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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. Investigating the potential of ancestral state reconstruction algorithms in historical linguistics

    OpenAIRE

    Jäger, Gerhard; List, Johann-Mattis

    2016-01-01

    Current efforts in computational historical linguistics are predominantly concerned with phylogenetic inference. However, methods for ancestral state reconstruction have been only sporadically applied. This is surprising since reconstruction is considered essential both in evolutionary biology and in classical historical linguistics. In contradistinction to phylogenetic algorithms, automatic reconstruction methods presuppose phylogenetic information in order to explain what has evolved whe...

  3. Reconstructing the ancestral germ line methylation state of young repeats.

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    Feuerbach, Lars; Lyngsø, Rune B; Lengauer, Thomas; Hein, Jotun

    2011-06-01

    One of the key objectives of comparative genomics is the characterization of the forces that shape genomes over the course of evolution. In the last decades, evidence has been accumulated that for vertebrate genomes also epigenetic modifications have to be considered in this context. Especially, the elevated mutation frequency of 5-methylcytosine (5mC) is assumed to facilitate the depletion of CpG dinucleotides in species that exhibit global DNA methylation. For instance, the underrepresentation of CpG dinucleotides in many mammalian genomes is attributed to this effect, which is only neutralized in so-called CpG islands (CGIs) that are preferentially unmethylated and thus partially protected from rapid CpG decay. For primate-specific CpG-rich transposable elements from the ALU family, it is unclear whether their elevated CpG frequency is caused by their small age or by the absence of DNA methylation. In consequence, these elements are often misclassified in CGI annotations. We present a method for the estimation of germ line methylation from pairwise ancestral-descendant alignments. The approach is validated in a simulation study and tested on DNA repeats from the AluSx family. We conclude that a predicted unmethylated state in the germ line is highly correlated with epigenetic activity of the respective genomic region. Thus, CpG-rich repeats can be facilitated as in silico probes for the epigenetic potential of their genomic neighborhood. PMID:21212152

  4. 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

  5. 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

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

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    Wei Song Hwang

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

  7. 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

  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. Reconstruction of ancestral protein sequences and its applications

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    Grishin Nick V

    2004-09-01

    Full Text Available Abstract Background Modern-day proteins were selected during long evolutionary history as descendants of ancient life forms. In silico reconstruction of such ancestral protein sequences facilitates our understanding of evolutionary processes, protein classification and biological function. Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference. Results We developed ANCESCON, a package for distance-based phylogenetic inference and reconstruction of ancestral protein sequences that takes into account the observed variation of evolutionary rates between positions that more precisely describes the evolution of protein families. To improve the accuracy of evolutionary distance estimation and ancestral sequence reconstruction, two approaches are proposed to estimate position-specific evolutionary rates. Comparisons show that at large evolutionary distances our method gives more accurate ancestral sequence reconstruction than PAML, PHYLIP and PAUP*. We apply the reconstructed ancestral sequences to homology inference and functional site prediction. We show that the usage of hypothetical ancestors together with the present day sequences improves profile-based sequence similarity searches; and that ancestral sequence reconstruction methods can be used to predict positions with functional specificity. Conclusions As a computational tool to reconstruct ancestral protein sequences from a given multiple sequence alignment, ANCESCON shows high accuracy in tests and helps detection of remote homologs and prediction of functional sites. ANCESCON is freely available for non-commercial use. Pre-compiled versions for several platforms can be downloaded from ftp://iole.swmed.edu/pub/ANCESCON/.

  10. Reconstruction of ancestral protein sequences and its applications

    OpenAIRE

    Grishin Nick V; Pei Jimin; Cai Wei

    2004-01-01

    Abstract Background Modern-day proteins were selected during long evolutionary history as descendants of ancient life forms. In silico reconstruction of such ancestral protein sequences facilitates our understanding of evolutionary processes, protein classification and biological function. Additionally, reconstructed ancestral protein sequences could serve to fill in sequence space thus aiding remote homology inference. Results We developed ANCESCON, a package for distance-based phylogenetic ...

  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. Comparative analysis of rosaceous genomes and the reconstruction of a putative ancestral genome for the family

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    Velasco Riccardo

    2011-01-01

    Full Text Available Abstract Background Comparative genome mapping studies in Rosaceae have been conducted until now by aligning genetic maps within the same genus, or closely related genera and using a limited number of common markers. The growing body of genomics resources and sequence data for both Prunus and Fragaria permits detailed comparisons between these genera and the recently released Malus × domestica genome sequence. Results We generated a comparative analysis using 806 molecular markers that are anchored genetically to the Prunus and/or Fragaria reference maps, and physically to the Malus genome sequence. Markers in common for Malus and Prunus, and Malus and Fragaria, respectively were 784 and 148. The correspondence between marker positions was high and conserved syntenic blocks were identified among the three genera in the Rosaceae. We reconstructed a proposed ancestral genome for the Rosaceae. Conclusions A genome containing nine chromosomes is the most likely candidate for the ancestral Rosaceae progenitor. The number of chromosomal translocations observed between the three genera investigated was low. However, the number of inversions identified among Malus and Prunus was much higher than any reported genome comparisons in plants, suggesting that small inversions have played an important role in the evolution of these two genera or of the Rosaceae.

  14. 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

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

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

    2013-09-01

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

  16. 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...

  17. Permutationally invariant state reconstruction

    DEFF Research Database (Denmark)

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

    2012-01-01

    Feasible tomography schemes for large particle numbers must possess, besides an appropriate data acquisition protocol, an efficient way to reconstruct the density operator from the observed finite data set. Since state reconstruction typically requires the solution of a nonlinear large-scale opti......Feasible tomography schemes for large particle numbers must possess, besides an appropriate data acquisition protocol, an efficient way to reconstruct the density operator from the observed finite data set. Since state reconstruction typically requires the solution of a nonlinear large......-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...

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

    Science.gov (United States)

    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

  19. 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

  20. 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

  1. 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

    infectious RNA transcripts. Full length sequencing of cDNA clones and deep sequencing of the parental population identified substitutions important for the observed phenotypes. The investigated cDNA clones were furthermore used as the basis for inferring the sequence of functional viruses. Since each unique......-fitness, functional cDNAs and may also pose problems for sequence-based analysis of viral evolution. To address these challenges we have performed a study of the evolution of classical swine fever virus (CSFV) using deep sequencing and analysis of 84 full-length cDNA clones, each representing individual genomes from...... clone must necessarily be the descendant of a functional ancestor, we hypothesized that it should be possible to produce functional clones by reconstructing ancestral sequences. To test this we used phylogenetic methods to infer two ancestral sequences, which were then reconstructed as cDNA clones...

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

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    Keightley Peter D

    2008-09-01

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

  3. 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.

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    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

  4. Genomic reconstruction of the history of extant populations of India reveals five distinct ancestral components and a complex structure.

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    Basu, Analabha; Sarkar-Roy, Neeta; Majumder, Partha P

    2016-02-01

    India, occupying the center stage of Paleolithic and Neolithic migrations, has been underrepresented in genome-wide studies of variation. Systematic analysis of genome-wide data, using multiple robust statistical methods, on (i) 367 unrelated individuals drawn from 18 mainland and 2 island (Andaman and Nicobar Islands) populations selected to represent geographic, linguistic, and ethnic diversities, and (ii) individuals from populations represented in the Human Genome Diversity Panel (HGDP), reveal four major ancestries in mainland India. This contrasts with an earlier inference of two ancestries based on limited population sampling. A distinct ancestry of the populations of Andaman archipelago was identified and found to be coancestral to Oceanic populations. Analysis of ancestral haplotype blocks revealed that extant mainland populations (i) admixed widely irrespective of ancestry, although admixtures between populations was not always symmetric, and (ii) this practice was rapidly replaced by endogamy about 70 generations ago, among upper castes and Indo-European speakers predominantly. This estimated time coincides with the historical period of formulation and adoption of sociocultural norms restricting intermarriage in large social strata. A similar replacement observed among tribal populations was temporally less uniform. PMID:26811443

  5. 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

  6. 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…

  7. Quantum Conditional Mutual Information, Reconstructed States, and State Redistribution.

    Science.gov (United States)

    Brandão, Fernando G S L; Harrow, Aram W; Oppenheim, Jonathan; Strelchuk, Sergii

    2015-07-31

    We give two strengthenings of an inequality for the quantum conditional mutual information of a tripartite quantum state recently proved by Fawzi and Renner, connecting it with the ability to reconstruct the state from its bipartite reductions. Namely, we show that the conditional mutual information is an upper bound on the regularized relative entropy distance between the quantum state and its reconstructed version. It is also an upper bound for the measured relative entropy distance of the state to its reconstructed version. The main ingredient of the proof is the fact that the conditional mutual information is the optimal quantum communication rate in the task of state redistribution. PMID:26274402

  8. First attempt of neutron quantum state reconstruction

    International Nuclear Information System (INIS)

    The neutron interferometer set-up S18 at the ILL reactor has been used for the first neutron quantum state reconstruction experiment. By a simultaneous measurement of the coherence function and of the modulated momentum distribution behind the interferometer, the Wigner function of various quantum states can be reconstructed. This is equivalent to knowledge of the particle wavefunction. Its spatial dimension follows from the measurement of the coherence function, which is the autocorrelation function of the wavefunction and the shape in momentum space follows from momentum post-selection experiments. Non-orthogonal traces through the (x, k)-phase space have to be measured for an unambiguous reconstruction. Nearly classical (coherent) and non-classical states in the form of Schroedinger cat-like states have been identified. Comparisons of calculated and measured Wigner functions will be shown

  9. 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 ...

  10. 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.

  11. 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

  12. 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...

  13. 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...

  14. 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...

  15. Reconstruction of spin states and its conceptual implications

    OpenAIRE

    Weigert, Stefan

    1998-01-01

    State reconstruction for quantum spins is reviewed. Emphasis is on non-tomographic approaches which are based on measurements performed with a Stern-Gerlach apparatus. Two consequences of successfully implemented state reconstruction are pointed out. First, it allows one to determine experimentally the expectation value of an arbitrary operator without a device measuring it. Second, state reconstruction suggests a reformulation of Schroedinger's equation in terms of expectation values only, w...

  16. Reconstruction of spin states and its conceptual implications

    CERN Document Server

    Weigert, S

    1998-01-01

    State reconstruction for quantum spins is reviewed. Emphasis is on non-tomographic approaches which are based on measurements performed with a Stern-Gerlach apparatus. Two consequences of successfully implemented state reconstruction are pointed out. First, it allows one to determine experimentally the expectation value of an arbitrary operator without a device measuring it. Second, state reconstruction suggests a reformulation of Schroedinger's equation in terms of expectation values only, without explicit reference to a wave function or a density operator.

  17. Coherent States and the Reconstruction of Pure Spin States

    CERN Document Server

    Amiet, J P; Amiet, Jean-Pierre; Weigert, Stefan

    1999-01-01

    Coherent states provide an appealing method to reconstruct efficiently a pure state of a quantum mechanical spin s. A Stern-Gerlach apparatus is used to measure (4s+1) expectations of projection operators on appropriate coherent states in the unknown state. These measurements are compatible with a finite number of states which can be distinguished, in the generic case, by measuring one more probability. In addition, the present technique shows that the zeroes of a Husimi distribution do have an operational meaning: they can be identified directly by measurements with a Stern-Gerlach apparatus. This result comes down to saying that it is possible to resolve experimentally structures in quantum phase-space which are smaller than hbar.

  18. 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...

  19. 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

  20. 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...... due to finite size of the ancestral population and connections between populations. This complicates the conciliation of both approaches and, in particular, combining pedigree with genomic relationships. We present a coherent theoretical framework to consider base population in pedigree relationships....... We suggest a conceptual framework that considers each ancestral population as a finite-sized pool of gametes. This generates across-individual relationships and contrasts with the classical view where each population is considered as an infinite, unrelated pool. Several ancestral populations may be...

  1. Gait identification by using spectrum analysis on state space reconstruction

    OpenAIRE

    Ruiz Vegas, Francisco Javier; Samà Monsonís, Albert; Pérez López, Carlos; Català Mallofré, Andreu

    2011-01-01

    This paper describes a method for identifying a person while walking by means of a triaxial accelerometer attached to the waist. Human gait is considered as a dynamical system whose attractor is reconstructed by time delay vectors. A Spectral Analysis on the state space reconstruction is used to characterize the attractor. Parameters involved in the reconstruction and characterization process are evaluated to examine the effect in gait identification. The method is tested in...

  2. 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)

  3. 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.

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

    OpenAIRE

    Adrian USATYI; Marin USATYI; Oleg CREPIS; Mihail SHATUNOVSKII; Alexandr BOBYREV; Aurel CEBANU

    2010-01-01

    Bream, Abramis brama L., is a key species in fish communities of Moldovian Rivers and a main component of bottom food chains of river and lake ecosystems. With the reconstruction of water bodies, mainly for hydroelectric power stations needs, the ecological conditions changed substantially, which results in modifications in population state of biota. The negative effects of water bodies’ reconstruction upon population status of bream in several Moldovian Rivers and reservoirs were studied. Th...

  5. Gait recognition by using spectrum analysis on state space reconstruction

    OpenAIRE

    Samà Monsonís, Albert; Ruiz Vegas, Francisco Javier; Pérez López, Carlos; Català Mallofré, Andreu

    2011-01-01

    This paper describes a method for identifying a person while walking by means of a triaxial accelerometer attached to the waist. Human gait is considered as a dynamical system whose attractor is reconstructed by time delay vectors. A Spectral Analysis on the state space reconstruction is used to characterize the attractor. The method is compared to other common methods used in gait recognition tasks through a preliminary test.

  6. Quantum reconstruction of an intense polarization squeezed optical state

    DEFF Research Database (Denmark)

    Marquardt, Ch.; Heersink, J.; Dong, R.; Chekhova, M.V.; Klimov, A.B.; Sanchez-Soto, L.L.; Andersen, Ulrik Lund; Leuchs, G.

    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...... characterization of the measured polarization state....

  7. An ancestral HIV-2/simian immunodeficiency virus peptide with potent HIV-1 and HIV-2 fusion inhibitor activity

    OpenAIRE

    Borrego, Pedro; Calado, Rita; Marcelino, José M.; Pereira, Patrícia MR; Quintas, Alexandre; Barroso, Helena; Taveira, Nuno

    2013-01-01

    "Objectives: To produce new fusion inhibitor peptides for HIV-1 and HIV-2 based on ancestral envelope sequences. Methods: HIV-2/simian immunodeficiency virus (SIV) ancestral transmembrane protein sequences were reconstructed and ancestral peptides were derived from the helical region 2 (HR2). The activity of one ancestral peptide (named P3) was examined against a panel of HIV-1 and HIV-2 primary isolates in TZM-bl cells and peripheral blood mononuclear cells and compared to ...

  8. 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...

  9. 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...

  10. 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

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

    Directory of Open Access Journals (Sweden)

    Adrian USATYI

    2010-11-01

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

  12. 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.

  13. 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).

  14. 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...

  15. The role of initial state reconstruction in short and long time deviations from exponential decay

    OpenAIRE

    Muga, J. G.; Delgado, F.; Del Campo, A.; Garcia-Calderon, G.

    2005-01-01

    We consider the role of the reconstruction of the initial state in the deviation from exponential decay at short and long times. The long time decay can be attributed to a wave that was, in a classical-like, probabilistic sense, fully outside the initial state or the inner region at intermediate times, i.e., to a completely reconstructed state, whereas the decay during the exponential regime is due instead to a non-reconstructed wave. At short times quantum interference between regenerated an...

  16. A robust state-space kinetics-guided framework for dynamic PET image reconstruction

    International Nuclear Information System (INIS)

    Dynamic PET image reconstruction is a challenging issue due to the low SNR and the large quantity of spatio-temporal data. We propose a robust state-space image reconstruction (SSIR) framework for activity reconstruction in dynamic PET. Unlike statistically-based frame-by-frame methods, tracer kinetic modeling is incorporated to provide physiological guidance for the reconstruction, harnessing the temporal information of the dynamic data. Dynamic reconstruction is formulated in a state-space representation, where a compartmental model describes the kinetic processes in a continuous-time system equation, and the imaging data are expressed in a discrete measurement equation. Tracer activity concentrations are treated as the state variables, and are estimated from the dynamic data. Sampled-data H∞ filtering is adopted for robust estimation. H∞ filtering makes no assumptions on the system and measurement statistics, and guarantees bounded estimation error for finite-energy disturbances, leading to robust performance for dynamic data with low SNR and/or errors. This alternative reconstruction approach could help us to deal with unpredictable situations in imaging (e.g. data corruption from failed detector blocks) or inaccurate noise models. Experiments on synthetic phantom and patient PET data are performed to demonstrate feasibility of the SSIR framework, and to explore its potential advantages over frame-by-frame statistical reconstruction approaches.

  17. A skull might lie: modelling ancestral ranges and diet from genes and shape of tree squirrels

    Czech Academy of Sciences Publication Activity Database

    Pečnerová, Patrícia; Moravec, Jiří C.; Martínková, Natália

    2015-01-01

    Roč. 64, č. 6 (2015), s. 1074-1088. ISSN 1063-5157 EU Projects: European Commission(XE) CZ.1.07/2.4.00/17.0138 Institutional support: RVO:68081766 Keywords : Sciurini * multilocus phylogeny * geometric morphometry * speciation * ancestral range reconstruction * diet modelling Subject RIV: EG - Zoology Impact factor: 14.387, year: 2014

  18. Reconstructing the quantum state of a Bose-Einstein condensate of atoms in two hyperfine levels

    International Nuclear Information System (INIS)

    We describe an atomic interferometer based on Raman transitions between two hyperfine states. We show how atom count probabilities at the output of the interferometer can be used to reconstruct the joint, entangled multi-particle state of a Bose-Einstein condensate with fixed total number. Two data collection schemes are compared, by numerically solving for the density matrix from the probability data and making analytical estimates of the errors. When only the phase of the interferometer is varied, state reconstruction is possible but ill-conditioned for the case of an unbalanced beamsplitter. When both the phase and transmission parameters are varied, the two-mode Q-function can be measured directly and the reconstruction of the state is well-conditioned. (author)

  19. 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.

  20. 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.

  1. Reconstructing a pure state of a spin s through three Stern-Gerlach measurements

    Energy Technology Data Exchange (ETDEWEB)

    Amiet, Jean-Pierre; Weigert, Stefan [Institut de Physique de l' Universite de Neuchatel, Neuchatel (Switzerland)

    1999-04-16

    Consider a spin s prepared in a pure state. It is shown that, generically, the moduli of the (2s+1) spin components along three directions in space determine the state unambiguously. These probabilities are accessible experimentally by means of a standard Stern-Gerlach apparatus. It is therefore possible to reconstruct a generic pure state on the basis of 6s independent measured intensities. (author)

  2. Reconstructing a pure state of a spin s through three Stern-Gerlach measurements

    CERN Document Server

    Amiet, J P; Amiet, Jean-Pierre; Weigert, Stefan

    1999-01-01

    Consider a spin s prepared in a pure state. It is shown that, generically, the moduli of the (2s+1) spin components along three directions in space determine the state unambiguously. These probabilities are accessible experimentally by means of a standard Stern-Gerlach apparatus. To reconstruct a pure spin state is therefore possible on the basis of 3(2s+1) measured intensities.

  3. 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.

  4. 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.

  5. 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...

  6. 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

  7. 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

  8. 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.

  9. 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.

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

    OpenAIRE

    Stig Thøgersen

    2010-01-01

    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...

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

    OpenAIRE

    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 ance...

  12. 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...

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

    DEFF Research Database (Denmark)

    Kwok, Kawai; Boccaccini, Dino; Persson, Åsa Helen; Frandsen, Henrik Lund

    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 of...... model size, representativeness, and boundary conditions on the numerical results are investigated. Two analytical models for creep rate of porous bodies are derived by extending the Hashin-Shtrikman bound and the Ramakrishnan-Arunchalam model in linear elasticity to steady-state creep based on nonlinear...

  14. 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...

  15. 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

  16. Targeted vessel reconstruction in non-contrast-enhanced steady-state free precession angiography.

    Science.gov (United States)

    Ilicak, Efe; Cetin, Suheyla; Bulut, Elif; Oguz, Kader Karli; Saritas, Emine Ulku; Unal, Gozde; Çukur, Tolga

    2016-05-01

    Image quality in non-contrast-enhanced (NCE) angiograms is often limited by scan time constraints. An effective solution is to undersample angiographic acquisitions and to recover vessel images with penalized reconstructions. However, conventional methods leverage penalty terms with uniform spatial weighting, which typically yield insufficient suppression of aliasing interference and suboptimal blood/background contrast. Here we propose a two-stage strategy where a tractographic segmentation is employed to auto-extract vasculature maps from undersampled data. These maps are then used to incur spatially adaptive sparsity penalties on vascular and background regions. In vivo steady-state free precession angiograms were acquired in the hand, lower leg and foot. Compared with regular non-adaptive compressed sensing (CS) reconstructions (CSlow ), the proposed strategy improves blood/background contrast by 71.3 ± 28.9% in the hand (mean ± s.d. across acceleration factors 1-8), 30.6 ± 11.3% in the lower leg and 28.1 ± 7.0% in the foot (signed-rank test, P < 0.05 at each acceleration). The proposed targeted reconstruction can relax trade-offs between image contrast, resolution and scan efficiency without compromising vessel depiction. Copyright © 2016 John Wiley & Sons, Ltd. PMID:26854004

  17. 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.

  18. Computation of Effective Steady-State Creep of Porous Ni–YSZ Composites with Reconstructed Microstructures

    DEFF Research Database (Denmark)

    Kwok, Kawai; Jørgensen, Peter Stanley; Frandsen, Henrik Lund

    2015-01-01

    This paper investigates the effective steady-state creep response of porous Ni–YSZ composites used in solid oxide fuel cell applications by numerical homogenization based on three-dimensional microstructural reconstructions and steadystate creep properties of the constituent phases. The Ni phase is...... found to carry insignificant stress in the composite and has a negligible role in the effective creep behavior. Thus, when determining effective creep, porous Ni–YSZ composites can be regarded as porous YSZ in which the Ni phase is counted as additional porosity. The stress exponents of porous YSZ are...

  19. 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.

  20. 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.

  1. 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.

  2. 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 ...

  3. 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

  4. 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. PMID:26273952

  5. 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)

  6. 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

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

    DEFF Research Database (Denmark)

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

    2011-01-01

    lower 147Sm/144Nd values of ~0.11, a source which is strongly affected by continentally derived input. Chromium isotopes provide a powerful tool for reconstructing the redox state of ancient seawater since positive values indicate that, at least locally, Neoproterozoic shallow ocean waters were...

  8. 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.

  9. A Discrete Phase-Space Calculus for Quantum Spins based on a Reconstruction Method using Coherent States

    OpenAIRE

    Weigert, Stefan

    1999-01-01

    To reconstruct a mixed or pure quantum state of a spin s is possible through coherent states: its density matrix is fixed by the probabilities to measure the value s along 4s(s+1) appropriately chosen directions in space. Thus, after inverting the experimental data, the statistical operator is parametrized entirely by expectation values. On this basis, a symbolic calculus for quantum spins is developed, the `expectation-value representation.' It resembles the Moyal representation for SU(2) bu...

  10. 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.

  11. 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.

  12. 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...

  13. 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

  14. 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.

  15. 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.

  16. 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.; Zengler, Karsten; Palsson, Bernhard

    2014-01-01

    promoters, we do not yet have a genome-scale assessment of their function. Results: Using multiple genome-scale measurements, we elucidated the network of s-factor and promoter interactions in Escherichia coli. The reconstructed network includes 4,724 sigma-factor-specific promoters corresponding to...

  17. 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...

