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Sample records for ancestral state reconstruction

  1. Global Alignment of Molecular Sequences via Ancestral State Reconstruction

    CERN Document Server

    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...

  2. 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

  3. Ancestral state reconstruction of body size in the Caniformia (Carnivora, Mammalia): the effects of incorporating data from the fossil record.

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    Finarelli, John A; Flynn, John J

    2006-04-01

    A recent molecular phylogeny of the mammalian order Carnivora implied large body size as the ancestral condition for the caniform subclade Arctoidea using the distribution of species mean body sizes among living taxa. "Extant taxa-only" approaches such as these discount character state observations for fossil members of living clades and completely ignore data from extinct lineages. To more rigorously reconstruct body sizes of ancestral forms within the Caniformia, body size and first appearance data were collected for 149 extant and 367 extinct taxa. Body sizes were reconstructed for four ancestral nodes using weighted squared-change parsimony on log-transformed body mass data. Reconstructions based on extant taxa alone favored large body sizes (on the order of 10 to 50 kg) for the last common ancestors of both the Caniformia and Arctoidea. In contrast, reconstructions incorporating fossil data support small body sizes (fossil data was discarded, body size reconstructions became ambiguous, demonstrating that incorporating both character state and temporal information from fossil taxa unambiguously supports a small ancestral body size, thereby falsifying hypotheses derived from extant taxa alone. Body size reconstructions for Caniformia, Arctoidea, and Musteloidea were not sensitive to potential errors introduced by uncertainty in the position of extinct lineages relative to the molecular topology, or to missing body size data for extinct members of an entire major clade (the aquatic Pinnipedia). Incorporating character state observations and temporal information from the fossil record into hypothesis testing has a significant impact on the ability to reconstruct ancestral characters and constrains the range of potential hypotheses of character evolution. Fossil data here provide the evidence to reliably document trends of both increasing and decreasing body size in several caniform clades. More generally, including fossils in such analyses incorporates evidence of

  4. Ancestral reconstruction of tick lineages.

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    Mans, Ben J; de Castro, Minique H; Pienaar, Ronel; de Klerk, Daniel; Gaven, Philasande; Genu, Siyamcela; Latif, Abdalla A

    2016-06-01

    Ancestral reconstruction in its fullest sense aims to describe the complete evolutionary history of a lineage. This depends on accurate phylogenies and an understanding of the key characters of each parental lineage. An attempt is made to delineate our current knowledge with regard to the ancestral reconstruction of the tick (Ixodida) lineage. Tick characters may be assigned to Core of Life, Lineages of Life or Edges of Life phenomena depending on how far back these characters may be assigned in the evolutionary Tree of Life. These include housekeeping genes, sub-cellular systems, heme processing (Core of Life), development, moulting, appendages, nervous and organ systems, homeostasis, respiration (Lineages of Life), specific adaptations to a blood-feeding lifestyle, including the complexities of salivary gland secretions and tick-host interactions (Edges of Life). The phylogenetic relationships of lineages, their origins and importance in ancestral reconstruction are discussed. Uncertainties with respect to systematic relationships, ancestral reconstruction and the challenges faced in comparative transcriptomics (next-generation sequencing approaches) are highlighted. While almost 150 years of information regarding tick biology have been assembled, progress in recent years indicates that we are in the infancy of understanding tick evolution. Even so, broad reconstructions can be made with relation to biological features associated with various lineages. Conservation of characters shared with sister and parent lineages are evident, but appreciable differences are present in the tick lineage indicating modification with descent, as expected for Darwinian evolutionary theory. Many of these differences can be related to the hematophagous lifestyle of ticks. PMID:26868413

  5. Hidden State Prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses

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    Jesse Robert Zaneveld

    2014-08-01

    Full Text Available Complex symbioses between animal or plant hosts and their associated microbiotas can involve thousands of species and millions of genes. Because of the number of interacting partners, it is often impractical to study all organisms or genes in these host-microbe symbioses individually. Yet new phylogenetic predictive methods can use the wealth of accumulated data on diverse model organisms to make inferences into the properties of less well-studied species and gene families. Predictive functional profiling methods use evolutionary models based on the properties of studied relatives to put bounds on the likely characteristics of an organism or gene that has not yet been studied in detail. These techniques have been applied to predict diverse features of host-associated microbial communities ranging from the enzymatic function of uncharacterized genes to the gene content of uncultured microorganisms. We consider these phylogenetically-informed predictive techniques from disparate fields as examples of a general class of algorithms for Hidden State Prediction (HSP, and argue that HSP methods have broad value in predicting organismal traits in a variety of contexts, including the study of complex host-microbe symbioses.

  6. Hidden state prediction: a modification of classic ancestral state reconstruction algorithms helps unravel complex symbioses.

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    Zaneveld, Jesse R R; Thurber, Rebecca L V

    2014-01-01

    Complex symbioses between animal or plant hosts and their associated microbiotas can involve thousands of species and millions of genes. Because of the number of interacting partners, it is often impractical to study all organisms or genes in these host-microbe symbioses individually. Yet new phylogenetic predictive methods can use the wealth of accumulated data on diverse model organisms to make inferences into the properties of less well-studied species and gene families. Predictive functional profiling methods use evolutionary models based on the properties of studied relatives to put bounds on the likely characteristics of an organism or gene that has not yet been studied in detail. These techniques have been applied to predict diverse features of host-associated microbial communities ranging from the enzymatic function of uncharacterized genes to the gene content of uncultured microorganisms. We consider these phylogenetically informed predictive techniques from disparate fields as examples of a general class of algorithms for Hidden State Prediction (HSP), and argue that HSP methods have broad value in predicting organismal traits in a variety of contexts, including the study of complex host-microbe symbioses. PMID:25202302

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

    Institute of Scientific and Technical Information of China (English)

    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.

  8. Algorithms of Ancestral Gene Length Reconstruction

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    Alexander Bolshoy

    2013-01-01

    Full Text Available Ancestral sequence reconstruction is a well-known problem in molecular evolution. The problem presented in this study is inspired by sequence reconstruction, but instead of leaf-associated sequences we consider only their lengths. We call this problem ancestral gene length reconstruction. It is a problem of finding an optimal labeling which minimizes the total length’s sum of the edges, where both a tree and nonnegative integers associated with corresponding leaves of the tree are the input. In this paper we give a linear algorithm to solve the problem on binary trees for the Manhattan cost function .

  9. An experimental phylogeny to benchmark ancestral sequence reconstruction.

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    Randall, Ryan N; Radford, Caelan E; Roof, Kelsey A; Natarajan, Divya K; Gaucher, Eric A

    2016-01-01

    Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed many key mechanisms of molecular evolution. One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation. Here we build an experimental phylogeny using the gene of a single red fluorescent protein to address this criticism. The evolved phylogeny consists of 19 operational taxonomic units (leaves) and 17 ancestral bifurcations (nodes) that display a wide variety of fluorescent phenotypes. The 19 leaves then serve as 'modern' sequences that we subject to ASR analyses using various algorithms and to benchmark against the known ancestral genotypes and ancestral phenotypes. We confirm computer simulations that show all algorithms infer ancient sequences with high accuracy, yet we also reveal wide variation in the phenotypes encoded by incorrectly inferred sequences. Specifically, Bayesian methods incorporating rate variation significantly outperform the maximum parsimony criterion in phenotypic accuracy. Subsampling of extant sequences had minor effect on the inference of ancestral sequences. PMID:27628687

  10. 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.

  11. Fast phylogeny reconstruction through learning of ancestral sequences

    CERN Document Server

    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...

  12. Reconstructed Ancestral Enzymes Impose a Fitness Cost upon Modern Bacteria Despite Exhibiting Favourable Biochemical Properties.

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    Hobbs, Joanne K; Prentice, Erica J; Groussin, Mathieu; Arcus, Vickery L

    2015-10-01

    Ancestral sequence reconstruction has been widely used to study historical enzyme evolution, both from biochemical and cellular perspectives. Two properties of reconstructed ancestral proteins/enzymes are commonly reported--high thermostability and high catalytic activity--compared with their contemporaries. Increased protein stability is associated with lower aggregation rates, higher soluble protein abundance and a greater capacity to evolve, and therefore, these proteins could be considered "superior" to their contemporary counterparts. In this study, we investigate the relationship between the favourable in vitro biochemical properties of reconstructed ancestral enzymes and the organismal fitness they confer in vivo. We have previously reconstructed several ancestors of the enzyme LeuB, which is essential for leucine biosynthesis. Our initial fitness experiments revealed that overexpression of ANC4, a reconstructed LeuB that exhibits high stability and activity, was only able to partially rescue the growth of a ΔleuB strain, and that a strain complemented with this enzyme was outcompeted by strains carrying one of its descendants. When we expanded our study to include five reconstructed LeuBs and one contemporary, we found that neither in vitro protein stability nor the catalytic rate was correlated with fitness. Instead, fitness showed a strong, negative correlation with estimated evolutionary age (based on phylogenetic relationships). Our findings suggest that, for reconstructed ancestral enzymes, superior in vitro properties do not translate into organismal fitness in vivo. The molecular basis of the relationship between fitness and the inferred age of ancestral LeuB enzymes is unknown, but may be related to the reconstruction process. We also hypothesise that the ancestral enzymes may be incompatible with the other, contemporary enzymes of the metabolic network. PMID:26349578

  13. 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.

  14. 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.

  15. 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.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  18. The imperfect ancestral recombination graph reconstruction problem: upper bounds for recombination and homoplasy.

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    Lam, Fumei; Tarpine, Ryan; Istrail, Sorin

    2010-06-01

    One of the central problems in computational biology is the reconstruction of evolutionary histories. While models incorporating recombination and homoplasy have been studied separately, a missing component in the theory is a robust and flexible unifying model which incorporates both of these major biological events shaping genetic diversity. In this article, we introduce the first such unifying model and develop algorithms to find the optimal ancestral recombination graph incorporating recombinations and homoplasy events. The power of our framework is the connection between our formulation and the Directed Steiner Arborescence Problem in combinatorial optimization. We implement linear programming techniques as well as heuristics for the Directed Steiner Arborescence Problem, and use our methods to construct evolutionary histories for both simulated and real data sets. PMID:20583925

  19. Permutationally invariant state reconstruction

    CERN Document Server

    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...

  20. 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.

  1. Permutationally invariant state reconstruction

    DEFF Research Database (Denmark)

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

    2012-01-01

    -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...

  2. Reconstruction of the ancestral plastid genome in Geraniaceae reveals a correlation between genome rearrangements, repeats, and nucleotide substitution rates.

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    Weng, Mao-Lun; Blazier, John C; Govindu, Madhumita; Jansen, Robert K

    2014-03-01

    Geraniaceae plastid genomes are highly rearranged, and each of the four genera already sequenced in the family has a distinct genome organization. This study reports plastid genome sequences of six additional species, Francoa sonchifolia, Melianthus villosus, and Viviania marifolia from Geraniales, and Pelargonium alternans, California macrophylla, and Hypseocharis bilobata from Geraniaceae. These genome sequences, combined with previously published species, provide sufficient taxon sampling to reconstruct the ancestral plastid genome organization of Geraniaceae and the rearrangements unique to each genus. The ancestral plastid genome of Geraniaceae has a 4 kb inversion and a reduced, Pelargonium-like small single copy region. Our ancestral genome reconstruction suggests that a few minor rearrangements occurred in the stem branch of Geraniaceae followed by independent rearrangements in each genus. The genomic comparison demonstrates that a series of inverted repeat boundary shifts and inversions played a major role in shaping genome organization in the family. The distribution of repeats is strongly associated with breakpoints in the rearranged genomes, and the proportion and the number of large repeats (>20 bp and >60 bp) are significantly correlated with the degree of genome rearrangements. Increases in the degree of plastid genome rearrangements are correlated with the acceleration in nonsynonymous substitution rates (dN) but not with synonymous substitution rates (dS). Possible mechanisms that might contribute to this correlation, including DNA repair system and selection, are discussed. PMID:24336877

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

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    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.

  4. AAV ancestral reconstruction library enables selection of broadly infectious viral variants.

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    Santiago-Ortiz, J; Ojala, D S; Westesson, O; Weinstein, J R; Wong, S Y; Steinsapir, A; Kumar, S; Holmes, I; Schaffer, D V

    2015-12-01

    Adeno-associated virus (AAV) vectors have achieved clinical efficacy in treating several diseases. However, enhanced vectors are required to extend these landmark successes to other indications and protein engineering approaches may provide the necessary vector improvements to address such unmet medical needs. To generate new capsid variants with potentially enhanced infectious properties and to gain insights into AAV's evolutionary history, we computationally designed and experimentally constructed a putative ancestral AAV library. Combinatorial variations at 32 amino acid sites were introduced to account for uncertainty in their identities. We then analyzed the evolutionary flexibility of these residues, the majority of which have not been previously studied, by subjecting the library to iterative selection on a representative cell line panel. The resulting variants exhibited transduction efficiencies comparable to the most efficient extant serotypes and, in general, ancestral libraries were broadly infectious across the cell line panel, indicating that they favored promiscuity over specificity. Interestingly, putative ancestral AAVs were more thermostable than modern serotypes and did not use sialic acids, galactose or heparan sulfate proteoglycans for cellular entry. Finally, variants mediated 19- to 31-fold higher gene expression in the muscle compared with AAV1, a clinically used serotype for muscle delivery, highlighting their promise for gene therapy. PMID:26186661

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

    Science.gov (United States)

    Hanson-Smith, Victor; Johnson, Alexander

    2016-01-01

    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. PMID:27472806

  6. 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.

  7. 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. PMID:27472806

  8. The forebrain of the Pacific hagfish: a cladistic reconstruction of the ancestral craniate forebrain.

    Science.gov (United States)

    Wicht, H; Northcutt, R G

    1992-01-01

    The forebrain of the Pacific hagfish is described with regard to its morphology, cytoarchitecture, and secondary olfactory projections. The forebrain ventricular system is greatly reduced in adult hagfishes, although vestiges of ventricular structures can still be recognized. In order to clarify topographical relationships within the forebrain, we provide a three-dimensional reconstruction of the ventricular system, including the vestigial portions. Topography and embryology lead us to conclude that the 'primordium hippocampi' of previous authors is a diencephalic structure. For topographical and hodological reasons, we interpret the 'area basalis' of previous authors to be part of the preoptic region, and we identify a part of the so-called 'nucleus olfactorius anterior' as the homologue of the striatum. The laminated pallium is dominated by secondary olfactory projections and shows a high degree of regional cytoarchitectural specialization, as does the entire forebrain. In all, 42 cell groups are identified in the forebrain of hagfishes (compared to only about 25 in lampreys, for example). This surprisingly high degree of cytoarchitectural complexity prompted us to re-examine the phylogenetic history of craniate brains with this complexity in mind. In this paper we use cladistic methodology to reconstruct a morphotype, and we conclude that the forebrains of the earliest craniates may have been more complex than previously believed. This reconstruction includes hypotheses regarding the general morphology, secondary olfactory system, and visual system, as well as the relative sizes of major divisions of the forebrain in the earliest craniates.

  9. 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...

  10. 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

  11. 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…

  12. 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

  13. Quantum State Reconstruction From Incomplete Data

    CERN Document Server

    Buzek, V; Derka, R; Adam, G; Wiedemann, H

    1998-01-01

    Knowing and guessing, these are two essential epistemological pillars in the theory of quantum-mechanical measurement. As formulated quantum mechanics is a statistical theory. In general, a priori unknown states can be completely determined only when measurements on infinite ensembles of identically prepared quantum systems are performed. But how one can estimate (guess) quantum state when just incomplete data are available (known)? What is the most reliable estimation based on a given measured data? What is the optimal measurement providing only a finite number of identically prepared quantum objects are available? These are some of the questions we address. We present several schemes for a reconstruction of states of quantum systems from measured data: (1) We show how the maximum entropy (MaxEnt) principle can be efficiently used for an estimation of quantum states on incomplete observation levels. (2) We show how Bayesian inference can be used for reconstruction of quantum states when only a finite number ...

  14. Generalized theorems for nonlinear state space reconstruction.

    Directory of Open Access Journals (Sweden)

    Ethan R Deyle

    Full Text Available Takens' theorem (1981 shows how lagged variables of a single time series can be used as proxy variables to reconstruct an attractor for an underlying dynamic process. State space reconstruction (SSR from single time series has been a powerful approach for the analysis of the complex, non-linear systems that appear ubiquitous in the natural and human world. The main shortcoming of these methods is the phenomenological nature of attractor reconstructions. Moreover, applied studies show that these single time series reconstructions can often be improved ad hoc by including multiple dynamically coupled time series in the reconstructions, to provide a more mechanistic model. Here we provide three analytical proofs that add to the growing literature to generalize Takens' work and that demonstrate how multiple time series can be used in attractor reconstructions. These expanded results (Takens' theorem is a special case apply to a wide variety of natural systems having parallel time series observations for variables believed to be related to the same dynamic manifold. The potential information leverage provided by multiple embeddings created from different combinations of variables (and their lags can pave the way for new applied techniques to exploit the time-limited, but parallel observations of natural systems, such as coupled ecological systems, geophysical systems, and financial systems. This paper aims to justify and help open this potential growth area for SSR applications in the natural sciences.

  15. 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

  16. Quantum State Reconstruction Using Atom Optics

    OpenAIRE

    Varcoe, B. T. H.; Sang, R. T.; MacGillivray, W. R.; Stadage, M C

    1999-01-01

    We present a novel technique in which the total internal quantum state of an atom may be reconstructed via the measurement of the momentum transferred to an atom following its interaction with a near resonant travelling wave laser beam. We present the first such measurement and demonstrate the feasibility of the technique.

  17. Character State Reconstruction of Call Diversity in the Neoconocephalus Katydids Reveals High Levels of Convergence.

    Science.gov (United States)

    Frederick, Katy; Schul, Johannes

    2016-01-01

    The katydid genus Neoconocephalus is characterized by high diversity of the acoustic communication system. Both male signals and female preferences have been thoroughly studied in the past. This study used Bayesian character state reconstruction to elucidate the evolutionary history of diverse call traits, based on an existing, well supported phylogenetic hypothesis. The most common male call pattern consisted of continuous calls comprising one fast pulse rate; this pattern is the likely ancestral state in this genus. Three lines of call divergence existed among the species of the genus. First, four species had significantly slower pulse rates. Second, five species had alternating pulse periods, resulting in a double pulse rhythm. Third, several species had discontinuous calls, when pulses were grouped into rhythmically repeated verses. Bayesian character state reconstruction revealed that the double-pulse pattern likely evolved convergently five times; the slow pulse rate also evolved four times independently. Discontinuous calls have evolved twice and occur in two clades; each of which contains reversals to the ancestral continuous calls. Pairwise phylogenetically independent contrast analyses among the three call traits found no significant correlations among the character states of the different traits, supporting the independent evolution of the three call traits. PMID:27110432

  18. 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...

  19. 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.

  20. 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...

  1. Shrinkage Effect in Ancestral Maximum Likelihood

    CERN Document Server

    Mossel, Elchanan; Steel, Mike

    2008-01-01

    Ancestral maximum likelihood (AML) is a method that simultaneously reconstructs a phylogenetic tree and ancestral sequences from extant data (sequences at the leaves). The tree and ancestral sequences maximize the probability of observing the given data under a Markov model of sequence evolution, in which branch lengths are also optimized but constrained to take the same value on any edge across all sequence sites. AML differs from the more usual form of maximum likelihood (ML) in phylogenetics because ML averages over all possible ancestral sequences. ML has long been known to be statistically consistent -- that is, it converges on the correct tree with probability approaching 1 as the sequence length grows. However, the statistical consistency of AML has not been formally determined, despite informal remarks in a literature that dates back 20 years. In this short note we prove a general result that implies that AML is statistically inconsistent. In particular we show that AML can `shrink' short edges in a t...

  2. Estimating Ancestral Population Parameters

    OpenAIRE

    Wakeley, J.; Hey, J.

    1997-01-01

    The expected numbers of different categories of polymorphic sites are derived for two related models of population history: the isolation model, in which an ancestral population splits into two descendents, and the size-change model, in which a single population undergoes an instantaneous change in size. For the isolation model, the observed numbers of shared, fixed, and exclusive polymorphic sites are used to estimate the relative sizes of the three populations, ancestral plus two descendent...

  3. Breast reconstruction: State of the arts

    International Nuclear Information System (INIS)

    Radical mastectomy is still required in many cases, such as inflammatory breast cancer, multicentric breast cancer, large tumour volume and small breast size. In this setting, immediate breast reconstruction is more and more offered for breast cancer patients. But such plastic surgery is still debated, owing to risks of implant complications when postoperative radiotherapy of chest wall is mandatory in locoregional breast cancer management. Here, the review is focused on different type of immediate breast reconstruction and on risk of implants complications with or without postoperative radiotherapy. (authors)

  4. Detection of "punctuated equilibrium" by bayesian estimation of speciation and extinction rates, ancestral character states, and rates of anagenetic and cladogenetic evolution on a molecular phylogeny.

    Science.gov (United States)

    Bokma, Folmer

    2008-11-01

    Algorithms are presented to simultaneously estimate probabilities of speciation and extinction, rates of anagenetic and cladogenetic phenotypic evolution, as well as ancestral character states, from a complete ultrametric species-level phylogeny with dates assigned to all bifurcations and one or more phenotypes in three or more extant species, using Metropolis-Hastings Markov Chain Monte Carlo sampling. The algorithms also estimate missing phenotypes of extant species and numbers of speciation events that occurred on all branches of the phylogeny. The algorithms are discussed and their performance is evaluated using simulated data. That evaluation shows that precise estimation of rates of evolution of one or a few phenotypes requires large phylogenies. Estimation accuracy improves with the number of species on the phylogeny. PMID:18752617

  5. Optimal approach to rotational state reconstruction of linear molecules

    Institute of Scientific and Technical Information of China (English)

    Qin Xiao; Gao Jun-Yi

    2011-01-01

    We present a simulation for the reconstruction of the rotational quantum state of linear molecules to retrieve the density matrix. An optimal approach in the sense of minimal error limit is proposed, in which a variable set of angular frequency is properly chosen and the least square inversion is then applied. This approach of reconstruction from time-dependent molecular-axis angular distribution is proved adaptable for various object states, which has a good numerical stability independent of the selected rotational space.

  6. 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

  7. Phase Transitions in q-States Signal Reconstruction

    Institute of Scientific and Technical Information of China (English)

    孙怡帆

    2012-01-01

    Compressed sensing is a new signM acquisition method that acquires signal in a compressed form and then recovers the signal by the use of computational tools and techniques. This means fewer measurements of signal are needed and thus it will save huge amount of time and storage space. We, in this paper, consider the compressed sensing of sparse integer-valued signal (referred as "q-states signal" throughout the paper). In order to accelerate the speed of reconstruction, we adopt the sparse rather than dense measurement matrices. Using methods and tools developed in statistical physics, we locate the reconstruction limit for Lo-reconstruction method and propose a belief propagation- based algorithm that can deal with instance with large size and its typical reconstruction performance are also analyzed.

  8. 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

  9. 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

  10. Measurement of cardiovascular state using attractor reconstruction analysis

    OpenAIRE

    Charlton, Peter Harcourt; Camporota, Luigi; Smith, John; Nandi, Manasi; Christie, Mark Ian; Aston, Philip; Beale, Richard

    2015-01-01

    Attractor reconstruction (AR) analysis has been used previously to quantify the variability in arterial blood pressure (ABP) signals. Since ABP signals are only available in a minority of clinical scenarios, we sought to determine whether AR could also be performed on more widely available photoplethysmogram (PPG) signals. AR analysis was performed on simultaneous ABP and PPG signals before, during and after a change in cardiovascular state. A novel quality metric was used to eliminate window...

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

    OpenAIRE

    E. Bagan; Baig, M.; A. Monras; Munoz-Tapia, 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 sch...

  12. Reconstructing dynamic molecular states from single-cell time series.

    Science.gov (United States)

    Huang, Lirong; Pauleve, Loic; Zechner, Christoph; Unger, Michael; Hansen, Anders S; Koeppl, Heinz

    2016-09-01

    The notion of state for a system is prevalent in the quantitative sciences and refers to the minimal system summary sufficient to describe the time evolution of the system in a self-consistent manner. This is a prerequisite for a principled understanding of the inner workings of a system. Owing to the complexity of intracellular processes, experimental techniques that can retrieve a sufficient summary are beyond our reach. For the case of stochastic biomolecular reaction networks, we show how to convert the partial state information accessible by experimental techniques into a full system state using mathematical analysis together with a computational model. This is intimately related to the notion of conditional Markov processes and we introduce the posterior master equation and derive novel approximations to the corresponding infinite-dimensional posterior moment dynamics. We exemplify this state reconstruction approach using both in silico data and single-cell data from two gene expression systems in Saccharomyces cerevisiae, where we reconstruct the dynamic promoter and mRNA states from noisy protein abundance measurements. PMID:27605167

  13. 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.

  14. 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.

  15. Decay patterns of edge states at reconstructed armchair graphene edges

    Science.gov (United States)

    Park, Changwon; Ihm, Jisoon; Kim, Gunn

    Density functional theory calculations are used to investigate the electronic structures of localized states at reconstructed armchair graphene edges. We consider graphene nanoribbons with two different edge types and obtain the energy band structures and charge densities of the edge states. By examining the imaginary part of the wave vector in the forbidden energy region, we reveal the decay behavior of the wave functions in graphene. The complex band structures of graphene in the armchair and zigzag directions are presented in the first-principles framework. G.K. acknowledges the support of the Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education (Grant No. 2013R1A1A2009131) and the Priority Research Center Program (Grant No. 2010-0020207).

  16. Mapping ancestral genomes with massive gene loss: a matrix sandwich problem.

    OpenAIRE

    Gavranović, Haris; Chauve, Cedric; Salse, Jérôme; Tannier, Eric

    2011-01-01

    MOTIVATION: Ancestral genomes provide a better way to understand the structural evolution of genomes than the simple comparison of extant genomes. Most ancestral genome reconstruction methods rely on universal markers, that is, homologous families of DNA segments present in exactly one exemplar in every considered species. Complex histories of genes or other markers, undergoing duplications and losses, are rarely taken into account. It follows that some ancestors are inaccessible by these met...

  17. 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...

  18. 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.

  19. 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.

  20. Fables of reconstruction: controlling bias in the dark energy equation of state

    CERN Document Server

    Crittenden, Robert G; Pogosian, Levon; Samushia, Lado; Zhang, Xinmin

    2011-01-01

    We develop an efficient, non-parametric Bayesian method for reconstructing the time evolution of the dark energy equation of state w(z) from observational data. Of particular importance is the choice of prior, which must be chosen carefully to minimise variance and bias in the reconstruction. Using a principal component analysis, we show how a correlated prior can be used to create a smooth reconstruction and also avoid bias in the mean behaviour of w(z). We test our method using Wiener reconstructions based on Fisher matrix projections, and also against more realistic MCMC analyses of simulated data sets for Planck and a future space-based dark energy mission. While the accuracy of our reconstruction depends on the smoothness of the assumed w(z), the relative error for typical dark energy models is <10% out to redshift z=1.5.

  1. The influence of reconstruction on the surface state of Au(110)

    Energy Technology Data Exchange (ETDEWEB)

    Nuber, Andreas; Forster, Frank [Experimentelle Physik II, Universitaet Wuerzburg (Germany); Higashiguchi, Mitsuharu [Graduate School of Science, Hiroshima University, Higashi-Hiroshima (Japan); Blaha, Peter [Institute of Materials Chemistry, Vienna University of Technology (Austria); Shimada, Kenya [Hiroshima Synchrotron Radiation Center, Hiroshima University, Higashi-Hiroshima (Japan); Reinert, Friedrich [Experimentelle Physik II, Universitaet Wuerzburg (Germany); Forschungszentrum Karlsruhe (Germany). Gemeinschaftslabor fuer Nanoanalytik

    2009-07-01

    We present high-resolution angle-resolved photoelectron spectroscopy on Au(110). The unreconstructed surface shows a Shockley-type surface state at E{sub 0}=590 meV whereas on the (2 x 1) missing-row reconstructed surface no such surface state below E{sub F} can be detected. We performed relativistic LDA calculations which agree well with our experimental data. Adsorption of 1 ML Ag on the (2 x 1) reconstructed surface results in a destruction to a (1 x 1) surface structure and a Shockley state appears at E{sub 0}=475 meV. Shifting down the surface state from just above to below E{sub F} by Na adsorption allowed to extrapolate a binding energy on the reconstructed surface of E{sub 0}=-120 meV above the Fermi level.

  2. An algorithm for permutationally invariant state reconstruction for larger qubit numbers

    Energy Technology Data Exchange (ETDEWEB)

    Moroder, Tobias [IQOQI, Innsbruck (Austria); Hyllus, Philipp [Department Theoretical Physics, Bilbao (Spain); IKERBASQUE, Bilbao (Spain); Toth, Geza [Department Theoretical Physics, Bilbao (Spain); IKERBASQUE, Bilbao (Spain); Research Institute for Solid State Physics and Optics, Budapest (Hungary); Schwemmer, Christian; Niggebaum, Alexander; Weinfurter, Harald [MPQ, Garching (Germany); Fakultaet Physik, LMU, Muenchen (Germany); Gaile, Stefanie [DTU Mathematics, Lyngby (Denmark); Guehne, Otfried [IQOQI, Innsbruck (Austria); Department Physik, Siegen (Germany)

    2012-07-01

    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 this state reconstruction task typically requires the solution of a non-linear large-scale optimization problem, this becomes another major challenge in the design of scalable tomography schemes. In this talk we present an efficient state reconstruction scheme for permutationally invariant tomography [PRL 105, 250403]. It works for common state-of-the-art reconstruction principles, including, among others, maximum likelihood and least squares which are the preferred choices in experiments. This is achieved by greatly reducing the dimensionality of the problem employing a particular representation of permutationally invariant states known from spin-coupling and moreover by using convex optimization, which has clear advantages regarding speed, control and accuracy in comparison to commonly employed numerical routines. First prototype implementations allow state reconstruction of 20 qubits in about 20 minutes on a standard computer.

  3. Encoding the states of interacting proteins to facilitate biological pathways reconstruction

    Directory of Open Access Journals (Sweden)

    Termanini Alberto

    2010-08-01

    Full Text Available Abstract Background In a systems biology perspective, protein-protein interactions (PPI are encoded in machine-readable formats to avoid issues encountered in their retrieval for the reconstruction of comprehensive interaction maps and biological pathways. However, the information stored in electronic formats currently used doesn't allow a valid automatic reconstruction of biological pathways. Results We propose a logical model of PPI that takes into account the "state" of proteins before and after the interaction. This information is necessary for proper reconstruction of the pathway. Conclusions The adoption of the proposed model, which can be easily integrated into existing machine-readable formats used to store the PPI data, would facilitate the automatic or semi-automated reconstruction of biological pathways. Reviewers This article was reviewed by Dr. Wen-Yu Chung (nominated by Kateryna Makova, Dr. Carl Herrmann (nominated by Dr. Purificación López-García and Dr. Arcady Mushegian.

  4. Reconstruction in the Southern United States: A Comparative Perspective.

    Science.gov (United States)

    Pressly, Thomas J.

