericanos son manifestaciones corporales que han sido exploradasprincipalmente desde perspectivas arqueológicas e históricas, pero también han sido retomadosdesde distintas iniciativas para ponerlos en práctica. Desde la frontera entre Estados Unidos conMéxico, pasando por distintos Estados del país “azteca”, son practicadas diferentes modalidades deeste juego. Sin embargo, decir que el chaaj en Mesoamérica es hoy en día una alternativa recreativay deportiva, es quedarse corto respecto a su ya demostrado potencial. La sacralidad manifestada através de los movimientos corporales está ofreciendo opciones de innovación en varios espacios de lassociedades actuales. En su dimensión ceremonial, revela una comunicación ancestral muy actual. Allíse ponen en juego los códices, las interpretaciones arqueológicas y los conocimientos territoriales depersonas sabedoras de las comunidades. En su dimensión lúdica, el juego reúne elementos culturales,deportivos y pedagógicos. Ha sido una práctica corporal, técnica y motora ejecutada constantementeen algunas regiones mexicanas y guatemaltecas. No obstante su antigüedad, en los últimos años seviene registrando una promoción inusitada, en medio de los actuales tiempos de cambio que fueronanunciados desde tiempos inmemoriales por los sabedores y las sabedoras mayas.

  10. Toxic and nontoxic components of botulinum neurotoxin complex are evolved from a common ancestral zinc protein

    Energy Technology Data Exchange (ETDEWEB)

    Inui, Ken [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Japan Society for the Promotion of Science, 1-8 Chiyoda-ku, Tokyo 102-8472 (Japan); Sagane, Yoshimasa [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Miyata, Keita [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Japan Society for the Promotion of Science, 1-8 Chiyoda-ku, Tokyo 102-8472 (Japan); Miyashita, Shin-Ichiro [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Suzuki, Tomonori [Department of Bacteriology, Okayama University Graduate School of Medicine, Dentistry and Pharmaceutical Sciences, 2-5-1 Shikata-cho, Kita-ku, Okayama 700-8558 (Japan); Shikamori, Yasuyuki [Agilent Technologies International Japan, Ltd. Takaura-cho 9-1, Hachioji-shi, Tokyo 192-0033 (Japan); Ohyama, Tohru; Niwa, Koichi [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan); Watanabe, Toshihiro, E-mail: t-watana@bioindustry.nodai.ac.jp [Department of Food and Cosmetic Science, Faculty of Bioindustry, Tokyo University of Agriculture, 196 Yasaka, Abashiri 099-2493 (Japan)

    2012-03-16

    Highlights: Black-Right-Pointing-Pointer BoNT and NTNHA proteins share a similar protein architecture. Black-Right-Pointing-Pointer NTNHA and BoNT were both identified as zinc-binding proteins. Black-Right-Pointing-Pointer NTNHA does not have a classical HEXXH zinc-coordinating motif similar to that found in all serotypes of BoNT. Black-Right-Pointing-Pointer Homology modeling implied probable key residues involved in zinc coordination. -- Abstract: Zinc atoms play an essential role in a number of enzymes. Botulinum neurotoxin (BoNT), the most potent toxin known in nature, is a zinc-dependent endopeptidase. Here we identify the nontoxic nonhemagglutinin (NTNHA), one of the BoNT-complex constituents, as a zinc-binding protein, along with BoNT. A protein structure classification database search indicated that BoNT and NTNHA share a similar domain architecture, comprising a zinc-dependent metalloproteinase-like, BoNT coiled-coil motif and concanavalin A-like domains. Inductively coupled plasma-mass spectrometry analysis demonstrated that every single NTNHA molecule contains a single zinc atom. This is the first demonstration of a zinc atom in this protein, as far as we know. However, the NTNHA molecule does not possess any known zinc-coordinating motif, whereas all BoNT serotypes possess the classical HEXXH motif. Homology modeling of the NTNHA structure implied that a consensus K-C-L-I-K-X{sub 35}-D sequence common among all NTNHA serotype molecules appears to coordinate a single zinc atom. These findings lead us to propose that NTNHA and BoNT may have evolved distinct functional specializations following their branching out from a common ancestral zinc protein.

  11. Are Hox genes ancestrally involved in axial patterning? Evidence from the hydrozoan Clytia hemisphaerica (Cnidaria.

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    Roxane Chiori

    Full Text Available BACKGROUND: The early evolution and diversification of Hox-related genes in eumetazoans has been the subject of conflicting hypotheses concerning the evolutionary conservation of their role in axial patterning and the pre-bilaterian origin of the Hox and ParaHox clusters. The diversification of Hox/ParaHox genes clearly predates the origin of bilaterians. However, the existence of a "Hox code" predating the cnidarian-bilaterian ancestor and supporting the deep homology of axes is more controversial. This assumption was mainly based on the interpretation of Hox expression data from the sea anemone, but growing evidence from other cnidarian taxa puts into question this hypothesis. METHODOLOGY/PRINCIPAL FINDINGS: Hox, ParaHox and Hox-related genes have been investigated here by phylogenetic analysis and in situ hybridisation in Clytia hemisphaerica, an hydrozoan species with medusa and polyp stages alternating in the life cycle. Our phylogenetic analyses do not support an origin of ParaHox and Hox genes by duplication of an ancestral ProtoHox cluster, and reveal a diversification of the cnidarian HOX9-14 genes into three groups called A, B, C. Among the 7 examined genes, only those belonging to the HOX9-14 and the CDX groups exhibit a restricted expression along the oral-aboral axis during development and in the planula larva, while the others are expressed in very specialised areas at the medusa stage. CONCLUSIONS/SIGNIFICANCE: Cross species comparison reveals a strong variability of gene expression along the oral-aboral axis and during the life cycle among cnidarian lineages. The most parsimonious interpretation is that the Hox code, collinearity and conservative role along the antero-posterior axis are bilaterian innovations.

  12. Delayed breast implant reconstruction

    DEFF Research Database (Denmark)

    Hvilsom, Gitte B.; Hölmich, Lisbet R.; Steding-Jessen, Marianne;

    2012-01-01

    We evaluated the association between radiation therapy and severe capsular contracture or reoperation after 717 delayed breast implant reconstruction procedures (288 1- and 429 2-stage procedures) identified in the prospective database of the Danish Registry for Plastic Surgery of the Breast during...... reconstruction approaches other than implants should be seriously considered among women who have received radiation therapy....

  13. Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates.

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    Jia-Yu Chen

    2015-07-01

    Full Text Available While some human-specific protein-coding genes have been proposed to originate from ancestral lncRNAs, the transition process remains poorly understood. Here we identified 64 hominoid-specific de novo genes and report a mechanism for the origination of functional de novo proteins from ancestral lncRNAs with precise splicing structures and specific tissue expression profiles. Whole-genome sequencing of dozens of rhesus macaque animals revealed that these lncRNAs are generally not more selectively constrained than other lncRNA loci. The existence of these newly-originated de novo proteins is also not beyond anticipation under neutral expectation, as they generally have longer theoretical lifespan than their current age, due to their GC-rich sequence property enabling stable ORFs with lower chance of non-sense mutations. Interestingly, although the emergence and retention of these de novo genes are likely driven by neutral forces, population genetics study in 67 human individuals and 82 macaque animals revealed signatures of purifying selection on these genes specifically in human population, indicating a proportion of these newly-originated proteins are already functional in human. We thus propose a mechanism for creation of functional de novo proteins from ancestral lncRNAs during the primate evolution, which may contribute to human-specific genetic novelties by taking advantage of existed genomic contexts.

  14. When ancestral heritage is a source of discomfort: culture, pre-object relatedness, and self-alienation.

    Science.gov (United States)

    Kradin, Richard L

    2012-04-01

    The ancestral claims on an individual can evoke mental conflict when they involve separating from an ethnic group whose beliefs and customs are devalued by the dominant culture. However, these claims are engraved on the psyche early in development by caretakers to the level of pre-object relatedness, where contents and affect tones are implicit and may be unavailable for later psychoanalytical interventions. In addition, as the anthropologist Clifford Geertz notes, one's culture of origin precedes the development of psyche and creates its own set of claims that must be renegotiated when one encounters a different domain of cultural symbols, a confrontation that can produce psychological dissonance and self-alienation. In this paper, three cases are examined in which mental conflicts were evoked by attempts at divesting ancestral claims in response to conscious efforts to assimilate into the dominant culture. These patients suffered from separation guilt and unstable self-esteem and reported dream imagery suggesting psychological imbalance. The requirement to carefully delineate the ancestral claims on psyche as well as those contents and affects that may not be accessible to therapeutic intervention is emphasized, and the importance of compromise and acceptance with respect to the psychological demands of the unconscious are considered.

  15. The capability to synthesize phytochelatins and the presence of constitutive and functional phytochelatin synthases are ancestral (plesiomorphic) characters for basal land plants.

    Science.gov (United States)

    Petraglia, Alessandro; De Benedictis, Maria; Degola, Francesca; Pastore, Giovanni; Calcagno, Margherita; Ruotolo, Roberta; Mengoni, Alessio; Sanità di Toppi, Luigi

    2014-03-01

    Bryophytes, a paraphyletic group which includes liverworts, mosses, and hornworts, have been stated as land plants that under metal stress (particularly cadmium) do not synthesize metal-binding peptides such as phytochelatins. Moreover, very little information is available to date regarding phytochelatin synthesis in charophytes, postulated to be the direct ancestors of land plants, or in lycophytes, namely very basal tracheophytes. In this study, it was hypothesized that basal land plants and charophytes have the capability to produce phytochelatins and possess constitutive and functional phytochelatin synthases. To verify this hypothesis, twelve bryophyte species (six liverworts, four mosses, and two hornworts), three charophytes, and two lycophyte species were exposed to 0-36 μM cadmium for 72 h, and then assayed for: (i) glutathione and phytochelatin quali-quantitative content by HPLC and mass spectrometry; (ii) the presence of putative phytochelatin synthases by western blotting; and (iii) in vitro activity of phytochelatin synthases. Of all the species tested, ten produced phytochelatins in vivo, while the other seven did not. The presence of a constitutively expressed and functional phytochelatin synthase was demonstrated in all the bryophyte lineages and in the lycophyte Selaginella denticulata, but not in the charophytes. Hence, current knowledge according to phytochelatins have been stated as being absent in bryophytes was therefore confuted by this work. It is argued that the capability to synthesize phytochelatins, as well as the presence of active phytochelatin synthases, are ancestral (plesiomorphic) characters for basal land plants.

  16. Study of |Vtd/Vts| Using a Sum of Exclusive B → X Gamma Final States Reconstructed With the BaBar Detector

    Energy Technology Data Exchange (ETDEWEB)

    Tibbetts, Mark James [Imperial College, London (United Kingdom)

    2013-06-01

    Experimental data collected with the BABAR detector consisting of 470.9 ± 2.8 million BB events are used to measure the sum of seven exclusive B → Xd(s) γ transitions, where Xd(s) is any non-strange (strange) charmless hadronic state. For each transition avour, measurements are made in the hadronic mass ranges 0.5 ≤ mX < 1.0 GeV=c2 and 1.0 ≤ mX ≤ 2.0 GeV=c2. These are extrapolated and combined in a model-dependent way to obtain the ratio of the total branching fractions, B(B→ X)=B(B→ X ) = 0.0456 ± 0.0110 ± 0.0097 where the first error is statistical and the second error is systematic. This is interpreted as a measurement of the ratio of CKM matrix elements |Vtd/Vts| = 0.211 ± 0.023 ± 0.022 ± 0.001 where the final error is due to theoretical uncertainty.

  17. Reconstruction of Intima and Adventitia Models into a State Undeformed by a Catheter by Using CT, IVUS, and Biplane X-Ray Angiogram Images

    Directory of Open Access Journals (Sweden)

    Jinwon Son

    2017-01-01

    Full Text Available The number of studies on blood flow analysis using fluid-structure interaction (FSI analysis is increasing. Though a 3D blood vessel model that includes intima and adventitia is required for FSI analysis, there are difficulties in generating it using only one type of medical imaging. In this paper, we propose a 3D modeling method for accurate FSI analysis. An intravascular ultrasound (IVUS image is used with biplane X-ray angiogram images to calculate the position and orientation of the blood vessel. However, these images show that the blood vessel is deformed by the catheter inserted into the blood vessel for IVUS imaging. To eliminate such deformation, a CT image was added and the two models were registered. First, a 3D model of the undeformed intima was generated using a CT image. In the second stage, a model of intima and adventitia deformed by the catheter was generated by combining the IVUS image and the X-ray angiogram images. A 3D model of intima and adventitia with the deformation caused by insertion of the catheter eliminated was generated by matching these 3D blood vessel models in different states. In addition, a 3D blood vessel model including bifurcation was generated using the proposed method.

  18. Reconstructing the neutron-star equation of state with gravitational-wave detectors from a realistic population of inspiralling binary neutron stars

    CERN Document Server

    Lackey, Benjamin D

    2014-01-01

    Gravitational-wave observations of inspiralling binary neutron star systems can be used to measure the neutron-star equation of state (EOS) through the tidally induced shift in the waveform phase that depends on the tidal deformability parameter $\\lambda$. Previous work has shown that $\\lambda$, a function of the neutron-star EOS and mass, is measurable by Advanced LIGO for a single event when including tidal information up to the merger frequency. In this work, we describe a method for stacking measurements of $\\lambda$ from multiple inspiral events to measure the EOS. We use Markov chain Monte Carlo simulations to estimate the parameters of a 4-parameter piecewise polytrope EOS that matches theoretical EOS models to a few percent. We find that, for "realistic" event rates ($\\sim 40$ binary neutron star inspiral events per year with signal-to-noise ratio $> 8$ in a single Advanced LIGO detector), combining a year of gravitational-wave data from a three-detector network with the constraints from causality and...

  19. 美國專利產品的修理與再製之區分與案例類型 Distinction between Repair and Reconstruction of a Patented Product and Category of Cases in United States

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    陳佳麟 Jia-Lin Chen

    2006-12-01

    Full Text Available 專利權人或其被授權人所銷售之專利產品,如於銷售時未附加有效限制,購買者可以任意使用、拋棄或再銷售該專利產品,其中使用之權利包含修理或改裝,但不包含再製(或稱:再造)一新的專利產品,此即所謂的可允許修理理論(doctrine of permissible repair)。可允許修理理論源自於專利權耗盡理論和默示授權理論。可允許修理或改裝專利產品,包含拆解和清洗專利產品,並更換其中未受個別專利保護之零組件,不論該零組件是否已耗損或使用過;不可允許再製專利產品係指,當專利產品整體已經耗損後,對其重新製造以致於實質上製造一個新産品。美國最高法院於1850 年第一次處理修理和再製區分案例至今已逾150 年,各級法院已累積了相當多的判決。本文整理與分析美國近年來有關於區分專利產品修理與再製之糾紛案例,藉以歸納出美國最高法院與美國聯邦巡迴上訴法院所發展之判斷準則及應注意事項。 The purchaser of a patented product sold by the patentee or its licensees without effective restriction thereon has the rights to use it, discard it, or resell it. The right to use the patented product includes replacement or modification, but does not include the right to construct an essentially new article on the template of the original one. This is so-called the doctrine of permissible repair, which originates from the patent exhaustion doctrine and implied license. Permissible repair of a patented product includes disassembly and clean of the product as well as replacement of unpatented components, regardless of whether the replaced components are spent or not. Reconstruction of a patented product is basically to make a new article, after the entity, viewed as a whole, has become spent. The Supreme Court of United States first addressed the issue about distinction between repair

  20. Reformulating and Reconstructing Quantum Theory

    CERN Document Server

    Hardy, Lucien

    2011-01-01

    We provide a reformulation of finite dimensional quantum theory in the circuit framework in terms of mathematical axioms, and a reconstruction of quantum theory from operational postulates. The mathematical axioms for quantum theory are the following: [Axiom 1] Operations correspond to operators. [Axiom 2] Every complete set of positive operators corresponds to a complete set of operations. The following operational postulates are shown to be equivalent to these mathematical axioms: [P1] Definiteness. Associated with any given pure state is a unique maximal effect giving probability equal to one. This maximal effect does not give probability equal to one for any other pure state. [P2] Information locality. A maximal measurement on a composite system is effected if we perform maximal measurements on each of the components. [P3] Tomographic locality. The state of a composite system can be determined from the statistics collected by making measurements on the components. [P4] Compound permutatability. There exis...

  1. A Common Ancestral Mutation in CRYBB3 Identified in Multiple Consanguineous Families with Congenital Cataracts.

    Directory of Open Access Journals (Sweden)

    Xiaodong Jiao

    report a common ancestral mutation in CRYBB3 associated with autosomal recessive congenital cataracts identified in four familial cases of Pakistani origin.

  2. 大学生健康人格现状及重构策略%Reconstruction Strategies of College and University Students' State of Personality Health

    Institute of Scientific and Technical Information of China (English)

    吴梅生

    2012-01-01

    For college and university students, the construction of healthy personality is essential for self-development and a historical mission in the new century. On the basis of international studies on personality health and scholars' surveys about college and university students' state of personality, this essay points out that the healthy personality college and university students must construct is as follows: raising self-awareness, accomplishing self-identity, forming benign morality, enhancing the ability of self-control and self-regulation, cultivating sense of optimism and responsibility. The strategies that college and university students may devise are: incorporating a healthy personality into their plans, focusing on the acquisition of personality health theory so as to increase wisdom, obtaining a correct self-knowledge and self-evaluation, having an objective knowledge and confrontation of the reality, enriching social experiences and undergoing a regular self-reflection.%指出健康人格的建构既是大学生自身发展的需要,也是新世纪赋予他们的历史使命。根据国内外专家对健康人格的研究以及学者对当前大学生人格的调查,大学生应努力建构的健康人格内容是:提高自我意识的水平、完成自我同一性、形成良好的品德、提高自控和调节能力、乐观进取的精神、高度责任感。大学生建构健康人格的策略有:把发展健康人格纳入目标和计划中;重视健康人格理论知识的学习、提升智慧;正确地认识自我和评价自我;客观地认识现实和面对现实;丰富社会实践体验;经常进行自我反恩。

  3. Reconstruction of hydrologic responses to late-Glacial (9-33ka) abrupt climate transitions in the coastal southwest United States

    Science.gov (United States)

    Wu, M.; Feakins, S. J.; Kirby, M. E.

    2013-12-01

    A sediment core retrieved from Lake Elsinore, the largest natural freshwater lake in southern California, spans an age of 9 to 33ka BP. The period includes several late-Glacial abrupt climate transitions such as the Heinrich events (HEs) 1-3, the Bølling-Allerød (B-A), and the Younger Dryas (YD). This terrestrial site provides a unique opportunity to evaluate changes in hydrology in coastal southwest United States across these key abrupt climate transition events. Hydrogen isotopic ratios (δDwax) of the long-chain C28 alkanoic acid, a biomarker for terrestrial leaf wax, extracted from the sediments, were analyzed to reveal the δD of precipitation water in the past (δDprecip). In the modern climate, higher δDprecip values are associated with moisture sourced from the tropical Pacific, which brings a drier and warmer climate, whereas lower δDprecip values are associated with moisture sourced from north Pacific brought by polar jet stream, causing a wetter and colder climate. δDwax ranges from about -210‰ to -100‰ between late-Glacial HEs and the beginning of Holocene. The pattern generally correlates with Greenland ice core and regional speleothem records, with lower δDwax values corresponding to colder periods (HEs), and higher δDwax values corresponding to warmer periods (B-A and early Holocene). We infer cold and wet climate with north Pacific sourced moisture during the glacial, followed by gradual warming and drying into the B-A and Holocene, when the moisture sources shifted to the tropical Pacific. There is no substantive response to the YD. The fluctuations of δDwax into and out of the HEs can be as large as about 60‰, suggesting greatly variable hydrology across these late-Glacial abrupt climate transition events. The large shifts in δDwax signal during deglaciation and HEs indicate that hydrology in the coastal southwest US has responded sensitively to climate change, and therefore has important implications for water resources in this

  4. Strains of JC virus in Amerind-speakers of North America (Salish) and South America (Guaraní), Na-Dene-speakers of New Mexico (Navajo), and modern Japanese suggest links through an ancestral Asian population.

    Science.gov (United States)

    Fernandez-Cobo, Mariana; Agostini, Hansjürgen T; Britez, Graciela; Ryschkewitsch, Caroline F; Stoner, Gerald L

    2002-06-01

    Previously we showed that strains of human polyoma virus JC among the Navajo in New Mexico, speakers of an Athapaskan language in the Na-Dene language phylum, and among the Salish people in Montana, speakers of a language of the Salishan group in the Amerind family, were mainly of a northeast Asian genotype found in Japan (type 2A). We now report partial VP1-gene, regulatory region, and complete genome sequences of JC virus (JCV) from the Guaraní Indians of Argentina. The Tupí-Guaraní language represents the Equatorial branch of the Amerind language family proposed by Greenberg ([1987] Language in the Americas, Stanford: Stanford University Press). The partial VP1 gene sequences of the Guaraní revealed several variants of strains found in northeast Asia (Japan), as did the Salish. In contrast, the strains in the Navajo largely conformed to the prototype type 2A sequence (MY). Phylogenetic reconstruction with both the neighbor-joining and maximum parsimony methods utilized three complete Guaraní JCV genome sequences, three genomes from the Salish people, and 27 other complete JCV genomes, including three from the Navajo and three from Japan. Both trees showed that all type 2A JCV strains from the North and South Americans are closely related phylogenetically to strains in present-day Japan. However, variant sites in the coding regions, the T-antigen intron, and the regulatory region link the type 2A strains in Amerind groups (Guaraní and Salish), but differentiate them from those in a Na-Dene-speaking (Navajo) population. The data suggest separation from a population ancestral to modern Japanese, followed by a second division within the ancestral group that led to Amerind- and Na-Dene-speaking groups. The data cannot, however, localize the latter split to the Asian mainland (two migrations) or to North America (one migration).

  5. Luminosity Spectrum Reconstruction at Linear Colliders

    CERN Document Server

    Poss, Stéphane

    2014-01-01

    A good knowledge of the luminosity spectrum is mandatory for many measurements at future e+e- colliders. As the beam-parameters determining the luminosity spectrum cannot be measured precisely, the luminosity spectrum has to be measured through a gauge process with the detector. The measured distributions, used to reconstruct the spectrum, depend on Initial State Radiation, cross-section, and Final State Radiation. To extract the basic luminosity spectrum, a parametric model of the luminosity spectrum is created, in this case the spectrum at the 3 TeV Compact Linear Collider (CLIC). The model is used within a reweighting technique to extract the luminosity spectrum from measured Bhabha event observables, taking all relevant effects into account. The centre-of-mass energy spectrum is reconstructed within 5% over the full validity range of the model. The reconstructed spectrum does not result in a significant bias or systematic uncertainty in the exemplary physics benchmark process of smuon pair production.

  6. Prairie Reconstruction Initiative Project

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of the Prairie Reconstruction Initiative Advisory Team (PRIAT) is to identify and take steps to resolve uncertainties in the process of prairie...

  7. On TPC cluster reconstruction

    CERN Document Server

    Dydak, F; Nefedov, Y; Wotschack, J; Zhemchugov, A

    2004-01-01

    For a bias-free momentum measurement of TPC tracks, the correct determination of cluster positions is mandatory. We argue in particular that (i) the reconstruction of the entire longitudinal signal shape in view of longitudinal diffusion, electronic pulse shaping, and track inclination is important both for the polar angle reconstruction and for optimum r phi resolution; and that (ii) self-crosstalk of pad signals calls for special measures for the reconstruction of the z coordinate. The problem of 'shadow clusters' is resolved. Algorithms are presented for accepting clusters as 'good' clusters, and for the reconstruction of the r phi and z cluster coordinates, including provisions for 'bad' pads and pads next to sector boundaries, respectively.

  8. Reconstructions of eyelid defects

    Directory of Open Access Journals (Sweden)

    Nirmala Subramanian

    2011-01-01

    Full Text Available Eyelids are the protective mechanism of the eyes. The upper and lower eyelids have been formed for their specific functions by Nature. The eyelid defects are encountered in congenital anomalies, trauma, and postexcision for neoplasm. The reconstructions should be based on both functional and cosmetic aspects. The knowledge of the basic anatomy of the lids is a must. There are different techniques for reconstructing the upper eyelid, lower eyelid, and medial and lateral canthal areas. Many a times, the defects involve more than one area. For the reconstruction of the lid, the lining should be similar to the conjunctiva, a cover by skin and the middle layer to give firmness and support. It is important to understand the availability of various tissues for reconstruction. One layer should have the vascularity to support the other layer which can be a graft. A proper plan and execution of it is very important.

  9. Prairie Reconstruction Initiative

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of the Prairie Reconstruction Initiative Advisory Team (PRIAT) is to identify and take steps to resolve uncertainties in the process of prairie...

  10. Breast Reconstruction After Mastectomy

    Science.gov (United States)

    ... It also does not involve cutting of the abdominal muscle and is a free flap. This type of ... NCI fact sheet Mammograms . What are some new developments in breast reconstruction after mastectomy? Oncoplastic surgery. In ...

  11. Head and face reconstruction

    Science.gov (United States)

    ... work together. Head and neck surgeons also perform craniofacial reconstruction operations. The surgery is done while you are deep asleep and pain-free (under general anesthesia ). The surgery may take ...

  12. La modernidad, el cuidado de la salud y la cultura ancestral.

    Directory of Open Access Journals (Sweden)

    Ana Cecilia Becerra

    2009-11-01

    Full Text Available La modernidad es tanto un período histórico como un concepto filosófico y sociológico que impuso la razón y el método formal sobre todos los actos políticos, sociales y epistemológicos de las distintas culturas del mundo. La modernidad se construyó en su momento sobre el imaginario de la superioridad europea1 y durante el período colonial fue la causante del proceso avasallador de exterminio y de desconocimiento de las sociedades y culturas indígenas de América. Ella, con sus valores patriarcales y formales, desplazó la ética del cuidado y del abrigo de los pueblos autóctonos imponiendo una lógica racional, calculadora e impersonal. Al desconocer y casi negar en su totalidad la cosmovisión ancestral de curar y cuidar, relegó los ejercicios profesionalizantes de la salud bajo el amparo de la mercantilización del capitalismo mundial integrado. La modernidad, desde el inicio y en la actualidad, ha impregnado la cultura de todos los pueblos y ha condicionado todos los actos académicos en las instituciones escolares y universitarias. La perpetuación de un modelo positivista y occidentalizado ha sido una constante en las aulas universitarias y en las disciplinas, sobre todo en las ciencias de la salud. Históricamente el conocimiento en salud ha sido construido con base en el enfoque positivista y la concepción biologista del proceso salud-enfermedad, lo cual lleva a una fragmentación del saber, disyunción del sujeto y el objeto en la producción del conocimiento, y a una incapacidad de asumir al ser humano en todas sus dimensiones, razón de ser de la acción en salud, como totalidad y unidad integral2. Este panorama aquí planteado deja un gran reto epistemológico a los profesionales y a los docentes de las ciencias de la salud en general y de enfermería en particular. Vista la enfermería desde la fundamentación del cuidado de la salud, no se puede descontextualizar ni escindir de nuestra propia cultura, pretendiendo

  13. La modernidad, el cuidado de la salud y la cultura ancestral

    Directory of Open Access Journals (Sweden)

    Ana Cecilia Becerra

    2008-09-01

    Full Text Available La modernidad es tanto un período histórico como un concepto filosófico y sociológico que impuso la razón y el método formal sobre todos los actos políticos, sociales y epistemológicos de las distintas culturas del mundo. La modernidad se construyó en su momento sobre el imaginario de la superioridad europea1 y durante el período colonial fue la causante del proceso avasallador de exterminio y de desconocimiento de las sociedades y culturas indígenas de América.Ella, con sus valores patriarcales y formales, desplazó la ética del cuidado y del abrigo de los pueblos autóctonos imponiendo una lógica racional, calculadora e impersonal. Al desconocer y casi negar en su totalidad la cosmovisión ancestral de curar y cuidar, relegó los ejercicios profesionalizantes de la salud bajo el amparo de la mercantilización del capitalismo mundial integrado.La modernidad, desde el inicio y en la actualidad, ha impregnado la cultura de todos los pueblos y ha condicionado todos los actos académicos en las instituciones escolares y universitarias. La perpetuación de un modelo positivista y occidentalizado ha sido una constante en las aulas universitarias y en las disciplinas, sobre todo en las ciencias de la salud. Históricamente el conocimiento en salud ha sido construido con base en el enfoque positivista y la concepción biologista del proceso salud-enfermedad, lo cual lleva a una fragmentación del saber, disyunción del sujeto y el objeto en la producción del conocimiento, y a una incapacidad de asumir al ser humano en todas sus dimensiones, razón de ser de la acción en salud, como totalidad y unidad integral2.Este panorama aquí planteado deja un gran reto epistemológico a los profesionales y a los docentes de las ciencias de la salud en general y de enfermería en particular. Vista la enfermería desde la fundamentación del cuidado de la salud, no se puede descontextualizar ni escindir de nuestra propia cultura, pretendiendo

  14. Reconstruction Setting Out

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The earthquake-hit Yushu shifts its focus from rescuing survivors to post-quake reconstruction The first phase of earthquake relief, in which rescuing lives was the priority, finished 12 days after a 7.1-magnitude earthquake struck the Tibetan Autonomous Prefecture of Yushu in northwest China’s Qinghai Province on April 14, and reconstruction of the area is now ready to begin.

  15. Iterative wavelet thresholding for rapid MRI reconstruction

    Science.gov (United States)

    Kayvanrad, Mohammad H.; McKenzie, Charles A.; Peters, Terry M.

    2011-03-01

    According to the developments in the field of compressed sampling and and sparse recovery, one might take advantage of the sparsity of an object, as an additional a priori knowledge about the object, to reconstruct it from fewer samples than that needed by the traditional sampling strategies. Since most magnetic resonance (MR) images are sparse in some domain, in this work we consider the problem of MR reconstruction and how one could apply this idea to accelerate the process of MR image/map acquisition. In particular, based on the Paupolis-Gerchgerg algorithm, an iterative thresholding algorithm for reconstruction of MR images from limited k-space observations is proposed. The proposed method takes advantage of the sparsity of most MR images in the wavelet domain. Initializing with a minimum-energy reconstruction, the object of interest is reconstructed by going through a sequence of thresholding and recovery iterations. Furthermore, MR studies often involve acquisition of multiple images in time that are highly correlated. This correlation can be used as additional knowledge on the object beside the sparsity to further reduce the reconstruction time. The performance of the proposed algorithms is experimentally evaluated and compared to other state-of-the-art methods. In particular, we show that the quality of reconstruction is increased compared to total variation (TV) regularization, and the conventional Papoulis-Gerchberg algorithm both in the absence and in the presence of noise. Also, phantom experiments show good accuracy in the reconstruction of relaxation maps from a set of highly undersampled k-space observations.

  16. Return flight to the Canary Islands--the key role of peripheral populations of Afrocanarian blue tits (Aves: Cyanistes teneriffae) in multi-gene reconstructions of colonization pathways.

    Science.gov (United States)

    Päckert, Martin; Martens, Jochen; Hering, Jens; Kvist, Laura; Illera, Juan Carlos

    2013-05-01

    Afrocanarian blue tits (Cyanistes teneriffae) have a scattered distribution on the Canary Islands and on the North African continent. To date, the Canary Islands have been considered the species' main Pleistocene evolutionary center, but their colonization pathways remain uncertain. We set out to reconstruct a dated multi-gene phylogeny and ancestral ranges for Cyanistes tit species including the currently unstudied, peripheral Libyan population of C. t. cyrenaicae. In all reconstructions the most easterly and westerly peripheral populations (in Libya and on La Palma) represented basal offshoots of C. teneriffae. These two peripheral populations shared all four major indels and differed in this respect from all other members of the Afrocanarian core group. The basal split of Afrocanarian blue tits from their European relatives was dated to the early Pliocene. The two ancestral area reconstructions were contradictory and suggested either a Canarian or a North African origin of C. teneriffae - but unambiguously ruled out a continental European ancestral range. We conclude that the peripheral populations of C. teneriffae represent relic lineages of a first faunal interchange, presumably downstream colonization from North Africa to the Canary Islands. Subsequent eastward stepping-stone colonization within the Canarian Archipelago culminated in a very recent late (possibly even post-) Pleistocene back-colonization from the Canary Islands to North Africa.

  17. Estimation of hominoid ancestral population sizes under bayesian coalescent models incorporating mutation rate variation and sequencing errors.

    Science.gov (United States)

    Burgess, Ralph; Yang, Ziheng

    2008-09-01

    Estimation of population parameters for the common ancestors of humans and the great apes is important in understanding our evolutionary history. In particular, inference of population size for the human-chimpanzee common ancestor may shed light on the process by which the 2 species separated and on whether the human population experienced a severe size reduction in its early evolutionary history. In this study, the Bayesian method of ancestral inference of Rannala and Yang (2003. Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics. 164:1645-1656) was extended to accommodate variable mutation rates among loci and random species-specific sequencing errors. The model was applied to analyze a genome-wide data set of approximately 15,000 neutral loci (7.4 Mb) aligned for human, chimpanzee, gorilla, orangutan, and macaque. We obtained robust and precise estimates for effective population sizes along the hominoid lineage extending back approximately 30 Myr to the cercopithecoid divergence. The results showed that ancestral populations were 5-10 times larger than modern humans along the entire hominoid lineage. The estimates were robust to the priors used and to model assumptions about recombination. The unusually low X chromosome divergence between human and chimpanzee could not be explained by variation in the male mutation bias or by current models of hybridization and introgression. Instead, our parameter estimates were consistent with a simple instantaneous process for human-chimpanzee speciation but showed a major reduction in X chromosome effective population size peculiar to the human-chimpanzee common ancestor, possibly due to selective sweeps on the X prior to separation of the 2 species.

  18. Human Genetic Ancestral Composition Correlates with the Origin of Mycobacterium leprae Strains in a Leprosy Endemic Population

    Science.gov (United States)

    Cardona-Castro, Nora; Cortés, Edwin; Beltrán, Camilo; Romero, Marcela; Badel-Mogollón, Jaime E.; Bedoya, Gabriel

    2015-01-01

    Recent reports have suggested that leprosy originated in Africa, extended to Asia and Europe, and arrived in the Americas during European colonization and the African slave trade. Due to colonization, the contemporary Colombian population is an admixture of Native-American, European and African ancestries. Because microorganisms are known to accompany humans during migrations, patterns of human migration can be traced by examining genomic changes in associated microbes. The current study analyzed 118 leprosy cases and 116 unrelated controls from two Colombian regions endemic for leprosy (Atlantic and Andean) in order to determine possible associations of leprosy with patient ancestral background (determined using 36 ancestry informative markers), Mycobacterium leprae genotype and/or patient geographical origin. We found significant differences between ancestral genetic composition. European components were predominant in Andean populations. In contrast, African components were higher in the Atlantic region. M. leprae genotypes were then analyzed for cluster associations and compared with the ancestral composition of leprosy patients. Two M. leprae principal clusters were found: haplotypes C54 and T45. Haplotype C54 associated with African origin and was more frequent in patients from the Atlantic region with a high African component. In contrast, haplotype T45 associated with European origin and was more frequent in Andean patients with a higher European component. These results suggest that the human and M. leprae genomes have co-existed since the African and European origins of the disease, with leprosy ultimately arriving in Colombia during colonization. Distinct M. leprae strains followed European and African settlement in the country and can be detected in contemporary Colombian populations. PMID:26360617

  19. The ear region of earliest known elephant relatives: new light on the ancestral morphotype of proboscideans and afrotherians.