  18. United states-assisted studies on dose reconstruction in the former Soviet Union

    International Nuclear Information System (INIS)

    Following the Chernobyl accident, the US and the USSR entered into an agreement to work on the safety of civilian nuclear reactors; one aspect of that work was to study the environmental transport and health effects of radionuclides released by the accident. After the break-up of the USSR separate agreements were established between the US and Ukraine, Belarus, and Russia to continue work on dose reconstruction and epidemiologic studies of health effects from exposure to external radiation and the incorporation of radionuclides. Studies in Belarus and Ukraine related to the Chernobyl accident now emphasize epidemiologic studies of childhood-thyroid cancer and leukemia, and eye-lens-cataract formation in liquidators. Supporting studies on dose reconstruction emphasize a variety of ecological, physical, and biological techniques. Studies being conducted in Russia currently emphasize health effects in the workers and the population around the Mayak Industrial Association. As this production complex is an analogue of the US Hanford Works, advantage is being taken of the US experience in conducting a similar, recently completed dose-reconstruction study. In all cases the primary work on dose reconstruction is being performed by scientists from the former Soviet Union. US assistance is in the form of expert consultation and participation, exchange visits, provision of supplies and equipment, and other forms of local assistance

  19. 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.

  20. Improving the quality of the experimental reconstructions as the initial equilibrium state for the NIMROD code

    Science.gov (United States)

    King, Jacob; Kruger, Scott; NIMROD Team

    2014-10-01

    High quality equilibria are essential for extended-MHD modeling with the initial-value NIMROD code. Typically the spatial resolution requirements for extended-MHD modeling, which must resolve singular-layer physics and highly anisotropic diffusion, are more stringent than the resolution of equilibrium reconstructions from experimental discharges. With the current workflow, reconstructed fields are mapped onto the NIMROD finite-element grid, and the disparity between the coarse resolution reconstruction and the fine resolution FE grid can create artificial small-scale artifacts. Extended-MHD modeling, which contains many high-order differential operators, can be corrupted by the mapping errors. We describe efforts to re-solve the Grad-Shafranov equation with open-flux regions using the NIMEQ solver to generate a new equilibrium while using the mapped results for both an initial guess and to specify the boundary conditions. Effects on computations with and without the re-solving for force balance will be described. Work funded by US DOE.

  1. Testing multivariate analysis in paleoenvironmental reconstructions using pollen records from Lagoa Salgada, NE Rio de Janeiro State, Brazil.

    Science.gov (United States)

    Toledo, Mauro B de; Barth, Ortrud M; Silva, Cleverson G; Barros, Marcia A

    2009-12-01

    Despite the indisputable significance of identification of modern analogs for Paleoecology research, relatively few studies attempted to integrate modern and fossil samples on paleoenvironmental reconstructions. In Palynology, this general pattern is not different from other fields of Paleoecology. This study demonstrates the practical application of modern pollen deposition data on paleoenvironmental reconstructions based on fossil pollen by using multivariate analysis. The main goal of this study was to use Detrended Correspondence Analysis (DCA) to compare pollen samples from two sediment cores collected at Lagoa Salgada, a coastal lagoon located at northeastern Rio de Janeiro State. Furthermore, modern surface samples were also statistically compared with samples from both cores, providing new paleoecological insights. DCA demonstrated that samples from both cores are more similar than previously expected, and that a strong pattern, related to a paleoenvironmental event, is present within the fossil data, clearly identifying in the scatter plot samples that represent pre- and post-environmental change. Additionally, it became apparent that modern vegetation and environmental conditions were established in this region 2500 years before present (BP). Multivariate Analysis allowed a more reliable integration of modern and fossil pollen data, proving to be a powerful tool in Paleoecology studies that should be employed more often on paleoclimate and paleoenvironmental reconstructions. PMID:19893900

  2. 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.

  3. 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

  4. 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.

  5. 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

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

    Science.gov (United States)

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

    2015-01-01

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

  7. Post-conflict Reconstruction through State-and Nation-building: The Case of Bosnia and Herzegovina

    Directory of Open Access Journals (Sweden)

    Joseph Marko

    2005-12-01

    Full Text Available The article analyses the effects of the implementation of the Dayton Peace Agreement, which had been based on a "political" compromise with various static and dynamic elements, with regard to the functioning of institutions, developments in the party system, rule of law, effective administration and the economy. In particular the role of the High Representative and the Constitutional Court´s jurisprudence are highlighted for post-conflict reconstruction through state- and nation-building. Finally, based also on a critique of the role of the International Community, the remaining problems are addressed such as the economic viability and attractiveness for foreign investment and the need to shift the balance more from ethnic power-sharing to state effectiveness. In this regard, lessons to be learned from the Bosnian case study are drawn and put into a prospective context for further integration into the European Union.

  8. A Discrete Phase-Space Calculus for Quantum Spins based on a Reconstruction Method using Coherent States

    CERN Document Server

    Weigert, S

    1999-01-01

    To reconstruct a mixed or pure quantum state of a spin s is possible through coherent states: its density matrix is fixed by the probabilities to measure the value s along 4s(s+1) appropriately chosen directions in space. Thus, after inverting the experimental data, the statistical operator is parametrized entirely by expectation values. On this basis, a symbolic calculus for quantum spins is developed, the `expectation-value representation.' It resembles the Moyal representation for SU(2) but two important differences exist. On the one hand, the symbols take values on a discrete set of points in phase space only. On the other hand, no quasi-probabilities - that is, phase-space distributions with negative values - are encountered in this approach.

  9. 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...

  10. 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

  11. Reconstructing the evolution of laughter in great apes and humans.

    Science.gov (United States)

    Davila Ross, Marina; Owren, Michael J; Zimmermann, Elke

    2009-07-14

    Human emotional expressions, such as laughter, are argued to have their origins in ancestral nonhuman primate displays. To test this hypothesis, the current work examined the acoustics of tickle-induced vocalizations from infant and juvenile orangutans, gorillas, chimpanzees, and bonobos, as well as tickle-induced laughter produced by human infants. Resulting acoustic data were then coded as character states and submitted to quantitative phylogenetic analysis. Acoustic outcomes revealed both important similarities and differences among the five species. Furthermore, phylogenetic trees reconstructed from the acoustic data matched the well-established trees based on comparative genetics. Taken together, the results provide strong evidence that tickling-induced laughter is homologous in great apes and humans and support the more general postulation of phylogenetic continuity from nonhuman displays to human emotional expressions. Findings also show that distinctively human laughter characteristics such as predominantly regular, stable voicing and consistently egressive airflow are nonetheless traceable to characteristics of shared ancestors with great apes. PMID:19500987

  12. 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.

  13. 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

  14. 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...

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

    OpenAIRE

    Lougovski, Pavel

    2004-01-01

    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 "Schrödinger 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 ...

  16. 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.

  17. 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

  18. 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

  19. 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

  20. 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

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

    DEFF Research Database (Denmark)

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

    -prone nature of the RNA-dependent RNA polymerase resulting in the majority of circulating forms being non-functional. However, since any infectious virus particle should necessarily be the offspring of a functional virus, we hypothesized that it should be possible to synthesize a highly virulent form 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 cDNA by...... site directed mutagenesis, removing non-synonymous mutations step by step. In vitro testing of modified constructs did indeed lead to fully functional viruses with similar growth kinetics as the wild-type strain. Moreover, viruses rescued from the construct had the ancestral amino acid sequence and...

  2. 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

  3. 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

  4. 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...

  5. 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...

  6. 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...

  7. 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

  8. 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.

  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. 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

  11. Haplotype ancestral AH8.1 dans la mucoviscidose

    OpenAIRE

    Beucher, Julie

    2012-01-01

    La mucoviscidose est une maladie à transmission autosomique récessive, due à des mutations du gène CFTR. Les patients, partageant de mêmes mutations de CFTR et un même environnement, ont une expression phénotypique variable, suggérant l'influence d'autres gènes modifiant la sévérité de la maladie, appelés gènes modificateurs. L'atteinte respiratoire, caractérisée par une inflammation exacerbée, est un facteur principal de morbimortalité. L'haplotype ancestral AH8.1, impliqué dans la réponse i...

  12. The CMS Muon Reconstruction Software

    CERN Document Server

    Trocino, Daniele

    2009-01-01

    Muonic final states will provide clean signatures for many physics processes at the LHC. One of the main goals of the Compact Muon Solenoid (CMS) design is thus to ensure efficient and accurate identification and reconstruction of muons. A sophisticated muon system is used for muon identification and stand-alone reconstruction and the inner silicon tracker exploits the high magnetic field to ensure a very precise transverse momentum resolution. The global reconstruction algorithms combine muons reconstructed in the dedicated spectrometer with tracks reconstructed in the inner detector. The CMS reconstruction software is well suited for both offline reconstruction and online event selection (HLT) and its performance has been studied in detail using Monte Carlo simulations. The muon reconstruction has also been employed successfully to reconstruct cosmic muons traversing the CMS detector. The design of the CMS muon identification and reconstruction is presented, as well as its performance on simulated and cosmi...

  13. 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.

  14. 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.

  15. 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.

  16. 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

    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...

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

    Directory of Open Access Journals (Sweden)

    Hsu Tsai-Wen

    2009-07-01

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

  18. 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

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  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. 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.

  7. 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

  8. Distinct Reconstruction Patterns and Spin-Resolved Electronic States along the Zigzag Edges of Transition Metal Dichalcogenides

    Science.gov (United States)

    Cui, Ping; Choi, Jin-Ho; Chen, Wei; Zeng, Jiang; Zhang, Chendong; Shih, Chih-Kang; Li, Zhenyu; Zhang, Zhenyu

    Two-dimensional transition metal dichalcogenides are a new class of materials exhibiting various intriguing physical, chemical, and mechanical properties. Integration of such materials for potential device applications will necessarily encounter creation of different boundaries. Using first-principles approaches, here we investigate the structural, electronic, and magnetic properties along two inequivalent M- or X-terminated zigzag edges of MX2 (M =Mo, W; X =S, Se). Along the M-terminated edges, we discover a previously unrecognized but energetically strongly preferred (2x1) reconstruction pattern, which is universal for all the MX2, characterized by place exchanges of the outmost X and M edge atoms. In contrast, the X-terminated edges undergo a more moderate (2x1) or (3x1) reconstruction for MoX2 or WX2, respectively. We further use the prototypical examples of zigzag MoX2 nanoribbons to demonstrate that the M- and X-terminated edges possess distinctly different electronic and magnetic properties, which can be exploited for a broad range of spintronic and catalytic applications Supported by NNSF of China, MOST, and USNSF.

  9. Evidence from cyclostomes for complex regionalization of the ancestral vertebrate brain.

    Science.gov (United States)

    Sugahara, Fumiaki; Pascual-Anaya, Juan; Oisi, Yasuhiro; Kuraku, Shigehiro; Aota, Shin-ichi; Adachi, Noritaka; Takagi, Wataru; Hirai, Tamami; Sato, Noboru; Murakami, Yasunori; Kuratani, Shigeru

    2016-03-01

    The vertebrate brain is highly complex, but its evolutionary origin remains elusive. Because of the absence of certain developmental domains generally marked by the expression of regulatory genes, the embryonic brain of the lamprey, a jawless vertebrate, had been regarded as representing a less complex, ancestral state of the vertebrate brain. Specifically, the absence of a Hedgehog- and Nkx2.1-positive domain in the lamprey subpallium was thought to be similar to mouse mutants in which the suppression of Nkx2-1 leads to a loss of the medial ganglionic eminence. Here we show that the brain of the inshore hagfish (Eptatretus burgeri), another cyclostome group, develops domains equivalent to the medial ganglionic eminence and rhombic lip, resembling the gnathostome brain. Moreover, further investigation of lamprey larvae revealed that these domains are also present, ruling out the possibility of convergent evolution between hagfish and gnathostomes. Thus, brain regionalization as seen in crown gnathostomes is not an evolutionary innovation of this group, but dates back to the latest vertebrate ancestor before the divergence of cyclostomes and gnathostomes more than 500 million years ago. PMID:26878236

  10. Penile reconstruction

    OpenAIRE

    Garaffa, Giulio; Sansalone, Salvatore; Ralph, David J.

    2012-01-01

    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.

  11. 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.

  12. 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...

  13. 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 $...

  14. 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

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

    International Nuclear Information System (INIS)

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

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

    Directory of Open Access Journals (Sweden)

    Kang Ji Hyoun

    2013-01-01

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

  17. 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...

  18. 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...

  19. 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

  20. 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.

  1. 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.

  2. 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...

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

    OpenAIRE

    Kolte, Astrid M.; Nielsen, Henriette S.; Steffensen, Rudi; Crespi, Bernard; Christiansen, Ole B

    2015-01-01

    A segment of DNA called the 8.1 ancestral haplotype is hypothesized to cause fetal loss due to a ‘selfish gene’ effect. The hypothesis was not supported, although the haplotype tended to be inherited more often than expected among girls (p=0.11) in a study of 110 mother-child pairs. Further studies are warranted.

  4. The significance of 14 C dating on the reconstruction of paleo-sea level and in the quaternary barrier evolution in the State of Parana, Brazil

    International Nuclear Information System (INIS)

    The C-14 datations are one of the main tools to reconstruct paleo-seal level and to understand the Quaternary barriers evolution. Thi paper discuss the significant of 33 14 C date dated samples on paleo-sea level reconstruction and in the interpretation of Upper Pleistocene and Holocene barrier evolution in the State of Parana. We have concluded that: it is unlikely that humic and fulvic acids are influencing the dating of wood samples from sediments impregnated with organic matter; in situ reef remains, composed mainly of vermetid tubes of Petaloconchus (Macrophragma) varians, are the most precise and reliable paleo-sea level indicators found in the coast of Parana, showing a margin of error around ± 1,0 m; the height of the shell banks, composed mainly of Anamalocardia brasiliana and containing abundant shells in live position, indicates a paleo-sea level equal or higher than the mean sea level during the organisms lifetime; interpretation of paleo-sea level through composed indicators provide only maximum ages because the dated-sample could be older than the sedimentary structure used determine paleo-sea level; the marine paleo-sea level indicators suggest that, during the late Pleistocene, the sea reached > 4.0 m above present sea level; dating of vermetid tubes indicates that the maximum Holocene sea level on the Parana coast occurred between 5370 and 4630 years B.P.; the Holocene high maximum was about 3.5-3.6 ± 1.0 m; after the maximum, the sea level gradually dropped, but the possibility of the occurrence of decimeter oscillations is not rejected; the paleo-seal level inferred from mollusk banks, mainly composed of Anomalocardia brasiliana, and composed indicators, such as sedimentary structures associated with transported shells and wood fragment, agree with paleo-sea levels inferred from vermetid tubes on the Parana coast. (author)

  5. Frequency of carriers of 8.1 ancestral haplotype and its fragments in two Caucasian populations.

    Science.gov (United States)

    Kiszel, Petra; Kovács, Margit; Szalai, Csaba; Yang, Yan; Pozsonyi, Eva; Blaskó, Bernadett; Laki, Judit; Prohászka, Zoltán; Fazakas, Adám; Pánczél, Pál; Hosszúfalusi, Nóra; Rajczy, Katalin; Wu, Yee-Ling; Chung, Erwin K; Zhou, Bi; Blanchong, Carol A; Vatay, Agnes; Yu, C Yung; Füst, G

    2007-01-01

    Within the human MHC region larger stretches of conserved DNA, called conserved ancestral haplotypes exist. However, many MHC haplotypes contain only fragments of an ancestral haplotype. Little is known, however, on relative distribution of the ancestral haplotypes to their fragments. Therefore we determined the frequency of carriers of the whole ancestral haplotype 8.1 (AH8.1) and its fragments in 127 healthy Hungarian people, 101 healthy Ohioian females, and in nine Hungarian families. The HLA-DQ2, HLA-DR3(17), RAGE -429C allele, the mono-S-C4B genotype, the HSP70-2 1267G allele and the TNF -308A (TNF2) allele were used as markers of the AH8.1. Frequency of carriers of the whole AH8.1 and its fragments was similar in the both populations. 18% of the subjects carried the whole AH8.1 in at least one chromosome, while 17-20%, 36-39%, and 24-29%, respectively carried two or three constituents of the haplotype, only one constituent or none of them. Similar results were obtained in the family study. In addition, marked differences were found in the relationship of the constituents' alleles to the whole AH8.1. In both populations, 29%, 50-59%, 52-56% and 76-96%, respectively of the carriers of HSP70-2 1267G, RAGE-429C, TNF2, and mono-S carriers carried the whole 8.1 haplotype. These findings may have important implications for studies of the disease associations with different MHC ancestral haplotypes. PMID:17558713

  6. 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)

  7. 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.

  8. 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

  9. ACL reconstruction - discharge

    Science.gov (United States)

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

  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. 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...

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

    Science.gov (United States)

    Evans, M. Y.

    2009-04-01

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

  13. Punctuated evolution and transitional hybrid network in an ancestral cell cycle of fungi

    Science.gov (United States)

    Medina, Edgar M; Turner, Jonathan J; Gordân, Raluca; Skotheim, Jan M; Buchler, Nicolas E

    2016-01-01

    Although cell cycle control is an ancient, conserved, and essential process, some core animal and fungal cell cycle regulators share no more sequence identity than non-homologous proteins. Here, we show that evolution along the fungal lineage was punctuated by the early acquisition and entrainment of the SBF transcription factor through horizontal gene transfer. Cell cycle evolution in the fungal ancestor then proceeded through a hybrid network containing both SBF and its ancestral animal counterpart E2F, which is still maintained in many basal fungi. We hypothesize that a virally-derived SBF may have initially hijacked cell cycle control by activating transcription via the cis-regulatory elements targeted by the ancestral cell cycle regulator E2F, much like extant viral oncogenes. Consistent with this hypothesis, we show that SBF can regulate promoters with E2F binding sites in budding yeast. DOI: http://dx.doi.org/10.7554/eLife.09492.001 PMID:27162172

  14. Diaspora of diaspora: Adyge-Abkhaz returnees in the ancestral homeland

    OpenAIRE

    Erciyes, Cemre

    2008-01-01

    Focusing on the diasporic characteristics shown by ancestral return migrants, this case study looks at the Abkhaz-Adyge (Circassian) returnees from Turkey to the Caucasus and how they become the “diaspora of the diaspora.” The next generations of diasporans continue to dream of return, and, with recent developments in communication technologies and cheaper transportation, many find ways to realize this dream. There are many different forms of return, but some “return-migrate” and settle in an...

  15. COMPONENTES NUTRICIONALES Y ANTIOXIDANTES DE DOS ESPECIES DE GUAJE (Leucaena spp.): UN RECURSO ANCESTRAL SUBUTILIZADO

    OpenAIRE

    Nallely Román-Cortés; María del Rosario García-Mateos; Ana María Castillo-González; Jaime Sahagún-Castellanos; Adelina Jiménez-Arellanes

    2014-01-01

    El guaje ( Leucaena spp.) es una planta de vaina y semillas comestibles, un recurso ancestral subutilizado por los pueblos mesoamericanos. El valor nutricional y nutracéutico del guaje se desconoce pese a su consumo vigente en las poblaciones rurales. El objetivo de este trabajo fue evaluar el contenido de minerales, compo - nentes nutricionales y antioxidantes para contribuir a la revalorización alimentaria del guaje rojo ( L. esculenta Benth.) y verde ( L. leucocephala Lam.). Los contenidos...

  16. 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.

  17. 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.

  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. 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

  20. 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]. PMID:27046809

  1. High-Performance Phylogeny Reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Tiffani L. Williams

    2004-11-10

    Under the Alfred P. Sloan Fellowship in Computational Biology, I have been afforded the opportunity to study phylogenetics--one of the most important and exciting disciplines in computational biology. A phylogeny depicts an evolutionary relationship among a set of organisms (or taxa). Typically, a phylogeny is represented by a binary tree, where modern organisms are placed at the leaves and ancestral organisms occupy internal nodes, with the edges of the tree denoting evolutionary relationships. The task of phylogenetics is to infer this tree from observations upon present-day organisms. Reconstructing phylogenies is a major component of modern research programs in many areas of biology and medicine, but it is enormously expensive. The most commonly used techniques attempt to solve NP-hard problems such as maximum likelihood and maximum parsimony, typically by bounded searches through an exponentially-sized tree-space. For example, there are over 13 billion possible trees for 13 organisms. Phylogenetic heuristics that quickly analyze large amounts of data accurately will revolutionize the biological field. This final report highlights my activities in phylogenetics during the two-year postdoctoral period at the University of New Mexico under Prof. Bernard Moret. Specifically, this report reports my scientific, community and professional activities as an Alfred P. Sloan Postdoctoral Fellow in Computational Biology.

  2. Vulvovaginal reconstruction for neoplastic disease.

    Science.gov (United States)

    Höckel, Michael; Dornhöfer, Nadja

    2008-06-01

    Current treatment of neoplastic disease that involves the external female genitalia aims to achieve local disease control, but not to restore form and function of these organs. Despite a growing trend to reduce the extent of surgical resection, impaired quality of life after surgery due to severe sexual dysfunction and disturbed body image is common. We postulate that the integration of surgical techniques for vulvar and vaginal reconstruction into primary treatment would improve aesthetic and functional results and therefore quality of life. We systematically searched the literature for surgical procedures designed and validated for vulvovaginal reconstruction. Various skin flaps, both with random vascularisation and those based on vascular territories (ie, axial pattern, fasciocutaneous, musculocutaneous, and bowel flaps), can restore important parts of vulvovaginal form and function with acceptable morbidity at the donor and recipient sites. Appropriate vulvovaginal reconstruction cannot be achieved by doing a few standardised procedures; rather, it necessitates specialists who are familiar with general principles of reconstructive surgery to master many techniques to select the optimum procedure for the individual patient. Vulvovaginal reconstructive surgery has limitations, particularly achievement of functional restoration in irradiated tissue. Physicians who treat women with neoplastic disease of the external genitalia should be aware of the current state of vulvovaginal reconstructive surgery. Prospective controlled clinical trials are warranted to assess the effect of vulvovaginal reconstruction on morbidity and quality of life after treatment. PMID:18510987

  3. 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.

  4. Breast Reconstruction and Prosthesis

    Science.gov (United States)

    ... have breast reconstruction If you choose to have reconstructive surgery, follow these steps: STEP 1 — Ask your doctor to refer you to a plastic surgeon who is an expert in breast reconstruction. ...

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

    Science.gov (United States)

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

    2013-11-01

    Analyses of the genetic relationships among modern humans, Neanderthals and Denisovans have suggested that 1-4% of the non-Sub-Saharan African gene pool may be Neanderthal derived, while 6-8% of the Melanesian gene pool may be the product of admixture between the Denisovans and the direct ancestors of Melanesians. In the present study, we analyzed single nucleotide polymorphism (SNP) diversity among a worldwide collection of contemporary human populations with respect to the genetic constitution of these two archaic hominins and Pan troglodytes (chimpanzee). We partitioned SNPs into subsets, including those that are derived in both archaic lineages, those that are ancestral in both archaic lineages and those that are only derived in one archaic lineage. By doing this, we have conducted separate examinations of subsets of mutations with higher probabilities of divergent phylogenetic origins. While previous investigations have excluded SNPs from common ancestors in principal component analyses, we included common ancestral SNPs in our analyses to visualize the relative placement of the Neanderthal and Denisova among human populations. To assess the genetic similarities among the various hominin lineages, we performed genetic structure analyses to provide a comparison of genetic patterns found within contemporary human genomes that may have archaic or common ancestral roots. Our results indicate that 3.6% of the Neanderthal genome is shared with roughly 65.4% of the average European gene pool, which clinally diminishes with distance from Europe. Our results suggest that Neanderthal genetic associations with contemporary non-Sub-Saharan African populations, as well as the genetic affinities observed between Denisovans and Melanesians most likely result from the retention of ancient mutations in these populations. PMID:23872234

  6. 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.