    1989-01-01

    Compares post-emancipation societies in Haiti, Jamaica, Russia, the southern United States, Cuba, Brazil, and Zaria, relative to the acquisition of land by former slaves. Suggests that this information might provide a comparative perspective for instruction about the efforts of Blacks and Whites after abolition. (KO)

  5. 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...

  6. Acceleration of the universe: a reconstruction of the effective equation of state

    CERN Document Server

    Mukherjee, Ankan

    2016-01-01

    The present work is based upon a parametric reconstruction of the effective or total equation of state in a model for the universe with accelerated expansion. The constraints on the model parameters are obtained by maximum likelihood analysis using the supernova distance modulus data, observational Hubble data, baryon acoustic oscillation data and cosmic microwave background shift parameter data. For statistical comparison, the same analysis has also been carried out for the wCDM dark energy model. Different model selection criteria (Akaike information criterion (AIC)) and (Bayesian Information Criterion (BIC)) give the clear indication that the reconstructed model is well consistent with the wCDM model. Then both the models (w_{eff}(z) model and wCDM model) have also been presented through (q_0 ,j_0 ) parameter space. Tighter constraint on the present values of dark energy equation of state parameter (w_{DE}(z = 0)) and cosmological jerk (j_0) have been achieved for the reconstructed model.

  7. 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.

  8. HISTORICAL RECONSTRUCTION OF STATE INTERVENTION IN THE OFFICIAL

    Directory of Open Access Journals (Sweden)

    Enriqueta Tello García

    2010-05-01

    Full Text Available Water it´s one of the main factors involved in agriculturalproduction, this is way the users of this resource weredeveloping various ways of management that allow them tohave access to it in traditional way. After the greenrevolution, widespread during the second half of the XIXcentury, there is a break that modifies the economical formsof conceiving the water as resource for farmers as well asmanagers and technicians (Naredo, 1998: 65. In this sense,the present work has the objective to make a historicalreconstruction of how the state has been involve in theofficial control for the use and management of water in SanMiguel Xoxhitecatitla, Tlaxcala.

  9. 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 ...

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

    OpenAIRE

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

    2011-01-01

    The non-linearity 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 cann...

  11. 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.

  12. Revisiting a Dramatic Triangle: The State, Villagers, and Social Activists in Chinese Rural Reconstruction Projects

    Directory of Open Access Journals (Sweden)

    Stig Thøgersen

    2009-01-01

    Full Text Available As part of the movement to “construct a new socialist countryside”, Chinese officials and social activists are experimenting with transforming rural social and economic relations. They often draw on discourses dating back to the Rural Reconstruction Movement of the 1920s and 1930s, which saw urban intellectuals making similar efforts to modernize the villages and their inhabitants. This paper analyses the different types of relationships between the state, social activists, and villagers in a number of rural reconstruction projects. The state is still the major player in this field, but traditional top-down procedures are often perceived to be unproductive when it comes to micro-level community building, so state actors are forced to find allies among village elites and social activists.

  13. 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.

  14. Reconstructing the highly virulent Classical Swine Fever Virus strain Koslov

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Pedersen, Anders Gorm; Nielsen, Jens;

    by reconstructing ancestral sequences. To test this hypothesis, we inferred sequences that correspond to ancestral nodes in a phylogenetic tree built from full-length nucleotide sequences of non-functional Koslov cDNAs and then proceeded to test the reconstructions. Specifically, we altered a non-functional c...

  15. 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

  16. 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...

  17. Phylogenetic analysis of a newfound bat-borne hantavirus supports a laurasiatherian host association for ancestral mammalian hantaviruses.

    Science.gov (United States)

    Witkowski, Peter T; Drexler, Jan F; Kallies, René; Ličková, Martina; Bokorová, Silvia; Mananga, Gael D; Szemes, Tomáš; Leroy, Eric M; Krüger, Detlev H; Drosten, Christian; Klempa, Boris

    2016-07-01

    Until recently, hantaviruses (family Bunyaviridae) were believed to originate from rodent reservoirs. However, genetically distinct hantaviruses were lately found in shrews and moles, as well as in bats from Africa and Asia. Bats (order Chiroptera) are considered important reservoir hosts for emerging human pathogens. Here, we report on the identification of a novel hantavirus, provisionally named Makokou virus (MAKV), in Noack's Roundleaf Bat (Hipposideros ruber) in Gabon, Central Africa. Phylogenetic analysis of the genomic l-segment showed that MAKV was the most closely related to other bat-borne hantaviruses and shared a most recent common ancestor with the Asian hantaviruses Xuan Son and Laibin. Breakdown of the virus load in a bat animal showed that MAKV resembles rodent-borne hantaviruses in its organ distribution in that it predominantly occurred in the spleen and kidney; this provides a first insight into the infection pattern of bat-borne hantaviruses. Ancestral state reconstruction based on a tree of l gene sequences of all relevant hantavirus lineages was combined with phylogenetic fossil host hypothesis testing, leading to a statistically significant rejection of the mammalian superorder Euarchontoglires (including rodents) but not the superorder Laurasiatheria (including shrews, moles, and bats) as potential hosts of ancestral hantaviruses at most basal tree nodes. Our data supports the emerging concept of bats as previously overlooked hantavirus reservoir hosts. PMID:27051047

  18. Reconstruction of an excited-state molecular wave packet with attosecond transient absorption spectroscopy

    Science.gov (United States)

    Cheng, Yan; Chini, Michael; Wang, Xiaowei; González-Castrillo, Alberto; Palacios, Alicia; Argenti, Luca; Martín, Fernando; Chang, Zenghu

    2016-08-01

    Attosecond science promises to allow new forms of quantum control in which a broadband isolated attosecond pulse excites a molecular wave packet consisting of a coherent superposition of multiple excited electronic states. This electronic excitation triggers nuclear motion on the molecular manifold of potential energy surfaces and can result in permanent rearrangement of the constituent atoms. Here, we demonstrate attosecond transient absorption spectroscopy (ATAS) as a viable probe of the electronic and nuclear dynamics initiated in excited states of a neutral molecule by a broadband vacuum ultraviolet pulse. Owing to the high spectral and temporal resolution of ATAS, we are able to reconstruct the time evolution of a vibrational wave packet within the excited B'Σ1u+ electronic state of H2 via the laser-perturbed transient absorption spectrum.

  19. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun

    DEFF Research Database (Denmark)

    Li, Ruiqiang; Ye, Jia; Li, Songgang;

    2005-01-01

    in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences. Udgivelsesdato: 2005-Sep...

  20. Reconstructed State Space Model for Recognition of Consonant - Vowel (Cv Utterances Using Support Vector Machines

    Directory of Open Access Journals (Sweden)

    N K Narayanan

    2012-04-01

    Full Text Available This paper presents a study on the use of Support Vector Machines (SVMs in classifying Malayalam Consonant – Vowel (CV speech unit by comparing it to two other classification algorithms namely Artificial Neural Network (ANN and k – Nearest Neighbourhood (k – NN. We extend SVM to combine many two class classifiers into multiclass classifier using Decision Directed Acyclic Graph (DDAG algorithm. A feature extraction technique using Reconstructed State Space(RSS based State Space PointDistribution (SSPD parameters are studied. We obtain an average recognition accuracy of 90% using SSPD for SVM based Malayalam CV speech unit database in speaker independent environments. The result shows that the efficiency of the proposed technique is capable for increasing speaker independent consonant speech recognition accuracy and can be effectively used for developing a complete speech recognition system for Malayalam language.

  1. 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.

  2. Ancestral genome inference using a genetic algorithm approach.

    Science.gov (United States)

    Gao, Nan; Yang, Ning; Tang, Jijun

    2013-01-01

    Recent advancement of technologies has now made it routine to obtain and compare gene orders within genomes. Rearrangements of gene orders by operations such as reversal and transposition are rare events that enable researchers to reconstruct deep evolutionary histories. An important application of genome rearrangement analysis is to infer gene orders of ancestral genomes, which is valuable for identifying patterns of evolution and for modeling the evolutionary processes. Among various available methods, parsimony-based methods (including GRAPPA and MGR) are the most widely used. Since the core algorithms of these methods are solvers for the so called median problem, providing efficient and accurate median solver has attracted lots of attention in this field. The "double-cut-and-join" (DCJ) model uses the single DCJ operation to account for all genome rearrangement events. Because mathematically it is much simpler than handling events directly, parsimony methods using DCJ median solvers has better speed and accuracy. However, the DCJ median problem is NP-hard and although several exact algorithms are available, they all have great difficulties when given genomes are distant. In this paper, we present a new algorithm that combines genetic algorithm (GA) with genomic sorting to produce a new method which can solve the DCJ median problem in limited time and space, especially in large and distant datasets. Our experimental results show that this new GA-based method can find optimal or near optimal results for problems ranging from easy to very difficult. Compared to existing parsimony methods which may severely underestimate the true number of evolutionary events, the sorting-based approach can infer ancestral genomes which are much closer to their true ancestors. The code is available at http://phylo.cse.sc.edu. PMID:23658708

  3. Nonparametric Reconstruction of the Dark Energy Equation of State from Diverse Data Sets

    CERN Document Server

    Holsclaw, Tracy; Sanso, Bruno; Lee, Herbie; Heitmann, Katrin; Habib, Salman; Higdon, David

    2011-01-01

    The cause of the accelerated expansion of the Universe poses one of the most fundamental questions in physics today. In the absence of a compelling theory to explain the observations, a first task is to develop a robust phenomenology. If the acceleration is driven by some form of dark energy, then, the phenomenology is determined by the dark energy equation of state w. A major aim of ongoing and upcoming cosmological surveys is to measure w and its time dependence at high accuracy. Since w(z) is not directly accessible to measurement, powerful reconstruction methods are needed to extract it reliably from observations. We have recently introduced a new reconstruction method for w(z) based on Gaussian process modeling. This method can capture nontrivial time-dependences in w(z) and, most importantly, it yields controlled and unbaised error estimates. In this paper we extend the method to include a diverse set of measurements: baryon acoustic oscillations, cosmic microwave background measurements, and supernova ...

  4. Reconstruction of Heel With Propeller Flap in Postfasciotomy and Popliteal Artery Revascularization State.

    Science.gov (United States)

    Kang, Jin Seok; Choi, Hwan Jun; Tak, Min Sung

    2016-06-01

    Free flaps are still the gold standard for large defects of the lower limb, but propeller perforator flaps have become a simpler and faster alternative to free flaps because of some advantages such as reliable vascular pedicle, wide mobilization and rotation, great freedom in design, low donor site morbidity, and easy harvest with no requirement for anastomosis. But when the vessels show insufficient findings in preoperative evaluation using a Doppler probe or the vessel is injured, the surgeon should avoid performing free flap surgery to prevent flap failure and should select a propeller perforator flap as an alternative method on the condition that more than one perforator is intact. In this study, we report reconstruction of soft tissue defects of the heel with a pedicled propeller flap in postfasciotomy and popliteal artery revascularization state by making an incision on the central portion above the Achilles tendon, which can be covered by the posterior tibial artery perforator or the peroneal artery perforator based flaps. In conclusion, we showed that although the popliteal artery was injured, the soft tissue defect can be reconstructed using a perforator propeller flap if intact distal flow in the anastomosis site was confirmed. PMID:25673623

  5. ReAS: Recovery of ancestral sequences for transposable elements from the unassembled reads of a whole genome shotgun.

    Directory of Open Access Journals (Sweden)

    Ruiqiang Li

    2005-09-01

    Full Text Available We describe an algorithm, ReAS, to recover ancestral sequences for transposable elements (TEs from the unassembled reads of a whole genome shotgun. The main assumptions are that these TEs must exist at high copy numbers across the genome and must not be so old that they are no longer recognizable in comparison to their ancestral sequences. Tested on the japonica rice genome, ReAS was able to reconstruct all of the high copy sequences in the Repbase repository of known TEs, and increase the effectiveness of RepeatMasker in identifying TEs from genome sequences.

  6. 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.

  7. Almost complete coherent state subsystems and partial reconstruction of wavefunctions in the Fock–Bargmann phase-number representation

    International Nuclear Information System (INIS)

    We provide (partial) reconstruction formulas and discrete Fourier transforms for wavefunctions in standard Fock–Bargmann (holomorphic) phase-number representation from a finite number N of phase samples {θk = 2πk/N}N−1k=0 for a given mean number p of particles. The resulting coherent state subsystem S={|zk=p1/2eiθk>} is complete (a frame) for truncated Hilbert spaces (finite number of particles) and reconstruction formulas are exact. For an unbounded number of particles, S is ‘almost complete’ (a pseudo-frame) and partial reconstruction formulas are provided along with a study of the accuracy of the approximation, which tends to be exact when p < N and/or N → ∞. This article is part of a special issue of Journal of Physics A: Mathematical and Theoretical devoted to ‘Coherent states: mathematical and physical aspects’. (paper)

  8. Improved Algorithms for Radar-Based Reconstruction of Asteroid Spin States and Shapes

    Science.gov (United States)

    Greenberg, Adam; Margot, Jean-Luc

    2015-11-01

    Earth-based radar is a powerful tool for gathering information about bodies in the Solar System. Radar observations can dramatically improve the determination of the physical properties and orbital elements of small bodies (such as asteroids and comets). An important development in the past two decades has been the formulation and implementation of algorithms for asteroid shape reconstruction based on radar data.Because of the nature of radar data, recovery of the spin state depends on knowledge of the shape and vice versa. Even with perfect spin state information, certain peculiarities of radar images (such as the two-to-one or several-to-one mapping between surface elements on the object and pixels within the radar image) make recovery of the physical shape challenging. This is a computationally intensive problem, potentially involving hundreds to thousands of free parameters and millions of data points.The method by which radar-based shape and spin state modelling is currently accomplished, a Sequential Parameter Fit (SPF), is relatively slow, and incapable of determining the spin state of an asteroid from radar images without substantial user intervention.We implemented a global-parameter optimizer and Square Root Information Filter (SRIF) into the asteroid-modelling software shape. This optimizer can find shapes more quickly than the current method and can determine the asteroid’s spin state.We ran our new algorithm, along with the existing SPF, through several tests, composed of both real and simulated data. The simulated data were composed of noisy images of procedurally generated shapes, as well as noisy images of existing shape models. The real data included recent observations of both 2000 ET70 and 1566 Icarus.These tests indicate that SRIF is faster and more accurate than SPF. In addition, SRIF can autonomously determine the spin state of an asteroid from a variety of starting conditions, a considerable advance over the existing algorithm. We will

  9. 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.

  10. 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.

  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. 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

    2008-06-01

    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 range (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-year 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 identified conditions when the proposed approach does not yield spectral reconstruction with sufficient accuracy.

  13. Reconstructing Ancient Forms of Life

    Science.gov (United States)

    Benner, Steven A.

    1998-01-01

    Progress in the past three months has occurred in two areas, reconstruction of ancestral proteins and improved understanding of chemical features that are likely to be universal in generic matter regardless of its genesis. Ancestral ribonucleases have been reconstructed, and an example has been developed that shows how physiological function can be assigned to in vitro behaviors observed in biological systems. Sequence data have been collected to permit the reconstruction of src homology 2 domains that underwent radiative divergence at the time of the radiative divergence of chordates. New studies have been completed that show how genetic matter (or its remnants) might be detected on Mars (or other non-terrean locations.) Last, the first in vitro selection experiments have been completed using a nucleoside library carrying positively charged functionality, illustrating the importance of non-standard nucleotides to those attempting to obtain evidence for an "RNA world" as an early episode of life on earth.

  14. 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

  15. 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

    and negative regulation by alternative s-factors. Comparison with sigma-factor binding in Klebsiella pneumoniae showed that transcriptional regulation of conserved genes in closely related species is unexpectedly divergent. Conclusions: The reconstructed network reveals the regulatory complexity...

  16. Ancestral Genomes, Sex, and the Population Structure of Trypanosoma cruzi.

    Directory of Open Access Journals (Sweden)

    2006-03-01

    Full Text Available Acquisition of detailed knowledge of the structure and evolution of Trypanosoma cruzi populations is essential for control of Chagas disease. We profiled 75 strains of the parasite with five nuclear microsatellite loci, 24Salpha RNA genes, and sequence polymorphisms in the mitochondrial cytochrome oxidase subunit II gene. We also used sequences available in GenBank for the mitochondrial genes cytochrome B and NADH dehydrogenase subunit 1. A multidimensional scaling plot (MDS based in microsatellite data divided the parasites into four clusters corresponding to T. cruzi I (MDS-cluster A, T. cruzi II (MDS-cluster C, a third group of T. cruzi strains (MDS-cluster B, and hybrid strains (MDS-cluster BH. The first two clusters matched respectively mitochondrial clades A and C, while the other two belonged to mitochondrial clade B. The 24Salpha rDNA and microsatellite profiling data were combined into multilocus genotypes that were analyzed by the haplotype reconstruction program PHASE. We identified 141 haplotypes that were clearly distributed into three haplogroups (X, Y, and Z. All strains belonging to T. cruzi I (MDS-cluster A were Z/Z, the T. cruzi II strains (MDS-cluster C were Y/Y, and those belonging to MDS-cluster B (unclassified T. cruzi had X/X haplogroup genotypes. The strains grouped in the MDS-cluster BH were X/Y, confirming their hybrid character. Based on these results we propose the following minimal scenario for T. cruzi evolution. In a distant past there were at a minimum three ancestral lineages that we may call, respectively, T. cruzi I, T. cruzi II, and T. cruzi III. At least two hybridization events involving T. cruzi II and T. cruzi III produced evolutionarily viable progeny. In both events, the mitochondrial recipient (as identified by the mitochondrial clade of the hybrid strains was T. cruzi II and the mitochondrial donor was T. cruzi III.

  17. 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.

  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. Waveguiding of hot surface state electrons by the Au(111) reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Geringer, Viktor; Subramaniam, Dinesh; Liebmann, Marcus; Morgenstern, Markus [II. Institute of Physics, RWTH Aachen University, Otto-Blumenthal-Str., 52074 Aachen (Germany); JARA, Fundamentals of Future Information Technology (Germany); Libisch, Florian [Institute for Theoretical Physics, Vienna University of Technology, Wiedner Hauptstrasse 8-10/136, A-1040 Vienna (Austria)

    2011-07-01

    Using scanning tunneling spectroscopy (STS) we perform a spatial and energy dependent study of the electronic scattering behavior on the Au(111) surface. In spite of the small surface reconstruction potential (35 meV), our measurements reveal a surprising effect of wave guiding. Electrons with energies up to twenty times larger than the corrugation of the potential follow the geometry of the reconstruction, observable through a strong anisotropy in the distribution of the wave vectors. In order to explain this behavior we calculated the square of the electronic wave function evidencing quantum-mechanical orthogonality as the origin of the waveguiding effect.

  20. Molecular paleontology: a biochemical model of the ancestral ribosome

    OpenAIRE

    Hsiao, Chiaolong; Lenz, Timothy K.; Peters, Jessica K; Fang, Po-Yu; Schneider, Dana M.; Anderson, Eric J.; Preeprem, Thanawadee; Bowman, Jessica C.; O'Neill, Eric B.; Lie, Lively; Athavale, Shreyas S.; Gossett, J. Jared; Trippe, Catherine; Murray, Jason; Anton S. Petrov

    2013-01-01

    Ancient components of the ribosome, inferred from a consensus of previous work, were constructed in silico, in vitro and in vivo. The resulting model of the ancestral ribosome presented here incorporates ∼20% of the extant 23S rRNA and fragments of five ribosomal proteins. We test hypotheses that ancestral rRNA can: (i) assume canonical 23S rRNA-like secondary structure, (ii) assume canonical tertiary structure and (iii) form native complexes with ribosomal protein fragments. Footprinting exp...

  1. 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.

  2. 75 FR 52797 - State-68, Office of the Coordinator for Reconstruction and Stabilization Records

    Science.gov (United States)

    2010-08-27

    ... Organization (NATO) or similar international organizations for the purpose of coordinating personnel engaged in specific reconstruction and stabilization activities. (3) U.S. and NATO military installations for the... Register its standard routine uses that apply to all of its Privacy Act systems of records. These...

  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. Ancestral Rocky Mountian Tectonics: A Sedimentary Record of Ancestral Front Range and Uncompahgre Exhumation

    Science.gov (United States)

    Smith, T. M.; Saylor, J. E.; Lapen, T. J.

    2015-12-01

    The Ancestral Rocky Mountains (ARM) encompass multiple crustal provinces with characteristic crystallization ages across the central and western US. Two driving mechanisms have been proposed to explain ARM deformation. (1) Ouachita-Marathon collision SE of the ARM uplifts has been linked to an E-to-W sequence of uplift and is consistent with proposed disruption of a larger Paradox-Central Colorado Trough Basin by exhumation of the Uncompahgre Uplift. Initial exhumation of the Amarillo-Wichita Uplift to the east would provide a unique ~530 Ma signal absent from source areas to the SW, and result in initial exhumation of the Ancestral Front Range. (2) Alternatively, deformation due to flat slab subduction along a hypothesized plate boundary to the SW suggests a SW-to-NE younging of exhumation. This hypothesis suggests a SW-derived Grenville signature, and would trigger uplift of the Uncompahgre first. We analyzed depositional environments, sediment dispersal patterns, and sediment and basement zircon U-Pb and (U-Th)/He ages in 3 locations in the Paradox Basin and Central Colorado Trough (CCT). The Paradox Basin exhibits an up-section transition in fluvial style that suggests a decrease in overbank stability and increased lateral migration. Similarly, the CCT records a long-term progradation of depositional environments from marginal marine to fluvial, indicating that sediment supply in both basins outpaced accommodation. Preliminary provenance results indicate little to no input from the Amarillo-Wichita uplift in either basin despite uniformly westward sediment dispersal systems in both basins. Results also show that the Uncompahgre Uplift was the source for sediment throughout Paradox Basin deposition. These observations are inconsistent with the predictions of scenario 1 above. Rather, they suggest either a synchronous response to tectonic stress across the ARM provinces or an SW-to-NE pattern of deformation.

  5. 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.

  6. 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

    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...

  7. 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.

  8. 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.

  9. Reconstruction of Initial Wave Field of a Nonsteady-State Wave Propagation from Limited Measurements at a Specific Spatial Point Based on Stochastic Inversion

    Directory of Open Access Journals (Sweden)

    S. L. Han

    2013-01-01

    Full Text Available This paper studies an inverse problem that can be used for reconstructing initial wave field of a nonsteady-state wave propagation. The inverse problem is ill posed in the sense that small changes in the input data can greatly affect the solution of the problem. To address the difficulty, the problem is formulated in the form of an inference problem in an appropriately constructed stochastic model. It is shown that the stochastic inverse model enables the initial surface disturbance to be reconstructed, including its confidence intervals given the noisy measurements. The reconstruction procedure is illustrated through applications to some simulated data for two- and three-dimensional problem.

  10. Are survival processing memory advantages based on ancestral priorities?

    Science.gov (United States)

    Soderstrom, Nicholas C; McCabe, David P

    2011-06-01

    Recent research has suggested that our memory systems are especially tuned to process information according to its survival relevance, and that inducing problems of "ancestral priorities" faced by our ancestors should lead to optimal recall performance (Nairne & Pandeirada, Cognitive Psychology, 2010). The present study investigated the specificity of this idea by comparing an ancestor-consistent scenario and a modern survival scenario that involved threats that were encountered by human ancestors (e.g., predators) or threats from fictitious creatures (i.e., zombies). Participants read one of four survival scenarios in which the environment and the explicit threat were either consistent or inconsistent with ancestrally based problems (i.e., grasslands-predators, grasslands-zombies, city-attackers, city-zombies), or they rated words for pleasantness. After rating words based on their survival relevance (or pleasantness), the participants performed a free recall task. All survival scenarios led to better recall than did pleasantness ratings, but recall was greater when zombies were the threat, as compared to predators or attackers. Recall did not differ for the modern (i.e., city) and ancestral (i.e., grasslands) scenarios. These recall differences persisted when valence and arousal ratings for the scenarios were statistically controlled as well. These data challenge the specificity of ancestral priorities in survival-processing advantages in memory. PMID:21327372

  11. Isolation of ancestral sylvatic dengue virus type 1, Malaysia.

    Science.gov (United States)

    Teoh, Boon-Teong; Sam, Sing-Sin; Abd-Jamil, Juraina; AbuBakar, Sazaly

    2010-11-01

    Ancestral sylvatic dengue virus type 1, which was isolated from a monkey in 1972, was isolated from a patient with dengue fever in Malaysia. The virus is neutralized by serum of patients with endemic DENV-1 infection. Rare isolation of this virus suggests a limited spillover infection from an otherwise restricted sylvatic cycle. PMID:21029545

  12. Isolation of Ancestral Sylvatic Dengue Virus Type 1, Malaysia

    OpenAIRE

    Teoh, Boon-Teong; Sam, Sing-Sin; Abd-Jamil, Juraina; AbuBakar, Sazaly

    2010-01-01

    Ancestral sylvatic dengue virus type 1, which was isolated from a monkey in 1972, was isolated from a patient with dengue fever in Malaysia. The virus is neutralized by serum of patients with endemic DENV-1 infection. Rare isolation of this virus suggests a limited spillover infection from an otherwise restricted sylvatic cycle.

  13. New Paradigm for Edge Reconstruction of Fractional States: Part Two - Noise

    OpenAIRE

    Sabo, Ron; Gurman, Itamar; Rosenblatt, Amir; Lafont, Fabien; Banitt, Daniel; Park, Jinhong; Heiblum, Moty; Gefen, Yuval; Umansky, Vladimir; Mahalu, Diana

    2016-01-01

    The recent, unexpected, findings of upstream neutral modes in particle-like fractional quantum Hall states, led to a realization that the nature of the neutral modes is far from being understood. Moreover, the observation of spatially separated of (at least) two downstream charge modes in hole-conjugate states (see Part One - Conductance), still faces unresolved contradictions between conductance and noise measurements. In this work we show how current fluctuations measured in various configu...

  14. 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.

  15. 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

  16. 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

  17. 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)

    OpenAIRE

    Beklemisheva, Violetta R.; Perelman, Polina L.; Lemskaya, Natalya A.; Kulemzina, Anastasia I.; Proskuryakova, Anastasia A.; Burkanov, Vladimir N.; Alexander S Graphodatsky

    2016-01-01

    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 li...

  18. 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. PMID:26363082

  19. 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…

  20. Multiway admixture deconvolution using phased or unphased ancestral panels.

    Science.gov (United States)

    Churchhouse, Claire; Marchini, Jonathan

    2013-01-01

    We describe a novel method for inferring the local ancestry of admixed individuals from dense genome-wide single nucleotide polymorphism data. The method, called MULTIMIX, allows multiple source populations, models population linkage disequilibrium between markers and is applicable to datasets in which the sample and source populations are either phased or unphased. The model is based upon a hidden Markov model of switches in ancestry between consecutive windows of loci. We model the observed haplotypes within each window using a multivariate normal distribution with parameters estimated from the ancestral panels. We present three methods to fit the model-Markov chain Monte Carlo sampling, the Expectation Maximization algorithm, and a Classification Expectation Maximization algorithm. The performance of our method on individuals simulated to be admixed with European and West African ancestry shows it to be comparable to HAPMIX, the ancestry calls of the two methods agreeing at 99.26% of loci across the three parameter groups. In addition to it being faster than HAPMIX, it is also found to perform well over a range of extent of admixture in a simulation involving three ancestral populations. In an analysis of real data, we estimate the contribution of European, West African and Native American ancestry to each locus in the Mexican samples of HapMap, giving estimates of ancestral proportions that are consistent with those previously reported. PMID:23136122

  1. State-of-the-art materials used for maxillofacial prosthetic reconstruction.

    Science.gov (United States)

    Lontz, J F

    1990-04-01

    The present state-of-the-art rests primarily on three general types of polymeric materials based on chemical configurations, that of polyacrylates, polydimethylsiloxane, and segmented block polyetherurethanes. Each of these types is currently prominent in a wide range of dental prosthodontics and surgical prosthetics with continued chemical variants emerging to attain enhanced biocompatibility for safety and effectiveness. However, owing to the disproportionally lower demand, the state-of-the-art for maxillofacial restorative prosthetics has not focused adequately on the specific array of the properties needed for the ideal prosthesis. To approach the ideality will require synthesizing new molecular configurations adjusted with component structures either as block copolymers or as intermediate oligomers. The synthetic effects must have a comprehensive plan of immediate assessments on terms of biocompatibility for safety to orofacial tissues and effective durability against all conceivable deterioration of the chemical structure. Above all, inasmuch as the skilled art and techniques of maxillofacial prosthetics is a custom-made specialty allied to the prosthodontics, the improved material for ideality should be readily amenable to molding by the well-established dental stone mold technology, for reasons of cost and simplicity. PMID:2186936

  2. 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.

  3. Ancestral gene and "complementary" antibody dominate early ontogeny.

    Science.gov (United States)

    Arend, Peter

    2013-05-01

    According to N.K. Jerne the somatic generation of immune recognition occurs in conjunction with germ cell evolution and precedes the formation of the zygote, i.e. operates before clonal selection. We propose that it is based on interspecies inherent, ancestral forces maintaining the lineage. Murine oogenesis may be offered as a model. So in C57BL/10BL sera an anti-A reactive, mercapto-ethanol sensitive glycoprotein of up to now unknown cellular origin, but exhibiting immunoglobulin M character, presents itself "complementary" to a syngeneic epitope, which encoded by histocompatibility gene A or meanwhile accepted ancestor of the ABO gene family, arises predominantly in ovarian tissue and was detected statistically significant exclusively in polar glycolipids. Reports either on loss, pronounced expressions or de novo appearances of A-type structures in various conditions of accelerated growth like germ cell evolution, wound healing, inflammation and tumor proliferation in man and ABO related animals might show the dynamics of ancestral functions guarantying stem cell fidelity in maturation and tissue renewal processes. Procedures vice versa generating pluripotent stem cells for therapeutical reasons may indicate, that any artificially started growth should somehow pass through the germ line from the beginning, where according to growing knowledge exclusively the oocyte's genome provides a completely channeling ancestral information. In predatory animals such as the modern-day sea anemone, ancestral proteins, particularly those of the p53 gene family govern the reproduction processes, and are active up to the current mammalian female germ line. Lectins, providing the dual function of growth promotion and defense in higher plants, are suggested to represent the evolutionary precursors of the mammalian immunoglobulin M molecules, or protein moiety implying the greatest functional diversity in nature. And apart from any established mammalian genetic tree, a common vetch

  4. Contrasting determinants of abundance in ancestral and colonized ranges of an invasive brood parasite

    Science.gov (United States)

    Hahn, D.C.; O'Connor, R.J.