    Science.gov (United States)

    Schmitt, Arnaud; Gheerbrant, Emmanuel

    2016-01-01

    One of the last major clades of placental mammals recognized was the Afrotheria, which comprises all main endemic African mammals. This group includes the ungulate-like paenungulates, and among them the elephant order Proboscidea. Among afrotherians, the petrosal anatomy remains especially poorly known in Proboscidea. We provide here the first comparative CT scan study of the ear region of the two earliest known proboscideans (and paenungulates), Eritherium and Phosphatherium, from the mid Palaeocene and early Eocene of Morocco. It is helpful to characterize the ancestral morphotype of Proboscidea to understand petrosal evolution within proboscideans and afrotherians. The petrosal structure of these two taxa shows several differences. Eritherium is more primitive than Phosphatherium and closer to the basal paenungulate Ocepeia in several traits (inflated tegmen tympani, very deep fossa subarcuata and ossified canal for ramus superior of stapedial artery). Phosphatherium, however, retains plesiomorphies such as a true crus commune secundaria. A cladistic analysis of petrosal traits of Eritherium and Phosphatherium among Proboscidea results in a single tree with a low level of homoplasy in which Eritherium, Phosphatherium and Numidotherium are basal. This contrasts with previous phylogenetic studies showing homoplasy in petrosal evolution among Tethytheria. It suggests that evolutionary modalities of petrosal characters differ with the taxonomic level among Afrotheria: noticeable convergences occurred among the paenungulate orders, whereas little homoplasy seems to have occurred at intra-ordinal level in orders such as Proboscidea. Most petrosal features of both Eritherium and Phosphatherium are primitive. The ancestral petrosal morphotype of Proboscidea was not specialized but was close to the generalized condition of paenungulates, afrotherians, and even eutherians. This is consistent with cranial and dental characters of Eritherium, suggesting that the ancestral

  20. Saccharomyces cerevisiae Bat1 and Bat2 aminotransferases have functionally diverged from the ancestral-like Kluyveromyces lactis orthologous enzyme.

    Directory of Open Access Journals (Sweden)

    Maritrini Colón

    Full Text Available BACKGROUND: Gene duplication is a key evolutionary mechanism providing material for the generation of genes with new or modified functions. The fate of duplicated gene copies has been amply discussed and several models have been put forward to account for duplicate conservation. The specialization model considers that duplication of a bifunctional ancestral gene could result in the preservation of both copies through subfunctionalization, resulting in the distribution of the two ancestral functions between the gene duplicates. Here we investigate whether the presumed bifunctional character displayed by the single branched chain amino acid aminotransferase present in K. lactis has been distributed in the two paralogous genes present in S. cerevisiae, and whether this conservation has impacted S. cerevisiae metabolism. PRINCIPAL FINDINGS: Our results show that the KlBat1 orthologous BCAT is a bifunctional enzyme, which participates in the biosynthesis and catabolism of branched chain aminoacids (BCAAs. This dual role has been distributed in S. cerevisiae Bat1 and Bat2 paralogous proteins, supporting the specialization model posed to explain the evolution of gene duplications. BAT1 is highly expressed under biosynthetic conditions, while BAT2 expression is highest under catabolic conditions. Bat1 and Bat2 differential relocalization has favored their physiological function, since biosynthetic precursors are generated in the mitochondria (Bat1, while catabolic substrates are accumulated in the cytosol (Bat2. Under respiratory conditions, in the presence of ammonium and BCAAs the bat1Δ bat2Δ double mutant shows impaired growth, indicating that Bat1 and Bat2 could play redundant roles. In K. lactis wild type growth is independent of BCAA degradation, since a Klbat1Δ mutant grows under this condition. CONCLUSIONS: Our study shows that BAT1 and BAT2 differential expression and subcellular relocalization has resulted in the distribution of the

  1. Human Genetic Ancestral Composition Correlates with the Origin of Mycobacterium leprae Strains in a Leprosy Endemic Population.

    Science.gov (United States)

    Cardona-Castro, Nora; Cortés, Edwin; Beltrán, Camilo; Romero, Marcela; Badel-Mogollón, Jaime E; Bedoya, Gabriel

    2015-01-01

    Recent reports have suggested that leprosy originated in Africa, extended to Asia and Europe, and arrived in the Americas during European colonization and the African slave trade. Due to colonization, the contemporary Colombian population is an admixture of Native-American, European and African ancestries. Because microorganisms are known to accompany humans during migrations, patterns of human migration can be traced by examining genomic changes in associated microbes. The current study analyzed 118 leprosy cases and 116 unrelated controls from two Colombian regions endemic for leprosy (Atlantic and Andean) in order to determine possible associations of leprosy with patient ancestral background (determined using 36 ancestry informative markers), Mycobacterium leprae genotype and/or patient geographical origin. We found significant differences between ancestral genetic composition. European components were predominant in Andean populations. In contrast, African components were higher in the Atlantic region. M. leprae genotypes were then analyzed for cluster associations and compared with the ancestral composition of leprosy patients. Two M. leprae principal clusters were found: haplotypes C54 and T45. Haplotype C54 associated with African origin and was more frequent in patients from the Atlantic region with a high African component. In contrast, haplotype T45 associated with European origin and was more frequent in Andean patients with a higher European component. These results suggest that the human and M. leprae genomes have co-existed since the African and European origins of the disease, with leprosy ultimately arriving in Colombia during colonization. Distinct M. leprae strains followed European and African settlement in the country and can be detected in contemporary Colombian populations.

  2. Estimating Divergence Time and Ancestral Effective Population Size of Bornean and Sumatran Orangutan Subspecies Using a Coalescent Hidden Markov Model

    DEFF Research Database (Denmark)

    Mailund, Thomas; Dutheil, Julien; Hobolth, Asger

    2011-01-01

    event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may......ue to genetic variation in the ancestor of two populations or two species, the divergence time for DNA sequences from two populations is variable along the genome. Within genomic segments all bases will share the same divergence—because they share a most recent common ancestor—when no recombination...

  3. A practical local tomography reconstruction algorithm based on known subregion

    CERN Document Server

    Paleo, Pierre; Mirone, Alessandro

    2016-01-01

    We propose a new method to reconstruct data acquired in a local tomography setup. This method uses an initial reconstruction and refines it by correcting the low frequency artifacts known as the cupping effect. A basis of Gaussian functions is used to correct the initial reconstruction. The coefficients of this basis are iteratively optimized under the constraint of a known subregion. Using a coarse basis reduces the degrees of freedom of the problem while actually correcting the cupping effect. Simulations show that the known region constraint yields an unbiased reconstruction, in accordance to uniqueness theorems stated in local tomography.

  4. Primordial density and BAO reconstruction

    CERN Document Server

    Zhu, Hong-Ming; Chen, Xuelei

    2016-01-01

    We present a new method to reconstruct the primordial (linear) density field using the estimated nonlinear displacement field. The divergence of the displacement field gives the reconstructed density field. We solve the nonlinear displacement field in the 1D cosmology and show the reconstruction results. The new reconstruction algorithm recovers a lot of linear modes and reduces the nonlinear damping scale significantly. The successful 1D reconstruction results imply the new algorithm should also be a promising technique in the 3D case.

  5. Reconstructing and deconstructing dark energy

    Energy Technology Data Exchange (ETDEWEB)

    Linder, Eric V.

    2004-06-07

    The acceleration of the expansion of the universe, ascribed to a dark energy, is one of the most intriguing discoveries in science. In addition to precise, systematics controlled data, clear, robust interpretation of the observations is required to reveal the nature of dark energy. Even for the simplest question: is the data consistent with the cosmological constant? there are important subtleties in the reconstruction of the dark energy properties. We discuss the roles of analysis both in terms of the Hubble expansion rate or dark energy density {rho}DE(z) and in terms of the dark energy equation of state w(z), arguing that each has its carefully defined place. Fitting the density is best for learning about the density, but using it to probe the equation of state can lead to instability and bias.

  6. Scheduling reconstruction operations with modes of execution

    OpenAIRE

    A D Chaney; R F Deckro; Moore, J T

    2013-01-01

    Since the decline of the Cold War, the risk of major conflict between powerful, industrialized nations has decreased. Insecurities in the 21st century are more apt to arise from the debris of imploding states. Such situations may require intervention—military or otherwise—by concerned states. To meet this new operational challenge, nations must adapt their planning procedures to account for Security, Stabilization, Transition, and Reconstruction Operations (SSTRO). This paper develops a proje...

  7. Augmented Likelihood Image Reconstruction.

    Science.gov (United States)

    Stille, Maik; Kleine, Matthias; Hägele, Julian; Barkhausen, Jörg; Buzug, Thorsten M

    2016-01-01

    The presence of high-density objects remains an open problem in medical CT imaging. Data of projections passing through objects of high density, such as metal implants, are dominated by noise and are highly affected by beam hardening and scatter. Reconstructed images become less diagnostically conclusive because of pronounced artifacts that manifest as dark and bright streaks. A new reconstruction algorithm is proposed with the aim to reduce these artifacts by incorporating information about shape and known attenuation coefficients of a metal implant. Image reconstruction is considered as a variational optimization problem. The afore-mentioned prior knowledge is introduced in terms of equality constraints. An augmented Lagrangian approach is adapted in order to minimize the associated log-likelihood function for transmission CT. During iterations, temporally appearing artifacts are reduced with a bilateral filter and new projection values are calculated, which are used later on for the reconstruction. A detailed evaluation in cooperation with radiologists is performed on software and hardware phantoms, as well as on clinically relevant patient data of subjects with various metal implants. Results show that the proposed reconstruction algorithm is able to outperform contemporary metal artifact reduction methods such as normalized metal artifact reduction.

  8. Topologies of the conditional ancestral trees and full-likelihood-based inference in the general coalescent tree framework.

    Science.gov (United States)

    Sargsyan, Ori

    2010-08-01

    The general coalescent tree framework is a family of models for determining ancestries among random samples of DNA sequences at a nonrecombining locus. The ancestral models included in this framework can be derived under various evolutionary scenarios. Here, a computationally tractable full-likelihood-based inference method for neutral polymorphisms is presented, using the general coalescent tree framework and the infinite-sites model for mutations in DNA sequences. First, an exact sampling scheme is developed to determine the topologies of conditional ancestral trees. However, this scheme has some computational limitations and to overcome these limitations a second scheme based on importance sampling is provided. Next, these schemes are combined with Monte Carlo integrations to estimate the likelihood of full polymorphism data, the ages of mutations in the sample, and the time of the most recent common ancestor. In addition, this article shows how to apply this method for estimating the likelihood of neutral polymorphism data in a sample of DNA sequences completely linked to a mutant allele of interest. This method is illustrated using the data in a sample of DNA sequences at the APOE gene locus.

  9. Conservation of shh cis-regulatory architecture of the coelacanth is consistent with its ancestral phylogenetic position

    Directory of Open Access Journals (Sweden)

    Lang Michael

    2010-11-01

    Full Text Available Abstract Background The modern coelacanth (Latimeria is the extant taxon of a basal sarcopterygian lineage and sister group to tetrapods. Apart from certain apomorphic traits, its morphology is characterized by a high degree of retention of ancestral vertebrate structures and little morphological change. An insight into the molecular evolution that may explain the unchanged character of Latimeria morphology requires the analysis of the expression patterns of developmental regulator genes and their cis-regulatory modules (CRMs. Results We describe the comparative and functional analysis of the sonic hedgehog (shh genomic region of Latimeria menadoensis. Several putative enhancers in the Latimeria shh locus have been identified by comparisons to sarcopterygian and actinopterygian extant species. Specific sequence conservation with all known actinopterygian enhancer elements has been detected. However, these elements are selectively missing in more recently diverged actinopterygian and sarcopterygian species. The functionality of the putative Latimeria enhancers was confirmed by reporter gene expression analysis in transient transgenic zebrafish and chick embryos. Conclusions Latimeria shh CRMs represent the ancestral set of enhancers that have emerged before the split of lobe-finned and ray-finned fishes. In contrast to lineage-specific losses and differentiations in more derived lineages, Latimeria shh enhancers reveal low levels of sequence diversification. High overall sequence conservation of shh conserved noncoding elements (CNE is consistent with the general trend of high levels of conservation of noncoding DNA in the slowly evolving Latimeria genome.

  10. Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History

    Science.gov (United States)

    Risso, Valeria A.; Manssour-Triedo, Fadia; Delgado-Delgado, Asunción; Arco, Rocio; Barroso-delJesus, Alicia; Ingles-Prieto, Alvaro; Godoy-Ruiz, Raquel; Gavira, Jose A.; Gaucher, Eric A.; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M.

    2015-01-01

    Local protein interactions (“molecular context” effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations. PMID:25392342

  11. Reconstruction of inflation models

    Energy Technology Data Exchange (ETDEWEB)

    Myrzakulov, Ratbay; Sebastiani, Lorenzo [Eurasian National University, Department of General and Theoretical Physics and Eurasian Center for Theoretical Physics, Astana (Kazakhstan); Zerbini, Sergio [Universita di Trento, Dipartimento di Fisica, Trento (Italy); TIFPA, Istituto Nazionale di Fisica Nucleare, Trento (Italy)

    2015-05-15

    In this paper, we reconstruct viable inflationary models by starting from spectral index and tensor-to-scalar ratio from Planck observations. We analyze three different kinds of models: scalar field theories, fluid cosmology, and f(R)-modified gravity. We recover the well-known R{sup 2} inflation in Jordan-frame and Einstein-frame representation, the massive scalar inflaton models and two models of inhomogeneous fluid. A model of R{sup 2} correction to Einstein's gravity plus a ''cosmological constant'' with an exact solution for early-time acceleration is reconstructed. (orig.)

  12. The evolving breast reconstruction

    DEFF Research Database (Denmark)

    Thomsen, Jørn Bo; Gunnarsson, Gudjon Leifur

    2014-01-01

    The aim of this editorial is to give an update on the use of the propeller thoracodorsal artery perforator flap (TAP/TDAP-flap) within the field of breast reconstruction. The TAP-flap can be dissected by a combined use of a monopolar cautery and a scalpel. Microsurgical instruments are generally...... not needed. The propeller TAP-flap can be designed in different ways, three of these have been published: (I) an oblique upwards design; (II) a horizontal design; (III) an oblique downward design. The latissimus dorsi-flap is a good and reliable option for breast reconstruction, but has been criticized...

  13. Upper Eyelid Reconstruction.

    Science.gov (United States)

    Espinoza, Gabriela Mabel; Prost, Angela Michelle

    2016-05-01

    Reconstruction of the upper eyelid is complicated because the eyelid must retain mobility, flexibility, function, and a suitable mucosal surface over the delicate cornea. Defects of the upper eyelid may be due to congenital defects or traumatic injury or follow oncologic resection. This article focuses on reconstruction due to loss of tissue. Multiple surgeries may be needed to reach the desired results, addressing loss of tissue and then loss of function. Each defect is unique and the laxity and availability of surrounding tissue vary. Knowing the most common techniques for repair assists surgeons in the multifaceted planning that takes place.

  14. 4D image reconstruction for emission tomography

    Science.gov (United States)

    Reader, Andrew J.; Verhaeghe, Jeroen

    2014-11-01

    An overview of the theory of 4D image reconstruction for emission tomography is given along with a review of the current state of the art, covering both positron emission tomography and single photon emission computed tomography (SPECT). By viewing 4D image reconstruction as a matter of either linear or non-linear parameter estimation for a set of spatiotemporal functions chosen to approximately represent the radiotracer distribution, the areas of so-called ‘fully 4D’ image reconstruction and ‘direct kinetic parameter estimation’ are unified within a common framework. Many choices of linear and non-linear parameterization of these functions are considered (including the important case where the parameters have direct biological meaning), along with a review of the algorithms which are able to estimate these often non-linear parameters from emission tomography data. The other crucial components to image reconstruction (the objective function, the system model and the raw data format) are also covered, but in less detail due to the relatively straightforward extension from their corresponding components in conventional 3D image reconstruction. The key unifying concept is that maximum likelihood or maximum a posteriori (MAP) estimation of either linear or non-linear model parameters can be achieved in image space after carrying out a conventional expectation maximization (EM) update of the dynamic image series, using a Kullback-Leibler distance metric (comparing the modeled image values with the EM image values), to optimize the desired parameters. For MAP, an image-space penalty for regularization purposes is required. The benefits of 4D and direct reconstruction reported in the literature are reviewed, and furthermore demonstrated with simple simulation examples. It is clear that the future of reconstructing dynamic or functional emission tomography images, which often exhibit high levels of spatially correlated noise, should ideally exploit these 4D

  15. Explicit reconstruction of the entanglement wedge

    CERN Document Server

    Kim, Jung-Wook

    2016-01-01

    The problem of bulk locality, or how the boundary encodes the bulk in AdS/CFT, is still a subject of study today. One of the major issues that needs more elucidation is the problem of subregion duality; what information of the bulk a given boundary subregion encodes. Although proofs given by two teams of researchers, Dong, Harlow, and Wall and Bao, and Kim, state that the entanglement wedge of the bulk should be reconstructible from boudnary subregions, no explicit procedure for reconstructing the entanglement wedge was as of yet given. In this paper, mode sum approach to obtaining smearing functions is generalised to include bulk reconstruction in the entanglement wedge of boundary subregions. It is generally expectated that solutions to the wave equation on a complicated coordinate patch are needed, but this hard problem has been transferred to a less hard but tractable problem of matrix inversion.

  16. On unitary reconstruction of linear optical networks

    CERN Document Server

    Tillmann, Max; Walther, Philip

    2015-01-01

    Linear optical elements are pivotal instruments in the manipulation of classical and quantum states of light. The vast progress in integrated quantum photonic technology enables the implementation of large numbers of such elements on chip while providing interferometric stability. As a trade-off these structures face the intrinsic challenge of characterizing their optical transformation as individual optical elements are not directly accessible. Thus the unitary transformation needs to be reconstructed from a dataset generated with having access to the input and output ports of the device only. Here we present a novel approach to unitary reconstruction that significantly improves upon existing approaches. We compare its performance to several approaches via numerical simulations for networks up to 14 modes. We show that an adapted version of our approach allows to recover all mode-dependent losses and to obtain highest reconstruction fidelities under such conditions.

  17. Bayesian Cosmic Web Reconstruction: BARCODE for Clusters

    CERN Document Server

    Bos, E G Patrick; Kitaura, Francisco; Cautun, Marius

    2016-01-01

    We describe the Bayesian BARCODE formalism that has been designed towards the reconstruction of the Cosmic Web in a given volume on the basis of the sampled galaxy cluster distribution. Based on the realization that the massive compact clusters are responsible for the major share of the large scale tidal force field shaping the anisotropic and in particular filamentary features in the Cosmic Web. Given the nonlinearity of the constraints imposed by the cluster configurations, we resort to a state-of-the-art constrained reconstruction technique to find a proper statistically sampled realization of the original initial density and velocity field in the same cosmic region. Ultimately, the subsequent gravitational evolution of these initial conditions towards the implied Cosmic Web configuration can be followed on the basis of a proper analytical model or an N-body computer simulation. The BARCODE formalism includes an implicit treatment for redshift space distortions. This enables a direct reconstruction on the ...

  18. Reconstruction of the electron spectrum in a metal hydrogen sulfide

    Science.gov (United States)

    Kudryashov, N. A.; Kutukov, A. A.; Mazur, E. A.

    2017-01-01

    Generalized Eliashberg theory of the normal properties of a metal electron-phonon system with a non constant electron density of states has been used to study the effect of the conduction band reconstruction. The electron density of states of the metallic phase of the hydrogen sulfide renormalized by the strong electron-phonon coupling at a pressure of P = 225 GPa has been calculated. It has been found that the reconstructed conduction band contains a series of narrow energy pockets.

  19. Two Rounds of Whole Genome Duplication in the AncestralVertebrate

    Energy Technology Data Exchange (ETDEWEB)

    Dehal, Paramvir; Boore, Jeffrey L.

    2005-04-12

    The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, then determined when each gene duplicated relative to the evolutionary tree of the organisms. We confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. However, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish-tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of 4-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage.

  20. Reconstruction Setting Out

    Institute of Scientific and Technical Information of China (English)

    YIN PUMIN

    2010-01-01

    @@ The first phase of earthquake relief,in which rescuing lives was the priority,finished 12 days after a 7.1-magnitude earthquake struck the Tibetan Autonomous Prefecture of Yushu in northwest China's Qinghai Province on April 14,and reconstruction of the area is now ready to begin.

  1. Urogenital Reconstructive Surgery

    DEFF Research Database (Denmark)

    Jakobsen, Lotte Kaasgaard

    Urogenital reconstructive surgery Lotte Kaasgaard Jakobsen1 Professor Henning Olsen1 Overlæge Gitte Hvistendahl1 Professor Karl-Erik Andersson2 1 – Dept. of Urology, Aarhus University Hospital 2 – Dept. of Gynecology and Obstetrics, Aarhus University hospital Background: Congenital obstruction...

  2. Photoacoustic image reconstruction based on Bayesian compressive sensing algorithm

    Institute of Scientific and Technical Information of China (English)

    Mingjian Sun; Naizhang Feng; Yi Shen; Jiangang Li; Liyong Ma; Zhenghua Wu

    2011-01-01

    The photoacoustic tomography (PAT) method, based on compressive sensing (CS) theory, requires that,for the CS reconstruction, the desired image should have a sparse representation in a known transform domain. However, the sparsity of photoacoustic signals is destroyed because noises always exist. Therefore,the original sparse signal cannot be effectively recovered using the general reconstruction algorithm. In this study, Bayesian compressive sensing (BCS) is employed to obtain highly sparse representations of photoacoustic images based on a set of noisy CS measurements. Results of simulation demonstrate that the BCS-reconstructed image can achieve superior performance than other state-of-the-art CS-reconstruction algorithms.%@@ The photoacoustic tomography (PAT) method, based on compressive sensing (CS) theory, requires that,for the CS reconstruction, the desired image should have a sparse representation in a known transform domain.However, the sparsity of photoacoustic signals is destroyed because noises always exist.Therefore,the original sparse signal cannot be effectively recovered using the general reconstruction algorithm.In this study, Bayesian compressive sensing (BCS) is employed to obtain highly sparse representations of photoacoustic inages based on a set of noisy CS measurements.Results of simulation demonstrate that the BCS-reconstructed image can achieve superior performance than other state-of-the-art CS-reconstruction algorithms.

  3. Preparing for Breast Reconstruction Surgery

    Science.gov (United States)

    ... Cancer Breast Reconstruction Surgery Preparing for Breast Reconstruction Surgery Your surgeon can help you know what to ... The plan for follow-up Costs Understanding your surgery costs Health insurance policies often cover most or ...

  4. Hanford Environmental Dose Reconstruction Project

    Energy Technology Data Exchange (ETDEWEB)

    Finch, S.M.; McMakin, A.H. (comps.)

    1991-01-01

    The objective of the Hanford Environmental Dose Reconstruction Project is to estimate the radiation doses that individuals and populations could have received from nuclear operations at Hanford since 1944. The project is being managed and conducted by the Pacific Northwest Laboratory (PNL) under the direction of an independent Technical Steering Panel (TSP). The TSP consists of experts in environmental pathways, epidemiology, surface-water transport, ground-water transport, statistics, demography, agriculture, meteorology, nuclear engineering, radiation dosimetry, and cultural anthropology. Included are appointed technical members representing the states of Oregon and Washington, a representative of Native American tribes, and an individual representing the public. The project is divided into the following technical tasks. These tasks correspond to the path radionuclides followed, from release to impact on human (dose estimates): Source Terms; Environmental Transport; Environmental Monitoring Data; Demographics, Agriculture, Food Habits and; Environmental Pathways and Dose Estimates.

  5. State-reconstruction-based robust backstepping control of air-breathing hypersonic vehicles%基于状态重构的吸气式高超声速飞行器鲁棒反演控制

    Institute of Scientific and Technical Information of China (English)

    卜祥伟; 吴晓燕; 马震; 张蕊

    2015-01-01

    A robust backstepping controller was designed based on state reconstruction for flexible air⁃breathing hypersonic ve⁃hicles considering that only the velocity,altitude and pitch rate were observable. Firstly,the controlled plant was rewritten as a strict feedback form,and the actual control laws and virtual control laws were designed based on dynamic inversion and backstepping re⁃spectively. Secondly,arctangent tracking differentiator was introduced to estimate the derivatives of virtual control laws and recon⁃struct the states of flight⁃path angle and angle of attack.Finally,in order to guarantee the backstepping controller'robustness,a new nonlinear disturbance observer was designed based on nonlinear⁃linear tracking differentiator to estimate and compensate uncertain⁃ties of the model precisely.Simulation results show that a high precise state construction can be obtained by the proposed strategy and the presented control methodology can provide a stable altitude and velocity tracking,and eliminate the influence of the uncer⁃tainties of the model.%针对吸气式高超声速飞行器参数不确定弹性体模型,仅考虑速度、高度和俯仰角速度可测的情况,提出了一种基于状态重构的鲁棒反演控制器设计方法。首先,将被控对象模型表示为严格反馈形式,分别采用动态逆和反演设计实际控制律和虚拟控制律;其次,引入反正切跟踪微分器来简化虚拟控制律求导运算,并用于对弹道角和攻角进行状态重构;最后,为了保证反演控制器的鲁棒性,基于非线性⁃线性跟踪微分器,设计了一种新型非线性干扰观测器,可实现对模型不确定项的精确估计和补偿。仿真结果表明,所提策略取得了较高的状态重构精度,控制器能够克服模型不确定项的影响,且能保证速度和高度对参考输入的稳定跟踪。

  6. On Cultural Perspective of Ancestral Hall Couplets in Sanming%三明宗祠楹联的文化透视

    Institute of Scientific and Technical Information of China (English)

    金文凯

    2012-01-01

    宗祠楹联是宋元以后宗族社会特有的一种艺术形式,是祠堂文化的典型产物。三明宗祠楹联文化蕴涵丰富。有的反映祠堂的祭祀功能;有的追祖溯源,崇仰故土祖根;有的表彰先贤,表达对先人的顶礼膜拜;有的则训勉后人,激励家族不断进取。它们在一定程度上记录着各家族的繁衍生息、荣衰变迁,为我们探知三明祠堂文化、了解三明宗族发展的历史以及研究三明历史文化名人等提供了珍贵的资料;同时,它们又以宗经明道、敦品立德为要旨,对促进社会和谐有序与可持续发展也具有重要意义,值得重视。%The ancestral hall couplet is a unique art form in clan society of the Song and Yuan dynasties,which is a typical product of the ancestral temple culture.The ancestral hall couplets in Sanming have rich cultural implications,such as reflecting the ritual function of the ancestral hall,recovering ancestral source,enshrining the homeland ancestral root,the recognition of the sages,the expression of pay homage to the ancestors,encouraging future generations and inspiring family to make progress.To a certain extent,they are a record of the development of each family as well as their changes in prosperity and decline,which provide valuable information for probing the ancestral hall culture in Sanming,understanding the history of ancestral hall couplets' development and studying the historical and cultural celebrities in Sanming.What's more,their following traditional ideas and regulating ethical conduct have important significance to promote harmonious society and sustainable development,which deserves attention.

  7. Mating animals by minimising the covariance between ancestral contributions generates less inbreeding without compromising genetic gain in breeding schemes with truncation selection

    DEFF Research Database (Denmark)

    Henryon, M; Berg, P; Sørensen, A C

    2009-01-01

    We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis by stoch......We reasoned that mating animals by minimising the covariance between ancestral contributions (MCAC mating) will generate less inbreeding and at least as much genetic gain as minimum-coancestry mating in breeding schemes where the animals are truncation-selected. We tested this hypothesis...

  8. Ancestral mutations as a tool for solubilizing proteins: The case of a hydrophobic phosphate-binding protein

    Directory of Open Access Journals (Sweden)

    Daniel Gonzalez

    2014-01-01

    Full Text Available Stable and soluble proteins are ideal candidates for functional and structural studies. Unfortunately, some proteins or enzymes can be difficult to isolate, being sometimes poorly expressed in heterologous systems, insoluble and/or unstable. Numerous methods have been developed to address these issues, from the screening of various expression systems to the modification of the target protein itself. Here we use a hydrophobic, aggregation-prone, phosphate-binding protein (HPBP as a case study. We describe a simple and fast method that selectively uses ancestral mutations to generate a soluble, stable and functional variant of the target protein, here named sHPBP. This variant is highly expressed in Escherichia coli, is easily purified and its structure was solved at much higher resolution than its wild-type progenitor (1.3 versus 1.9 Å, respectively.

  9. ¿Con o sin ancestros? Vigencia de lo ancestral en la Amazonía peruana

    Directory of Open Access Journals (Sweden)

    Thomas Mouriès

    2014-07-01

    Full Text Available The existence —or not— of the concept of ancestors in the indigenous Amazon has been the subject of much debate. However, regional leaders do not hesitate to call upon ‘ancestral’ knowledge, customs, or territories in the sense that, from an academic point of view, could appear enigmatic. «Ancestral, but… with or without ancestors?» is the question a confused anthropologist might ask. In this article, I propose to offer elements of a response to this question,based on a case study in Peru. First I analyze how Amazonian indigenous leaders, following international law, have adopted the legal notion of ‘ancestral possession’ of their territory to adapt it to the political sphere. This approach accounts for the recent generalization and uniformization of the term ‘ancestral’, but poses the problem of how it articulates with the indigenous cosmologies that it supposes to reflect. For this reason, I explore in the second section the pertinence of the category of ‘ancestor’ in the indigenous Amazon, briefly drawing upon the academic debate in order to define inwhat way this category takes on meaning. Based on testimony from an experienced Awajún leader, we thus return in the third section more explicitly to the different meanings and planes of reference that unfold when one uses the term ‘ancestral’, showing how Amazonian indigenous people not only adopt external conceptual elements and arguments, but also transform them based on their own cosmological singularities and political perspectives.

  10. The impact of ancestral population size and incomplete lineage sorting on Bayesian estimation of species divergence times

    Institute of Scientific and Technical Information of China (English)

    Konstantinos ANGELIS; Mario DOS REIS

    2015-01-01

    Although the effects of the coalescent process on sequence divergence and genealogies are well understood, the vir-tual majority of studies that use molecular sequences to estimate times of divergence among species have failed to account for the coalescent process. Here we study the impact of ancestral population size and incomplete lineage sorting on Bayesian estimates of species divergence times under the molecular clock when the inference model ignores the coalescent process. Using a combi-nation of mathematical analysis, computer simulations and analysis of real data, we find that the errors on estimates of times and the molecular rate can be substantial when ancestral populations are large and when there is substantial incomplete lineage sort-ing. For example, in a simple three-species case, we find that if the most precise fossil calibration is placed on the root of the phylogeny, the age of the internal node is overestimated, while if the most precise calibration is placed on the internal node, then the age of the root is underestimated. In both cases, the molecular rate is overestimated. Using simulations on a phylogeny of nine species, we show that substantial errors in time and rate estimates can be obtained even when dating ancient divergence events. We analyse the hominoid phylogeny and show that estimates of the neutral mutation rate obtained while ignoring the coalescent are too high. Using a coalescent-based technique to obtain geological times of divergence, we obtain estimates of the mutation rate that are within experimental estimates and we also obtain substantially older divergence times within the phylogeny [Current Zoology 61 (5): 874–885, 2015].

  11. A Medaka Gene Map: The Trace of Ancestral Vertebrate Proto-Chromosomes Revealed by Comparative Gene Mapping

    OpenAIRE

    Naruse, Kiyoshi; Tanaka, Minoru; Mita, Kazuei; Shima, Akihiro; Postlethwait, John; Mitani, Hiroshi

    2004-01-01

    The mapping of Hox clusters and many duplicated genes in zebrafish indicated an extra whole-genome duplication in ray-fined fish. However, to reconstruct the preduplication chromosomes (proto-chromosomes), the comparative genomic studies of more distantly related teleosts are essential. Medaka and zebrafish are ideal for this purpose, because their lineages separated from their last common ancestor ∼140 million years ago. To reconstruct ancient vertebrate chromosomes, including the chromosome...

  12. Arctic Sea Level Reconstruction

    DEFF Research Database (Denmark)

    Svendsen, Peter Limkilde

    method.For oceanographic purposes, the altimetric record over the Arctic Ocean is inferiorin quality to that of moderate latitudes, but nonetheless an invaluable set of observations. During this project, newly processed Arctic altimetry from the ERS-1/-2 and Envisat missions has become available......Reconstruction of historical Arctic sea level is very difficult due to the limited coverage and quality of tide gauge and altimetry data in the area. This thesis addresses many of these issues, and discusses strategies to help achieve a stable and plausible reconstruction of Arctic sea level from...... 1950 to today.The primary record of historical sea level, on the order of several decades to a few centuries, is tide gauges. Tide gauge records from around the world are collected in the Permanent Service for Mean Sea Level (PSMSL) database, and includes data along the Arctic coasts. A reasonable...

  13. Autologous Costochondral Microtia Reconstruction.

    Science.gov (United States)

    Patel, Sapna A; Bhrany, Amit D; Murakami, Craig S; Sie, Kathleen C Y

    2016-04-01

    Reconstruction with autologous costochondral cartilage is one of the mainstays of surgical management of congenital microtia. We review the literature, present our current technique for microtia reconstruction with autologous costochondral graft, and discuss the evolution of our technique over the past 20 years. We aim to minimize donor site morbidity and create the most durable and natural appearing ear possible using a stacked framework to augment the antihelical fold and antitragal-tragal complex. Assessment of outcomes is challenging due to the paucity of available objective measures with which to evaluate aesthetic outcomes. Various instruments are used to assess outcomes, but none is universally accepted as the standard. The challenges we continue to face are humbling, but ongoing work on tissue engineering, application of 3D models, and use of validated questionnaires can help us get closer to achieving a maximal aesthetic outcome.

  14. Stochastic reconstruction of sandstones

    Science.gov (United States)

    Manwart; Torquato; Hilfer

    2000-07-01

    A simulated annealing algorithm is employed to generate a stochastic model for a Berea sandstone and a Fontainebleau sandstone, with each a prescribed two-point probability function, lineal-path function, and "pore size" distribution function, respectively. We find that the temperature decrease of the annealing has to be rather quick to yield isotropic and percolating configurations. A comparison of simple morphological quantities indicates good agreement between the reconstructions and the original sandstones. Also, the mean survival time of a random walker in the pore space is reproduced with good accuracy. However, a more detailed investigation by means of local porosity theory shows that there may be significant differences of the geometrical connectivity between the reconstructed and the experimental samples.

  15. Reconstructing the Tengger calendar

    Directory of Open Access Journals (Sweden)

    Ian Proudfoot

    2008-12-01

    Full Text Available The survival of an Indic calendar among the Tengger people of the Brama highlands in east Java opens a window on Java’s calendar history. Its hybrid form reflects accommodations between this non-Muslim Javanese group and the increasingly dominant Muslim Javanese culture. Reconstruction is challenging because of this hybridity, because of inconsistencies in practice, and because the historical evidence is sketchy and often difficult to interpret.