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

    Science.gov (United States)

    2012-01-01

    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. PMID:22429690

  8. Ancestral polymorphism and recent invasion of transposable elements in Drosophila species

    Directory of Open Access Journals (Sweden)

    Dias Elaine

    2012-07-01

    Full Text Available Abstract Background During the evolution of transposable elements, some processes, such as ancestral polymorphisms and horizontal transfer of sequences between species, can produce incongruences in phylogenies. We investigated the evolutionary history of the transposable elements Bari and 412 in the sequenced genomes of the Drosophila melanogaster group and in the sibling species D. melanogaster and D. simulans using traditional phylogenetic and network approaches. Results Maximum likelihood (ML phylogenetic analyses revealed incongruences and unresolved relationships for both the Bari and 412 elements. The DNA transposon Bari within the D. ananassae genome is more closely related to the element of the melanogaster complex than to the sequence in D. erecta, which is inconsistent with the species phylogeny. Divergence analysis and the comparison of the rate of synonymous substitutions per synonymous site of the Bari and host gene sequences explain the incongruence as an ancestral polymorphism that was inherited stochastically by the derived species. Unresolved relationships were observed in the ML phylogeny of both elements involving D. melanogaster, D. simulans and D. sechellia. A network approach was used to attempt to resolve these relationships. The resulting tree suggests recent transfers of both elements between D. melanogaster and D. simulans. The divergence values of the elements between these species support this conclusion. Conclusions We showed that ancestral polymorphism and recent invasion of genomes due to introgression or horizontal transfer between species occurred during the evolutionary history of the Bari and 412 elements in the melanogaster group. These invasions likely occurred in Africa during the Pleistocene, before the worldwide expansion of D. melanogaster and D. simulans.

  9. 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

  10. 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...

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Sporadic inclusion body myositis in Japanese is associated with the MHC ancestral haplotype 52.1.

    Science.gov (United States)

    Scott, Adrian Phillip; Allcock, Richard James Nigel; Mastaglia, Frank; Nishino, Ichizo; Nonaka, Ikuya; Laing, Nigel

    2006-05-01

    In Caucasians, sporadic inclusion body myositis has been associated with the MHC ancestral haplotypes; HLA-A1, B8, DR3 (8.1AH) and HLA-B35, DR1 (35.2AH). It is not known whether these haplotypes carry susceptibility for the disease in other ethnic groups. We report here the results of HLA-B and -DRB1 typing using a high-resolution sequence-based technique in a cohort of 31 Japanese patients with definite sIBM. Patient allele frequencies were 40.3% for HLA-B*5201 (10.7% in controls: pHLA-DRB1*1502 (10% in controls: p<0.001). Both alleles were found together as part of a conserved haplotype (52.1AH) at a frequency of 37.1% in patients (8.4% in controls: p<0.001). This is the first description of a haplotypic MHC association with sporadic inclusion body myositis in Japanese patients. These findings indicate that different MHC ancestral haplotypes are associated with sIBM in different ethnic groups and further emphasize the importance of genetic factors in this condition. PMID:16564169

  16. Contributions of ancestral inter-species recombination to the genetic diversity of extant Streptomyces lineages.

    Science.gov (United States)

    Andam, Cheryl P; Choudoir, Mallory J; Vinh Nguyen, Anh; Sol Park, Han; Buckley, Daniel H

    2016-07-01

    Streptomyces species produce many important antibiotics and have a crucial role in soil nutrient cycling. However, their evolutionary history remains poorly characterized. We have evaluated the impact of homologous recombination on the evolution of Streptomyces using multi-locus sequence analysis of 234 strains that represent at least 11 species clusters. Evidence of inter-species recombination is widespread but not uniform within the genus and levels of mosaicism vary between species clusters. Most phylogenetically incongruent loci are monophyletic at the scale of species clusters and their subclades, suggesting that these recombination events occurred in shared ancestral lineages. Further investigation of two mosaic species clusters suggests that genes acquired by inter-species recombination may have become fixed in these lineages during periods of demographic expansion; implicating a role for phylogeography in determining contemporary patterns of genetic diversity. Only by examining the phylogeny at the scale of the genus is apparent that widespread phylogenetically incongruent loci in Streptomyces are derived from a far smaller number of ancestral inter-species recombination events. PMID:26849310

  17. 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

  18. RNA-DNA differences in human mitochondria restore ancestral form of 16S ribosomal RNA.

    Science.gov (United States)

    Bar-Yaacov, Dan; Avital, Gal; Levin, Liron; Richards, Allison L; Hachen, Naomi; Rebolledo Jaramillo, Boris; Nekrutenko, Anton; Zarivach, Raz; Mishmar, Dan

    2013-11-01

    RNA transcripts are generally identical to the underlying DNA sequences. Nevertheless, RNA-DNA differences (RDDs) were found in the nuclear human genome and in plants and animals but not in human mitochondria. Here, by deep sequencing of human mitochondrial DNA (mtDNA) and RNA, we identified three RDD sites at mtDNA positions 295 (C-to-U), 13710 (A-to-U, A-to-G), and 2617 (A-to-U, A-to-G). Position 2617, within the 16S rRNA, harbored the most prevalent RDDs (>30% A-to-U and ∼15% A-to-G of the reads in all tested samples). The 2617 RDDs appeared already at the precursor polycistrone mitochondrial transcript. By using traditional Sanger sequencing, we identified the A-to-U RDD in six different cell lines and representative primates (Gorilla gorilla, Pongo pigmaeus, and Macaca mulatta), suggesting conservation of the mechanism generating such RDD. Phylogenetic analysis of more than 1700 vertebrate mtDNA sequences supported a thymine as the primate ancestral allele at position 2617, suggesting that the 2617 RDD recapitulates the ancestral 16S rRNA. Modeling U or G (the RDDs) at position 2617 stabilized the large ribosomal subunit structure in contrast to destabilization by an A (the pre-RDDs). Hence, these mitochondrial RDDs are likely functional. PMID:23913925

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

    Directory of Open Access Journals (Sweden)

    Teresa Almeida

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

  20. In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes.

    Science.gov (United States)

    Daly, Toni K; Sutherland-Smith, Andrew J; Penny, David

    2013-01-01

    Vaults are very large oligomeric ribonucleoproteins conserved among a variety of species. The rat vault 3D structure shows an ovoid oligomeric particle, consisting of 78 major vault protein monomers, each of approximately 861 amino acids. Vaults are probably the largest ribonucleoprotein structures in eukaryote cells, being approximately 70 nm in length with a diameter of 40 nm--the size of three ribosomes and with a lumen capacity of 50 million Å(3). We use both protein sequences and inferred ancestral sequences for in silico virtual resurrection of tertiary and quaternary structures to search for vaults in a wide variety of eukaryotes. We find that the vault's phylogenetic distribution is widespread in eukaryotes, but is apparently absent in some notable model organisms. Our conclusion from the distribution of vaults is that they were present in the last eukaryote common ancestor but they have apparently been lost from a number of groups including fungi, insects, and probably plants. Our approach of inferring ancestral 3D and quaternary structures is expected to be useful generally. PMID:23887922

  1. 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...

  2. 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.

  3. [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

  4. 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.

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

    Science.gov (United States)

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

    2006-03-01

    The biogeography of pungency in three species of wild chili in the chaco and surrounding highland habitats of southeastern Bolivia is described. We report that Capsicum chacoense, C. baccatum, and C. eximium are polymorphic for production of capsaicin and its analogs, such that completely pungent and completely nonpungent individuals co-occur in some populations. In C. chacoense, the density of plants and the proportion of pungent plants increased with elevation. Above 900 m, all individuals in all populations except two were pungent; nonpungent individuals in at least one of the two polymorphic populations were likely a result of spreading by humans. The occurrence of pungent and nonpungent individuals in three species of ancestral Capsicum and the geographic variation of pungency within species suggest that production of capsaicin and its analogs entails both costs and benefits, which shift from one locality to another. Determining the selection pressures behind such shifts is necessary to understand the evolution of pungency in chilies. PMID:16572297

  6. Characterisation of monotreme caseins reveals lineage-specific expansion of an ancestral casein locus in mammals.

    Science.gov (United States)

    Lefèvre, Christophe M; Sharp, Julie A; Nicholas, Kevin R

    2009-01-01

    Using a milk-cell cDNA sequencing approach we characterised milk-protein sequences from two monotreme species, platypus (Ornithorhynchus anatinus) and echidna (Tachyglossus aculeatus) and found a full set of caseins and casein variants. The genomic organisation of the platypus casein locus is compared with other mammalian genomes, including the marsupial opossum and several eutherians. Physical linkage of casein genes has been seen in the casein loci of all mammalian genomes examined and we confirm that this is also observed in platypus. However, we show that a recent duplication of beta-casein occurred in the monotreme lineage, as opposed to more ancient duplications of alpha-casein in the eutherian lineage, while marsupials possess only single copies of alpha- and beta-caseins. Despite this variability, the close proximity of the main alpha- and beta-casein genes in an inverted tail-tail orientation and the relative orientation of the more distant kappa-casein genes are similar in all mammalian genome sequences so far available. Overall, the conservation of the genomic organisation of the caseins indicates the early, pre-monotreme development of the fundamental role of caseins during lactation. In contrast, the lineage-specific gene duplications that have occurred within the casein locus of monotremes and eutherians but not marsupials, which may have lost part of the ancestral casein locus, emphasises the independent selection on milk provision strategies to the young, most likely linked to different developmental strategies. The monotremes therefore provide insight into the ancestral drivers for lactation and how these have adapted in different lineages. PMID:19874726

  7. 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

  8. 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.

  9. Antiquity of Ediacaran Fossils, Early Shelled Organisms, Recent Radiometric Age-Dates from India and Ancestral Biota

    Science.gov (United States)

    Basu, A.

    2008-03-01

    U-Pb zircon ages and Pb-Pb limestone ages assign Ediacaran and shelly fossils reported from India between 1750 and 950 Ma indicating ancestral diversification of metazoans. Simple bacterial life must have began earlier and may be found in meteorites.

  10. 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 ...

  11. 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.

  12. 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

  13. Surfaces, Digitisations and Reconstructions

    DEFF Research Database (Denmark)

    Christensen, Sabrina Tang

    2015-01-01

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

  14. Eleven ancestral gene families lost in mammals and vertebrates while otherwise universally conserved in animals

    Directory of Open Access Journals (Sweden)

    Danchin Etienne GJ

    2006-01-01

    Full Text Available Abstract Background Gene losses played a role which may have been as important as gene and genome duplications and rearrangements, in modelling today species' genomes from a common ancestral set of genes. The set and diversity of protein-coding genes in a species has direct output at the functional level. While gene losses have been reported in all the major lineages of the metazoan tree of life, none have proposed a focus on specific losses in the vertebrates and mammals lineages. In contrast, genes lost in protostomes (i.e. arthropods and nematodes but still present in vertebrates have been reported and extensively detailed. This probable over-anthropocentric way of comparing genomes does not consider as an important phenomena, gene losses in species that are usually described as "higher". However reporting universally conserved genes throughout evolution that have recently been lost in vertebrates and mammals could reveal interesting features about the evolution of our genome, particularly if these losses can be related to losses of capability. Results We report 11 gene families conserved throughout eukaryotes from yeasts (such as Saccharomyces cerevisiae to bilaterian animals (such as Drosophila melanogaster or Caenorhabditis elegans. This evolutionarily wide conservation suggests they were present in the last common ancestors of fungi and metazoan animals. None of these 11 gene families are found in human nor mouse genomes, and their absence generally extends to all vertebrates. A total of 8 out of these 11 gene families have orthologs in plants, suggesting they were present in the Last Eukaryotic Common Ancestor (LECA. We investigated known functional information for these 11 gene families. This allowed us to correlate some of the lost gene families to loss of capabilities. Conclusion Mammalian and vertebrate genomes lost evolutionary conserved ancestral genes that are probably otherwise not dispensable in eukaryotes. Hence, the human

  15. 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

  16. 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

  17. 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.

  18. 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.

  19. 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

  20. 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.

  1. 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

  2. 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.

  3. The hypothetical ancestral animal. the Urmetazoa: telomerase activity in sponges (Porifera

    Directory of Open Access Journals (Sweden)

    ISABEL M. MÜLLER

    2003-05-01

    Full Text Available Sponges (Porifera represent the lowest metazoan phylum, characterized by a pronounced plasticity in the determination of cell lineages, and they are the closest related taxon to the hypothetical ancestral animal, the Urmetazoa, from which the metazoan lineages diverged. In a first approach to elucidate the molecular mechanisms controlling the switch from the cell lineage with a putative indefinite growth capacity to senescent, somatic cells, the activity of the telomerase as an indicator for immortality has been determined. The studies were performed with the marine demosponges Suberites domuncula and Geodia cydonium, in vivo with tissue but also in vitro using the primmorph system. Primmorphs are formed from dissociated cells which have retained their proliferation potency. It was found that the activity of telomerase in tissue of both sponges is high. Based on this and additional findings it is assumed that the separation of the senescent sponge cell lineage from the immortal germ-/somatic cell lineage is triggered by the loss of contact to cell adhesion factors. First evidence is included which suggests that the final progress of the senescent, telomerase-negative cells to cell death is caused by apoptosis.

  4. 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.

  5. 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.

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

    DEFF Research Database (Denmark)

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

    2015-01-01

    BACKGROUND AND OBJECTIVES: The 8.1 ancestral haplotype (AH) (HLA-A1, C7, B8, C4AQ0, C4B1, DR3, DQ2) is a remarkably long and conserved haplotype in the human major histocompatibility complex. It has been associated with both beneficial and detrimental effects, consistent with antagonistic....... The objective was to test the gestational drive theory for the 8.1AH in women with RPL and their live born children. METHODOLOGY: We investigated the inheritance of the 8.1AH from 82 heterozygous RPL women to 110 live born children. All participants were genotyped for HLA-A, -B and -DRB1 in DNA from...... EDTA-treated blood or buccal swaps. Inheritance was compared with a Mendelian inheritance of 50% using a two-sided exact binomial test. RESULTS: We found that 55% of the live born children had inherited the 8.1AH, which was not significantly higher than the expected 50% (P = 0.29). Interestingly, we...

  7. 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.

  8. 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

  9. 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.

  10. Cosmic Tidal Reconstruction

    CERN Document Server

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

    2015-01-01

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

  11. 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).

  12. 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 ...

  13. 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...

  14. 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...

  15. Impacts of plant-based foods in ancestral hominin diets on the metabolism and function of gut microbiota in vitro

    OpenAIRE

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

    2014-01-01

    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 plant-based d...

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

    Science.gov (United States)

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

    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 lion (Eumetopias jubatus, Otariidae) and the endemic Baikal seal (Pusa sibirica, Phocidae) using combination of human, domestic dog and stone marten whole-chromosome painting probes. The earliest karyological studies of Pinnipedia showed that pinnipeds were characterized by a pronounced karyological conservatism that is confirmed here with species from Phocidae, Otariidae and Odobenidae sharing same low number of conserved human autosomal segments (32). Chromosome painting in Pinnipedia and comparison with non-pinniped carnivore karyotypes provide strong support for refined structure of ACK with 2n = 38. Constructed comparative chromosome maps show that pinniped karyotype evolution was characterized by few tandem fusions, seemingly absent inversions and slow rate of genome rearrangements (less then one rearrangement per 10 million years). Integrative comparative analyses with published chromosome painting of Phoca vitulina revealed common cytogenetic signature for Phoca/Pusa branch and supports Phocidae and Otaroidea (Otariidae/Odobenidae) as sister groups. We revealed rearrangements specific for walrus karyotype and found the chromosomal signature linking together families Otariidae and Odobenidae. The Steller sea lion karyotype is the most conserved among three studied species and differs from the ACK by single fusion. The study underlined the strikingly slow karyotype evolution of the Pinnipedia in general and the Otariidae in particular. PMID:26821159

  17. 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. 

  18. 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

  19. 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.

  20. 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.

  1. Placental expression of pituitary hormones is an ancestral feature of therian mammals

    Directory of Open Access Journals (Sweden)

    Menzies Brandon R

    2011-08-01

    Full Text Available Abstract Background The placenta is essential for supplying nutrients and gases to the developing mammalian young before birth. While all mammals have a functional placenta, only in therian mammals (marsupials and eutherians does the placenta closely appose or invade the uterine endometrium. The eutherian placenta secretes hormones that are structurally and functionally similar to pituitary growth hormone (GH, prolactin (PRL and luteinizing hormone (LH. Marsupial and eutherian mammals diverged from a common ancestor approximately 125 to 148 million years ago and developed distinct reproductive strategies. As in eutherians, marsupials rely on a short-lived but functional placenta for embryogenesis. Results We characterized pituitary GH, GH-R, IGF-2, PRL and LHβ in a macropodid marsupial, the tammar wallaby, Macropus eugenii. These genes were expressed in the tammar placenta during the last third of gestation when most fetal growth occurs and active organogenesis is initiated. The mRNA of key growth genes GH, GH-R, IGF-2 and PRL were expressed during late pregnancy. We found significant up-regulation of GH, GH-R and IGF-2 after the start of the rapid growth phase of organogenesis which suggests that the placental growth hormones regulate the rapid phase of fetal growth. Conclusions This is the first demonstration of the existence of pituitary hormones in the marsupial placenta. Placental expression of these pituitary hormones has clearly been conserved in marsupials as in eutherian mammals, suggesting an ancestral origin of the evolution of placental expression and a critical function of these hormones in growth and development of all therian mammals.

  2. An Ancestral Role for CONSTITUTIVE TRIPLE RESPONSE1 Proteins in Both Ethylene and Abscisic Acid Signaling.

    Science.gov (United States)

    Yasumura, Yuki; Pierik, Ronald; Kelly, Steven; Sakuta, Masaaki; Voesenek, Laurentius A C J; Harberd, Nicholas P

    2015-09-01

    Land plants have evolved adaptive regulatory mechanisms enabling the survival of environmental stresses associated with terrestrial life. Here, we focus on the evolution of the regulatory CONSTITUTIVE TRIPLE RESPONSE1 (CTR1) component of the ethylene signaling pathway that modulates stress-related changes in plant growth and development. First, we compare CTR1-like proteins from a bryophyte, Physcomitrella patens (representative of early divergent land plants), with those of more recently diverged lycophyte and angiosperm species (including Arabidopsis [Arabidopsis thaliana]) and identify a monophyletic CTR1 family. The fully sequenced P. patens genome encodes only a single member of this family (PpCTR1L). Next, we compare the functions of PpCTR1L with that of related angiosperm proteins. We show that, like angiosperm CTR1 proteins (e.g. AtCTR1 of Arabidopsis), PpCTR1L modulates downstream ethylene signaling via direct interaction with ethylene receptors. These functions, therefore, likely predate the divergence of the bryophytes from the land-plant lineage. However, we also show that PpCTR1L unexpectedly has dual functions and additionally modulates abscisic acid (ABA) signaling. In contrast, while AtCTR1 lacks detectable ABA signaling functions, Arabidopsis has during evolution acquired another homolog that is functionally distinct from AtCTR1. In conclusion, the roles of CTR1-related proteins appear to have functionally diversified during land-plant evolution, and angiosperm CTR1-related proteins appear to have lost an ancestral ABA signaling function. Our study provides new insights into how molecular events such as gene duplication and functional differentiation may have contributed to the adaptive evolution of regulatory mechanisms in plants. PMID:26243614

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

    Directory of Open Access Journals (Sweden)

    Coggill Penny

    2006-08-01

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

  4. 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.

  5. 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.

  6. 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.

  7. 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

  8. Bitzer's Model Reconstructed.

    Science.gov (United States)

    Lybarger, Scott; Smith, Craig R.

    1996-01-01

    Reconstructs Lloyd Bitzer's situational model to serve as a guide for the generation of multiperspectival critical assessments of rhetorical discourse. Uses two of President Bush's speeches on the drug crisis to illustrate how the reconstructed model can account for such modern problems as multiple audiences, perceptions, and exigencies. (PA)

  9. The CMS Reconstruction Software

    Science.gov (United States)

    Lange, David J.; CMS Collaboration

    2011-12-01

    We report on the status and plans for the event reconstruction software of the CMS experiment. The CMS reconstruction algorithms are the basis for a wide range of data analysis approaches currently under study by the CMS collaboration using the first high-energy run of the LHC. These algorithms have been primarily developed and validated using simulated data samples, and are now being commissioned with LHC proton-proton collision data samples. The CMS reconstruction is now operated routinely on all events triggered by the CMS detector, both in a close to real-time prompt reconstruction processing and in frequent passes over the full recorded CMS data set. We discuss the overall software design, development cycle, computational requirements and performance, recent operational performance, and planned improvements of the CMS reconstruction software.

  10. 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.

  11. 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

  12. 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

  13. 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

  14. 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

  15. Delayed breast implant reconstruction

    DEFF Research Database (Denmark)

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

    2011-01-01

    -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 the......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...

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

    Energy Technology Data Exchange (ETDEWEB)

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

    2013-06-01

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

  17. 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

  18. 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

  19. Relaxation and edge reconstruction in integer quantum Hall systems

    OpenAIRE

    Karzig, Torsten; Levchenko, Alex; Glazman, Leonid I.; von Oppen, Felix

    2012-01-01

    The interplay between the confinement potential and electron-electron interactions causes reconstructions of Quantum Hall edges. We study the consequences of this edge reconstruction for the relaxation of hot electrons injected into integer quantum Hall edge states. In translationally invariant edges, the relaxation of hot electrons is governed by three-body collisions which are sensitive to the electron dispersion and thus to reconstruction effects. We show that the relaxation rates are sign...

  20. 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

  1. 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...... proteins showed that the lethal temperature for yeast is around 49°C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number...

  2. Surgical Ventricular Reconstruction

    Medline Plus

    Full Text Available SURGICAL VENTRICULAR RECONSTRUCTION MONTEFIORE-EINSTEIN HEART CENTER NEW YORK CITY, NEW YORK February 13, 2008 00:00:09 NARRATOR: Welcome to the Montefiore-Einstein Heart Center in ...

  3. Surgical Ventricular Reconstruction

    Medline Plus

    Full Text Available SURGICAL VENTRICULAR RECONSTRUCTION MONTEFIORE-EINSTEIN HEART CENTER NEW YORK CITY, NEW YORK February 13, 2008 00:00:09 NARRATOR: Welcome to the Montefiore-Einstein Heart Center in New York City. In ...

  4. 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...

  5. 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)

  6. Surgical Ventricular Reconstruction

    Medline Plus

    Full Text Available ... reconstruction. This study is going to be a land…landmark study. And in all likelihood will influence ... improve postoperatively. But, nevertheless, this is an acute change and may take some time for the myocardium ...

  7. Overview of image reconstruction

    International Nuclear Information System (INIS)

    Image reconstruction (or computerized tomography, etc.) is any process whereby a function, f, on R/sup n/ 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

  8. Breast reconstruction - natural tissue

    Science.gov (United States)

    After a mastectomy , some women choose to have cosmetic surgery to remake their breast. This type of surgery ... Risks of anesthesia and surgery are: Reactions to medicines Breathing problems Bleeding, blood clots , or infection Risks of breast reconstruction with ...

  9. Surgical Ventricular Reconstruction

    Medline Plus

    Full Text Available ... a better procedure, the ventricular reconstruction or heart transplantation. This particular viewer actually saw our previous video on heart transplantation. And to answer that question, they are both ...

  10. 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.

  11. Surgical Ventricular Reconstruction

    Medline Plus

    Full Text Available ... He has not been readmitted for any reasons related to heart failure. 00:41:57 ROBERT E. ... question, because it really deals with whether anything related to surgical ventricular reconstruction would add to the ...

  12. 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 ...

  13. 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...

  14. 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...

  15. 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.

  16. 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.

  17. 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

  18. 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…

  19. 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.

  20. Nipple-areola complex reconstruction

    OpenAIRE

    Nimboriboonporn, Anongporn; Chuthapisith, Suebwong

    2014-01-01

    Nipple areolar reconstruction (NAC) was introduced since 1940s and evolved as parallel with breast reconstruction since era of breast cancer treatment. It consists of nipple and areolar reconstruction. Ideal reconstruction of the NAC requires symmetry in position, size, shape, texture, and pigmentation and permanent projection. There are many innovative ways to create a nipple and each method has its unique characteristics that apply to certain breast types. NAC reconstruction techniques comp...