    2002-01-01

    Avian species distributions are typically regarded as constrained by spatially extensive variables such as climate, habitat, spatial patchiness, and microhabitat attributes. We hypothesized that the distribution of a brood parasite depends as strongly on host distribution patterns as on biophysical factors and examined this hypothesis with respect to the national distribution of the Brown-headed Cowbird (Molothrus ater). We applied a classification and regression (CART) analysis to data from the Breeding Bird Survey (BBS) and the Christmas Bird Count (CBC) and derived hierarchically organized statistical models of the influence of climate and weather, cropping and land use, and host abundance and distribution on the distribution of the Brown-headed Cowbird within the conterminous United States. The model accounted for 47.2% of the variation in cowbird incidence, and host abundance was the top predictor with an R2 of 18.9%. The other predictors identified by the model (crops 15.7%, weather and climate 14.3%, and region 9.6%) fit the ecological profile of this cowbird. We showed that host abundance was independent of these environmental predictors of cowbird distribution. At the regional scale host abundance played a very strong role in determining cowbird abundance in the cowbird?s colonized range east and west of their ancestral range in the Great Plains (26.6%). Crops were not a major predictor for cowbirds in their ancestral range, although they are the most important predictive factor (33%) for the grassland passerines that are the cowbird?s ancestral hosts. Consequently our findings suggest that the distribution of hosts does indeed take precedence over habitat attributes in shaping the cowbird?s distribution at a national scale, within an envelope of constraint set by biophysical factors.

  5. 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...

  6. Magnetic Investigation of Ancestral Puebloan Rio Grande (New Mexico) Glaze Wares

    Science.gov (United States)

    Dyer, J. B.; Geissman, J. W.; Ramenofsky, A. F.

    2007-12-01

    In geologically heterogeneous regions, such as the Rio Grande, archaeologists typically rely on petrographic analyses to determine ceramic provenance and reconstruct prehistoric trade patterns. Even in these regions, other methods are useful for elucidating trade patterns and/or resolving ambiguities from the petrographic data. Magnetic properties of Ancestral central Rio Grande Puebloan ceramics are being acquired to assess their use in identifying provenance, trade patterns, composition, manufacturing techniques, and firing conditions of ceramics, before and during the early European contact period (ca. A.D. 1325-1700) in New Mexico. Similar to the study of Moskowitz et al. (1987), we use a combination of bulk susceptibility, NRM, ARM, and SIRM intensity, AF response by NRM, ARM, and SIRM, thermal demagnetization of NRM and SIRM, and coercivity of remanence, to study temporal change in Rio Grande glaze wares from four archaeological sites in the northern Rio Grande (approximately 90 sherds per site). Rio Grande glaze wares were widely traded among Ancestral Puebloan groups before and during the European contact period. The ceramics are from the two earliest Spanish administrative centers in New Mexico, San Gabriel del Yungue and Palace of the Governors, and two mission pueblos, Pecos Pueblo and San Marcos Pueblo. Magnetic property data are being compared with petrographic observations to test the effectiveness of several magnetic measurements to identify, among other things, ceramic provenance. A tentative observation in our study is that bulk susceptibility values correlate with different ceramic provenances. The mean bulk susceptibility values for Galisteo Basin ceramics, tempered with augite monzonite and hornblende latite, are significantly higher (5.56E-04 and 4.91E-04 SI mass, respectively) than those for Pajarito Plateau ceramics, tempered with glassy tuff, tuff rocks, and andesite, (1.79E-04, 2.53E-04, and 2.58E-04 SI mass, respectively). This study is

  7. Wiring a periscope--ocelli, retinula axons, visual neuropils and the ancestrality of sea spiders.

    Directory of Open Access Journals (Sweden)

    Tobias Lehmann

    Full Text Available The Pycnogonida or sea spiders are cryptic, eight-legged arthropods with four median ocelli in a 'periscope' or eye tubercle. In older attempts at reconstructing phylogeny they were Arthropoda incertae sedis, but recent molecular trees placed them as the sister group either to all other euchelicerates or even to all euarthropods. Thus, pycnogonids are among the oldest extant arthropods and hold a key position for the understanding of arthropod evolution. This has stimulated studies of new sets of characters conductive to cladistic analyses, e.g. of the chelifores and of the hox gene expression pattern. In contrast knowledge of the architecture of the visual system is cursory. A few studies have analysed the ocelli and the uncommon "pseudoinverted" retinula cells. Moreover, analyses of visual neuropils are still at the stage of Hanström's early comprehensive works. We have therefore used various techniques to analyse the visual fibre pathways and the structure of their interrelated neuropils in several species. We found that pycnogonid ocelli are innervated to first and second visual neuropils in close vicinity to an unpaired midline neuropil, i.e. possibly the arcuate body, in a way very similar to ancestral euarthropods like Euperipatoides rowelli (Onychophora and Limulus polyphemus (Xiphosura. This supports the ancestrality of pycnogonids and sheds light on what eyes in the pycnogonid ground plan might have 'looked' like. Recently it was suggested that arthropod eyes originated from simple ocelli similar to larval eyes. Hence, pycnogonid eyes would be one of the early offshoots among the wealth of more sophisticated arthropod eyes.

  8. 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

  9. Exploring dynamic property of traffic flow time series in multi-states based on complex networks: Phase space reconstruction versus visibility graph

    Science.gov (United States)

    Tang, Jinjun; Liu, Fang; Zhang, Weibin; Zhang, Shen; Wang, Yinhai

    2016-05-01

    A new method based on complex network theory is proposed to analyze traffic flow time series in different states. We use the data collected from loop detectors on freeway to establish traffic flow model and classify the flow into three states based on K-means method. We then introduced two widely used methods to convert time series into networks: phase space reconstruction and visibility graph. Furthermore, in phase space reconstruction, we discuss how to determine delay time constant and embedding dimension and how to select optimal critical threshold in terms of cumulative degree distribution. In the visibility graph, we design a method to construct network from multi-variables time series based on logical OR. Finally, we study and compare the statistic features of the networks converted from original traffic time series in three states based on phase space and visibility by using the degree distribution, network structure, correlation of the cluster coefficient to betweenness and degree-degree correlation.

  10. Do Pere David's deer lose memories of their ancestral predators?

    Directory of Open Access Journals (Sweden)

    Chunwang Li

    Full Text Available Whether prey retains antipredator behavior after a long period of predator relaxation is an important question in predator-prey evolution. Père David's deer have been raised in enclosures for more than 1200 years and this isolation provides an opportunity to study whether Père David's deer still respond to the cues of their ancestral predators or to novel predators. We played back the sounds of crows (familiar sound and domestic dogs (familiar non-predators, of tigers and wolves (ancestral predators, and of lions (potential naïve predator to Père David's deer in paddocks, and blank sounds to the control group, and videoed the behavior of the deer during the experiment. We also showed life-size photo models of dog, leopard, bear, tiger, wolf, and lion to the deer and video taped their responses after seeing these models. Père David's deer stared at and approached the hidden loudspeaker when they heard the roars of tiger or lion. The deer listened to tiger roars longer, approached to tiger roars more and spent more time staring at the tiger model. The stags were also found to forage less in the trials of tiger roars than that of other sound playbacks. Additionally, it took longer for the deer to restore their normal behavior after they heard tiger roars, which was longer than that after the trial of other sound playbacks. Moreover, the deer were only found to walk away after hearing the sounds of tiger and wolf. Therefore, the tiger was probably the main predator for Père David's deer in ancient time. Our study implies that Père David's deer still retain the memories of the acoustic and visual cues of their ancestral predators in spite of the long term isolation from natural habitat.

  11. Ancestral Origins and Genetic History of Tibetan Highlanders.

    Science.gov (United States)

    Lu, Dongsheng; Lou, Haiyi; Yuan, Kai; Wang, Xiaoji; Wang, Yuchen; Zhang, Chao; Lu, Yan; Yang, Xiong; Deng, Lian; Zhou, Ying; Feng, Qidi; Hu, Ya; Ding, Qiliang; Yang, Yajun; Li, Shilin; Jin, Li; Guan, Yaqun; Su, Bing; Kang, Longli; Xu, Shuhua

    2016-09-01

    The origin of Tibetans remains one of the most contentious puzzles in history, anthropology, and genetics. Analyses of deeply sequenced (30×-60×) genomes of 38 Tibetan highlanders and 39 Han Chinese lowlanders, together with available data on archaic and modern humans, allow us to comprehensively characterize the ancestral makeup of Tibetans and uncover their origins. Non-modern human sequences compose ∼6% of the Tibetan gene pool and form unique haplotypes in some genomic regions, where Denisovan-like, Neanderthal-like, ancient-Siberian-like, and unknown ancestries are entangled and elevated. The shared ancestry of Tibetan-enriched sequences dates back to ∼62,000-38,000 years ago, predating the Last Glacial Maximum (LGM) and representing early colonization of the plateau. Nonetheless, most of the Tibetan gene pool is of modern human origin and diverged from that of Han Chinese ∼15,000 to ∼9,000 years ago, which can be largely attributed to post-LGM arrivals. Analysis of ∼200 contemporary populations showed that Tibetans share ancestry with populations from East Asia (∼82%), Central Asia and Siberia (∼11%), South Asia (∼6%), and western Eurasia and Oceania (∼1%). Our results support that Tibetans arose from a mixture of multiple ancestral gene pools but that their origins are much more complicated and ancient than previously suspected. We provide compelling evidence of the co-existence of Paleolithic and Neolithic ancestries in the Tibetan gene pool, indicating a genetic continuity between pre-historical highland-foragers and present-day Tibetans. In particular, highly differentiated sequences harbored in highlanders' genomes were most likely inherited from pre-LGM settlers of multiple ancestral origins (SUNDer) and maintained in high frequency by natural selection. PMID:27569548

  12. 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. PMID:22109873

  13. AAV ancestral reconstruction library enables selection of broadly infectious viral variants

    OpenAIRE

    Santiago-Ortiz, J; Ojala, DS; Westesson, O; Weinstein, JR; Wong, SY; Steinsapir, A; S. Kumar; Holmes, I; Schaffer, DV

    2015-01-01

    © 2015 Macmillan Publishers Limited Adeno-associated virus (AAV) vectors have achieved clinical efficacy in treating several diseases. However, enhanced vectors are required to extend these landmark successes to other indications and protein engineering approaches may provide the necessary vector improvements to address such unmet medical needs. To generate new capsid variants with potentially enhanced infectious properties and to gain insights into AAV’s evolutionary history, we computationa...

  14. 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...

  15. 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...

  16. Reconstruction of false spring occurrences over the southeastern United States, 1901-2007: an increasing risk of spring freeze damage?

    International Nuclear Information System (INIS)

    Near-record warmth over much of the United States during March 2007 promoted early growth of crops and vegetation. A widespread arctic air outbreak followed in early April, resulting in extensive agricultural losses over much of the south-central and southeastern US. This 'false spring' event also resulted in widespread damage to newly grown tissues of native deciduous forest species, shown by previous researchers to have had measurable effects on the terrestrial carbon cycle. The current study reconstructed the historical occurrence of false springs over most of the southeastern quarter of the conterminous US (32-39 deg. N; 75-98 deg. W) from 1901 to 2007 using daily maximum and minimum temperature records from 176 stations in the Global Historical Climatology Network database, and enhanced vegetation index (EVI) data derived from Moderate Resolution Imaging Spectroradiometer (MODIS) satellite observations. A false spring index was derived that examined the timing of the start of the growing season (SGS), or leaf emergence, relative to the timing of a potentially damaging last hard freeze (minimum temperature ≤ - 2.2 deg. C). SGS was modeled for the domain by combining EVI data with ground-based temperature 'degree day' calculations reflecting the rate of springtime warming. No significant area-wide, long-term SGS trend was found; however, over much of a contiguous region stretching from Mississippi eastward to the Carolinas, the timing of the last hard freeze was found to occur significantly later, this change occurring along with increased frequency of false springs. Earlier last hard freeze dates and decreased frequency of false springs were found over much of the northwestern part of the study region, including Arkansas and southern Missouri.

  17. Reconstruction of false spring occurrences over the southeastern United States, 1901-2007: an increasing risk of spring freeze damage?

    Energy Technology Data Exchange (ETDEWEB)

    Marino, Garrett P [Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA (United States); Kaiser, Dale P; Gu, Lianhong; Ricciuto, Daniel M, E-mail: kaiserdp@ornl.gov [Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN (United States)

    2011-04-15

    Near-record warmth over much of the United States during March 2007 promoted early growth of crops and vegetation. A widespread arctic air outbreak followed in early April, resulting in extensive agricultural losses over much of the south-central and southeastern US. This 'false spring' event also resulted in widespread damage to newly grown tissues of native deciduous forest species, shown by previous researchers to have had measurable effects on the terrestrial carbon cycle. The current study reconstructed the historical occurrence of false springs over most of the southeastern quarter of the conterminous US (32-39 deg. N; 75-98 deg. W) from 1901 to 2007 using daily maximum and minimum temperature records from 176 stations in the Global Historical Climatology Network database, and enhanced vegetation index (EVI) data derived from Moderate Resolution Imaging Spectroradiometer (MODIS) satellite observations. A false spring index was derived that examined the timing of the start of the growing season (SGS), or leaf emergence, relative to the timing of a potentially damaging last hard freeze (minimum temperature {<=} - 2.2 deg. C). SGS was modeled for the domain by combining EVI data with ground-based temperature 'degree day' calculations reflecting the rate of springtime warming. No significant area-wide, long-term SGS trend was found; however, over much of a contiguous region stretching from Mississippi eastward to the Carolinas, the timing of the last hard freeze was found to occur significantly later, this change occurring along with increased frequency of false springs. Earlier last hard freeze dates and decreased frequency of false springs were found over much of the northwestern part of the study region, including Arkansas and southern Missouri.

  18. Reconstruction of false spring occurrences over the southeastern United States, 1901 2007: an increasing risk of spring freeze damage?

    Energy Technology Data Exchange (ETDEWEB)

    Marino, Garrett P [ORNL; Kaiser, Dale Patrick [ORNL; Gu, Lianhong [ORNL; Ricciuto, Daniel M [ORNL

    2011-01-01

    Near-record warmth over much of the United States during March 2007 promoted early growth of crops and vegetation. A widespread arctic air outbreak followed in early April, resulting in extensive agricultural losses over much of the south-central and southeastern US. This false spring event also resulted in widespread damage to newly grown tissues of native deciduous forest species, shown by previous researchers to have had measurable effects on the terrestrial carbon cycle. The current study reconstructed the historical occurrence of false springs over most of the southeastern quarter of the conterminous US (32 39 N; 75 98 W) from 1901 to 2007 using daily maximum and minimum temperature records from 176 stations in the Global Historical Climatology Network database, and enhanced vegetation index (EVI) data derived from Moderate Resolution Imaging Spectroradiometer (MODIS) satellite observations. A false spring index was derived that examined the timing of the start of the growing season (SGS), or leaf emergence, relative to the timing of a potentially damaging last hard freeze (minimum temperature 2.2 C). SGS was modeled for the domain by combining EVI data with ground-based temperature degree day calculations reflecting the rate of springtime warming. No significant area-wide, long-term SGS trend was found; however, over much of a contiguous region stretching from Mississippi eastward to the Carolinas, the timing of the last hard freeze was found to occur significantly later, this change occurring along with increased frequency of false springs. Earlier last hard freeze dates and decreased frequency of false springs were found over much of the northwestern part of the study region, including Arkansas and southern Missouri.

  19. 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

  20. The vomeronasal complex of nocturnal strepsirhines and implications for the ancestral condition in primates.

    Science.gov (United States)

    Garrett, Eva C; Dennis, John C; Bhatnagar, Kunwar P; Durham, Emily L; Burrows, Anne M; Bonar, Christopher J; Steckler, Natalie K; Morrison, Edward E; Smith, Timothy D

    2013-12-01

    This study investigates the vomeronasal organ in extant nocturnal strepsirhines as a model for ancestral primates. Cadaveric samples from 10 strepsirhine species, ranging from fetal to adult ages, were studied histologically. Dimensions of structures in the vomeronasal complex, such as the vomeronasal neuroepithelium (VNNE) and vomeronasal cartilage (VNC) were measured in serial sections and selected specimens were studied immunohistochemically to determine physiological aspects of the vomeronasal sensory neurons (VSNs). Osteological features corresponding to vomeronasal structures were studied histologically and related to 3-D CT reconstructions. The VNC consistently rests in a depression on the palatal portion of the maxilla, which we refer to as the vomeronasal groove (VNG). Most age comparisons indicate that in adults VNNE is about twice the length compared with perinatal animals. In VNNE volume, adults are 2- to 3-fold larger compared with perinatal specimens. Across ages, a strong linear relationship exists between VNNE dimensions and body length, mass, and midfacial length. Results indicate that the VNNE of nocturnal strepsirhines is neurogenic postnatally based on GAP43 expression. In addition, based on Olfactory Marker Protein expression, terminally differentiated VSNs are present in the VNNE. Therefore, nocturnal strepsirhines have basic similarities to rodents in growth and maturational characteristics of VSNs. These results indicate that a functional vomeronasal system is likely present in all nocturnal strepsirhines. Finally, given that osteological features such as the VNG are visible on midfacial bones, primate fossils can be assessed to determine whether primate ancestors possessed a vomeronasal complex morphologically similar to that of modern nocturnal strepsirhines. PMID:24249398

  1. 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.

  2. 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.

  3. 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

  4. Operational production of equipments in the topographic reconstruction of degraded areas for mineral exploration in the national forest of Jamari, State of Rondonia, Brazil

    Directory of Open Access Journals (Sweden)

    Antônio José da Silva Maciel

    2004-06-01

    Full Text Available The topographic reconstruction of surfaces is the initial stage in a recovery’s programs of degraded areas. Few studies exist in this knowledge area because geology forms associated to the landscape are not possible of be re-done. Areas of mine pit are usually quite irregular and compacted, this fact is associated with the intense traffic of machines in the mineral exploration. The present work had for objective evaluate the operational production of different equipments in the topographic reconstruction of degraded areas in the National Forest of Jamari, State of Rondonia, Brazil, by means of a conjoint tractor-blade equipped with riper, it was evaluated to following operations: leveling of the land, construction and terraces and subsoiling. The operational production of the equipments analyzed for topographic reconstruction presented high acting in mine pit, and the use of the studied equipments showed important for the recovery of the initial conditions of the physical properties of the soil. However, high operational acting, it cannot be considered as the only technical factor of selection of machines in the moment of the mechanization of a degraded soil, other factors as: the final quality of the executed work and the interaction soil-plant can be decisive in the adoption and acting of the machines and recovery techniques.

  5. 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. PMID:25472831

  6. 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.

  7. Color vision of ancestral organisms of higher primates.

    Science.gov (United States)

    Nei, M; Zhang, J; Yokoyama, S

    1997-06-01

    The color vision of mammals is controlled by photosensitive proteins called opsins. Most mammals have dichromatic color vision, but hominoids and Old World (OW) monkeys enjoy trichromatic vision, having the blue-, green-, and red-sensitive opsin genes. Most New World (NW) monkeys are either dichromatic or trichromatic, depending on the sex and genotype. Trichromacy in higher primates is believed to have evolved to facilitate the detection of yellow and red fruits against dappled foliage, but the process of evolutionary change from dichromacy to trichromacy is not well understood. Using the parsimony and the newly developed Bayesian methods, we inferred the amino acid sequences of opsins of ancestral organisms of higher primates. The results suggest that the ancestors of OW and NW monkeys lacked the green gene and that the green gene later evolved from the red gene. The fact that the red/green opsin gene has survived the long nocturnal stage of mammalian evolution and that it is under strong purifying selection in organisms that live in dark environments suggests that this gene has another important function in addition to color vision, probably the control of circadian rhythms. PMID:9190062

  8. 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

  9. 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.

  10. Features of the ancestral bilaterian inferred from Platynereis dumerilii ParaHox genes

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    Magdelenat Ghislaine

    2009-07-01

    Full Text Available Abstract Background The ParaHox gene cluster is the evolutionary sister to the Hox cluster. Whilst the role of the Hox cluster in patterning the anterior-posterior axis of bilaterian animals is well established, and the organisation of vertebrate Hox clusters is intimately linked to gene regulation, much less is known about the more recently discovered ParaHox cluster. ParaHox gene clustering, and its relationship to expression, has only been described in deuterostomes. Conventional protostome models (Drosophila melanogaster and Caenorhabditis elegans are secondarily derived with respect to ParaHox genes, suffering gene loss and cluster break-up. Results We provide the first evidence for ParaHox gene clustering from a less-derived protostome animal, the annelid Platynereis dumerilii. Clustering of these genes is thus not a sole preserve of the deuterostome lineage within Bilateria. This protostome ParaHox cluster is not entirely intact however, with Pdu-Cdx being on the opposite end of the same chromosome arm from Pdu-Gsx and Pdu-Xlox. From the genomic sequence around the P. dumerilii ParaHox genes the neighbouring genes are identified, compared with other taxa, and the ancestral arrangement deduced. Conclusion We relate the organisation of the ParaHox genes to their expression, and from comparisons with other taxa hypothesise that a relatively complex pattern of ParaHox gene expression existed in the protostome-deuterostome ancestor, which was secondarily simplified along several invertebrate lineages. Detailed comparisons of the gene content around the ParaHox genes enables the reconstruction of the genome surrounding the ParaHox cluster of the protostome-deuterostome ancestor, which existed over 550 million years ago.

  11. 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.

  12. Genome-wide inference of ancestral recombination graphs.

    Science.gov (United States)

    Rasmussen, Matthew D; Hubisz, Melissa J; Gronau, Ilan; Siepel, Adam

    2014-01-01

    The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of [Formula: see text] chromosomes conditional on an ARG of [Formula: see text] chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective sweeps. PMID:24831947

  13. Genome-wide inference of ancestral recombination graphs.

    Directory of Open Access Journals (Sweden)

    Matthew D Rasmussen

    Full Text Available The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG, a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of [Formula: see text] chromosomes conditional on an ARG of [Formula: see text] chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the posterior distribution over ARGs and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. The patterns we observe near protein-coding genes are consistent with a primary influence from background selection rather than hitchhiking, although we cannot rule out a contribution from recurrent selective

  14. β-Propeller blades as ancestral peptides in protein evolution.

    Directory of Open Access Journals (Sweden)

    Klaus O Kopec

    Full Text Available Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. Despite the large size range of β-propellers, their blades frequently show sequence similarity indicative of a common ancestry and it has been proposed that the majority of β-propellers arose divergently by amplification and diversification of an ancestral blade. Given the structural versatility of β-propellers and the hypothesis that the first folded proteins evolved from a simpler set of peptides, we investigated whether this blade may have given rise to other folds as well. Using sequence comparisons, we identified proteins of four other folds as potential homologs of β-propellers: the luminal domain of inositol-requiring enzyme 1 (IRE1-LD, type II β-prisms, β-pinwheels, and WW domains. Because, with increasing evolutionary distance and decreasing sequence length, the statistical significance of sequence comparisons becomes progressively harder to distinguish from the background of convergent similarities, we complemented our analyses with a new method that evaluates possible homology based on the correlation between sequence and structure similarity. Our results indicate a homologous relationship of IRE1-LD and type II β-prisms with β-propellers, and an analogous one for β-pinwheels and WW domains. Whereas IRE1-LD most likely originated by fold-changing mutations from a fully formed PQQ motif β-propeller, type II β-prisms originated by amplification and differentiation of a single blade, possibly also of the PQQ type. We conclude that both β-propellers and type II β-prisms arose by independent amplification of a blade-sized fragment, which represents a remnant of an ancient peptide world.

  15. β-Propeller Blades as Ancestral Peptides in Protein Evolution

    Science.gov (United States)

    Kopec, Klaus O.; Lupas, Andrei N.

    2013-01-01

    Proteins of the β-propeller fold are ubiquitous in nature and widely used as structural scaffolds for ligand binding and enzymatic activity. This fold comprises between four and twelve four-stranded β-meanders, the so called blades that are arranged circularly around a central funnel-shaped pore. Despite the large size range of β-propellers, their blades frequently show sequence similarity indicative of a common ancestry and it has been proposed that the majority of β-propellers arose divergently by amplification and diversification of an ancestral blade. Given the structural versatility of β-propellers and the hypothesis that the first folded proteins evolved from a simpler set of peptides, we investigated whether this blade may have given rise to other folds as well. Using sequence comparisons, we identified proteins of four other folds as potential homologs of β-propellers: the luminal domain of inositol-requiring enzyme 1 (IRE1-LD), type II β-prisms, β-pinwheels, and WW domains. Because, with increasing evolutionary distance and decreasing sequence length, the statistical significance of sequence comparisons becomes progressively harder to distinguish from the background of convergent similarities, we complemented our analyses with a new method that evaluates possible homology based on the correlation between sequence and structure similarity. Our results indicate a homologous relationship of IRE1-LD and type II β-prisms with β-propellers, and an analogous one for β-pinwheels and WW domains. Whereas IRE1-LD most likely originated by fold-changing mutations from a fully formed PQQ motif β-propeller, type II β-prisms originated by amplification and differentiation of a single blade, possibly also of the PQQ type. We conclude that both β-propellers and type II β-prisms arose by independent amplification of a blade-sized fragment, which represents a remnant of an ancient peptide world. PMID:24143202

  16. 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.

  17. 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.

  18. 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.

  19. Orangutan fish eating, primate aquatic fauna eating, and their implications for the origins of ancestral hominin fish eating.

    Science.gov (United States)

    Russon, Anne E; Compost, Alain; Kuncoro, Purwo; Ferisa, Agnes

    2014-12-01

    This paper presents new evidence of fish eating in rehabilitant orangutans living on two Bornean islands and explores its contributions to understanding nonhuman primates' aquatic fauna eating and the origins of ancestral hominin fish eating. We assessed the prevalence of orangutans' fish eating, their techniques for obtaining fish, and possible contributors (ecology, individual differences, humans). We identified 61 events in which orangutans tried to obtain fish, including 19 in which they ate fish. All the orangutans were juvenile-adolescent; all the fish were disabled catfish; and most were obtained and eaten in drier seasons in or near shallow, slow-moving water. Orangutans used several techniques to obtain fish (inadvertent, opportunistic and deliberate hand-catch, scrounge, tool-assisted catch) and probably learned them in that order. Probable contributing factors were orangutan traits (age, pre-existing water or tool skills), island features (social density, water accessibility), and local human fishing. Our review of primates' aquatic fauna eating showed orangutans to be one of 20 species that eat aquatic fauna, one of nine confirmed to eat fish, and one of three that use tools to obtain fish. Primate fish eating is also site-specific within species, partly as a function of habitat (e.g., marine-freshwater, seasonality) and human influence (possibly fostered eating fish or other aquatic fauna at most sites, clearly induced it at some). At tropical freshwater sites, fish eating occurred most often in drier seasons around shallow water. Orangutan and primate findings are generally consistent with Stewart's (2010) reconstruction of the origins of ancestral hominin fish eating, but suggest that it, and tool-assisted fish catching, were possible much earlier. PMID:25038033

  20. 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

  1. Reconstruction of symmetric Potts Models

    OpenAIRE

    Sly, Allan

    2008-01-01

    The reconstruction problem on the tree has been studied in numerous contexts including statistical physics, information theory and computational biology. However, rigorous reconstruction thresholds have only been established in a small number of models. We prove the first exact reconstruction threshold in a non-binary model establishing the Kesten-Stigum bound for the 3-state Potts model on regular trees of large degree. We further establish that the Kesten-Stigum bound is not tight for the $...

  2. 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...

  3. Laryngopharyngeal reconstruction

    OpenAIRE

    Kazi, Rehan A

    2006-01-01

    There is a high incidence of hypopharyngeal cancer is our country due to the habits of tobacco and alcohol. Moreover these cases are often detected in the late stages thereby making the issue of reconstruction very tedious and unpredictable. There are a number of options for laryngopharyngeal reconstruction available now including the use of microvascular flaps depending upon the patient’s fitness, motivation, technical expertise, size and extent of the defect. This article reviews the differ...

  4. 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.

  5. 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).

  6. 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...

  7. State failure and success in Uganda and Zimbabwe: the logic of political decay and reconstruction in Africa

    OpenAIRE

    Brett, Edwin

    2006-01-01

    This article uses an interdisciplinary approach to the post-colonial history of Uganda and Zimbabwe and shows that the way in which regimes responded to contradictory political and economic demands explain the processes that led to state failure or consolidation. It provides a review of the claims of the competing theories used to explain these processes, and shows that they all explain some, but not all, of the critical changes that occurred. The outcome of interventionist or neo-liberal pol...

  8. 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.

  9. Social capital and health: evidence that ancestral trust promotes health among children of immigrants.

    Science.gov (United States)

    Ljunge, Martin

    2014-12-01

    This paper presents evidence that generalized trust promotes health. Children of immigrants in a broad set of European countries with ancestry from across the world are studied. Individuals are examined within country of residence using variation in trust across countries of ancestry. The approach addresses reverse causality and concerns that the trust measure picks up institutional factors in the individual's contextual setting. There is a significant positive estimate of ancestral trust in explaining self-assessed health. The finding is robust to accounting for individual, parental, and extensive ancestral country characteristics. Individuals with higher ancestral trust are also less likely to be hampered by health problems in their daily life, providing evidence of trust influencing real life outcomes. Individuals with high trust feel and act healthier, enabling a more productive life. PMID:25464341

  10. 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.

  11. Project Reconstruct.

    Science.gov (United States)

    Helisek, Harriet; Pratt, Donald

    1994-01-01

    Presents a project in which students monitor their use of trash, input and analyze information via a database and computerized graphs, and "reconstruct" extinct or endangered animals from recyclable materials. The activity was done with second-grade students over a period of three to four weeks. (PR)

  12. Vaginal reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Lesavoy, M.A.

    1985-05-01

    Vaginal reconstruction can be an uncomplicated and straightforward procedure when attention to detail is maintained. The Abbe-McIndoe procedure of lining the neovaginal canal with split-thickness skin grafts has become standard. The use of the inflatable Heyer-Schulte vaginal stent provides comfort to the patient and ease to the surgeon in maintaining approximation of the skin graft. For large vaginal and perineal defects, myocutaneous flaps such as the gracilis island have been extremely useful for correction of radiation-damaged tissue of the perineum or for the reconstruction of large ablative defects. Minimal morbidity and scarring ensue because the donor site can be closed primarily. With all vaginal reconstruction, a compliant patient is a necessity. The patient must wear a vaginal obturator for a minimum of 3 to 6 months postoperatively and is encouraged to use intercourse as an excellent obturator. In general, vaginal reconstruction can be an extremely gratifying procedure for both the functional and emotional well-being of patients.

  13. Vaginal reconstruction

    International Nuclear Information System (INIS)

    Vaginal reconstruction can be an uncomplicated and straightforward procedure when attention to detail is maintained. The Abbe-McIndoe procedure of lining the neovaginal canal with split-thickness skin grafts has become standard. The use of the inflatable Heyer-Schulte vaginal stent provides comfort to the patient and ease to the surgeon in maintaining approximation of the skin graft. For large vaginal and perineal defects, myocutaneous flaps such as the gracilis island have been extremely useful for correction of radiation-damaged tissue of the perineum or for the reconstruction of large ablative defects. Minimal morbidity and scarring ensue because the donor site can be closed primarily. With all vaginal reconstruction, a compliant patient is a necessity. The patient must wear a vaginal obturator for a minimum of 3 to 6 months postoperatively and is encouraged to use intercourse as an excellent obturator. In general, vaginal reconstruction can be an extremely gratifying procedure for both the functional and emotional well-being of patients

  14. 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

  15. Radio Reconstructions

    OpenAIRE

    Bulley, James; Jones, Daniel

    2013-01-01

    Radio Reconstructions is a sound installation which use indeterminate radio broadcasts as its raw material. Each piece is structured by a notated score, which controls its rhythm, dynamics and melodic contour over time. The audio elements used to enact this score are selected in real-time from unknown radio transmissions, by an autonomous software system which is continuously scanning the radio waves in search of similar fragments of audio. Using a technique known as audio mosaicing, hund...