  16. Undersampled MR Image Reconstruction with Data-Driven Tight Frame

    Directory of Open Access Journals (Sweden)

    Jianbo Liu

    2015-01-01

    Full Text Available Undersampled magnetic resonance image reconstruction employing sparsity regularization has fascinated many researchers in recent years under the support of compressed sensing theory. Nevertheless, most existing sparsity-regularized reconstruction methods either lack adaptability to capture the structure information or suffer from high computational load. With the aim of further improving image reconstruction accuracy without introducing too much computation, this paper proposes a data-driven tight frame magnetic image reconstruction (DDTF-MRI method. By taking advantage of the efficiency and effectiveness of data-driven tight frame, DDTF-MRI trains an adaptive tight frame to sparsify the to-be-reconstructed MR image. Furthermore, a two-level Bregman iteration algorithm has been developed to solve the proposed model. The proposed method has been compared to two state-of-the-art methods on four datasets and encouraging performances have been achieved by DDTF-MRI.

  17. Undersampled MR Image Reconstruction with Data-Driven Tight Frame.

    Science.gov (United States)

    Liu, Jianbo; Wang, Shanshan; Peng, Xi; Liang, Dong

    2015-01-01

    Undersampled magnetic resonance image reconstruction employing sparsity regularization has fascinated many researchers in recent years under the support of compressed sensing theory. Nevertheless, most existing sparsity-regularized reconstruction methods either lack adaptability to capture the structure information or suffer from high computational load. With the aim of further improving image reconstruction accuracy without introducing too much computation, this paper proposes a data-driven tight frame magnetic image reconstruction (DDTF-MRI) method. By taking advantage of the efficiency and effectiveness of data-driven tight frame, DDTF-MRI trains an adaptive tight frame to sparsify the to-be-reconstructed MR image. Furthermore, a two-level Bregman iteration algorithm has been developed to solve the proposed model. The proposed method has been compared to two state-of-the-art methods on four datasets and encouraging performances have been achieved by DDTF-MRI.

  18. Photostatistics Reconstruction via Loop Detector Signatures

    CERN Document Server

    Webb, J G; 10.1364/OE.17.011799

    2009-01-01

    Photon-number resolving detectors are a fundamental building-block of optical quantum information processing protocols. A loop detector, combined with appropriate statistical processing, can be used to convert a binary on/off photon counter into a photon-number-resolving detector. Here we describe the idea of a signature of photon-counts, which may be used to more robustly reconstruct the photon number distribution of a quantum state. The methodology is applied experimentally in a 9-port loop detector operating at a telecommunications wavelength and compared directly to the approach whereby only the number of photon-counts is used to reconstruct the input distribution. The signature approach is shown to be more robust against calibration errors, exhibit reduced statistical uncertainty, and reduced reliance on a-priori assumptions about the input state.

  19. Reconstructing building mass models from UAV images

    KAUST Repository

    Li, Minglei

    2015-07-26

    We present an automatic reconstruction pipeline for large scale urban scenes from aerial images captured by a camera mounted on an unmanned aerial vehicle. Using state-of-the-art Structure from Motion and Multi-View Stereo algorithms, we first generate a dense point cloud from the aerial images. Based on the statistical analysis of the footprint grid of the buildings, the point cloud is classified into different categories (i.e., buildings, ground, trees, and others). Roof structures are extracted for each individual building using Markov random field optimization. Then, a contour refinement algorithm based on pivot point detection is utilized to refine the contour of patches. Finally, polygonal mesh models are extracted from the refined contours. Experiments on various scenes as well as comparisons with state-of-the-art reconstruction methods demonstrate the effectiveness and robustness of the proposed method.

  20. Canal Wall Reconstruction Mastoidectomy

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    Objective To investigate the advantages of canal wall reconstruction (CWR) mastoidectomy, a single-stage technique for cholesteatoma removal and posterior external canal wall reconstruction, over the open and closed procedures in terms of cholesteatoma recurrence. Methods: Between June 2002 and December 2005, 38 patients (40 ears) with cholesteatoma were admited to Sun Yat-Sen Memorial Hospital and received surgical treatments. Of these patients, 25 were male with ages ranging between 11 and 60 years (mean = 31.6 years) and 13 were female with ages ranging between 20 and 65 years (mean = 38.8 years). Canal wall reconstruction (CWR)mastoidectomy was performed in 31 ears and canal wall down (CWD) mastoidectomy in 9 ears. Concha cartilage was used for ear canal wall reconstruction in 22 of the 31 CWR procedures and cortical mastoid bone was used in the remaining 9 cases. Results At 0.5 to 4 years follow up, all but one patients remained free of signs of cholesteatoma recurrence, i.e., no retraction pocket or cholesteatoma matrix. One patient, a smoker, needed revision surgery due to cholesteatoma recurrence 1.5 year after the initial operation. The recurrence rate was therefore 3.2% (1/31). Cholesteatoma recurrence was monitored using postoperative CT scans whenever possible. In the case that needed a revision procedure, a retraction pocket was identified by otoendoscopy in the pars flacida area that eventually evolved into a cholesteatoma. A pocket extending to the epitympanum filled with cholesteatoma matrix was confirmed during the revision operation, A decision to perform a modified mastoidectomy was made as the patient refused to quit smoking. The mean air-bone gap in pure tone threshold was 45 dB before surgery and 25 dB after (p < 0.05). There was no difference between using concha cartilage and cortical mastoid bone for the reconstruction regarding air-bone gap improvement, CT findings and otoendoscopic results. Conclusion CWR mastoidectomy can be used for

  1. Posteromedial Corner Reconstruction

    Science.gov (United States)

    Ferrer, Gonzalo; Leon, Agustín; Wirth, Hans; Mena, Adolfo; Tuca, María José; Espinoza, Gonzalo

    2017-01-01

    Objective: Report the experience, after 1-year follow-up, of 30 patients who underwent anatomical knee reconstruction of posteromedial corner (PMC) injuries, using La Prade´s Technique. Methods: Retrospective cohort study of 30 consecutive patients with PMC injuries operated between November 2010 and May 2014 by the same surgical team. Inclusion criteria: patients with clinical presentation and images (stress radiographs and MRI) compatible with PMC injury, who maintained a grade III chronic instability in spite of at least 3 months of orthopedic treatment, who were reconstructed using La Prade’s anatomical technique, and completed at least 12 months of follow-up. Exclusion criteria: discordance between clinical and image studies, grade I or II medial instability, and surgery performed through a different technique. Data was collected by reviewing the electronic files and images. Functional scores (IKDC and Lysholm) were applied and registered in the preoperative evaluation, and then 6 and 12 months after surgery. Results: Thirty patients (28 men and 2 women) met the inclusion criteria. Mean age was 43 years (24-69). The vast majority (28 patients) had a high-energy mechanism of injury. Twenty patients were diagnosed in the acute setting, while 10 had a delayed diagnosis after poor results of concomitant ligament reconstructions. With the exception of 2 patients, who presented with isolated PMC injury, the majority had associated injuries as detailed: 11 cases had PMC + anterior cruciate ligament (ACL) injury, 3 patients had PMC + posterior cruciate ligament (PCL) injury, 3 patients had PMC + meniscal tears, 9 patients had PMC + ACL + PCL injuries, and there were 2 cases of PMC + ACL + PCL + lateral collateral ligament injuries. Mean time for PMC reconstruction surgery was 5 months (range 2-32). Lysholm and IKDC scores were 18,2 (2-69) and 24,3 (9,2-52,9) respectively in the preoperative setting, improving to 76,7 (44-94) and 70,7 (36,8-95,4) after 1-year follow

  2. 3D VIRTUAL RECONSTRUCTION OF ARCHAEOLOGICAL MONUMENTS

    OpenAIRE

    2014-01-01

    3D Virtual Models are the future of the representation of the existing and destroyed architectural heritage. The term reconstruction defines the re-building of a monument to its state at the time of its history chosen for that particular representation. In recent years the evolution of the technology, has contributed significantly in many aspects of the field of cultural heritage preservation and recording. Techniques like digital image processing, digital orthophoto production, terrestrial l...

  3. War and reconstruction in northern Mozambique

    OpenAIRE

    2006-01-01

    The article discusses some of the economic effects of war in northern Mozambique. It indicates how the historical and structural features of the economy of northern Mozambique restricted post-war reconstruction and post-war poverty alleviation. These features include the dominance of only a few cash crops for export, the absence of much rural trading, poor communication infrastructure, and weak political and state institutions. The specific nature of the internal war further weakened the stat...

  4. Complete tribal sampling reveals basal split in Muscidae (Diptera), confirms saprophagy as ancestral feeding mode, and reveals an evolutionary correlation between instar numbers and carnivory

    DEFF Research Database (Denmark)

    Kutty, Sujatha Narayanan; Pont, Adrian C.; Meier, Rudolf;

    2014-01-01

    of the number of larval instars from three (ancestral) to two and one. The genus Achanthiptera which was previously in its own subfamily is shown to be closely related to Azeliini. However, it appears that Azeliinae is paraphyletic because Muscinae is sister-group to the Azeliini while the azeliine...

  5. Local motion-compensated method for high-quality 3D coronary artery reconstruction.

    Science.gov (United States)

    Liu, Bo; Bai, Xiangzhi; Zhou, Fugen

    2016-12-01

    The 3D reconstruction of coronary artery from X-ray angiograms rotationally acquired on C-arm has great clinical value. While cardiac-gated reconstruction has shown promising results, it suffers from the problem of residual motion. This work proposed a new local motion-compensated reconstruction method to handle this issue. An initial image was firstly reconstructed using a regularized iterative reconstruction method. Then a 3D/2D registration method was proposed to estimate the residual vessel motion. Finally, the residual motion was compensated in the final reconstruction using the extended iterative reconstruction method. Through quantitative evaluation, it was found that high-quality 3D reconstruction could be obtained and the result was comparable to state-of-the-art method.

  6. Computerized craniofacial reconstruction: Conceptual framework and review.

    Science.gov (United States)

    Claes, Peter; Vandermeulen, Dirk; De Greef, Sven; Willems, Guy; Clement, John Gerald; Suetens, Paul

    2010-09-10

    When confronted with a corpse that is unrecognizable due to its state of decomposition, soft-tissue mutilation or incineration, and if no other identification evidence is available, craniofacial reconstruction (CFR) can be a useful tool in the identification of the body. Traditional methods are based on manual reconstruction by physically modelling a face on a skull replica with clay or plasticine. The progress in computer science and the improvement of medical imaging technologies during recent years has had a significant impact on this domain. New, fast, flexible and computer-based objective reconstruction programs are under development. Employing the newer technologies and permanently evaluating the obtained results will hopefully lead to more accurate reconstructions, beneficial to the added value of CFR methods during crime-scene investigations. A general model-based workflow is observed, when analysing computerized CFR techniques today. The main purpose of this paper is to give an overview of existing computer-based CFR methods up to date defined within a common framework using a general taxonomy. The paper will also discuss the various alternatives and problems which arise during the process of designing a CFR program.

  7. Wavefront reconstruction using computer-generated holograms

    Science.gov (United States)

    Schulze, Christian; Flamm, Daniel; Schmidt, Oliver A.; Duparré, Michael

    2012-02-01

    We propose a new method to determine the wavefront of a laser beam, based on modal decomposition using computer-generated holograms (CGHs). Thereby the beam under test illuminates the CGH with a specific, inscribed transmission function that enables the measurement of modal amplitudes and phases by evaluating the first diffraction order of the hologram. Since we use an angular multiplexing technique, our method is innately capable of real-time measurements of amplitude and phase, yielding the complete information about the optical field. A measurement of the Stokes parameters, respectively of the polarization state, provides the possibility to calculate the Poynting vector. Two wavefront reconstruction possibilities are outlined: reconstruction from the phase for scalar beams and reconstruction from the Poynting vector for inhomogeneously polarized beams. To quantify single aberrations, the reconstructed wavefront is decomposed into Zernike polynomials. Our technique is applied to beams emerging from different kinds of multimode optical fibers, such as step-index, photonic crystal and multicore fibers, whereas in this work results are exemplarily shown for a step-index fiber and compared to a Shack-Hartmann measurement that serves as a reference.