  1. 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.

  2. Alternative reconstruction after pancreaticoduodenectomy

    Directory of Open Access Journals (Sweden)

    Cooperman Avram M

    2008-01-01

    Full Text Available Abstract Background Pancreaticoduodenectomy is the procedure of choice for tumors of the head of the pancreas and periampulla. Despite advances in surgical technique and postoperative care, the procedure continues to carry a high morbidity rate. One of the most common morbidities is delayed gastric emptying with rates of 15%–40%. Following two prolonged cases of delayed gastric emptying, we altered our reconstruction to avoid this complication altogether. Subsequently, our patients underwent a classic pancreaticoduodenectomy with an undivided Roux-en-Y technique for reconstruction. Methods We reviewed the charts of our last 13 Whipple procedures evaluating them for complications, specifically delayed gastric emptying. We compared the outcomes of those patients to a control group of 15 patients who underwent the Whipple procedure with standard reconstruction. Results No instances of delayed gastric emptying occurred in patients who underwent an undivided Roux-en-Y technique for reconstruction. There was 1 wound infection (8%, 1 instance of pneumonia (8%, and 1 instance of bleeding from the gastrojejunal staple line (8%. There was no operative mortality. Conclusion Use of the undivided Roux-en-Y technique for reconstruction following the Whipple procedure may decrease the incidence of delayed gastric emptying. In addition, it has the added benefit of eliminating bile reflux gastritis. Future randomized control trials are recommended to further evaluate the efficacy of the procedure.

  3. Auricular reconstruction for microtia: Part II. Surgical techniques.

    Science.gov (United States)

    Walton, Robert L; Beahm, Elisabeth K

    2002-07-01

    Reconstruction of the microtic ear represents one of the most demanding challenges in reconstructive surgery. In this review the two most commonly used techniques for ear reconstruction, the Brent and Nagata techniques, are addressed in detail. Unique to this endeavor, the originator of each technique has been allowed to submit representative case material and to address the pros and cons of the other's technique. What follows is a detailed, insightful overview of microtia reconstruction, as a state of the art. The review then details commonly encountered problems in ear reconstruction and pertinent technical points. Finally, a glimpse into the future is offered with an accounting of the advances made in tissue engineering as this technology applies to auricular reconstruction. PMID:12087261

  4. Breast Reconstruction with Microvascular

    Directory of Open Access Journals (Sweden)

    David W. Chang

    2012-01-01

    Full Text Available The free muscle-sparing transverse rectus abdominis myocutaneous (MS-TRAM and deepinferior epigastric perforator (DIEP flaps involve transferring skin and subcutaneous tissuefrom the lower abdominal area and have many features that make them well suited forbreast reconstruction. The robust blood supply of the free flap reduces the risk of fat necrosisand also enables aggressive shaping of the flap for breast reconstruction to optimize theaesthetic outcome. In addition, the free MS-TRAM flap and DIEP flap require minimal donorsitesacrifice in most cases. With proper patient selection and safe surgical technique, the freeMS-TRAM flap and DIEP flap can transfer the lower abdominal skin and subcutaneous tissueto provide an aesthetically pleasing breast reconstruction with minimal donor-site morbidity.

  5. Reconstructing random media

    International Nuclear Information System (INIS)

    We formulate a procedure to reconstruct the structure of general random heterogeneous media from limited morphological information by extending the methodology of Rintoul and Torquato [J. Colloid Interface Sci. 186, 467 (1997)] developed for dispersions. The procedure has the advantages that it is simple to implement and generally applicable to multidimensional, multiphase, and anisotropic structures. Furthermore, an extremely useful feature is that it can incorporate any type and number of correlation functions in order to provide as much morphological information as is necessary for accurate reconstruction. We consider a variety of one- and two-dimensional reconstructions, including periodic and random arrays of rods, various distribution of disks, Debye random media, and a Fontainebleau sandstone sample. We also use our algorithm to construct heterogeneous media from specified hypothetical correlation functions, including an exponentially damped, oscillating function as well as physically unrealizable ones. copyright 1998 The American Physical Society

  6. 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.

  7. 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...

  8. Reconstruction of dynamical systems from interspike intervals

    International Nuclear Information System (INIS)

    Attractor reconstruction from interspike interval (ISI) data is described, in rough analogy with Taken's theorem for attractor reconstruction from time series. Assuming a generic integrate-and-fire model coupling the dynamical system to the spike train, there is a one-to-one correspondence between the system states and interspike interval vectors of sufficiently large dimension. The correspondence has an important implication: interspike intervals can be forecast from past history. We show that deterministically driven ISI series can be distinguished from stochastically driven ISI series on the basis of prediction error

  9. 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

  10. 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.

  11. 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...

  12. 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.)

  13. 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

  14. Current Sensor Fault Reconstruction for PMSM Drives.

    Science.gov (United States)

    Huang, Gang; Luo, Yi-Ping; Zhang, Chang-Fan; He, Jing; Huang, Yi-Shan

    2016-01-01

    This paper deals with a current sensor fault reconstruction algorithm for the torque closed-loop drive system of an interior PMSM. First, sensor faults are equated to actuator ones by a new introduced state variable. Then, in αβ coordinates, based on the motor model with active flux linkage, a current observer is constructed with a specific sliding mode equivalent control methodology to eliminate the effects of unknown disturbances, and the phase current sensor faults are reconstructed by means of an adaptive method. Finally, an αβ axis current fault processing module is designed based on the reconstructed value. The feasibility and effectiveness of the proposed method are verified by simulation and experimental tests on the RT-LAB platform. PMID:26840317

  15. Current Sensor Fault Reconstruction for PMSM Drives

    Directory of Open Access Journals (Sweden)

    Gang Huang

    2016-01-01

    Full Text Available This paper deals with a current sensor fault reconstruction algorithm for the torque closed-loop drive system of an interior PMSM. First, sensor faults are equated to actuator ones by a new introduced state variable. Then, in αβ coordinates, based on the motor model with active flux linkage, a current observer is constructed with a specific sliding mode equivalent control methodology to eliminate the effects of unknown disturbances, and the phase current sensor faults are reconstructed by means of an adaptive method. Finally, an αβ axis current fault processing module is designed based on the reconstructed value. The feasibility and effectiveness of the proposed method are verified by simulation and experimental tests on the RT-LAB platform.

  16. 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.

  17. 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.

  18. 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...

  19. An Interpretation of the Ancestral Codon from Miller’s Amino Acids and Nucleotide Correlations in Modern Coding Sequences

    Science.gov (United States)

    Carels, Nicolas; de Leon, Miguel Ponce

    2015-01-01

    Purine bias, which is usually referred to as an “ancestral codon”, is known to result in short-range correlations between nucleotides in coding sequences, and it is common in all species. We demonstrate that RWY is a more appropriate pattern than the classical RNY, and purine bias (Rrr) is the product of a network of nucleotide compensations induced by functional constraints on the physicochemical properties of proteins. Through deductions from universal correlation properties, we also demonstrate that amino acids from Miller’s spark discharge experiment are compatible with functional primeval proteins at the dawn of living cell radiation on earth. These amino acids match the hydropathy and secondary structures of modern proteins. PMID:25922573

  20. Surgical Ventricular Reconstruction

    Medline Plus

    Full Text Available ... VENTRICULAR RECONSTRUCTION MONTEFIORE-EINSTEIN HEART CENTER NEW YORK CITY, NEW YORK February 13, 2008 00:00:09 ... the Montefiore-Einstein Heart Center in New York City. In just moments, you'll see an expert ...

  1. 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

  2. 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].

  3. Stem cell-specific activation of an ancestral myc protooncogene with conserved basic functions in the early metazoan Hydra

    Science.gov (United States)

    Hartl, Markus; Mitterstiller, Anna-Maria; Valovka, Taras; Breuker, Kathrin; Hobmayer, Bert; Bister, Klaus

    2010-01-01

    The c-myc protooncogene encodes a transcription factor (Myc) with oncogenic potential. Myc and its dimerization partner Max are bHLH-Zip DNA binding proteins controlling fundamental cellular processes. Deregulation of c-myc leads to tumorigenesis and is a hallmark of many human cancers. We have identified and extensively characterized ancestral forms of myc and max genes from the early diploblastic cnidarian Hydra, the most primitive metazoan organism employed so far for the structural, functional, and evolutionary analysis of these genes. Hydra myc is specifically activated in all stem cells and nematoblast nests which represent the rapidly proliferating cell types of the interstitial stem cell system and in proliferating gland cells. In terminally differentiated nerve cells, nematocytes, or epithelial cells, myc expression is not detectable by in situ hybridization. Hydra max exhibits a similar expression pattern in interstitial cell clusters. The ancestral Hydra Myc and Max proteins display the principal design of their vertebrate derivatives, with the highest degree of sequence identities confined to the bHLH-Zip domains. Furthermore, the 314-amino acid Hydra Myc protein contains basic forms of the essential Myc boxes I through III. A recombinant Hydra Myc/Max complex binds to the consensus DNA sequence CACGTG with high affinity. Hybrid proteins composed of segments from the retroviral v-Myc oncoprotein and the Hydra Myc protein display oncogenic potential in cell transformation assays. Our results suggest that the principal functions of the Myc master regulator arose very early in metazoan evolution, allowing their dissection in a simple model organism showing regenerative ability but no senescence. PMID:20142507

  4. ¿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.

  5. 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.

  6. Anthropometric study of cephalometric indices among Idoma and Igede ethnic groups of Benue State, Nigeria

    Directory of Open Access Journals (Sweden)

    Obaje S.G

    2015-04-01

    Full Text Available Background: Anthropometric variables are important biometric characteristics that varies with age, sex, and tribe. Aim: Following the paucity of research in cephalometry as subdivisions of biological and forensic anthropology, this study was undertaken due to lack of adequate cephalometry among Nigerians. Methods: Four hundred and twenty five subjects were used for the study of which 158 were Igede and 267 were Idoma with mean age of 22.6, 0.45 and 23.0 0.47 year respectively. The anthropometric variables measured were head length, head width, bizygomatic distance, upper facial length, lower facial length, total facial length, nose width and skull height from which the cephalometric indices were calculated. Result: The result showed that there were statistically significant differences (P<0.05 in some of the measured variables between the Igede and Idoma tribes of Benue State as head length, head width. The result also showed a positive correlation between the head width and bizygomatic distance and other anthropometric variables which could be used to predict cephalic indices among the Igede and Idoma ethnic groups of Benue State, Nigeria. These results showed that the dominant head form among the Idoma and Igede Ethnic groups were mexocephalic respectively. Facial indices showed dominant hypereuriprosopic face. Conclusion: The present study could be used in forensic anthropology, establishing ancestral relationship and reconstructive surgeries of the face, head and neck of the two ethnic groups of Idoma and Igede of Benue State in north-central of Nigeria.

  7. Breast Reconstruction with Tissue Expansion

    Medline Plus

    Full Text Available ... planning to do a left breast reconstruction, so lift up the flaps here and go underneath the ... breast reconstruction. In this case, we would usually lift the skin flap and the pectoralis major muscle ...

  8. 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

  9. 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

  10. Anterior cruciate ligament reconstruction

    International Nuclear Information System (INIS)

    This paper determines the efficacy of MR imaging in evaluation of the anterior cruciate ligament (ACL) following reconstructive surgery. Forty-three MR examinations were performed in 33 patients who had undergone previous arthroscopic ACL reconstruction with patellar bone-tendon- bone autografts (postoperative period, 1-24 months; mean, 5.2 months). Of the 40 studies performed in clinically stable knees (30 patients), MR demonstrated a well-defined, signal void ACL graft in 36. Of the three studies performed in three patients with clinical ACL laxity or suspected tear, the neoligament was of intermediate definition in one and nondiscernible in the other two. As in the native knee, buckling of the PCL was suggestive of ACL insufficiency. Bone tunnel placement, patellar tendon changes, and joint effusions were also evaluated

  11. Stochastic reconstruction of sandstones

    International Nuclear Information System (INIS)

    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. (c) 2000 The American Physical Society

  12. 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. PMID:11088546

  13. Reconstructing the Tengger calendar

    Directory of Open Access Journals (Sweden)

    Ian Proudfoot

    2008-12-01

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

  14. Reconstructing the Tengger calendar

    OpenAIRE

    Ian Proudfoot

    2008-01-01

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

  15. 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 ...

  16. 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.

  17. Stochastic reconstruction of sandstones

    OpenAIRE

    Manwart, C.; Torquato, S.; Hilfer, R.

    2000-01-01

    A simulated annealing algorithm is employed to generate a stochastic model for a Berea and a Fontainebleau sandstone with 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 sandston...

  18. 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...

  19. Reconstruction of vaginal agenesis.

    Science.gov (United States)

    Ozkan, Ozlenen; Erman Akar, Münire; Ozkan, Omer; Doğan, N Utku

    2011-06-01

    Vaginal ageneses are by no means rare anomalies. Complete Mullerian agenesis is the most common reason for vaginal agenesis requiring reconstruction. Patients usually present with pain, hematocolpos, or hematometra in puberty, and later with amenorrhea and dyspareunia. Detailed information is given here regarding etiologies, timing of surgery, and current treatment options for vaginal agenesis. Outcomes and short- and long-term complications of recent treatment options are also discussed. PMID:21372677

  20. 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...

  1. 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

  2. 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. PMID:26973693

  3. 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.

  4. 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.

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

    Science.gov (United States)

    Song, Xiaowei; Tang, Yezhong; Wang, Yajun

    2016-08-22

    The vertebrate FoxP subfamily genes play important roles in the construction of essential functional modules involved in physiological and developmental processes. To explore the adaptive evolution of functional modules associated with the FoxP subfamily member genes, it is necessary to study the gene duplication process. We detected four member genes of the FoxP subfamily in sea lampreys (a representative species of jawless vertebrates) through genome screenings and phylogenetic analyses. Reliable paralogons (i.e. paralogous chromosome segments) have rarely been detected in scaffolds of FoxP subfamily member genes in sea lampreys due to the considerable existence of HTH_Tnp_Tc3_2 transposases. However, these transposases did not alter gene numbers of the FoxP subfamily in sea lampreys. The coincidence between the "1-4" gene duplication pattern of FoxP subfamily genes from invertebrates to vertebrates and two rounds of ancestral whole genome duplication (1R- and 2R-WGD) events reveal that the FoxP subfamily of vertebrates was quadruplicated in the 1R- and 2R-WGD events. Furthermore, we deduced that a synchronous gene duplication process occurred for the FoxP subfamily and for three linked gene families/subfamilies (i.e. MIT family, mGluR group III and PLXNA subfamily) in the 1R- and 2R-WGD events using phylogenetic analyses and mirror-dendrogram methods (i.e. algorithms to test protein-protein interactions). Specifically, the ancestor of FoxP1 and FoxP3 and the ancestor of FoxP2 and FoxP4 were generated in 1R-WGD event. In the subsequent 2R-WGD event, these two ancestral genes were changed into FoxP1, FoxP2, FoxP3 and FoxP4. The elucidation of these gene duplication processes shed light on the phylogenetic relationships between functional modules of the FoxP subfamily member genes. PMID:27188254

  6. Climate Field Reconstruction via Data Assimilation

    Science.gov (United States)

    Steiger, N. J.; Hakim, G. J.; Steig, E. J.; Battisti, D. S.; Roe, G.

    2012-12-01

    We illustrate the utility of a data assimilation (DA) technique in producing climate field reconstructions (CFR) of surface temperature. Our "off-line" DA technique assimilates time-averaged observations with a novel Ensemble Square-root Filter. We perform several pseudoproxy experiments with both general circulation model (GCM) and 20th Century Reanalysis data (20CR). These experiments highlight some advantages of our DA approach with reference to a conventional CFR approach based on Principal Component Analysis. We find important agreements as well as disparities: both approaches reproduce GCM global mean temperature with similar magnitudes and correlation coefficients; DA improves GCM temperature reconstructions around isolated pseudoproxies; DA has much higher correlations in the global mean and in most geographical regions when reconstructing 20CR temperatures. Our results suggest that pseudoproxy experiments which rely solely on GCM data may give a false impression of reconstruction skill. Additionally, we present CFRs with our DA approach based on actual proxy data and discuss the results. While we employ "off-line" DA via the "state-update" step, our DA technique can be extended to "live" climate models.

  7. Wavefront reconstruction using computer-generated holograms

    Science.gov (United States)

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

    2012-02-01

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

  8. Analysis of the 8.1 ancestral MHC haplotype in severe, pneumonia-related sepsis.

    Science.gov (United States)

    Aladzsity, István; Madách, Krisztina; Szilágyi, Agnes; Gál, János; Pénzes, István; Prohászka, Zoltán; Fust, George

    2011-06-01

    The most frequent Caucasian MHC haplotype, AH8.1 - associated with numerous immunopathological differences and certain autoimmune diseases - was recently linked to the delayed onset of bacterial colonization in cystic fibrosis. Based on this observation, we hypothesized that the carriers of AH8.1 have lower risk for a worse outcome in sepsis. AH8.1 carrier state was determined in 207 Caucasian patients with severe, pneumonia-related sepsis. Our data showed that in patients without chronic obstructive pulmonary disease (COPD), septic shock - a serious consequence of the bacterial infection - occurred significantly less frequently (OR=0.3383; 95% CI=0.1141-0.995; p=0.043) in carriers of AH8.1, than in non-carriers. According to the multivariate logistic regression analysis, this haplotype had an independent protective role against septic shock in all patients (OR=0.315; 95% CI=0.100-0.992; p=0.048), particularly in COPD-free patients (OR=0.117; 95% CI=0.025-0.554; p=0.007). These results indicate that AH8.1 may confer protection against the progression of bacterial infection, and this could explain, at least partially, its high frequency in the Caucasian population. PMID:21414845

  9. On Stack Reconstruction Problem

    Directory of Open Access Journals (Sweden)

    V. D. Аkeliev

    2014-06-01

    Full Text Available The paper describes analytical investigations that study relation of fuel combustion regimes with concentration values of sulphur anhydride in flue gases and acid dew point. Coefficients of convective heat transfer at internal and external surfaces of stacks have been determined in the paper. The paper reveals the possibility to reconstruct stacks while using gas discharging channel made of composite material on the basis of glass-reinforced plastic which permits to reduce thermo-stressed actions on reinforced concrete and increase volume of released gases due to practically two-fold reduction of gas-dynamic pressure losses along the pipe length.

  10. Evolutionary tree reconstruction

    Science.gov (United States)

    Cheeseman, Peter; Kanefsky, Bob

    1990-01-01

    It is described how Minimum Description Length (MDL) can be applied to the problem of DNA and protein evolutionary tree reconstruction. If there is a set of mutations that transform a common ancestor into a set of the known sequences, and this description is shorter than the information to encode the known sequences directly, then strong evidence for an evolutionary relationship has been found. A heuristic algorithm is described that searches for the simplest tree (smallest MDL) that finds close to optimal trees on the test data. Various ways of extending the MDL theory to more complex evolutionary relationships are discussed.

  11. Influence of finite spatial coherence on ptychographic reconstruction

    Energy Technology Data Exchange (ETDEWEB)

    Stachnik, K., E-mail: karolina.stachnik@desy.de; Stuebe, N.; Meyer, J.; Warmer, M.; Meents, A. [DESY Photon Science, Deutsches Elektronen-Synchrotron DESY, Notkestr. 85, 22607 Hamburg (Germany); Mohacsi, I.; Vartiainen, I.; David, C. [Paul Scherrer Institut, 5232 Villigen PSI (Switzerland)

    2015-07-06

    X-ray ptychography is an ultrahigh-resolution scanning coherent diffractive imaging technique, allowing quantitative measurements of extended samples and a simultaneous reconstruction of the illuminating wavefront. Recent development of the mixed-state reconstruction algorithm has triggered a certain interest in utilizing partially coherent X-ray sources for ptychography. Here, we study how finite spatial coherence influences the reconstructed image of a test structure. Our work shows that use of a highly coherent illumination provides images with better spatial resolution and fewer artefacts than the approach with partial coherence.

  12. Influence of finite spatial coherence on ptychographic reconstruction

    International Nuclear Information System (INIS)

    X-ray ptychography is an ultrahigh-resolution scanning coherent diffractive imaging technique, allowing quantitative measurements of extended samples and a simultaneous reconstruction of the illuminating wavefront. Recent development of the mixed-state reconstruction algorithm has triggered a certain interest in utilizing partially coherent X-ray sources for ptychography. Here, we study how finite spatial coherence influences the reconstructed image of a test structure. Our work shows that use of a highly coherent illumination provides images with better spatial resolution and fewer artefacts than the approach with partial coherence