  16. 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.

  17. Tracheal reconstructions.

    Science.gov (United States)

    Srikrishna, S V; Shekar, P S; Shetty, N

    1998-12-01

    Surgical reconstruction of the trachea is a relatively complex procedure. We had 20 cases of tracheal stenosis. We have a modest experience of 16 tracheal reconstructions for acquired tracheal stenosis. Two patients underwent laser treatment while another two died before any intervention. The majority of these cases were a result of prolonged ventilation (14 cases), following organophosphorous poisoning (11 cases), Guillain-Barré syndrome, bullet injury, fat embolism and surprisingly only one tumor, a case of mucoepidermoid carcinoma, who had a very unusual presentation. There were 12 males and 4 females in this series, age ranging from 12-35 years. The duration of ventilation ranged from 1-21 days and the interval from decannulation to development of stridor was between 5-34 days. Six of them were approached by the cervical route, 5 by thoracotomy and cervical approach, 2 via median sternotomy and 3 by thoracotomy alone. Five of them required an additional laryngeal drop and 1 required pericardiotomy and release of pulmonary veins to gain additional length. The excised segments of trachea measured 3 to 5 cms in length. All were end to end anastomosis with interrupted Vicryl sutures. We have had no experience with stents or prosthetic tubes. Three patients developed anastomotic leaks which were controlled conservatively. Almost all of them required postoperative tracheo-bronchial suctioning with fibreoptic bronchoscope. We had one death in this series due to sepsis. PMID:9914459

  18. 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.

  19. Defining the ancestral eutherian karyotype: a cladistic interpretation of chromosome painting and genome sequence assembly data.

    Science.gov (United States)

    Robinson, Terence J; Ruiz-Herrera, Aurora

    2008-01-01

    A cladistic analysis of genome assemblies (syntenic associations) for eutherian mammals against two distant outgroup species--opossum and chicken--permitted a refinement of the 46-chromosome karyotype formerly inferred in the ancestral eutherian. We show that two intact chromosome pairs (corresponding to human chromosomes 13 and 18) and three conserved chromosome segments (10q, 19p and 8q in the human karyotype) are probably symplesiomorphic for Eutheria because they are also present as unaltered orthologues in one or both outgroups. Seven additional syntenies (4q/8p/4pq, 3p/21, 14/15, 10p/12pq/22qt, 19q/16q, 16p/7a and 12qt/22q), each involving human chromosomal segments that in various combinations correspond to complete chromosomes in the ancestral eutherian karyotype, are also present in one or both outgroup taxa and thus are probable symplesiomorphies for Eutheria. Interestingly, several of the symplesiomorphic characters identified in chicken and/or opossum are present in more distant outgroups such as pufferfish and zebrafish (for example 3p/21, 14/15, 19q/16q and 16p/7a), suggesting their retention since vertebrate common ancestry approximately 450 million years ago. However, eight intact pairs (corresponding to human chromosomes 1, 5, 6, 9, 11, 17, 20 and the X) and three chromosome segments (7b, 2p-q13 and 2q13-qter) are derived characters potentially consistent with eutherian monophyly. Our analyses clarify the distinction between shared-ancestral and shared-derived homology in the eutherian ancestral karyotype.

  20. Late Paleozoic deformation of interior North America: The greater Ancestral Rocky Mountains

    Energy Technology Data Exchange (ETDEWEB)

    Ye, Hongzhuan [Massachusetts Inst. of Technology, Cambridge, MA (United States)]|[Univ. of Texas at Dallas, Richardson, TX (United States); Royden, L.; Burchfiel, C. [Massachusetts Inst. of Technology, Cambridge, MA (United States); Schuepbach, M. [MAXUS Energy Co., Dallas, TX (United States)

    1996-09-01

    Late Paleozoic deformation within interior North America has produced a series of north-northwest- to northwest-trending elongate basins that cover much of Oklahoma, Texas, New Mexico, Colorado, and Utah. Each basin thickens asymmetrically toward an adjacent region of coeval basement uplift from which it is separated by synsedimentary faults with great vertical relief. The remarkable coincidence in timing, geometry, and apparent structural style throughout the region of late Paleozoic deformation strongly suggests that these paired regions of basin subsidence and basement uplift form a unified system of regional deformation, the greater Ancestral Rocky Mountains. Over this region, basin subsidence and basement uplift were approximately synchronous, beginning in the Chesterian-Morrowan, continuing through the Pennsylvanian, and ending in the Wolfcampian (although minor post-Wolfcampian deformation occurs locally). The basement uplifts show evidence for folding and faulting in the Pennsylvanian and Early Permian. Reverse faults and thrust faults have been drilled over many of the uplifts, but only in the Anadarko region has thrusting of the basement uplifts over the adjacent basin been clearly documented. Extensive basement-involved thrusting also occurs along the margins of the Delaware and Midland basins, and suggests that the entire greater Ancestral Rocky Mountains region probably formed as the result of northeast-southwest-directed-intraplate shortening. Deformation within the greater Ancestral Rocky Mountains was coeval with late Paleozoic subduction along much of the North American plate margin, and has traditionally been related to emplacement of thrust sheets within the Ouachita-Marathon orogenic belt. The nature, timing, and orientation of events along the Ouachita-Marathon belt make it difficult to drive the deformation of the greater Ancestral Rocky Mountains by emplacement of the Ouachita-Marathon belt along the southern margin of North America.

  1. 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.

  2. 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.

  3. Distinct actions of ancestral vinclozolin and juvenile stress on neural gene expression in the male rat

    Directory of Open Access Journals (Sweden)

    Ross eGillette

    2015-03-01

    Full Text Available Exposure to the endocrine disrupting chemical vinclozolin during gestation of an F0 generation and/or chronic restraint stress during adolescence of the F3 descendants affects behavior, physiology, and gene expression in the brain. Genes related to the networks of growth factors, signaling peptides and receptors, steroid hormone receptors and enzymes, and epigenetic related factors were measured using quantitative polymerase chain reaction via Taqman low density arrays targeting 48 genes in the central amygdaloid nucleus, medial amygdaloid nucleus, medial preoptic area, lateral hypothalamus, and the ventromedial nucleus of the hypothalamus. We found that growth factors are particularly vulnerable to ancestral exposure in the central and medial amygdala; restraint stress during adolescence affected neural growth factors in the medial amygdala. Signaling peptides were affected by both ancestral exposure and stress during adolescence primarily in hypothalamic nuclei. Steroid hormone receptors and enzymes were strongly affected by restraint stress in the medial preoptic area. Epigenetic related genes were affected by stress in the ventromedial hypothalamus and by both ancestral exposure and stress during adolescence independently in the central amygdala. It is noteworthy that the lateral hypothalamus showed no effects of either manipulation. Gene expression is discussed in the context of behavioral and physiological measures previously published.

  4. 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].

  5. 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.

  6. 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

  7. The Reconstruction of Local Government Powers under State Governance System%国家治理体系下的地方政府权力重构

    Institute of Scientific and Technical Information of China (English)

    赵豪

    2014-01-01

    power system of “sharing the equal responsibility and equal power between the superior and the subordinate”has greatly hindered the multicenter lateral configuration of local governments’ power. Therefore, the vertical power separation between the local governments at all levels and enhancing the government's autonomy at the local level have become the primary task of the reconstruction of local governments’ power. In addition, the State Governance System also has a great influence on the basic principles of administration law. In the new era, it should be stressed to restrict the abuse of local government powers and prevent local government wantonly breaking up the boundary of powers under the rule of law of local government power configuration. Moreover, the principle of legal hold and ultra vires invalidity will be more valuable and relevant legislation will be more perfect.

  8. 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.

  9. 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.

  10. 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.

  11. Noise-enhanced reconstruction of attractors

    CERN Document Server

    Castro, R G

    1997-01-01

    In principle, the state space of a chaotic attractor can be partially or wholly reconstructed from interspike intervals recorded from experiment. Under certain conditions, the quality of a partial reconstruction, as measured by the spike train prediction error, can be increased by adding noise to the spike creation process. This phenomenon for chaotic systems is an analogue of stochastic resonance.

  12. Evolution of sexes from an ancestral mating-type specification pathway.

    Directory of Open Access Journals (Sweden)

    Sa Geng

    2014-07-01

    Full Text Available Male and female sexes have evolved repeatedly in eukaryotes but the origins of dimorphic sexes and their relationship to mating types in unicellular species are not understood. Volvocine algae include isogamous species such as Chlamydomonas reinhardtii, with two equal-sized mating types, and oogamous multicellular species such as Volvox carteri with sperm-producing males and egg-producing females. Theoretical work predicts genetic linkage of a gamete cell-size regulatory gene(s to an ancestral mating-type locus as a possible step in the evolution of dimorphic gametes, but this idea has not been tested. Here we show that, contrary to predictions, a single conserved mating locus (MT gene in volvocine algae-MID, which encodes a RWP-RK domain transcription factor-evolved from its ancestral role in C. reinhardtii as a mating-type specifier, to become a determinant of sperm and egg development in V. carteri. Transgenic female V. carteri expressing male MID produced functional sperm packets during sexual development. Transgenic male V. carteri with RNA interference (RNAi-mediated knockdowns of VcMID produced functional eggs, or self-fertile hermaphrodites. Post-transcriptional controls were found to regulate cell-type-limited expression and nuclear localization of VcMid protein that restricted its activity to nuclei of developing male germ cells and sperm. Crosses with sex-reversed strains uncoupled sex determination from sex chromosome identity and revealed gender-specific roles for male and female mating locus genes in sexual development, gamete fitness and reproductive success. Our data show genetic continuity between the mating-type specification and sex determination pathways of volvocine algae, and reveal evidence for gender-specific adaptations in the male and female mating locus haplotypes of Volvox. These findings will enable a deeper understanding of how a master regulator of mating-type determination in an ancestral unicellular species was

  13. The mitochondrial genome structure of Xenoturbella bocki (phylum Xenoturbellida is ancestral within the deuterostomes

    Directory of Open Access Journals (Sweden)

    Lanfear Robert

    2009-05-01

    Full Text Available Abstract Background Mitochondrial genome comparisons contribute in multiple ways when inferring animal relationships. As well as primary sequence data, rare genomic changes such as gene order, shared gene boundaries and genetic code changes, which are unlikely to have arisen through convergent evolution, are useful tools in resolving deep phylogenies. Xenoturbella bocki is a morphologically simple benthic marine worm recently found to belong among the deuterostomes. Here we present analyses comparing the Xenoturbella bocki mitochondrial gene order, genetic code and control region to those of other metazoan groups. Results The complete mitochondrial genome sequence of Xenoturbella bocki was determined. The gene order is most similar to that of the chordates and the hemichordates, indicating that this conserved mitochondrial gene order might be ancestral to the deuterostome clade. Using data from all phyla of deuterostomes, we infer the ancestral mitochondrial gene order for this clade. Using inversion and breakpoint analyses of metazoan mitochondrial genomes, we test conflicting hypotheses for the phylogenetic placement of Xenoturbella and find a closer affinity to the hemichordates than to other metazoan groups. Comparative analyses of the control region reveal similarities in the transcription initiation and termination sites and origin of replication of Xenoturbella with those of the vertebrates. Phylogenetic analyses of the mitochondrial sequence indicate a weakly supported placement as a basal deuterostome, a result that may be the effect of compositional bias. Conclusion The mitochondrial genome of Xenoturbella bocki has a very conserved gene arrangement in the deuterostome group, strikingly similar to that of the hemichordates and the chordates, and thus to the ancestral deuterostome gene order. Similarity to the hemichordates in particular is suggested by inversion and breakpoint analysis. Finally, while phylogenetic analyses of the

  14. The mammary gland-specific marsupial ELP and eutherian CTI share a common ancestral gene

    Directory of Open Access Journals (Sweden)

    Pharo Elizabeth A

    2012-06-01

    Full Text Available Abstract Background The marsupial early lactation protein (ELP gene is expressed in the mammary gland and the protein is secreted into milk during early lactation (Phase 2A. Mature ELP shares approximately 55.4% similarity with the colostrum-specific bovine colostrum trypsin inhibitor (CTI protein. Although ELP and CTI both have a single bovine pancreatic trypsin inhibitor (BPTI-Kunitz domain and are secreted only during the early lactation phases, their evolutionary history is yet to be investigated. Results Tammar ELP was isolated from a genomic library and the fat-tailed dunnart and Southern koala ELP genes cloned from genomic DNA. The tammar ELP gene was expressed only in the mammary gland during late pregnancy (Phase 1 and early lactation (Phase 2A. The opossum and fat-tailed dunnart ELP and cow CTI transcripts were cloned from RNA isolated from the mammary gland and dog CTI from cells in colostrum. The putative mature ELP and CTI peptides shared 44.6%-62.2% similarity. In silico analyses identified the ELP and CTI genes in the other species examined and provided compelling evidence that they evolved from a common ancestral gene. In addition, whilst the eutherian CTI gene was conserved in the Laurasiatherian orders Carnivora and Cetartiodactyla, it had become a pseudogene in others. These data suggest that bovine CTI may be the ancestral gene of the Artiodactyla-specific, rapidly evolving chromosome 13 pancreatic trypsin inhibitor (PTI, spleen trypsin inhibitor (STI and the five placenta-specific trophoblast Kunitz domain protein (TKDP1-5 genes. Conclusions Marsupial ELP and eutherian CTI evolved from an ancestral therian mammal gene before the divergence of marsupials and eutherians between 130 and 160 million years ago. The retention of the ELP gene in marsupials suggests that this early lactation-specific milk protein may have an important role in the immunologically naïve young of these species.

  15. 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.

  16. Analysis of Ancestral and Functionally Relevant CD5 Variants in Systemic Lupus Erythematosus Patients

    OpenAIRE

    Maria Carmen Cenit; Mario Martínez-Florensa; Marta Consuegra; Lizette Bonet; Elena Carnero-Montoro; Noelia Armiger; Miguel Caballero-Baños; Maria Teresa Arias; Daniel Benitez; Norberto Ortego-Centeno; Enrique de Ramón; José Mario Sabio; García-Hernández, Francisco J; Carles Tolosa; Ana Suárez

    2014-01-01

    Objective: CD5 plays a crucial role in autoimmunity and is a well-established genetic risk factor of developing RA. Recently, evidence of positive selection has been provided for the CD5 Pro224-Val471 haplotype in East Asian populations. The aim of the present work was to further analyze the functional relevance of non-synonymous CD5 polymorphisms conforming the ancestral and the newly derived haplotypes (Pro224-Ala471 and Pro224-Val471, respectively) as well as to investigate the potential r...

  17. Ancestral heritage saves tribes during 1 April 2007 Solomon Islands tsunami

    Science.gov (United States)

    Fritz, Hermann M.; Kalligeris, Nikos

    2008-01-01

    The 1 April 2007 magnitude Ms 8.1 earthquake off the New Georgia Group in the Solomon Islands generated a tsunami that killed 52 with locally focused run-up heights of 12 m, local flow depths of 5 m as well as tectonic uplift up to 3.6 m and subsidence down to -1.5 m. A reconnaissance team deployed within one week investigated 65 coastal settlements on 13 remote Islands. The ancestral heritage ``run to high ground after an earthquake'' passed on to younger generations by survivors of smaller historic tsunamis triggered an immediate spontaneous self evacuation containing the death toll.

  18. 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.

  19. 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. PMID:27086043

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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. PMID:23130614

  6. 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.

  7. 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.

  8. Individualized internal exposure doses reconstruction for the persons of Ukraine State Register: Report 2. Locally-specific models and doses of persons living in Kozelets and Ripky raions of Chernihiv oblast.

    Science.gov (United States)

    Likhtarov, I A; Kovgan, L N; Masiuk, S V; Ivanova, O N; Chepurny, M I; Boyko, Z N; Gerasymenko, V B; Tereshchenko, S A; Kravchenko, I G; Kortushin, G I; Marcenjyk, O D

    2014-09-01

    Study objective. Development a system of models and procedures for the individualized internal exposure doses reconstruction for the subjects of Ukrainian State Register of persons, affected due to the Chornobyl accident (SRU) and residing in radioactive contaminated territories of Kozelets and Ripky raions of Chernihiv oblast. Materials and methods. A description the schematic diagram and mathematical equations of ecological-dosimetric models are given that allow to reconstruct the individualized exposure doses from consumption of food contaminated with radiocesium of Chornobyl origin for inhabitants of two raions of Chernihiv oblast. Parameterization of the reconstruction models is based on the mathematical analysis of results for radioecological (radiocesium milk contamination) and dosimetric (radiocesium human body burden) monitorings, that were calculated in the period of 1986-2012 in the settlements of raions under consideration. Due to quite low level of radioactive cesium depositions on the ground in 1986, the territory of these raions was divided into two "territorial zones": TZ-1, an area where the 137Cs ground depositions density in 1986 exceeds 37 kBq/m2, and TZ-2, an area where this rate does not exceeds 37 kBq/m2. For each territorial zone in each raion, the initial time moment (year) was introduced in the reconstruction model. Since this year the concept of the so-called "reference dose" has been using. Its value was assigned to all persons, regardless of the results and availability of monitoring. The results of radioecological and dosimetric monitorings were used for setting in raion specific functions: the annual average concentration of 137Cs in milk per unit of 137Cs ground depositions for Kozelets raion, function of the temporary dynamic of 137Cs concentration in milk for Ripky raion, absolute raion milk equivalent of the diet (ARMEr), and relative age dependent intake of radiocesium with the diet. Results and conclusions. Models for

  9. [Symbiogenesis as a Model for Reconstructing the Early Stages of Genome Evolution].

    Science.gov (United States)

    Provorov, N A; Tikhonovich, I A; Vorobyov, N I

    2016-02-01

    Symbiogenic evolution, which involves transformations of bacteria into the cellular organelles, is represented as a model for reconstructing the early stages of genome evolution, including the origin of DNA genomes from RNA genomes and the emergence of template processes on the basis of self-replicating molecular complexes in the ancestral metabolic systems. The antiquity of RNA genomes is supported by an increased evolutionary stability of ribosomal protein synthesis (translation) with respect to the DNA-dependent template processes (replication, transcription, recombination, and reparation). This stability is demonstrated by analysis of the deeply reduced genomes of symbiotic bacteria and cellular organelles as well as the "minimal" genomes which are common to phylogenetically diverse organisms. Higher evolutionary conservation of template biosynthetic processes with respect to step processes determining the metabolism and development in cells does not support the hypothesis about emergence ofgenomes within the ancestral cellular metabolic systems which are thought to be of abiogenic origin, instead suggesting dualistic origin of life on Earth. We suppose that the genome-free organelles of some eukaryotes (mitosomes, many hydrogenosomes, and some plastids) represent the products of reversion of symbiotic bacteria into ancestral forms which implemented their basic cellular functions using the informational macromolecules of exogenic origin. In the framework of this hypothesis the eukaryotic cells functioning based on the massive transfer of gene products (RNAs, proteins) from cytosol to organelles may represent the analogs of ancestral biocenoses that possessed integral hereditary systems (metagenomes). PMID:27215028

  10. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific.

    OpenAIRE

    Rapacz, J; Chen, L.; Butler-Brunner, E; Wu, M J; Hasler-Rapacz, J O; Butler, R.; Schumaker, V N

    1991-01-01

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB ha...

  11. 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

    adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses...... 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...

  12. 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.

  13. Breast Reconstruction After Mastectomy

    Science.gov (United States)

    ... reconstruction with or without radiotherapy. Current Opinion in Obstetrics and Gynecology 2011;23(1):44–50. [PubMed Abstract] Barry M, Kell MR. Radiotherapy and breast reconstruction: a meta-analysis. Breast ...

  14. 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.

  15. 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.

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  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. 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.

  3. 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.

  4. In Silico Reconstruction of the Viral Evolutionary Lineage Yields a Potent Gene Therapy Vector.

    Science.gov (United States)

    Zinn, Eric; Pacouret, Simon; Khaychuk, Vadim; Turunen, Heikki T; Carvalho, Livia S; Andres-Mateos, Eva; Shah, Samiksha; Shelke, Rajani; Maurer, Anna C; Plovie, Eva; Xiao, Ru; Vandenberghe, Luk H

    2015-08-11

    Adeno-associated virus (AAV) vectors have emerged as a gene-delivery platform with demonstrated safety and efficacy in a handful of clinical trials for monogenic disorders. However, limitations of the current generation vectors often prevent broader application of AAV gene therapy. Efforts to engineer AAV vectors have been hampered by a limited understanding of the structure-function relationship of the complex multimeric icosahedral architecture of the particle. To develop additional reagents pertinent to further our insight into AAVs, we inferred evolutionary intermediates of the viral capsid using ancestral sequence reconstruction. In-silico-derived sequences were synthesized de novo and characterized for biological properties relevant to clinical applications. This effort led to the generation of nine functional putative ancestral AAVs and the identification of Anc80, the predicted ancestor of the widely studied AAV serotypes 1, 2, 8, and 9, as a highly potent in vivo gene therapy vector for targeting liver, muscle, and retina. PMID:26235624

  5. Reconstructing the Alcatraz escape

    Science.gov (United States)

    Baart, F.; Hoes, O.; Hut, R.; Donchyts, G.; van Leeuwen, E.

    2014-12-01

    In the night of June 12, 1962 three inmates used a raft made of raincoatsto escaped the ultimate maximum security prison island Alcatraz in SanFrancisco, United States. History is unclear about what happened tothe escapees. At what time did they step into the water, did theysurvive, if so, where did they reach land? The fate of the escapees has been the subject of much debate: did theymake landfall on Angel Island, or did the current sweep them out ofthe bay and into the cold pacific ocean? In this presentation, we try to shed light on this historic case using avisualization of a high-resolution hydrodynamic simulation of the San Francisco Bay, combined with historical tidal records. By reconstructing the hydrodynamic conditions and using a particle based simulation of the escapees we show possible scenarios. The interactive model is visualized using both a 3D photorealistic and web based visualization. The "Escape from Alcatraz" scenario demonstrates the capabilities of the 3Di platform. This platform is normally used for overland flooding (1D/2D). The model engine uses a quad tree structure, resulting in an order of magnitude speedup. The subgrid approach takes detailed bathymetry information into account. The inter-model variability is tested by comparing the results with the DFlow Flexible Mesh (DFlowFM) San Francisco Bay model. Interactivity is implemented by converting the models from static programs to interactive libraries, adhering to the Basic ModelInterface (BMI). Interactive models are more suitable for answeringexploratory research questions such as this reconstruction effort. Although these hydrodynamic simulations only provide circumstantialevidence for solving the mystery of what happened during the foggy darknight of June 12, 1962, it can be used as a guidance and provides aninteresting testcase to apply interactive modelling.

  6. 周代宗庙礼制考%The Research on the Etiquettes of Zhou Dynasty’s Ancestral Temple

    Institute of Scientific and Technical Information of China (English)

    王启敏

    2015-01-01

    周代社会中与宗庙相关的礼制多种多样。宗庙始成要举行落成典礼,作歌诗以纪之。祭庙的形式可谓五花八门,而且祭者的态度要十分的恭敬、严谨。诸侯有丧事了,要在宗庙吊唁,规矩也很多。此外,如天子即位,天子(或诸侯)娶妻、嫁女、出国、归国、出征、凯旋等都要在宗庙举行郑重的祭告仪式。在宗庙的守护、装饰、迁移等方面,在当时也有着严格的、不同的礼节制度要遵守。%In Zhou dynasty the related ancestral temple customs are various. After the completion of ancestral temple, it should be inaugurated and poems should be made to memorize. The forms of memorial temples are varied. The attitude of the emperor and monarch muse be very respectful. The same was the monarch’s condolences at the ancestral temple. In addition, the ascending to the throne as emperor, or monarch, getting married or married abroad, returning to the homeland and triumphing must be held in the ancestral temple solemnly and be reported to ancestral temple. The temple’s guardian, decoration, migration and the others also have restricted rules to obey.

  7. 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).

  8. 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...

  9. Re-construction

    OpenAIRE

    Bernadette Marie Devilat

    2013-01-01

    Re-construct: to build again. The necessary reconstruction process after an earthquake can be seen as an opportunity to improve previous conditions. All damaged buildings undergo a renovation process in which every piece is carefully returned to its original place. The photograph shows roof reconstruction work in San Pedro de Alcántara, a heritage area in the central valley of Chile, which was particularly affected by the 2010 earthquake. 

  10. Temperature reconstruction analysis

    CERN Document Server

    Scafetta, N; Grigolini, P; Roberts, J; Scafetta, Nicola; Imholt, Tim; Grigolini, Paolo; Roberts, Jim

    2002-01-01

    This paper presents a wavelet multiresolution analysis of a time series dataset to study the correlation between the real temperature data and three temperature model reconstructions at different scales. We show that the Mann et.al. model reconstructs the temperature better at all temporal resolutions. We show and discuss the wavelet multiresolution analysis of the Mann's temperature reconstruction for the period from 1400 to 2000 A.D.E.

  11. Flexor pulley reconstruction.

    Science.gov (United States)

    Dy, Christopher J; Daluiski, Aaron

    2013-05-01

    Flexor pulley reconstruction is a challenging surgery. Injuries often occur after traumatic lacerations or forceful extension applied to an acutely flexed finger. Surgical treatment is reserved for patients with multiple closed pulley ruptures, persistent pain, or dysfunction after attempted nonoperative management of a single pulley rupture, or during concurrent or staged flexor tendon repair or reconstruction. If the pulley cannot be repaired primarily, pulley reconstruction can be performed using graft woven into remnant pulley rim or looping graft around the phalanx. Regardless of the reconstructive technique, the surgeon should emulate the length, tension, and glide of the native pulley. PMID:23660059

  12. 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

    2016-01-01

    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. PMID:27352946

  13. 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.

  14. 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

    2016-01-01

    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. PMID:27352946

  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. 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.

  17. 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.

  18. The ancestral circadian clock of monarch butterflies: role in time-compensated sun compass orientation.

    Science.gov (United States)

    Reppert, S M

    2007-01-01

    The circadian clock has a vital role in monarch butterfly (Danaus plexippus) migration by providing the timing component of time-compensated sun compass orientation, which contributes to navigation to the overwintering grounds. The location of circadian clock cells in monarch brain has been identified in the dorsolateral protocerebrum (pars lateralis); these cells express PERIOD, TIMELESS, and a Drosophila-like cryptochrome designated CRY1. Monarch butterflies, like all other nondrosophilid insects examined so far, express a second cry gene (designated insect CRY2) that encodes a vertebrate-like CRY that is also expressed in pars lateralis. An ancestral circadian clock mechanism has been defined in monarchs, in which CRY1 functions as a blue light photoreceptor for photic entrainment, whereas CRY2 functionswithin the clockwork as themajor transcriptional repressor of an intracellular negative transcriptional feedback loop. A CRY1-staining neural pathway has been identified that may connect the circadian (navigational) clock to polarized light input important for sun compass navigation, and a CRY2-positive neural pathway has been discovered that may communicate circadian information directly from the circadian clock to the central complex, the likely site of the sun compass. The monarch butterfly may thus use the CRY proteins as components of the circadian mechanism and also as output molecules that connect the clock to various aspects of the sun compass apparatus. PMID:18419268

  19. WEB LOG PREPROCESSING BASED ON PARTIAL ANCESTRAL GRAPH TECHNIQUE FOR SESSION CONSTRUCTION

    Directory of Open Access Journals (Sweden)

    S.Chitra

    2012-10-01

    Full Text Available Web access log analysis is to analyze the patterns of web site usage and the features of users behavior. It is the fact that the normal Log data is very noisy and unclear and it is vital to preprocess the log data for efficient web usage mining process. Preprocessing comprises of three phases which includes data cleaning, user identification and session construction. Session construction is very vital and numerous real world problems can be modeled as traversals on graph and mining from these traversals would provide the requirement for preprocessing phase. On the other hand, the traversals on unweighted graph have been taken into consideration in existing works. This paper oversimplifies this to the case where vertices of graph are given weights to reflect their significance. The proposed method constructs sessions as a Partial Ancestral Graph which contains pages with calculated weights. This will help site administrators to find the interesting pages for users and to redesign their web pages. After weighting each page according to browsing time a PAG structure is constructed for each user session. Existing system in which there is a problem of learning with the latent variables of the data and the problem can be overcome by the proposed method.

  20. 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.

  1. 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.

  2. Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European.

    Science.gov (United States)

    Olalde, Iñigo; Allentoft, Morten E; Sánchez-Quinto, Federico; Santpere, Gabriel; Chiang, Charleston W K; DeGiorgio, Michael; Prado-Martinez, Javier; Rodríguez, Juan Antonio; Rasmussen, Simon; Quilez, Javier; Ramírez, Oscar; Marigorta, Urko M; Fernández-Callejo, Marcos; Prada, María Encina; Encinas, Julio Manuel Vidal; Nielsen, Rasmus; Netea, Mihai G; Novembre, John; Sturm, Richard A; Sabeti, Pardis; Marquès-Bonet, Tomàs; Navarro, Arcadi; Willerslev, Eske; Lalueza-Fox, Carles

    2014-03-13

    Ancient genomic sequences have started to reveal the origin and the demographic impact of farmers from the Neolithic period spreading into Europe. The adoption of farming, stock breeding and sedentary societies during the Neolithic may have resulted in adaptive changes in genes associated with immunity and diet. However, the limited data available from earlier hunter-gatherers preclude an understanding of the selective processes associated with this crucial transition to agriculture in recent human evolution. Here we sequence an approximately 7,000-year-old Mesolithic skeleton discovered at the La Braña-Arintero site in León, Spain, to retrieve a complete pre-agricultural European human genome. Analysis of this genome in the context of other ancient samples suggests the existence of a common ancient genomic signature across western and central Eurasia from the Upper Paleolithic to the Mesolithic. The La Braña individual carries ancestral alleles in several skin pigmentation genes, suggesting that the light skin of modern Europeans was not yet ubiquitous in Mesolithic times. Moreover, we provide evidence that a significant number of derived, putatively adaptive variants associated with pathogen resistance in modern Europeans were already present in this hunter-gatherer. PMID:24463515

  3. 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.

  4. 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.