  8. Performance of $\\tau$-lepton reconstruction and identification in CMS

    CERN Document Server

    Chatrchyan, Serguei; Sirunyan, Albert M; Tumasyan, Armen; Adam, Wolfgang; Bergauer, Thomas; Dragicevic, Marko; Erö, Janos; Fabjan, Christian; Friedl, Markus; Fruehwirth, Rudolf; Ghete, Vasile Mihai; Hammer, Josef; Haensel, Stephan; Hoch, Michael; Hörmann, Natascha; Hrubec, Josef; Jeitler, Manfred; Kiesenhofer, Wolfgang; Krammer, Manfred; Liko, Dietrich; Mikulec, Ivan; Pernicka, Manfred; Rahbaran, Babak; Rohringer, Herbert; Schöfbeck, Robert; Strauss, Josef; Taurok, Anton; Teischinger, Florian; Trauner, Christine; Wagner, Philipp; Waltenberger, Wolfgang; Walzel, Gerhard; Widl, Edmund; Wulz, Claudia-Elisabeth; Mossolov, Vladimir; Shumeiko, Nikolai; Suarez Gonzalez, Juan; Bansal, Sunil; Benucci, Leonardo; De Wolf, Eddi A; Janssen, Xavier; Luyckx, Sten; Maes, Thomas; Mucibello, Luca; Ochesanu, Silvia; Roland, Benoit; Rougny, Romain; Selvaggi, Michele; Van Haevermaet, Hans; Van Mechelen, Pierre; Van Remortel, Nick; Blekman, Freya; Blyweert, Stijn; D'Hondt, Jorgen; Gonzalez Suarez, Rebeca; Kalogeropoulos, Alexis; Maes, Michael; Olbrechts, Annik; Van Doninck, Walter; Van Mulders, Petra; Van Onsem, Gerrit Patrick; Villella, Ilaria; Charaf, Otman; Clerbaux, Barbara; De Lentdecker, Gilles; Dero, Vincent; Gay, Arnaud; Hammad, Gregory Habib; Hreus, Tomas; Marage, Pierre Edouard; Raval, Amita; Thomas, Laurent; Vander Marcken, Gil; Vander Velde, Catherine; Vanlaer, Pascal; Adler, Volker; Cimmino, Anna; Costantini, Silvia; Grunewald, Martin; Klein, Benjamin; Lellouch, Jérémie; Marinov, Andrey; Mccartin, Joseph; Ryckbosch, Dirk; Thyssen, Filip; Tytgat, Michael; Vanelderen, Lukas; Verwilligen, Piet; Walsh, Sinead; Zaganidis, Nicolas; Basegmez, Suzan; Bruno, Giacomo; Caudron, Julien; Ceard, Ludivine; Cortina Gil, Eduardo; De Favereau De Jeneret, Jerome; Delaere, Christophe; Favart, Denis; Giammanco, Andrea; Grégoire, Ghislain; Hollar, Jonathan; Lemaitre, Vincent; Liao, Junhui; Militaru, Otilia; Nuttens, Claude; Ovyn, Severine; Pagano, Davide; Pin, Arnaud; Piotrzkowski, Krzysztof; Schul, Nicolas; Beliy, Nikita; Caebergs, Thierry; Daubie, Evelyne; Alves, Gilvan; Brito, Lucas; De Jesus Damiao, Dilson; Pol, Maria Elena; Henrique Gomes E Souza, Moacyr; Aldá Júnior, Walter Luiz; Carvalho, Wagner; Da Costa, Eliza Melo; De Oliveira Martins, Carley; Fonseca De Souza, Sandro; Matos Figueiredo, Diego; Mundim, Luiz; Nogima, Helio; Oguri, Vitor; Prado Da Silva, Wanda Lucia; Santoro, Alberto; Silva Do Amaral, Sheila Mara; Sznajder, Andre; Souza Dos Anjos, Tiago; Bernardes, Cesar Augusto; De Almeida Dias, Flavia; Tomei, Thiago; De Moraes Gregores, Eduardo; Lagana, Caio; Da Cunha Marinho, Franciole; Mercadante, Pedro G; Novaes, Sergio F; Padula, Sandra; Darmenov, Nikolay; Genchev, Vladimir; Iaydjiev, Plamen; Piperov, Stefan; Rodozov, Mircho; Stoykova, Stefka; Sultanov, Georgi; Tcholakov, Vanio; Trayanov, Rumen; Vutova, Mariana; Dimitrov, Anton; Hadjiiska, Roumyana; Karadzhinova, Aneliya; Kozhuharov, Venelin; Litov, Leander; Mateev, Matey; Pavlov, Borislav; Petkov, Peicho; Bian, Jian-Guo; Chen, Guo-Ming; Chen, He-Sheng; Jiang, Chun-Hua; Liang, Dong; Liang, Song; Meng, Xiangwei; Tao, Junquan; Wang, Jian; Wang, Jian; Wang, Xianyou; Wang, Zheng; Xiao, Hong; Xu, Ming; Zang, Jingjing; Zhang, Zhen; Ban, Yong; Guo, Shuang; Guo, Yifei; Li, Wenbo; Mao, Yajun; Qian, Si-Jin; Teng, Haiyun; Zhu, Bo; Zou, Wei; Cabrera, Andrés; Gomez Moreno, Bernardo; Ocampo Rios, Alberto Andres; Osorio Oliveros, Andres Felipe; Sanabria, Juan Carlos; Godinovic, Nikola; Lelas, Damir; Lelas, Karlo; Plestina, Roko; Polic, Dunja; Puljak, Ivica; Antunovic, Zeljko; Dzelalija, Mile; Kovac, Marko; Brigljevic, Vuko; Duric, Senka; Kadija, Kreso; Luetic, Jelena; Morovic, Srecko; Attikis, Alexandros; Galanti, Mario; Mousa, Jehad; Nicolaou, Charalambos; Ptochos, Fotios; Razis, Panos A; Finger, Miroslav; Finger Jr, Michael; Assran, Yasser; Ellithi Kamel, Ali; Khalil, Shaaban; Mahmoud, Mohammed; Radi, Amr; Hektor, Andi; Kadastik, Mario; Müntel, Mait; Raidal, Martti; Rebane, Liis; Tiko, Andres; Azzolini, Virginia; Eerola, Paula; Fedi, Giacomo; Voutilainen, Mikko; Czellar, Sandor; Härkönen, Jaakko; Heikkinen, Mika Aatos; Karimäki, Veikko; Kinnunen, Ritva; Kortelainen, Matti J; Lampén, Tapio; Lassila-Perini, Kati; Lehti, Sami; Lindén, Tomas; Luukka, Panja-Riina; Mäenpää, Teppo; Tuominen, Eija; Tuominiemi, Jorma; Tuovinen, Esa; Ungaro, Donatella; Wendland, Lauri; Banzuzi, Kukka; Karjalainen, Ahti; Korpela, Arja; Tuuva, Tuure; Sillou, Daniel; Besancon, Marc; Choudhury, Somnath; Dejardin, Marc; Denegri, Daniel; Fabbro, Bernard; Faure, Jean-Louis; Ferri, Federico; Ganjour, Serguei; Givernaud, Alain; Gras, Philippe; Hamel de Monchenault, Gautier; Jarry, Patrick; Locci, Elizabeth; Malcles, Julie; Marionneau, Matthieu; Millischer, Laurent; Rander, John; Rosowsky, André; Shreyber, Irina; Titov, Maksym; Baffioni, Stephanie; Beaudette, Florian; Benhabib, Lamia; Bianchini, Lorenzo; Bluj, Michal; Broutin, Clementine; Busson, Philippe; Charlot, Claude; Dahms, Torsten; Dobrzynski, Ludwik; Elgammal, Sherif; Granier de Cassagnac, Raphael; Haguenauer, Maurice; Miné, Philippe; Mironov, Camelia; Ochando, Christophe; Paganini, Pascal; Sabes, David; Salerno, Roberto; Sirois, Yves; Thiebaux, Christophe; Veelken, Christian; Zabi, Alexandre; Agram, Jean-Laurent; Andrea, Jeremy; Bloch, Daniel; Bodin, David; Brom, Jean-Marie; Cardaci, Marco; Chabert, Eric Christian; Collard, Caroline; Conte, Eric; Drouhin, Frédéric; Ferro, Cristina; Fontaine, Jean-Charles; Gelé, Denis; Goerlach, Ulrich; Greder, Sebastien; Juillot, Pierre; Karim, Mehdi; Le Bihan, Anne-Catherine; Mikami, Yoshinari; Van Hove, Pierre; Fassi, Farida; Mercier, Damien; Baty, Clement; Beauceron, Stephanie; Beaupere, Nicolas; Bedjidian, Marc; Bondu, Olivier; Boudoul, Gaelle; Boumediene, Djamel; Brun, Hugues; Chasserat, Julien; Chierici, Roberto; Contardo, Didier; Depasse, Pierre; El Mamouni, Houmani; Fay, Jean; Gascon, Susan; Ille, Bernard; Kurca, Tibor; Le Grand, Thomas; Lethuillier, Morgan; Mirabito, Laurent; Perries, Stephane; Sordini, Viola; Tosi, Silvano; Tschudi, Yohann; Verdier, Patrice; Viret, Sébastien; Lomidze, David; Anagnostou, Georgios; Beranek, Sarah; Edelhoff, Matthias; Feld, Lutz; Heracleous, Natalie; Hindrichs, Otto; Jussen, Ruediger; Klein, Katja; Merz, Jennifer; Mohr, Niklas; Ostapchuk, Andrey; Perieanu, Adrian; Raupach, Frank; Sammet, Jan; Schael, Stefan; Sprenger, Daniel; Weber, Hendrik; Weber, Martin; Wittmer, Bruno; Zhukov, Valery; Ata, Metin; Dietz-Laursonn, Erik; Erdmann, Martin; Hebbeker, Thomas; Heidemann, Carsten; Hinzmann, Andreas; Hoepfner, Kerstin; Klimkovich, Tatsiana; Klingebiel, Dennis; Kreuzer, Peter; Lanske, Dankfried; Lingemann, Joschka; Magass, Carsten; Merschmeyer, Markus; Meyer, Arnd; Papacz, Paul; Pieta, Holger; Reithler, Hans; Schmitz, Stefan Antonius; Sonnenschein, Lars; Steggemann, Jan; Teyssier, Daniel; Bontenackels, Michael; Cherepanov, Vladimir; Davids, Martina; Flügge, Günter; Geenen, Heiko; Giffels, Manuel; Haj Ahmad, Wael; Hoehle, Felix; Kargoll, Bastian; Kress, Thomas; Kuessel, Yvonne; Linn, Alexander; Nowack, Andreas; Perchalla, Lars; Pooth, Oliver; Rennefeld, Jörg; Sauerland, Philip; Stahl, Achim; Tornier, Daiske; Zoeller, Marc Henning; Aldaya Martin, Maria; Behrenhoff, Wolf; Behrens, Ulf; Bergholz, Matthias; Bethani, Agni; Borras, Kerstin; Cakir, Altan; Campbell, Alan; Castro, Elena; Dammann, Dirk; Eckerlin, Guenter; Eckstein, Doris; Flossdorf, Alexander; Flucke, Gero; Geiser, Achim; Hauk, Johannes; Jung, Hannes; Kasemann, Matthias; Katsas, Panagiotis; Kleinwort, Claus; Kluge, Hannelies; Knutsson, Albert; Krämer, Mira; Krücker, Dirk; Kuznetsova, Ekaterina; Lange, Wolfgang; Lohmann, Wolfgang; Lutz, Benjamin; Mankel, Rainer; Marienfeld, Markus; Melzer-Pellmann, Isabell-Alissandra; Meyer, Andreas Bernhard; Mnich, Joachim; Mussgiller, Andreas; Olzem, Jan; Petrukhin, Alexey; Pitzl, Daniel; Raspereza, Alexei; Rosin, Michele; Schmidt, Ringo; Schoerner-Sadenius, Thomas; Sen, Niladri; Spiridonov, Alexander; Stein, Matthias; Tomaszewska, Justyna; Walsh, Roberval; Wissing, Christoph; Autermann, Christian; Blobel, Volker; Bobrovskyi, Sergei; Draeger, Jula; Enderle, Holger; Gebbert, Ulla; Görner, Martin; Hermanns, Thomas; Kaschube, Kolja; Kaussen, Gordon; Kirschenmann, Henning; Klanner, Robert; Lange, Jörn; Mura, Benedikt; Naumann-Emme, Sebastian; Nowak, Friederike; Pietsch, Niklas; Sander, Christian; Schettler, Hannes; Schleper, Peter; Schlieckau, Eike; Schröder, Matthias; Schum, Torben; Stadie, Hartmut; Steinbrück, Georg; Thomsen, Jan; Barth, Christian; Bauer, Julia; Berger, Joram; Buege, Volker; Chwalek, Thorsten; De Boer, Wim; Dierlamm, Alexander; Dirkes, Guido; Feindt, Michael; Gruschke, Jasmin; Hackstein, Christoph; Hartmann, Frank; Heinrich, Michael; Held, Hauke; Hoffmann, Karl-Heinz; Honc, Simon; Katkov, Igor; Komaragiri, Jyothsna Rani; Kuhr, Thomas; Martschei, Daniel; Mueller, Steffen; Müller, Thomas; Niegel, Martin; Oberst, Oliver; Oehler, Andreas; Ott, Jochen; Peiffer, Thomas; Quast, Gunter; Rabbertz, Klaus; Ratnikov, Fedor; Ratnikova, Natalia; Renz, Manuel; Röcker, Steffen; Saout, Christophe; Scheurer, Armin; Schieferdecker, Philipp; Schilling, Frank-Peter; Schmanau, Mike; Schott, Gregory; Simonis, Hans-Jürgen; Stober, Fred-Markus Helmut; Troendle, Daniel; Wagner-Kuhr, Jeannine; Weiler, Thomas; Zeise, Manuel; Ziebarth, Eva Barbara; Daskalakis, Georgios; Geralis, Theodoros; Kesisoglou, Stilianos; Kyriakis, Aristotelis; Loukas, Demetrios; Manolakos, Ioannis; Markou, Athanasios; Markou, Christos; Mavrommatis, Charalampos; Ntomari, Eleni; Petrakou, Eleni; Gouskos, Loukas; Mertzimekis, Theodoros; Panagiotou, Apostolos; Saoulidou, Niki; Stiliaris, Efstathios; Evangelou, Ioannis; Foudas, Costas; Kokkas, Panagiotis; Manthos, Nikolaos; Papadopoulos, Ioannis; Patras, Vaios; Triantis, Frixos A; Aranyi, Attila; Bencze, Gyorgy; Boldizsar, Laszlo; Hajdu, Csaba; Hidas, Pàl; Horvath, Dezso; Kapusi, Anita; Krajczar, Krisztian; Sikler, Ferenc; Veres, Gabor Istvan; Vesztergombi, Gyorgy; Beni, Noemi; Molnar, Jozsef; Palinkas, Jozsef; Szillasi, Zoltan; Veszpremi, Viktor; Karancsi, János; Raics, Peter; Trocsanyi, Zoltan Laszlo; Ujvari, Balazs; Beri, Suman Bala; Bhatnagar, Vipin; Dhingra, Nitish; Gupta, Ruchi; Jindal, Monika; Kaur, Manjit; Kohli, Jatinder Mohan; Mehta, Manuk Zubin; Nishu, Nishu; Saini, Lovedeep Kaur; Sharma, Archana; Singh, Anil; Singh, Jasbir; Singh, Supreet Pal; Ahuja, Sudha; Choudhary, Brajesh C; Gupta, Pooja; Kumar, Ashok; Kumar, Arun; Malhotra, Shivali; Naimuddin, Md; Ranjan, Kirti; Shivpuri, Ram Krishen; Banerjee, Sunanda; Bhattacharya, Satyaki; Dutta, Suchandra; Gomber, Bhawna; Jain, Sandhya; Jain, Shilpi; Khurana, Raman; Sarkar, Subir; Choudhury, Rajani Kant; Dutta, Dipanwita; Kailas, Swaminathan; Kumar, Vineet; Mehta, Pourus; Mohanty, Ajit Kumar; Pant, Lalit Mohan; Shukla, Prashant; Aziz, Tariq; Guchait, Monoranjan; Gurtu, Atul; Maity, Manas; Majumder, Devdatta; Majumder, Gobinda; Mathew, Thomas; Mazumdar, Kajari; Mohanty, Gagan Bihari; Parida, Bibhuti; Saha, Anirban; Sudhakar, Katta; Wickramage, Nadeesha; Banerjee, Sudeshna; Dugad, Shashikant; Mondal, Naba Kumar; Arfaei, Hessamaddin; Bakhshiansohi, Hamed; Etesami, Seyed Mohsen; Fahim, Ali; Hashemi, Majid; Hesari, Hoda; Jafari, Abideh; Khakzad, Mohsen; Mohammadi, Abdollah; Mohammadi Najafabadi, Mojtaba; Paktinat Mehdiabadi, Saeid; Safarzadeh, Batool; Zeinali, Maryam; Abbrescia, Marcello; Barbone, Lucia; Calabria, Cesare; Colaleo, Anna; Creanza, Donato; De Filippis, Nicola; De Palma, Mauro; Fiore, Luigi; Iaselli, Giuseppe; Lusito, Letizia; Maggi, Giorgio; Maggi, Marcello; Manna, Norman; Marangelli, Bartolomeo; My, Salvatore; Nuzzo, Salvatore; Pacifico, Nicola; Pierro, Giuseppe Antonio; Pompili, Alexis; Pugliese, Gabriella; Romano, Francesco; Roselli, Giuseppe; Selvaggi, Giovanna; Silvestris, Lucia; Trentadue, Raffaello; Tupputi, Salvatore; Zito, Giuseppe; Abbiendi, Giovanni; Benvenuti, Alberto; Bonacorsi, Daniele; Braibant-Giacomelli, Sylvie; Brigliadori, Luca; Capiluppi, Paolo; Castro, Andrea; Cavallo, Francesca Romana; Cuffiani, Marco; Dallavalle, Gaetano-Marco; Fabbri, Fabrizio; Fanfani, Alessandra; Fasanella, Daniele; Giacomelli, Paolo; Giunta, Marina; Grandi, Claudio; Marcellini, Stefano; Masetti, Gianni; Meneghelli, Marco; Montanari, Alessandro; Navarria, Francesco; Odorici, Fabrizio; Perrotta, Andrea; Primavera, Federica; Rossi, Antonio; Rovelli, Tiziano; Siroli, Gianni; Travaglini, Riccardo; Albergo, Sebastiano; Cappello, Gigi; Chiorboli, Massimiliano; Costa, Salvatore; Potenza, Renato; Tricomi, Alessia; Tuve, Cristina; Barbagli, Giuseppe; Ciulli, Vitaliano; Civinini, Carlo; D'Alessandro, Raffaello; Focardi, Ettore; Frosali, Simone; Gallo, Elisabetta; Gonzi, Sandro; Meschini, Marco; Paoletti, Simone; Sguazzoni, Giacomo; Tropiano, Antonio; Benussi, Luigi; Bianco, Stefano; Colafranceschi, Stefano; Fabbri, Franco; Piccolo, Davide; Fabbricatore, Pasquale; Musenich, Riccardo; Benaglia, Andrea; De Guio, Federico; Di Matteo, Leonardo; Gennai, Simone; Ghezzi, Alessio; Malvezzi, Sandra; Martelli, Arabella; Massironi, Andrea; Menasce, Dario; Moroni, Luigi; Paganoni, Marco; Pedrini, Daniele; Ragazzi, Stefano; Redaelli, Nicola; Sala, Silvano; Tabarelli de Fatis, Tommaso; Buontempo, Salvatore; Carrillo Montoya, Camilo Andres; Cavallo, Nicola; De Cosa, Annapaola; Fabozzi, Francesco; Iorio, Alberto Orso Maria; Lista, Luca; Merola, Mario; Paolucci, Pierluigi; Azzi, Patrizia; Bacchetta, Nicola; Bellan, Paolo; Bisello, Dario; Branca, Antonio; Carlin, Roberto; Checchia, Paolo; Dorigo, Tommaso; Dosselli, Umberto; Fanzago, Federica; Gasparini, Fabrizio; Gasparini, Ugo; Gozzelino, Andrea; Lacaprara, Stefano; Lazzizzera, Ignazio; Margoni, Martino; Mazzucato, Mirco; Meneguzzo, Anna Teresa; Nespolo, Massimo; Perrozzi, Luca; Pozzobon, Nicola; Ronchese, Paolo; Simonetto, Franco; Torassa, Ezio; Tosi, Mia; Vanini, Sara; Zotto, Pierluigi; Zumerle, Gianni; Baesso, Paolo; Berzano, Umberto; Ratti, Sergio P; Riccardi, Cristina; Torre, Paola; Vitulo, Paolo; Viviani, Claudio; Biasini, Maurizio; Bilei, Gian Mario; Caponeri, Benedetta; Fanò, Livio; Lariccia, Paolo; Lucaroni, Andrea; Mantovani, Giancarlo; Menichelli, Mauro; Nappi, Aniello; Romeo, Francesco; Santocchia, Attilio; Taroni, Silvia; Valdata, Marisa; Azzurri, Paolo; Bagliesi, Giuseppe; Bernardini, Jacopo; Boccali, Tommaso; Broccolo, Giuseppe; Castaldi, Rino; D'Agnolo, Raffaele Tito; Dell'Orso, Roberto; Fiori, Francesco; Foà, Lorenzo; Giassi, Alessandro; Kraan, Aafke; Ligabue, Franco; Lomtadze, Teimuraz; Martini, Luca; Messineo, Alberto; Palla, Fabrizio; Palmonari, Francesco; Segneri, Gabriele; Serban, Alin Titus; Spagnolo, Paolo; Tenchini, Roberto; Tonelli, Guido; Venturi, Andrea; Verdini, Piero Giorgio; Barone, Luciano; Cavallari, Francesca; Del Re, Daniele; Di Marco, Emanuele; Diemoz, Marcella; Franci, Daniele; Grassi, Marco; Longo, Egidio; Meridiani, Paolo; Nourbakhsh, Shervin; Organtini, Giovanni; Pandolfi, Francesco; Paramatti, Riccardo; Rahatlou, Shahram; Sigamani, Michael; Amapane, Nicola; Arcidiacono, Roberta; Argiro, Stefano; Arneodo, Michele; Biino, Cristina; Botta, Cristina; Cartiglia, Nicolo; Castello, Roberto; Costa, Marco; Demaria, Natale; Graziano, Alberto; Mariotti, Chiara; Maselli, Silvia; Migliore, Ernesto; Monaco, Vincenzo; Musich, Marco; Obertino, Maria Margherita; Pastrone, Nadia; Pelliccioni, Mario; Potenza, Alberto; Romero, Alessandra; Ruspa, Marta; Sacchi, Roberto; Sola, Valentina; Solano, Ada; Staiano, Amedeo; Vilela Pereira, Antonio; Belforte, Stefano; Cossutti, Fabio; Della Ricca, Giuseppe; Gobbo, Benigno; Marone, Matteo; Montanino, Damiana; Penzo, Aldo; Heo, Seong Gu; Nam, Soon-Kwon; Chang, Sunghyun; Chung, Jin Hyuk; Kim, Dong Hee; Kim, Gui Nyun; Kim, Ji Eun; Kong, Dae Jung; Park, Hyangkyu; Ro, Sang-Ryul; Son, Dong-Chul; Son, Taejin; Kim, Jae Yool; Kim, Zero Jaeho; Song, Sanghyeon; Jo, Hyun Yong; Choi, Suyong; Gyun, Dooyeon; Hong, Byung-Sik; Jo, Mihee; Kim, Hyunchul; Kim, Ji Hyun; Kim, Tae Jeong; Lee, Kyong Sei; Moon, Dong Ho; Park, Sung Keun; Seo, Eunsung; Sim, Kwang Souk; Choi, Minkyoo; Kang, Seokon; Kim, Hyunyong; Park, Chawon; Park, Inkyu; Park, Sangnam; Ryu, Geonmo; Cho, Yongjin; Choi, Young-Il; Choi, Young Kyu; Goh, Junghwan; Kim, Min Suk; Lee, Byounghoon; Lee, Jongseok; Lee, Sungeun; Seo, Hyunkwan; Yu, Intae; Bilinskas, Mykolas Jurgis; Grigelionis, Ignas; Janulis, Mindaugas; Martisiute, Dalia; Petrov, Pavel; Polujanskas, Mindaugas; Sabonis, Tomas; Castilla-Valdez, Heriberto; De La Cruz-Burelo, Eduard; Heredia-de La Cruz, Ivan; Lopez-Fernandez, Ricardo; Magaña Villalba, Ricardo; Martínez-Ortega, Jorge; Sánchez-Hernández, Alberto; Villasenor-Cendejas, Luis Manuel; Carrillo Moreno, Salvador; Vazquez Valencia, Fabiola; Salazar Ibarguen, Humberto Antonio; Casimiro Linares, Edgar; Morelos Pineda, Antonio; Reyes-Santos, Marco A; Krofcheck, David; Tam, Jason; Butler, Philip H; Doesburg, Robert; Silverwood, Hamish; Ahmad, Muhammad; Ahmed, Ijaz; Ansari, Muhammad Hamid; Asghar, Muhammad Irfan; Hoorani, Hafeez R; Khalid, Shoaib; Khan, Wajid Ali; Khurshid, Taimoor; Qazi, Shamona; Shah, Mehar Ali; Shoaib, Muhammad; Brona, Grzegorz; Cwiok, Mikolaj; Dominik, Wojciech; Doroba, Krzysztof; Kalinowski, Artur; Konecki, Marcin; Krolikowski, Jan; Frueboes, Tomasz; Gokieli, Ryszard; Górski, Maciej; Kazana, Malgorzata; Nawrocki, Krzysztof; Romanowska-Rybinska, Katarzyna; Szleper, Michal; Wrochna, Grzegorz; Zalewski, Piotr; Almeida, Nuno; Bargassa, Pedrame; David Tinoco Mendes, Andre; Faccioli, Pietro; Ferreira Parracho, Pedro Guilherme; Gallinaro, Michele; Musella, Pasquale; Nayak, Aruna; Pela, Joao; Ribeiro, Pedro Quinaz; Seixas, Joao; Varela, Joao; Afanasiev, Serguei; Belotelov, Ivan; Bunin, Pavel; Gavrilenko, Mikhail; Golutvin, Igor; Kamenev, Alexey; Karjavin, Vladimir; Kozlov, Guennady; Lanev, Alexander; Moisenz, Petr; Palichik, Vladimir; Perelygin, Victor; Shmatov, Sergey; Smirnov, Vitaly; Volodko, Anton; Zarubin, Anatoli; Golovtsov, Victor; Ivanov, Yury; Kim, Victor; Levchenko, Petr; Murzin, Victor; Oreshkin, Vadim; Smirnov, Igor; Sulimov, Valentin; Uvarov, Lev; Vavilov, Sergey; Vorobyev, Alexey; Vorobyev, Andrey; Andreev, Yuri; Dermenev, Alexander; Gninenko, Sergei; Golubev, Nikolai; Kirsanov, Mikhail; Krasnikov, Nikolai; Matveev, Viktor; Pashenkov, Anatoli; Toropin, Alexander; Troitsky, Sergey; Epshteyn, Vladimir; Erofeeva, Maria; Gavrilov, Vladimir; Kaftanov, Vitali; Kossov, Mikhail; Krokhotin, Andrey; Lychkovskaya, Natalia; Popov, Vladimir; Safronov, Grigory; Semenov, Sergey; Stolin, Viatcheslav; Vlasov, Evgueni; Zhokin, Alexander; Belyaev, Andrey; Boos, Edouard; Dubinin, Mikhail; Dudko, Lev; Ershov, Alexander; Gribushin, Andrey; Kodolova, Olga; Lokhtin, Igor; Markina, Anastasia; Obraztsov, Stepan; Perfilov, Maxim; Petrushanko, Sergey; Sarycheva, Ludmila; Savrin, Viktor; Snigirev, Alexander; Andreev, Vladimir; Azarkin, Maksim; Dremin, Igor; Kirakosyan, Martin; Leonidov, Andrey; Mesyats, Gennady; Rusakov, Sergey V; Vinogradov, Alexey; Azhgirey, Igor; Bayshev, Igor; Bitioukov, Sergei; Grishin, Viatcheslav; Kachanov, Vassili; Konstantinov, Dmitri; Korablev, Andrey; Krychkine, Victor; Petrov, Vladimir; Ryutin, Roman; Sobol, Andrei; Tourtchanovitch, Leonid; Troshin, Sergey; Tyurin, Nikolay; Uzunian, Andrey; Volkov, Alexey; Adzic, Petar; Djordjevic, Milos; Krpic, Dragomir; Milosevic, Jovan; Aguilar-Benitez, Manuel; Alcaraz Maestre, Juan; Arce, Pedro; Battilana, Carlo; Calvo, Enrique; Cerrada, Marcos; Chamizo Llatas, Maria; Colino, Nicanor; De La Cruz, Begona; Delgado Peris, Antonio; Diez Pardos, Carmen; Domínguez Vázquez, Daniel; Fernandez Bedoya, Cristina; Fernández Ramos, Juan Pablo; Ferrando, Antonio; Flix, Jose; Fouz, Maria Cruz; Garcia-Abia, Pablo; Gonzalez Lopez, Oscar; Goy Lopez, Silvia; Hernandez, Jose M; Josa, Maria Isabel; Merino, Gonzalo; Puerta Pelayo, Jesus; Redondo, Ignacio; Romero, Luciano; Santaolalla, Javier; Soares, Mara Senghi; Willmott, Carlos; Albajar, Carmen; Codispoti, Giuseppe; de Trocóniz, Jorge F; Cuevas, Javier; Fernandez Menendez, Javier; Folgueras, Santiago; Gonzalez Caballero, Isidro; Lloret Iglesias, Lara; Vizan Garcia, Jesus Manuel; Brochero Cifuentes, Javier Andres; Cabrillo, Iban Jose; Calderon, Alicia; Chuang, Shan-Huei; Duarte Campderros, Jordi; Felcini, Marta; Fernandez, Marcos; Gomez, Gervasio; Gonzalez Sanchez, Javier; Jorda, Clara; Lobelle Pardo, Patricia; Lopez Virto, Amparo; Marco, Jesus; Marco, Rafael; Martinez Rivero, Celso; Matorras, Francisco; Munoz Sanchez, Francisca Javiela; Piedra Gomez, Jonatan; Rodrigo, Teresa; Rodríguez-Marrero, Ana Yaiza; Ruiz-Jimeno, Alberto; Scodellaro, Luca; Sobron Sanudo, Mar; Vila, Ivan; Vilar Cortabitarte, Rocio; Abbaneo, Duccio; Auffray, Etiennette; Auzinger, Georg; Baillon, Paul; Ball, Austin; Barney, David; Bell, Alan James; Benedetti, Daniele; Bernet, Colin; Bialas, Wojciech; Bloch, Philippe; Bocci, Andrea; Bolognesi, Sara; Bona, Marcella; Breuker, Horst; Bunkowski, Karol; Camporesi, Tiziano; Cerminara, Gianluca; Christiansen, Tim; Coarasa Perez, Jose Antonio; Curé, Benoît; D'Enterria, David; De Roeck, Albert; Di Guida, Salvatore; Dupont-Sagorin, Niels; Elliott-Peisert, Anna; Frisch, Benjamin; Funk, Wolfgang; Gaddi, Andrea; Georgiou, Georgios; Gerwig, Hubert; Gigi, Dominique; Gill, Karl; Giordano, Domenico; Glege, Frank; Gomez-Reino Garrido, Robert; Gouzevitch, Maxime; Govoni, Pietro; Gowdy, Stephen; Guida, Roberto; Guiducci, Luigi; Hansen, Magnus; Hartl, Christian; Harvey, John; Hegeman, Jeroen; Hegner, Benedikt; Hoffmann, Hans Falk; Innocente, Vincenzo; Janot, Patrick; Kaadze, Ketino; Karavakis, Edward; Lecoq, Paul; Lenzi, Piergiulio; Lourenco, Carlos; Maki, Tuula; Malberti, Martina; Malgeri, Luca; Mannelli, Marcello; Masetti, Lorenzo; Maurisset, Aurelie; Mavromanolakis, Georgios; Meijers, Frans; Mersi, Stefano; Meschi, Emilio; Moser, Roland; Mozer, Matthias Ulrich; Mulders, Martijn; Nesvold, Erik; Nguyen, Matthew; Orimoto, Toyoko; Orsini, Luciano; Palencia Cortezon, Enrique; Perez, Emmanuelle; Petrilli, Achille; Pfeiffer, Andreas; Pierini, Maurizio; Pimiä, Martti; Piparo, Danilo; Polese, Giovanni; Quertenmont, Loic; Racz, Attila; Reece, William; Rodrigues Antunes, Joao; Rolandi, Gigi; Rommerskirchen, Tanja; Rovelli, Chiara; Rovere, Marco; Sakulin, Hannes; Schäfer, Christoph; Schwick, Christoph; Segoni, Ilaria; Sharma, Archana; Siegrist, Patrice; Silva, Pedro; Simon, Michal; Sphicas, Paraskevas; Spiga, Daniele; Spiropulu, Maria; Stoye, Markus; Tsirou, Andromachi; Vichoudis, Paschalis; Wöhri, Hermine Katharina; Worm, Steven; Zeuner, Wolfram Dietrich; Bertl, Willi; Deiters, Konrad; Erdmann, Wolfram; Gabathuler, Kurt; Horisberger, Roland; Ingram, Quentin; Kaestli, Hans-Christian; König, Stefan; Kotlinski, Danek; Langenegger, Urs; Meier, Frank; Renker, Dieter; Rohe, Tilman; Sibille, Jennifer; Bäni, Lukas; Bortignon, Pierluigi; Caminada, Lea; Casal, Bruno; Chanon, Nicolas; Chen, Zhiling; Cittolin, Sergio; Dissertori, Günther; Dittmar, Michael; Eugster, Jürg; Freudenreich, Klaus; Grab, Christoph; Hintz, Wieland; Lecomte, Pierre; Lustermann, Werner; Marchica, Carmelo; Martinez Ruiz del Arbol, Pablo; Milenovic, Predrag; Moortgat, Filip; Nägeli, Christoph; Nef, Pascal; Nessi-Tedaldi, Francesca; Pape, Luc; Pauss, Felicitas; Punz, Thomas; Rizzi, Andrea; Ronga, Frederic Jean; Rossini, Marco; Sala, Leonardo; Sanchez, Ann - Karin; Sawley, Marie-Christine; Starodumov, Andrei; Stieger, Benjamin; Takahashi, Maiko; Tauscher, Ludwig; Thea, Alessandro; Theofilatos, Konstantinos; Treille, Daniel; Urscheler, Christina; Wallny, Rainer; Weber, Matthias; Wehrli, Lukas; Weng, Joanna; Aguilo, Ernest; Amsler, Claude; Chiochia, Vincenzo; De Visscher, Simon; Favaro, Carlotta; Ivova Rikova, Mirena; Jaeger, Andreas; Millan Mejias, Barbara; Otiougova, Polina; Robmann, Peter; Schmidt, Alexander; Snoek, Hella; Chang, Yuan-Hann; Chen, Kuan-Hsin; Kuo, Chia-Ming; Li, Syue-Wei; Lin, Willis; Liu, Zong-Kai; Lu, Yun-Ju; Mekterovic, Darko; Volpe, Roberta; Yu, Shin-Shan; Bartalini, Paolo; Chang, Paoti; Chang, You-Hao; Chang, Yu-Wei; Chao, Yuan; Chen, Kai-Feng; Dietz, Charles; Grundler, Ulysses; Hou, George Wei-Shu; Hsiung, Yee; Kao, Kai-Yi; Lei, Yeong-Jyi; Lu, Rong-Shyang; Shiu, Jing-Ge; Tzeng, Yeng-Ming; Wan, Xia; Wang, Minzu; Adiguzel, Aytul; Bakirci, Mustafa Numan; Cerci, Salim; Dozen, Candan; Dumanoglu, Isa; Eskut, Eda; Girgis, Semiray; Gokbulut, Gul; Hos, Ilknur; Kangal, Evrim Ersin; Kayis Topaksu, Aysel; Onengut, Gulsen; Ozdemir, Kadri; Ozturk, Sertac; Polatoz, Ayse; Sogut, Kenan; Sunar Cerci, Deniz; Tali, Bayram; Topakli, Huseyin; Uzun, Dilber; Vergili, Latife Nukhet; Vergili, Mehmet; Akin, Ilina Vasileva; Aliev, Takhmasib; Bilin, Bugra; Bilmis, Selcuk; Deniz, Muhammed; Gamsizkan, Halil; Guler, Ali Murat; Ocalan, Kadir; Ozpineci, Altug; Serin, Meltem; Sever, Ramazan; Surat, Ugur Emrah; Yalvac, Metin; Yildirim, Eda; Zeyrek, Mehmet; Deliomeroglu, Mehmet; Demir, Durmus; Gülmez, Erhan; Isildak, Bora; Kaya, Mithat; Kaya, Ozlem; Özbek, Melih; Ozkorucuklu, Suat; Sonmez, Nasuf; Levchuk, Leonid; Bostock, Francis; Brooke, James John; Cheng, Teh Lee; Clement, Emyr; Cussans, David; Frazier, Robert; Goldstein, Joel; Grimes, Mark; Heath, Greg P; Heath, Helen F; Kreczko, Lukasz; Metson, Simon; Newbold, Dave M; Nirunpong, Kachanon; Poll, Anthony; Senkin, Sergey; Smith, Vincent J; Basso, Lorenzo; Bell, Ken W; Belyaev, Alexander; Brew, Christopher; Brown, Robert M; Camanzi, Barbara; Cockerill, David JA; Coughlan, John A; Harder, Kristian; Harper, Sam; Jackson, James; Kennedy, Bruce W; Olaiya, Emmanuel; Petyt, David; Radburn-Smith, Benjamin Charles; Shepherd-Themistocleous, Claire; Tomalin, Ian R; Womersley, William John; Bainbridge, Robert; Ball, Gordon; Ballin, Jamie; Beuselinck, Raymond; Buchmuller, Oliver; Colling, David; Cripps, Nicholas; Cutajar, Michael; Davies, Gavin; Della Negra, Michel; Ferguson, William; Fulcher, Jonathan; Futyan, David; Gilbert, Andrew; Guneratne Bryer, Arlo; Hall, Geoffrey; Hatherell, Zoe; Hays, Jonathan; Iles, Gregory; Jarvis, Martyn; Karapostoli, Georgia; Lyons, Louis; Magnan, Anne-Marie; Marrouche, Jad; Mathias, Bryn; Nandi, Robin; Nash, Jordan; Nikitenko, Alexander; Papageorgiou, Anastasios; Pesaresi, Mark; Petridis, Konstantinos; Pioppi, Michele; Raymond, David Mark; Rogerson, Samuel; Rompotis, Nikolaos; Rose, Andrew; Ryan, Matthew John; Seez, Christopher; Sharp, Peter; Sparrow, Alex; Tapper, Alexander; Tourneur, Stephane; Vazquez Acosta, Monica; Virdee, Tejinder; Wakefield, Stuart; Wardle, Nicholas; Wardrope, David; Whyntie, Tom; Barrett, Matthew; Chadwick, Matthew; Cole, Joanne; Hobson, Peter R; Khan, Akram; Kyberd, Paul; Leslie, Dawn; Martin, William; Reid, Ivan; Teodorescu, Liliana; Hatakeyama, Kenichi; Liu, Hongxuan; Henderson, Conor; Bose, Tulika; Carrera Jarrin, Edgar; Fantasia, Cory; Heister, Arno; St John, Jason; Lawson, Philip; Lazic, Dragoslav; Rohlf, James; Sperka, David; Sulak, Lawrence; Avetisyan, Aram; Bhattacharya, Saptaparna; Chou, John Paul; Cutts, David; Ferapontov, Alexey; Heintz, Ulrich; Jabeen, Shabnam; Kukartsev, Gennadiy; Landsberg, Greg; Luk, Michael; Narain, Meenakshi; Nguyen, Duong; Segala, Michael; Sinthuprasith, Tutanon; Speer, Thomas; Tsang, Ka Vang; Breedon, Richard; Breto, Guillermo; Calderon De La Barca Sanchez, Manuel; Chauhan, Sushil; Chertok, Maxwell; Conway, John; Conway, Rylan; Cox, Peter Timothy; Dolen, James; Erbacher, Robin; Houtz, Rachel; Ko, Winston; Kopecky, Alexandra; Lander, Richard; Liu, Haidong; Mall, Orpheus; Maruyama, Sho; Miceli, Tia; Nikolic, Milan; Pellett, Dave; Robles, Jorge; Rutherford, Britney; Salur, Sevil; Searle, Matthew; Smith, John; Squires, Michael; Tripathi, Mani; Vasquez Sierra, Ricardo; Andreev, Valeri; Arisaka, Katsushi; Cline, David; Cousins, Robert; Deisher, Amanda; Duris, Joseph; Erhan, Samim; Farrell, Chris; Hauser, Jay; Ignatenko, Mikhail; Jarvis, Chad; Plager, Charles; Rakness, Gregory; Schlein, Peter; Tucker, Jordan; Valuev, Vyacheslav; Babb, John; Clare, Robert; Ellison, John Anthony; Gary, J William; Giordano, Ferdinando; Hanson, Gail; Jeng, Geng-Yuan; Kao, Shih-Chuan; Liu, Hongliang; Long, Owen Rosser; Luthra, Arun; Nguyen, Harold; Paramesvaran, Sudarshan; Sturdy, Jared; Sumowidagdo, Suharyo; Wilken, Rachel; Wimpenny, Stephen; Andrews, Warren; Branson, James G; Cerati, Giuseppe Benedetto; Evans, David; Golf, Frank; Holzner, André; Kelley, Ryan; Lebourgeois, Matthew; Letts, James; Mangano, Boris; Padhi, Sanjay; Palmer, Christopher; Petrucciani, Giovanni; Pi, Haifeng; Pieri, Marco; Ranieri, Riccardo; Sani, Matteo; Sharma, Vivek; Simon, Sean; Sudano, Elizabeth; Tadel, Matevz; Tu, Yanjun; Vartak, Adish; Wasserbaech, Steven; Würthwein, Frank; Yagil, Avraham; Yoo, Jaehyeok; Barge, Derek; Bellan, Riccardo; Campagnari, Claudio; D'Alfonso, Mariarosaria; Danielson, Thomas; Flowers, Kristen; Geffert, Paul; Incandela, Joe; Justus, Christopher; Kalavase, Puneeth; Koay, Sue Ann; Kovalskyi, Dmytro; Krutelyov, Vyacheslav; Lowette, Steven; Mccoll, Nickolas; Mullin, Sam Daniel; Pavlunin, Viktor; Rebassoo, Finn; Ribnik, Jacob; Richman, Jeffrey; Rossin, Roberto; Stuart, David; To, Wing; Vlimant, Jean-Roch; West, Christopher; Apresyan, Artur; Bornheim, Adolf; Bunn, Julian; Chen, Yi; Duarte, Javier; Gataullin, Marat; Ma, Yousi; Mott, Alexander; Newman, Harvey B; Rogan, Christopher; Shin, Kyoungha; Timciuc, Vladlen; Traczyk, Piotr; Veverka, Jan; Wilkinson, Richard; Yang, Yong; Zhu, Ren-Yuan; Akgun, Bora; Carroll, Ryan; Ferguson, Thomas; Iiyama, Yutaro; Jang, Dong Wook; Jun, Soon Yung; Liu, Yueh-Feng; Paulini, Manfred; Russ, James; Vogel, Helmut; Vorobiev, Igor; Cumalat, John Perry; Dinardo, Mauro Emanuele; Drell, Brian Robert; Edelmaier, Christopher; Ford, William T; Gaz, Alessandro; Heyburn, Bernadette; Luiggi Lopez, Eduardo; Nauenberg, Uriel; Smith, James; Stenson, Kevin; Ulmer, Keith; Wagner, Stephen Robert; Zang, Shi-Lei; Agostino, Lorenzo; Alexander, James; Chatterjee, Avishek; Eggert, Nicholas; Gibbons, Lawrence Kent; Heltsley, Brian; Hopkins, Walter; Khukhunaishvili, Aleko; Kreis, Benjamin; Nicolas Kaufman, Gala; Patterson, Juliet Ritchie; Puigh, Darren; Ryd, Anders; Salvati, Emmanuele; Shi, Xin; Sun, Werner; Teo, Wee Don; Thom, Julia; Thompson, Joshua; Vaughan, Jennifer; Weng, Yao; Winstrom, Lucas; Wittich, Peter; Biselli, Angela; Cirino, Guy; Winn, Dave; Abdullin, Salavat; Albrow, Michael; Anderson, Jacob; Apollinari, Giorgio; Atac, Muzaffer; Bakken, Jon Alan; Bauerdick, Lothar AT; Beretvas, Andrew; Berryhill, Jeffrey; Bhat, Pushpalatha C; Bloch, Ingo; Burkett, Kevin; Butler, Joel Nathan; Chetluru, Vasundhara; Cheung, Harry; Chlebana, Frank; Cihangir, Selcuk; Cooper, William; Eartly, David P; Elvira, Victor Daniel; Esen, Selda; Fisk, Ian; Freeman, Jim; Gao, Yanyan; Gottschalk, Erik; Green, Dan; Gutsche, Oliver; Hanlon, Jim; Harris, Robert M; Hirschauer, James; Hooberman, Benjamin; Jensen, Hans; Jindariani, Sergo; Johnson, Marvin; Joshi, Umesh; Klima, Boaz; Kousouris, Konstantinos; Kunori, Shuichi; Kwan, Simon; Leonidopoulos, Christos; Limon, Peter; Lincoln, Don; Lipton, Ron; Lykken, Joseph; Maeshima, Kaori; Marraffino, John Michael; Mason, David; McBride, Patricia; Miao, Ting; Mishra, Kalanand; Mrenna, Stephen; Musienko, Yuri; Newman-Holmes, Catherine; O'Dell, Vivian; Pivarski, James; Pordes, Ruth; Prokofyev, Oleg; Schwarz, Thomas; Sexton-Kennedy, Elizabeth; Sharma, Seema; Spalding, William J; Spiegel, Leonard; Tan, Ping; Taylor, Lucas; Tkaczyk, Slawek; Uplegger, Lorenzo; Vaandering, Eric Wayne; Vidal, Richard; Whitmore, Juliana; Wu, Weimin; Yang, Fan; Yumiceva, Francisco; Yun, Jae Chul; Acosta, Darin; Avery, Paul; Bourilkov, Dimitri; Chen, Mingshui; Das, Souvik; De Gruttola, Michele; Di Giovanni, Gian Piero; Dobur, Didar; Drozdetskiy, Alexey; Field, Richard D; Fisher, Matthew; Fu, Yu; Furic, Ivan-Kresimir; Gartner, Joseph; Goldberg, Sean; Hugon, Justin; Kim, Bockjoo; Konigsberg, Jacobo; Korytov, Andrey; Kropivnitskaya, Anna; Kypreos, Theodore; Low, Jia Fu; Matchev, Konstantin; Mitselmakher, Guenakh; Muniz, Lana; Myeonghun, Park; Remington, Ronald; Rinkevicius, Aurelijus; Schmitt, Michael; Scurlock, Bobby; Sellers, Paul; Skhirtladze, Nikoloz; Snowball, Matthew; Wang, Dayong; Yelton, John; Zakaria, Mohammed; Gaultney, Vanessa; Lebolo, Luis Miguel; Linn, Stephan; Markowitz, Pete; Martinez, German; Rodriguez, Jorge Luis; Adams, Todd; Askew, Andrew; Bochenek, Joseph; Chen, Jie; Diamond, Brendan; Gleyzer, Sergei V; Haas, Jeff; Hagopian, Sharon; Hagopian, Vasken; Jenkins, Merrill; Johnson, Kurtis F; Prosper, Harrison; Sekmen, Sezen; Veeraraghavan, Venkatesh; Baarmand, Marc M; Dorney, Brian; Hohlmann, Marcus; Kalakhety, Himali; Vodopiyanov, Igor; Adams, Mark Raymond; Anghel, Ioana Maria; Apanasevich, Leonard; Bai, Yuting; Bazterra, Victor Eduardo; Betts, Russell Richard; Callner, Jeremy; Cavanaugh, Richard; Dragoiu, Cosmin; Gauthier, Lucie; Gerber, Cecilia Elena; Hofman, David Jonathan; Khalatyan, Samvel; Kunde, Gerd J; Lacroix, Florent; Malek, Magdalena; O'Brien, Christine; Silkworth, Christopher; Silvestre, Catherine; Smoron, Agata; Strom, Derek; Varelas, Nikos; Akgun, Ugur; Albayrak, Elif Asli; Bilki, Burak; Clarida, Warren; Duru, Firdevs; Lae, Chung Khim; McCliment, Edward; Merlo, Jean-Pierre; Mermerkaya, Hamit; Mestvirishvili, Alexi; Moeller, Anthony; Nachtman, Jane; Newsom, Charles Ray; Norbeck, Edwin; Olson, Jonathan; Onel, Yasar; Ozok, Ferhat; Sen, Sercan; Wetzel, James; Yetkin, Taylan; Yi, Kai; Barnett, Bruce Arnold; Blumenfeld, Barry; Bonato, Alessio; Eskew, Christopher; Fehling, David; Giurgiu, Gavril; Gritsan, Andrei; Guo, Zijin; Hu, Guofan; Maksimovic, Petar; Rappoccio, Salvatore; Swartz, Morris; Tran, Nhan Viet; Whitbeck, Andrew; Baringer, Philip; Bean, Alice; Benelli, Gabriele; Grachov, Oleg; Kenny Iii, Raymond Patrick; Murray, Michael; Noonan, Daniel; Sanders, Stephen; Stringer, Robert; Wood, Jeffrey Scott; Zhukova, Victoria; Barfuss, Anne-Fleur; Bolton, Tim; Chakaberia, Irakli; Ivanov, Andrew; Khalil, Sadia; Makouski, Mikhail; Maravin, Yurii; Shrestha, Shruti; Svintradze, Irakli; Gronberg, Jeffrey; Lange, David; Wright, Douglas; Baden, Drew; Boutemeur, Madjid; Eno, Sarah Catherine; Ferencek, Dinko; Gomez, Jaime; Hadley, Nicholas John; Kellogg, Richard G; Kirn, Malina; Lu, Ying; Mignerey, Alice; Rossato, Kenneth; Rumerio, Paolo; Santanastasio, Francesco; Skuja, Andris; Temple, Jeffrey; Tonjes, Marguerite; Tonwar, Suresh C; Twedt, Elizabeth; Alver, Burak; Bauer, Gerry; Bendavid, Joshua; Busza, Wit; Butz, Erik; Cali, Ivan Amos; Chan, Matthew; Dutta, Valentina; Everaerts, Pieter; Gomez Ceballos, Guillelmo; Goncharov, Maxim; Hahn, Kristan Allan; Harris, Philip; Kim, Yongsun; Klute, Markus; Lee, Yen-Jie; Li, Wei; Loizides, Constantinos; Luckey, Paul David; Ma, Teng; Nahn, Steve; Paus, Christoph; Ralph, Duncan; Roland, Christof; Roland, Gunther; Rudolph, Matthew; Stephans, George; Stöckli, Fabian; Sumorok, Konstanty; Sung, Kevin; Velicanu, Dragos; Wenger, Edward Allen; Wolf, Roger; Wyslouch, Bolek; Xie, Si; Yang, Mingming; Yilmaz, Yetkin; Yoon, Sungho; Zanetti, Marco; Cooper, Seth; Cushman, Priscilla; Dahmes, Bryan; De Benedetti, Abraham; Franzoni, Giovanni; Gude, Alexander; Haupt, Jason; Klapoetke, Kevin; Kubota, Yuichi; Mans, Jeremy; Pastika, Nathaniel; Rekovic, Vladimir; Rusack, Roger; Sasseville, Michael; Singovsky, Alexander; Tambe, Norbert; Turkewitz, Jared; Cremaldi, Lucien Marcus; Godang, Romulus; Kroeger, Rob; Perera, Lalith; Rahmat, Rahmat; Sanders, David A; Summers, Don; Bloom, Kenneth; Bose, Suvadeep; Butt, Jamila; Claes, Daniel R; Dominguez, Aaron; Eads, Michael; Jindal, Pratima; Keller, Jason; Kelly, Tony; Kravchenko, Ilya; Lazo-Flores, Jose; Malbouisson, Helena; Malik, Sudhir; Snow, Gregory R; Baur, Ulrich; Godshalk, Andrew; Iashvili, Ia; Jain, Supriya; Kharchilava, Avto; Kumar, Ashish; Smith, Kenneth; Wan, Zongru; Alverson, George; Barberis, Emanuela; Baumgartel, Darin; Boeriu, Oana; Chasco, Matthew; Reucroft, Steve; Swain, John; Trocino, Daniele; Wood, Darien; Zhang, Jinzhong; Anastassov, Anton; Kubik, Andrew; Mucia, Nicholas; Odell, Nathaniel; Ofierzynski, Radoslaw Adrian; Pollack, Brian; Pozdnyakov, Andrey; Schmitt, Michael; Stoynev, Stoyan; Velasco, Mayda; Won, Steven; Antonelli, Louis; Berry, Douglas; Brinkerhoff, Andrew; Hildreth, Michael; Jessop, Colin; Karmgard, Daniel John; Kolb, Jeff; Kolberg, Ted; Lannon, Kevin; Luo, Wuming; Lynch, Sean; Marinelli, Nancy; Morse, David Michael; Pearson, Tessa; Ruchti, Randy; Slaunwhite, Jason; Valls, Nil; Wayne, Mitchell; Ziegler, Jill; Bylsma, Ben; Durkin, Lloyd Stanley; Hill, Christopher; Killewald, Phillip; Kotov, Khristian; Ling, Ta-Yung; Rodenburg, Marissa; Vuosalo, Carl; Williams, Grayson; Adam, Nadia; Berry, Edmund; Elmer, Peter; Gerbaudo, Davide; Halyo, Valerie; Hebda, Philip; Hunt, Adam; Laird, Edward; Lopes Pegna, David; Marlow, Daniel; Medvedeva, Tatiana; Mooney, Michael; Olsen, James; Piroué, Pierre; Quan, Xiaohang; Safdi, Ben; Saka, Halil; Stickland, David; Tully, Christopher; Werner, Jeremy Scott; Zuranski, Andrzej; Acosta, Jhon Gabriel; Huang, Xing Tao; Lopez, Angel; Mendez, Hector; Oliveros, Sandra; Ramirez Vargas, Juan Eduardo; Zatserklyaniy, Andriy; Alagoz, Enver; Barnes, Virgil E; Bolla, Gino; Borrello, Laura; Bortoletto, Daniela; De Mattia, Marco; Everett, Adam; Gutay, Laszlo; Hu, Zhen; Jones, Matthew; Koybasi, Ozhan; Kress, Matthew; Laasanen, Alvin T; Leonardo, Nuno; Maroussov, Vassili; Merkel, Petra; Miller, David Harry; Neumeister, Norbert; Shipsey, Ian; Silvers, David; Svyatkovskiy, Alexey; Vidal Marono, Miguel; Yoo, Hwi Dong; Zablocki, Jakub; Zheng, Yu; Guragain, Samir; Parashar, Neeti; Adair, Antony; Boulahouache, Chaouki; Ecklund, Karl Matthew; Geurts, Frank JM; Padley, Brian Paul; Redjimi, Radia; Roberts, Jay; Zabel, James; Betchart, Burton; Bodek, Arie; Chung, Yeon Sei; Covarelli, Roberto; de Barbaro, Pawel; Demina, Regina; Eshaq, Yossof; Flacher, Henning; Garcia-Bellido, Aran; Goldenzweig, Pablo; Gotra, Yury; Han, Jiyeon; Harel, Amnon; Miner, Daniel Carl; Petrillo, Gianluca; Sakumoto, Willis; Vishnevskiy, Dmitry; Zielinski, Marek; Bhatti, Anwar; Ciesielski, Robert; Demortier, Luc; Goulianos, Konstantin; Lungu, Gheorghe; Malik, Sarah; Mesropian, Christina; Arora, Sanjay; Atramentov, Oleksiy; Barker, Anthony; Contreras-Campana, Christian; Contreras-Campana, Emmanuel; Duggan, Daniel; Gershtein, Yuri; Gray, Richard; Halkiadakis, Eva; Hidas, Dean; Hits, Dmitry; Lath, Amitabh; Panwalkar, Shruti; Park, Michael; Patel, Rishi; Richards, Alan; Rose, Keith; Schnetzer, Steve; Somalwar, Sunil; Stone, Robert; Thomas, Scott; Cerizza, Giordano; Hollingsworth, Matthew; Spanier, Stefan; Yang, Zong-Chang; York, Andrew; Eusebi, Ricardo; Flanagan, Will; Gilmore, Jason; Gurrola, Alfredo; Kamon, Teruki; Khotilovich, Vadim; Montalvo, Roy; Osipenkov, Ilya; Pakhotin, Yuriy; Perloff, Alexx; Roe, Jeffrey; Safonov, Alexei; Sengupta, Sinjini; Suarez, Indara; Tatarinov, Aysen; Toback, David; Akchurin, Nural; Bardak, Cemile; Damgov, Jordan; Dudero, Phillip Russell; Jeong, Chiyoung; Kovitanggoon, Kittikul; Lee, Sung Won; Libeiro, Terence; Mane, Poonam; Roh, Youn; Sill, Alan; Volobouev, Igor; Wigmans, Richard; Yazgan, Efe; Appelt, Eric; Brownson, Eric; Engh, Daniel; Florez, Carlos; Gabella, William; Issah, Michael; Johns, Willard; Johnston, Cody; Kurt, Pelin; Maguire, Charles; Melo, Andrew; Sheldon, Paul; Snook, Benjamin; Tuo, Shengquan; Velkovska, Julia; Arenton, Michael Wayne; Balazs, Michael; Boutle, Sarah; Cox, Bradley; Francis, Brian; Goadhouse, Stephen; Goodell, Joseph; Hirosky, Robert; Ledovskoy, Alexander; Lin, Chuanzhe; Neu, Christopher; Wood, John; Yohay, Rachel; Gollapinni, Sowjanya; Harr, Robert; Karchin, Paul Edmund; Kottachchi Kankanamge Don, Chamath; Lamichhane, Pramod; Mattson, Mark; Milstène, Caroline; Sakharov, Alexandre; Anderson, Michael; Bachtis, Michail; Belknap, Donald; Bellinger, James Nugent; Carlsmith, Duncan; Cepeda, Maria; Dasu, Sridhara; Efron, Jonathan; Friis, Evan; Gray, Lindsey; Grogg, Kira Suzanne; Grothe, Monika; Hall-Wilton, Richard; Herndon, Matthew; Hervé, Alain; Klabbers, Pamela; Klukas, Jeffrey; Lanaro, Armando; Lazaridis, Christos; Leonard, Jessica; Loveless, Richard; Mohapatra, Ajit; Ojalvo, Isabel; Parker, William; Ross, Ian; Savin, Alexander; Smith, Wesley H; Swanson, Joshua; Weinberg, Marc

    2012-01-01

    The performance of tau-lepton reconstruction and identification algorithms is studied using a data sample of proton-proton collisions at sqrt(s)=7 TeV, corresponding to an integrated luminosity of 36 inverse picobarns collected with the CMS detector at the LHC. The tau leptons that decay into one or three charged hadrons, zero or more short-lived neutral hadrons, and a neutrino are identified using final-state particles reconstructed in the CMS tracker and electromagnetic calorimeter. The reconstruction efficiency of the algorithms is measured using tau leptons produced in Z-boson decays. The tau-lepton misidentification rates for jets and electrons are determined.