  13. 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

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

    CERN Document Server

    Chatrchyan, Serguei; Sirunyan, Albert M; Tumasyan, Armen; Adam, Wolfgang; Bergauer, Thomas; Dragicevic, Marko; Erö, Janos; Fabjan, Christian; Friedl, Markus; Fruehwirth, Rudolf; Ghete, Vasile Mihai; Hammer, Josef; Haensel, Stephan; Hoch, Michael; Hörmann, Natascha; Hrubec, Josef; Jeitler, Manfred; Kiesenhofer, Wolfgang; Krammer, Manfred; Liko, Dietrich; Mikulec, Ivan; Pernicka, Manfred; Rahbaran, Babak; Rohringer, Herbert; Schöfbeck, Robert; Strauss, Josef; Taurok, Anton; Teischinger, Florian; Trauner, Christine; Wagner, Philipp; Waltenberger, Wolfgang; Walzel, Gerhard; Widl, Edmund; Wulz, Claudia-Elisabeth; Mossolov, Vladimir; Shumeiko, Nikolai; Suarez Gonzalez, Juan; Bansal, Sunil; Benucci, Leonardo; De Wolf, Eddi A; Janssen, Xavier; Luyckx, Sten; Maes, Thomas; Mucibello, Luca; Ochesanu, Silvia; Roland, Benoit; Rougny, Romain; Selvaggi, Michele; Van Haevermaet, Hans; Van Mechelen, Pierre; Van Remortel, Nick; Blekman, Freya; Blyweert, Stijn; D'Hondt, Jorgen; Gonzalez Suarez, Rebeca; Kalogeropoulos, Alexis; Maes, Michael; Olbrechts, Annik; Van Doninck, Walter; Van Mulders, Petra; Van Onsem, Gerrit Patrick; Villella, Ilaria; Charaf, Otman; Clerbaux, Barbara; De Lentdecker, Gilles; Dero, Vincent; Gay, Arnaud; Hammad, Gregory Habib; Hreus, Tomas; Marage, Pierre Edouard; Raval, Amita; Thomas, Laurent; Vander Marcken, Gil; Vander Velde, Catherine; Vanlaer, Pascal; Adler, Volker; Cimmino, Anna; Costantini, Silvia; Grunewald, Martin; Klein, Benjamin; Lellouch, Jérémie; Marinov, Andrey; Mccartin, Joseph; Ryckbosch, Dirk; Thyssen, Filip; Tytgat, Michael; Vanelderen, Lukas; Verwilligen, Piet; Walsh, Sinead; Zaganidis, Nicolas; Basegmez, Suzan; Bruno, Giacomo; Caudron, Julien; Ceard, Ludivine; Cortina Gil, Eduardo; De Favereau De Jeneret, Jerome; Delaere, Christophe; Favart, Denis; Giammanco, Andrea; Grégoire, Ghislain; Hollar, Jonathan; Lemaitre, Vincent; Liao, Junhui; Militaru, Otilia; Nuttens, Claude; Ovyn, Severine; Pagano, Davide; Pin, Arnaud; Piotrzkowski, Krzysztof; Schul, Nicolas; Beliy, Nikita; Caebergs, Thierry; Daubie, Evelyne; Alves, Gilvan; Brito, Lucas; De Jesus Damiao, Dilson; Pol, Maria Elena; Henrique Gomes E Souza, Moacyr; Aldá Júnior, Walter Luiz; Carvalho, Wagner; Da Costa, Eliza Melo; De Oliveira Martins, Carley; Fonseca De Souza, Sandro; Matos Figueiredo, Diego; Mundim, Luiz; Nogima, Helio; Oguri, Vitor; Prado Da Silva, Wanda Lucia; Santoro, Alberto; Silva Do Amaral, Sheila Mara; Sznajder, Andre; Souza Dos Anjos, Tiago; Bernardes, Cesar Augusto; De Almeida Dias, Flavia; Tomei, Thiago; De Moraes Gregores, Eduardo; Lagana, Caio; Da Cunha Marinho, Franciole; Mercadante, Pedro G; Novaes, Sergio F; Padula, Sandra; Darmenov, Nikolay; Genchev, Vladimir; Iaydjiev, Plamen; Piperov, Stefan; Rodozov, Mircho; Stoykova, Stefka; Sultanov, Georgi; Tcholakov, Vanio; Trayanov, Rumen; Vutova, Mariana; Dimitrov, Anton; Hadjiiska, Roumyana; Karadzhinova, Aneliya; Kozhuharov, Venelin; Litov, Leander; Mateev, Matey; Pavlov, Borislav; Petkov, Peicho; Bian, Jian-Guo; Chen, Guo-Ming; Chen, He-Sheng; Jiang, Chun-Hua; Liang, Dong; Liang, Song; Meng, Xiangwei; Tao, Junquan; Wang, Jian; Wang, Jian; Wang, Xianyou; Wang, Zheng; Xiao, Hong; Xu, Ming; Zang, Jingjing; Zhang, Zhen; Ban, Yong; Guo, Shuang; Guo, Yifei; Li, Wenbo; Mao, Yajun; Qian, Si-Jin; Teng, Haiyun; Zhu, Bo; Zou, Wei; Cabrera, Andrés; Gomez Moreno, Bernardo; Ocampo Rios, Alberto Andres; Osorio Oliveros, Andres Felipe; Sanabria, Juan Carlos; Godinovic, Nikola; Lelas, Damir; Lelas, Karlo; Plestina, Roko; Polic, Dunja; Puljak, Ivica; Antunovic, Zeljko; Dzelalija, Mile; Kovac, Marko; Brigljevic, Vuko; Duric, Senka; Kadija, Kreso; Luetic, Jelena; Morovic, Srecko; Attikis, Alexandros; Galanti, Mario; Mousa, Jehad; Nicolaou, Charalambos; Ptochos, Fotios; Razis, Panos A; Finger, Miroslav; Finger Jr, Michael; Assran, Yasser; Ellithi Kamel, Ali; Khalil, Shaaban; Mahmoud, Mohammed; Radi, Amr; Hektor, Andi; Kadastik, Mario; Müntel, Mait; Raidal, Martti; Rebane, Liis; Tiko, Andres; Azzolini, Virginia; Eerola, Paula; Fedi, Giacomo; Voutilainen, Mikko; Czellar, Sandor; Härkönen, Jaakko; Heikkinen, Mika Aatos; Karimäki, Veikko; Kinnunen, Ritva; Kortelainen, Matti J; Lampén, Tapio; Lassila-Perini, Kati; Lehti, Sami; Lindén, Tomas; Luukka, Panja-Riina; Mäenpää, Teppo; Tuominen, Eija; Tuominiemi, Jorma; Tuovinen, Esa; Ungaro, Donatella; Wendland, Lauri; Banzuzi, Kukka; Karjalainen, Ahti; Korpela, Arja; Tuuva, Tuure; Sillou, Daniel; Besancon, Marc; Choudhury, Somnath; Dejardin, Marc; Denegri, Daniel; Fabbro, Bernard; Faure, Jean-Louis; Ferri, Federico; Ganjour, Serguei; Givernaud, Alain; Gras, Philippe; Hamel de Monchenault, Gautier; Jarry, Patrick; Locci, Elizabeth; Malcles, Julie; Marionneau, Matthieu; Millischer, Laurent; Rander, John; Rosowsky, André; Shreyber, Irina; Titov, Maksym; Baffioni, Stephanie; Beaudette, Florian; Benhabib, Lamia; Bianchini, Lorenzo; Bluj, Michal; Broutin, Clementine; Busson, Philippe; Charlot, Claude; Dahms, Torsten; Dobrzynski, Ludwik; Elgammal, Sherif; Granier de Cassagnac, Raphael; Haguenauer, Maurice; Miné, Philippe; Mironov, Camelia; Ochando, Christophe; Paganini, Pascal; Sabes, David; Salerno, Roberto; Sirois, Yves; Thiebaux, Christophe; Veelken, Christian; Zabi, Alexandre; Agram, Jean-Laurent; Andrea, Jeremy; Bloch, Daniel; Bodin, David; Brom, Jean-Marie; Cardaci, Marco; Chabert, Eric Christian; Collard, Caroline; Conte, Eric; Drouhin, Frédéric; Ferro, Cristina; Fontaine, Jean-Charles; Gelé, Denis; Goerlach, Ulrich; Greder, Sebastien; Juillot, Pierre; Karim, Mehdi; Le Bihan, Anne-Catherine; Mikami, Yoshinari; Van Hove, Pierre; Fassi, Farida; Mercier, Damien; Baty, Clement; Beauceron, Stephanie; Beaupere, Nicolas; Bedjidian, Marc; Bondu, Olivier; Boudoul, Gaelle; Boumediene, Djamel; Brun, Hugues; Chasserat, Julien; Chierici, Roberto; Contardo, Didier; Depasse, Pierre; El Mamouni, Houmani; Fay, Jean; Gascon, Susan; Ille, Bernard; Kurca, Tibor; Le Grand, Thomas; Lethuillier, Morgan; Mirabito, Laurent; Perries, Stephane; Sordini, Viola; Tosi, Silvano; Tschudi, Yohann; Verdier, Patrice; Viret, Sébastien; Lomidze, David; Anagnostou, Georgios; Beranek, Sarah; Edelhoff, Matthias; Feld, Lutz; Heracleous, Natalie; Hindrichs, Otto; Jussen, Ruediger; Klein, Katja; Merz, Jennifer; Mohr, Niklas; Ostapchuk, Andrey; Perieanu, Adrian; Raupach, Frank; Sammet, Jan; Schael, Stefan; Sprenger, Daniel; Weber, Hendrik; Weber, Martin; Wittmer, Bruno; Zhukov, Valery; Ata, Metin; Dietz-Laursonn, Erik; Erdmann, Martin; Hebbeker, Thomas; Heidemann, Carsten; Hinzmann, Andreas; Hoepfner, Kerstin; Klimkovich, Tatsiana; Klingebiel, Dennis; Kreuzer, Peter; Lanske, Dankfried; Lingemann, Joschka; Magass, Carsten; Merschmeyer, Markus; Meyer, Arnd; Papacz, Paul; Pieta, Holger; Reithler, Hans; Schmitz, Stefan Antonius; Sonnenschein, Lars; Steggemann, Jan; Teyssier, Daniel; Bontenackels, Michael; Cherepanov, Vladimir; Davids, Martina; Flügge, Günter; Geenen, Heiko; Giffels, Manuel; Haj Ahmad, Wael; Hoehle, Felix; Kargoll, Bastian; Kress, Thomas; Kuessel, Yvonne; Linn, Alexander; Nowack, Andreas; Perchalla, Lars; Pooth, Oliver; Rennefeld, Jörg; Sauerland, Philip; Stahl, Achim; Tornier, Daiske; Zoeller, Marc Henning; Aldaya Martin, Maria; Behrenhoff, Wolf; Behrens, Ulf; Bergholz, Matthias; Bethani, Agni; Borras, Kerstin; Cakir, Altan; Campbell, Alan; Castro, Elena; Dammann, Dirk; Eckerlin, Guenter; Eckstein, Doris; Flossdorf, Alexander; Flucke, Gero; Geiser, Achim; Hauk, Johannes; Jung, Hannes; Kasemann, Matthias; Katsas, Panagiotis; Kleinwort, Claus; Kluge, Hannelies; Knutsson, Albert; Krämer, Mira; Krücker, Dirk; Kuznetsova, Ekaterina; Lange, Wolfgang; Lohmann, Wolfgang; Lutz, Benjamin; Mankel, Rainer; Marienfeld, Markus; Melzer-Pellmann, Isabell-Alissandra; Meyer, Andreas Bernhard; Mnich, Joachim; Mussgiller, Andreas; Olzem, Jan; Petrukhin, Alexey; Pitzl, Daniel; Raspereza, Alexei; Rosin, Michele; Schmidt, Ringo; Schoerner-Sadenius, Thomas; Sen, Niladri; Spiridonov, Alexander; Stein, Matthias; Tomaszewska, Justyna; Walsh, Roberval; Wissing, Christoph; Autermann, Christian; Blobel, Volker; Bobrovskyi, Sergei; Draeger, Jula; Enderle, Holger; Gebbert, Ulla; Görner, Martin; Hermanns, Thomas; Kaschube, Kolja; Kaussen, Gordon; Kirschenmann, Henning; Klanner, Robert; Lange, Jörn; Mura, Benedikt; Naumann-Emme, Sebastian; Nowak, Friederike; Pietsch, Niklas; Sander, Christian; Schettler, Hannes; Schleper, Peter; Schlieckau, Eike; Schröder, Matthias; Schum, Torben; Stadie, Hartmut; Steinbrück, Georg; Thomsen, Jan; Barth, Christian; Bauer, Julia; Berger, Joram; Buege, Volker; Chwalek, Thorsten; De Boer, Wim; Dierlamm, Alexander; Dirkes, Guido; Feindt, Michael; Gruschke, Jasmin; Hackstein, Christoph; Hartmann, Frank; Heinrich, Michael; Held, Hauke; Hoffmann, Karl-Heinz; Honc, Simon; Katkov, Igor; Komaragiri, Jyothsna Rani; Kuhr, Thomas; Martschei, Daniel; Mueller, Steffen; Müller, Thomas; Niegel, Martin; Oberst, Oliver; Oehler, Andreas; Ott, Jochen; Peiffer, Thomas; Quast, Gunter; Rabbertz, Klaus; Ratnikov, Fedor; Ratnikova, Natalia; Renz, Manuel; Röcker, Steffen; Saout, Christophe; Scheurer, Armin; Schieferdecker, Philipp; Schilling, Frank-Peter; Schmanau, Mike; Schott, Gregory; Simonis, Hans-Jürgen; Stober, Fred-Markus Helmut; Troendle, Daniel; Wagner-Kuhr, Jeannine; Weiler, Thomas; Zeise, Manuel; Ziebarth, Eva Barbara; Daskalakis, Georgios; Geralis, Theodoros; Kesisoglou, Stilianos; Kyriakis, Aristotelis; Loukas, Demetrios; Manolakos, Ioannis; Markou, Athanasios; Markou, Christos; Mavrommatis, Charalampos; Ntomari, Eleni; Petrakou, Eleni; Gouskos, Loukas; Mertzimekis, Theodoros; Panagiotou, Apostolos; Saoulidou, Niki; Stiliaris, Efstathios; Evangelou, Ioannis; Foudas, Costas; Kokkas, Panagiotis; Manthos, Nikolaos; Papadopoulos, Ioannis; Patras, Vaios; Triantis, Frixos A; Aranyi, Attila; Bencze, Gyorgy; Boldizsar, Laszlo; Hajdu, Csaba; Hidas, Pàl; Horvath, Dezso; Kapusi, Anita; Krajczar, Krisztian; Sikler, Ferenc; Veres, Gabor Istvan; Vesztergombi, Gyorgy; Beni, Noemi; Molnar, Jozsef; Palinkas, Jozsef; Szillasi, Zoltan; Veszpremi, Viktor; Karancsi, János; Raics, Peter; Trocsanyi, Zoltan Laszlo; Ujvari, Balazs; Beri, Suman Bala; Bhatnagar, Vipin; Dhingra, Nitish; Gupta, Ruchi; Jindal, Monika; Kaur, Manjit; Kohli, Jatinder Mohan; Mehta, Manuk Zubin; Nishu, Nishu; Saini, Lovedeep Kaur; Sharma, Archana; Singh, Anil; Singh, Jasbir; Singh, Supreet Pal; Ahuja, Sudha; Choudhary, Brajesh C; Gupta, Pooja; Kumar, Ashok; Kumar, Arun; Malhotra, Shivali; Naimuddin, Md; Ranjan, Kirti; Shivpuri, Ram Krishen; Banerjee, Sunanda; Bhattacharya, Satyaki; Dutta, Suchandra; Gomber, Bhawna; Jain, Sandhya; Jain, Shilpi; Khurana, Raman; Sarkar, Subir; Choudhury, Rajani Kant; Dutta, Dipanwita; Kailas, Swaminathan; Kumar, Vineet; Mehta, Pourus; Mohanty, Ajit Kumar; Pant, Lalit Mohan; Shukla, Prashant; Aziz, Tariq; Guchait, Monoranjan; Gurtu, Atul; Maity, Manas; Majumder, Devdatta; Majumder, Gobinda; Mathew, Thomas; Mazumdar, Kajari; Mohanty, Gagan Bihari; Parida, Bibhuti; Saha, Anirban; Sudhakar, Katta; Wickramage, Nadeesha; Banerjee, Sudeshna; Dugad, Shashikant; Mondal, Naba Kumar; Arfaei, Hessamaddin; Bakhshiansohi, Hamed; Etesami, Seyed Mohsen; Fahim, Ali; Hashemi, Majid; Hesari, Hoda; Jafari, Abideh; Khakzad, Mohsen; Mohammadi, Abdollah; Mohammadi Najafabadi, Mojtaba; Paktinat Mehdiabadi, Saeid; Safarzadeh, Batool; Zeinali, Maryam; Abbrescia, Marcello; Barbone, Lucia; Calabria, Cesare; Colaleo, Anna; Creanza, Donato; De Filippis, Nicola; De Palma, Mauro; Fiore, Luigi; Iaselli, Giuseppe; Lusito, Letizia; Maggi, Giorgio; Maggi, Marcello; Manna, Norman; Marangelli, Bartolomeo; My, Salvatore; Nuzzo, Salvatore; Pacifico, Nicola; Pierro, Giuseppe Antonio; Pompili, Alexis; Pugliese, Gabriella; Romano, Francesco; Roselli, Giuseppe; Selvaggi, Giovanna; Silvestris, Lucia; Trentadue, Raffaello; Tupputi, Salvatore; Zito, Giuseppe; Abbiendi, Giovanni; Benvenuti, Alberto; Bonacorsi, Daniele; Braibant-Giacomelli, Sylvie; Brigliadori, Luca; Capiluppi, Paolo; Castro, Andrea; Cavallo, Francesca Romana; Cuffiani, Marco; Dallavalle, Gaetano-Marco; Fabbri, Fabrizio; Fanfani, Alessandra; Fasanella, Daniele; Giacomelli, Paolo; Giunta, Marina; Grandi, Claudio; Marcellini, Stefano; Masetti, Gianni; Meneghelli, Marco; Montanari, Alessandro; Navarria, Francesco; Odorici, Fabrizio; Perrotta, Andrea; Primavera, Federica; Rossi, Antonio; Rovelli, Tiziano; Siroli, Gianni; Travaglini, Riccardo; Albergo, Sebastiano; Cappello, Gigi; Chiorboli, Massimiliano; Costa, Salvatore; Potenza, Renato; Tricomi, Alessia; Tuve, Cristina; Barbagli, Giuseppe; Ciulli, Vitaliano; Civinini, Carlo; D'Alessandro, Raffaello; Focardi, Ettore; Frosali, Simone; Gallo, Elisabetta; Gonzi, Sandro; Meschini, Marco; Paoletti, Simone; Sguazzoni, Giacomo; Tropiano, Antonio; Benussi, Luigi; Bianco, Stefano; Colafranceschi, Stefano; Fabbri, Franco; Piccolo, Davide; Fabbricatore, Pasquale; Musenich, Riccardo; Benaglia, Andrea; De Guio, Federico; Di Matteo, Leonardo; Gennai, Simone; Ghezzi, Alessio; Malvezzi, Sandra; Martelli, Arabella; Massironi, Andrea; Menasce, Dario; Moroni, Luigi; Paganoni, Marco; Pedrini, Daniele; Ragazzi, Stefano; Redaelli, Nicola; Sala, Silvano; Tabarelli de Fatis, Tommaso; Buontempo, Salvatore; Carrillo Montoya, Camilo Andres; Cavallo, Nicola; De Cosa, Annapaola; Fabozzi, Francesco; Iorio, Alberto Orso Maria; Lista, Luca; Merola, Mario; Paolucci, Pierluigi; Azzi, Patrizia; Bacchetta, Nicola; Bellan, Paolo; Bisello, Dario; Branca, Antonio; Carlin, Roberto; Checchia, Paolo; Dorigo, Tommaso; Dosselli, Umberto; Fanzago, Federica; Gasparini, Fabrizio; Gasparini, Ugo; Gozzelino, Andrea; Lacaprara, Stefano; Lazzizzera, Ignazio; Margoni, Martino; Mazzucato, Mirco; Meneguzzo, Anna Teresa; Nespolo, Massimo; Perrozzi, Luca; Pozzobon, Nicola; Ronchese, Paolo; Simonetto, Franco; Torassa, Ezio; Tosi, Mia; Vanini, Sara; Zotto, Pierluigi; Zumerle, Gianni; Baesso, Paolo; Berzano, Umberto; Ratti, Sergio P; Riccardi, Cristina; Torre, Paola; Vitulo, Paolo; Viviani, Claudio; Biasini, Maurizio; Bilei, Gian Mario; Caponeri, Benedetta; Fanò, Livio; Lariccia, Paolo; Lucaroni, Andrea; Mantovani, Giancarlo; Menichelli, Mauro; Nappi, Aniello; Romeo, Francesco; Santocchia, Attilio; Taroni, Silvia; Valdata, Marisa; Azzurri, Paolo; Bagliesi, Giuseppe; Bernardini, Jacopo; Boccali, Tommaso; Broccolo, Giuseppe; Castaldi, Rino; D'Agnolo, Raffaele Tito; Dell'Orso, Roberto; Fiori, Francesco; Foà, Lorenzo; Giassi, Alessandro; Kraan, Aafke; Ligabue, Franco; Lomtadze, Teimuraz; Martini, Luca; Messineo, Alberto; Palla, Fabrizio; Palmonari, Francesco; Segneri, Gabriele; Serban, Alin Titus; Spagnolo, Paolo; Tenchini, Roberto; Tonelli, Guido; Venturi, Andrea; Verdini, Piero Giorgio; Barone, Luciano; Cavallari, Francesca; Del Re, Daniele; Di Marco, Emanuele; Diemoz, Marcella; Franci, Daniele; Grassi, Marco; Longo, Egidio; Meridiani, Paolo; Nourbakhsh, Shervin; Organtini, Giovanni; Pandolfi, Francesco; Paramatti, Riccardo; Rahatlou, Shahram; Sigamani, Michael; Amapane, Nicola; Arcidiacono, Roberta; Argiro, Stefano; Arneodo, Michele; Biino, Cristina; Botta, Cristina; Cartiglia, Nicolo; Castello, Roberto; Costa, Marco; Demaria, Natale; Graziano, Alberto; Mariotti, Chiara; Maselli, Silvia; Migliore, Ernesto; Monaco, Vincenzo; Musich, Marco; Obertino, Maria Margherita; Pastrone, Nadia; Pelliccioni, Mario; Potenza, Alberto; Romero, Alessandra; Ruspa, Marta; Sacchi, Roberto; Sola, Valentina; Solano, Ada; Staiano, Amedeo; Vilela Pereira, Antonio; Belforte, Stefano; Cossutti, Fabio; Della Ricca, Giuseppe; Gobbo, Benigno; Marone, Matteo; Montanino, Damiana; Penzo, Aldo; Heo, Seong Gu; Nam, Soon-Kwon; Chang, Sunghyun; Chung, Jin Hyuk; Kim, Dong Hee; Kim, Gui Nyun; Kim, Ji Eun; Kong, Dae Jung; Park, Hyangkyu; Ro, Sang-Ryul; Son, Dong-Chul; Son, Taejin; Kim, Jae Yool; Kim, Zero Jaeho; Song, Sanghyeon; Jo, Hyun Yong; Choi, Suyong; Gyun, Dooyeon; Hong, Byung-Sik; Jo, Mihee; Kim, Hyunchul; Kim, Ji Hyun; Kim, Tae Jeong; Lee, Kyong Sei; Moon, Dong Ho; Park, Sung Keun; Seo, Eunsung; Sim, Kwang Souk; Choi, Minkyoo; Kang, Seokon; Kim, Hyunyong; Park, Chawon; Park, Inkyu; Park, Sangnam; Ryu, Geonmo; Cho, Yongjin; Choi, Young-Il; Choi, Young Kyu; Goh, Junghwan; Kim, Min Suk; Lee, Byounghoon; Lee, Jongseok; Lee, Sungeun; Seo, Hyunkwan; Yu, Intae; Bilinskas, Mykolas Jurgis; Grigelionis, Ignas; Janulis, Mindaugas; Martisiute, Dalia; Petrov, Pavel; Polujanskas, Mindaugas; Sabonis, Tomas; Castilla-Valdez, Heriberto; De La Cruz-Burelo, Eduard; Heredia-de La Cruz, Ivan; Lopez-Fernandez, Ricardo; Magaña Villalba, Ricardo; Martínez-Ortega, Jorge; Sánchez-Hernández, Alberto; Villasenor-Cendejas, Luis Manuel; Carrillo Moreno, Salvador; Vazquez Valencia, Fabiola; Salazar Ibarguen, Humberto Antonio; Casimiro Linares, Edgar; Morelos Pineda, Antonio; Reyes-Santos, Marco A; Krofcheck, David; Tam, Jason; Butler, Philip H; Doesburg, Robert; Silverwood, Hamish; Ahmad, Muhammad; Ahmed, Ijaz; Ansari, Muhammad Hamid; Asghar, Muhammad Irfan; Hoorani, Hafeez R; Khalid, Shoaib; Khan, Wajid Ali; Khurshid, Taimoor; Qazi, Shamona; Shah, Mehar Ali; Shoaib, Muhammad; Brona, Grzegorz; Cwiok, Mikolaj; Dominik, Wojciech; Doroba, Krzysztof; Kalinowski, Artur; Konecki, Marcin; Krolikowski, Jan; Frueboes, Tomasz; Gokieli, Ryszard; Górski, Maciej; Kazana, Malgorzata; Nawrocki, Krzysztof; Romanowska-Rybinska, Katarzyna; Szleper, Michal; Wrochna, Grzegorz; Zalewski, Piotr; Almeida, Nuno; Bargassa, Pedrame; David Tinoco Mendes, Andre; Faccioli, Pietro; Ferreira Parracho, Pedro Guilherme; Gallinaro, Michele; Musella, Pasquale; Nayak, Aruna; Pela, Joao; Ribeiro, Pedro Quinaz; Seixas, Joao; Varela, Joao; Afanasiev, Serguei; Belotelov, Ivan; Bunin, Pavel; Gavrilenko, Mikhail; Golutvin, Igor; Kamenev, Alexey; Karjavin, Vladimir; Kozlov, Guennady; Lanev, Alexander; Moisenz, Petr; Palichik, Vladimir; Perelygin, Victor; Shmatov, Sergey; Smirnov, Vitaly; Volodko, Anton; Zarubin, Anatoli; Golovtsov, Victor; Ivanov, Yury; Kim, Victor; Levchenko, Petr; Murzin, Victor; Oreshkin, Vadim; Smirnov, Igor; Sulimov, Valentin; Uvarov, Lev; Vavilov, Sergey; Vorobyev, Alexey; Vorobyev, Andrey; Andreev, Yuri; Dermenev, Alexander; Gninenko, Sergei; Golubev, Nikolai; Kirsanov, Mikhail; Krasnikov, Nikolai; Matveev, Viktor; Pashenkov, Anatoli; Toropin, Alexander; Troitsky, Sergey; Epshteyn, Vladimir; Erofeeva, Maria; Gavrilov, Vladimir; Kaftanov, Vitali; Kossov, Mikhail; Krokhotin, Andrey; Lychkovskaya, Natalia; Popov, Vladimir; Safronov, Grigory; Semenov, Sergey; Stolin, Viatcheslav; Vlasov, Evgueni; Zhokin, Alexander; Belyaev, Andrey; Boos, Edouard; Dubinin, Mikhail; Dudko, Lev; Ershov, Alexander; Gribushin, Andrey; Kodolova, Olga; Lokhtin, Igor; Markina, Anastasia; Obraztsov, Stepan; Perfilov, Maxim; Petrushanko, Sergey; Sarycheva, Ludmila; Savrin, Viktor; Snigirev, Alexander; Andreev, Vladimir; Azarkin, Maksim; Dremin, Igor; Kirakosyan, Martin; Leonidov, Andrey; Mesyats, Gennady; Rusakov, Sergey V; Vinogradov, Alexey; Azhgirey, Igor; Bayshev, Igor; Bitioukov, Sergei; Grishin, Viatcheslav; Kachanov, Vassili; Konstantinov, Dmitri; Korablev, Andrey; Krychkine, Victor; Petrov, Vladimir; Ryutin, Roman; Sobol, Andrei; Tourtchanovitch, Leonid; Troshin, Sergey; Tyurin, Nikolay; Uzunian, Andrey; Volkov, Alexey; Adzic, Petar; Djordjevic, Milos; Krpic, Dragomir; Milosevic, Jovan; Aguilar-Benitez, Manuel; Alcaraz Maestre, Juan; Arce, Pedro; Battilana, Carlo; Calvo, Enrique; Cerrada, Marcos; Chamizo Llatas, Maria; Colino, Nicanor; De La Cruz, Begona; Delgado Peris, Antonio; Diez Pardos, Carmen; Domínguez Vázquez, Daniel; Fernandez Bedoya, Cristina; Fernández Ramos, Juan Pablo; Ferrando, Antonio; Flix, Jose; Fouz, Maria Cruz; Garcia-Abia, Pablo; Gonzalez Lopez, Oscar; Goy Lopez, Silvia; Hernandez, Jose M; Josa, Maria Isabel; Merino, Gonzalo; Puerta Pelayo, Jesus; Redondo, Ignacio; Romero, Luciano; Santaolalla, Javier; Soares, Mara Senghi; Willmott, Carlos; Albajar, Carmen; Codispoti, Giuseppe; de Trocóniz, Jorge F; Cuevas, Javier; Fernandez Menendez, Javier; Folgueras, Santiago; Gonzalez Caballero, Isidro; Lloret Iglesias, Lara; Vizan Garcia, Jesus Manuel; Brochero Cifuentes, Javier Andres; Cabrillo, Iban Jose; Calderon, Alicia; Chuang, Shan-Huei; Duarte Campderros, Jordi; Felcini, Marta; Fernandez, Marcos; Gomez, Gervasio; Gonzalez Sanchez, Javier; Jorda, Clara; Lobelle Pardo, Patricia; Lopez Virto, Amparo; Marco, Jesus; Marco, Rafael; Martinez Rivero, Celso; Matorras, Francisco; Munoz Sanchez, Francisca Javiela; Piedra Gomez, Jonatan; Rodrigo, Teresa; Rodríguez-Marrero, Ana Yaiza; Ruiz-Jimeno, Alberto; Scodellaro, Luca; Sobron Sanudo, Mar; Vila, Ivan; Vilar Cortabitarte, Rocio; Abbaneo, Duccio; Auffray, Etiennette; Auzinger, Georg; Baillon, Paul; Ball, Austin; Barney, David; Bell, Alan James; Benedetti, Daniele; Bernet, Colin; Bialas, Wojciech; Bloch, Philippe; Bocci, Andrea; Bolognesi, Sara; Bona, Marcella; Breuker, Horst; Bunkowski, Karol; Camporesi, Tiziano; Cerminara, Gianluca; Christiansen, Tim; Coarasa Perez, Jose Antonio; Curé, Benoît; D'Enterria, David; De Roeck, Albert; Di Guida, Salvatore; Dupont-Sagorin, Niels; Elliott-Peisert, Anna; Frisch, Benjamin; Funk, Wolfgang; Gaddi, Andrea; Georgiou, Georgios; Gerwig, Hubert; Gigi, Dominique; Gill, Karl; Giordano, Domenico; Glege, Frank; Gomez-Reino Garrido, Robert; Gouzevitch, Maxime; Govoni, Pietro; Gowdy, Stephen; Guida, Roberto; Guiducci, Luigi; Hansen, Magnus; Hartl, Christian; Harvey, John; Hegeman, Jeroen; Hegner, Benedikt; Hoffmann, Hans Falk; Innocente, Vincenzo; Janot, Patrick; Kaadze, Ketino; Karavakis, Edward; Lecoq, Paul; Lenzi, Piergiulio; Lourenco, Carlos; Maki, Tuula; Malberti, Martina; Malgeri, Luca; Mannelli, Marcello; Masetti, Lorenzo; Maurisset, Aurelie; Mavromanolakis, Georgios; Meijers, Frans; Mersi, Stefano; Meschi, Emilio; Moser, Roland; Mozer, Matthias Ulrich; Mulders, Martijn; Nesvold, Erik; Nguyen, Matthew; Orimoto, Toyoko; Orsini, Luciano; Palencia Cortezon, Enrique; Perez, Emmanuelle; Petrilli, Achille; Pfeiffer, Andreas; Pierini, Maurizio; Pimiä, Martti; Piparo, Danilo; Polese, Giovanni; Quertenmont, Loic; Racz, Attila; Reece, William; Rodrigues Antunes, Joao; Rolandi, Gigi; Rommerskirchen, Tanja; Rovelli, Chiara; Rovere, Marco; Sakulin, Hannes; Schäfer, Christoph; Schwick, Christoph; Segoni, Ilaria; Sharma, Archana; Siegrist, Patrice; Silva, Pedro; Simon, Michal; Sphicas, Paraskevas; Spiga, Daniele; Spiropulu, Maria; Stoye, Markus; Tsirou, Andromachi; Vichoudis, Paschalis; Wöhri, Hermine Katharina; Worm, Steven; Zeuner, Wolfram Dietrich; Bertl, Willi; Deiters, Konrad; Erdmann, Wolfram; Gabathuler, Kurt; Horisberger, Roland; Ingram, Quentin; Kaestli, Hans-Christian; König, Stefan; Kotlinski, Danek; Langenegger, Urs; Meier, Frank; Renker, Dieter; Rohe, Tilman; Sibille, Jennifer; Bäni, Lukas; Bortignon, Pierluigi; Caminada, Lea; Casal, Bruno; Chanon, Nicolas; Chen, Zhiling; Cittolin, Sergio; Dissertori, Günther; Dittmar, Michael; Eugster, Jürg; Freudenreich, Klaus; Grab, Christoph; Hintz, Wieland; Lecomte, Pierre; Lustermann, Werner; Marchica, Carmelo; Martinez Ruiz del Arbol, Pablo; Milenovic, Predrag; Moortgat, Filip; Nägeli, Christoph; Nef, Pascal; Nessi-Tedaldi, Francesca; Pape, Luc; Pauss, Felicitas; Punz, Thomas; Rizzi, Andrea; Ronga, Frederic Jean; Rossini, Marco; Sala, Leonardo; Sanchez, Ann - Karin; Sawley, Marie-Christine; Starodumov, Andrei; Stieger, Benjamin; Takahashi, Maiko; Tauscher, Ludwig; Thea, Alessandro; Theofilatos, Konstantinos; Treille, Daniel; Urscheler, Christina; Wallny, Rainer; Weber, Matthias; Wehrli, Lukas; Weng, Joanna; Aguilo, Ernest; Amsler, Claude; Chiochia, Vincenzo; De Visscher, Simon; Favaro, Carlotta; Ivova Rikova, Mirena; Jaeger, Andreas; Millan Mejias, Barbara; Otiougova, Polina; Robmann, Peter; Schmidt, Alexander; Snoek, Hella; Chang, Yuan-Hann; Chen, Kuan-Hsin; Kuo, Chia-Ming; Li, Syue-Wei; Lin, Willis; Liu, Zong-Kai; Lu, Yun-Ju; Mekterovic, Darko; Volpe, Roberta; Yu, Shin-Shan; Bartalini, Paolo; Chang, Paoti; Chang, You-Hao; Chang, Yu-Wei; Chao, Yuan; Chen, Kai-Feng; Dietz, Charles; Grundler, Ulysses; Hou, George Wei-Shu; Hsiung, Yee; Kao, Kai-Yi; Lei, Yeong-Jyi; Lu, Rong-Shyang; Shiu, Jing-Ge; Tzeng, Yeng-Ming; Wan, Xia; Wang, Minzu; Adiguzel, Aytul; Bakirci, Mustafa Numan; Cerci, Salim; Dozen, Candan; Dumanoglu, Isa; Eskut, Eda; Girgis, Semiray; Gokbulut, Gul; Hos, Ilknur; Kangal, Evrim Ersin; Kayis Topaksu, Aysel; Onengut, Gulsen; Ozdemir, Kadri; Ozturk, Sertac; Polatoz, Ayse; Sogut, Kenan; Sunar Cerci, Deniz; Tali, Bayram; Topakli, Huseyin; Uzun, Dilber; Vergili, Latife Nukhet; Vergili, Mehmet; Akin, Ilina Vasileva; Aliev, Takhmasib; Bilin, Bugra; Bilmis, Selcuk; Deniz, Muhammed; Gamsizkan, Halil; Guler, Ali Murat; Ocalan, Kadir; Ozpineci, Altug; Serin, Meltem; Sever, Ramazan; Surat, Ugur Emrah; Yalvac, Metin; Yildirim, Eda; Zeyrek, Mehmet; Deliomeroglu, Mehmet; Demir, Durmus; Gülmez, Erhan; Isildak, Bora; Kaya, Mithat; Kaya, Ozlem; Özbek, Melih; Ozkorucuklu, Suat; Sonmez, Nasuf; Levchuk, Leonid; Bostock, Francis; Brooke, James John; Cheng, Teh Lee; Clement, Emyr; Cussans, David; Frazier, Robert; Goldstein, Joel; Grimes, Mark; Heath, Greg P; Heath, Helen F; Kreczko, Lukasz; Metson, Simon; Newbold, Dave M; Nirunpong, Kachanon; Poll, Anthony; Senkin, Sergey; Smith, Vincent J; Basso, Lorenzo; Bell, Ken W; Belyaev, Alexander; Brew, Christopher; Brown, Robert M; Camanzi, Barbara; Cockerill, David JA; Coughlan, John A; Harder, Kristian; Harper, Sam; Jackson, James; Kennedy, Bruce W; Olaiya, Emmanuel; Petyt, David; Radburn-Smith, Benjamin Charles; Shepherd-Themistocleous, Claire; Tomalin, Ian R; Womersley, William John; Bainbridge, Robert; Ball, Gordon; Ballin, Jamie; Beuselinck, Raymond; Buchmuller, Oliver; Colling, David; Cripps, Nicholas; Cutajar, Michael; Davies, Gavin; Della Negra, Michel; Ferguson, William; Fulcher, Jonathan; Futyan, David; Gilbert, Andrew; Guneratne Bryer, Arlo; Hall, Geoffrey; Hatherell, Zoe; Hays, Jonathan; Iles, Gregory; Jarvis, Martyn; Karapostoli, Georgia; Lyons, Louis; Magnan, Anne-Marie; Marrouche, Jad; Mathias, Bryn; Nandi, Robin; Nash, Jordan; Nikitenko, Alexander; Papageorgiou, Anastasios; Pesaresi, Mark; Petridis, Konstantinos; Pioppi, Michele; Raymond, David Mark; Rogerson, Samuel; Rompotis, Nikolaos; Rose, Andrew; Ryan, Matthew John; Seez, Christopher; Sharp, Peter; 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Beretvas, Andrew; Berryhill, Jeffrey; Bhat, Pushpalatha C; Bloch, Ingo; Burkett, Kevin; Butler, Joel Nathan; Chetluru, Vasundhara; Cheung, Harry; Chlebana, Frank; Cihangir, Selcuk; Cooper, William; Eartly, David P; Elvira, Victor Daniel; Esen, Selda; Fisk, Ian; Freeman, Jim; Gao, Yanyan; Gottschalk, Erik; Green, Dan; Gutsche, Oliver; Hanlon, Jim; Harris, Robert M; Hirschauer, James; Hooberman, Benjamin; Jensen, Hans; Jindariani, Sergo; Johnson, Marvin; Joshi, Umesh; Klima, Boaz; Kousouris, Konstantinos; Kunori, Shuichi; Kwan, Simon; Leonidopoulos, Christos; Limon, Peter; Lincoln, Don; Lipton, Ron; Lykken, Joseph; Maeshima, Kaori; Marraffino, John Michael; Mason, David; McBride, Patricia; Miao, Ting; Mishra, Kalanand; Mrenna, Stephen; Musienko, Yuri; Newman-Holmes, Catherine; O'Dell, Vivian; Pivarski, James; Pordes, Ruth; Prokofyev, Oleg; Schwarz, Thomas; Sexton-Kennedy, Elizabeth; Sharma, Seema; Spalding, William J; Spiegel, Leonard; Tan, Ping; Taylor, Lucas; Tkaczyk, Slawek; Uplegger, Lorenzo; Vaandering, Eric Wayne; Vidal, Richard; Whitmore, Juliana; Wu, Weimin; Yang, Fan; Yumiceva, Francisco; Yun, Jae Chul; Acosta, Darin; Avery, Paul; Bourilkov, Dimitri; Chen, Mingshui; Das, Souvik; De Gruttola, Michele; Di Giovanni, Gian Piero; Dobur, Didar; Drozdetskiy, Alexey; Field, Richard D; Fisher, Matthew; Fu, Yu; Furic, Ivan-Kresimir; Gartner, Joseph; Goldberg, Sean; Hugon, Justin; Kim, Bockjoo; Konigsberg, Jacobo; Korytov, Andrey; Kropivnitskaya, Anna; Kypreos, Theodore; Low, Jia Fu; Matchev, Konstantin; Mitselmakher, Guenakh; Muniz, Lana; Myeonghun, Park; Remington, Ronald; Rinkevicius, Aurelijus; Schmitt, Michael; Scurlock, Bobby; Sellers, Paul; Skhirtladze, Nikoloz; Snowball, Matthew; Wang, Dayong; Yelton, John; Zakaria, Mohammed; Gaultney, Vanessa; Lebolo, Luis Miguel; Linn, Stephan; Markowitz, Pete; Martinez, German; Rodriguez, Jorge Luis; Adams, Todd; Askew, Andrew; Bochenek, Joseph; Chen, Jie; Diamond, Brendan; Gleyzer, Sergei V; Haas, Jeff; Hagopian, Sharon; Hagopian, Vasken; Jenkins, Merrill; Johnson, Kurtis F; Prosper, Harrison; Sekmen, Sezen; Veeraraghavan, Venkatesh; Baarmand, Marc M; Dorney, Brian; Hohlmann, Marcus; Kalakhety, Himali; Vodopiyanov, Igor; Adams, Mark Raymond; Anghel, Ioana Maria; Apanasevich, Leonard; Bai, Yuting; Bazterra, Victor Eduardo; Betts, Russell Richard; Callner, Jeremy; Cavanaugh, Richard; Dragoiu, Cosmin; Gauthier, Lucie; Gerber, Cecilia Elena; Hofman, David Jonathan; Khalatyan, Samvel; Kunde, Gerd J; Lacroix, Florent; Malek, Magdalena; O'Brien, Christine; Silkworth, Christopher; Silvestre, Catherine; Smoron, Agata; Strom, Derek; Varelas, Nikos; Akgun, Ugur; Albayrak, Elif Asli; Bilki, Burak; Clarida, Warren; Duru, Firdevs; Lae, Chung Khim; McCliment, Edward; Merlo, Jean-Pierre; Mermerkaya, Hamit; Mestvirishvili, Alexi; Moeller, Anthony; Nachtman, Jane; Newsom, Charles Ray; Norbeck, Edwin; Olson, Jonathan; Onel, Yasar; Ozok, Ferhat; Sen, Sercan; Wetzel, James; Yetkin, Taylan; Yi, Kai; Barnett, Bruce Arnold; Blumenfeld, Barry; Bonato, Alessio; Eskew, Christopher; Fehling, David; Giurgiu, Gavril; Gritsan, Andrei; Guo, Zijin; Hu, Guofan; Maksimovic, Petar; Rappoccio, Salvatore; Swartz, Morris; Tran, Nhan Viet; Whitbeck, Andrew; Baringer, Philip; Bean, Alice; Benelli, Gabriele; Grachov, Oleg; Kenny Iii, Raymond Patrick; Murray, Michael; Noonan, Daniel; Sanders, Stephen; Stringer, Robert; Wood, Jeffrey Scott; Zhukova, Victoria; Barfuss, Anne-Fleur; Bolton, Tim; Chakaberia, Irakli; Ivanov, Andrew; Khalil, Sadia; Makouski, Mikhail; Maravin, Yurii; Shrestha, Shruti; Svintradze, Irakli; Gronberg, Jeffrey; Lange, David; Wright, Douglas; Baden, Drew; Boutemeur, Madjid; Eno, Sarah Catherine; Ferencek, Dinko; Gomez, Jaime; Hadley, Nicholas John; Kellogg, Richard G; Kirn, Malina; Lu, Ying; Mignerey, Alice; Rossato, Kenneth; Rumerio, Paolo; Santanastasio, Francesco; Skuja, Andris; Temple, Jeffrey; Tonjes, Marguerite; Tonwar, Suresh C; Twedt, Elizabeth; Alver, Burak; Bauer, Gerry; Bendavid, Joshua; Busza, Wit; Butz, Erik; 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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; 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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.