  5. 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。

  6. Image Reconstruction. Chapter 13

    International Nuclear Information System (INIS)

    This chapter discusses how 2‑D or 3‑D images of tracer distribution can be reconstructed from a series of so-called projection images acquired with a gamma camera or a positron emission tomography (PET) system [13.1]. This is often called an ‘inverse problem’. The reconstruction is the inverse of the acquisition. The reconstruction is called an inverse problem because making software to compute the true tracer distribution from the acquired data turns out to be more difficult than the ‘forward’ direction, i.e. making software to simulate the acquisition. There are basically two approaches to image reconstruction: analytical reconstruction and iterative reconstruction. The analytical approach is based on mathematical inversion, yielding efficient, non-iterative reconstruction algorithms. In the iterative approach, the reconstruction problem is reduced to computing a finite number of image values from a finite number of measurements. That simplification enables the use of iterative instead of mathematical inversion. Iterative inversion tends to require more computer power, but it can cope with more complex (and hopefully more accurate) models of the acquisition process

  7. The Crystal Structure of Aq_328 from the Hyperthermophilic Bacteria Aquifex aeolicus Shows an Ancestral Histone Fold

    OpenAIRE

    Qiu, Yang; Tereshko, Valentina; Kim, Youngchang; Zhang, Rongguang; Collart, Frank; Yousef, Mohammed; Kossiakoff, Anthony; Joachimiak, Andrzej

    2006-01-01

    The structure of Aq_328, an uncharacterized protein from hyperthermophilic bacteria Aquifex aeolicus, has been determined to 1.9 Å by using multi-wavelength anomalous diffraction (MAD) phasing. Although the amino acid sequence analysis shows that Aq_328 has no significant similarity to proteins with a known structure and function, the structure comparison by using the Dali server reveals that it: (1) assumes a histone-like fold, and (2) is similar to an ancestral nuclear histone protein (PDB ...

  8. Impacts of Plant-Based Foods in Ancestral Hominin Diets on the Metabolism and Function of Gut Microbiota In Vitro

    OpenAIRE

    Gary S Frost; Walton, Gemma E; Jonathan R Swann; Psichas, Arianna; Costabile, Adele; Johnson, Laura P.; Sponheimer, Matt; Glenn R Gibson; Barraclough, Timothy G.

    2014-01-01

    ABSTRACT Ancestral human populations had diets containing more indigestible plant material than present-day diets in industrialized countries. One hypothesis for the rise in prevalence of obesity is that physiological mechanisms for controlling appetite evolved to match a diet with plant fiber content higher than that of present-day diets. We investigated how diet affects gut microbiota and colon cells by comparing human microbial communities with those from a primate that has an extreme plan...

  9. Genetic evidence for the ancestral loss of short-wavelength-sensitive cone pigments in mysticete and odontocete cetaceans.

    OpenAIRE

    Levenson, D H; Dizon, A

    2003-01-01

    All mammals ancestrally possessed two types of cone pigments, an arrangement that persists in nearly all contemporary species. However, the absence of one of these cone types, the short-wavelength-sensitive (SWS) cone, has recently been established in several delphinoid cetacean species, indicating that the loss of this pigment type may be widespread among cetaceans. To evaluate the functional condition of SWS cones in cetaceans, partial SWS cone-opsin gene sequences were obtained from nuclea...

  10. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    International Nuclear Information System (INIS)

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes

  11. Identification of the ancestral haplotype for apolipoprotein B suggests an African origin of Homo sapiens sapiens and traces their subsequent migration to Europe and the Pacific

    Energy Technology Data Exchange (ETDEWEB)

    Rapacz, J.; Hasler-Rapacz, J.O. (Univ. of Wisconsin, Madison (United States)); Chen, L.; Wu, Mingjiuan; Schumaker, V.N. (Univ. of California, Los Angeles (United States)); Butler-Brunner, E.; Butler, R. (Swiss Red Cross Blood Transfusion Service, Bern (Switzerland))

    1991-02-15

    The probable ancestral haplotype for human apolipoprotein B (apoB) has been identified through immunological analysis of chimpanzee and gorilla serum and sequence analysis of their DNA. Moreover, the frequency of this ancestral apoB haplotype among different human populations provides strong support for the African origin of Homo sapiens sapiens and their subsequent migration from Africa to Europe and to the Pacific. The approach used here for the identification of the ancestral human apoB haplotype is likely to be applicable to many other genes.

  12. 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

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

    Directory of Open Access Journals (Sweden)

    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.

  14. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    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.

  18. 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.

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

    International Nuclear Information System (INIS)

    Highlights: ► BoNT and NTNHA proteins share a similar protein architecture. ► NTNHA and BoNT were both identified as zinc-binding proteins. ► NTNHA does not have a classical HEXXH zinc-coordinating motif similar to that found in all serotypes of BoNT. ► 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-X35-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.

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

    Directory of Open Access Journals (Sweden)

    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.

  1. Functions of two distinct prolactin-releasing peptides evolved from a common ancestral gene

    Directory of Open Access Journals (Sweden)

    Tetsuya eTachibana

    2014-11-01

    Full Text Available Prolactin-releasing peptide (PrRP is one of the RF-amide peptides and was originally identified in the bovine hypothalamus as a stimulator of prolactin (PRL release. Independently, another RF-amide peptide was found in Japanese crucian carp and named Carassius RFa (C-RFa, which shows high homology to PrRP and stimulates PRL secretion in teleost fish. Therefore, C-RFa has been recognized as fish PrRP. However, recent work has revealed that PrRP and C-RFa in non-mammalian vertebrates are encoded by separate genes originated through duplication of an ancestral gene. Indeed, both PrRP and C-RFa are suggested to exist in teleost, amphibian, reptile, and avian species. Therefore, we propose that non-mammalian PrRP (C-RFa be renamed PrRP2. Despite a common evolutionary origin, PrRP2 appears to be a physiological regulator of PRL, whereas this is not a consistent role for PrRP itself. Further work revealed that the biological functions of PrRP and PrRP2 are not limited solely to PRL release, because they are also neuromodulators of several hypothalamus-pituitary axes and are involved in some brain circuits related to the regulation of food intake, stress, and cardiovascular functions. However, these actions appear to be different among vertebrates. For example, central injection of PrRP inhibits feeding behavior in rodents and teleosts while it stimulates it in chicks. Therefore, both PrRP and PrRP2 have acquired diverse actions through evolution. In this review, we integrate the burgeoning information of structures, expression profiles, and multiple biological actions of PrRP in higher vertebrates, as well as those of PrRP2 in non-mammals.

  2. Functions of two distinct "prolactin-releasing peptides" evolved from a common ancestral gene.

    Science.gov (United States)

    Tachibana, Tetsuya; Sakamoto, Tatsuya

    2014-01-01

    Prolactin-releasing peptide (PrRP) is one of the RF-amide peptides and was originally identified in the bovine hypothalamus as a stimulator of prolactin (PRL) release. Independently, another RF-amide peptide was found in Japanese crucian carp and named Carassius-RFa (C-RFa), which shows high homology to PrRP and stimulates PRL secretion in teleost fish. Therefore, C-RFa has been recognized as fish PrRP. However, recent work has revealed that PrRP and C-RFa in non-mammalian vertebrates are encoded by separate genes originated through duplication of an ancestral gene. Indeed, both PrRP and C-RFa are suggested to exist in teleost, amphibian, reptile, and avian species. Therefore, we propose that non-mammalian PrRP (C-RFa) be renamed PrRP2. Despite a common evolutionary origin, PrRP2 appears to be a physiological regulator of PRL, whereas this is not a consistent role for PrRP itself. Further work revealed that the biological functions of PrRP and PrRP2 are not limited solely to PRL release, because they are also neuromodulators of several hypothalamus-pituitary axes and are involved in some brain circuits related to the regulation of food intake, stress, and cardiovascular functions. However, these actions appear to be different among vertebrates. For example, central injection of PrRP inhibits feeding behavior in rodents and teleosts, while it stimulates it in chicks. Therefore, both PrRP and PrRP2 have acquired diverse actions through evolution. In this review, we integrate the burgeoning information of structures, expression profiles, and multiple biological actions of PrRP in higher vertebrates, as well as those of PrRP2 in non-mammals.

  3. 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.

  4. 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...

  5. Environment reconstruction for robot navigation

    Energy Technology Data Exchange (ETDEWEB)

    Bohn, S.; Thornton, E.

    1994-04-01

    The United State Department of Energy (DOE) is facing a large task in characterizing and remediating waste tanks and their contents. Because of the hazardous materials inside the waste tanks, all of the work must be done remotely. The purpose of this paper is to show how to reconstruct an enclosed environment from various scans of a Laser Range Finder (LRF). The reconstructed environment can then be used by a robot for path planning, and by an operator to monitor the progress of the waste remediation process. Environment reconstruction consists of two tasks: image processing and laser sculpting. The image processing task focuses first on reducing the quantity of low-confidence data and on smoothing random fluctuations in the data. Then the processed range data must be converted into an XYZ Cartesian coordinate space, a process for which we examined two methods. The first method is a geometrical transform of the LRF data. The second uses an artificial neural network to transform the data to XYZ coordinates. Once an XYZ data set is computed, laser sculpting can be performed. Laser sculpting employs a hierarchical tree structure formally called an octree. The octree structure allows efficient storage of volumetric data and the ability to fuse multiple data sets. Our research has allowed us to examine the difficulties of fusing multiple LRF scans into an octree and to develop algorithms for converting an octree structure into a representation of polygon surfaces.

  6. Acromioclavicular Joint Reconstruction.

    Science.gov (United States)

    Scillia, Anthony J; Cain, E Lyle

    2015-12-01

    Our technique for acromioclavicular joint reconstruction provides a variation on coracoclavicular ligament reconstruction to also include acromioclavicular ligament reconstruction. An oblique acromial tunnel is drilled, and the medial limb of the gracilis graft, after being crossed and passed beneath the coracoid and through the clavicle, is passed through this acromial tunnel and sutured to the trapezoid graft limb after appropriate tensioning. Tenodesis screws are not placed in the bone tunnels to avoid graft fraying, and initial forces on the graft are offloaded with braided absorbable sutures passed around the clavicle. PMID:27284528

  7. 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.

  8. 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...

  9. Overview of Image Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Marr, R. B.

    1980-04-01

    Image reconstruction (or computerized tomography, etc.) is any process whereby a function, f, on Rn is estimated from empirical data pertaining to its integrals, ∫f(x) dx, for some collection of hyperplanes of dimension k < n. The paper begins with background information on how image reconstruction problems have arisen in practice, and describes some of the application areas of past or current interest; these include radioastronomy, optics, radiology and nuclear medicine, electron microscopy, acoustical imaging, geophysical tomography, nondestructive testing, and NMR zeugmatography. Then the various reconstruction algorithms are discussed in five classes: summation, or simple back-projection; convolution, or filtered back-projection; Fourier and other functional transforms; orthogonal function series expansion; and iterative methods. Certain more technical mathematical aspects of image reconstruction are considered from the standpoint of uniqueness, consistency, and stability of solution. The paper concludes by presenting certain open problems. 73 references. (RWR)

  10. 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...... for oncoplastic and reconstructive breast surgery and will certainly become an invaluable addition to breast reconstructive methods....

  11. Delayed breast implant reconstruction

    DEFF Research Database (Denmark)

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

    2011-01-01

    Studies of complications following reconstructive surgery with implants among women with breast cancer are needed. As the, to our knowledge, first prospective long-term study we evaluated the occurrence of complications following delayed breast reconstruction separately for one- and two......-stage procedures. From the Danish Registry for Plastic Surgery of the Breast, which has prospectively registered data for women undergoing breast implantations since 1999, we identified 559 women without a history of radiation therapy undergoing 592 delayed breast reconstructions following breast cancer during...... of reoperation was significantly higher following the one-stage procedure. For both procedures, the majority of reoperations were due to asymmetry or displacement of the implant. In conclusion, non-radiated one- and two-stage delayed breast implant reconstructions are associated with substantial risks...

  12. 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.

  13. 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.

  14. Reconstructing baryon oscillations

    OpenAIRE

    Noh, Yookyung; White, Martin; Padmanabhan, Nikhil

    2009-01-01

    The baryon acoustic oscillation (BAO) method for constraining the expansion history is adversely affected by non-linear structure formation, which washes out the correlation function peak created at decoupling. To increase the constraining power of low z BAO experiments, it has been proposed that one use the observed distribution of galaxies to "reconstruct'' the acoustic peak. Recently Padmanabhan, White and Cohn provided an analytic formalism for understanding how reconstruction works withi...

  15. Reconstruction after mastectomy.

    Science.gov (United States)

    Bostwick, J

    1990-10-01

    Advances in materials and techniques, especially those involving transposition of muscle and skin flaps, have made breast reconstruction possible for most women who undergo mastectomy for breast cancer. The availability of this option can alleviate the breast and chest wall deformity that results from virtually all local treatment of breast cancer. It is essential that the reconstruction surgeon be part of the breast cancer management team from the beginning of treatment planning and that this surgeon work closely with the general surgeon, medical oncologist, and radiation therapist as well as the adjunctive treatment team members. The patient's clinical status and the type of local treatment will be significant determinants of the reconstructive options. For women with stage I breast cancer, these decisions may be based largely on the oncologist's local and adjunctive therapy procedures and the woman's desire to proceed or delay. For women with systemic disease, all members of the breast management team may need to agree on the advisability and timing of reconstruction. Central to all of the numerous decisions described in this paper regarding the timing, type, and extent of breast reconstruction is the primary goal of the entire team: the best possible management of the breast cancer itself. The promise of attractive, symmetric, and natural appearing breasts, complete with a symmetric nipple-areolar complex, has eased somewhat the diminishment of self-esteem and the threat to femininity that can accompany the loss of a breast. By lowering fear, the widely recognized availability of breast reconstruction may encourage more women to monitor their breasts and seek diagnosis of changes and may influence selection of the type of local treatment if cancer is detected. Because of the psychological and cultural significance of the breast, the reconstructive surgeon must be particularly sensitive to the psychological and aesthetic expectations of the patient. Even in

  16. Chalet. Reconstruction from Memory

    OpenAIRE

    Gheysen, Eva

    2015-01-01

    In the research project several design tactics are developed in order to counteract the phenomenon of experiential erosion. This particular project explored one of the tactics: Reconstruction from Memory. When reconstructing space from memory, isolated spatial fragments from the past are reformed into a new, decontextualized construct that represents the most memorable experiences evoked by that space. These memories give insight in which architectural features strongly affect our experience ...

  17. 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.

  18. Cosmic tidal reconstruction

    Science.gov (United States)

    Zhu, Hong-Ming; Pen, Ue-Li; Yu, Yu; Er, Xinzhong; Chen, Xuelei

    2016-05-01

    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 known to be 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 the theoretical framework of 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 ≲0.1 h /Mpc ), with the filter scale ˜1.25 Mpc /h . This is useful in the 21 cm intensity mapping survey, where the long-wavelength radial modes are lost due to a foreground subtraction process.

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

    Science.gov (United States)

    Irum, Bushra; Khan, Arif O.; Wang, Qiwei; Li, David; Khan, Asma A.; Husnain, Tayyab; Akram, Javed; Riazuddin, Sheikh

    2016-01-01

    development. Conclusion Here, we report a common ancestral mutation in CRYBB3 associated with autosomal recessive congenital cataracts identified in four familial cases of Pakistani origin. PMID:27326458

  20. 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.

  1. Control systems for membrane fusion in the ancestral eukaryote; evolution of tethering complexes and SM proteins

    Directory of Open Access Journals (Sweden)

    Coulson Richard MR

    2007-02-01

    Full Text Available Abstract Background In membrane trafficking, the mechanisms ensuring vesicle fusion specificity remain to be fully elucidated. Early models proposed that specificity was encoded entirely by SNARE proteins; more recent models include contributions from Rab proteins, Syntaxin-binding (SM proteins and tethering factors. Most information on membrane trafficking derives from an evolutionarily narrow sampling of model organisms. However, considering factors from a wider diversity of eukaryotes can provide both functional information on core systems and insight into the evolutionary history of the trafficking machinery. For example, the major Qa/syntaxin SNARE families are present in most eukaryotic genomes and likely each evolved via gene duplication from a single ancestral syntaxin before the existing eukaryotic groups diversified. This pattern is also likely for Rabs and various other components of the membrane trafficking machinery. Results We performed comparative genomic and phylogenetic analyses, when relevant, on the SM proteins and components of the tethering complexes, both thought to contribute to vesicle fusion specificity. Despite evidence suggestive of secondary losses amongst many lineages, the tethering complexes are well represented across the eukaryotes, suggesting an origin predating the radiation of eukaryotic lineages. Further, whilst we detect distant sequence relations between GARP, COG, exocyst and DSL1 components, these similarities most likely reflect convergent evolution of similar secondary structural elements. No similarity is found between the TRAPP and HOPS complexes and the other tethering factors. Overall, our data favour independent origins for the various tethering complexes. The taxa examined possess at least one homologue of each of the four SM protein families; since the four monophyletic families each encompass a wide diversity of eukaryotes, the SM protein families very likely evolved before the last common

  2. Effects of interleukin-10 on cutaneous wounds and scars in humans of African continental ancestral origin.

    Science.gov (United States)

    Kieran, Ingrid; Taylor, Catherine; Bush, Jim; Rance, Mark; So, Karen; Boanas, Adam; Metcalfe, Anthony; Hobson, Rosalind; Goldspink, Nick; Hutchison, John; Ferguson, Mark

    2014-01-01

    Scars in humans of African continental ancestry heal with an exaggerated inflammatory response and a generally wider scar. Interleukin-10 is an anti-inflammatory and antifibrotic cytokine. A randomized controlled trial in Caucasians found that exogenous interleukin-10 resulted in improved macroscopic scar appearance and reduced scar redness. We investigated the effects of interleukin-10 on cutaneous scarring in volunteers of African ancestral origin in an exploratory, single-center, within-subject, double-blind randomized controlled trial. Fifty-six subjects received two of four potential prerandomized concentrations of interleukin-10 (5, 25, 100, and 250 ng/100 µL) in two full-thickness incisions on the upper inner arms. Anatomically matching incisions on the contralateral arm were treated with placebo. Scars were excised at 1 month for histological analysis and were redosed with the same regimen. Resultant excision scars were followed up for 12 months for scar width measurement and scoring. Scoring was performed by trial doctors, subjects, and a panel. Incisions treated with 100 ng/100 µL interleukin-10 had significantly reduced microscopic scar widths. Incisions treated with 5 and 25 ng/100 µL interleukin-10 were also narrower, but not significantly. There were no differences observed in pro-inflammatory or pro-fibrotic markers between interleukin-10 and placebo treatment. There was no long-term evidence that 100 ng/100 µL interleukin-10 had a therapeutic effect on macroscopic scar width or appearance, as excisions treated with this concentration were significantly wider than placebo between 8 and 12 months of maturation. Doctors showed a trend toward favoring the macroscopic appearance of placebo-treated excisions compared with those treated with 250 ng/100 µL interleukin-10. Panelists scored placebo-treated excisions as significantly better-appearing than those treated with 250 ng/100 µL interleukin-10. Doctors' scores showed a

  3. Reconstruction in Dewey's Pragmatism: Home, Neighborhood, and Otherness

    Science.gov (United States)

    Saito, Naoko

    2009-01-01

    The purpose of this paper, states the author, is to revive and reconstruct John Dewey's pragmatism so that it becomes an alerting and inspiring voice in response to the nihilistic crisis of today's democracy and education. In other words this is a Deweyan task of reconstruction in philosophy, and it prompts the present endeavor in the continuing…

  4. Face reconstruction from image sequences for forensic face comparison

    NARCIS (Netherlands)

    Dam, van Chris; Veldhuis, Raymond; Spreeuwers, Luuk

    2015-01-01

    The authors explore the possibilities of a dense model-free three-dimensional (3D) face reconstruction method, based on image sequences from a single camera, to improve the current state of forensic face comparison. They propose a new model-free 3D reconstruction method for faces, based on the Lambe

  5. 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

  6. 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

  7. Randomization Resilient To Sensitive Reconstruction

    CERN Document Server

    Wang, Ke; Fu, Ada Waichee

    2012-01-01

    With the randomization approach, sensitive data items of records are randomized to protect privacy of individuals while allowing the distribution information to be reconstructed for data analysis. In this paper, we distinguish between reconstruction that has potential privacy risk, called micro reconstruction, and reconstruction that does not, called aggregate reconstruction. We show that the former could disclose sensitive information about a target individual, whereas the latter is more useful for data analysis than for privacy breaches. To limit the privacy risk of micro reconstruction, we propose a privacy definition, called (epsilon,delta)-reconstruction-privacy. Intuitively, this privacy notion requires that micro reconstruction has a large error with a large probability. The promise of this approach is that micro reconstruction is more sensitive to the number of independent trials in the randomization process than aggregate reconstruction is; therefore, reducing the number of independent trials helps a...

  8. Reconstruction of Nansan Oil Store Accomplished

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    @@ On June 15th 2005, Russian crude oil unloading reconstruction project of Nansan oil store, which has drawn much attention of the state, China National Petroleum Corporation (CNPC) and Daqing Oilfield, was successfully accomplished and put into operation, marking the start of large scale import of Russian crude and opening up a new era for Daqing Oilfield to involve in foreign crude trade.

  9. 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.

  10. Anchoring genome sequence to chromosomes of the central bearded dragon (Pogona vitticeps) enables reconstruction of ancestral squamate macrochromosomes and identifies sequence content of the Z chromosome

    OpenAIRE

    Deakin, Janine E; Edwards, Melanie J; Patel, Hardip; O’Meally, Denis; Lian, Jinmin; Stenhouse, Rachael; Ryan, Sam; Livernois, Alexandra M.; Azad, Bhumika; Clare E Holleley; Li, Qiye; Georges, Arthur

    2016-01-01

    Background Squamates (lizards and snakes) are a speciose lineage of reptiles displaying considerable karyotypic diversity, particularly among lizards. Understanding the evolution of this diversity requires comparison of genome organisation between species. Although the genomes of several squamate species have now been sequenced, only the green anole lizard has any sequence anchored to chromosomes. There is only limited gene mapping data available for five other squamates. This makes it diffic...

  11. 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.

  12. 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

  13. 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. PMID:18603620

  14. 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

  15. 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

  16. 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.

  17. Ancestral polymorphism at the major histocompatibility complex (MHCIIß in the Nesospiza bunting species complex and its sister species (Rowettia goughensis

    Directory of Open Access Journals (Sweden)

    van Rensburg Alexandra

    2012-08-01

    Full Text Available Abstract Background The major histocompatibility complex (MHC is an important component of the vertebrate immune system and is frequently used to characterise adaptive variation in wild populations due to its co-evolution with pathogens. Passerine birds have an exceptionally diverse MHC with multiple gene copies and large numbers of alleles compared to other avian taxa. The Nesospiza bunting species complex (two species on Nightingale Island; one species with three sub-species on Inaccessible Island represents a rapid adaptive radiation at a small, isolated archipelago, and is thus an excellent model for the study of adaptation and speciation. In this first study of MHC in Nesospiza buntings, we aim to characterize MHCIIß variation, determine the strength of selection acting at this gene region and assess the level of shared polymorphism between the Nesospiza species complex and its putative sister taxon, Rowettia goughensis, from Gough Island. Results In total, 23 unique alleles were found in 14 Nesospiza and 2 R. goughensis individuals encoding at least four presumably functional loci and two pseudogenes. There was no evidence of ongoing selection on the peptide binding region (PBR. Of the 23 alleles, 15 were found on both the islands inhabited by Nesospiza species, and seven in both Nesospiza and Rowettia; indications of shared, ancestral polymorphism. A gene tree of Nesospiza MHCIIß alleles with several other passerine birds shows three highly supported Nesospiza-specific groups. All R. goughensis alleles were shared with Nesospiza, and these alleles were found in all three Nesospiza sequence groups in the gene tree, suggesting that most of the observed variation predates their phylogenetic split. Conclusions Lack of evidence of selection on the PBR, together with shared polymorphism across the gene tree, suggests that population variation of MHCIIß among Nesospiza and Rowettia is due to ancestral polymorphism rather than local selective

  18. 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...

  19. Reconstructed Jets at RHIC

    CERN Document Server

    Salur, Sevil

    2010-01-01

    To precisely measure jets over a large background such as pile up in high luminosity p+p collisions at LHC, a new generation of jet reconstruction algorithms is developed. These algorithms are also applicable to reconstruct jets in the heavy ion environment where large event multiplicities are produced. Energy loss in the medium created in heavy ion collisions are already observed indirectly via inclusive hadron distributions and di-hadron correlations. Jets can be used to study this energy loss in detail with reduced biases. We review the latest results on jet-medium interactions as seen in A+A collisions at RHIC, focusing on the recent progress on jet reconstruction in heavy ion collisions.

  20. 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...... of radiation therapy was associated with a non-significantly increased risk of reoperation after both 1-stage (HR = 1.4; 95% CI: 0.7-2.5) and 2-stage (HR = 1.6; 95% CI: 0.9-3.1) procedures. Reconstruction failure was highest (13.2%) in the 2-stage procedures with a history of radiation therapy. Breast...

  1. 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.)

  2. 4D image reconstruction for emission tomography

    International Nuclear Information System (INIS)

    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

  3. 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.

  4. 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.

  5. 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 ...

  6. 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.

  7. 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

  8. 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.

  9. Breast reconstruction - natural tissue

    Science.gov (United States)

    ... muscle flap; TRAM; Latissimus muscle flap with a breast implant; DIEP flap; DIEAP flap; Gluteal free flap; ... If you are having breast reconstruction at the same time as mastectomy, the surgeon may do either of the following: Skin-sparing mastectomy. This means ...

  10. 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...

  11. Breast reconstruction: Correlation between different procedures, reconstruction timing and complications

    Directory of Open Access Journals (Sweden)

    Anđelkov Katarina

    2011-01-01

    Full Text Available Introduction. Improved psychophysical condition after breast reconstruction in women has been well documented Objective. To determine the most optimal technique with minimal morbidity, the authors examined their results and complications based on reconstruction timing (immediate and delayed reconstruction and three reconstruction methods: TRAM flap, latissimus dorsi flap and reconstruction with tissue expanders and implants. Methods. Reconstruction was performed in 60 women of mean age 51.1 years. We analyzed risk factors: age, body mass index (BMI, smoking history and radiation therapy in correlation with timing and method of reconstruction. Complications of all three methods of reconstruction were under 1.5-2-year follow-up after the reconstruction. All data were statistically analyzed. Results. Only radiation had significant influence on the occurrence of complications both before and after the reconstruction, while age, smoking and BMI had no considerable influence of the development of complications. There were no statistically significant correlation between the incidence of complications, time and method of reconstruction. Conclusion. Any of the aforementioned breast reconstruction techniques can yield good results and a low rate of re-operations. To choose the best method, the patient needs to be as well informed as possible about the options including the risks and benefits of each method.

  12. The age, ancestral distribution and radiation of Chimarra (Trichoptera: Philopotamidae) using molecular methods.

    Science.gov (United States)

    Wahlberg, Emma; Johanson, Kjell Arne

    2014-10-01

    The phylogeny of Chimarra has previously been examined using morphological characters for a smaller subset of taxa and geographical representativeness. Here molecular data from three genes (COI, CAD and POL-II) are used to reconstruct the phylogeny of the genus. The results show Chimarra to be monophyletic, and that some of the sister groups are paraphyletic. Previous hypotheses regarding the relationships of subgenera within the genus are corroborated but incongruences are also found compared to morphological characters that have been used in keys. The origin of the genus is explored using three different hypotheses of biogeographical region. The biogeography analyses reveal an origin in the Neotropical region and a subsequent rapid radiation, with dispersal into the Oriental, Palaearctic and Australasian regions and secondarily to the Nearctic region. The Afrotropical region has been colonized in several independent events. The molecular dating using a relaxed clock and calibration with four fossil species indicates that Chimarra is about 138million years old, and that the radiation out of the Neotropical region occurred approximately 124million years ago. PMID:25008108

  13. 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.

  14. Kinetid structure in Choanocytes of Sponges (Heteroscleromorpha): Toward the ancestral Kinetid of Demospongiae.

    Science.gov (United States)

    Pozdnyakov, Igor R; Karpov, Sergey A

    2016-07-01

    Every large clade of Eukarya has its own pattern of kinetid (flagellar apparatus) structure, which is stable and specific within the group, thereby being a good phylogenetic marker. The kinetid structure of sponge choanocytes might be a candidate for such marker for the phylogeny of Porifera. Kinetids of two heteroscleromorphs, Halichondria sp. (Suberitida) and Crellomima imparidens (Poecilosclerida), have been investigated here for the first time, and a reconstruction of the kinetid for each species is provided. The kinetids of both species comprise a flagellar kinetosome with a nuclear fibrillar root, a basal foot and satellite producing microtubules; a centriole is absent. Good resolution images reveal a new thin structure, the axial granule, in the flagellar transition zone which might be present in other sponges. The comparison of kinetids in investigated sponges revealed three types of kinetid in Demospongiae, and their distribution in the taxon has been shown on a molecular phylogenetic tree. Kinetid characters of the common ancestor of Demospongiae are discussed. J. Morphol. 277:925-934, 2016. © 2016 Wiley Periodicals, Inc. PMID:27091517

  15. 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.

  16. Hanford Environmental Dose Reconstruction Project

    International Nuclear Information System (INIS)

    The objective of the Hanford Environmental Dose Reconstruction (HEDR) Project is to estimate the radiation doses that individuals and populations could have received from nuclear operations at Hanford since 1944. 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, Washington, and Idaho, 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 humans (dose estimates): Source terms, environmental transport, environmental monitoring data, demography, food consumption, and agriculture, and environmental pathways and dose estimates. Progress is discussed

  17. 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。

  18. 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...

  19. 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.

  20. Reconstructing holographic quintessence

    OpenAIRE

    Zhang, Xin

    2006-01-01

    The holographic dark energy model is an attempt for probing the nature of dark energy within the framework of quantum gravity. The dimensionless parameter $c$ determines the main property of the holographic dark energy. With the choice of $c\\geq 1$, the holographic dark energy can be described completely by a quintessence scalar field. In this paper, we show this quintessential description of the holographic dark energy with $c\\geq 1$ and reconstruct the potential of the quintessence as well ...

  1. LOFAR sparse image reconstruction

    Science.gov (United States)

    Garsden, H.; Girard, J. N.; Starck, J. L.; Corbel, S.; Tasse, C.; Woiselle, A.; McKean, J. P.; van Amesfoort, A. S.; Anderson, J.; Avruch, I. M.; Beck, R.; Bentum, M. J.; Best, P.; Breitling, F.; Broderick, J.; Brüggen, M.; Butcher, H. R.; Ciardi, B.; de Gasperin, F.; de Geus, E.; de Vos, M.; Duscha, S.; Eislöffel, J.; Engels, D.; Falcke, H.; Fallows, R. A.; Fender, R.; Ferrari, C.; Frieswijk, W.; Garrett, M. A.; Grießmeier, J.; Gunst, A. W.; Hassall, T. E.; Heald, G.; Hoeft, M.; Hörandel, J.; van der Horst, A.; Juette, E.; Karastergiou, A.; Kondratiev, V. I.; Kramer, M.; Kuniyoshi, M.; Kuper, G.; Mann, G.; Markoff, S.; McFadden, R.; McKay-Bukowski, D.; Mulcahy, D. D.; Munk, H.; Norden, M. J.; Orru, E.; Paas, H.; Pandey-Pommier, M.; Pandey, V. N.; Pietka, G.; Pizzo, R.; Polatidis, A. G.; Renting, A.; Röttgering, H.; Rowlinson, A.; Schwarz, D.; Sluman, J.; Smirnov, O.; Stappers, B. W.; Steinmetz, M.; Stewart, A.; Swinbank, J.; Tagger, M.; Tang, Y.; Tasse, C.; Thoudam, S.; Toribio, C.; Vermeulen, R.; Vocks, C.; van Weeren, R. J.; Wijnholds, S. J.; Wise, M. W.; Wucknitz, O.; Yatawatta, S.; Zarka, P.; Zensus, A.