  9. Amino Acids in Hemagglutinin Antigenic Site B Determine Antigenic and Receptor Binding Differences between A(H3N2)v and Ancestral Seasonal H3N2 Influenza Viruses.

    Science.gov (United States)

    Wang, Xiaoquan; Ilyushina, Natalia A; Lugovtsev, Vladimir Y; Bovin, Nicolai V; Couzens, Laura K; Gao, Jin; Donnelly, Raymond P; Eichelberger, Maryna C; Wan, Hongquan

    2017-01-15

    Influenza A H3N2 variant [A(H3N2)v] viruses, which have caused human infections in the United States in recent years, originated from human seasonal H3N2 viruses that were introduced into North American swine in the mid-1990s, but they are antigenically distinct from both the ancestral and current circulating H3N2 strains. A reference A(H3N2)v virus, A/Minnesota/11/2010 (MN/10), and a seasonal H3N2 strain, A/Beijing/32/1992 (BJ/92), were chosen to determine the molecular basis for the antigenic difference between A(H3N2)v and the ancestral viruses. Viruses containing wild-type and mutant MN/10 or BJ/92 hemagglutinins (HAs) were constructed and probed for reactivity with ferret antisera against MN/10 and BJ/92 in hemagglutination inhibition assays. Among the amino acids that differ between the MN/10 and BJ/92 HAs, those in antigenic site A had little impact on the antigenic phenotype. Within antigenic site B, mutations at residues 156, 158, 189, and 193 of MN/10 HA to those in BJ/92 switched the MN/10 antigenic phenotype to that of BJ/92. Mutations at residues 156, 157, 158, 189, and 193 of BJ/92 HA to amino acids present in MN/10 were necessary for BJ/92 to become antigenically similar to MN/10. The HA amino acid substitutions responsible for switching the antigenic phenotype also impacted HA binding to sialyl receptors that are usually present in the human respiratory tract. Our study demonstrates that antigenic site B residues play a critical role in determining both the unique antigenic phenotype and receptor specificity of A(H3N2)v viruses, a finding that may facilitate future surveillance and risk assessment of novel influenza viruses.

  10. The Road to C4 Photosynthesis: Evolution of a Complex Trait via Intermediary States.

    Science.gov (United States)

    Schlüter, Urte; Weber, Andreas P M

    2016-05-01

    C4 photosynthesis enables high photosynthetic energy conversion efficiency as well as high nitrogen and water use efficiencies. Given the multitude of biochemical, structural and molecular changes in comparison with C3 photosynthesis, it appears unlikely that such a complex trait would evolve in a single step. C4 photosynthesis is therefore believed to have evolved from the ancestral C3 state via intermediary stages. Consequently, the identification and detailed characterization of plant species representing transitory states between C3 and C4 is important for the reconstruction of the sequence of evolutionary events, especially since C4 evolution occurred in very different phylogenetic backgrounds. There is also significant interest in engineering of C4 or at least C4-like elements into C3 crop plants. A detailed and mechanistic understanding of C3-C4 intermediates is likely to provide guidance for the experimental design of such approaches. Here we provide an overview on the most relevant results obtained on C3-C4 intermediates to date. Recent knowledge gains in this field will be described in more detail. We thereby concentrate especially on biochemical and physiological work. Finally, we will provide a perspective and outlook on the continued importance of research on C3-C4 intermediates.

  11. The ancestral cascades arc: Cenozoic evolution of the central Sierra Nevada (California) and the birth of the new plate boundary

    Science.gov (United States)

    Busby, C.J.; Hagan, J.C.; Putirka, K.; Pluhar, C.J.; Gans, P.B.; Wagner, D.L.; Rood, D.; DeOreo, S.B.; Skilling, I.

    2008-01-01

    We integrate new stratigraphic, structural, geochemical, geochronological, and magnetostratigraphic data on Cenozoic volcanic rocks in the central Sierra Nevada to arrive at closely inter-related new models for: (1) the paleogeography of the ancestral Cascades arc, (2) the stratigraphic record of uplift events in the Sierra Nevada, (3) the tectonic controls on volcanic styles and compositions in the arc, and (4) the birth of a new plate margin. Previous workers have assumed that the ancestral Cascades arc consisted of stratovolcanoes, similar to the modern Cascades arc, but we suggest that the arc was composed largely of numerous, very small centers, where magmas frequently leaked up strands of the Sierran frontal fault zone. These small centers erupted to produce andesite lava domes that collapsed to produce block-and-ash flows, which were reworked into paleocanyons as volcanic debris flows and streamflow deposits. Where intrusions rose up through water-saturated paleocanyon fill, they formed peperite complexes that were commonly destabilized to form debris flows. Paleocanyons that were cut into Cretaceous bedrock and filled with Oligocene to late Miocene strata not only provide a stratigraphic record of the ancestral Cascades arc volcanism, but also deep unconformities within them record tectonic events. Preliminary correlation of newly mapped unconformities and new geochronological, magnetostratigraphic, and structural data allow us to propose three episodes of Cenozoic uplift that may correspond to (1) early Miocene onset of arc magmatism (ca. 15 Ma), (2) middle Miocene onset of Basin and Range faulting (ca. 10 Ma), and (3) late Miocene arrival of the triple junction (ca. 6 Ma), perhaps coinciding with a second episode of rapid extension on the range front. Oligocene ignimbrites, which erupted from calderas in central Nevada and filled Sierran paleocanyons, were deeply eroded during the early Miocene uplift event. The middle Miocene event is recorded by growth

  12. Genesis of the vertebrate FoxP subfamily member genes occurred during two ancestral whole genome duplication events.

    Science.gov (United States)

    Song, Xiaowei; Tang, Yezhong; Wang, Yajun

    2016-08-22

    The vertebrate FoxP subfamily genes play important roles in the construction of essential functional modules involved in physiological and developmental processes. To explore the adaptive evolution of functional modules associated with the FoxP subfamily member genes, it is necessary to study the gene duplication process. We detected four member genes of the FoxP subfamily in sea lampreys (a representative species of jawless vertebrates) through genome screenings and phylogenetic analyses. Reliable paralogons (i.e. paralogous chromosome segments) have rarely been detected in scaffolds of FoxP subfamily member genes in sea lampreys due to the considerable existence of HTH_Tnp_Tc3_2 transposases. However, these transposases did not alter gene numbers of the FoxP subfamily in sea lampreys. The coincidence between the "1-4" gene duplication pattern of FoxP subfamily genes from invertebrates to vertebrates and two rounds of ancestral whole genome duplication (1R- and 2R-WGD) events reveal that the FoxP subfamily of vertebrates was quadruplicated in the 1R- and 2R-WGD events. Furthermore, we deduced that a synchronous gene duplication process occurred for the FoxP subfamily and for three linked gene families/subfamilies (i.e. MIT family, mGluR group III and PLXNA subfamily) in the 1R- and 2R-WGD events using phylogenetic analyses and mirror-dendrogram methods (i.e. algorithms to test protein-protein interactions). Specifically, the ancestor of FoxP1 and FoxP3 and the ancestor of FoxP2 and FoxP4 were generated in 1R-WGD event. In the subsequent 2R-WGD event, these two ancestral genes were changed into FoxP1, FoxP2, FoxP3 and FoxP4. The elucidation of these gene duplication processes shed light on the phylogenetic relationships between functional modules of the FoxP subfamily member genes.

  13. Reconstructing the Origin of Oxygenic Photosynthesis: Do Assembly and Photoactivation Recapitulate Evolution?

    Science.gov (United States)

    Cardona, Tanai

    2016-01-01

    Due to the great abundance of genomes and protein structures that today span a broad diversity of organisms, now more than ever before, it is possible to reconstruct the molecular evolution of protein complexes at an incredible level of detail. Here, I recount the story of oxygenic photosynthesis or how an ancestral reaction center was transformed into a sophisticated photochemical machine capable of water oxidation. First, I review the evolution of all reaction center proteins in order to highlight that Photosystem II and Photosystem I, today only found in the phylum Cyanobacteria, branched out very early in the history of photosynthesis. Therefore, it is very unlikely that they were acquired via horizontal gene transfer from any of the described phyla of anoxygenic phototrophic bacteria. Second, I present a new evolutionary scenario for the origin of the CP43 and CP47 antenna of Photosystem II. I suggest that the antenna proteins originated from the remodeling of an entire Type I reaction center protein and not from the partial gene duplication of a Type I reaction center gene. Third, I highlight how Photosystem II and Photosystem I reaction center proteins interact with small peripheral subunits in remarkably similar patterns and hypothesize that some of this complexity may be traced back to the most ancestral reaction center. Fourth, I outline the sequence of events that led to the origin of the Mn4CaO5 cluster and show that the most ancestral Type II reaction center had some of the basic structural components that would become essential in the coordination of the water-oxidizing complex. Finally, I collect all these ideas, starting at the origin of the first reaction center proteins and ending with the emergence of the water-oxidizing cluster, to hypothesize that the complex and well-organized process of assembly and photoactivation of Photosystem II recapitulate evolutionary transitions in the path to oxygenic photosynthesis.

  14. Reconstructing the origin of oxygenic photosynthesis: do assembly and photoactivation recapitulate evolution?

    Directory of Open Access Journals (Sweden)

    Tanai eCardona

    2016-03-01

    Full Text Available Due to the great abundance of genomes and protein structures that today span a broad diversity of organisms, now more than ever before, it is possible to reconstruct the molecular evolution of protein complexes at an incredible level of detail. Here, I recount the story of oxygenic photosynthesis or how an ancestral reaction center was transformed into a sophisticated photochemical machine capable of water oxidation. First, I review the evolution of all reaction center proteins in order to highlight that Photosystem II and Photosystem I, today only found in the phylum Cyanobacteria, branched out very early in the history of photosynthesis. Therefore, it is very unlikely that they were acquired via horizontal gene transfer from any of the described phyla of anoxygenic phototrophic bacteria. Second, I present a new evolutionary scenario for the origin of the CP43 and CP47 antenna of Photosystem II. I suggest that the antenna proteins originated from the remodeling of an entire Type I reaction center protein and not from the partial gene duplication of a Type I reaction center gene. Third, I highlight how Photosystem II and Photosystem I reaction center proteins interact with small peripheral subunits in remarkably similar patterns and hypothesize that some of this complexity may be traced back to the most ancestral reaction center. Fourth, I outline the sequence of events that led to the origin of the Mn4CaO5 cluster and show that the most ancestral Type II reaction center had some of the basic structural components that would become essential in the coordination of the water-oxidizing complex. Finally, I collect all these ideas, starting at the origin of the first reaction center proteins and ending with the emergence of the water-oxidizing cluster, to hypothesize that the complex and well-organized process of assembly and photoactivation of Photosystem II recapitulate evolutionary transitions in the path to oxygenic photosynthesis.

  15. Reconstruction in Fourier space

    Science.gov (United States)

    Burden, A.; Percival, W. J.; Howlett, C.

    2015-10-01

    We present a fast iterative fast Fourier transform (FFT) based reconstruction algorithm that allows for non-parallel redshift-space distortions (RSDs). We test our algorithm on both N-body dark matter simulations and mock distributions of galaxies designed to replicate galaxy survey conditions. We compare solenoidal and irrotational components of the redshift distortion and show that an approximation of this distortion leads to a better estimate of the real-space potential (and therefore faster convergence) than ignoring the RSD when estimating the displacement field. Our iterative reconstruction scheme converges in two iterations for the mock samples corresponding to Baryon Oscillation Spectroscopic Survey CMASS Data Release 11 when we start with an approximation of the RSD. The scheme takes six iterations when the initial estimate, measured from the redshift-space overdensity, has no RSD correction. Slower convergence would be expected for surveys covering a larger angle on the sky. We show that this FFT based method provides a better estimate of the real-space displacement field than a configuration space method that uses finite difference routines to compute the potential for the same grid resolution. Finally, we show that a lognormal transform of the overdensity, used as a proxy for the linear overdensity, is beneficial in estimating the full displacement field from a dense sample of tracers. However, the lognormal transform of the overdensity does not perform well when estimating the displacements from sparser simulations with a more realistic galaxy density.

  16. LHCb; LHCb Jet Reconstruction

    CERN Multimedia

    Augusto, O

    2012-01-01

    The Large Hadron Collider (LHC) is the most powerful particle accelerator in the world. It has been designed to collide proton beams at an energy up to 14 TeV in the center of mass. In 2011, the data taking was done with a center of mass energy of 7 TeV, the instant luminosity has reached values greater than $4 \\times 10^{32} cm^{-2} s^{-1}$ and the integrated luminosity reached the value of 1.02 $fb^{-1}$ on the LHCb. The jet reconstruction is fundamental to observe events that can be used to test pertubative QCD (pQCD). It also provides a way to observe standard model channels and searches for new physics like SUSY. The anti-kt algorithm is a jet reconstruction algorithm that is based on the distance of the particles on the space $\\eta \\times \\phi$ and on the transverse momentum of particles. To maximize the energy resolution all information about the trackers and the calo...

  17. Reconstructing Experiences through Sketching

    CERN Document Server

    Karapanos, Evangelos; Hassenzahl, Marc

    2009-01-01

    This paper presents iScale, a survey tool that aims at eliciting users' experiences with a product from memory. iScale employs sketching in imposing a process in the reconstruction of one's experiences. Two versions of iScale, the Constructive and the Value-Account iScale, were motivated by two distinct theories on how people reconstruct emotional experiences from memory. These two versions were tested in two separate studies. Study 1 aimed at providing qualitative insight into the use of iScale and compared its performance to that of free-hand sketching. Study 2 compared the two iScale versions to a control condition: that of reporting one's experiences without employing any form of sketching. Significant differences between iScale and the "no-sketching" tool were found. Overall, iScale resulted in a) an increase in the number of experience reports that subjects provided, b) an increase in the amount of contextual information for the reported experiences, and c) an increase in subjects' accuracy in recalling...

  18. Biomaterials for craniofacial reconstruction

    Directory of Open Access Journals (Sweden)

    Neumann, Andreas

    2009-01-01

    Full Text Available Biomaterials for reconstruction of bony defects of the skull comprise of osteosynthetic materials applied after osteotomies or traumatic fractures and materials to fill bony defects which result from malformation, trauma or tumor resections. Other applications concern functional augmentations for dental implants or aesthetic augmentations in the facial region.For ostheosynthesis, mini- and microplates made from titanium alloys provide major advantages concerning biocompatibility, stability and individual fitting to the implant bed. The necessity of removing asymptomatic plates and screws after fracture healing is still a controversial issue. Risks and costs of secondary surgery for removal face a low rate of complications (due to corrosion products when the material remains in situ. Resorbable osteosynthesis systems have similar mechanical stability and are especially useful in the growing skull.The huge variety of biomaterials for the reconstruction of bony defects makes it difficult to decide which material is adequate for which indication and for which site. The optimal biomaterial that meets every requirement (e.g. biocompatibility, stability, intraoperative fitting, product safety, low costs etc. does not exist. The different material types are (autogenic bone and many alloplastics such as metals (mainly titanium, ceramics, plastics and composites. Future developments aim to improve physical and biological properties, especially regarding surface interactions. To date, tissue engineered bone is far from routine clinical application.

  19. Quantum interferences reconstruction with low homodyne detection efficiency

    Energy Technology Data Exchange (ETDEWEB)

    Esposito, Martina; Randi, Francesco [Universita degli studi di Trieste, Dipartimento di Fisica, Trieste (Italy); Titimbo, Kelvin; Zimmermann, Klaus; Benatti, Fabio [Universita degli studi di Trieste, Dipartimento di Fisica, Trieste (Italy); Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, Trieste (Italy); Kourousias, Georgios; Curri, Alessio [Sincrotrone Trieste S.C.p.A., Trieste (Italy); Floreanini, Roberto [Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, Trieste (Italy); Parmigiani, Fulvio [Universita degli studi di Trieste, Dipartimento di Fisica, Trieste (Italy); Sincrotrone Trieste S.C.p.A., Trieste (Italy); University of Cologne, Institute of Physics II, Cologne (Germany); Fausti, Daniele [Universita degli studi di Trieste, Dipartimento di Fisica, Trieste (Italy); Sincrotrone Trieste S.C.p.A., Trieste (Italy)

    2016-12-15

    Optical homodyne tomography consists in reconstructing the quantum state of an optical field from repeated measurements of its amplitude at different field phases (homodyne data). The experimental noise, which unavoidably affects the homodyne data, leads to a detection efficiency η<1. The problem of reconstructing quantum states from noisy homodyne data sets prompted an intense scientific debate about the presence or absence of a lower homodyne efficiency bound (η>0.5) below which quantum features, like quantum interferences, cannot be retrieved. Here, by numerical experiments, we demonstrate that quantum interferences can be effectively reconstructed also for low homodyne detection efficiency. In particular, we address the challenging case of a Schroedinger cat state and test the minimax and adaptive Wigner function reconstruction technique by processing homodyne data distributed according to the chosen state but with an efficiency η>0.5. By numerically reproducing the Schroedinger's cat interference pattern, we give evidence that quantum state reconstruction is actually possible in these conditions, and provide a guideline for handling optical tomography based on homodyne data collected by low efficiency detectors. (orig.)

  20. Virtual 3-D Facial Reconstruction

    Directory of Open Access Journals (Sweden)

    Martin Paul Evison

    2000-06-01

    Full Text Available Facial reconstructions in archaeology allow empathy with people who lived in the past and enjoy considerable popularity with the public. It is a common misconception that facial reconstruction will produce an exact likeness; a resemblance is the best that can be hoped for. Research at Sheffield University is aimed at the development of a computer system for facial reconstruction that will be accurate, rapid, repeatable, accessible and flexible. This research is described and prototypical 3-D facial reconstructions are presented. Interpolation models simulating obesity, ageing and ethnic affiliation are also described. Some strengths and weaknesses in the models, and their potential for application in archaeology are discussed.

  1. Exercises in PET Image Reconstruction

    Science.gov (United States)

    Nix, Oliver

    These exercises are complementary to the theoretical lectures about positron emission tomography (PET) image reconstruction. They aim at providing some hands on experience in PET image reconstruction and focus on demonstrating the different data preprocessing steps and reconstruction algorithms needed to obtain high quality PET images. Normalisation, geometric-, attenuation- and scatter correction are introduced. To explain the necessity of those some basics about PET scanner hardware, data acquisition and organisation are reviewed. During the course the students use a software application based on the STIR (software for tomographic image reconstruction) library 1,2 which allows them to dynamically select or deselect corrections and reconstruction methods as well as to modify their most important parameters. Following the guided tutorial, the students get an impression on the effect the individual data precorrections have on image quality and what happens if they are forgotten. Several data sets in sinogram format are provided, such as line source data, Jaszczak phantom data sets with high and low statistics and NEMA whole body phantom data. The two most frequently used reconstruction algorithms in PET image reconstruction, filtered back projection (FBP) and the iterative OSEM (ordered subset expectation maximation) approach are used to reconstruct images. The exercise should help the students gaining an understanding what the reasons for inferior image quality and artefacts are and how to improve quality by a clever choice of reconstruction parameters.

  2. Resorbable extracellular matrix grafts in urologic reconstruction

    Directory of Open Access Journals (Sweden)

    Richard A. Santucci

    2005-06-01

    Full Text Available PURPOSE: There is an increasingly large body of literature concerning tissue-engineering products that may be used in urology. Some of these are quite complex (such as multilayer patient-specific cell-seeded implants yet the most simple and successful products to date are also the most uncomplicated: resorbable acellular extra-cellular matrices (ECMs harvested from animals. ECMs have been used in a variety of difficult urologic reconstruction problems, and this review is intended to summarize this complex literature for the practicing urologist. METHODS: Medline search of related terms such as "SIS, small intestinal submucosa, ECM, extracellular matrix, acellular matrix and urologic reconstruction". Manuscripts missed in the initial search were taken from the bibliographies of the primary references. RESULTS: Full review of potential clinical uses of resorbable extra-cellular matrices in urologic reconstruction. CONCLUSIONS: Currently, the "state of the art" in tissue engineering solutions for urologic reconstruction means resorbable acellular xenograft matrices. They show promise when used as a pubovaginal sling or extra bolstering layers in ureteral or urethral repairs, although recent problems with inflammation following 8-ply pubovaginal sling use and failures after 1- and 4-ply SIS repair of Peyronie's disease underscore the need for research before wide adoption. Preliminary data is mixed concerning the potential for ECM urethral patch graft, and more data is needed before extended uses such as bladder augmentation and ureteral replacement are contemplated. The distant future of ECMs in urology likely will include cell-seeded grafts with the eventual hope of producing "off the shelf" replacement materials. Until that day arrives, ECMs only fulfill some of the requirements for the reconstructive urologist.

  3. Diffusion archeology for diffusion progression history reconstruction.

    Science.gov (United States)

    Sefer, Emre; Kingsford, Carl

    2016-11-01

    Diffusion through graphs can be used to model many real-world processes, such as the spread of diseases, social network memes, computer viruses, or water contaminants. Often, a real-world diffusion cannot be directly observed while it is occurring - perhaps it is not noticed until some time has passed, continuous monitoring is too costly, or privacy concerns limit data access. This leads to the need to reconstruct how the present state of the diffusion came to be from partial diffusion data. Here, we tackle the problem of reconstructing a diffusion history from one or more snapshots of the diffusion state. This ability can be invaluable to learn when certain computer nodes are infected or which people are the initial disease spreaders to control future diffusions. We formulate this problem over discrete-time SEIRS-type diffusion models in terms of maximum likelihood. We design methods that are based on submodularity and a novel prize-collecting dominating-set vertex cover (PCDSVC) relaxation that can identify likely diffusion steps with some provable performance guarantees. Our methods are the first to be able to reconstruct complete diffusion histories accurately in real and simulated situations. As a special case, they can also identify the initial spreaders better than the existing methods for that problem. Our results for both meme and contaminant diffusion show that the partial diffusion data problem can be overcome with proper modeling and methods, and that hidden temporal characteristics of diffusion can be predicted from limited data.

  4. The minute brain of the copepod Tigriopus californicus supports a complex ancestral ground pattern of the tetraconate cerebral nervous systems.

    Science.gov (United States)

    Andrew, David R; Brown, Sheena M; Strausfeld, Nicholas J

    2012-10-15

    Copepods are a diverse and ecologically crucial group of minute crustaceans that are relatively neglected in terms of studies on nervous system organization. Recently, morphological neural characters have helped clarify evolutionary relationships within Arthropoda, particularly among Tetraconata (i.e., crustaceans and hexapods), and indicate that copepods occupy an important phylogenetic position relating to both Malacostraca and Hexapoda. This taxon therefore provides the opportunity to evaluate those neural characters common to these two clades likely to be results of shared ancestry (homology) versus convergence (homoplasy). Here we present an anatomical characterization of the brain and central nervous system of the well-studied harpacticoid copepod species Tigriopus californicus. We show that this species is endowed with a complex brain possessing a central complex comprising a protocerebral bridge and central body. Deutocerebral glomeruli are supplied by the antennular nerves, and a lateral protocerebral olfactory neuropil corresponds to the malacostracan hemiellipsoid body. Glomeruli contain synaptic specializations comparable to the presynaptic "T-bars" typical of dipterous insects, including Drosophila melanogaster. Serotonin-like immunoreactivity pervades the brain and ventral nervous system, with distinctive deutocerebral distributions. The present observations suggest that a suite of morphological characters typifying the Tigriopus brain reflect a ground pattern organization of an ancestral Tetraconata, which possessed an elaborate and structurally differentiated nervous system.

  5. Ancestral association between HLA and HFE H63D and C282Y gene mutations from northwest Colombia

    Directory of Open Access Journals (Sweden)

    Libia M Rodriguez

    2015-03-01

    Full Text Available A significant association between HFE gene mutations and the HLA-A*03-B*07 and HLA-A*29-B*44 haplotypes has been reported in the Spanish population. It has been proposed that these mutations are probably connected with Celtic and North African ancestry, respectively. We aimed to find the possible ancestral association between HLA alleles and haplotypes associated with the HFE gene (C282Y and H63D mutations in 214 subjects from Antioquia, Colombia. These were 18 individuals with presumed hereditary hemochromatosis (“HH” and 196 controls. The HLA-B*07 allele was in linkage disequilibrium (LD with C282Y, while HLA-A*23, A*29, HLA-B*44, and B*49 were in LD with H63D. Altogether, our results show that, although the H63D mutation is more common in the Antioquia population, it is not associated with any particular HLA haplotype, whereas the C282Y mutation is associated with HLA-A*03-B*07, this supporting a northern Spaniard ancestry.

  6. Natural environments, ancestral diets, and microbial ecology: is there a modern "paleo-deficit disorder"? Part II.

    Science.gov (United States)

    Logan, Alan C; Katzman, Martin A; Balanzá-Martínez, Vicent

    2015-03-10

    Famed microbiologist René J. Dubos (1901-1982) was an early pioneer in the developmental origins of health and disease (DOHaD) construct. In the 1960s, he conducted groundbreaking research concerning the ways in which early-life experience with nutrition, microbiota, stress, and other environmental variables could influence later-life health outcomes. He recognized the co-evolutionary relationship between microbiota and the human host. Almost 2 decades before the hygiene hypothesis, he suggested that children in developed nations were becoming too sanitized (vs. our ancestral past) and that scientists should determine whether the childhood environment should be "dirtied up in a controlled manner." He also argued that oft-celebrated growth chart increases via changes in the global food supply and dietary patterns should not be equated to quality of life and mental health. Here in the second part of our review, we reflect the words of Dubos off contemporary research findings in the areas of diet, the gut-brain-axis (microbiota and anxiety and depression) and microbial ecology. Finally, we argue, as Dubos did 40 years ago, that researchers should more closely examine the relevancy of silo-sequestered, reductionist findings in the larger picture of human quality of life. In the context of global climate change and the epidemiological transition, an allergy epidemic and psychosocial stress, our review suggests that discussions of natural environments, urbanization, biodiversity, microbiota, nutrition, and mental health, are often one in the same.

  7. Evolution of the human diet: linking our ancestral diet to modern functional foods as a means of chronic disease prevention.

    Science.gov (United States)

    Jew, Stephanie; AbuMweis, Suhad S; Jones, Peter J H

    2009-10-01

    The evolution of the human diet over the past 10,000 years from a Paleolithic diet to our current modern pattern of intake has resulted in profound changes in feeding behavior. Shifts have occurred from diets high in fruits, vegetables, lean meats, and seafood to processed foods high in sodium and hydrogenated fats and low in fiber. These dietary changes have adversely affected dietary parameters known to be related to health, resulting in an increase in obesity and chronic disease, including cardiovascular disease (CVD), diabetes, and cancer. Some intervention trials using Paleolithic dietary patterns have shown promising results with favorable changes in CVD and diabetes risk factors. However, such benefits may be offset by disadvantages of the Paleolithic diet, which is low in vitamin D and calcium and high in fish potentially containing environmental toxins. More advantageous would be promotion of foods and food ingredients from our ancestral era that have been shown to possess health benefits in the form of functional foods. Many studies have investigated the health benefits of various functional food ingredients, including omega-3 fatty acids, polyphenols, fiber, and plant sterols. These bioactive compounds may help to prevent and reduce incidence of chronic diseases, which in turn could lead to health cost savings ranging from $2 to $3 billion per year as estimated by case studies using omega-3 and plant sterols as examples. Thus, public health benefits should result from promotion of the positive components of Paleolithic diets as functional foods.

  8. Food-Nonfood Discrimination in Ancestral Vertebrates: Gamete Cannibalism and the Origin of the Adaptive Immune System.

    Science.gov (United States)

    Corcos, D

    2015-11-01

    Adaptive immunity is a complex system that appeared twice in vertebrates (in gnathostomes and in jawless fish) although it is not required for invertebrate defence. The adaptive immune system is tightly associated with self-non-self discrimination, and it is now clear that this interplay is not limited to the prevention of autoreactivity. Micro-organisms are usually considered for their pathogenicity or symbiotic ability, but, for most small metazoans, they mainly constitute food. Vertebrates are characterized by feeding by predation on larger preys, when compared to their ancestors who were filter feeders and ate micro-organisms. Predation gives a strong selective advantage, not only due to the availability of new food resources but also by the ability to eliminate competitors for environmental resources (intraguild predation (IGP)). Unlike size-structured IGP, intraspecific predation of juveniles, zygotes or gametes can be detrimental for species fitness in some circumstances. The ability of individuals to recognize highly polymorphic molecules on the surface of gametes present in the plankton and so distinguish self versus non-self gametes might have constituted a strong selective advantage in intraspecific competition. Here, I propose the theory that the capacity to rearrange receptors has been selected in ancestral vertebrates as a consequence of this strong need for discriminating between hetero-cannibalism versus filial cannibalism. This evolutionary origin sheds light on presently unexplained features of the immune system, including the existence of regulatory T cells and of non-pathogenic natural autoimmunity.

  9. Ancestral variation and the potential for genetic accommodation in larval amphibians: implications for the evolution of novel feeding strategies.

    Science.gov (United States)

    Ledon-Rettig, Cris C; Pfennig, David W; Nascone-Yoder, Nanette

    2008-01-01

    Few studies provide empirical evidence for phenotypic plasticity's role in the evolution of novel traits. One way to do so is to test whether latent plasticity is present in an ancestor that can be refined, enhanced, or diminished by selection in derived taxa (through "genetic accommodation"), thereby producing novel traits. Here, we evaluated whether gut plasticity preceded and promoted the evolution of a novel feeding strategy in spadefoot toad tadpoles. We studied Scaphiopus couchii, whose tadpoles develop an elongate gut and consume only detritus, and two derived species, Spea multiplicata and Sp. bombifrons, whose tadpoles also express a novel, short-gut phenotype in response to a novel resource (anostracan shrimp). Consistent with the expectations of plasticity-mediated trait evolution, we found that shrimp induced a range of phenotypes in Scaphiopus that were not produced with detritus. This plasticity was either suppressed or exaggerated in Spea depending on whether the induced phenotypes were adaptive. Moreover, in contrast to its effects on morphology, shrimp induced little or no functional plasticity, as assessed by gut cell proliferation, in Scaphiopus. Shrimp did, however, induce substantial proliferation in Sp. bombifrons, the species that consumes the most shrimp and that produces the short-gut phenotype the most frequently. Thus, if Spea had ancestral morphological plasticity in response to a novel diet, their shrimp-induced short-gut morphology may have undergone subsequent genetic accommodation that improved its functionality. Hence, diet-induced phenotypic plasticity may have preceded and even promoted the evolution of a novel phenotype.

  10. Facial anatomy of Victoriapithecus and its relevance to the ancestral cranial morphology of Old World monkeys and apes.

    Science.gov (United States)

    Benefit, B R; McCrossin, M L

    1993-11-01

    Recently discovered craniofacial fossils of the middle Miocene cercopithecoid Victoriapithecus are described. The frontal, zygomatic, maxilla, and premaxilla anatomy differ from the previously proposed colobine-like ancestral cercopithecoid morphotype in several significant respects. This morphotype was based on the assumption that features held in common by subordinate hominoid and cercopithecoid morphotypes (Colobinae and Hylobatidae) are primitive for Old World monkeys. Cranial similarities between Victoriapithecus, which represents the sister-group of both colobine and cercopithecine monkeys, and the shorter-snouted Cercopithecinae (Macaca and Cercopithecus) indicate that the last common ancestor of Old World monkeys possessed the following features: a narrow interorbital septum, moderately long snout, moderately long and anteriorly tapering premaxilla, large procumbent upper central incisors set anterior to and with longer roots than lateral incisors, moderately tall face below the orbits, teardrop-shaped nasal aperture of low height and moderate width, and probably long and narrow nasal bones. The Victoriapithecus cranium is also characterized by features not present in modern cercopithecids. These include a deep malar region of the zygomatic and the presence of a frontal trigon due to the occurrence of temporal lines that merge with supraorbital costae close to the midline of each orbit and converge anterior to bregma. These features are interpreted as primitive retentions from the basal catarrhine condition as indicated by the occurrence of these features among primitive catarrhines (Aegyptopithecus) and Miocene hominoids (Afropithecus).

  11. Natural epigenetic protection against the I-factor, a Drosophila LINE retrotransposon, by remnants of ancestral invasions.

    Science.gov (United States)

    Dramard, Xavier; Heidmann, Thierry; Jensen, Silke

    2007-03-21

    Transposable elements are major components of most eukaryotic genomes. Such sequences are generally defective for transposition and have little or no coding capacity. Because transposition can be highly mutagenic, mobile elements that remain functional are tightly repressed in all living species. Drosophila pericentromeric heterochromatin naturally contains transposition-defective, non-coding derivatives of a LINE retrotransposon related to the I-factor. The I-factor is a good model to study the regulation of transposition in vivo because, under specific conditions, current functional copies of this mobile element can transpose at high frequency, specifically in female germ cells, with deleterious effects including female sterility. However, this high transpositional activity becomes spontaneously repressed upon ageing or heat treatment, by a maternally transmitted, transgenerational epigenetic mechanism of unknown nature. We have analyzed, by quantitative real time RT-PCR, the RNA profile of the transposition-defective I-related sequences, in the Drosophila ovary during ageing and upon heat treatment, and also in female somatic tissues and in males, which are not permissive for I-factor transposition. We found evidence for a role of transcripts from these ancestral remnants in the natural epigenetic protection of the Drosophila melanogaster genome against the deleterious effects of new invasions by functional I-factors. These results provide a molecular basis for a probably widespread natural protection against transposable elements by persisting vestiges of ancient invasions.