  15. 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.

  16. Genetic control of immune response in carriers of ancestral haplotype 8.1: the study of chemotaxis.

    Science.gov (United States)

    Candore, Giuseppina; Balistreri, Carmela R; Campagna, Anna Maria; Colombo, Alfredo; Cuppari, Irene; Di-Carlo, Daniele; Grimaldi, Maria P; Orlando, Valentina; Piazza, Giuseppina; Vasto, Sonya; Lio, Domenico; Caruso, Calogero

    2006-11-01

    In all caucasian populations the association of an impressive number of autoimmune diseases with genes from the HLA-B8, DR3 haplotype that is part of the ancestral haplotype (AH) 8.1 HLA-A1, Cw7, B8, TNFAB*a2b3, TNFN*S, C2*C, Bf*s, C4A*Q0, C4B*1, DRB1*0301, DRB3*0101, DQA1*0501, DQB1*0201 has been reported by different research groups. This haplotype, which is more common in northern Europe, is also associated with a number of immune system dysfunctions in healthy subjects. Analyzing the data according to gender, some dysfunctions are observed in women but not in men, in agreement with the role of X-linked genes and/or estrogens in the development and progression of autoimmune diseases. It has been proposed that a small number of genes within the 8.1 AH modify immune responsiveness and hence affect multiple immunopathological diseases. In this article, we demonstrate that neutrophil chemotaxis is significantly decreased in carriers of this AH, suggesting that this impairment may also be related to the increased occurrence of autoimmune diseases in these individuals. PMID:17261794

  17. Comparative Genomics of Candidate Phylum TM6 Suggests That Parasitism Is Widespread and Ancestral in This Lineage.

    Science.gov (United States)

    Yeoh, Yun Kit; Sekiguchi, Yuji; Parks, Donovan H; Hugenholtz, Philip

    2016-04-01

    Candidate phylum TM6 is a major bacterial lineage recognized through culture-independent rRNA surveys to be low abundance members in a wide range of habitats; however, they are poorly characterized due to a lack of pure culture representatives. Two recent genomic studies of TM6 bacteria revealed small genomes and limited gene repertoire, consistent with known or inferred dependence on eukaryotic hosts for their metabolic needs. Here, we obtained additional near-complete genomes of TM6 populations from agricultural soil and upflow anaerobic sludge blanket reactor metagenomes which, together with the two publicly available TM6 genomes, represent seven distinct family level lineages in the TM6 phylum. Genome-based phylogenetic analysis confirms that TM6 is an independent phylum level lineage in the bacterial domain, possibly affiliated with the Patescibacteria superphylum. All seven genomes are small (1.0-1.5 Mb) and lack complete biosynthetic pathways for various essential cellular building blocks including amino acids, lipids, and nucleotides. These and other features identified in the TM6 genomes such as a degenerated cell envelope, ATP/ADP translocases for parasitizing host ATP pools, and protein motifs to facilitate eukaryotic host interactions indicate that parasitism is widespread in this phylum. Phylogenetic analysis of ATP/ADP translocase genes suggests that the ancestral TM6 lineage was also parasitic. We propose the name Dependentiae (phyl. nov.) to reflect dependence of TM6 bacteria on host organisms. PMID:26615204

  18. 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

  19. What was the ancestral function of decidual stromal cells? A model for the evolution of eutherian pregnancy.

    Science.gov (United States)

    Chavan, Arun Rajendra; Bhullar, Bhart-Anjan S; Wagner, Günter P

    2016-04-01

    In human and mouse, decidual stromal cells (DSC) are necessary for the establishment (implantation) and the maintenance of pregnancy by preventing inflammation and the immune rejection of the semi-allograft conceptus. DSC originated along the stem lineage of eutherian mammals, coincidental with the origin of invasive placentation. Surprisingly, in many eutherian lineages decidual cells are lost after the implantation phase of pregnancy, making it unlikely that DSC are necessary for the maintenance of pregnancy in these animals. In order to understand this variation, we review the literature on the fetal-maternal interface in all major eutherian clades Euarchontoglires, Laurasiatheria, Xenarthra and Afrotheria, as well as the literature about the ancestral eutherian species. We conclude that maintaining pregnancy may not be a shared derived function of DSC among all eutherian mammals. Rather, we propose that DSC originated to manage the inflammatory reaction associated with invasive implantation. We envision that this happened in a stem eutherian that had invasive placenta but still a short gestation. We further propose that extended gestation evolved independently in the major eutherian clades explaining why the major lineages of eutherian mammals differ with respect to the mechanisms maintaining pregnancy. PMID:27016782

  20. 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

  1. 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

  2. Localization of Type 1 Diabetes susceptibility in the ancestral haplotype 18.2 by high density SNP mapping.

    Science.gov (United States)

    Santiago, Jose Luis; Li, Wentian; Lee, Annette; Martinez, Alfonso; Chandrasekaran, Alamelu; Fernandez-Arquero, Miguel; Khalili, Houman; de la Concha, Emilio G; Urcelay, Elena; Gregersen, Peter K

    2009-10-01

    Previous studies have suggested that the ancestral haplotype 18.2 (AH18.2) carries additional susceptibility gene to Type 1 Diabetes (T1D) on the Major Histocompatibility Complex (MHC). We analyzed 10 DR3/TNFa1b5 homozygous subjects in order to establish the conservation of the AH18.2 and then compared this conserved region with other DR3 haplotype, the AH8.1. The Illumina's HumanHap550 Bead chip was used to perform an extensive genotyping of the MHC region. The AH18.2 was highly conserved between DDR1 and HLA-DQA1 genes; therefore most probably the second susceptibility gene is located within this region. We can exclude the region centromeric to HLA-DRA gene and telomeric to DDR1 gene. A comparison between the AH18.2 and AH8.1 haplotypes showed that 233 SNPs were different in the aforementioned conserved region. These data suggest that the 1.65 Mb MHC region between DDR1 and HLA-DRA genes is likely to carry additional susceptibility alleles for T1D on the AH18.2 haplotype. PMID:19591919

  3. 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.

  4. 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.

  5. 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...

  6. 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...

  7. 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.