    2015-03-01

    Context. The LOw Frequency ARray (LOFAR) radio telescope is a giant digital phased array interferometer with multiple antennas distributed in Europe. It provides discrete sets of Fourier components of the sky brightness. Recovering the original brightness distribution with aperture synthesis forms an inverse problem that can be solved by various deconvolution and minimization methods. Aims: Recent papers have established a clear link between the discrete nature of radio interferometry measurement and the "compressed sensing" (CS) theory, which supports sparse reconstruction methods to form an image from the measured visibilities. Empowered by proximal theory, CS offers a sound framework for efficient global minimization and sparse data representation using fast algorithms. Combined with instrumental direction-dependent effects (DDE) in the scope of a real instrument, we developed and validated a new method based on this framework. Methods: We implemented a sparse reconstruction method in the standard LOFAR imaging tool and compared the photometric and resolution performance of this new imager with that of CLEAN-based methods (CLEAN and MS-CLEAN) with simulated and real LOFAR data. Results: We show that i) sparse reconstruction performs as well as CLEAN in recovering the flux of point sources; ii) performs much better on extended objects (the root mean square error is reduced by a factor of up to 10); and iii) provides a solution with an effective angular resolution 2-3 times better than the CLEAN images. Conclusions: Sparse recovery gives a correct photometry on high dynamic and wide-field images and improved realistic structures of extended sources (of simulated and real LOFAR datasets). This sparse reconstruction method is compatible with modern interferometric imagers that handle DDE corrections (A- and W-projections) required for current and future instruments such as LOFAR and SKA.

  2. Orthotopic neobladder reconstruction

    OpenAIRE

    Chang, Dwayne T. S.; Nathan Lawrentschuk

    2015-01-01

    Orthotopic neobladder reconstruction is becoming an increasingly common urinary diversion following cystectomy for bladder cancer. This is in recognition of the potential benefits of neobladder surgery over creation of an ileal conduit related to quality of life (QoL), such as avoiding the need to form a stoma with its cosmetic, psychological and other potential complications. The PubMed database was searched using relevant search terms for articles published electronically between January 19...

  3. The art of reconstruction

    OpenAIRE

    Healey, Michael; Esson, Michael

    2011-01-01

    The ‘Art of Reconstruction Research Project’ is where re-skilling of plastic surgeons by artists is already in an embryonic phase. In integrating the required network of associated skills, expertise and experience, the research collaboration brings together artists within The Drawing Research Group of The Faculty of Art, Architecture and Design (AAD) and the distinguished work of Professor Mike Esson, Director, The International Drawing Research Institute (IDRI). Th...

  4. 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.

  5. Orientia tsutsugamushi, agent of scrub typhus, displays a single metapopulation with maintenance of ancestral haplotypes throughout continental South East Asia.

    Science.gov (United States)

    Wongprompitak, Patimaporn; Duong, Veasna; Anukool, Wichittra; Sreyrath, Lay; Mai, Trinh Thi Xuan; Gavotte, Laurent; Moulia, Catherine; Cornillot, Emmanuel; Ekpo, Pattama; Suputtamongkol, Yupin; Buchy, Philippe; Frutos, Roger

    2015-04-01

    Orientia tsutsugamushi is the causative agent of scrub typhus, a major cause of febrile illness in rural area of Asia-Pacific region. A multi-locus sequence typing (MLST) analysis was performed on strains isolated from human patients from 3 countries in Southeast Asia: Cambodia, Vietnam and Thailand. The phylogeny of the 56-kDa protein encoding gene was analyzed on the same strains and showed a structured topology with genetically distinct clusters. MLST analysis did not lead to the same conclusion. DNA polymorphism and phylogeny of individual gene loci indicated a significant level of recombination and genetic diversity whereas the ST distribution indicated the presence of isolated patches. No correlation was found with the geographic origin. This work suggests that weak divergence in core genome and ancestral haplotypes are maintained by permanent recombination in mites while the 56-kDa protein gene is diverging in higher speed due to selection by the mammalian immune system. PMID:25577986

  6. 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

    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...... 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...... be possible if we can decode the divergence times along a genomic alignment. Here, we present a new hidden Markov model that infers the changing divergence (coalescence) times along the genome alignment using a coalescent framework, in order to estimate the speciation time, the recombination rate...

  7. ¿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.

  8. Cis-by-Trans regulatory divergence causes the asymmetric lethal effects of an ancestral hybrid incompatibility gene.

    Directory of Open Access Journals (Sweden)

    Shamoni Maheshwari

    Full Text Available The Dobzhansky and Muller (D-M model explains the evolution of hybrid incompatibility (HI through the interaction between lineage-specific derived alleles at two or more loci. In agreement with the expectation that HI results from functional divergence, many protein-coding genes that contribute to incompatibilities between species show signatures of adaptive evolution, including Lhr, which encodes a heterochromatin protein whose amino acid sequence has diverged extensively between Drosophila melanogaster and D. simulans by natural selection. The lethality of D. melanogaster/D. simulans F1 hybrid sons is rescued by removing D. simulans Lhr, but not D. melanogaster Lhr, suggesting that the lethal effect results from adaptive evolution in the D. simulans lineage. It has been proposed that adaptive protein divergence in Lhr reflects antagonistic coevolution with species-specific heterochromatin sequences and that defects in LHR protein localization cause hybrid lethality. Here we present surprising results that are inconsistent with this coding-sequence-based model. Using Lhr transgenes expressed under native conditions, we find no evidence that LHR localization differs between D. melanogaster and D. simulans, nor do we find evidence that it mislocalizes in their interspecific hybrids. Rather, we demonstrate that Lhr orthologs are differentially expressed in the hybrid background, with the levels of D. simulans Lhr double that of D. melanogaster Lhr. We further show that this asymmetric expression is caused by cis-by-trans regulatory divergence of Lhr. Therefore, the non-equivalent hybrid lethal effects of Lhr orthologs can be explained by asymmetric expression of a molecular function that is shared by both orthologs and thus was presumably inherited from the ancestral allele of Lhr. We present a model whereby hybrid lethality occurs by the interaction between evolutionarily ancestral and derived alleles.

  9. Low pathogenic avian influenza (H9N2) in chicken: Evaluation of an ancestral H9-MVA vaccine.

    Science.gov (United States)

    Ducatez, Mariette F; Becker, Jens; Freudenstein, Astrid; Delverdier, Maxence; Delpont, Mattias; Sutter, Gerd; Guérin, Jean-Luc; Volz, Asisa

    2016-06-30

    Modified Vaccinia Ankara (MVA) has proven its efficacy as a recombinant vector vaccine for numerous pathogens including influenza virus. The present study aimed at evaluating a recombinant MVA candidate vaccine against low pathogenic avian influenza virus subtype H9N2 in the chicken model. As the high genetic and antigenic diversity of H9N2 viruses increases vaccine design complexity, one strategy to widen the range of vaccine coverage is to use an ancestor sequence. We therefore generated a recombinant MVA encoding for the gene sequence of an ancestral hemagglutinin H9 protein (a computationally derived amino acid sequence of the node of the H9N2 G1 lineage strains was obtained using the ANCESCON program). We analyzed the genetics and the growth properties of the MVA vector virus confirming suitability for use under biosafety level 1 and tested its efficacy when applied either as an intra-muscular (IM) or an oral vaccine in specific pathogen free chickens challenged with A/chicken/Tunisia/12/2010(H9N2). Two control groups were studied in parallel (unvaccinated and inoculated birds; unvaccinated and non-inoculated birds). IM vaccinated birds seroconverted as early as four days post vaccination and neutralizing antibodies were detected against A/chicken/Tunisia/12/2010(H9N2) in all the birds before challenge. The role of local mucosal immunity is unclear here as no antibodies were detected in eye drop or aerosol vaccinated birds. Clinical signs were not detected in any of the infected birds even in absence of vaccination. Virus replication was observed in both vaccinated and unvaccinated chickens, suggesting the MVA-ancestral H9 vaccine may not stop virus spread in the field. However vaccinated birds showed less histological damage, fewer influenza-positive cells and shorter virus shedding than their unvaccinated counterparts. PMID:27259828

  10. Tectonics vs. eustasy: Mid Pennsylvanian carbonate-ramp cycles, ancestral Rocky Mountains, north-central New Mexico

    Energy Technology Data Exchange (ETDEWEB)

    Wiberg, T.L. (PRC Environmental Management, Inc., Chicago, IL (United States). Dept. of Geology); Smith, G.A. (Univ. of Mexico, Albuquerque, NM (United States). Dept. of Geology)

    1992-01-01

    Detailed stratigraphic and sedimentologic analysis of measured sections within the Madera Limestone in the Sandia Mountains, New Mexico, characterize depositional environments and transgressive-regressive (T-R) cycles across a west-dipping ramp, situated approximately 70 kilometers west of the Pedernal uplift, a tectonically active element of the Ancestral Rocky Mountains. The ramp setting was separated from the Pedernal Uplift by the deep, clastic-filled Estancia Basin. T-R cycles are 2--12 meters thick and consist of asymmetric, shoaling-upward calcareous shales, thick skeletal wackestones, packstones-grainstones, and are capped by subaerial exposure surfaces or terrigenous clastics. The presence of subaerial exposure features upon subtidal carbonates argues for an allogenic control on cycle formation. 15 T-R cycles are interpreted to coincide with 3rd-order eustatic curves of Ross and Ross (1987). Following the convention of most workers, these 3rd-order cycles are herein referred to as 4th-order. No higher-order cycles have been recognized. Cycles exhibit a bundling of 4, 4th-order cycles into larger, asymmetric 3rd-order cycles, similar in pattern to those described by Ross and Ross (1987). Correlation of Madera Limestone cycles with those in other regions indicates that ancestral Rocky Mountains tectonism was less effective than eustasy in controlling the stratigraphy of Middle Pennsylvanian sediments. Using various time scales for the Desmoinesian, cycle periodicities range between 200,000--370,000 years. This average cycle periodicity is similar to other 4th-order cycles reported in the literature for the Pennsylvanian and suggests a Milankovitch orbital forcing mechanism.

  11. 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].

  12. 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

  13. Reconstruction of the perineum.

    Science.gov (United States)

    Wong, David Sau-Yan

    2014-09-01

    The pelvic and perineal regions are affected by a heterogeneous spectrum of pathologies, many with a tendency to recur. Extensive mutilation carries physical, sexual, and psychological sequelae. Primary reconstruction reduces morbidity and shortens recovery. Modern management calls for a multidisciplinary approach. Not uncommonly, patients come with previous surgery and/or chemoirradiation. They may also be elderly and debilitated. The literature on reconstruction of the perineum can be confusing because knowledge has evolved by an accumulation of isolated short reports of individual methods. This led to the lack of a unifying basis for nomenclature and a failure to relate specific techniques to their roles in repairing particular types of defects. This article gives an overall summary of the approaches in a structured and rational manner. Defects of the external pelvis and perineal lining are usually amenable to coverage with local or regional fasciocutaneous flaps, if primary closure or skin graft is not appropriate. These flaps depend on the integrity of the vascular territories of the internal pudendal, the upper medial thigh plexus, or the descending branches of the inferior gluteal. The location and extent of the resection usually determine the requirements of the reconstruction and may dictate the choice of options. When defects are pelviperineal, particularly when the vagina needs to be reconstructed, myocutaneous flaps are of proven advantage in dealing with both the resurfacing as well as providing the bulk needed to fill the pelvic cavity after extensive resections. The rectus, gluteus, and gracilis are the best known options. Owing to the intrinsic limitations with the gracilis flap, the rectus and gluteus flaps have largely superseded its role in most situations. The rectus flap, in particular, provides good bulk as well as reliable skin. The use of muscle sparing flaps based on the perforator principle in suitable instances has increasingly been

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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. PMID:20359837

  19. Breast reconstruction and post-mastectomy radiation practice

    International Nuclear Information System (INIS)

    The goal of this study was to explore the perspectives and practice of radiation oncologists who treat breast cancer patients who have had breast reconstruction. In 2010, an original electronic survey was sent to all physician members of the American Society of Radiation Oncology, National Cancer Research Institute-Breast Cancer Studies Group in the United Kingdom, Thai Society of Therapeutic Radiology and Oncology, Swiss Society of Radiation Oncology, and Turkish Radiation Oncology Society. We identified factors associated with radiation oncologists who treat breast cancer patients with reconstruction performed prior to radiation and obtained information regarding radiation management of the breast reconstruction. 358 radiation oncologists responded, and 60% of the physicians were from the United States. While 64% of participants agree or strongly agree that breast image affects a woman’s quality of life during radiation, 57% feel that reconstruction challenges their ability to deliver effective breast radiation. Compared with other countries, treatment within the United States was associated with a high reconstruction rate (>/= 50% of mastectomy patients) prior to radiation (p < 0.05). Delayed-immediate reconstruction with a temporary tissue expander was more common in the United States than in other countries (52% vs. 23%, p = 0.01). Among physicians who treat patients with tissue expanders, the majority (60%) prefer a moderately inflated implant with 150-250 cc of fluid rather than a completely deflated (13%) or inflated expander (28%) during radiation. Among radiation oncologists who treat reconstructions, 49% never use bolus and 40% never boost a breast reconstruction. United States physicians were more likely than physicians from other countries to boost or bolus the reconstruction irrespective of the type of reconstruction seen in their clinic patients (p < 0.01). Great variation in practice is evident from our study of radiation treatment for breast

  20. 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; 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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; 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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; 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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; 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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.

  1. 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...

  2. Broadening the New Perspective on Paul : Paul and the Ethnographical Debate of his Time - The Criticism of Jewish and Pagan Ancestral Customs (1 Thess 2:13-16)

    NARCIS (Netherlands)

    van Kooten, G.H.; van Kooten, G.H.; Goodman, M.; van Ruiten, J.T.A.G.M.

    2010-01-01

    George H. van Kooten, “Broadening the New Perspective on Paul: Paul and the Ethnographical Debate of His Time—The Criticism of Jewish and Pagan Ancestral Customs (1 Thess 2:13-16),” in Abraham, the Nations, and the Hagarites: Jewish, Christian, and Islamic Perspectives on Kinship with Abraham (ed. M

  3. Reconstructing the history of dark energy using maximum entropy

    OpenAIRE

    Zunckel, C.; Trotta, R.

    2007-01-01

    We present a Bayesian technique based on a maximum entropy method to reconstruct the dark energy equation of state $w(z)$ in a non--parametric way. This MaxEnt technique allows to incorporate relevant prior information while adjusting the degree of smoothing of the reconstruction in response to the structure present in the data. After demonstrating the method on synthetic data, we apply it to current cosmological data, separately analysing type Ia supernovae measurement from the HST/GOODS pro...

  4. Least-squares inversion for density-matrix reconstruction

    OpenAIRE

    Opatrny, T.; Welsch, D. -G.; Vogel, W.

    1997-01-01

    We propose a method for reconstruction of the density matrix from measurable time-dependent (probability) distributions of physical quantities. The applicability of the method based on least-squares inversion is - compared with other methods - very universal. It can be used to reconstruct quantum states of various systems, such as harmonic and and anharmonic oscillators including molecular vibrations in vibronic transitions and damped motion. It also enables one to take into account various s...

  5. Non-microsurgical breast reconstruction

    Directory of Open Access Journals (Sweden)

    Sharma Sheel

    2007-12-01

    Full Text Available Breast reconstruction after mastectomy should aim at resulting in an aesthetic outcome that matches the patient′s expectations and without interfering in the oncologic treatment. Whether the reconstruction is performed immediately or in a delayed fashion depends on various factors, which needs detailed attention. Autologous tissue, implants or both are used in the reconstruction. This article reviews the current concepts in these, with emphasis on non-microsurgical methods of using the autologous tissue for reconstruction. Breast conservation has become an accepted practice of treatment. Reconstruction in these situations as well as in an occasion when the surgery is done for failed breast conservation is discussed in detail. The article also reviews the various methods for nipple reconstruction available.

  6. 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...

  7. 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.

  8. 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...

  9. 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.

  10. 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.

  11. 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.

  12. Application of particle filtering algorithm in image reconstruction of EMT

    International Nuclear Information System (INIS)

    To improve the image quality of electromagnetic tomography (EMT), a new image reconstruction method of EMT based on a particle filtering algorithm is presented. Firstly, the principle of image reconstruction of EMT is analyzed. Then the search process for the optimal solution for image reconstruction of EMT is described as a system state estimation process, and the state space model is established. Secondly, to obtain the minimum variance estimation of image reconstruction, the optimal weights of random samples obtained from the state space are calculated from the measured information. Finally, simulation experiments with five different flow regimes are performed. The experimental results have shown that the average image error of reconstruction results obtained by the method mentioned in this paper is 42.61%, and the average correlation coefficient with the original image is 0.8706, which are much better than corresponding indicators obtained by LBP, Landweber and Kalman Filter algorithms. So, this EMT image reconstruction method has high efficiency and accuracy, and provides a new method and means for EMT research. (paper)

  13. 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.

  14. Unfavourable results in thumb reconstruction

    Directory of Open Access Journals (Sweden)

    Samir M Kumta

    2013-01-01

    Full Text Available The history of thumb reconstruction parallels the history of hand surgery. The attributes that make the thumb unique, and that the reconstructive surgeon must assess and try to restore when reconstructing a thumb, are: Position, stability, strength, length, motion, sensibility and appearance. Deficiency in any of these attributes can reduce the utility of the reconstructed thumb. A detailed assessment of the patient and his requirements needs to be performed before embarking on a thumb reconstruction. Most unsatisfactory results can be attributed to wrong choice of procedure. Component defects of the thumb are commonly treated by tissue from adjacent fingers, hand or forearm. With refinements in microsurgery, the foot has become a major source of tissue for component replacement in the thumb. Bone lengthening, osteoplastic reconstruction, pollicisation, and toe to hand transfers are the commonest methods of thumb reconstruction. Unfavourable results can be classified as functional and aesthetic. Some are common to all types of procedures. However each type of reconstruction has its own unique set of problems. Meticulous planning and execution is essential to give an aesthetic and functionally useful thumb. Secondary surgeries like tendon transfers, bone grafting, debulking, arthrodesis, may be required to correct deficiencies in the reconstruction. Attention needs to be paid to the donor site as well.

  15. 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.

  16. Set Reconstruction on the Hypercube

    OpenAIRE

    Pebody, Luke

    2016-01-01

    Given an action of a group $G$ on a set $S$, the $k$-deck of a subset $T$ of $S$ is the multiset of all subsets of $T$ of size $k$, each given up to translation by $G$. For a given subset $T$, the {\\em reconstruction number} of $T$ is the minimum $k$ such that the $k$-deck uniquely identifies $T$ up to translation by $G$, and the {\\em reconstruction number} of the action $G:S$ is the maximum reconstruction number of any subset of $S$. The concept of reconstruction number extends naturally to ...

  17. 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

  18. 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.)

  19. Quantum interferences reconstruction with low homodyne detection efficiency

    International Nuclear Information System (INIS)

    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. Nonparametric Dark Energy Reconstruction from Supernova Data

    CERN Document Server

    Holsclaw, Tracy; Sanso, Bruno; Lee, Herbert; Heitmann, Katrin; Habib, Salman; Higdon, David

    2010-01-01

    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.

  1. In Silico Reconstruction of the Viral Evolutionary Lineage Yields a Potent Gene Therapy Vector

    Directory of Open Access Journals (Sweden)

    Eric Zinn

    2015-08-01

    Full Text Available Adeno-associated virus (AAV vectors have emerged as a gene-delivery platform with demonstrated safety and efficacy in a handful of clinical trials for monogenic disorders. However, limitations of the current generation vectors often prevent broader application of AAV gene therapy. Efforts to engineer AAV vectors have been hampered by a limited understanding of the structure-function relationship of the complex multimeric icosahedral architecture of the particle. To develop additional reagents pertinent to further our insight into AAVs, we inferred evolutionary intermediates of the viral capsid using ancestral sequence reconstruction. In-silico-derived sequences were synthesized de novo and characterized for biological properties relevant to clinical applications. This effort led to the generation of nine functional putative ancestral AAVs and the identification of Anc80, the predicted ancestor of the widely studied AAV serotypes 1, 2, 8, and 9, as a highly potent in vivo gene therapy vector for targeting liver, muscle, and retina.

  2. Gender Mainstreaming and Sustainable Post Disaster Reconstruction,

    OpenAIRE

    Yumarni, Tri; Amaratunga, Dilanthi; Haigh, Richard

    2013-01-01

    Gender inequalities are barriers to achieve sustainable post disaster reconstruction. Mainstreaming gender equality within post disaster reconstruction process can enhance sustainability of reconstruction. Based on a detailed literature review on post disaster reconstruction, this paper identifies pre-requisite conditions for mainstreaming gender within sustainable post disaster reconstruction as ; awareness of gender needs and concerns, a strong gender policy framework, women ...

  3. Markov Random Field Surface Reconstruction

    DEFF Research Database (Denmark)

    Paulsen, Rasmus Reinhold; Bærentzen, Jakob Andreas; Larsen, Rasmus

    2010-01-01

    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...

  4. 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.

  5. Expression of segment polarity genes in brachiopods supports a non-segmental ancestral role of engrailed for bilaterians.

    Science.gov (United States)

    Vellutini, Bruno C; Hejnol, Andreas

    2016-01-01

    The diverse and complex developmental mechanisms of segmentation have been more thoroughly studied in arthropods, vertebrates and annelids-distantly related animals considered to be segmented. Far less is known about the role of "segmentation genes" in organisms that lack a segmented body. Here we investigate the expression of the arthropod segment polarity genes engrailed, wnt1 and hedgehog in the development of brachiopods-marine invertebrates without a subdivided trunk but closely related to the segmented annelids. We found that a stripe of engrailed expression demarcates the ectodermal boundary that delimits the anterior region of Terebratalia transversa and Novocrania anomala embryos. In T. transversa, this engrailed domain is abutted by a stripe of wnt1 expression in a pattern similar to the parasegment boundaries of insects-except for the expression of hedgehog, which is restricted to endodermal tissues of the brachiopod embryos. We found that pax6 and pax2/5/8, putative regulators of engrailed, also demarcate the anterior boundary in the two species, indicating these genes might be involved in the anterior patterning of brachiopod larvae. In a comparative phylogenetic context, these findings suggest that bilaterians might share an ancestral, non-segmental domain of engrailed expression during early embryogenesis. PMID:27561213

  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

    2015-01-01

    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. PMID:25889196

  7. 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.

  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. PMID:26286030

  9. Basin and range-age reactivation of the ancestral Rocky Mountains in Texas Panhandle: evidence from Ogallala Formation

    Energy Technology Data Exchange (ETDEWEB)

    Budnik, R.T.

    1984-04-01

    The Ogallala Formation (Neogene) is a widespread syntectonic alluvial apron that was shed eastward from the Rio Grande rift and related uplifts in Colorado and New Mexico during Basin and Range extension. In the Texas Panhandle, the Ogallala completely buried Ancestral Rocky Mountain (Pennsylvanian) structures. Renewed movement on these older structures during the Neogene influenced the thickness and facies distribution of the Ogallala. The Ogallala thickens into the Palo Duro, Dalhart, and Anadarko basins. Major distributary channels on Ogallala alluvial fans coincide with the axes of these basins, whereas major interchannel areas overlie intervening uplifts. Second-order structures subtly influenced the unit as well. For example, the Carson basin, a Pennsylvanian rhomb graben along the Amarillo uplift, the Ogallala is over 250 m (820 ft) thick compared with 90 m (275 ft) in adjacent areas. Within the Palo Duro basin, local highs controlled the distribution of thin, interchannel flood-basin and lacustrine deposits. Thicker, braided-stream channel deposits follow local lows. Later movement on the Amarillo uplift broadly folded the Ogallala. The southern high plains surface subtly reflects basement structure, with topographic highs overlying basement highs, suggesting post-Ogallala deformation within the Palo Duro basin. The Amarillo uplift is approximately perpendicular to the Rio Grande rift and parallel to the direction of Basin and Range extension. Thus, the stress field that produced the rift may have caused strike-slip movement and reactivation of the Carson basin along the Amarillo uplift.

  10. 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.

  11. 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

  12. 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.

  13. Ancestral polymorphisms and sex-biased migration shaped the demographic history of brown bears and polar bears.

    Directory of Open Access Journals (Sweden)

    Shigeki Nakagome

    Full Text Available Recent studies have reported discordant gene trees in the evolution of brown bears and polar bears. Genealogical histories are different among independent nuclear loci and between biparentally inherited autosomal DNA (aDNA and matrilineal mitochondrial DNA (mtDNA. Based on multi-locus genomic sequences from aDNA and mtDNA, we inferred the population demography of brown and polar bears and found that brown bears have 6 times (aDNA or more than 14 times (mtDNA larger population sizes than polar bears and that polar bear lineage is derived from within brown bear diversity. In brown bears, the effective population size ratio of mtDNA to aDNA was at least 0.62, which deviated from the expected value of 0.25, suggesting matriarchal population due to female philopatry and male-biased migration. These results emphasize that ancestral polymorphisms and sex-biased migration may have contributed to conflicting branching patterns in brown and polar bears across aDNA genes and mtDNA.

  14. 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.

  15. 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

  16. SEGMENTATION USING MULTISCALE MORPHOLOGICAL RECONSTRUCTION

    Directory of Open Access Journals (Sweden)

    NANMOZHI.R

    2013-04-01

    Full Text Available Image segmentation is a crucial step in the field of image processing and pattern recognition. Segmentation allows the identification of structures in an image which can be utilized for further processing. This paper proposes a technique for object segmentation from its background. We utilized both region-based and object-based segmentation capabilities to handle the object segmentation for large-scale database images in a robust and principled manner. MultiScalE Graylevel mOrphological recoNstructions (SEGON is used for segmenting an image. SEGON roughly identifies the background and object regions in the image. To further refine the boundaries of the objects mean-shift segmentation technique is applied on the SEGON processed image. Accuracy of segmentation is evaluated by computing structural similarity index (SSIM, for the image segmented with and without using SEGON. Images collected from Corel, Caltech, PASCAL, UCID and CMU-PIE databases are utilized for this work. Experimental results showed that the proposed object segmentation method outperforms the state-of-the-art image segmentation techniques.

  17. 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

  18. Evidence-Based ACL Reconstruction.

    Science.gov (United States)

    Rodriguez-Merchan, E Carlos

    2015-01-01

    There is controversy in the literature regarding a number of topics related to anterior cruciate ligament (ACL) reconstruction. The purpose of this article is to answer the following questions: 1) Bone-patellar tendon-bone reconstruction (BPTB-R) or hamstrimg reconstruction (H-R); 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-analyses focused 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. PMID:25692162

  19. 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...

  20. 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.

  1. AORTOILIAC AND AORTOFEMORAL RECONSTRUCTION OF OBSTRUCTIVE DISEASE

    NARCIS (Netherlands)

    VANDENAKKER, PJ; VANSCHILFGAARDE, R; BRAND, R; VANBOCKEL, JH; TERPSTRA, JL

    1994-01-01

    This retrospective study evaluates our strategy to limit prosthetic reconstructions for aortoiliac obstructive disease to the diseased segments in 518 patients. There were 363 (70%) reconstructions without femoral anastomotic sites (FEM-0), 107 (21%) reconstructions with one femoral anastomotic site

  2. 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.

  3. 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.

  4. 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.

  5. Bayesian Cosmic Web Reconstruction: BARCODE for Clusters

    Science.gov (United States)

    Patrick Bos, E. G.; 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.

  6. 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)

  7. Driving Organic Molecule Crystalliztion with Surface Reconstructions

    Science.gov (United States)

    Bickel, Jessica; Trovato, Gianfranco

    This work examines how surface reconstructions can drive crystallization of organic molecules via self-assembly. Organic electronic molecules have low conductivities compared to inorganic materials, but crystallizing these polymers increases their conductivity. This project uses surface reconstructions with periodically repeating topographies to drive the crystallization process. The samples are grown by placing a drop of a dilute PEDOT solution on the clean Si(001)-(2x1) or Si(111)-(7x7) surface reconstruction and heating the surface up to both evaporate the solvent and promote diffusion of the polymer to the thermodynamically defined lowest energy position. The resulting samples are characterized by scanning tunneling microscopy (STM) with respect to their crystallinity and electronic properties. Of particular interest is whether there is a preferential location for the PEDOT molecule to adsorb and whether there are any conformational changes upon adsorption that modify the HOMO-LUMO gap. This work is being done in a new pan-style RHK-STM enclosed in a glovebox at Cleveland State University. The glovebox has O2 and H2O levels of less than 1ppm. This allows for sample preparation and imaging in a controlled environment that is free from contamination.

  8. Genome-scale metabolic network reconstruction.

    Science.gov (United States)

    Fondi, Marco; Liò, Pietro

    2015-01-01

    Bacterial metabolism is an important source of novel products/processes for everyday life and strong efforts are being undertaken to discover and exploit new usable substances of microbial origin. Computational modeling and in silico simulations are powerful tools in this context since they allow the exploration and a deeper understanding of bacterial metabolic circuits. Many approaches exist to quantitatively simulate chemical reaction fluxes within the whole microbial metabolism and, regardless of the technique of choice, metabolic model reconstruction is the first step in every modeling pipeline. Reconstructing a metabolic network consists in drafting the list of the biochemical reactions that an organism can carry out together with information on cellular boundaries, a biomass assembly reaction, and exchange fluxes with the external environment. Building up models able to represent the different functional cellular states is universally recognized as a tricky task that requires intensive manual effort and much additional information besides genome sequence. In this chapter we present a general protocol for metabolic reconstruction in bacteria and the main challenges encountered during this process. PMID:25343869

  9. 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...

  10. 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. PMID:27093062

  11. Orthotopic neobladder reconstruction

    Directory of Open Access Journals (Sweden)

    Dwayne T. S. Chang

    2015-01-01

    Full Text Available Orthotopic neobladder reconstruction is becoming an increasingly common urinary diversion following cystectomy for bladder cancer. This is in recognition of the potential benefits of neobladder surgery over creation of an ileal conduit related to quality of life (QoL, such as avoiding the need to form a stoma with its cosmetic, psychological and other potential complications. The PubMed database was searched using relevant search terms for articles published electronically between January 1994 and April 2014. Full-text articles in English or with English translation were assessed for relevance to the topic before being included in the review. Patients with neobladders have comparable or better post-operative sexual function than those with ileal conduits. They also have comparable QoL to those with ileal conduits. Orthotopic neobladder is a good alternative to ileal conduit in suitable patients who do not want a stoma and are motivated to comply with neobladder training. However, the selection of a neobladder as the urinary diversion of choice requires that patients have good renal and liver functions and are likely to be compliant with neobladder training. With benefits also come potential risks of neobladder formation. These include electrolyte abnormalities and nocturnal incontinence. This short review highlights current aspects of neobladder formation and its potential advantages.

  12. 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.

  13. 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.