  12. What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy.

    Science.gov (United States)

    Chavan, Arun Rajendra; Bhullar, Bhart-Anjan S; Wagner, Günter P

    2016-04-01

    In human and mouse, decidual stromal cells (DSC) are necessary for the establishment (implantation) and the maintenance of pregnancy by preventing inflammation and the immune rejection of the semi-allograft conceptus. DSC originated along the stem lineage of eutherian mammals, coincidental with the origin of invasive placentation. Surprisingly, in many eutherian lineages decidual cells are lost after the implantation phase of pregnancy, making it unlikely that DSC are necessary for the maintenance of pregnancy in these animals. In order to understand this variation, we review the literature on the fetal-maternal interface in all major eutherian clades Euarchontoglires, Laurasiatheria, Xenarthra and Afrotheria, as well as the literature about the ancestral eutherian species. We conclude that maintaining pregnancy may not be a shared derived function of DSC among all eutherian mammals. Rather, we propose that DSC originated to manage the inflammatory reaction associated with invasive implantation. We envision that this happened in a stem eutherian that had invasive placenta but still a short gestation. We further propose that extended gestation evolved independently in the major eutherian clades explaining why the major lineages of eutherian mammals differ with respect to the mechanisms maintaining pregnancy.

  13. Hox Proteins Display a Common and Ancestral Ability to Diversify Their Interaction Mode with the PBC Class Cofactors

    Science.gov (United States)

    Hudry, Bruno; Remacle, Sophie; Delfini, Marie-Claire; Rezsohazy, René; Graba, Yacine; Merabet, Samir

    2012-01-01

    Hox transcription factors control a number of developmental processes with the help of the PBC class proteins. In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide (HX). This paradigm is at the basis of the vast majority of experimental approaches dedicated to the study of Hox protein function. Here we questioned the unique and general use of the HX for PBC recruitment by using the Bimolecular Fluorescence Complementation (BiFC) assay. This method allows analyzing Hox-PBC interactions in vivo and at a genome-wide scale. We found that the HX is dispensable for PBC recruitment in the majority of investigated Drosophila and mouse Hox proteins. We showed that HX-independent interaction modes are uncovered by the presence of Meis class cofactors, a property which was also observed with Hox proteins of the cnidarian sea anemone Nematostella vectensis. Finally, we revealed that paralog-specific motifs convey major PBC-recruiting functions in Drosophila Hox proteins. Altogether, our results highlight that flexibility in Hox-PBC interactions is an ancestral and evolutionary conserved character, which has strong implications for the understanding of Hox protein functions during normal development and pathologic processes. PMID:22745600

  14. Hox proteins display a common and ancestral ability to diversify their interaction mode with the PBC class cofactors.

    Directory of Open Access Journals (Sweden)

    Bruno Hudry

    Full Text Available Hox transcription factors control a number of developmental processes with the help of the PBC class proteins. In vitro analyses have established that the formation of Hox/PBC complexes relies on a short conserved Hox protein motif called the hexapeptide (HX. This paradigm is at the basis of the vast majority of experimental approaches dedicated to the study of Hox protein function. Here we questioned the unique and general use of the HX for PBC recruitment by using the Bimolecular Fluorescence Complementation (BiFC assay. This method allows analyzing Hox-PBC interactions in vivo and at a genome-wide scale. We found that the HX is dispensable for PBC recruitment in the majority of investigated Drosophila and mouse Hox proteins. We showed that HX-independent interaction modes are uncovered by the presence of Meis class cofactors, a property which was also observed with Hox proteins of the cnidarian sea anemone Nematostella vectensis. Finally, we revealed that paralog-specific motifs convey major PBC-recruiting functions in Drosophila Hox proteins. Altogether, our results highlight that flexibility in Hox-PBC interactions is an ancestral and evolutionary conserved character, which has strong implications for the understanding of Hox protein functions during normal development and pathologic processes.

  15. 论家族祠堂文化的教育与传承--以博白客家家族祠堂为例%Cultural Education and Inheritance of Family Ancestral Temple-- Take Bobai Hakka Family Ancestral Temple County as an Example

    Institute of Scientific and Technical Information of China (English)

    李春霞; 程丽秋

    2016-01-01

    祠堂是家族的中心和家族文化的载体,它践行着家族文化的教育与传承的重要使命。博白县客家的家族文化氛围特别浓厚,本文以其为例,论述博白客家祠堂文化及其教育与传承的方式。家族祠堂文化对可塑性极强的儿童的影响方式有环境熏陶、榜样示范以及教育期望等等,即论述家族祠堂文化的教育与传承,需要家族充分利用祠堂这个载体进行家族教育,以实现祠堂教育功能最大化的发挥。%Family ancestral temple is the center of the family and the isotopic carrier of family culture. It sustains the responsibility of the education and inheritance of family culture. Bobai county is selected as an example because Bobai Hakka people have a strong concept of family. This paper discusses culture, education and inheritance of the Hakka family ancestral temple culture in Bobai county. The culture of family ancestral temple has an influence on educable child and the influence way include environmental edifying, model demonstrating and educational expectation, etc. It needs the family to make full use of the isotopic carrier of the ancestral temple to educate the descendants when discussing the cultural education and inheritance of family ancestral temple. It aims to maximize the educational function of ancestral temple education.

  16. Nonparametric dark energy reconstruction from supernova data.

    Science.gov (United States)

    Holsclaw, Tracy; Alam, Ujjaini; Sansó, Bruno; Lee, Herbert; Heitmann, Katrin; Habib, Salman; Higdon, David

    2010-12-10

    Understanding the origin of the accelerated expansion of the Universe poses one of the greatest challenges in physics today. Lacking a compelling fundamental theory to test, observational efforts are targeted at a better characterization of the underlying cause. If a new form of mass-energy, dark energy, is driving the acceleration, the redshift evolution of the equation of state parameter w(z) will hold essential clues as to its origin. To best exploit data from observations it is necessary to develop a robust and accurate reconstruction approach, with controlled errors, for w(z). We introduce a new, nonparametric method for solving the associated statistical inverse problem based on Gaussian process modeling and Markov chain Monte Carlo sampling. Applying this method to recent supernova measurements, we reconstruct the continuous history of w out to redshift z=1.5.

  17. Biomatrices for bladder reconstruction.

    Science.gov (United States)

    Lin, Hsueh-Kung; Madihally, Sundar V; Palmer, Blake; Frimberger, Dominic; Fung, Kar-Ming; Kropp, Bradley P

    2015-03-01

    There is a demand for tissue engineering of the bladder needed by patients who experience a neurogenic bladder or idiopathic detrusor overactivity. To avoid complications from augmentation cystoplasty, the field of tissue engineering seeks optimal scaffolds for bladder reconstruction. Naturally derived biomaterials as well as synthetic and natural polymers have been explored as bladder substitutes. To improve regenerative properties, these biomaterials have been conjugated with functional molecules, combined with nanotechology, or seeded with exogenous cells. Although most studies reported complete and functional bladder regeneration in small-animal models, results from large-animal models and human clinical trials varied. For functional bladder regeneration, procedures for biomaterial fabrication, incorporation of biologically active agents, introduction of nanotechnology, and application of stem-cell technology need to be standardized. Advanced molecular and medical technologies such as next generation sequencing and magnetic resonance imaging can be introduced for mechanistic understanding and non-invasive monitoring of regeneration processes, respectively.

  18. CRUCIATE LIGAMENT RECONSTRUCTION

    Directory of Open Access Journals (Sweden)

    A. V. Korolev

    2016-01-01

    Full Text Available Purpose: To evaluate long-term results of meniscal repair during arthroscopic ACL reconstruction.Materials and methods: 45 patients who underwent meniscal repair during arthroscopic ACL reconstruction between 2007 and 2013 by the same surgeon were included in the study. In total, fifty meniscus were repaired (26 medial and 24 lateral. Procedures included use of one up to four Fast-Fix implants (Smith & Nephew. In five cases both medial and lateral meniscus were repaired. Cincinnati, IKDC and Lysholm scales were used for long-term outcome analysis.Results: 19 male and 26 female patients were included in the study aging from 15 to 59 years (mean age 33,2±1,5. Median time from injury to surgical procedure was zero months (ranging zero to one. Mean time from surgery to scale analysis was 55,9±3 months (ranged 20-102. Median Cincinnati score was 97 (ranged 90-100, with excellent results in 93% of cases (43 patients and good results in 7% (3 patients. Median IKDC score was 90,8 (ranged 86,2-95,4, with excellent outcomes in 51% of cases (23 patients, good in 33% (15 patients and satisfactory in 16% (7 patients. Median Lysholm score was 95 (ranged 90-100, with excellent outcomes in 76% of cases (34 patients and good in 24% (11 patients. Authors identified no statistical differences when comparing survey results in age, sex and time from trauma to surgery.Conclusions: Results of the present study match the data from orthopedic literature that prove meniscal repair as a safe and efficient procedure with good and excellent outcomes. All-inside meniscal repair can be used irrespectively of patients' age and is efficient even in case of delayed procedures.

  19. Ptychographic reconstruction of attosecond pulses

    CERN Document Server

    Lucchini, M; Ludwig, A; Gallmann, L; Keller, U; Feurer, T

    2015-01-01

    We demonstrate a new attosecond pulse reconstruction modality which uses an algorithm that is derived from ptychography. In contrast to other methods, energy and delay sampling are not correlated, and as a result, the number of electron spectra to record is considerably smaller. Together with the robust algorithm, this leads to a more precise and fast convergence of the reconstruction.

  20. The Challenge of Reconstructing "Failed" States Le défi de la reconstruction des États «faillis» : Quelles leçons tirer des erreurs commises en Afghanistan ? El desafío de la reconstrucción de estados fracasados

    Directory of Open Access Journals (Sweden)

    Serge Michailof

    2000-12-01

    Full Text Available While international aid has significantly increased its support for the reconstruction of fragile countries and "failed" states emerging from severe crises or civil war,  we begin today to realize that the disaster in Afghanistan is largely due to mistakes made by the Western coalition, and in particular, to the disorganization of its development support efforts in this country. In this uncompromising article, Serge Michailof undertakes a systematic analysis of international donors' mistakes in Afghanistan between 2002 and 2010. His purpose is to draw lessons that can be applied more broadly and thus avoid repeating the same mistakes in other contexts.After reminding the reader that aid efficiency in countries emerging from a crisis is a source of considerable disappointment, and that not only promises and flashy announcements but considerable financial resources are required to rebuild those countries, Serge Michailof next makes a candid analysis of donors’ poor performance in Afghanistan. He emphasizes the lack of a coherent strategy and clear goals to guide their actions. He stresses the fact that ensuring the safety of the people and providing a local administration is critical in these circumstances, although largely forgotten by donors. Since foreign forces cannot fulfill this need indefinitely, building reliable national security forces is essential. He then describes the consequences of the lack of coordination and strategic management of aid, which results in severe inconsistencies in resource allocation, and proposes a new aid model to address such deficiencies. From the Afghan case analysis, he draws general conclusions regarding the principles governing aid coordination in fragile countries and the inadequacy of the millennium development goals as a conceptual framework in such contexts. He stresses the dire consequences of approaches governed by donors' short-term concerns, which end up establishing a parallel donor

  1. Are temperature reconstructions regionally biased?

    CERN Document Server

    Bothe, O

    2012-01-01

    Are temperature reconstructions possibly biased due to regionally differing density of utilized proxy-networks? This question is assessed utilizing a simple process-based forward model of tree growth in the virtual reality of two simulations of the climate of the last millennium with different amplitude of solar forcing variations. The pseudo-tree ring series cluster in high latitudes of the northern hemisphere and east Asia. Only weak biases are found for the full network. However, for a strong solar forcing amplitude the high latitudes indicate a warmer first half of the last millennium while mid-latitudes and Asia were slightly colder than the extratropical hemispheric average. Reconstruction skill is weak or non-existent for two simple reconstruction schemes, and comparison of virtual reality target and reconstructions reveals strong deficiencies. The temporal resolution of the proxies has an influence on the reconstruction task and results are sensitive to the construction of the proxy-network. Existing ...

  2. Blob-enhanced reconstruction technique

    Science.gov (United States)

    Castrillo, Giusy; Cafiero, Gioacchino; Discetti, Stefano; Astarita, Tommaso

    2016-09-01

    A method to enhance the quality of the tomographic reconstruction and, consequently, the 3D velocity measurement accuracy, is presented. The technique is based on integrating information on the objects to be reconstructed within the algebraic reconstruction process. A first guess intensity distribution is produced with a standard algebraic method, then the distribution is rebuilt as a sum of Gaussian blobs, based on location, intensity and size of agglomerates of light intensity surrounding local maxima. The blobs substitution regularizes the particle shape allowing a reduction of the particles discretization errors and of their elongation in the depth direction. The performances of the blob-enhanced reconstruction technique (BERT) are assessed with a 3D synthetic experiment. The results have been compared with those obtained by applying the standard camera simultaneous multiplicative reconstruction technique (CSMART) to the same volume. Several blob-enhanced reconstruction processes, both substituting the blobs at the end of the CSMART algorithm and during the iterations (i.e. using the blob-enhanced reconstruction as predictor for the following iterations), have been tested. The results confirm the enhancement in the velocity measurements accuracy, demonstrating a reduction of the bias error due to the ghost particles. The improvement is more remarkable at the largest tested seeding densities. Additionally, using the blobs distributions as a predictor enables further improvement of the convergence of the reconstruction algorithm, with the improvement being more considerable when substituting the blobs more than once during the process. The BERT process is also applied to multi resolution (MR) CSMART reconstructions, permitting simultaneously to achieve remarkable improvements in the flow field measurements and to benefit from the reduction in computational time due to the MR approach. Finally, BERT is also tested on experimental data, obtaining an increase of the

  3. Robust sparse image reconstruction of radio interferometric observations with PURIFY

    CERN Document Server

    Pratley, Luke; d'Avezac, Mayeul; Carrillo, Rafael E; Onose, Alexandru; Wiaux, Yves

    2016-01-01

    Next-generation radio interferometers, such as the Square Kilometre Array (SKA), will revolutionise our understanding of the universe through their unprecedented sensitivity and resolution. However, to realise these goals significant challenges in image and data processing need to be overcome. The standard methods in radio interferometry for reconstructing images, such as CLEAN and its variants, have served the community well over the last few decades and have survived largely because they are pragmatic. However, they produce reconstructed interferometric images that are limited in quality and they are not scalable for big data. In this work we apply and evaluate alternative interferometric reconstruction methods that make use of state-of-the-art sparse image reconstruction algorithms motivated by compressive sensing, which have been implemented in the PURIFY software package. In particular, we implement and apply the proximal alternating direction method of multipliers (P-ADMM) algorithm presented in a recen...

  4. Fast reconstruction of low dose proton CT by sinogram interpolation

    Science.gov (United States)

    Hansen, David C.; Sangild Sørensen, Thomas; Rit, Simon

    2016-08-01

    Proton computed tomography (CT) has been demonstrated as a promising image modality in particle therapy planning. It can reduce errors in particle range calculations and consequently improve dose calculations. Obtaining a high imaging resolution has traditionally required computationally expensive iterative reconstruction techniques to account for the multiple scattering of the protons. Recently, techniques for direct reconstruction have been developed, but these require a higher imaging dose than the iterative methods. No previous work has compared the image quality of the direct and the iterative methods. In this article, we extend the methodology for direct reconstruction to be applicable for low imaging doses and compare the obtained results with three state-of-the-art iterative algorithms. We find that the direct method yields comparable resolution and image quality to the iterative methods, even at 1 mSv dose levels, while yielding a twentyfold speedup in reconstruction time over previously published iterative algorithms.

  5. Tomographic reconstruction of the Wigner function on the Bloch sphere

    CERN Document Server

    Schmied, Roman

    2011-01-01

    We present a filtered backprojection algorithm for reconstructing the Wigner function of a system of large angular momentum j from Stern-Gerlach-type measurements. Our method is advantageous over the full determination of the density matrix in that it is insensitive to experimental fluctuations in j, and allows for a natural elimination of high-frequency noise in the Wigner function by taking into account the experimental uncertainties in the determination of j, its projection m, and the quantization axis orientation. No data binning and no arbitrary smoothing parameters are necessary in this reconstruction. Using recently published data [Riedel et al., Nature 464:1170 (2010)] we reconstruct the Wigner function of a spin-squeezed state of a Bose-Einstein condensate of about 1250 atoms, demonstrating that measurements along quantization axes lying in a single plane are sufficient for performing this tomographic reconstruction.

  6. Porcelain three-dimensional shape reconstruction and its color reconstruction

    Science.gov (United States)

    Yu, Xiaoyang; Wu, Haibin; Yang, Xue; Yu, Shuang; Wang, Beiyi; Chen, Deyun

    2013-01-01

    In this paper, structured light three-dimensional measurement technology was used to reconstruct the porcelain shape, and further more the porcelain color was reconstructed. So the accurate reconstruction of the shape and color of porcelain was realized. Our shape measurement installation drawing is given. Because the porcelain surface is color complex and highly reflective, the binary Gray code encoding is used to reduce the influence of the porcelain surface. The color camera was employed to obtain the color of the porcelain surface. Then, the comprehensive reconstruction of the shape and color was realized in Java3D runtime environment. In the reconstruction process, the space point by point coloration method is proposed and achieved. Our coloration method ensures the pixel corresponding accuracy in both of shape and color aspects. The porcelain surface shape and color reconstruction experimental results completed by proposed method and our installation, show that: the depth range is 860 ˜ 980mm, the relative error of the shape measurement is less than 0.1%, the reconstructed color of the porcelain surface is real, refined and subtle, and has the same visual effect as the measured surface.

  7. The pig story (tiboi sakkoko Storytelling of kinship, memories of the past, and rights to plots of ancestral land in Mentawai

    Directory of Open Access Journals (Sweden)

    Juniator Tulius

    2016-07-01

    Full Text Available This paper examines some significant elements of the pig story (tiboi sakkoko. This tale contains crucial information about the collective identity, ancestors and historical events affecting particular Mentawai kin-groups. As families do not preserve their culture and traditions in written form, storytellers of kin-groups have narrated the pig story from generation to generation so as to preserve it carefully. In the course of time, storytellers establish particular ways of telling their stories so as to remember the content and plot of the stories easily. Through the pig story, members of kin groups also recollect their ancestral place of origin and plots of ancestral lands. The role of human memory is indispensable to recalling all these important elements. Therefore, this paper analyses memories of the past of different family generations. To achieve its aims, this paper also evaluates the roles of family stories in the culture and traditions of Mentawai society.

  8. Clan, ancestral hall, and sacrifice in the Song Dynasty%宋代的宗族祠堂、祭祀及其它

    Institute of Scientific and Technical Information of China (English)

    游彪

    2007-01-01

    The Song Dynasty is the most important period in Chinese history in terms of the establishment of a new type of clan system. During the Song, Chinese social organization, at the grass-roots level, experienced a fundamental change.In the wake of the late-Tang collapse of the local power system, it was necessary for the Song to replace the ancestral lineage structure and develop a new system to adapt itself to the new circumstances brought on by drastic changes in its economy. Song Confucians played a vital part in the changes. Not only did they gradually solve the theoretical problems of the new type of clan organization, but they also developed many feasible and standard models. Eventually this model would gain even wider acceptance after the Yuan Dynasty with the rise of Neo-Confucianism. Thus, ancestral halls, serving as the major centers for the new clan activities, became prevalent among common people.

  9. Quantum Teleportation of Tripartite Arbitrary State via W State

    Institute of Scientific and Technical Information of China (English)

    XUE Zheng-Yuan; YI You-Min; CAO Zhuo-Liang

    2005-01-01

    A scheme of teleportation of a tripartite state via W state is suggested. The W state serves as quantum channels. Standard Bell-state measurements and Von Neumann measurements are performed. After the sender operates the measurements and informs the receiver her results, he can reconstruct the original state by the corresponding unitary transformation. The probability of the successful teleportation is also obtained.

  10. Los no lugares y el mundo de las aguas: Aproximación al territorio ancestral de una comunidad amazónica

    OpenAIRE

    2015-01-01

    Characterization of an ancestral territory of the indigenous community of Macedonia was performed (Colombian Amazon located 57 km upstream from Leticia); through the cultural maps analysis obtained of ethnographic methodology based on social mapping and one analysis through intersubjective processes of consensus.As a result, georeferenced maps that generate an approximation of non-places that give access to shamanistic macro-space were obtained, which in turn is used to generate a local cultu...

  11. Tomographic reconstruction of time-bin-entangled qudits

    Science.gov (United States)

    Nowierski, Samantha J.; Oza, Neal N.; Kumar, Prem; Kanter, Gregory S.

    2016-10-01

    We describe an experimental implementation to generate and measure high-dimensional time-bin-entangled qudits. Two-photon time-bin entanglement is generated via spontaneous four-wave mixing in single-mode fiber. Unbalanced Mach-Zehnder interferometers transform selected time bins to polarization entanglement, allowing standard polarization-projective measurements to be used for complete quantum state tomographic reconstruction. Here we generate maximally entangled qubits (d =2 ) , qutrits (d =3 ) , and ququarts (d =4 ) , as well as other phase-modulated nonmaximally entangled qubits and qutrits. We reconstruct and verify all generated states using maximum-likelihood estimation tomography.

  12. Phylogenomic analysis of vertebrate thrombospondins reveals fish-specific paralogues, ancestral gene relationships and a tetrapod innovation

    Directory of Open Access Journals (Sweden)

    Adams Josephine C

    2006-04-01

    Full Text Available Abstract Background Thrombospondins (TSPs are evolutionarily-conserved, extracellular, calcium-binding glycoproteins with important roles in cell-extracellular matrix interactions, angiogenesis, synaptogenesis and connective tissue organisation. Five TSPs, designated TSP-1 through TSP-5, are encoded in the human genome. All but one have known roles in acquired or inherited human diseases. To further understand the roles of TSPs in human physiology and pathology, it would be advantageous to extend the repertoire of relevant vertebrate models. In general the zebrafish is proving an excellent model organism for vertebrate biology, therefore we set out to evaluate the status of TSPs in zebrafish and two species of pufferfish. Results We identified by bioinformatics that three fish species encode larger numbers of TSPs than vertebrates, yet all these sequences group as homologues of TSP-1 to -4. By phylogenomic analysis of neighboring genes, we uncovered that, in fish, a TSP-4-like sequence is encoded from the gene corresponding to the tetrapod TSP-5 gene. Thus, all TSP genes show conservation of synteny between fish and tetrapods. In the human genome, the TSP-1, TSP-3, TSP-4 and TSP-5 genes lie within paralogous regions that provide insight into the ancestral genomic context of vertebrate TSPs. Conclusion A new model for TSP evolution in vertebrates is presented. The TSP-5 protein sequence has evolved rapidly from a TSP-4-like sequence as an innovation in the tetrapod lineage. TSP biology in fish is complicated by the presence of additional lineage- and species-specific TSP paralogues. These novel results give deeper insight into the evolution of TSPs in vertebrates and open new directions for understanding the physiological and pathological roles of TSP-4 and TSP-5 in humans.

  13. Somatostatin signaling system as an ancestral mechanism: Myoregulatory activity of an Allatostatin-C peptide in Hydra.

    Science.gov (United States)

    Alzugaray, María Eugenia; Hernández-Martínez, Salvador; Ronderos, Jorge Rafael

    2016-08-01

    The coordination of physiological processes requires precise communication between cells. Cellular interactions allow cells to be functionally related, facilitating the maintaining of homeostasis. Neuropeptides functioning as intercellular signals are widely distributed in Metazoa. It is assumed that neuropeptides were the first intercellular transmitters, appearing early during the evolution. In Cnidarians, neuropeptides are mainly involved in neurotransmission, acting directly or indirectly on epithelial muscle cells, and thereby controlling coordinated movements. Allatostatins are a group of chemically unrelated neuropeptides that were originally characterized based on their ability to inhibit juvenil hormone synthesis in insects. Allatostatin-C has pleiotropic functions, acting as myoregulator in several insects. In these studies, we analyzed the myoregulatory effect of Aedes aegypti Allatostatin-C in Hydra sp., a member of the phylum Cnidaria. Allatostatin-C peptide conjugated with Qdots revealed specifically distributed cell populations that respond to the peptide in different regions of hydroids. In vivo physiological assays using Allatostatin-C showed that the peptide induced changes in shape and length in tentacles, peduncle and gastrovascular cavity. The observed changes were dose and time dependent suggesting the physiological nature of the response. Furthermore, at highest doses, Allatostatin-C induced peristaltic movements of the gastrovascular cavity resembling those that occur during feeding. In silico search of putative Allatostatin-C receptors in Cnidaria showed that genomes predict the existence of proteins of the somatostatin/Allatostatin-C receptors family. Altogether, these results suggest that Allatostatin-C has myoregulatory activity in Hydra sp, playing a role in the control of coordinated movements during feeding, indicating that Allatostatin-C/Somatostatin based signaling might be an ancestral mechanism.

  14. Phylogenetic analysis of glycerol 3-phosphate acyltransferases in opisthokonts reveals unexpected ancestral complexity and novel modern biosynthetic components.

    Directory of Open Access Journals (Sweden)

    Heather C Smart

    Full Text Available Glycerolipid synthesis represents a central metabolic process of all forms of life. In the last decade multiple genes coding for enzymes responsible for the first step of the pathway, catalyzed by glycerol 3-phosphate acyltransferase (GPAT, have been described, and characterized primarily in model organisms like Saccharomyces cerevisiae and mice. Notoriously, the fungal enzymes share low sequence identity with their known animal counterparts, and the nature of their homology is unclear. Furthermore, two mitochondrial GPAT isoforms have been described in animal cells, while no such enzymes have been identified in Fungi. In order to determine if the yeast and mammalian GPATs are representative of the set of enzymes present in their respective groups, and to test the hypothesis that metazoan orthologues are indeed absent from the fungal clade, a comparative genomic and phylogenetic analysis was performed including organisms spanning the breadth of the Opisthokonta supergroup. Surprisingly, our study unveiled the presence of 'fungal' orthologs in the basal taxa of the holozoa and 'animal' orthologues in the basal holomycetes. This includes a novel clade of fungal homologues, with putative peroxisomal targeting signals, of the mitochondrial/peroxisomal acyltransferases in Metazoa, thus potentially representing an undescribed metabolic capacity in the Fungi. The overall distribution of GPAT homologues is suggestive of high relative complexity in the ancestors of the opisthokont clade, followed by loss and sculpting of the complement in the descendent lineages. Divergence from a general versatile metabolic model, present in ancestrally deduced GPAT complements, points to distinctive contributions of each GPAT isoform to lipid metabolism and homeostasis in contemporary organisms like humans and their fungal pathogens.

  15. Amoebozoans Are Secretly but Ancestrally Sexual: Evidence for Sex Genes and Potential Novel Crossover Pathways in Diverse Groups of Amoebae

    Science.gov (United States)

    Wood, Fiona C.; Katz, Laura A.; Cerón-Romero, Mario A.; Gorfu, Lydia A.

    2017-01-01

    Sex is beneficial in eukaryotes as it can increase genetic diversity, reshuffle their genomes, and purge deleterious mutations. Yet, its evolution remains a mystery. The eukaryotic clade supergroup Amoebozoa encompasses diverse lineages of polymorphic amoeboid forms, including both free-living and parasitic lineages. The group is generally believed to be asexual, though recent studies show that some of its members are implicated in cryptic forms of sexual cycles. In this study, we conduct a comprehensive inventory and analysis of genes involved in meiosis and related processes, in order to investigate the evolutionary history of sex in the clade. We analyzed genomic and transcriptomic data of 39 amoebozoans representing all major subclades of Amoebozoa. Our results show that Amoebozoa possess most of the genes exclusive to meiosis but lack genes encoding synaptonemal complex (SC). The absence of SC genes is discussed in the context of earlier studies that reported ultrastructural evidence of SC in some amoebae. We also find interclade and intrageneric variation in sex gene distribution, indicating diversity in sexual pathways in the group. Particularly, members of Mycetozoa engage in a novel sexual pathway independent of the universally conserved meiosis initiator gene, SPO11. Our findings strongly suggest that not only do amoebozoans possess sex genes in their genomes, but also, based on the transcriptome evidence, the present sex genes are functional. We conclude that Amoebozoa is ancestrally sexual, contrary to the long held belief that most of its members are asexual. Thus, asexuality in Amoebozoa, if confirmed to be present, is a derived-trait that appeared later in their evolution. PMID:28087686

  16. Expansion and Functional Divergence of Jumonji C-Containing Histone Demethylases: Significance of Duplications in Ancestral Angiosperms and Vertebrates.

    Science.gov (United States)

    Qian, Shengzhan; Wang, Yingxiang; Ma, Hong; Zhang, Liangsheng

    2015-08-01

    Histone modifications, such as methylation and demethylation, are crucial mechanisms altering chromatin structure and gene expression. Recent biochemical and molecular studies have uncovered a group of histone demethylases called Jumonji C (JmjC) domain proteins. However, their evolutionary history and patterns have not been examined systematically. Here, we report extensive analyses of eukaryotic JmjC genes and define 14 subfamilies, including the Lysine-Specific Demethylase3 (KDM3), KDM5, JMJD6, Putative-Lysine-Specific Demethylase11 (PKDM11), and PKDM13 subfamilies, shared by plants, animals, and fungi. Other subfamilies are detected in plants and animals but not in fungi (PKDM12) or in animals and fungi but not in plants (KDM2 and KDM4). PKDM7, PKDM8, and PKDM9 are plant-specific groups, whereas Jumonji, AT-Rich Interactive Domain2, KDM6, and PKDM10 are animal specific. In addition to known domains, most subfamilies have characteristic conserved amino acid motifs. Whole-genome duplication (WGD) was likely an important mechanism for JmjC duplications, with four pairs from an angiosperm-wide WGD and others from subsequent WGDs. Vertebrates also experienced JmjC duplications associated with the vertebrate ancestral WGDs, with additional mammalian paralogs from tandem duplication and possible transposition. The sequences of paralogs have diverged in both known functional domains and other regions, showing evidence of selection pressure. The increases of JmjC copy number and the divergences in sequence and expression might have contributed to the divergent functions of JmjC genes, allowing the angiosperms and vertebrates to adapt to a great number of ecological niches and contributing to their evolutionary successes.

  17. Zebrafish Wnt9a,9b paralog comparisons suggest ancestral roles for Wnt9 in neural, oral-pharyngeal ectoderm and mesendoderm.

    Science.gov (United States)

    Cox, A A; Jezewski, P A; Fang, P-K; Payne-Ferreira, T L

    2010-09-01

    The Wnts are a highly conserved family of secreted glycoproteins involved in cell-cell signaling and pattern formation during early embryonic development. Teasing out the role of individual Wnt molecules through development is challenging. Gene duplications are one of the most important mechanisms for generating evolutionary variations. The current consensus suggests that most anatomical variation is generated by divergence of regulatory control regions rather than by coding sequence divergence. Thus phylogenetic comparisons of divergent gene expression patterns are essential to understanding ancestral morphogenetic patterns from which subsequent anatomy diversified in modern lineages. We previously demonstrated strongest expression of zebrafish wnt9b within its heart tube, limb bud and ventral/anterior ectoderm during oral and pharyngeal arch patterning. Our goal is to compare and contrast zwnt9b to its closest paralog, zwnt9a. Sequenced, fulllength zebrafish wnt9a and wnt9b cDNA clones were used for phylogenetic analysis, which suggests their derivation from a common pre-vertebrate archeolog by gene duplication and divergence. Here we demonstrate that zwnt9a expression is found within unique (CNS, pronephric ducts, sensory organs) and overlapping (pectoral fin buds) expression domains relative to zwnt9b. Apparently, Wnt9 paralogs differentially parsed common ancestral expression domains during their subsequent rounds of gene duplication, divergence and loss in different vertebrate lineages. This expression data suggests ancestral roles for Wnt9s in early patterning of neural/oral-pharyngeal ectoderm and mesendoderm derivatives.

  18. "Recuperación ancestral mapuche": Divergencias ideológicas y conflictos entre Mapuches y el Estado. El caso del Lof Inkaial WalMapu Meu (Parque Nacional Nahuel Huapí, Río Negro, Argentina "Recuperação ancestral Mapuche": O caso de Lof Inkaial WalMapu Meu (Parque Nacional Nahuel Huapí, Rio Negro, Argentina Mapuche Ancestral Recovery of Land: The Lof Inkaial WalMapu Meu case of study (Nahuel Huapí National Park, Río Negro, Argentina

    Directory of Open Access Journals (Sweden)

    Guido Galafassi

    2012-07-01

    ção por parte dos povoadores "vizinhos" da área recuperadaThe aim of this paper is to present and analyze the case of a recent social mobilization which involved a Mapuche community in the southern region of Argentina, known as Patagonia. An "ancestral recovery of land" was claimed to be the objective of the action. Several conflicts emerged due to the fact that the land in conflict is part of the Nahuel Huapi National Park, which implied a straightforward questioning of the National State rights over territory. Apart from that, the recovery process was strongly rejected by local residents. This brought about a new conflict that required the local government's mediation.