  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. 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...... the period between 1999 and 2006. A history of radiation therapy was associated with increased risk of severe capsular contracture for 1- and 2-stage procedures, with adjusted hazard ratios (HR) of 3.3 (95% confidence interval [CI]: 0.9-12.4) and 7.2 (95% CI: 2.4-21.4), respectively. Similarly, a...... history 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...

  10. 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...

  11. Three-dimensional ICT reconstruction

    International Nuclear Information System (INIS)

    The three-dimensional ICT reconstruction method is the hot topic of recent ICT technology research. In the context, qualified visual three-dimensional ICT pictures are achieved through multi-piece two-dimensional images accumulation by, combining with thresholding method and linear interpolation. Different direction and different position images of the reconstructed pictures are got by rotation and interception respectively. The convenient and quick method is significantly instructive to more complicated three-dimensional reconstruction of ICT images. (authors)

  12. Phase Retrieval Versus Phaseless Reconstruction

    OpenAIRE

    Botelho-Andrade, Sara; Casazza, Peter G.; Nguyen, Hanh; Tremain, Janet C.

    2015-01-01

    In 2006, Balan/Casazza/Edidin \\cite{BCE} introduced the frame theoretic study of phaseless reconstruction. Since then, this has turned into a very active area of research. Over the years, many people have replaced the term {\\it phaseless reconstruction} with {\\it phase retrieval}. Casazza then asked: {\\it Are these really the same?} In this paper, we will show that phase retrieval is equivalent to phaseless reconstruction. We then show, more generally, that phase retrieval by projections is e...

  13. 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.

  14. 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 ...

  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. 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)

  17. 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.

  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. Identifying variation in resistance to the take-all fungus, Gaeumannomyces graminis var. tritici, between different ancestral and modern wheat species

    OpenAIRE

    McMillan, Vanessa E; Gutteridge, Richard J; Hammond-Kosack, Kim E.

    2014-01-01

    Background Ancestral wheat relatives are important sources of genetic diversity for the introduction of novel traits for the improvement of modern bread wheat. In this study the aim was to assess the susceptibility of 34 accessions of the diploid wheat Triticum monococcum (A genome) to Gaeumannomyces graminis var. tritici (Ggt), the causal agent of take-all disease. The second aim was to explore the susceptibility of tetraploid wheat (T. durum) and the B genome progenitor species Aegilops spe...

  1. 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...

  2. 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.

  3. Optimal reconstruction angles

    International Nuclear Information System (INIS)

    The question of optimal projection angles has recently become of interest in the field of reconstruction from projections. Here, studies are concentrated on the n x n pixel space, where literative algorithms such as ART and direct matrix techniques due to Katz are considered. The best angles are determined in a Gauss--Markov statistical sense as well as with respect to a function-theoretical error bound. The possibility of making photon intensity a function of angle is also examined. Finally, the best angles to use in an ART-like algorithm are studied. A certain set of unequally spaced angles was found to be preferred in several contexts. 15 figures, 6 tables

  4. Urogenital Reconstructive Surgery

    DEFF Research Database (Denmark)

    Jakobsen, Lotte Kaasgaard

    the lower urinary tract causes voiding disabilities, renal failure and chronic bladder changes. Children with such malformations often require extensive treatment, and will experience side effects and not always satisfactory results. Aim: To develop an animal model of congenital infravesical......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 of...... the fetal bladder to those of the bladder from young pigs used in the animal model. Results: By further characterising the effect of congenital obstruction, regarding urodynamic properties of the bladder and structural changes in the bladder tissue and comparing the results after relief of obstruction...

  5. "Recuperación ancestral mapuche": Divergencias ideológicas y conflictos entre Mapuches y el Estado. El caso del Lof Inkaial WalMapu Meu (Parque Nacional Nahuel Huapí, Río Negro, Argentina "Recuperação ancestral Mapuche": O caso de Lof Inkaial WalMapu Meu (Parque Nacional Nahuel Huapí, Rio Negro, Argentina Mapuche Ancestral Recovery of Land: The Lof Inkaial WalMapu Meu case of study (Nahuel Huapí National Park, Río Negro, Argentina

    Directory of Open Access Journals (Sweden)

    Guido Galafassi

    2012-07-01

    ção por parte dos povoadores "vizinhos" da área recuperadaThe aim of this paper is to present and analyze the case of a recent social mobilization which involved a Mapuche community in the southern region of Argentina, known as Patagonia. An "ancestral recovery of land" was claimed to be the objective of the action. Several conflicts emerged due to the fact that the land in conflict is part of the Nahuel Huapi National Park, which implied a straightforward questioning of the National State rights over territory. Apart from that, the recovery process was strongly rejected by local residents. This brought about a new conflict that required the local government's mediation.

  6. 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 ...

  7. 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.

  8. 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

  9. Breast reconstruction - methods and imaging

    International Nuclear Information System (INIS)

    Silicon implants are used for breast reconstruction or for cosmetic operations. The contribution outlines the role of mammography, sonography and MR for defect assessment, tumour detection and monitoring after prosthesis implantation. Instrument adjustment for mammographic screening of patients with implants is gone into. Autologic reconstruction techniques and protocols of secondary and tertiary early detection are presented. (orig.)

  10. 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) and...

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. Reconstructing ENSO - Methods, Proxy Data and Teleconnections

    Science.gov (United States)

    Wilson, R.; Cook, E.; D'Arrigo, R.; Riedwyl, N.; Evans, M.; Tudhope, A.; Allan, R.

    2009-04-01

    The El Niño/Southern Oscillation (ENSO) is globally important and influences climate at interannual and decadal time-scales with resultant links with extreme weather events and associated socio-economic problems. An understanding of the ENSO system is therefore crucial to allow for a better understanding of how ENSO will ‘react' under current global warming. Palaeoclimate reconstructions of ENSO variability allow extension prior to the relatively short instrumental record. However, due to the paucity of relevant annually resolved proxy archives (e.g. corals) in the central and eastern Pacific, reconstructions must rely on proxy data that are located in regions where the local climate is teleconnected with the tropical Pacific. In this study we compare three newly developed independent NINO3.4 SST reconstructions using data from (1) the central Pacific (corals), (2) the TexMex region of the United States (tree-rings), and (3) other regions in the tropics (corals and an ice-core) which are teleconnected with central Pacific SSTs in the 20th century. Although these three reconstructions are strongly calibrated and well verified, inter-proxy comparison shows a significant weakening in inter-proxy coherence in the 19th century. This break down in common signal could be related to insufficient data, dating errors in some of the proxy records or a break down in ENSO's influence on other regions. However, spectral analysis indicates that each reconstruction portrays ENSO-like spectral properties. Superposed epoch analysis also shows that each reconstruction shows a generally consistent ‘El-Niño-like' response to major volcanic events in the following year, while during years T+4 to T+7, ‘La Niña-like' conditions prevail. These results suggest that each of the series expresses ENSO-like ‘behaviour' but this ‘behaviour' however does not appear to be spatially or temporally consistent. This result may reflect published observations that there appear to be

  16. 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.

  17. 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

  18. 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...

  19. 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.

  20. Reconstructive dosimetry for cutaneous radiation syndrome

    Energy Technology Data Exchange (ETDEWEB)

    Lima, C.M.A.; Lima, A.R.; Degenhardt, Ä.L.; Da Silva, F.C.A., E-mail: dasilva@ird.gov.br [Instituto de Radioprotecao e Dosimetria (IRD/CNEN-RJ), Rio de Janeiro, RJ (Brazil); Valverde, N.J. [Fundacao Eletronuclear de Assistencia Medica, Rio de Janeiro, RJ (Brazil)

    2015-10-15

    According to the International Atomic Energy Agency (IAEA), a relatively significant number of radiological accidents have occurred in recent years mainly because of the practices referred to as potentially high-risk activities, such as radiotherapy, large irradiators and industrial radiography, especially in gammagraphy assays. In some instances, severe injuries have occurred in exposed persons due to high radiation doses. In industrial radiography, 80 cases involving a total of 120 radiation workers, 110 members of the public including 12 deaths have been recorded up to 2014. Radiological accidents in industrial practices in Brazil have mainly resulted in development of cutaneous radiation syndrome (CRS) in hands and fingers. Brazilian data include 5 serious cases related to industrial gammagraphy, affecting 7 radiation workers and 19 members of the public; however, none of them were fatal. Some methods of reconstructive dosimetry have been used to estimate the radiation dose to assist in prescribing medical treatment. The type and development of cutaneous manifestations in the exposed areas of a person is the first achievable gross dose estimation. This review article presents the state-of-the-art reconstructive dosimetry methods enabling estimation of local radiation doses and provides guidelines for medical handling of the exposed individuals. The review also presents the Chilean and Brazilian radiological accident cases to highlight the importance of reconstructive dosimetry. (author)

  1. 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.

  2. 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

  3. Surgical Ventricular Reconstruction

    Medline Plus

    Full Text Available ... a few centers in the United States with innovations in the field if heart disease and heart ... handful of centers that have been involved in innovations in cardiac disease and heart surgery for over ...

  4. Surgical Ventricular Reconstruction

    Medline Plus

    Full Text Available ... a few centers in the United States with innovations in the field if heart disease and heart ... E. MICHLER, MD: Well, yes, indeed. And the importance of the STITCH Trial is that it is ...

  5. Surgical Ventricular Reconstruction

    Medline Plus

    Full Text Available ... a few centers in the United States with innovations in the field if heart disease and heart ... those cases we need to resort to alternative strategies such as this procedure. 00:34:07 ROBERT ...

  6. 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

  7. ¿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.

  8. ABO (histo) blood group phenotype development and human reproduction as they relate to ancestral IgM formation: A hypothesis.

    Science.gov (United States)

    Arend, Peter

    2016-01-01

    The formation of a histo (blood) group) ABO phenotype and the exclusion of an autoreactive IgM or isoagglutinin activity arise apparently in identical glycosylation of complementary domains on cell surfaces and plasma proteins. The fundamental O-glycan emptiness of the circulating IgM, which during the neonatal amino acid sequencing of the variable regions is exerting germline-specific O-GalNAc glycan-reactive serine/threonine residues that in the plasma of the adult human blood group O individuals apparently remain associated with the open glycosidic sites on the ABOH convertible red cell surface, must raise suggestions on a transient expression of developmental glycans, which have been "lost" over the course of maturation. In fact, while the mammalian non-somatic, embryogenic stem cell (ESC)- germ cell (GC) transformation is characterized by a transient and genetically as-yet-undefined trans-species-functional O-GalNAc glycan expression, in the C57BL/10 mouse such expression was potentially identified in growth-dependent, blood group A-like GalNAc glycan-bearing, ovarian glycolipids complementary with the syngeneic anti-A reactive IgM, which does not appear in early ovariectomized animals. This non-somatically encoded, polyreactive, ancestral IgM molecule has not undergone clonal selection and does primarily not differentiate between self and non-self and might, due to amino acid hydroxyl groups, highly suggest substrate competition with subsequent O-glycosylations in ongoing ESC-GC transformations and affecting GC maturation. However, the membrane-bound somatic N/O-glycotransferases, which initiate, after formation of the zygote, the complex construction of the human ABO phenotypes in the trans cisternae of the Golgi apparatus, are associated and/or completed with soluble enzyme versions exerting identical specificities in plasma and likely competing vice versa by glycosylation of neonatal IgM amino acids, where they suggest to accomplish the clearance of anti

  9. 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 ...

  10. Primary reconstruction with implants in breast cancer: aspects of oncological safety and aesthetic outcome.

    OpenAIRE

    Eriksen, Catharina

    2011-01-01

    Introduction: Despite the introduction of breast conserving surgery, in Sweden mastectomy is still annually recommended to 40–50 % (about 3000) of women with breast cancer. National guidelines state that, in the absence of contraindications, these women should be offered breast reconstruction. Immediate reconstruction has many advantages compared with delayed reconstruction but questions have been raised about the method’s oncological safety and which method is preferable. Aim: The first a...

  11. Reconstruction of instrumentation and control system (SKR)

    International Nuclear Information System (INIS)

    For the first time extensive upgrades have been performed in all safety related areas of units with WWER 440/230 reactors. One of the most important actions was the replacement of the safety and safety related instrumentation and control. The state of the art digital safety instrumentation and control system TELEPERM XS has been implemented in units 1 and 2 of the Bohunice V1 power plant. The requirements as deduced from safety assessments conducted by commissions of international experts have been fulfilled, so that Bohunice V1 after this gradual reconstruction has been upgraded to an internationally accepted safety level for the remainder of its service life. (author)

  12. ACL RECONSTRUCTION ‐ IT'S ALL ABOUT TIMING

    OpenAIRE

    Evans, Stephanie; Shaginaw, Justin; Bartolozzi, Arthur

    2014-01-01

    Injury to the anterior cruciate ligament (ACL) is the most common ligamentous injury, ranging from up to 200,000 injuries per year in the United States. Sports such as soccer, football, and skiing have been reported to be high‐risk sports that can cause injury to the ACL when compared to other sport activities. Due to the high incidence of ACL injuries, approximately 100,000 ACL reconstructions are performed each year. Although conservative treatment can potentially be successful in the appro...

  13. Reconstructing the Aalborg Model for PBL

    DEFF Research Database (Denmark)

    Kolmos, Anette; Holgaard, Jette Egelund; Dahl, Bettina

    2013-01-01

    . Therefore this paper focuses on what this implementation process can tell us about the drivers, challenges and prospects of reconstructing PBL curricula? We address this question by reporting on the experiences from the middle management level based on interview with three school leaders and 11 study board...... directors. Based on the results, we stress that although innovations obviously have to happen at a certain pace in order to reflect the state of art in society, the pace have to be adjusted to make room for i) pedagogical support and training, ii) a strong coordination to assure an aligned curricula iii...

  14. 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.

  15. 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.

  16. Breast Reconstruction with Tissue Expansion

    Medline Plus

    Full Text Available ... to go with Tamoxifen. At that point in time she did not want to get a reconstruction, ... her work and she's more comfortable with her time, she said she wanted to pursue the breast ...

  17. Breast Reconstruction with Tissue Expansion

    Medline Plus

    Full Text Available ... come to my practice a few months ago seeking a left breast reconstruction after mastectomy. She had ... Veritas Collagen Matrix sling in order to help support the expansion because there is possible radiation damage ...

  18. Submicron STIM tomography reconstruction techniques

    International Nuclear Information System (INIS)

    One-dimensional projections of ion energy loss have been converted to areal density using tabulated stopping powers in a scanning transmission ion microscopy (STIM) reconstruction of a test object, displaying a spatial resolution of 0.37 μm. Location and registration of the centre of areal mass density in each projection provides a means of overcoming (a) the misalignment of the specimen rotation axis with the centre of the scan path and (b) deviations of the specimen from its precession around the axis of rotation. Multiplicative algebraic reconstruction technique (ART), filtered backprojection and maximum-entropy algorithms for the reconstruction of the object are considered. Maximum entropy is shown to produce an image with the least number of artifacts. However, when time considerations are taken into account, it is found that filtered backprojection is the preferred algorithm for a tomographic reconstruction. (orig.)

  19. Reconstruction within the Zeldovich approximation

    CERN Document Server

    White, Martin

    2015-01-01

    The Zeldovich approximation, 1st order Lagrangian perturbation theory, provides a good description of the clustering of matter and galaxies on large scales. The acoustic feature in the large-scale correlation function of galaxies imprinted by sound waves in the early Universe has been successfully used as a `standard ruler' to constrain the expansion history of the Universe. The standard ruler can be improved if a process known as density field reconstruction is employed. In this paper we develop the Zeldovich formalism to compute the correlation function of biased tracers in both real- and redshift-space using the simplest reconstruction algorithm with a Gaussian kernel and compare to N-body simulations. The model qualitatively describes the effects of reconstruction on the simulations, though its quantitative success depends upon how redshift-space distortions are handled in the reconstruction algorithm.

  20. 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

  1. 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.

  2. 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,...

  3. Current Concepts in ACL Reconstruction

    OpenAIRE

    Fu, Freddie H; Cohen, Steven B.

    2008-01-01

    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 con...

  4. 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.

  5. Reconstructing pedigrees: a stochastic perspective

    OpenAIRE

    Thatte, Bhalchandra D.; Steel, Mike

    2007-01-01

    A pedigree is a directed graph that describes how individuals are related through ancestry in a sexually-reproducing population. In this paper we explore the question of whether one can reconstruct a pedigree by just observing sequence data for present day individuals. This is motivated by the increasing availability of genomic sequences, but in this paper we take a more theoretical approach and consider what models of sequence evolution might allow pedigree reconstruction (given sufficiently...

  6. Technical basis for dose reconstruction

    International Nuclear Information System (INIS)

    The purpose of this paper is to consider two general topics: technical considerations of why dose-reconstruction studies should or should not be performed and methods of dose reconstruction. The first topic is of general and growing interest as the number of dose-reconstruction studies increases, and one asks the question whether it is necessary to perform a dose reconstruction for virtually every site at which, for example, the Department of Energy (DOE) has operated a nuclear-related facility. And there is the broader question of how one might logically draw the line at performing or not performing dose-reconstruction (radiological and chemical) studies for virtually every industrial complex in the entire country. The second question is also of general interest. There is no single correct way to perform a dose-reconstruction study, and it is important not to follow blindly a single method to the point that cheaper, faster, more accurate, and more transparent methods might not be developed and applied

  7. Lip Reconstruction after Tumor Ablation

    Science.gov (United States)

    Ebrahimi, Ali; Kalantar Motamedi, Mohammad Hossein; Ebrahimi, Azin; Kazemi, Mohammad; Shams, Amin; Hashemzadeh, Haleh

    2016-01-01

    Approximately 25% of all oral cavity carcinomas involve the lips, and the primary management of these lesions is complete surgical resection. Loss of tissue in the lips after resection is treated with a variety of techniques, depending on the extension and location of the defect. Here we review highly accepted techniques of lip reconstruction and some of new trials with significant clinical results. Reconstruction choice is primarily depend to size of the defect, localization of defect, elasticity of tissues. But patient’s age, comorbidities, and motivation are also important. According to the defect location and size, different reconstruction methods can be used. For defects involved less than 30% of lips, primary closures are sufficient. In defects with 35–70% lip involvement, the Karapandzic, Abbe, Estlander, McGregor or Gillies’ fan flaps or their modifications can be used. When lip remaining tissues are insufficient, cheek tissue can be used in Webster and Bernard advancement flaps and their various modifications. Deltopectoral or radial forearm free flaps can be options for large defects of the lip extending to the Jaws. To achieve best functional and esthetic results, surgeons should be able to choose most appropriate reconstruction method. Considering defects’ size and location, patients’ expects and surgeon’s ability and knowledge, a variety of flaps are presented in order to reconstruct defects resulted from tumor ablation. It’s necessary for surgeons to trace the recent innovations in lip reconstruction to offer best choices to patients. PMID:27308236

  8. A fast sparse reconstruction algorithm for electrical tomography

    International Nuclear Information System (INIS)

    Electrical tomography (ET) has been widely investigated due to its advantages of being non-radiative, low-cost and high-speed. However, the image reconstruction of ET is a nonlinear and ill-posed inverse problem and the imaging results are easily affected by measurement noise. A sparse reconstruction algorithm based on L1 regularization is robust to noise and consequently provides a high quality of reconstructed images. In this paper, a sparse reconstruction by separable approximation algorithm (SpaRSA) is extended to solve the ET inverse problem. The algorithm is competitive with the fastest state-of-the-art algorithms in solving the standard L2−L1 problem. However, it is computationally expensive when the dimension of the matrix is large. To further improve the calculation speed of solving inverse problems, a projection method based on the Krylov subspace is employed and combined with the SpaRSA algorithm. The proposed algorithm is tested with image reconstruction of electrical resistance tomography (ERT). Both simulation and experimental results demonstrate that the proposed method can reduce the computational time and improve the noise robustness for the image reconstruction. (paper)

  9. A fast sparse reconstruction algorithm for electrical tomography

    Science.gov (United States)

    Zhao, Jia; Xu, Yanbin; Tan, Chao; Dong, Feng

    2014-08-01

    Electrical tomography (ET) has been widely investigated due to its advantages of being non-radiative, low-cost and high-speed. However, the image reconstruction of ET is a nonlinear and ill-posed inverse problem and the imaging results are easily affected by measurement noise. A sparse reconstruction algorithm based on L1 regularization is robust to noise and consequently provides a high quality of reconstructed images. In this paper, a sparse reconstruction by separable approximation algorithm (SpaRSA) is extended to solve the ET inverse problem. The algorithm is competitive with the fastest state-of-the-art algorithms in solving the standard L2-L1 problem. However, it is computationally expensive when the dimension of the matrix is large. To further improve the calculation speed of solving inverse problems, a projection method based on the Krylov subspace is employed and combined with the SpaRSA algorithm. The proposed algorithm is tested with image reconstruction of electrical resistance tomography (ERT). Both simulation and experimental results demonstrate that the proposed method can reduce the computational time and improve the noise robustness for the image reconstruction.

  10. Pre-and post-Missoula flood geomorphology of the Pre-Holocene ancestral Columbia River Valley in the Portland forearc basin, Oregon and Washington, USA

    Science.gov (United States)

    Peterson, Curt D.; Minor, Rick; Peterson, Gary L.; Gates, Edward B.

    2011-06-01

    Geomorphic landscape development in the pre-Holocene ancestral Columbia River Valley (1-5 km width) in the Portland forearc basin (~ 50 km length) is established from depositional sequences, which pre-date and post-date the glacial Lake Missoula floods. The sequences are observed from selected borehole logs (150 in number) and intact terrace soil profiles (56 in number) in backhoe trenches. Four sequences are widespread, including (1) a vertically aggraded Pleistocene alluvial plain, (2) a steep sided valley that is incised (125-150 m) into the Pleistocene gravel plain, (3) Missoula flood terraces (19-13 ka) abandoned on the sides of the ancestral valley, and (4) Holocene flooding surfaces (11-8 ka) buried at 70-30 m depth in the axial Columbia River Valley. Weathering rims and cementation are used for relative dating of incised Pleistocene gravel units. Soil development on the abandoned Missoula flood terraces is directly related to terrace deposit lithology, including thin Bw horizons in gravel, irregular podzols in sand, and multiple Bw horizons in thicker loess-capping layers. Radiocarbon dating of sand and mud alluvium in the submerged axial valley ties Holocene flooding surfaces to a local sea level curve and establishes Holocene sedimentation rates of 1.5 cm year- 1 during 11-9 ka and 0.3 cm year- 1 during 9-0 ka. The sequences of Pleistocene gravel aggradation, river valley incision, cataclysmic Missoula flooding, and Holocene submergence yield complex geomorphic landscapes in the ancestral lower Columbia River Valley.

  11. 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.

  12. New time constraints for the age of metamorphism at the ancestral Pacific Gondwana margin of southern Chile (42-52°S)

    OpenAIRE

    Stuart N. Thomson; Francisco Hervé

    2002-01-01

    Fission-track (FT) analysis was performed on ten samples of detrital zircons from several pre-Late Jurassic metamorphic accretionary complexes at the ancestral Pacific margin of Gondwana in southern Chile (42-52°S) previously dated by U-Pb SHRIMP. Post-metamorphic zircon FT cooling ages combined with published U-Pb provenance ages allow the estimation of the following maximum and minimum ages of deposition and metamorphism: the Eastern Andes metamorphic complex (EAMC), 364 to 250 Ma (Late Dev...

  13. The Influence of the Autoimmunity-Associated Ancestral HLA Haplotype AH8.1 on the Human Gut Microbiota: A Cross-Sectional Study

    OpenAIRE

    Hov, Johannes R; Zhong, Huanzi; Qin, Bingcai; Anmarkrud, Jarl Andreas; Holm, Kristian; Franke, Andre; Benedicte A Lie; Karlsen, Tom H.