  14. 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

  15. Personal and Social Transformation in the Health Area through Education: A Brief Journey from the Ancestral Indigenous Wisdom to the Modern Tyranny of Healthiness

    OpenAIRE

    Andrés de Muller

    2015-01-01

    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 abu...

  16. Broadening the New Perspective on Paul: Paul and the Ethnographical Debate of his Time - The Criticism of Jewish and Pagan Ancestral Customs (1 Thess 2:13-16)

    OpenAIRE

    van Kooten, G.H.; Goodman, M.(Argonne National Laboratory, Argonne, Illinois, 60439, U.S.A.); Ruiten, J.T.A.G.M. van

    2010-01-01

    George H. van Kooten, “Broadening the New Perspective on Paul: Paul and the Ethnographical Debate of His Time—The Criticism of Jewish and Pagan Ancestral Customs (1 Thess 2:13-16),” in Abraham, the Nations, and the Hagarites: Jewish, Christian, and Islamic Perspectives on Kinship with Abraham (ed. Martin Goodman, George H. van Kooten, and Jacques T.A.G.M. van Ruiten; Themes in Biblical Narrative 13; Leiden and Boston: Brill, 2010), 319-344.

  17. Reconstruction tomography from incomplete projections

    International Nuclear Information System (INIS)

    In some instances, reconstruction radionuclide tomography must be carried out from projections that do not include projection values for all portions of the object to be reconstructed. This may occur, for example, when the field of view of the detector is limited, or when an opaque foreign body is present within the object. The effects of such incomplete projections upon reconstructions of computer-simulated phantoms were studied, using iterative and convolution methods. Several methods for reducing the resulting artifacts and inaccuracies are discussed

  18. 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.

  19. 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

  20. High Performance Reconstruction Framework for Straight Ray Tomography: from Micro to Nano Resolution Imaging

    OpenAIRE

    Nilchian, Masih

    2015-01-01

    We develop a high-performance scheme to reconstruct straight-ray tomographic scans. We preserve the quality of the state-of-the-art schemes typically found in traditional computed tomography but reduce the computational cost substantially. Our approach is based on 1) a rigorous discretization of the forward model using a generalized sampling scheme; 2) a variational formulation of the reconstruction problem; and 3) iterative reconstruction algorithms that use the alternating-direction method ...

  1. 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.

  2. 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.

  3. 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.

  4. 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. PMID:27288244

  5. 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.

  6. 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.

  7. 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.”

  8. Ancestral Relationships Using Metafounders

    DEFF Research Database (Denmark)

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

    2015-01-01

    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...

  9. 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.

  10. Reconstruction techniques for optoacoustic imaging

    Science.gov (United States)

    Frenz, Martin; Koestli, Kornel P.; Paltauf, Guenther; Schmidt-Kloiber, Heinz; Weber, Heinz P.

    2001-06-01

    Optoacoustics is a method to gain information from inside a tissue. This is done by irradiating a tissue with a short light pulse, which generates a pressure distribution inside the tissue that mirrors the absorber distribution. The pressure distribution measured on the tissue-surface allows, by applying a back-projection method, to calculate a tomography image of the absorber distribution. This study presents a novel computational algorithm based on Fourier transform, which, at least in principle, yields an exact 3D reconstruction of the distribution of absorbed energy density inside turbid media. The reconstruction is based on 2D pressure distributions captured outside at different times. The FFT reconstruction algorithm is first tested in the back projection of simulated pressure transients of small model absorbers, and finally applied to reconstruct the distribution of artificial blood vessels in three dimensions.

  11. Vermilion Reconstruction with Genital Mucosa.

    Science.gov (United States)

    Müller-Richter, Urs D A; Weyandt, Gerhard H; Woeckel, Achim; Kübler, Alexander C

    2016-05-01

    Functional and aesthetical reconstruction, especially of the upper lip after ablative tumor surgery, can be very challenging. The skin of the lip might be sufficiently reconstructed by transpositional flaps from the nasolabial or facial area. Large defects of the lip mucosa, including the vestibule, are even more challenging due to the fact that flaps from the inner lining of the oral cavity often lead to functional impairments. We present a case of multiple vermilion and skin resections of the upper lip. At the last step, we had to resect even the whole vermilion mucosa, including parts of the oral mucosa of the vestibule, leaving a bare orbicularis oris muscle. To reconstruct the mucosal layer, we used a mucosal graft from the labia minora and placed it on the compromised lip and the former transpositional flaps for the reconstructed skin of the upper lip with very good functional and aesthetic results. PMID:27579226

  12. 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.

  13. 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.

  14. Provincial reconstruction teams improving effectiveness

    OpenAIRE

    Sellers, Cameron S.

    2007-01-01

    Provincial Reconstruction Teams (PRTs) are currently prominent constructs for stabilization and reconstruction in Afghanistan and Iraq. PRTs are composed of civil-military teams, including elements from coalition partners and the host-nation, and involve multiple military services and civilian agencies. Their missions are to extend the legitimacy of the central government throughout the country and to use Civil Military Operations (CMO) to counter anti-government forces. PRTs are prominent,...

  15. Erectile function after urethral reconstruction

    Institute of Scientific and Technical Information of China (English)

    Joshua Carlton; Maharshi Patel; Allen F. Morey

    2008-01-01

    Advances in urogenital plastic surgical tissue transfer techniques have enabled urethral reconstruction surgery to become the new gold-standard for treatment of refractory urethral stricture disease. Questions remain, however,regarding the long-term implications on sexual function after major genital reconstructive surgery. In this article, we review the pathologic features of urethral stricture disease and urologic trauma that may affect erectile function (EF) and assess the impact of various specific contemporary urethroplasty surgical techniques on male sexual function.

  16. Equilibrium Reconstruction in EAST Tokamak

    Institute of Scientific and Technical Information of China (English)

    QIAN Jinping; WAN Baonian; L. L. LAO; SHEN Biao; S. A. SABBAGH; SUN Youwen; LIU Dongmei; XIAO Singjia; REN Qilong; GONG Xianzu; LI Jiangang

    2009-01-01

    Reconstruction of experimental axisymmetric equilibria is an important part of toka-mak data analysis. Fourier expansion is applied to reconstruct the vessel current distribution in EFIT code. Benchmarking and testing calculations are performed to evaluate and validate this algorithm. Two cases for circular and non-circular plasma discharges are presented. Fourier ex-pansion used to fit the eddy current is a robust method and the real time EFIT can be introduced to the plasma control system in the coming campaign.

  17. Direct Reconstruction of the Dark Energy Scalar-Field Potential

    CERN Document Server

    Li, C; Cooray, A R; Li, Chao; Holz, Daniel E.; Cooray, Asantha

    2006-01-01

    While the accelerated expansion of the Universe is by now well established, an underlying scalar field potential possibly responsible for this acceleration remains unconstrained. We present an attempt to reconstruct this potential using recent SN data, under the assumption that the acceleration is driven by a single scalar field. Current approaches to such reconstructions are based upon simple parametric descriptions of either the luminosity distance or the dark energy equation of state. We find that these various approximations lead to different derived evolutionary histories of the dark energy equation of state (although there is considerable overlap between the different potential shapes allowed by the data). Depending upon one's assumptions, the same SN data set can lead to divergent statements about properties of the dark energy. Instead of these indirect reconstruction schemes, we discuss a technique to determine the potential directly from the data by expressing it in terms of a binned scalar field. In...

  18. 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...

  19. Intraplate mountain building in response to continent continent collision—the Ancestral Rocky Mountains (North America) and inferences drawn from the Tien Shan (Central Asia)

    Science.gov (United States)

    Dickerson, Patricia Wood

    2003-04-01

    The intraplate Ancestral Rocky Mountains of western North America extend from British Columbia, Canada, to Chihuahua, Mexico, and formed during Early Carboniferous through Early Permian time in response to continent-continent collision of Laurentia with Gondwana—the conjoined masses of Africa and South America, including Yucatán and Florida. Uplifts and flanking basins also formed within the Laurentian Midcontinent. On the Gondwanan continent, well inboard from the marginal fold belts, a counterpart structural array developed during the same period. Intraplate deformation began when full collisional plate coupling had been achieved along the continental margin; the intervening ocean had been closed and subduction had ceased—that is, the distinction between upper versus lower plates became moot. Ancestral Rockies deformation was not accompanied by volcanism. Basement shear zones that formed during Mesoproterozoic rifting of Laurentia were reactivated and exerted significant control on the locations, orientations, and modes of displacement on late Paleozoic faults. Ancestral Rocky Mountain uplifts extend as far south as Chihuahua and west Texas (28° to 33°N, 102° to 109°W) and include the Florida-Moyotes, Placer de Guadalupe-Carrizalillo, Ojinaga-Tascotal and Hueco Mountain blocks, as well as the Diablo and Central Basin Platforms. All are cored with Laurentian Proterozoic crystalline basement rocks and host correlative Paleozoic stratigraphic successions. Pre-late Paleozoic deformational, thermal, and metamorphic histories are similar as well. Southern Ancestral Rocky Mountain structures terminate along a line that trends approximately N 40°E (present coordinates), a common orientation for Mesoproterozoic extensional structures throughout southern to central North America. Continuing Tien Shan intraplate deformation (Central Asia) has created an analogous array of uplifts and basins in response to the collision of India with Eurasia, beginning in late

  20. 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。

  1. 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.

  2. 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...

  3. On an algorithm for dynamic reconstruction of the input

    OpenAIRE

    Blizorukova, M. S.; V.I. Maksimov

    2013-01-01

    We consider the problem of dynamic reconstruction of the input in a system described by a vector differential equation and nonlinear in the state variable. We indicate an algorithm that is stable under information noises and computational errors and is aimed at infinite system operation time. The algorithm is based on the dynamic regularization method. © 2013 Pleiades Publishing, Ltd.

  4. On combination of the processes of reconstruction and guaranteeing control

    OpenAIRE

    Kryazhimskii, A. V.; V.I. Maksimov

    2013-01-01

    Consideration was given to the problem of controlling a system of ordinary differential equations under incomplete information about the phase states. Given was an algorithm to solve it on the basis of a combination of the "real-time" reconstruction processes and feedback control. © 2013 Pleiades Publishing, Ltd.

  5. ¿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.

  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. 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.

  8. 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.

  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. PMID:27274452

  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. The reconstruction of inflationary potentials

    Science.gov (United States)

    Lin, Jianmang; Gao, Qing; Gong, Yungui

    2016-07-01

    The observational data on the anisotropy of the cosmic microwave background constraints the scalar spectral tilt ns and the tensor to scalar ratio r which depend on the first and second derivatives of the inflaton potential. The information can be used to reconstruct the inflaton potential in the polynomial form up to some orders. However, for some classes of potentials, ns and r behave as ns(N) and r(N) universally in terms of the number of e-folds N. The universal behaviour of ns(N) can be used to reconstruct a class of inflaton potentials. By parametrizing one of the parameters ns(N), ɛ(N) and φ(N), and fitting the parameters in the models to the observational data, we obtain the constraints on the parameters and reconstruct the classes of the inflationary models which include the chaotic inflation, T-model, hilltop inflation, s-dual inflation, natural inflation and R2 inflation.

  13. 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...

  14. 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

  15. 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.

  16. Reconstructing WKB from topological recursion

    CERN Document Server

    Bouchard, Vincent

    2016-01-01

    We prove that the topological recursion reconstructs the WKB expansion of a quantum curve for all spectral curves whose Newton polygons have no interior point (and that are smooth as affine curves). This includes nearly all previously known cases in the literature, and many more; in particular, it includes many quantum curves of order greater than two. We also explore the connection between the choice of ordering in the quantization of the spectral curve and the choice of integration divisor to reconstruct the WKB expansion.

  17. 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...

  18. 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

  19. 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

  20. 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.

  1. The Integration of Traditional and New in Neoteric Pudong Ancestral Buildings%浦东近代祠堂建筑的传统与新统

    Institute of Scientific and Technical Information of China (English)

    王凤席; 曹永康

    2011-01-01

    祠堂是在中国传统社会中具有极为重要意义的一种建筑类型,在传统社会中具有维护社会稳定关系的重要社会职能.因此祠堂作为一种建筑类型具有超级稳定的特点.然而这种稳定的建筑类型在近代外来文化的冲击下也发生了一定的改变.该文对浦东区6座近代祠堂进行案例研究,通过对这种变化的描述与分析,理清祠堂建筑中表发生变化的部分与发生了变化部分.以及变化的程度,并进一步探讨这种变与不变背后的深层原因.在一定程度上有助于了解建筑文化交流与嬗变之中的变迁特点与模式.%The ancestral hall is a very important building type, which maintains the function of social stability in traditional Chinese society. Therefore, as an architecture type,the ancestral hall is super-stable. However,under the impact of foreign culture in modern times, certain changes have taken place in this construction too. This paper studies six cases of neoteric ancestral halls in Pudong District. Through the description and analysis of such changes, the issue which part of ancestral buildings has changed, and which did not, is clarified, as well as the degree of change. And the Underlying reasons are investigated .Hope that this study will help to understand the exchanges and Evolution of Architectural cultural in characteristics and mode to some extent.

  2. 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

  3. 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.

  4. 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.

  5. 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

  6. 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...

  7. Reconstructing the Population Genetic History of the Caribbean

    Science.gov (United States)

    Moreno-Estrada, Andrés; Gravel, Simon; Zakharia, Fouad; McCauley, Jacob L.; Byrnes, Jake K.; Gignoux, Christopher R.; Ortiz-Tello, Patricia A.; Martínez, Ricardo J.; Hedges, Dale J.; Morris, Richard W.; Eng, Celeste; Sandoval, Karla; Acevedo-Acevedo, Suehelay; Norman, Paul J.; Layrisse, Zulay; Parham, Peter; Martínez-Cruzado, Juan Carlos; Burchard, Esteban González; Cuccaro, Michael L.; Martin, Eden R.; Bustamante, Carlos D.

    2013-01-01

    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

  8. Reconstructing mammalian sleep dynamics with data assimilation.

    Directory of Open Access Journals (Sweden)

    Madineh Sedigh-Sarvestani

    Full Text Available Data assimilation is a valuable tool in the study of any complex system, where measurements are incomplete, uncertain, or both. It enables the user to take advantage of all available information including experimental measurements and short-term model forecasts of a system. Although data assimilation has been used to study other biological systems, the study of the sleep-wake regulatory network has yet to benefit from this toolset. We present a data assimilation framework based on the unscented Kalman filter (UKF for combining sparse measurements together with a relatively high-dimensional nonlinear computational model to estimate the state of a model of the sleep-wake regulatory system. We demonstrate with simulation studies that a few noisy variables can be used to accurately reconstruct the remaining hidden variables. We introduce a metric for ranking relative partial observability of computational models, within the UKF framework, that allows us to choose the optimal variables for measurement and also provides a methodology for optimizing framework parameters such as UKF covariance inflation. In addition, we demonstrate a parameter estimation method that allows us to track non-stationary model parameters and accommodate slow dynamics not included in the UKF filter model. Finally, we show that we can even use observed discretized sleep-state, which is not one of the model variables, to reconstruct model state and estimate unknown parameters. Sleep is implicated in many neurological disorders from epilepsy to schizophrenia, but simultaneous observation of the many brain components that regulate this behavior is difficult. We anticipate that this data assimilation framework will enable better understanding of the detailed interactions governing sleep and wake behavior and provide for better, more targeted, therapies.

  9. 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.

  10. 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

  11. 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.

  12. Breast Reconstruction with Tissue Expansion

    Medline Plus

    Full Text Available RECONSTRUCTIVE BREAST SURGERY ALBANY MEDICAL CENTER HOSPITAL ALBANY, NY July 31, 2008 00:00:10 ANNOUNCER: Welcome to this OR-Live webcast presentation, brought to ... webcast screen and open the door to informed medical care. 00:00:28 DIMITRI KOUMANIS, M.D.: ...

  13. 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.

  14. Deep Reconstruction Models for Image Set Classification.

    Science.gov (United States)

    Hayat, Munawar; Bennamoun, Mohammed; An, Senjian

    2015-04-01

    Image set classification finds its applications in a number of real-life scenarios such as classification from surveillance videos, multi-view camera networks and personal albums. Compared with single image based classification, it offers more promises and has therefore attracted significant research attention in recent years. Unlike many existing methods which assume images of a set to lie on a certain geometric surface, this paper introduces a deep learning framework which makes no such prior assumptions and can automatically discover the underlying geometric structure. Specifically, a Template Deep Reconstruction Model (TDRM) is defined whose parameters are initialized by performing unsupervised pre-training in a layer-wise fashion using Gaussian Restricted Boltzmann Machines (GRBMs). The initialized TDRM is then separately trained for images of each class and class-specific DRMs are learnt. Based on the minimum reconstruction errors from the learnt class-specific models, three different voting strategies are devised for classification. Extensive experiments are performed to demonstrate the efficacy of the proposed framework for the tasks of face and object recognition from image sets. Experimental results show that the proposed method consistently outperforms the existing state of the art methods. PMID:26353289

  15. 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

    2011-01-01

    The origin of pairing in a superconductor resides in the underlying normal state. In the cuprate high-temperature superconductor YBa2Cu3Oy (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 La1.8−xEu0.2SrxCuO4 (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. PMID:21847106

  16. Stability indicators in network reconstruction.

    Science.gov (United States)

    Filosi, Michele; Visintainer, Roberto; Riccadonna, Samantha; Jurman, Giuseppe; Furlanello, Cesare

    2014-01-01

    The number of available algorithms to infer a biological network from a dataset of high-throughput measurements is overwhelming and keeps growing. However, evaluating their performance is unfeasible unless a 'gold standard' is available to measure how close the reconstructed network is to the ground truth. One measure of this is the stability of these predictions to data resampling approaches. We introduce NetSI, a family of Network Stability Indicators, to assess quantitatively the stability of a reconstructed network in terms of inference variability due to data subsampling. In order to evaluate network stability, the main NetSI methods use a global/local network metric in combination with a resampling (bootstrap or cross-validation) procedure. In addition, we provide two normalized variability scores over data resampling to measure edge weight stability and node degree stability, and then introduce a stability ranking for edges and nodes. A complete implementation of the NetSI indicators, including the Hamming-Ipsen-Mikhailov (HIM) network distance adopted in this paper is available with the R package nettools. We demonstrate the use of the NetSI family by measuring network stability on four datasets against alternative network reconstruction methods. First, the effect of sample size on stability of inferred networks is studied in a gold standard framework on yeast-like data from the Gene Net Weaver simulator. We also consider the impact of varying modularity on a set of structurally different networks (50 nodes, from 2 to 10 modules), and then of complex feature covariance structure, showing the different behaviours of standard reconstruction methods based on Pearson correlation, Maximum Information Coefficient (MIC) and False Discovery Rate (FDR) strategy. Finally, we demonstrate a strong combined effect of different reconstruction methods and phenotype subgroups on a hepatocellular carcinoma miRNA microarray dataset (240 subjects), and we validate the

  17. Stability indicators in network reconstruction.

    Directory of Open Access Journals (Sweden)

    Michele Filosi

    Full Text Available The number of available algorithms to infer a biological network from a dataset of high-throughput measurements is overwhelming and keeps growing. However, evaluating their performance is unfeasible unless a 'gold standard' is available to measure how close the reconstructed network is to the ground truth. One measure of this is the stability of these predictions to data resampling approaches. We introduce NetSI, a family of Network Stability Indicators, to assess quantitatively the stability of a reconstructed network in terms of inference variability due to data subsampling. In order to evaluate network stability, the main NetSI methods use a global/local network metric in combination with a resampling (bootstrap or cross-validation procedure. In addition, we provide two normalized variability scores over data resampling to measure edge weight stability and node degree stability, and then introduce a stability ranking for edges and nodes. A complete implementation of the NetSI indicators, including the Hamming-Ipsen-Mikhailov (HIM network distance adopted in this paper is available with the R package nettools. We demonstrate the use of the NetSI family by measuring network stability on four datasets against alternative network reconstruction methods. First, the effect of sample size on stability of inferred networks is studied in a gold standard framework on yeast-like data from the Gene Net Weaver simulator. We also consider the impact of varying modularity on a set of structurally different networks (50 nodes, from 2 to 10 modules, and then of complex feature covariance structure, showing the different behaviours of standard reconstruction methods based on Pearson correlation, Maximum Information Coefficient (MIC and False Discovery Rate (FDR strategy. Finally, we demonstrate a strong combined effect of different reconstruction methods and phenotype subgroups on a hepatocellular carcinoma miRNA microarray dataset (240 subjects, and we

  18. δ-Conotoxin SuVIA suggests an evolutionary link between ancestral predator defence and the origin of fish-hunting behaviour in carnivorous cone snails.

    Science.gov (United States)

    Jin, Ai-Hua; Israel, Mathilde R; Inserra, Marco C; Smith, Jennifer J; Lewis, Richard J; Alewood, Paul F; Vetter, Irina; Dutertre, Sébastien

    2015-07-22

    Some venomous cone snails feed on small fishes using an immobilizing combination of synergistic venom peptides that target Kv and Nav channels. As part of this envenomation strategy, δ-conotoxins are potent ichtyotoxins that enhance Nav channel function. δ-Conotoxins belong to an ancient and widely distributed gene superfamily, but any evolutionary link from ancestral worm-eating cone snails to modern piscivorous species has not been elucidated. Here, we report the discovery of SuVIA, a potent vertebrate-active δ-conotoxin characterized from a vermivorous cone snail (Conus suturatus). SuVIA is equipotent at hNaV1.3, hNaV1.4 and hNaV1.6 with EC50s in the low nanomolar range. SuVIA also increased peak hNaV1.7 current by approximately 75% and shifted the voltage-dependence of activation to more hyperpolarized potentials from -15 mV to -25 mV, with little effect on the voltage-dependence of inactivation. Interestingly, the proximal venom gland expression and pain-inducing effect of SuVIA in mammals suggest that δ-conotoxins in vermivorous cone snails play a defensive role against higher order vertebrates. We propose that δ-conotoxins originally evolved in ancestral vermivorous cones to defend against larger predators including fishes have been repurposed to facilitate a shift to piscivorous behaviour, suggesting an unexpected underlying mechanism for this remarkable evolutionary transition. PMID:26156767

  19. Patient Race and Provider Predict Patient Satisfaction Following Post-Mastectomy Breast Reconstruction

    Science.gov (United States)

    Shaterian, Ashkaun; Gandy, Jessica; Lalezari, Shadi; Smith, Sarah; Paydar, Keyianoosh

    2016-01-01

    BACKGROUND Post-mastectomy breast reconstruction is commonly performed in the United States with numerous options available to patients and providers. This study evaluated patient race and provider in prediction of patient satisfaction following post-mastectomy breast reconstruction. METHODS The patient satisfaction for women who underwent post mastectomy breast reconstruction at University of California, Irvine Medical Center was evaluated between 2012 and 2014, randomly using Press Ganey Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) surveys. Patient demographics and surgery related variables including type of reconstruction received were determined. RESULTS Between 2012 and 2014, ninety breast reconstruction patients completed a HCAHPS satisfaction survey. Average satisfaction score was 9.67/10. Multivariate linear regression analyses revealed that 34% of the variability in satisfaction scores was accounted for by the variables included in our statistical model. Analyses revealed race/ethnicity and provider to be independent predictors of satisfaction (pvariables were included, but did not influence patient satisfaction: type, timing, or laterality of reconstruction, presence of post-operative complication, body mass index (BMI), age, presence of comorbidity, and insurance type. CONCLUSION Achieving patient satisfaction is an important outcome of breast reconstruction. This study is one of the first to identify provider and race/ethnicity as predictors of patient satisfaction following breast reconstruction. The information provided here can help inform providers and improve satisfaction for patients undergoing breast reconstruction.

  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. Reconstructing the inflaton potential: Perturbative reconstruction to second order

    Energy Technology Data Exchange (ETDEWEB)

    Copeland, Edmund J.; Kolb, Edward W.; Liddle, Andrew R.; Lidsey, James E.

    1993-08-01

    One method to reconstruct the scalar field potential of inflation is a perturbative approach, where the values of the potential and its derivatives are calculated as an expansion in departures from the slow-roll approximation. They can then be expressed in terms of observable quantities, such as the square of the ratio of the gravitational wave amplitude to the density perturbation amplitude, the deviation of the spectral index from the Harrison--Zel'dovich value, etc. Here, we calculate complete expressions for the second-order contributions to the coefficients of the expansion by including for the first time corrections to the standard expressions for the perturbation spectra. As well as offering an improved result, these corrections indicate the expected accuracy of the reconstruction. Typically the corrections are only a few percent.

  2. Thermographic image reconstruction using ultrasound reconstruction from virtual waves

    CERN Document Server

    Burgholzer, Peter; Gruber, Jürgen; Mayr, Günther

    2016-01-01

    Reconstruction of subsurface features from ultrasound signals measured on the surface is widely used in medicine and non-destructive testing. In this work, we introduce a concept how to use image reconstruction methods known from ultrasonic imaging for thermographic signals, i.e. on the measured temperature evolution on a sample surface. Before using these imaging methods a virtual signal is calculated by applying a transformation to the measured temperature evolution. The virtual signal is calculated locally for every detection point and has the same initial temperature distribution as the measured signal, but is a solution of the wave equation. The introduced transformation can be used for every shape of the detection surface and in every dimension. It describes all the irreversibility of the heat diffusion, which is responsible that the spatial resolution gets worse with increasing depth. Up to now, for thermographic imaging mostly one-dimensional methods, e.g., for depth-profiling were used, which are sui...

  3. 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 CMS analyses are described and the performance of different variables and top taggers are shown.

  4. SOCIAL RECONSTRUCTION THROUGH EDUCATION

    Directory of Open Access Journals (Sweden)

    Јована Милутиновић

    2013-12-01

    Full Text Available The focus of the paper is social reconstructionism, which represented the radical wing of the broader Movement for Progressive Education in the United States in the twenties of the twentieth century. Starting from understanding of social reconstructionism as an educational and social program, which presupposes support to socially democratic political economy, cooperative cul­ture, socially-based approach to education, and view of the role and importance of the school in directing the social and political changes, the aim of this paper refers to the examination and evaluation of socially democratic educational reconstructionism practice. The new learning para­digm, which is implied in the socially reconstructionism theory and practice, is also a focus of interest of this paper. Namely, according to social reconstructionism, the basic aim of education is to promote the program of social reforms, resulting in an emphasis on the social role of the school, i.e. the emphasis on the activist role of the school in the implementation of progressive social changes. The teacher’s role is not to be a disseminator of information, but an activist of social changes who should actively involve pupils in the research process through open discussions and experiential learning. In that context, the reconstructionism emphasis on providing the experi­ences in experimentation and reflective research is consistent with the idea on pupils as active constructors of their own knowledge. The way in which social reconstructionism supports democracy is illustrated by concrete pos­sibilities for application of these theoretical positions in practice. From a pedagogical point of view, the most important example of embedding socially reconstructionism ideas into the school curriculum certainly represents a unique curricular experiment conducted by Theodore Brameld in 1944, in a high school in Floodwood (Minnesota, USA. Regardless of many difficulties that have arisen in

  5. Neural process reconstruction from sparse user scribbles.

    Science.gov (United States)

    Roberts, Mike; Jeong, Won-Ki; Vázquez-Reina, Amelio; Unger, Markus; Bischof, Horst; Lichtman, Jeff; Pfister, Hanspeter

    2011-01-01

    We present a novel semi-automatic method for segmenting neural processes in large, highly anisotropic EM (electron microscopy) image stacks. Our method takes advantage of sparse scribble annotations provided by the user to guide a 3D variational segmentation model, thereby allowing our method to globally optimally enforce 3D geometric constraints on the segmentation. Moreover, we leverage a novel algorithm for propagating segmentation constraints through the image stack via optimal volumetric pathways, thereby allowing our method to compute highly accurate 3D segmentations from very sparse user input. We evaluate our method by reconstructing 16 neural processes in a 1024 x 1024 x 50 nanometer-scale EM image stack of a mouse hippocampus. We demonstrate that, on average, our method is 68% more accurate than previous state-of-the-art semi-automatic methods. PMID:22003670

  6. Optimized Quasi-Interpolators for Image Reconstruction.

    Science.gov (United States)

    Sacht, Leonardo; Nehab, Diego

    2015-12-01

    We propose new quasi-interpolators for the continuous reconstruction of sampled images, combining a narrowly supported piecewise-polynomial kernel and an efficient digital filter. In other words, our quasi-interpolators fit within the generalized sampling framework and are straightforward to use. We go against standard practice and optimize for approximation quality over the entire Nyquist range, rather than focusing exclusively on the asymptotic behavior as the sample spacing goes to zero. In contrast to previous work, we jointly optimize with respect to all degrees of freedom available in both the kernel and the digital filter. We consider linear, quadratic, and cubic schemes, offering different tradeoffs between quality and computational cost. Experiments with compounded rotations and translations over a range of input images confirm that, due to the additional degrees of freedom and the more realistic objective function, our new quasi-interpolators perform better than the state of the art, at a similar computational cost. PMID:26390452

  7. Reconstructing Deweyan Pragmatism: A Review Essay

    Science.gov (United States)

    Neubert, Stefan

    2009-01-01

    In this essay Stefan Neubert argues that John Dewey was a philosopher of reconstruction and that the best use we can make of him today is to reconstruct his work in and for our own contexts. Neubert distinguishes three necessary and equally important components of the overall project of reconstructing Deweyan pragmatism: first, to make strong and…

  8. Set-reconstructibility of Post classes

    OpenAIRE

    Couceiro, Miguel; Lehtonen, Erkko; Schölzel, Karsten

    2013-01-01

    The clones of Boolean functions are classified in regard to set-reconstructibility via a strong dichotomy result: the clones containing only affine functions, conjunctions, disjunctions or constant functions are set-reconstructible, whereas the remaing clones are not weakly reconstructible.

  9. Vertex Reconstruction in ATLAS Run II

    CERN Document Server

    Zhang, Matt; The ATLAS collaboration

    2016-01-01

    Vertex reconstruction is the process of taking reconstructed tracks and using them to determine the locations of proton collisions. In this poster we present the performance of our current vertex reconstruction algorithm, and look at investigations into potential improvements from a new seed finding method.

  10. 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. PMID:26827632

  11. Genotyping-by-sequencing as a tool to infer phylogeny and ancestral hybridization: a case study in Carex (Cyperaceae).