  19. Historical reconstruction of ocean acidification in the Australian region

    Directory of Open Access Journals (Sweden)

    A. Lenton

    2015-06-01

    Full Text Available The increase in atmospheric greenhouse gases over the last 200 years has caused an increase in ocean acidity levels. Documenting how the ocean has changed is critical for assessing how these changes could impact marine ecosystems and for the management of marine resources. We use present day ocean carbon observations from shelf and offshore waters around Australia, combined with neural network mapping of CO2, to estimate the current seasonal and regional distributions of carbonate chemistry (pH and aragonite saturation state. These predicted changes in carbonate chemistry are combined with atmospheric CO2 concentration changes since to reconstruct pH and aragonite saturation state changes over the last 140 years (1870–2013. The comparison with data collected at Integrated Marine Observing System National Reference Station sites located on the shelf around Australia shows both the mean state and seasonality for the present day is well represented by our reconstruction, with the exception of sites such as the Great Barrier Reef. Our reconstruction predicts that since 1870 an average decrease in aragonite saturation state of 0.48 and of 0.09 in pH has occurred in response to increasing oceanic uptake of atmospheric CO2. Our reconstruction shows that seasonality is the dominant mode of variability, with only small interannual variability present. Large seasonal variability in pH and aragonite saturation state occur in Southwestern Australia driven by ocean dynamics (mixing and in the Tasman Sea by seasonal warming (in the case of aragonite saturation state. The seasonal and historical changes in aragonite saturation state and pH have different spatial patterns and suggest that the biological responses to ocean acidification are likely to be non-uniform depending on the relative sensitivity of organisms to shifts in pH and saturation state. This new historical reconstruction provides an important to link to biological observations to help elucidate

  20. Reconstructive dosimetry for cutaneous radiation syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Lima, C.M.A.; Lima, A.R.; Degenhardt, Ä.L.; Da Silva, F.C.A., E-mail: dasilva@ird.gov.br [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Valverde, N.J. [Fundacao Eletronuclear de Assistencia Medica, Rio de Janeiro, RJ (Brazil)

    2015-10-15

    According to the International Atomic Energy Agency (IAEA), a relatively significant number of radiological accidents have occurred in recent years mainly because of the practices referred to as potentially high-risk activities, such as radiotherapy, large irradiators and industrial radiography, especially in gammagraphy assays. In some instances, severe injuries have occurred in exposed persons due to high radiation doses. In industrial radiography, 80 cases involving a total of 120 radiation workers, 110 members of the public including 12 deaths have been recorded up to 2014. Radiological accidents in industrial practices in Brazil have mainly resulted in development of cutaneous radiation syndrome (CRS) in hands and fingers. Brazilian data include 5 serious cases related to industrial gammagraphy, affecting 7 radiation workers and 19 members of the public; however, none of them were fatal. Some methods of reconstructive dosimetry have been used to estimate the radiation dose to assist in prescribing medical treatment. The type and development of cutaneous manifestations in the exposed areas of a person is the first achievable gross dose estimation. This review article presents the state-of-the-art reconstructive dosimetry methods enabling estimation of local radiation doses and provides guidelines for medical handling of the exposed individuals. The review also presents the Chilean and Brazilian radiological accident cases to highlight the importance of reconstructive dosimetry. (author)

  1. Bayesian Cosmic Web Reconstruction: BARCODE for Clusters

    Science.gov (United States)

    Bos, E. G. Patrick; van de Weygaert, Rien; Kitaura, Francisco; Cautun, Marius

    2016-10-01

    We describe the Bayesian \\barcode\\ formalism that has been designed towards the reconstruction of the Cosmic Web in a given volume on the basis of the sampled galaxy cluster distribution. Based on the realization that the massive compact clusters are responsible for the major share of the large scale tidal force field shaping the anisotropic and in particular filamentary features in the Cosmic Web. Given the nonlinearity of the constraints imposed by the cluster configurations, we resort to a state-of-the-art constrained reconstruction technique to find a proper statistically sampled realization of the original initial density and velocity field in the same cosmic region. Ultimately, the subsequent gravitational evolution of these initial conditions towards the implied Cosmic Web configuration can be followed on the basis of a proper analytical model or an N-body computer simulation. The BARCODE formalism includes an implicit treatment for redshift space distortions. This enables a direct reconstruction on the basis of observational data, without the need for a correction of redshift space artifacts. In this contribution we provide a general overview of the the Cosmic Web connection with clusters and a description of the Bayesian BARCODE formalism. We conclude with a presentation of its successful workings with respect to test runs based on a simulated large scale matter distribution, in physical space as well as in redshift space.

  2. Evidence-Based ACL Reconstruction

    Directory of Open Access Journals (Sweden)

    E. Carlos RODRIGUEZ-MERCHAN

    2015-01-01

    Full Text Available There is controversy in the literature regarding a number of topics related to anterior cruciate ligament (ACLreconstruction. The purpose of this article is to answer the following questions: 1 Bone patellar tendon bone (BPTB reconstruction or hamstring reconstruction (HR; 2 Double bundle or single bundle; 3 Allograft or authograft; 4 Early or late reconstruction; 5 Rate of return to sports after ACL reconstruction; 6 Rate of osteoarthritis after ACL reconstruction. A Cochrane Library and PubMed (MEDLINE search of systematic reviews and meta-analysis related to ACL reconstruction was performed. The key words were: ACL reconstruction, systematic reviews and meta-analysis. The main criteria for selection were that the articles were systematic reviews and meta-analysesfocused on the aforementioned questions. Sixty-nine articles were found, but only 26 were selected and reviewed because they had a high grade (I-II of evidence. BPTB-R was associated with better postoperative knee stability but with a higher rate of morbidity. However, the results of both procedures in terms of functional outcome in the long-term were similar. The double-bundle ACL reconstruction technique showed better outcomes in rotational laxity, although functional recovery was similar between single-bundle and double-bundle. Autograft yielded better results than allograft. There was no difference between early and delayed reconstruction. 82% of patients were able to return to some kind of sport participation. 28% of patients presented radiological signs of osteoarthritis with a follow-up of minimum 10 years.

  3. Reconstruction of B mesons

    Science.gov (United States)

    Albrecht, H.; Binder, U.; Böckmann, P.; Gläser, R.; Harder, G.; Lembke-Koppitz, I.; Schmidt-Parzefall, W.; Schröder, H.; Schulz, H. D.; Wurth, R.; Yagil, A.; Donker, J. P.; Drescher, A.; Kamp, D.; Matthiesen, U.; Scheck, H.; Spaan, B.; Spengler, J.; Wegener, D.; Gabriel, J. C.; Schubert, K. R.; Stiewe, J.; Strahl, K.; Waldi, R.; Weseler, S.; Edwards, K. W.; Frisken, W. R.; Gilkinson, D. J.; Gingrich, D. M.; Kapitza, H.; Kim, P. C. H.; Kutschke, R.; Macfarlane, D. B.; McKenna, J. A.; McLean, K. W.; Nilsson, A. W.; Orr, R. S.; Padley, P.; Parsons, J. A.; Patel, P. M.; Prentice, J. D.; Seywerd, H. C. J.; Swain, J. D.; Tsipolitis, G.; Yoon, T.-S.; Yun, J. C.; Ammar, R.; Coppage, D.; Davis, R.; Kanekal, S.; Kwak, N.; Boštjančič, B.; Kernel, G.; Pleško, M.; Jönsson, L.; Babaev, A.; Danilov, M.; Golutvin, A.; Gorelov, I.; Lubimov, V.; Matveev, V.; Nagovitsin, V.; Ryltsov, V.; Semenov, A.; Shevchenko, V.; Soloshenko, V.; Tchistilin, V.; Tichomirov, I.; Zaitzev, Yu.; Childers, R.; Darden, C. W.; Oku, Y.; Gennow, H.; Argus Collaboration

    1987-02-01

    B mesons have been reconstructed in five decay channels of the type B→D ∗±nπ(n=1,2,3) using data accumulated by the ARGUS experiment at the e +e - storage ring DORIS II at DESY. In total, we find 40 neutral B mesons above a background of 15±6 events with a mass of (5278.2±1.0±3.0) MeV/ c2 and 32 charged B mesons above a background of 17±6 events with a mass of (5275.8±1.3±3.0) MeV/ c2. The decays overlineB0D∗+π -π 0, overlineB0D∗+π -π -π +, and B-→ D∗+π -π -π 0 have been observed for the first time. We find substantially smaller branching ratios for the decay modes overlineB0→ D∗+π - and B-→ D∗+π -π - than previously published by the CLEO collaboration.

  4. Reconstructing human evolution

    CERN Document Server

    Cavalli-Sforza, M

    1999-01-01

    One can reconstruct human evolution using modern genetic data and models based on the mathematical theory of evolution and its four major factors : mutation, natural selection, statistical fluctuations in finite populations (random genetic drift), and migration. Archaeology gives some help on the major dates and events of the process. Chances of studying ancient DNA are very limited but there have been a few successful results. Studying DNA instead of proteins, as was done until a few years ago, and in particular the DNA of mitochondria and of the Y chromosome which are transmitted, respectively, by the maternal line and the paternal line, has greatly simplified the analysis. It is now possible to carry the analysis on individuals, while earlier studies were of necessity based on populations. Also the evolution of ÒcultureÓ (i.e. what we learn from others), in particular that of languages, gives some help and can be greatly enlightened by genetic studies. Even though it is largely based on mechanisms of mut...

  5. Facial Reconstruction and Rehabilitation.

    Science.gov (United States)

    Guntinas-Lichius, Orlando; Genther, Dane J; Byrne, Patrick J

    2016-01-01

    Extracranial infiltration of the facial nerve by salivary gland tumors is the most frequent cause of facial palsy secondary to malignancy. Nevertheless, facial palsy related to salivary gland cancer is uncommon. Therefore, reconstructive facial reanimation surgery is not a routine undertaking for most head and neck surgeons. The primary aims of facial reanimation are to restore tone, symmetry, and movement to the paralyzed face. Such restoration should improve the patient's objective motor function and subjective quality of life. The surgical procedures for facial reanimation rely heavily on long-established techniques, but many advances and improvements have been made in recent years. In the past, published experiences on strategies for optimizing functional outcomes in facial paralysis patients were primarily based on small case series and described a wide variety of surgical techniques. However, in the recent years, larger series have been published from high-volume centers with significant and specialized experience in surgical and nonsurgical reanimation of the paralyzed face that have informed modern treatment. This chapter reviews the most important diagnostic methods used for the evaluation of facial paralysis to optimize the planning of each individual's treatment and discusses surgical and nonsurgical techniques for facial rehabilitation based on the contemporary literature.

  6. Reconstruction of anterior cruciate ligament repairs knee sports injury:clinical state and future%前交叉韧带重建修复运动性膝关节损伤:临床现状与未来

    Institute of Scientific and Technical Information of China (English)

    张海灵

    2014-01-01

    BACKGROUND:The cruciate ligament of the knee joint has a poor capacity of self-healing after injury, and the main treatment is grafting to reconstruct cruciate ligament. OBJECTIVE:To summarize the structure, function, and mechanical characteristics of anterior cruciate ligament of the knee joint, the present research of artificial ligament reconstruction fol owing damage, and to provide evidences for clinical application of artificial ligament. METHODS:An online computer-based retrieval was performed with the key words of“artificial y synthetic materials, knee joint cruciate ligament, exercise, ligament repair, ligament reconstruction”. Articles related to knee ligament treatment approach, materials science characteristics, biocompatibility and application were included. A total of 25 articles addressing the properties of biological materials applied in knee cruciate ligament reconstruction were screened. RESULTS AND CONCLUSION:As an effective treatment for anterior cruciate ligament injuries, technique of anterior cruciate ligament reconstruction has been developed in recent years. Implants for repairing anterior cruciate ligament injuries include autologous ligaments, ligament al ograft, artificial ligaments, and tissue engineered ligament. Artificial materials and tissue engineered ligaments are the hotspots in recent years. Biological artificial ligament is effective to treat the knee ligament injury. celland molecular biology techniques as wel as the use of gene therapy wil become a new direction in the treatment of knee ligament injury and rehabilitation.%背景:膝关节交叉韧带损伤后自愈能力较差,治疗上以移植物植入重建交叉韧带为主。  目的:总结膝关节前交叉韧带的功能、结构,力学特点,及其缺损后人工韧带重建研究的进展,为人工韧带的临床应用提供依据。  方法:作者应用计算机检索数据库,检索关键词“人工合成材料;膝交叉韧带,韧

  7. Image Interpolation Through Surface Reconstruction

    Institute of Scientific and Technical Information of China (English)

    ZHANG Ling; LI Xue-mei

    2013-01-01

    Reconstructing an HR (high-resolution) image which preserves the image intrinsic structures from its LR ( low-resolution) counterpart is highly challenging. This paper proposes a new surface reconstruction algorithm applied to image interpolation. The interpolation surface for the whole image is generated by putting all the quadratic polynomial patches together. In order to eliminate the jaggies of the edge, a new weight function containing edge information is incorporated into the patch reconstruction procedure as a constraint. Extensive experimental results demonstrate that our method produces better results across a wide range of scenes in terms of both quantitative evaluation and subjective visual quality.

  8. Dynamical numerical model for nematic order reconstruction

    Science.gov (United States)

    Lombardo, G.; Ayeb, H.; Barberi, R.

    2008-05-01

    In highly frustrated calamitic nematic liquid crystals, a strong elastic distortion can be confined on a few nanometers. The classical elastic theory fails to describe such systems and a more complete description based on the tensor order parameter Q is required. A finite element method is used to implement the Q dynamics by a variational principle and it is shown that a uniaxial nematic configuration can evolve passing through transient biaxial states. This solution, which connects two competing uniaxial nematic textures, is known as “nematic order reconstruction.”

  9. Hadronization systematics and top mass reconstruction

    Directory of Open Access Journals (Sweden)

    Corcella Gennaro

    2014-01-01

    Full Text Available I discuss a few issues related to the systematic error on the top mass mea- surement at hadron colliders, due to hadronization effects. Special care is taken about the impact of bottom-quark fragmentation in top decays, especially on the reconstruction relying on final states with leptons and J/Ψ in the dilepton channel. I also debate the relation between the measured mass and its theoretical definition, and report on work in progress, based on the Monte Carlo simulation of fictitious top-flavoured hadrons, which may shed light on this issue and on the hadronization systematics.

  10. Ensemble data assimilation for the reconstruction of mantle circulation

    Science.gov (United States)

    Bocher, Marie; Coltice, Nicolas; Fournier, Alexandre; Tackley, Paul

    2016-04-01

    The surface tectonics of the Earth is the result of mantle dynamics. This link between internal and surface dynamics can be used to reconstruct the evolution of mantle circulation. This is classically done by imposing plate tectonics reconstructions as boundary conditions on numerical models of mantle convection. However, this technique does not account for uncertainties in plate tectonics reconstructions and does not allow any dynamical feedback of mantle dynamics on surface tectonics to develop. Mantle convection models are now able to produce surface tectonics comparable to that of the Earth to first order. We capitalize on these convection models to propose a more consistent integration of plate tectonics reconstructions into mantle convection models. For this purpose, we use the ensemble Kalman filter. This method has been developed and successfully applied to meteorology, oceanography and even more recently outer core dynamics. It consists in integrating sequentially a time series of data into a numerical model, starting from an ensemble of possible initial states. The initial ensemble of states is designed to represent an approximation of the probability density function (pdf) of the a priori state of the system. Whenever new observations are available, each member of the ensemble states is corrected considering both the approximated pdf of the state, and the pdf of the new data. Between two observation times, each ensemble member evolution is computed independently, using the convection model. This technique provides at each time an approximation of the pdf of the state of the system, in the form of a finite ensemble of states. We perform synthetic experiments to assess the efficiency of this method for the reconstruction of mantle circulation.

  11. Reconstruction and modernization of factory "Hartija Kocani", Macedonia

    Directory of Open Access Journals (Sweden)

    Krgović Milorad

    2007-01-01

    Full Text Available This work presents the reconstruction and modernization of Factory HARTIJA Kocani, for production of high quality graphic paper. Part one analyses the goal of modernization and the approach to its realization. Part two describes the pre-reconstruction state and points to the trouble spots and technical shortcomings of the paper machine. Part three shows the state of technology after the modernization. Here, the companies that took part in realization of project are presented and the quality of their engagement is graded. The final part gives the evaluation of usefulness of the reconstruction and modernization. The evaluation is given for reaching projected capacity and quality, as well as for financial efficiency of the investment, i.e. the price of the execution of the project assignment.

  12. Zigzag graphene nanoribbon edge reconstruction with Stone-Wales defects

    DEFF Research Database (Denmark)

    Rodrigues, J. N. B.; Gonçalves, P. A. D; Rodrigues, N. F. G.;

    2011-01-01

    In this paper, we study zigzag graphene nanoribbons with edges reconstructed with Stone-Wales defects, by means of an empirical (first-neighbor) tight-binding method, with parameters determined by ab initio calculations of very narrow ribbons. We explore the characteristics of the electronic band...... structure with a focus on the nature of edge states. Edge reconstruction allows the appearance of a new type of edge states. They are dispersive, with nonzero amplitudes in both sublattices; furthermore, the amplitudes have two components that decrease with different decay lengths with the distance from...... the edge; at the Dirac points one of these lengths diverges, whereas the other remains finite, of the order of the lattice parameter. We trace this curious effect to the doubling of the unit cell along the edge, brought about by the edge reconstruction. In the presence of a magnetic field, the zero...

  13. Hologram-reconstruction signal enhancement

    Science.gov (United States)

    Mezrich, R. S.

    1977-01-01

    Principle of heterodyne detection is used to combine object beam and reconstructed virtual image beam. All light valves in page composer are opened, and virtual-image beam is allowed to interfere with light from valves.

  14. Arapahoe NWR diversion reconstruction : Preliminary

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — This is a preliminary plan for a diversion reconstruction for Hubbard #2. Oklahoma #1, Dryer, Hill and Crowder sites on the Arapahoe National Wildlife Refuge.

  15. Rational reconstructions of modern physics

    CERN Document Server

    Mittelstaedt, Peter

    2013-01-01

    Newton’s classical physics and its underlying ontology are loaded with several metaphysical hypotheses that cannot be justified by rational reasoning nor by experimental evidence. Furthermore, it is well known that some of these hypotheses are not contained in the great theories of Modern Physics, such as the theory of Special Relativity and Quantum Mechanics. This book shows that, on the basis of Newton’s classical physics and by rational reconstruction, the theory of Special Relativity as well as Quantum Mechanics can be obtained by partly eliminating or attenuating the metaphysical hypotheses. Moreover, it is shown that these reconstructions do not require additional hypotheses or new experimental results. In the second edition the rational reconstructions are completed with respect to General Relativity and Cosmology. In addition, the statistics of quantum objects is elaborated in more detail with respect to the rational reconstruction of quantum mechanics. The new material completes the approach of t...

  16. Iterative image reconstruction and its role in cardiothoracic computed tomography.

    Science.gov (United States)

    Singh, Sarabjeet; Khawaja, Ranish Deedar Ali; Pourjabbar, Sarvenaz; Padole, Atul; Lira, Diego; Kalra, Mannudeep K

    2013-11-01

    Revolutionary developments in multidetector-row computed tomography (CT) scanner technology offer several advantages for imaging of cardiothoracic disorders. As a result, expanding applications of CT now account for >85 million CT examinations annually in the United States alone. Given the large number of CT examinations performed, concerns over increase in population-based risk for radiation-induced carcinogenesis have made CT radiation dose a top safety concern in health care. In response to this concern, several technologies have been developed to reduce the dose with more efficient use of scan parameters and the use of "newer" image reconstruction techniques. Although iterative image reconstruction algorithms were first introduced in the 1970s, filtered back projection was chosen as the conventional image reconstruction technique because of its simplicity and faster reconstruction times. With subsequent advances in computational speed and power, iterative reconstruction techniques have reemerged and have shown the potential of radiation dose optimization without adversely influencing diagnostic image quality. In this article, we review the basic principles of different iterative reconstruction algorithms and their implementation for various clinical applications in cardiothoracic CT examinations for reducing radiation dose.

  17. ¿Con o sin ancestros?: vigencia de lo ancestral en la Amazonía peruana

    Directory of Open Access Journals (Sweden)

    Thomas Mouriès

    2014-06-01

    Full Text Available La existencia o no de ancestros en la Amazonía indígena ha sido objeto de importantes debates. Sin embargo, los líderes de la región no dudan en llamar ‘ancestrales’ sus saberes, normas o territorios, en un sentido que, desde un punto de vista académico, puede parecer enigmático. «Ancestrales, pero… ¿con o sin ancestros?», preguntaría entonces, confuso, el antropólogo. En este artículo propongo aportar elementos de respuesta a esta pregunta a través del caso peruano. Primero analizo cómo los líderes indígenas amazónicos, conectándose al circuito del derecho internacional, adoptan la noción jurídica de ‘posesión ancestral’ del territorio para adaptarla al ámbito político. Este planteamiento rinde cuenta de la generalización y uniformización reciente del vocablo ‘ancestral’ pero deja pendiente el problema de su eventual articulación con las cosmologías indígenas que pretende reflejar. Por eso, en la segunda parte, intento sondear sobre la pertinencia de la categoría de ‘ancestro’ en la Amazonía indígena, recordando brevemente el debate académico para ir definiendo en qué medida esta categoría puede cobrar sentido. A partir del testimonio de un experimentado líder awajún, la tercera parte permite, entonces, volver más explícitos los diferentes sentidos y planos referenciales que despliega la referencia a lo ancestral, mostrando cómo los indígenas amazónicos no solo adoptan elementos conceptuales y discursivos externos, sino que al mismo tiempo los transforman a partir de sus propias singularidades cosmológicas y perspectivas políticas.

  18. ABO (histo) blood group phenotype development and human reproduction as they relate to ancestral IgM formation: A hypothesis.

    Science.gov (United States)

    Arend, Peter

    2016-01-01

    The formation of a histo (blood) group) ABO phenotype and the exclusion of an autoreactive IgM or isoagglutinin activity arise apparently in identical glycosylation of complementary domains on cell surfaces and plasma proteins. The fundamental O-glycan emptiness of the circulating IgM, which during the neonatal amino acid sequencing of the variable regions is exerting germline-specific O-GalNAc glycan-reactive serine/threonine residues that in the plasma of the adult human blood group O individuals apparently remain associated with the open glycosidic sites on the ABOH convertible red cell surface, must raise suggestions on a transient expression of developmental glycans, which have been "lost" over the course of maturation. In fact, while the mammalian non-somatic, embryogenic stem cell (ESC)- germ cell (GC) transformation is characterized by a transient and genetically as-yet-undefined trans-species-functional O-GalNAc glycan expression, in the C57BL/10 mouse such expression was potentially identified in growth-dependent, blood group A-like GalNAc glycan-bearing, ovarian glycolipids complementary with the syngeneic anti-A reactive IgM, which does not appear in early ovariectomized animals. This non-somatically encoded, polyreactive, ancestral IgM molecule has not undergone clonal selection and does primarily not differentiate between self and non-self and might, due to amino acid hydroxyl groups, highly suggest substrate competition with subsequent O-glycosylations in ongoing ESC-GC transformations and affecting GC maturation. However, the membrane-bound somatic N/O-glycotransferases, which initiate, after formation of the zygote, the complex construction of the human ABO phenotypes in the trans cisternae of the Golgi apparatus, are associated and/or completed with soluble enzyme versions exerting identical specificities in plasma and likely competing vice versa by glycosylation of neonatal IgM amino acids, where they suggest to accomplish the clearance of anti

  19. Discussion on Embedded Phenomenon of Ancestral Culture and Public Culture---Taking Cangpo Country Cultural Hall in Wenzhou’s Yongjia County of Zhejiang as an Example%宗祠文化与公共文化的互嵌现象--以浙江温州永嘉苍坡村文化礼堂为例

    Institute of Scientific and Technical Information of China (English)

    李晓云; 王鹏

    2016-01-01

    To construct a beautiful country, in 2013, the government of Zhejiang Province puts forward the policy of expanding the community’s public culture service system by establishing culture hall to inherit the local culture and carry forward the modern civilization. The measures of changing old ancestral temple into culture hall cause great response from the society. Based on the reconstruction of Cangpo country cultural hall (Lee’s ancestral temple)in Yongjia county, Wenzhou, it is to explore its rationality and discuss the necessity both folk culture and public culture service from the perspective of folklore that mean improve the quality of public cultural services with the basis of protecting the folk culture.%为建设美丽乡村,浙江省人民政府2013年出台了通过建立文化礼堂来拓展社区公共文化服务体系的政策,以此传承乡土文化,弘扬现代文明。其中将旧祠堂改建为文化礼堂这一措施,在社会各界引起了很大反响。为进一步探讨这一做法的合理性,本文以温州永嘉苍坡村文化礼堂(李氏宗祠)改建为例,从民俗学角度探讨民俗文化与公共文化服务相结合的必要性,即在保护民俗文化的基础上提高公共文化服务的质量。

  20. Improving outcomes in aesthetic facial reconstruction.

    Science.gov (United States)

    Hofer, Stefan O P; Mureau, Marc A M

    2009-07-01

    Aesthetic facial reconstruction is a challenging art. Improving outcomes in aesthetic facial reconstruction requires a thorough understanding of the basic principles of the functional and aesthetic requirements for facial reconstruction. From there, further refinement and attention to detail can be provided. This paper discusses basic principles of aesthetic facial reconstruction.

  1. On $\\mathfrak{I}$-reconstruction Property

    OpenAIRE

    L. K. Vashisht; Khattar, Geetika

    2013-01-01

    Reconstruction property in Banach spaces introduced and studied by Casazza and Christensen in [1]. In this paper we introduce reconstruction property in Banach spaces which satisfy $\\mathfrak{I}$-property. A characterization of reconstruction property in Banach spaces which satisfy $\\mathfrak{I}$-property in terms of frames in Banach spaces is obtained. Banach frames associated with reconstruction property are discussed.

  2. Comparison of preoperative anxiety in reconstructive and cosmetic surgery patients.

    Science.gov (United States)

    Sönmez, Ahmet; Bişkin, Nurdan; Bayramiçli, Mehmet; Numanoğlu, Ayhan

    2005-02-01

    Surgery is a serious stressor and a cause of anxiety for the patients. Reconstructive surgery patients are mostly operated on because of certain functional impairment or disability; on the contrary, cosmetic surgery patients do not have any physical impairment and they are operated on because of mostly psychologic reasons. The aim of this study was to compare the anxiety levels in the reconstructive surgery patients and cosmetic surgery patients preoperatively. Thirty-two patients in the reconstructive surgery group and 30 patients in the cosmetic surgery group were included in the study. State Trait Anxiety Inventory was used to measure the anxiety levels in these 2 groups preoperatively. The 2 groups were similar in characteristics such as age, gender distribution, number of previous operations, and trait anxiety scores. Mean state anxiety scores obtained for the reconstructive surgery group was 38.0 +/- 8.7, while it was 44.2 +/- 10.79 for the cosmetic surgery group (t test, degrees of freedom = 60, P = 0.015). This study reveals that preoperative anxiety levels in the cosmetic surgery patients are higher than those of the reconstructive surgery patients. Therefore, adequate preoperative preparation for cosmetic surgery should include attempts to cope with anxiety. Anxiolytics may be used more liberally and professional psychologic assistance may be required.

  3. EEG Source Reconstruction using Sparse Basis Function Representations

    DEFF Research Database (Denmark)

    Hansen, Sofie Therese; Hansen, Lars Kai

    2014-01-01

    State of the art performance of 3D EEG imaging is based on reconstruction using spatial basis function representations. In this work we augment the Variational Garrote (VG) approach for sparse approximation to incorporate spatial basis functions. As VG handles the bias variance trade-off with cross...

  4. Subtotal Nasal Reconstruction: Military-civilian Collaboration in Care of an Afghan-American Woman's Plight.

    Science.gov (United States)

    Latham, Kerry P; Valerio, Ian; Martin, Barry D; Burget, Gary; VanderKolk, Craig

    2015-07-01

    Military plastic surgeons perform reconstructive surgeries for various congenital, oncologic, and traumatic craniofacial injuries or deformities. Recently, our Walter Reed National Military Medical Center Plastic Surgery team was tasked to care for a woman who bravely sought a new and better life in the United States after she suffered amputation of her nose and bilateral ears while in her home country of Afghanistan. A military-civilian team collaborated throughout her reconstructive planning, treatment, and postoperative course to create both an aesthetically acceptable and functional subtotal nasal reconstruction. This case report details the patient's unique journey, her reconstructive course, and highlights her reintegration into a new life and society.

  5. An Algorithm for Automated Reconstruction of Particle Cascades in High Energy Physics Experiments

    CERN Document Server

    Actis, O; Henrichs, A; Hinzmann, A; Kirsch, M; Müller, G; Steggemann, J

    2008-01-01

    We present an algorithm for reconstructing particle cascades from event data of a high energy physics experiment. For a given physics process, the algorithm reconstructs all possible configurations of the cascade from the final state objects. We describe the procedure as well as examples of physics processes of different complexity studied at hadron-hadron colliders. We estimate the performance of the algorithm by 20 microseconds per reconstructed decay vertex, and 0.6 kByte per reconstructed particle in the decay trees.

  6. Fast algorithms for nonconvex compression sensing: MRI reconstruction from very few data

    Energy Technology Data Exchange (ETDEWEB)

    Chartrand, Rick [Los Alamos National Laboratory

    2009-01-01

    Compressive sensing is the reconstruction of sparse images or signals from very few samples, by means of solving a tractable optimization problem. In the context of MRI, this can allow reconstruction from many fewer k-space samples, thereby reducing scanning time. Previous work has shown that nonconvex optimization reduces still further the number of samples required for reconstruction, while still being tractable. In this work, we extend recent Fourier-based algorithms for convex optimization to the nonconvex setting, and obtain methods that combine the reconstruction abilities of previous nonconvex approaches with the computational speed of state-of-the-art convex methods.

  7. RETHINKING VIOLENCE, RECONCILIATION AND RECONSTRUCTION IN BURUNDI

    Directory of Open Access Journals (Sweden)

    Leah Ndimurwimo

    2015-11-01

    Full Text Available Armed violence and genocide are among the on-going problems that are still facing contemporary Africa and the world. In the aftermath of the outrages, devastation and appalling carnage of the Second World War, member states of the United Nations (UN undertook radical steps, inter alia, "to save succeeding generations from the scourge of war and to reaffirm faith in fundamental human rights". Subsequently, the International Bill of Human Rights was proclaimed in order to lay down international human rights norms and standards of conduct and to prevent the recurrence of mass killings. Although Burundi is a State Party to the UN and African Union and is a signatory to a number of international and regional human rights treaties, the post-colonial history of Burundi is an epic tale of indescribable human suffering and misery as a result of systematic mass killings. At least every family or household in Burundi has been negatively affected by the mass killings of the 1960s, 1972, 1988 and 1990s, which have created a significant number of refugees and internally displaced persons (IDPs.This article traces the root causes of Burundi's systemic armed violence and argues that despite several UN Security Council Resolutions and peace agreements aimed at national reconciliation and reconstruction, mass killings and other heinous crimes remain unaddressed. The article recommends that a comprehensive transitional justice model is required in post-conflict Burundi in order to bring about national reconciliation, healing and reconstruction.

  8. What Would Women Choose When Given a Choice in Breast Reconstruction?

    Science.gov (United States)

    Winch, Caleb J.

    2016-01-01

    Background: Reconstruction after mastectomy is an important milestone for many women treated for breast cancer. However, because many surgeons only offer their preferred method of reconstruction, it is not clear which approach women would choose if offered a genuine choice. Methods: Between 1998 and 2010, the breast reconstruction service at a major Australian teaching hospital was staffed by a single plastic surgeon trained in both prosthetic and autologous breast reconstruction techniques. The choices of all 837 women who underwent reconstruction were compared across time for publicly and privately funded patients using binary logistic regression. Results: Overall, women chose prosthetic over autologous reconstruction at a ratio of 4.7:1. This ratio increasingly favored prosthetic reconstruction over time, though less strongly for private patients who did not face a 3-year waiting list for autologous reconstruction. Conclusions: Financial constraints affected these women’s reconstruction choices. Nevertheless, and in contrast to the situation in the United States, these women clearly favored prosthetic over autologous reconstruction.

  9. Two-Stage Revision Anterior Cruciate Ligament Reconstruction: Bone Grafting Technique Using an Allograft Bone Matrix.

    Science.gov (United States)

    Chahla, Jorge; Dean, Chase S; Cram, Tyler R; Civitarese, David; O'Brien, Luke; Moulton, Samuel G; LaPrade, Robert F

    2016-02-01

    Outcomes of primary anterior cruciate ligament (ACL) reconstruction have been reported to be far superior to those of revision reconstruction. However, as the incidence of ACL reconstruction is rapidly increasing, so is the number of failures. The subsequent need for revision ACL reconstruction is estimated to occur in up to 13,000 patients each year in the United States. Revision ACL reconstruction can be performed in one or two stages. A two-stage approach is recommended in cases of improper placement of the original tunnels or in cases of unacceptable tunnel enlargement. The aim of this study was to describe the technique for allograft ACL tunnel bone grafting in patients requiring a two-stage revision ACL reconstruction.

  10. Probing CP Violation with Kinematic Reconstruction at the LHC

    CERN Document Server

    Rolbiecki, K; Tattersall, J; Wienemann, P

    2010-01-01

    We discuss the potential of observing effects of CP-violation phases in squark decay chains at the LHC. As the CP-odd observable, we use the asymmetry composed by triple products of final state momenta. There are good prospects of observing these effects using the method of kinematic reconstruction for the final and intermediate state particles. We also discuss the main experimental factors and the expected sensitivity.

  11. Probing CP violation with kinematic reconstruction at the LHC

    Energy Technology Data Exchange (ETDEWEB)

    Moortgat-Pick, G.; Tattersall, J. [IPPP, Department of Physics, University of Durham, South Road, Durham DH1 3LE (United Kingdom); Wienemann, P. [Department of Physics, University of Bonn, Nussallee 12, 53115 Bonn (Germany); Rolbiecki, K.

    2010-07-15

    We discuss the potential of observing effects of CP-violation phases in squark decay chains at the LHC[1]. As the CP-odd observable, we use the asymmetry composed by triple products of final state momenta. There are good prospects of observing these effects using the method of kinematic reconstruction for the final and intermediate state particles. We also discuss the main experimental factors and the expected sensitivity. (Abstract Copyright [2010], Wiley Periodicals, Inc.)

  12. An ancestral miR-1304 allele present in Neanderthals regulates genes involved in enamel formation and could explain dental differences with modern humans.

    Science.gov (United States)

    Lopez-Valenzuela, Maria; Ramírez, Oscar; Rosas, Antonio; García-Vargas, Samuel; de la Rasilla, Marco; Lalueza-Fox, Carles; Espinosa-Parrilla, Yolanda

    2012-07-01

    Genetic changes in regulatory elements are likely to result in phenotypic effects that might explain population-specific as well as species-specific traits. MicroRNAs (miRNAs) are posttranscriptional repressors involved in the control of almost every biological process. These small noncoding RNAs are present in various phylogenetic groups, and a large number of them remain highly conserved at the sequence level. MicroRNA-mediated regulation depends on perfect matching between the seven nucleotides of its seed region and the target sequence usually located at the 3' untranslated region of the regulated gene. Hence, even single changes in seed regions are predicted to be deleterious as they may affect miRNA target specificity. In accordance to this, purifying selection has strongly acted on these regions. Comparison between the genomes of present-day humans from various populations, Neanderthal, and other nonhuman primates showed an miRNA, miR-1304, that carries a polymorphism on its seed region. The ancestral allele is found in Neanderthal, nonhuman primates, at low frequency (~5%) in modern Asian populations and rarely in Africans. Using miRNA target site prediction algorithms, we found that the derived allele increases the number of putative target genes for the derived miRNA more than ten-fold, indicating an important functional evolution for miR-1304. Analysis of the predicted targets for derived miR-1304 indicates an association with behavior and nervous system development and function. Two of the predicted target genes for the ancestral miR-1304 allele are important genes for teeth formation, enamelin, and amelotin. MicroRNA overexpression experiments using a luciferase-based assay showed that the ancestral version of miR-1304 reduces the enamelin- and amelotin-associated reporter gene expression by 50%, whereas the derived miR-1304 does not have any effect. Deletion of the corresponding target sites for miR-1304 in these dental genes avoided their repression

  13. Personal and Social Transformation in the Health Area through Education: A Brief Journey from the Ancestral Indigenous Wisdom to the Modern Tyranny of Healthiness

    Directory of Open Access Journals (Sweden)

    Andrés de Muller

    2015-09-01

    Full Text Available This paper aims at claiming the ancestral wisdom of indigenous people in the health area. It analyzes how health has been commodified in the interest of large companies (particularly those related to the pharmaceutical industry to the detriment of a holistic definition of wellness through education. Furthermore, the concept of health as a right disagrees with such commodification or sale to the highest bidder, which prompts dehumanization of health services and public misinformation. The abundance of self-proclaimed gurus or healers who appeal to autosuggestion contributes both to confusion and to an unhealthy cult of healthiness.