    Science.gov (United States)

    Escudero, Marcial; Eaton, Deren A R; Hahn, Marlene; Hipp, Andrew L

    2014-10-01

    Determining phylogenetic relationships among very closely related species has remained a challenge for evolutionary biologists due to interlocus phylogenetic discordance and the difficulty of obtaining variable markers. Here, we used a Genotyping-by-Sequencing (GBS) approach to sample a reduced representation genomic data set and infer the phylogeny of seven closely related species in the genus Carex (Cyperaceae). Past attempts to reconstruct phylogenetic relationships among these species produced conflicting and poorly-supported results. We inferred a robust phylogeny based on >3000 GBS loci and >1300 SNPs (with a minimum sequence depth within individuals of 10) using maximum likelihood and Bayesian inference. We also tested for historical introgression using the D-statistic test. We compared these analyses with partitioned RAD analysis, which is designed to identify suboptimal trees reflecting secondary phylogenetic signal that may be obscured by the dominant signal in the data. Phylogenetic analyses yielded fully resolved trees with high support. We found two main clades, one grouping Carex scoparia populations and C. waponahkikensis, and a second clade grouping C. longii, C. vexans, C. suberecta and C. albolutescens. We detected marginally significant signals of introgression between C. scoparia and C. suberecta or C. albolutescens, and we rejected a hybrid origin hypothesis for C. waponahkikensis. Our results demonstrate the power of NGS data sets for resolving some of the most difficult phylogenetic challenges where traditional phylogenetic markers have failed. PMID:25010772

  12. Atmospheric muons reconstruction with Antares

    International Nuclear Information System (INIS)

    The ANTARES collaboration is building a neutrino telescope in the Mediterranean Sea. This detector contains 900 photomultiplier tubes, dispatched on 12 lines, in order to detect Cerenkov light from muon induced by neutrino interactions in the the vicinity of the detector. Currently the first 5 lines have been deployed. A first task consists in studying the stability of the detector calibration, which is a necessary step to understand the detector response. Then we studied optical properties of water, for this we developed a reconstruction method dedicated to LED Beacon. The extracted parameters are compatible with earlier measurements. A quality criteria to reject badly reconstructed track has been developed based on the likelihood of the tracks fit versus point fit. This has been applied to real data and a preliminary analysis of atmospheric muons with a 5-lines detector is performed. (author)

  13. Reconstruction of complete interval tournaments

    CERN Document Server

    Iványi, Antal

    2010-01-01

    Let $a, b$ and $n$ be nonnegative integers $(b \\geq a, \\ b > 0, \\ n \\geq 1)$, $\\mathcal{G}_n(a,b)$ be a multigraph on $n$ vertices in which any pair of vertices is connected with at least $a$ and at most $b$ edges and \\textbf{v =} $(v_1, v_2, ..., v_n)$ be a vector containing $n$ nonnegative integers. We give a necessary and sufficient condition for the existence of such orientation of the edges of $\\mathcal{G}_n(a,b)$, that the resulted out-degree vector equals to \\textbf{v}. We describe a reconstruction algorithm. In worst case checking of \\textbf{v} requires $\\Theta(n)$ time and the reconstruction algorithm works in $O(bn^3)$ time. Theorems of H. G. Landau (1953) and J. W. Moon (1963) on the score sequences of tournaments are special cases $b = a = 1$ resp. $b = a \\geq 1$ of our result.

  14. Blind reconstruction of linear scrambler

    Institute of Scientific and Technical Information of China (English)

    Hui Xie; Fenghua Wang; Zhitao Huang

    2014-01-01

    An algorithm based on eigenanalysis technique and Walsh-Hadamard transform (WHT) is proposed. The algorithm contains two steps. Firstly, the received sequence is divided into temporal windows, and a covariance matrix is computed. The li-near feedback shift register (LFSR) sequence is reconstructed from the first eigenvector of this matrix. Secondly, equations ac-cording to the recovered LFSR sequence are constructed, and the Walsh spectrum corresponding to the equations is computed. The feedback polynomial of LFSR is estimated from the Walsh spec-trum. The validity of the algorithm is verified by the simulation result. Final y, case studies are presented to il ustrate the perfor-mance of the blind reconstruction method.

  15. Ear Reconstruction in Young Children.

    Science.gov (United States)

    Reinisch, John

    2015-12-01

    The use of a porous high-density polyethylene ear implant, rather than a costal cartilage framework, allows ear reconstruction in young children before they enter school. The fact that the growth of the normal ear matures early allows for good symmetry. If the implant is covered completely with a large, well-vascularized superficial parietal fascia flap and appropriately color-matched skin, an ear with excellent projection and definition can be obtained with minimal complications and long-term viability. Ear reconstruction in young children is preferred by the author because the necessary fascial flap coverage is thinner, easier to harvest than in older patients, and can be done in a single outpatient procedure with minimal discomfort or psychological trauma. PMID:26667634

  16. Optimal Reconstruction of Inviscid Vortices

    CERN Document Server

    Danaila, Ionut

    2014-01-01

    This study addresses the question whether, given {some} measurements of the velocity field induced by a vortex, one can stably determine the structure of the vortex. Assuming that the flow is incompressible, inviscid and stationary in the frame of reference moving with the vortex, the "structure" of the vortex is uniquely characterized by the functional relation between the streamfunction and vorticity. It is demonstrated how the inverse problem of reconstructing this functional relation from data can be framed as an optimization problem which can be efficiently solved using variational techniques. To focus attention, we consider 3D axisymmetric vortex rings and use measurements of the tangential velocity on the boundary of the vortex bubble. In contrast to earlier studies, the vorticity function defining the streamfunction-vorticity relation is reconstructed in the continuous setting subject to a minimum number of assumptions. To validate our approach, two test cases are presented, involving Hill's and Norbu...

  17. Growing self-reconstruction maps.

    Science.gov (United States)

    do Rêgo, Renata Lúcia Mendonça Ernesto; Araújo, Aluizio Fausto Ribeiro; de Lima Neto, Fernando Buarque

    2010-02-01

    In this paper, we propose a new method for surface reconstruction based on growing self-organizing maps (SOMs), called growing self-reconstruction maps (GSRMs). GSRM is an extension of growing neural gas (GNG) that includes the concept of triangular faces in the learning algorithm and additional conditions in order to include and remove connections, so that it can produce a triangular two-manifold mesh representation of a target object given an unstructured point cloud of its surface. The main modifications concern competitive Hebbian learning (CHL), the vertex insertion operation, and the edge removal mechanism. The method proposed is able to learn the geometry and topology of the surface represented in the point cloud and to generate meshes with different resolutions. Experimental results show that the proposed method can produce models that approximate the shape of an object, including its concave regions, boundaries, and holes, if any. PMID:20007030

  18. Network reconstruction via density sampling

    CERN Document Server

    Squartini, Tiziano; Gabrielli, Andrea; Garlaschelli, Diego

    2016-01-01

    Reconstructing weighted networks from partial information is necessary in many important circumstances, e.g. for a correct estimation of systemic risk. It has been shown that, in order to achieve an accurate reconstruction, it is crucial to reliably replicate the empirical degree sequence, which is however unknown in many realistic situations. More recently, it has been found that the knowledge of the degree sequence can be replaced by the knowledge of the strength sequence, which is typically accessible, complemented by that of the total number of links, thus considerably relaxing the observational requirements. Here we further relax these requirements and devise a procedure valid when even the the total number of links is unavailable. We assume that, apart from the heterogeneity induced by the degree sequence itself, the network is homogeneous, so that its link density can be estimated by sampling subsets of nodes with representative density. We show that the best way of sampling nodes is the random selecti...

  19. Oak Ridge Dose Reconstruction Project Summary Report; Reports of the Oak Ridge Dose Reconstruction, Vol. 7

    International Nuclear Information System (INIS)

    In the early 1990s, concern about the Oak Ridge Reservation's past releases of contaminants to the environment prompted Tennessee's public health officials to pursue an in-depth study of potential off-site health effects at Oak Ridge. This study, the Oak Ridge dose reconstruction, was supported by an agreement between the U.S. Department of Energy (DOE) and the State of Tennessee, and was overseen by a 12-member panel of individuals appointed by Tennessee's Commissioner of Health. The panel requested that the principal investigator for the project prepare the following report, ''Oak Ridge Dose Reconstruction Project Summary Report,'' to serve the following purposes: (1) summarize in a single, less technical report, the methods and results of the various investigations that comprised the Phase II of the dose reconstruction; (2) describe the systematic searching of classified and unclassified historical records that was a vital component of the project; and (3) summarize the less detailed, screening-level assessments that were performed to evaluate the potential health significance of a number of materials, such a uranium, whose priority did not require a complete dose reconstruction effort. This report describes each major step of the dose reconstruction study: (1) the review of thousands of historical records to obtain information relating to past operations at each facility; (2) estimation of the quantity and timing of releases of radioiodines from X-10, of mercury from Y-12, of PCB's from all facilities, and of cesium-137 and other radionuclides from White Oak Creek; (3) evaluation of the routes taken by these contaminants through the environment to nearby populations; and (4) estimation of doses and health risks to exposed groups. Calculations found the highest excess cancer risks for a female born in 1952 who drank goat milk; the highest non-cancer health risk was for children in a farm family exposed to PCBs in and near East Fork Poplar Creek. More detailed

  20. Bayes reconstruction of missing teeth

    DEFF Research Database (Denmark)

    Sporring, Jon; Jensen, Katrine Hommelhoff

    2008-01-01

     We propose a method for restoring the surface of tooth crowns in a 3D model of a human denture, so that the pose and anatomical features of the tooth will work well for chewing. This is achieved by including information about the position and anatomy of the other teeth in the mouth. Our system...... of a missing tooth based on the best match with our shape model on the known data, and we superior improved reconstructions of our full system....

  1. [Plastic reconstructive surgery for burn injuries].

    Science.gov (United States)

    Niederbichler, A D; Vogt, P M

    2009-06-01

    The stage-adjusted therapy of thermal injuries is based on pathophysiologic mechanisms as well as functional and aesthetic requirements. Plastic reconstructive surgical approaches are highly important in the prevention of the frequent grave sequelae of thermal trauma and to achieve optimal functional rehabilitation and favourable outcome. In reconstructive surgery of burns operative goals are subdivided into acute, secondary reconstructive, functional and aesthetic indications. The achievement of early wound closure to preserve functional skin and soft tissue components is an essential part of acute reconstructive procedures. Functional reconstructive and aesthetic procedures supplement the conservative treatment modalities of the secondary phase of burn care with physical therapy, ergotherapy and psychological support. PMID:19543874

  2. Photogrammetric Reconstruction with Bayesian Information

    Science.gov (United States)

    Masiero, A.; Fissore, F.; Guarnieri, A.; Pirotti, F.; Vettore, A.

    2016-06-01

    Nowadays photogrammetry and laser scanning methods are the most wide spread surveying techniques. Laser scanning methods usually allow to obtain more accurate results with respect to photogrammetry, but their use have some issues, e.g. related to the high cost of the instrumentation and the typical need of high qualified personnel to acquire experimental data on the field. Differently, photogrammetric reconstruction can be achieved by means of low cost devices and by persons without specific training. Furthermore, the recent diffusion of smart devices (e.g. smartphones) embedded with imaging and positioning sensors (i.e. standard camera, GNSS receiver, inertial measurement unit) is opening the possibility of integrating more information in the photogrammetric reconstruction procedure, in order to increase its computational efficiency, its robustness and accuracy. In accordance with the above observations, this paper examines and validates new possibilities for the integration of information provided by the inertial measurement unit (IMU) into the photogrammetric reconstruction procedure, and, to be more specific, into the procedure for solving the feature matching and the bundle adjustment problems.

  3. Femoral Reconstruction Using External Fixation

    Directory of Open Access Journals (Sweden)

    Yevgeniy Palatnik

    2011-01-01

    Full Text Available Background. The use of an external fixator for the purpose of distraction osteogenesis has been applied to a wide range of orthopedic problems caused by such diverse etiologies as congenital disease, metabolic conditions, infections, traumatic injuries, and congenital short stature. The purpose of this study was to analyze our experience of utilizing this method in patients undergoing a variety of orthopedic procedures of the femur. Methods. We retrospectively reviewed our experience of using external fixation for femoral reconstruction. Three subgroups were defined based on the primary reconstruction goal lengthening, deformity correction, and repair of nonunion/bone defect. Factors such as leg length discrepancy (LLD, limb alignment, and external fixation time and complications were evaluated for the entire group and the 3 subgroups. Results. There was substantial improvement in the overall LLD, femoral length discrepancy, and limb alignment as measured by mechanical axis deviation (MAD and lateral distal femoral angle (LDFA for the entire group as well as the subgroups. Conclusions. The Ilizarov external fixator allows for decreased surgical exposure and preservation of blood supply to bone, avoidance of bone grafting and internal fixation, and simultaneous lengthening and deformity correction, making it a very useful technique for femoral reconstruction.

  4. Historical reconstruction of ocean acidification in the Australian region

    Science.gov (United States)

    Lenton, Andrew; Tilbrook, Bronte; Matear, Richard J.; Sasse, Tristan P.; Nojiri, Yukihiro

    2016-03-01

    The ocean has become more acidic over the last 200 years in response increasing atmospheric carbon dioxide (CO2) levels. Documenting how the ocean has changed is critical for assessing how these changes impact marine ecosystems and for the management of marine resources. Here we use present-day ocean carbon observations, from shelf and offshore waters around Australia, combined with neural network mapping of CO2, sea surface temperature, and salinity to estimate the current seasonal and regional distributions of carbonate chemistry (pH and aragonite saturation state). The observed changes in atmospheric CO2 and sea surface temperature (SST) and climatological salinity are then used 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 that both the mean state and seasonality in the present day are well represented, with the exception of sites such as the Great Barrier Reef. Our reconstruction predicts that since 1870 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. 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 the 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 link to biological observations that will help to elucidate the consequences of ocean acidification.

  5. Alpha image reconstruction (AIR): A new iterative CT image reconstruction approach using voxel-wise alpha blending

    International Nuclear Information System (INIS)

    factor for contrast-resolution plots. Furthermore, the authors calculate the contrast-to-noise ratio with the low contrast disks and the authors compare the agreement of the reconstructions with the ground truth by calculating the normalized cross-correlation and the root-mean-square deviation. To evaluate the clinical performance of the proposed method, the authors reconstruct patient data acquired with a Somatom Definition Flash dual source CT scanner (Siemens Healthcare, Forchheim, Germany). Results: The results of the simulation study show that among the compared algorithms AIR achieves the highest resolution and the highest agreement with the ground truth. Compared to the reference FBP reconstruction AIR is able to reduce the relative pixel noise by up to 50% and at the same time achieve a higher resolution by maintaining the edge information from the basis images. These results can be confirmed with the patient data. Conclusions: To evaluate the AIR algorithm simulated and measured patient data of a state-of-the-art clinical CT system were processed. It is shown, that generating CT images through the reconstruction of weighting coefficients has the potential to improve the resolution noise trade-off and thus to improve the dose usage in clinical CT

  6. Reconstruction of defects by ultrasonic testing using synthetic aperture procedures

    International Nuclear Information System (INIS)

    The three methods ALOK (Amplitude Time Locus Curves), PHASED ARRAY and LSAFT (Line-Synthetic-Aperture-Focusing-Technique) use the method of synthesizing a large aperture by moving a probe. All methods are based on the time-of-flight or phase information and less to amplitude information. They differ in the state of development, in the complexity of data acquisition and reconstruction. The ALOK method is closest to those ultrasonic inspection methods used today in inservice inspection of nuclear pressure vessels. PHASED ARRAY combined with the compound scan synthesizes the divergent beam too and insonifies a reflector from many different insonification directions with high energy. LSAFT, like the others, reconstructs a B-scan image. For all three methods examples have been shown which demonstrate the state of development of these systems

  7. Phylogenetic reconstruction of the wolf spiders (Araneae: Lycosidae) using sequences from the 12S rRNA, 28S rRNA, and NADH1 genes: implications for classification, biogeography, and the evolution of web building behavior.

    Science.gov (United States)

    Murphy, Nicholas P; Framenau, Volker W; Donnellan, Stephen C; Harvey, Mark S; Park, Yung-Chul; Austin, Andrew D

    2006-03-01

    Current knowledge of the evolutionary relationships amongst the wolf spiders (Araneae: Lycosidae) is based on assessment of morphological similarity or phylogenetic analysis of a small number of taxa. In order to enhance the current understanding of lycosid relationships, phylogenies of 70 lycosid species were reconstructed by parsimony and Bayesian methods using three molecular markers; the mitochondrial genes 12S rRNA, NADH1, and the nuclear gene 28S rRNA. The resultant trees from the mitochondrial markers were used to assess the current taxonomic status of the Lycosidae and to assess the evolutionary history of sheet-web construction in the group. The results suggest that a number of genera are not monophyletic, including Lycosa, Arctosa, Alopecosa, and Artoria. At the subfamilial level, the status of Pardosinae needs to be re-assessed, and the position of a number of genera within their respective subfamilies is in doubt (e.g., Hippasa and Arctosa in Lycosinae and Xerolycosa, Aulonia and Hygrolycosa in Venoniinae). In addition, a major clade of strictly Australasian taxa may require the creation of a new subfamily. The analysis of sheet-web building in Lycosidae revealed that the interpretation of this trait as an ancestral state relies on two factors: (1) an asymmetrical model favoring the loss of sheet-webs and (2) that the suspended silken tube of Pirata is directly descended from sheet-web building. Paralogous copies of the nuclear 28S rRNA gene were sequenced, confounding the interpretation of the phylogenetic analysis and suggesting that a cautionary approach should be taken to the further use of this gene for lycosid phylogenetic analysis.

  8. Reconstructing Rodinia by Fitting Neoproterozoic Continental Margins

    Science.gov (United States)

    Stewart, John H.

    2009-01-01

    Reconstructions of Phanerozoic tectonic plates can be closely constrained by lithologic correlations across conjugate margins by paleontologic information, by correlation of orogenic belts, by paleomagnetic location of continents, and by ocean floor magmatic stripes. In contrast, Proterozoic reconstructions are hindered by the lack of some of these tools or the lack of their precision. To overcome some of these difficulties, this report focuses on a different method of reconstruction, namely the use of the shape of continents to assemble the supercontinent of Rodinia, much like a jigsaw puzzle. Compared to the vast amount of information available for Phanerozoic systems, such a limited approach for Proterozoic rocks, may seem suspect. However, using the assembly of the southern continents (South America, Africa, India, Arabia, Antarctica, and Australia) as an example, a very tight fit of the continents is apparent and illustrates the power of the jigsaw puzzle method. This report focuses on Neoproterozoic rocks, which are shown on two new detailed geologic maps that constitute the backbone of the study. The report also describes the Neoproterozoic, but younger or older rocks are not discussed or not discussed in detail. The Neoproterozoic continents and continental margins are identified based on the distribution of continental-margin sedimentary and magmatic rocks that define the break-up margins of Rodinia. These Neoproterozoic continental exposures, as well as critical Neo- and Meso-Neoproterozoic tectonic features shown on the two new map compilations, are used to reconstruct the Mesoproterozoic supercontinent of Rodinia. This approach differs from the common approach of using fold belts to define structural features deemed important in the Rodinian reconstruction. Fold belts are difficult to date, and many are significantly younger than the time frame considered here (1,200 to 850 Ma). Identifying Neoproterozoic continental margins, which are primarily

  9. On Reconstruction of Enterprise Legal Counsel Membership Mechanism--Based on the Angle of View for Settings of State-owned Enterprise Legal Counsel Membership%论重构企业法律顾问的隶属体制--以国有企业法律顾问机构的设置为视角

    Institute of Scientific and Technical Information of China (English)

    李远和

    2014-01-01

    idea in a new angle that balancing the relative detached position of state-owned enterprise legal advisers and enterprise independent management,in order to reconstruct the state-owned enterprise legal adviser membership system,and create new work system of state-owned enterprise legal adviser institute.

  10. The aftermath of Hurricane Ivan: reconstructing roadways while recovering species

    OpenAIRE

    Mittiga, Mary; Sharpe, Vicki

    2005-01-01

    Reconstructing roadways following Hurricane Ivan presented both challenges and opportunities for protected-species recovery. A major challenge was balancing the desire for rapid restoration of major transportation linkages with the regulatory need to minimize harm to rare coastal species. Animals like the Perdido Key beach mouse (PKBM) were already severely impacted by the storm and additional losses could have affected their continued survival. Lessons learned from Ivan will assist state and...

  11. Genome-scale models of bacterial metabolism: reconstruction and applications

    OpenAIRE

    Durot, Maxime; Bourguignon, Pierre-Yves; Schachter, Vincent

    2008-01-01

    Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety...

  12. Twenty-fold acceleration of 3D projection reconstruction MPI

    OpenAIRE

    Konkle, Justin J.; Goodwill, Patrick W.; Saritas, Emine Ulku; Zheng, Bo; Lu, Kuan; Conolly, Steven M.

    2013-01-01

    We experimentally demonstrate a 20-fold improvement in acquisition time in projection reconstruction (PR) magnetic particle imaging (MPI) relative to the state-of-the-art PR MPI imaging results. We achieve this acceleration in our imaging system by introducing an additional Helmholtz electromagnet pair, which creates a slow shift (focus) field. Because of magnetostimulation limits in humans, we show that scan time with three-dimensional (3D) PR MPI is theoretically within the same order of ma...

  13. Study of State Audit Serving Economic Development:Rethink and Reconstruction%国家审计服务经济建设的路径研究:反思与重构

    Institute of Scientific and Technical Information of China (English)

    刘杉

    2014-01-01

    Since the establishment,the national audit offices has been playing the important role in supervising financial income and expenses of every department of the State Council,governments in different levels,fiscal and financial institutions, enterprises and public institutions. In the new era and social condition,according to the requirement of comprehensively deepening reform,national audit offices should redesign the focuses and service path,namely strengthening public responsibility and strengthening national economic governance by standardizing market economic order, supervising the operation of government economic power,promoting the fiscal and financial sustainability,guaranteeing financial safety,preserving or increasing the value of public resources,combating corruption and upholding integrity,deepening economic institutional reform, and so on.%国家审计机关自成立以来,在监督国务院各部门和地方各级政府财政收支、国家财政金融机构和企业事业单位的财务收支等方面发挥了积极作用。在新的时代背景和社会条件下,按照全面深化改革的目标要求,国家审计应重新定位在经济建设中的着力点和服务路径,即通过规范市场经济秩序、监督政府经济权力的运行、促进财政的可持续性、保障金融安全、维护公共资源保值增值、促进反腐倡廉建设、深化经济体制改革等强化政府及相关部门的公共责任,加强国家经济治理。

  14. 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 stochastic simulation and compared the mating criteria in hierarchical and factorial breeding schemes, where the animals were selected based on breeding values predicted by animal-model BLUP. Random mating was included as a reference-mating criterion. We found that MCAC mating generated 4% to 8% less...... they can be achieved without extra costs or practical constraints. MCAC mating merely uses pedigree information to pair the animals more appropriately and is clearly a worthy alternative to minimum-coancestry mating and probably any other mating criterion. We believe, therefore, that MCAC mating should...

  15. 济南市闵子骞祠堂东汉墓%Eastern Han Tomb in the Min Ziqian Ancestral Temple in Jinan City

    Institute of Scientific and Technical Information of China (English)

    济南市考古研究所

    2004-01-01

    In 2000, the Jinan Municipal Institute of Archaeology carried out a rescuing excavation to explore a tomb in the Min Ziqian ancestral temple, Jinan City. The grave is built of brick and stone, consists of an anterior, a middle, a back and two side rooms, and has a "凸"-shaped plan. It has been seriously robbed, but still above 60 pottery objects and copper coins are left over from the grave goods. Among them pottery domestic fowls and animals come first in number, and four pictorial stones remain in the tomb. The tomb shape, the features of the objects and those of the pictorial stones suggest that the burial belongs to the late Eastern Han period.

  16. Reconstructing geographical boundary conditions for palaeoclimate modelling during the Cenozoic

    Science.gov (United States)

    Baatsen, Michiel; van Hinsbergen, Douwe J. J.; von der Heydt, Anna S.; Dijkstra, Henk A.; Sluijs, Appy; Abels, Hemmo A.; Bijl, Peter K.

    2016-08-01

    Studies on the palaeoclimate and palaeoceanography using numerical model simulations may be considerably dependent on the implemented geographical reconstruction. Because building the palaeogeographic datasets for these models is often a time-consuming and elaborate exercise, palaeoclimate models frequently use reconstructions in which the latest state-of-the-art plate tectonic reconstructions, palaeotopography and -bathymetry, or vegetation have not yet been incorporated. In this paper, we therefore provide a new method to efficiently generate a global geographical reconstruction for the middle-late Eocene. The generalised procedure is also reusable to create reconstructions for other time slices within the Cenozoic, suitable for palaeoclimate modelling. We use a plate-tectonic model to make global masks containing the distribution of land, continental shelves, shallow basins and deep ocean. The use of depth-age relationships for oceanic crust together with adjusted present-day topography gives a first estimate of the global geography at a chosen time frame. This estimate subsequently needs manual editing of areas where existing geological data indicate that the altimetry has changed significantly over time. Certain generic changes (e.g. lowering mountain ranges) can be made relatively easily by defining a set of masks while other features may require a more specific treatment. Since the discussion regarding many of these regions is still ongoing, it is crucial to make it easy for changes to be incorporated without having to redo the entire procedure. In this manner, a complete reconstruction can be made that suffices as a boundary condition for numerical models with a limited effort. This facilitates the interaction between experts in geology and palaeoclimate modelling, keeping reconstructions up to date and improving the consistency between different studies. Moreover, it facilitates model inter-comparison studies and sensitivity tests regarding certain

  17. Temperature response to external forcing in simulations and reconstructions of the last millennium

    Directory of Open Access Journals (Sweden)

    L. Fernández-Donado

    2012-08-01

    Full Text Available The understanding of natural climate variability and its driving factors is crucial to assess future climate change. Therefore, comparing proxy-based climate reconstructions with forcing factors as well as comparing these with paleoclimate model simulations is key to gain insights into the relative roles of internal versus forced variability. A review of the state of modeling of the last millennium climate previous to the CMIP5-PMIP3 coordinated effort is presented and compared to the available temperature reconstructions. Simulations and reconstructions broadly agree on reproducing the major temperature changes and suggest an overall linear response to external forcing on multidecadal or longer timescales. Internal variability is found to have an important influence at hemispheric and global scales. The spatial distribution of simulated temperature changes during the transition of the Medieval Climate Anomaly to the Little Ice Age disagrees with that found in the reconstructions, thus advocating for internal variability as a possible major player in shaping temperature changes through the millennium.

    A paleo transient climate response (PTCR is defined to provide a quantitative framework for analysing the consistency between simulated and reconstructed climate. Beyond an overall agreement between simulated and reconstructed PTCR ranges, this analysis is able to single out specific discrepancies between some reconstructions and the ensemble of simulations. The disagreement is found in the cases where the reconstructions show reduced covariability with external forcings or when they present high rates of temperature change.

  18. Use of an object model in three dimensional image reconstruction. Application in medical imaging

    International Nuclear Information System (INIS)

    Threedimensional image reconstruction from projections corresponds to a set of techniques which give information on the inner structure of the studied object. These techniques are mainly used in medical imaging or in non destructive evaluation. Image reconstruction is an ill-posed problem. So the inversion has to be regularized. This thesis deals with the introduction of a priori information within the reconstruction algorithm. The knowledge is introduced through an object model. The proposed scheme is applied to the medical domain for cone beam geometry. We address two specific problems. First, we study the reconstruction of high contrast objects. This can be applied to bony morphology (bone/soft tissue) or to angiography (vascular structures opacified by injection of contrast agent). With noisy projections, the filtering steps of standard methods tend to smooth the natural transitions of the investigated object. In order to regularize the reconstruction but to keep contrast, we introduce a model of classes which involves the Markov random fields theory. We develop a reconstruction scheme: analytic reconstruction-reprojection. Then, we address the case of an object changing during the acquisition. This can be applied to angiography when the contrast agent is moving through the vascular tree. The problem is then stated as a dynamic reconstruction. We define an evolution AR model and we use an algebraic reconstruction method. We represent the object at a particular moment as an intermediary state between the state of the object at the beginning and at the end of the acquisition. We test both methods on simulated and real data, and we prove how the use of an a priori model can improve the results. (author)

  19. Clusters of ancestrally related genes that show paralogy in whole or in part are a major feature of the genomes of humans and other species.

    Directory of Open Access Journals (Sweden)

    Michael B Walker

    Full Text Available Arrangements of genes along chromosomes are a product of evolutionary processes, and we can expect that preferable arrangements will prevail over the span of evolutionary time, often being reflected in the non-random clustering of structurally and/or functionally related genes. Such non-random arrangements can arise by two distinct evolutionary processes: duplications of DNA sequences that give rise to clusters of genes sharing both sequence similarity and common sequence features and the migration together of genes related by function, but not by common descent. To provide a background for distinguishing between the two, which is important for future efforts to unravel the evolutionary processes involved, we here provide a description of the extent to which ancestrally related genes are found in proximity.Towards this purpose, we combined information from five genomic datasets, InterPro, SCOP, PANTHER, Ensembl protein families, and Ensembl gene paralogs. The results are provided in publicly available datasets (http://cgd.jax.org/datasets/clustering/paraclustering.shtml describing the extent to which ancestrally related genes are in proximity beyond what is expected by chance (i.e. form paraclusters in the human and nine other vertebrate genomes, as well as the D. melanogaster, C. elegans, A. thaliana, and S. cerevisiae genomes. With the exception of Saccharomyces, paraclusters are a common feature of the genomes we examined. In the human genome they are estimated to include at least 22% of all protein coding genes. Paraclusters are far more prevalent among some gene families than others, are highly species or clade specific and can evolve rapidly, sometimes in response to environmental cues. Altogether, they account for a large portion of the functional clustering previously reported in several genomes.

  20. Coalescent models reveal the relative roles of ancestral polymorphism, vicariance, and dispersal in shaping phylogeographical structure of an African montane forest robin.

    Science.gov (United States)

    Bowie, Rauri C K; Fjeldså, Jon; Hackett, Shannon J; Bates, John M; Crowe, Timothy M

    2006-01-01

    Although many studies have documented the effect of glaciation on the evolutionary history of Northern Hemisphere flora and fauna, this study is the first to investigate how the indirect aridification of Africa caused by global cooling in response to glacial cycles at higher latitudes has influenced the evolutionary history of an African montane bird. Mitochondrial DNA sequences from the NADH 3 gene were collected from 283 individual Starred Robins (Pogonocichla stellata, Muscicapoidea). At least two major vicariant events, one that separated the Albertine Rift from all but the Kenyan Highlands around 1.3-1.2 Myrs BP, and another that separated the Kenyan Highlands from the northern Eastern Arc, and the northern Eastern Arc from the south-central Eastern Arc between 0.9 and 0.8 Myrs BP appear to underlie much of the observed genetic diversity and structure within Starred Robin populations. These dates of divergence suggest a lack of recurrent gene flow; although the Albertine Rift and south-central Eastern Arc share haplotypes, based on coalescent analyses this can confidently be accounted for by ancestral polymorphism as opposed to recurrent gene flow. Taken collectively, strong evidence exists for recognition of four major ancestral populations: (1) Kenyan Highlands (subspecies keniensis), (2) Albertine Rift (ruwenzori), (3) northern Eastern Arc (helleri), and (4) south-central Eastern Arc, Ufipa and the Malawi Rift (orientalis). The estimated divergence times cluster remarkably around one of the three estimated peaks of aridification in Africa during the Plio-Pleistocene centred on 1 Myrs BP. Further, time to most recent common ancestor (TMRCA) estimates (1.7-1.6 Myrs BP) of gene divergence between the Albertine Rift and the other montane highlands corresponds closely with a second estimated peak of aridification at about 1.7 Myrs BP. Collectively, these results suggest that aridification of Africa in response to glaciation at higher latitudes during the