  14. Latest Miocene-earliest Pliocene evolution of the ancestral Rio Grande at the Española-San Luis Basin boundary, northern New Mexico

    Science.gov (United States)

    Daniel J. Koning,; Scott Aby,; Grauch, V. J.; Matthew J. Zimmerer,

    2016-01-01

    We use stratigraphic relations, paleoflow data, and 40Ar/39Ar dating to interpret net aggradation, punctuated by at least two minor incisional events, along part of the upper ancestral Rio Grande fluvial system between 5.5 and 4.5 Ma (in northern New Mexico). The studied fluvial deposits, which we informally call the Sandlin unit of the Santa Fe Group, overlie a structural high between the San Luis and Española Basins. The Sandlin unit was deposited by two merging, west- to southwest-flowing, ancestral Rio Grande tributaries respectively sourced in the central Taos Mountains and southern Taos Mountains-northeastern Picuris Mountains. The river confluence progressively shifted southwestward (downstream) with time, and the integrated river (ancestral Rio Grande) flowed southwards into the Española Basin to merge with the ancestral Rio Chama. Just prior to the end of the Miocene, this fluvial system was incised in the southern part of the study area (resulting in an approximately 4–7 km wide paleovalley), and had sufficient competency to transport cobbles and boulders. Sometime between emplacement of two basalt flows dated at 5.54± 0.38 Ma and 4.82±0.20 Ma (groundmass 40Ar/39Ar ages), this fluvial system deposited 10–12 m of sandier sediment (lower Sandlin subunit) preserved in the northern part of this paleovalley. The fluvial system widened between 4.82±0.20 and 4.50±0.07 Ma, depositing coarse sand and fine gravel up to 14 km north of the present-day Rio Grande. This 10–25 m-thick sediment package (upper Sandlin unit) buried earlier south- to southeast-trending paleovalleys (500–800 m wide) inferred from aeromagnetic data. Two brief incisional events are recognized. The first was caused by the 4.82±0.20 Ma basalt flow impounding south-flowing paleodrainages, and the second occurred shortly after emplacement of a 4.69±0.09 Ma basalt flow in the northern study area. Drivers responsible for Sandlin unit aggradation may include climate

  15. Robust and accurate multi-view reconstruction by prioritized matching

    DEFF Research Database (Denmark)

    Ylimaki, Markus; Kannala, Juho; Holappa, Jukka;

    2012-01-01

    a prioritized matching method which expands the most promising seeds first. The output of the method is a three-dimensional point cloud. Unlike previous correspondence growing approaches our method allows to use the best-first matching principle in the generic multi-view stereo setting with arbitrary number...... of input images. Our experiments show that matching the most promising seeds first provides very robust point cloud reconstructions efficiently with just a single expansion step. A comparison to the current state-of-the-art shows that our method produces reconstructions of similar quality but significantly...

  16. Queueing interpretation of adaptive reconstructive multiparameter τ-opening filters

    Science.gov (United States)

    Chen, Yidong; Dougherty, Edward R.

    1998-04-01

    A multiparameter binary (tau) -opening is a union of parameterized openings in which parameters for each opening are individually defined and a structuring element can be parameterized relative to both size and shape. The reconstructive filter corresponding to an opening is defined by fully passing any grain not eliminated by the opening and deleting all other grains. Adaptive design results from treating the parameter vector of a reconstructive multiparameter (tau) -opening as the state space of a Markov chain. The present paper considers the relationship between Markovian queueing networks and adaptive multiparameter (tau) - openings for the signal-union-noise model.

  17. An evaluation of GPU acceleration for sparse reconstruction

    Science.gov (United States)

    Braun, Thomas R.

    2010-04-01

    Image processing applications typically parallelize well. This gives a developer interested in data throughput several different implementation options, including multiprocessor machines, general purpose computation on the graphics processor, and custom gate-array designs. Herein, we will investigate these first two options for dictionary learning and sparse reconstruction, specifically focusing on the K-SVD algorithm for dictionary learning and the Batch Orthogonal Matching Pursuit for sparse reconstruction. These methods have been shown to provide state of the art results for image denoising, classification, and object recognition. We'll explore the GPU implementation and show that GPUs are not significantly better or worse than CPUs for this application.

  18. Network reconstruction from infection cascades

    CERN Document Server

    Braunstein, Alfredo

    2016-01-01

    Reconstructing propagation networks from observations is a fundamental inverse problem, and it's crucial to understand and control dynamics in complex systems. Here we show that it is possible to reconstruct the whole structure of an interaction network and to simultaneously infer the complete time course of activation spreading, relying just on single snapshots of a small number of activity cascades. The method, that we called Inverse Dynamics Network Reconstruction (IDNR), is shown to work successfully on several synthetic and real networks, inferring the networks and the sources of infection based on sparse observations, including single snapshots. IDNR is built on a Belief Propagation approximation, that has an impressive performance in a wide variety of topological structures. The method can be applied in absence of complete time-series data by providing a detailed modeling of the posterior distribution of trajectories conditioned to the observations. Furthermore, we show by experiments that the informat...

  19. Track Reconstruction Performance in CMS

    CERN Document Server

    Azzurri, Paolo

    2008-01-01

    The expected performance of track reconstruction with LHC events using the CMS silicon tracker is presented. Track finding and fitting is accomplished with Kalman Filter techniques that achieve efficiencies above 99\\% on single muons with $p_T >$1~GeV/c. Difficulties arise in the context of standard LHC events with a high density of charged particles, where the rate of fake combinatorial tracks is very large for low $p_T$ tracks, and nuclear interactions in the tracker material reduce the tracking efficiency for charged hadrons. Recent improvements with the CMS track reconstruction now allow to efficiently reconstruct charged tracks with $p_T$ down to few hundred MeV/c and as few as three crossed layers, with a very small fake fraction, by making use of an optimal rejection of fake tracks in conjunction with an iterative tracking procedure.

  20. CURRENT CONCEPTS IN ACL RECONSTRUCTION

    Directory of Open Access Journals (Sweden)

    Freddie H. Fu

    2008-09-01

    Full Text Available Current Concepts in ACL Reconstruction is a complete reference text composed of the most thorough collection of topics on the ACL and its surgical reconstruction compiled, with contributions from some of the world's experts and most experienced ACL surgeons. Various procedures mentioned throughout the text are also demonstrated in an accompanying video CD-ROM. PURPOSE Composing a single, comprehensive and complete information source on ACL including basic sciences, clinical issues, latest concepts and surgical techniques, from evaluation to outcome, from history to future, editors and contributors have targeted to keep the audience pace with the latest concepts and techniques for the evaluation and the treatment of ACL injuries. FEATURES The text is composed of 27 chapters in 6 sections. The first section is mostly about basic sciences, also history of the ACL, imaging, clinical approach to adolescent and pediatric patients are subjected. In the second section, Graft Choices and Arthroscopy Portals for ACL Reconstruction are mentioned. The third section is about the technique and the outcome of the single-bundle ACL reconstruction. The fourth chapter includes the techniques and outcome of the double-bundle ACL reconstruction. In the fifth chapter revision, navigation technology, rehabilitation and the evaluation of the outcome of ACL reconstruction is subjected. The sixth/the last chapter is about the future advances to reach: What We Have Learned and the Future of ACL Reconstruction. AUDIENCE Orthopedic residents, sports traumatology and knee surgery fellows, orthopedic surgeons, also scientists in basic sciences or clinicians who are studying or planning a research on ACL forms the audience group of this book. ASSESSMENT This is the latest, the most complete and comprehensive textbook of ACL reconstruction produced by the editorial work up of two pioneer and masters "Freddie H. Fu MD and Steven B. Cohen MD" with the contribution of world

  1. Probabilistic remote state preparation by W states

    Institute of Scientific and Technical Information of China (English)

    Liu Jin-Ming; Wang Yu-Zhu

    2004-01-01

    In this paper we consider a scheme for probabilistic remote state preparation of a general qubit by using W states. The scheme consists of the sender, Alice, and two remote receivers Bob and Carol. Alice performs a projective measurement on her qubit in the basis spanned by the state she wants to prepare and its orthocomplement. This allows either Bob or Carol to reconstruct the state with finite success probability. It is shown that for some special ensembles of qubits, the remote state preparation scheme requires only two classical bits, unlike the case in the scheme of quantum teleportation where three classical bits are needed.

  2. Reconstruction of Vees, Kinks, XI sup - 's, and OMEGA sup - 's in the FOCUS spectrometer

    CERN Document Server

    Link, J M; Alimonti, G; Anjos, J C; Arena, V; Bediaga, I; Bianco, S; Boca, G; Bonomi, G; Boschini, M; Butler, J N; Carrillo, S; Casimiro, E; Cawlfield, C; Cheung, H W K; Cho, K; Chung, Y S; Cinquini, L; Cuautle, E; Cumalat, J P; D'Angelo, P; Di Corato, M; Dini, P; Engh, D; Fabbri, Franco Luigi; Gaines, I; Garbincius, P H; Gardner, R; Garren, L A; Giammarchi, M; Gianini, G; Gottschalk, E; Göbel, C; Handler, T; Hernández, H; Hosack, M; Inzani, P; Johns, W E; Kang, J S; Kasper, P H; Kim, D Y; Ko, B R; Kreymer, A E; Kryemadhi, A; Kutschke, R; Kwak, J W; Lee, K B; Leveraro, F; Liguori, G; Magnin, J; Malvezzi, S; Massafferri, A; Menasce, D; Merlo, M M; Mezzadri, M; Milazzo, L; Miranda, J M D; Mitchell, R; Montiel, E; Moroni, L; Méndez, H; Méndez, L; Nehring, M; O'Reilly, B; Olaya, D; Pantea, D; Paris, A; Park, H; Pedrini, D; Pepe, I M; Pontoglio, C; Prelz, F; Quinones, J; Rahimi, A; Ramírez, J E; Ratti, S P; Reis, A C D; Reyes, M; Riccardi, C; Rivera, C; Rovere, M; Sala, S; Sarwar, S; Segoni, I; Sheaff, M; Sheldon, P D; Stenson, K; Sánchez-Hernández, A; Uribe, C; Vaandering, E W; Vitulo, P; Vázquez, F; Webster, M; Wilson, J R; Wiss, J; Xiong, W; Yager, P M; Zallo, A; Zhang, Y

    2002-01-01

    We describe the various techniques developed in the Fermilab Wideband Experiments, E687 and FOCUS, to reconstruct long-lived states. The techniques all involve modifications to standard tracking techniques and are useful to report for future experiments.

  3. Clinical applications of iterative reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Eberl, S. [Royal Prince Alfred Hospital, Camperdown, NSW (Australia). Department of PET and Nuclear Medicine

    1998-03-01

    Expectation maximisation (EM) reconstruction largely eliminates the hot and cold streaking artifacts characteristic of filtered-back projection (FBP) reconstruction around localised hot areas, such as the bladder. It also substantially reduces the problem of decreased inferior wall counts in MIBI myocardial perfusion studies due to ``streaking`` from high liver uptake. Non-uniform attenuation and scatter correction, resolution recovery, anatomical information, e.g. from MRI or CT tracer kinetic modelling, can all be built into the EM reconstruction imaging model. The properties of ordered subset EM (OSEM) have also been used to correct for known patient motion as part of the reconstruction process. These uses of EM are elaborated more fully in some of the other abstracts of this meeting. Currently we use OSEM routinely for: (i) studies where streaking is a problem, including all MIBI myocardial perfusion studies, to avoid hot liver inferior wall artifact, (ii) all whole body FDG PET, all lung V/Q SPECT (which have a short acquisition time) and all gated {sup 201}TI myocardial perfusion studies due to improved noise characteristics of OSEM in these studies; (iii) studies with measured, non-uniform attenuation correction. With the accelerated OSEM algorithm, iterative reconstruction is practical for routine clinical applications and we have found OSEM to provide clearly superior reconstructions for the areas listed above and are investigating its application to other studies. In clinical use, we have not found OSEM to introduce artifacts which would not also occur with FBP, e.g. uncorrected patient motion will cause artifacts with both OSEM and FBP.

  4. Adaptive Adjustment of Relaxation Parameters for Algebraic Reconstruction Technique and its Possible Application to Sparsity Prior X-ray CT Reconstruction

    CERN Document Server

    Saha, Sajib; Lambert, Andrew; Pickering, Mark

    2015-01-01

    In this paper, we systematically evaluate the performance of adaptive adjustment of the relaxation parameters of various iterative algorithms for X-ray CT reconstruction relying on sparsity priors. Sparsity prior has been found to be an efficient strategy in CT reconstruction where significantly fewer attenuation measurements are available. Sparsity prior CT reconstruction relies on iterative algorithms such as the algebraic reconstruction technique (ART) to produce a crude reconstruction based on which a sparse approximation is performed. Data driven adjustment of relaxation has been found to ensure better convergence than traditional relaxation for ART. In this paper, we study the performance of such data driven relaxation on a (CS) compressed sensing environment. State-of-the-art algorithms are implemented and their performance analyzed in regard to conventional and data-driven relaxation. Experiments are performed both on simulated and real environments. For the simulated case, experiments are conducted w...

  5. Nuclear introns outperform mitochondrial DNA in inter-specific phylogenetic reconstruction: Lessons from horseshoe bats (Rhinolophidae: Chiroptera).

    Science.gov (United States)

    Dool, Serena E; Puechmaille, Sebastien J; Foley, Nicole M; Allegrini, Benjamin; Bastian, Anna; Mutumi, Gregory L; Maluleke, Tinyiko G; Odendaal, Lizelle J; Teeling, Emma C; Jacobs, David S

    2016-04-01

    Despite many studies illustrating the perils of utilising mitochondrial DNA in phylogenetic studies, it remains one of the most widely used genetic markers for this purpose. Over the last decade, nuclear introns have been proposed as alternative markers for phylogenetic reconstruction. However, the resolution capabilities of mtDNA and nuclear introns have rarely been quantified and compared. In the current study we generated a novel ∼5kb dataset comprising six nuclear introns and a mtDNA fragment. We assessed the relative resolution capabilities of the six intronic fragments with respect to each other, when used in various combinations together, and when compared to the traditionally used mtDNA. We focused on a major clade in the horseshoe bat family (Afro-Palaearctic clade; Rhinolophidae) as our case study. This old, widely distributed and speciose group contains a high level of conserved morphology. This morphological stasis renders the reconstruction of the phylogeny of this group with traditional morphological characters complex. We sampled multiple individuals per species to represent their geographic distributions as best as possible (122 individuals, 24 species, 68 localities). We reconstructed the species phylogeny using several complementary methods (partitioned Maximum Likelihood and Bayesian and Bayesian multispecies-coalescent) and made inferences based on consensus across these methods. We computed pairwise comparisons based on Robinson-Foulds tree distance metric between all Bayesian topologies generated (27,000) for every gene(s) and visualised the tree space using multidimensional scaling (MDS) plots. Using our supported species phylogeny we estimated the ancestral state of key traits of interest within this group, e.g. echolocation peak frequency which has been implicated in speciation. Our results revealed many potential cryptic species within this group, even in taxa where this was not suspected a priori and also found evidence for mt

  6. Markov Random Field Surface Reconstruction

    DEFF Research Database (Denmark)

    Paulsen, Rasmus Reinhold; Bærentzen, Jakob Andreas; Larsen, Rasmus

    2010-01-01

    ) and knowledge about data (the observation model) in an orthogonal fashion. Local models that account for both scene-specific knowledge and physical properties of the scanning device are described. Furthermore, how the optimal distance field can be computed is demonstrated using conjugate gradients, sparse......A method for implicit surface reconstruction is proposed. The novelty in this paper is the adaption of Markov Random Field regularization of a distance field. The Markov Random Field formulation allows us to integrate both knowledge about the type of surface we wish to reconstruct (the prior...

  7. Tragal reconstruction after tumor excision.

    Science.gov (United States)

    Coombs, Christopher J; Lin, Frank

    2015-02-01

    The tragus forms a distinct and important landmark in the overall artistic and anatomical landscape of the ear. Despite its small size, it functions to cover and prevent direct access to the ear canal. Aesthetically, it has an important role in defining the morphology of the auricle in 3 dimensions, not only covering the meatus but also casting a shadow into the conchal bowl that gives the impression of depth. Most of the techniques for tragal reconstruction are associated with creation of a tragus in patients with microtia. We present here a new technique for tragal reconstruction in the setting of tumor ablation.

  8. Vascular Reconstruction in Hepatic Malignancy.

    Science.gov (United States)

    Berumen, Jennifer; Hemming, Alan

    2016-04-01

    With surgery for hepatic malignancy, there are poor options for chemotherapy; many patients are deemed unresectable because of vascular involvement or location of tumors. Over the past few decades, advances in surgical technique have allowed resection of these tumors with vascular reconstruction to achieve negative margins and improve chances for survival. This article reviews those reconstruction techniques and outcomes in detail, including in situ perfusion and ex vivo liver surgery, and provides a discussion of implications and operative planning for patients with hepatic malignancy in order to provide surgeons with better understanding of these complicated operations.

  9. Rational Reconstructions of Modern Physics

    CERN Document Server

    Mittelstaedt, Peter

    2011-01-01

    Newton’s classical physics and its underlying ontology are loaded with several metaphysical hypotheses that cannot be justified by rational reasoning nor by experimental evidence. Furthermore, it is well known that some of these hypotheses are not contained in the great theories of modern physics, such as the theory of relativity and quantum mechanics. This book shows that, on the basis of Newton’s classical physics and by rational reconstruction, the theory of relativity as well as quantum mechanics can be obtained by partly eliminating or attenuating the metaphysical hypotheses. Moreover, it is shown that these reconstructions do not require additional hypotheses or new experimental results.

  10. On ECG reconstruction using weighted-compressive sensing.

    Science.gov (United States)

    Zonoobi, Dornoosh; Kassim, Ashraf A

    2014-06-01

    The potential of the new weighted-compressive sensing approach for efficient reconstruction of electrocardiograph (ECG) signals is investigated. This is motivated by the observation that ECG signals are hugely sparse in the frequency domain and the sparsity changes slowly over time. The underlying idea of this approach is to extract an estimated probability model for the signal of interest, and then use this model to guide the reconstruction process. The authors show that the weighted-compressive sensing approach is able to achieve reconstruction performance comparable with the current state-of-the-art discrete wavelet transform-based method, but with substantially less computational cost to enable it to be considered for use in the next generation of miniaturised wearable ECG monitoring devices.

  11. Analysis Operator Learning and Its Application to Image Reconstruction

    CERN Document Server

    Hawe, Simon; Diepold, Klaus

    2012-01-01

    Exploiting a priori known structural information lies at the core of many image reconstruction methods that can be stated as inverse problems. The synthesis model, which assumes that images can be decomposed into a linear combination of very few atoms of some dictionary, is now a well established tool for the design of image reconstruction algorithms. An interesting alternative is the analysis model, where the signal is multiplied by an analysis operator and the outcome is assumed to be the sparse. This approach has only recently gained increasing interest. The quality of reconstruction methods based on an analysis model severely depends on the right choice of the suitable operator. In this work, we present an algorithm for learning an analysis operator from training images. Our method is based on an $\\ell_p$-norm minimization on the set of full rank matrices with normalized columns. We carefully introduce the employed conjugate gradient method on manifolds, and explain the underlying geometry of the constrai...

  12. Human Metabolic Network: Reconstruction, Simulation, and Applications in Systems Biology

    Science.gov (United States)

    Wu, Ming; Chan, Christina

    2012-01-01

    Metabolism is crucial to cell growth and proliferation. Deficiency or alterations in metabolic functions are known to be involved in many human diseases. Therefore, understanding the human metabolic system is important for the study and treatment of complex diseases. Current reconstructions of the global human metabolic network provide a computational platform to integrate genome-scale information on metabolism. The platform enables a systematic study of the regulation and is applicable to a wide variety of cases, wherein one could rely on in silico perturbations to predict novel targets, interpret systemic effects, and identify alterations in the metabolic states to better understand the genotype-phenotype relationships. In this review, we describe the reconstruction of the human metabolic network, introduce the constraint based modeling approach to analyze metabolic networks, and discuss systems biology applications to study human physiology and pathology. We highlight the challenges and opportunities in network reconstruction and systems modeling of the human metabolic system. PMID:24957377

  13. The Role of the Army in North Carolina Reconstruction 1865-1877

    Science.gov (United States)

    1991-01-01

    17. Edward McPherson, The Political History of the United States of America during the Period of Reconstruction (Washington D.C.: Philp & Solomons...the United States of America during the Period of Reconstruction (Washin% ton D.C.: Philp & Solomons, 1871), 192. 4. McPherson, 192, 335-336. 5...unreliable figure. Acting under department orders, Lieutenant Paul Hambrick, a native of the area, arrived to investigate the situation.6 To this point

  14. Reconstructing the population genetic history of the Caribbean.

    Directory of Open Access Journals (Sweden)

    Andrés Moreno-Estrada

    2013-11-01

    Full Text Available The Caribbean basin is home to some of the most complex interactions in recent history among previously diverged human populations. Here, we investigate the population genetic history of this region by characterizing patterns of genome-wide variation among 330 individuals from three of the Greater Antilles (Cuba, Puerto Rico, Hispaniola, two mainland (Honduras, Colombia, and three Native South American (Yukpa, Bari, and Warao populations. We combine these data with a unique database of genomic variation in over 3,000 individuals from diverse European, African, and Native American populations. We use local ancestry inference and tract length distributions to test different demographic scenarios for the pre- and post-colonial history of the region. We develop a novel ancestry-specific PCA (ASPCA method to reconstruct the sub-continental origin of Native American, European, and African haplotypes from admixed genomes. We find that the most likely source of the indigenous ancestry in Caribbean islanders is a Native South American component shared among inland Amazonian tribes, Central America, and the Yucatan peninsula, suggesting extensive gene flow across the Caribbean in pre-Columbian times. We find evidence of two pulses of African migration. The first pulse--which today is reflected by shorter, older ancestry tracts--consists of a genetic component more similar to coastal West African regions involved in early stages of the trans-Atlantic slave trade. The second pulse--reflected by longer, younger tracts--is more similar to present-day West-Central African populations, supporting historical records of later transatlantic deportation. Surprisingly, we also identify a Latino-specific European component that has significantly diverged from its parental Iberian source populations, presumably as a result of small European founder population size. We demonstrate that the ancestral components in admixed genomes can be traced back to distinct sub

  15. Concluding Report: Quantitative Tomography Simulations and Reconstruction Algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Aufderheide, M B; Martz, H E; Slone, D M; Jackson, J A; Schach von Wittenau, A E; Goodman, D M; Logan, C M; Hall, J M

    2002-02-01

    In this report we describe the original goals and final achievements of this Laboratory Directed Research and Development project. The Quantitative was Tomography Simulations and Reconstruction Algorithms project (99-ERD-015) funded as a multi-directorate, three-year effort to advance the state of the art in radiographic simulation and tomographic reconstruction by improving simulation and including this simulation in the tomographic reconstruction process. Goals were to improve the accuracy of radiographic simulation, and to couple advanced radiographic simulation tools with a robust, many-variable optimization algorithm. In this project, we were able to demonstrate accuracy in X-Ray simulation at the 2% level, which is an improvement of roughly a factor of 5 in accuracy, and we have successfully coupled our simulation tools with the CCG (Constrained Conjugate Gradient) optimization algorithm, allowing reconstructions that include spectral effects and blurring in the reconstructions. Another result of the project was the assembly of a low-scatter X-Ray imaging facility for use in nondestructive evaluation applications. We conclude with a discussion of future work.

  16. Fermi-surface reconstruction by stripe order in cuprate superconductors.

    Science.gov (United States)

    Laliberté, F; Chang, J; Doiron-Leyraud, N; Hassinger, E; Daou, R; Rondeau, M; Ramshaw, B J; Liang, R; Bonn, D A; Hardy, W N; Pyon, S; Takayama, T; Takagi, H; Sheikin, I; Malone, L; Proust, C; Behnia, K; Taillefer, Louis

    2011-08-16

    The origin of pairing in a superconductor resides in the underlying normal state. In the cuprate high-temperature superconductor YBa(2)Cu(3)O(y) (YBCO), application of a magnetic field to suppress superconductivity reveals a ground state that appears to break the translational symmetry of the lattice, pointing to some density-wave order. Here we use a comparative study of thermoelectric transport in the cuprates YBCO and La(1.8-x)Eu(0.2)Sr(x)CuO(4) (Eu-LSCO) to show that the two materials exhibit the same process of Fermi-surface reconstruction as a function of temperature and doping. The fact that in Eu-LSCO this reconstruction coexists with spin and charge modulations that break translational symmetry shows that stripe order is the generic non-superconducting ground state of hole-doped cuprates.

  17. Continuous Variable Quantum State Sharing via Quantum Disentanglement

    CERN Document Server

    Lance, A M; Bowen, W P; Sanders, B C; Tyc, T; Ralph, T C; Lam, P K; Lance, Andrew M.; Symul, Thomas; Bowen, Warwick P.; Sanders, Barry C.; Tyc, Tomas; Ralph, Timothy C.; Lam, Ping Koy

    2004-01-01

    Quantum state sharing is a protocol where perfect reconstruction of quantum states is achieved with incomplete or partial information in a multi-partite quantum networks. Quantum state sharing allows for secure communication in a quantum network where partial information is lost or acquired by malicious parties. This protocol utilizes entanglement for the secret state distribution, and a class of "quantum disentangling" protocols for the state reconstruction. We demonstrate a quantum state sharing protocol in which a tripartite entangled state is used to encode and distribute a secret state to three players. Any two of these players can collaborate to reconstruct the secret state, whilst individual players obtain no information. We investigate a number of quantum disentangling processes and experimentally demonstrate quantum state reconstruction using two of these protocols. We experimentally measure a fidelity, averaged over all reconstruction permutations, of F = 0.73. A result achievable only by using quan...

  18. Reconstructing Native American Population History

    Science.gov (United States)

    Reich, David; Patterson, Nick; Campbell, Desmond; Tandon, Arti; Mazieres, Stéphane; Ray, Nicolas; Parra, Maria V.; Rojas, Winston; Duque, Constanza; Mesa, Natalia; García, Luis F.; Triana, Omar; Blair, Silvia; Maestre, Amanda; Dib, Juan C.; Bravi, Claudio M.; Bailliet, Graciela; Corach, Daniel; Hünemeier, Tábita; Bortolini, Maria-Cátira; Salzano, Francisco M.; Petzl-Erler, María Luiza; Acuña-Alonzo, Victor; Aguilar-Salinas, Carlos; Canizales-Quinteros, Samuel; Tusié-Luna, Teresa; Riba, Laura; Rodríguez-Cruz, Maricela; Lopez-Alarcón, Mardia; Coral-Vazquez, Ramón; Canto-Cetina, Thelma; Silva-Zolezzi, Irma; Fernandez-Lopez, Juan Carlos; Contreras, Alejandra V.; Jimenez-Sanchez, Gerardo; Gómez-Vázquez, María José; Molina, Julio; Carracedo, Ángel; Salas, Antonio; Gallo, Carla; Poletti, Giovanni; Witonsky, David B.; Alkorta-Aranburu, Gorka; Sukernik, Rem I.; Osipova, Ludmila; Fedorova, Sardana; Vasquez, René; Villena, Mercedes; Moreau, Claudia; Barrantes, Ramiro; Pauls, David; Excoffier, Laurent; Bedoya, Gabriel; Rothhammer, Francisco; Dugoujon, Jean Michel; Larrouy, Georges; Klitz, William; Labuda, Damian; Kidd, Judith; Kidd, Kenneth; Rienzo, Anna Di; Freimer, Nelson B.; Price, Alkes L.; Ruiz-Linares, Andrés

    2013-01-01

    The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved1–5. One contentious issue is whether the settlement occurred via a single6–8 or multiple streams of migration from Siberia9–15. The pattern of dispersals within the Americas is also poorly understood. To address these questions at higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. We show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call “First American”. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan-speakers on both sides of the Panama Isthmus, who have ancestry from both North and South America. PMID:22801491

  19. Reconstructing Native American population history.

    Science.gov (United States)

    Reich, David; Patterson, Nick; Campbell, Desmond; Tandon, Arti; Mazieres, Stéphane; Ray, Nicolas; Parra, Maria V; Rojas, Winston; Duque, Constanza; Mesa, Natalia; García, Luis F; Triana, Omar; Blair, Silvia; Maestre, Amanda; Dib, Juan C; Bravi, Claudio M; Bailliet, Graciela; Corach, Daniel; Hünemeier, Tábita; Bortolini, Maria Cátira; Salzano, Francisco M; Petzl-Erler, María Luiza; Acuña-Alonzo, Victor; Aguilar-Salinas, Carlos; Canizales-Quinteros, Samuel; Tusié-Luna, Teresa; Riba, Laura; Rodríguez-Cruz, Maricela; Lopez-Alarcón, Mardia; Coral-Vazquez, Ramón; Canto-Cetina, Thelma; Silva-Zolezzi, Irma; Fernandez-Lopez, Juan Carlos; Contreras, Alejandra V; Jimenez-Sanchez, Gerardo; Gómez-Vázquez, Maria José; Molina, Julio; Carracedo, Angel; Salas, Antonio; Gallo, Carla; Poletti, Giovanni; Witonsky, David B; Alkorta-Aranburu, Gorka; Sukernik, Rem I; Osipova, Ludmila; Fedorova, Sardana A; Vasquez, René; Villena, Mercedes; Moreau, Claudia; Barrantes, Ramiro; Pauls, David; Excoffier, Laurent; Bedoya, Gabriel; Rothhammer, Francisco; Dugoujon, Jean-Michel; Larrouy, Georges; Klitz, William; Labuda, Damian; Kidd, Judith; Kidd, Kenneth; Di Rienzo, Anna; Freimer, Nelson B; Price, Alkes L; Ruiz-Linares, Andrés

    2012-08-16

    The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

  20. Estimating ancestral distributions of lineages with uncertain sister groups: a statistical approach to Dispersal-Vicariance Analysis and a case using Aesculus L. (Sapindaceae) including fossils

    Institute of Scientific and Technical Information of China (English)

    A.J. HARRIS; Qiu-Yun (Jenny) XIANG

    2009-01-01

    We propose a simple statistical approach for using Dispersal-Vicariance Analysis (DIVA) software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as P(rY)= Σnt=1 F(rY)tPt where Y is a node, and F(rY) is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage "x", where x may vary due to phylogenetic uncertainty (polytomies and nodes with posterior probability <100%). Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp* F(rY) on the Bayesian consensus tree when both variables are < 100%, where pp is the posterior probability and F(rY) is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and ofAesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages.Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the

  1. A survey of urban reconstruction

    KAUST Repository

    Musialski, Przemyslaw

    2013-05-10

    This paper provides a comprehensive overview of urban reconstruction. While there exists a considerable body of literature, this topic is still under active research. The work reviewed in this survey stems from the following three research communities: computer graphics, computer vision and photogrammetry and remote sensing. Our goal is to provide a survey that will help researchers to better position their own work in the context of existing solutions, and to help newcomers and practitioners in computer graphics to quickly gain an overview of this vast field. Further, we would like to bring the mentioned research communities to even more interdisciplinary work, since the reconstruction problem itself is by far not solved. This paper provides a comprehensive overview of urban reconstruction. While there exists a considerable body of literature, this topic is still under active research. The work reviewed in this survey stems from the following three research communities: computer graphics, computer vision and photogrammetry and remote sensing. Our goal is to provide a survey that will help researchers to better position their own work in the context of existing solutions, and to help newcomers and practitioners in computer graphics to quickly gain an overview of this vast field. Further, we would like to bring the mentioned research communities to even more interdisciplinary work, since the reconstruction problem itself is by far not solved. © 2013 The Eurographics Association and John Wiley & Sons Ltd.

  2. Reconstructing Death in Postmodern Society.

    Science.gov (United States)

    Kastenbaum, Robert

    1993-01-01

    Examines interaction between emerging thanatological movement and its sociohistorical context. Notes that thanatology will take on new shape as individuals and society attempt to cope with postmodernistic forces and deconstructive mentality. Considers prospect for authentic solidarity against distress in reconstructed death system. (Author/NB)

  3. Dating the origin and dispersal of Human Papillomavirus type 16 on the basis of ancestral human migrations.

    Science.gov (United States)

    Zehender, Gianguglielmo; Frati, Elena Rosanna; Martinelli, Marianna; Bianchi, Silvia; Amendola, Antonella; Ebranati, Erika; Ciccozzi, Massimo; Galli, Massimo; Lai, Alessia; Tanzi, Elisabetta

    2016-04-01

    A major limitation when reconstructing the origin and evolution of HPV-16 is the lack of reliable substitution rate estimates for the viral genes. On the basis of the hypothesis of human HPV-16 co-divergence, we estimated a mean evolutionary rate of 1.47×10(-7) (95% HPD=0.64-2.47×10(-7)) subs/site/year for the viral LCR region. The results of a Bayesian phylogeographical analysis suggest that the currently circulating HPV-16 most probably originated in Africa about 110 thousand years ago (Kya), before giving rise to four known geographical lineages: the Asian/European lineage, which most probably originated in Asia a mean 38 Kya, and the Asian/American and two African lineages, which probably respectively originated about 33 and 27 Kya. These data closely reflect current hypotheses concerning modern human expansion based on studies of mitochondrial DNA phylogeny. The correlation between ancient human migration and the present HPV phylogeny may be explained by the co-existence of modes of transmission other than sexual transmission.

  4. Mandibular reconstruction in adults: a review.

    NARCIS (Netherlands)

    Goh, B.T.; Lee, S.; Tideman, H.; Stoelinga, P.J.W.

    2008-01-01

    Mandibular defects may result from trauma, inflammatory disease and benign or malignant tumours. Mastication, speech and facial aesthetics are often severely compromised without reconstruction. The goal of mandibular reconstruction is to restore facial form and function, implying repair of mandibula

  5. Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica

    Directory of Open Access Journals (Sweden)

    Victoria Sosa

    2016-11-01

    Full Text Available Background Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Methods Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Results Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from

  6. Reconstructing the interaction term between dark matter and dark energy

    CERN Document Server

    Cueva, Freddy

    2010-01-01

    We apply a parametric reconstruction method to a homogeneous, isotropic and spatially flat Friedmann-Robertson-Walker (FRW) cosmological model filled of a fluid of dark energy (DE) with constant equation of state parameter interacting with dark matter (DM). The reconstruction method is based on expansions of the general interaction term and the relevant cosmological variables in terms of Chebyshev polynomials which form a complete set orthonormal functions. This interaction term describes an exchange of energy flow between the DE and DM within dark sector. To show how the method works we do the reconstruction of the interaction function expanding it in terms of only the first three Chebyshev polynomials and obtain the best estimation for the coefficients of the expansion as well as for the DE equation of the state constant parameter w using the type Ia Supernova SCP Union data set (307 SNe-Ia). The preliminary reconstruction shows that in the best scenario there is an energy transfer from DM to DE which worse...

  7. Top reconstruction and boosted top experimental overview

    CERN Document Server

    Skinnari, Louise

    2015-01-01

    An overview of techniques used to reconstruct resolved and boosted top quarks is presented. Techniques for resolved top quark reconstruction include kinematic likelihood fitters and pseudo- top reconstruction. Many tools and methods are available for the reconstruction of boosted top quarks, such as jet grooming techniques, jet substructure variables, and dedicated top taggers. Different techniques as used by ATLAS and C