    2015-01-01

    Multiple immune-related genes are encoded in the HLA complex on chromosome 6p21. The 8.1 ancestral haplotype (AH8.1) include the classical HLA alleles HLA-B*08:01 and HLA-DRB1*03:01, and has been associated with a large number of autoimmune diseases, but the underlying mechanisms for this association are largely unknown. Given the recently established links between the gut microbiota and inflammatory diseases, we hypothesized that the AH8.1 influences the host gut microbial community composit...

  14. On $\\mathfrak{I}$-reconstruction Property

    OpenAIRE

    Vashisht, L. K.; Khattar, Geetika

    2013-01-01

    Reconstruction property in Banach spaces introduced and studied by Casazza and Christensen in [1]. In this paper we introduce reconstruction property in Banach spaces which satisfy $\\mathfrak{I}$-property. A characterization of reconstruction property in Banach spaces which satisfy $\\mathfrak{I}$-property in terms of frames in Banach spaces is obtained. Banach frames associated with reconstruction property are discussed.

  15. Ulnar Collateral Ligament Reconstruction

    Science.gov (United States)

    Erickson, Brandon J.; Bach, Bernard R.; Cohen, Mark S.; Bush-Joseph, Charles A.; Cole, Brian J.; Verma, Nikhil N.; Nicholson, Gregory P.; Romeo, Anthony A.

    2016-01-01

    Background: Ulnar collateral ligament reconstruction (UCLR) is a common surgery performed in professional, collegiate, and high school athletes. Purpose: To report patient demographics, surgical techniques, and outcomes of all UCLRs performed at a single institution from 2004 to 2014. Study Design: Case series; Level of evidence, 4. Methods: All patients who underwent UCLR from January 1, 2004, through December 31, 2014, at a single institution were identified. Charts were reviewed to determine patient age, sex, date of surgery, sport played, athletic level, surgical technique, graft type, and complications. Data were collected prospectively, and patients were contacted via phone calls to obtain the return-to-sport rate, Conway-Jobe score, Andrews-Timmerman score, and Kerlan-Jobe Orthopaedic Clinic (KJOC) Shoulder and Elbow score. Continuous variable data were reported as weighted means, and categorical variable data were reported as frequencies with percentages. Results: A total of 187 patients (188 elbows) underwent UCLR during the study period (92% male; mean age, 19.6 ± 4.7 years; 78.2% right elbows). There were 165 baseball players (87.8% of all patients), 155 of whom were pitchers (82.5% of all patients). Ninety-seven (51.6%) were college athletes, 68 (36.2%) high school athletes, and 7 (3.7%) professional athletes at the time of surgery. The docking technique was used in 110 (58.5%) patients while the double-docking technique was used in 78 (41.5%). An ipsilateral palmaris longus graft was used in 110 (58.5%) patients while a hamstring autograft was used in 48 (25.5%) patients. The ulnar nerve was subcutaneously transposed in 79 (42%) patients. Clinical follow-up data were available on 85 patients. Mean follow-up was 60 ± 30.8 months. Overall, 94.1% of patients were able to return to sport and had a Conway-Jobe score of good/excellent while 4.3% had a score of fair. The mean KJOC score was 90.4 ± 6.7 and mean Andrews-Timmerman score was 92.5 ± 7

  16. Tracing the origin and geographic distribution of an ancestral form of the modern human Y chromosome Reconstrucción del origen y distribución geográfica de una forma ancestral del cromosoma Y del hombre moderno

    OpenAIRE

    Bravi, Claudio M.; GRACIELA BAILLIET; VERÓNICA L MARTÍNEZ-MARIGNAC; Bianchi, Nestor O.

    2001-01-01

    We screened a total of 841 Y chromosomes representing 36 human populations of wide geographical distribution for the presence of a Y-specific Alu insert (YAP+ chromosomes). The Alu element was found in 77 cases. We tested five biallelic and eight polyallelic markers in 70 out of the 77 YAP+ chromosomes. We could identify the existence of a hierarchical and chronological structuring of ancestral and derived YAP+ lineages giving rise to four haplogroups, 14 subhaplogroups and 60 haplotypes. Mor...

  17. 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...

  18. 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.

  19. 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.

  20. RETHINKING VIOLENCE, RECONCILIATION AND RECONSTRUCTION IN BURUNDI

    Directory of Open Access Journals (Sweden)

    Leah Ndimurwimo

    2015-11-01

    Full Text Available Armed violence and genocide are among the on-going problems that are still facing contemporary Africa and the world. In the aftermath of the outrages, devastation and appalling carnage of the Second World War, member states of the United Nations (UN undertook radical steps, inter alia, "to save succeeding generations from the scourge of war and to reaffirm faith in fundamental human rights". Subsequently, the International Bill of Human Rights was proclaimed in order to lay down international human rights norms and standards of conduct and to prevent the recurrence of mass killings. Although Burundi is a State Party to the UN and African Union and is a signatory to a number of international and regional human rights treaties, the post-colonial history of Burundi is an epic tale of indescribable human suffering and misery as a result of systematic mass killings. At least every family or household in Burundi has been negatively affected by the mass killings of the 1960s, 1972, 1988 and 1990s, which have created a significant number of refugees and internally displaced persons (IDPs.This article traces the root causes of Burundi's systemic armed violence and argues that despite several UN Security Council Resolutions and peace agreements aimed at national reconciliation and reconstruction, mass killings and other heinous crimes remain unaddressed. The article recommends that a comprehensive transitional justice model is required in post-conflict Burundi in order to bring about national reconciliation, healing and reconstruction.

  1. Reconstructive inverse dynamics in feedwater control

    International Nuclear Information System (INIS)

    The history of nuclear reactor operations during the last two decades has indicated the need to use advanced control, monitoring, and diagnostics techniques to achieve major improvements in power plant performance. In this paper, the authors present an application of reconstructive inverse dynamics (RID) to the feedwater-train control system for a typical pressurized water reactor (PWR). Existing controllers used in power plants, such as proportional-integral-derivative (PID) controllers, are designed using linear techniques. Although PIDs have proven simple and reliable in reactor operations, their limitation is related to the degree of linearity of the system dynamics. When the system undergoes a state-transition caused by a significant nonlinearity, the linear controller gains may not provide adequate compensation on the system dynamics, regardless of how sophisticated the control designs are. This fact is the main motivation behind searching for an appropriate nonlinear control law. The RID is a version of the inverse-dynamics method currently used in robotics. The power of RID lies in its unique control law for any system with plant nonlinearities. The control law includes inverse dynamics and state reconstruction to follow a demanded trajectory. The RID structure is best understood with a coupled system dynamics

  2. 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

  3. Titanium template for scaphoid reconstruction.

    Science.gov (United States)

    Haefeli, M; Schaefer, D J; Schumacher, R; Müller-Gerbl, M; Honigmann, P

    2015-06-01

    Reconstruction of a non-united scaphoid with a humpback deformity involves resection of the non-union followed by bone grafting and fixation of the fragments. Intraoperative control of the reconstruction is difficult owing to the complex three-dimensional shape of the scaphoid and the other carpal bones overlying the scaphoid on lateral radiographs. We developed a titanium template that fits exactly to the surfaces of the proximal and distal scaphoid poles to define their position relative to each other after resection of the non-union. The templates were designed on three-dimensional computed tomography reconstructions and manufactured using selective laser melting technology. Ten conserved human wrists were used to simulate the reconstruction. The achieved precision measured as the deviation of the surface of the reconstructed scaphoid from its virtual counterpart was good in five cases (maximal difference 1.5 mm), moderate in one case (maximal difference 3 mm) and inadequate in four cases (difference more than 3 mm). The main problems were attributed to the template design and can be avoided by improved pre-operative planning, as shown in a clinical case. PMID:25167978

  4. 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

  5. The secreted proteins of Achlya hypogyna and Thraustotheca clavata identify the ancestral oomycete secretome and reveal gene acquisitions by horizontal gene transfer.

    Science.gov (United States)

    Misner, Ian; Blouin, Nic; Leonard, Guy; Richards, Thomas A; Lane, Christopher E

    2015-01-01

    Saprotrophic and parasitic microorganisms secrete proteins into the environment to breakdown macromolecules and obtain nutrients. The molecules secreted are collectively termed the "secretome" and the composition and function of this set of proteins varies depending on the ecology, life cycle, and environment of an organism. Beyond the function of nutrient acquisition, parasitic lineages must also secrete molecules to manipulate their host. Here, we use a combination of de novo genome and transcriptome sequencing and bioinformatic identification of signal peptides to identify the putative secreted proteome of two oomycetes, the facultative parasite Achlya hypogyna and free-living Thraustotheca clavata. By comparing the secretomes of these saprolegnialean oomycetes with that of eight other oomycetes, we were able to characterize the evolution of this protein set across the oomycete clade. These species span the last common ancestor of the two major oomycete families allowing us to identify the ancestral secretome. This putative ancestral secretome consists of at least 84 gene families. Only 11 of these gene families are conserved across all 10 secretomes analyzed and the two major branches in the oomycete radiation. Notably, we have identified expressed elicitin-like effector genes in the saprotrophic decomposer, T. clavata. Phylogenetic analyses show six novel horizontal gene transfers to the oomycete secretome from bacterial and fungal donor lineages, four of which are specific to the Saprolegnialeans. Comparisons between free-living and pathogenic taxa highlight the functional changes of oomycete secretomes associated with shifts in lifestyle. PMID:25527045

  6. 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

  7. 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

  8. 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

  9. 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.

  10. 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...

  11. Shape Reconstruction from Generalized Projections

    Science.gov (United States)

    Viikinkoski, Matti

    2016-01-01

    In this thesis we develop methods for recovering the three-dimensional shape of an object from generalized projections. We particularly focus on the problems encountered when data are presented as discrete image fields. We demonstrate the usefulness of the Fourier transform in transferring the image data and shape model projections to a domain more suitable for gradient based optimization. To substantiate the general applicability of our methods to observational astronomy, we reconstruct shape models for several asteroids observed with adaptive optics, thermal infrared interferometry, or range-Doppler radar. The reconstructions are carried out with the ADAM software package that we have designed for general use.

  12. 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.

  13. 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...

  14. Inconsistencies between Pangean reconstructions and basic climate controls.

    Science.gov (United States)

    Rowe, Clinton M; Loope, David B; Oglesby, Robert J; Van der Voo, Rob; Broadwater, Charles E

    2007-11-23

    The supercontinent Pangea dominated our planet from the Permian into the Jurassic. Paleomagnetic reconstructions have been used to estimate the latitudinal position of Pangea during this 100-million-year period. Atmospheric circulation, recorded by eolian sandstones in the southwestern United States, shows a broad sweep of northeasterly winds over their northernmost extent, curving to become northwesterly in the south: This evidence is consistent with paleomagnetic reconstructions of the region straddling the equator in the Early Permian but is at odds with its northward movement to about 20 degrees N by the Early Jurassic. At least one of the following scenarios must be true: The latitude based on paleomagnetism is incorrect; the interpretation of how winds shaped the dunes is mistaken; the basic climate controls in the Jurassic were different from those of today; or the paleogeographic reconstructions available are insufficient to adequately reproduce the wind fields responsible for dune formation. PMID:18033879

  15. 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...

  16. Optimization of reconstruction algorithms using Monte Carlo simulation

    International Nuclear Information System (INIS)

    A method for optimizing reconstruction algorithms is presented that is based on how well a specified task can be performed using the reconstructed images. Task performance is numerically assessed by a Monte Carlo simulation of the complete imaging process including the generation of scenes appropriate to the desired application, subsequent data taking, reconstruction, and performance of the stated task based on the final image. The use of this method is demonstrated through the optimization of the Algebraic Reconstruction Technique (ART), which reconstructs images from their projections by a iterative procedure. The optimization is accomplished by varying the relaxation factor employed in the updating procedure. In some of the imaging situations studied, it is found that the optimization of constrained ART, in which a nonnegativity constraint is invoked, can vastly increase the detectability of objects. There is little improvement attained for unconstrained ART. The general method presented may be applied to the problem of designing neutron-diffraction spectrometers. 11 refs., 6 figs., 2 tabs

  17. 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.

  18. Paleoenvironmental reconstruction using microfossils : terrestrial

    International Nuclear Information System (INIS)

    The following section provides a brief summary of the use of pollen and chironomids in terrestrial paleoenvironmental reconstruction and lists some key references and general text addressing the history, methods and development of these techniques in Quaternary paleoclimate research and their application in New Zealand. (author). 52 refs., 8 figs

  19. Reconstructing Indo-European Syllabification

    Science.gov (United States)

    Byrd, Andrew Miles

    2010-01-01

    The chief concern of this dissertation is to investigate a fundamental, yet unsolved problem within the phonology of Proto-Indo-European (PIE): the process of syllabification. I show that by analyzing the much more easily reconstructable word-edge clusters we may predict which types of consonant clusters can occur word-medially, provided that we…

  20. 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.

  1. 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.: ...

  2. Tomographic reconstruction of polar plumes

    Science.gov (United States)

    Auchère, F.; Guennou, C.; Barbey, N.

    2012-06-01

    We present a tomographic reconstruction of polar plumes as observed in the Extreme Ultraviolet in January 2010. Plumes are elusive structures visible in polar coronal holes that may play an important role in the acceleration of the solar wind. However, despite numerous observations, little is irrefutably known about them. Because of line of sight effects, even their geometry is subject to debate. Are they genuine cylindrical features of the corona or are they only chance alignments along the line of sight? Tomography provides a means to reconstruct the volume of an optically thin object from a set of observations taken from different vantage points. In the case of the Sun, these are typically obtained by using a solar rotation worth of images, which limits the ability to reconstruct short lived structures. We present here a tomographic inversion of the solar corona obtained using only 6 days of data. This is achieved by using simultaneously three space telescopes (EUVI/STEREO and SWAP/PROBA2) in a very specific orbital configuration. The result is the shortest possible tomographic snapshot of polar plumes. The 3D reconstruction shows both quasi-cylindrical plumes and a network pattern that can mimic them by line of sight superimpositions. This suggests that the controversy on plume geometry is due to the coexistence of both types of structures.

  3. Dating the origin and dispersal of Human Papillomavirus type 16 on the basis of ancestral human migrations.

    Science.gov (United States)

    Zehender, Gianguglielmo; Frati, Elena Rosanna; Martinelli, Marianna; Bianchi, Silvia; Amendola, Antonella; Ebranati, Erika; Ciccozzi, Massimo; Galli, Massimo; Lai, Alessia; Tanzi, Elisabetta

    2016-04-01

    A major limitation when reconstructing the origin and evolution of HPV-16 is the lack of reliable substitution rate estimates for the viral genes. On the basis of the hypothesis of human HPV-16 co-divergence, we estimated a mean evolutionary rate of 1.47×10(-7) (95% HPD=0.64-2.47×10(-7)) subs/site/year for the viral LCR region. The results of a Bayesian phylogeographical analysis suggest that the currently circulating HPV-16 most probably originated in Africa about 110 thousand years ago (Kya), before giving rise to four known geographical lineages: the Asian/European lineage, which most probably originated in Asia a mean 38 Kya, and the Asian/American and two African lineages, which probably respectively originated about 33 and 27 Kya. These data closely reflect current hypotheses concerning modern human expansion based on studies of mitochondrial DNA phylogeny. The correlation between ancient human migration and the present HPV phylogeny may be explained by the co-existence of modes of transmission other than sexual transmission. PMID:26827632

  4. 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

  5. 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

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Current Trends in Anterior Cruciate Ligament Reconstruction

    OpenAIRE

    Kim, Ha Sung; Seon, Jong Keun; Jo, Ah Reum

    2013-01-01

    The advances in the knowledge of anatomy, surgical techniques, and fixation devices have led to the improvement of anterior cruciate ligament (ACL) reconstruction over the past 10 years. Nowadays, double bundle and anatomical single bundle ACL reconstruction that more closely restores the normal anatomy of the ACL are becoming popular. Although there is still no definite conclusion whether double bundle ACL reconstruction provides better clinical results than single bundle reconstruction, the...

  11. Multi-resolution Compressive Sensing Reconstruction

    OpenAIRE

    Gonzalez, Adriana; Jiang, Hong; Huang, Gang; Jacques, Laurent

    2016-01-01

    We consider the problem of reconstructing an image from compressive measurements using a multi-resolution grid. In this context, the reconstructed image is divided into multiple regions, each one with a different resolution. This problem arises in situations where the image to reconstruct contains a certain region of interest (RoI) that is more important than the rest. Through a theoretical analysis and simulation experiments we show that the multi-resolution reconstruction provides a higher ...

  12. 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

  13. 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

    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......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...

  14. 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.

  15. 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…

  16. 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.

  17. Reconstruction of semileptonic b→u decays

    International Nuclear Information System (INIS)

    Using the ARGUS detector at the e+e- storage ring DORIS II at DESY we have updated our result on charmless semileptonic B decays and searched for direct evidence for b→u transitions through reconstruction of complete events. This approach has successfully identified two Υ (4S) events which contain B meson decays to a non-charm final state. In one case, a B0 meson is found in the channel π+μ- anti ν, while in the other a decay B+ → ωμ+ν is seen. These events show that the previously observed signal of charmless semileptonic B decays is due to b → u transitions from which we obtain vertical strokeVub/Vcbvertical stroke = 0.11±0.012 using the model of Altarelli et al. (orig.)

  18. 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

  19. Mandibular reconstruction using bone allografts

    International Nuclear Information System (INIS)

    Further understanding of bone healing mechanisms, bone physiology and bone biology, transplantation immunology, and development of Tissue Banking procedures has enabled oral and maxillofacial surgeons to reconstruct even the most difficult bony defects successfully with the preserved allogeneic bone implant. Although it had been known that bone allografts were clinically effective, its application has not been widespread until the reports of Inclan (I 942), Hyatt and Butler (I 950), and Wilson (I 95 1). Tissue Banking provides the surgeon with a readily available, relatively inexpensive, and relatively safe selection of allogeneic bone for clinical use. Now autogenous bone and allogeneic bone implants present a wide variety of surgical options to surgeons, whether used separately or in combination. The surgeons are able to make judicious and fruitful choices, only with a thorough knowledge of the above-mentioned biological principles and skillful techniques. Many kinds of bone grafting techniques have been tried for reconstructing defective osseous tissues of the oral and maxillofacial region, though they have varying degrees of success. The osseous defects which require grafting include those of various size, shape, position, or amount. Unlike autogenous grafts, whose function is to provide osteogenic cells, allografts are purely passive, offering only a matrix for the inductive phase of bone healing. The condition of the recipient bed is of primary importance, because the host must produce all of the essential elements for the bone allograft to become incorporated. Depending on the processing methods of the allogeneic bone, the bone graft materials have different qualities, different healing potentials and different indications. Proper selection of grafts and surgical techniques requires an understanding of graft immunology and the mechanisms of graft healing. The surgeons should know about the biological principles to raise the clinical success rate

  20. X-Ray Crystal Structure of the Ancestral 3-Ketosteroid Receptor-Progesterone-Mifepristone Complex Shows Mifepristone Bound at the Coactivator Binding Interface

    Energy Technology Data Exchange (ETDEWEB)

    Colucci, Jennifer K.; Ortlund, Eric A. [Emory-MED

    2013-12-12

    Steroid receptors are a subfamily of nuclear receptors found throughout all metazoans. They are highly important in the regulation of development, inflammation, and reproduction and their misregulation has been implicated in hormone insensitivity syndromes and cancer. Steroid binding to SRs drives a conformational change in the ligand binding domain that promotes nuclear localization and subsequent interaction with coregulator proteins to affect gene regulation. SRs are important pharmaceutical targets, yet most SR-targeting drugs have off-target pharmacology leading to unwanted side effects. A better understanding of the structural mechanisms dictating ligand specificity and the evolution of the forces that created the SR-hormone pairs will enable the design of better pharmaceutical ligands. In order to investigate this relationship, we attempted to crystallize the ancestral 3-ketosteroid receptor (ancSR2) with mifepristone, a SR antagonist. Here, we present the x-ray crystal structure of the ancestral 3-keto steroid receptor (ancSR2)-progesterone complex at a resolution of 2.05 Å. This improves upon our previously reported structure of the ancSR2-progesterone complex, permitting unambiguous assignment of the ligand conformation within the binding pocket. Surprisingly, we find mifepristone, fortuitously docked at the protein surface, poised to interfere with coregulator binding. Recent attention has been given to generating pharmaceuticals that block the coregulator binding site in order to obstruct coregulator binding and achieve tissue-specific SR regulation independent of hormone binding. Mifepristone’s interaction with the coactivator cleft of this SR suggests that it may be a useful molecular scaffold for further coactivator binding inhibitor development.

  1. Comparison with ancestral diets suggests dense acellular carbohydrates promote an inflammatory microbiota, and may be the primary dietary cause of leptin resistance and obesity.

    Science.gov (United States)

    Spreadbury, Ian

    2012-01-01

    A novel hypothesis of obesity is suggested by consideration of diet-related inflammation and evolutionary medicine. The obese homeostatically guard their elevated weight. In rodent models of high-fat diet-induced obesity, leptin resistance is seen initially at vagal afferents, blunting the actions of satiety mediators, then centrally, with gastrointestinal bacterial-triggered SOCS3 signaling implicated. In humans, dietary fat and fructose elevate systemic lipopolysaccharide, while dietary glucose also strongly activates SOCS3 signaling. Crucially however, in humans, low-carbohydrate diets spontaneously decrease weight in a way that low-fat diets do not. Furthermore, nutrition transition patterns and the health of those still eating diverse ancestral diets with abundant food suggest that neither glycemic index, altered fat, nor carbohydrate intake can be intrinsic causes of obesity, and that human energy homeostasis functions well without Westernized foods containing flours, sugar, and refined fats. Due to being made up of cells, virtually all "ancestral foods" have markedly lower carbohydrate densities than flour- and sugar-containing foods, a property quite independent of glycemic index. Thus the "forgotten organ" of the gastrointestinal microbiota is a prime candidate to be influenced by evolutionarily unprecedented postprandial luminal carbohydrate concentrations. The present hypothesis suggests that in parallel with the bacterial effects of sugars on dental and periodontal health, acellular flours, sugars, and processed foods produce an inflammatory microbiota via the upper gastrointestinal tract, with fat able to effect a "double hit" by increasing systemic absorption of lipopolysaccharide. This model is consistent with a broad spectrum of reported dietary phenomena. A diet of grain-free whole foods with carbohydrate from cellular tubers, leaves, and fruits may produce a gastrointestinal microbiota consistent with our evolutionary condition, potentially

  2. 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.

  3. Conserved intron positions in FGFR genes reflect the modular structure of FGFR and reveal stepwise addition of domains to an already complex ancestral FGFR.

    Science.gov (United States)

    Rebscher, Nicole; Deichmann, Christina; Sudhop, Stefanie; Fritzenwanker, Jens Holger; Green, Stephen; Hassel, Monika

    2009-10-01

    We have analyzed the evolution of fibroblast growth factor receptor (FGFR) tyrosine kinase genes throughout a wide range of animal phyla. No evidence for an FGFR gene was found in Porifera, but we tentatively identified an FGFR gene in the placozoan Trichoplax adhaerens. The gene encodes a protein with three immunoglobulin-like domains, a single-pass transmembrane, and a split tyrosine kinase domain. By superimposing intron positions of 20 FGFR genes from Placozoa, Cnidaria, Protostomia, and Deuterostomia over the respective protein domain structure, we identified ten ancestral introns and three conserved intron groups. Our analysis shows (1) that the position of ancestral introns correlates to the modular structure of FGFRs, (2) that the acidic domain very likely evolved in the last common ancestor of triploblasts, (3) that splicing of IgIII was enabled by a triploblast-specific insertion, and (4) that IgI is subject to substantial loss or duplication particularly in quickly evolving genomes. Moreover, intron positions in the catalytic domain of FGFRs map to the borders of protein subdomains highly conserved in other serine/threonine kinases. Nevertheless, these introns were introduced in metazoan receptor tyrosine kinases exclusively. Our data support the view that protein evolution dating back to the Cambrian explosion took place in such a short time window that only subtle changes in the domain structure are detectable in extant representatives of animal phyla. We propose that the first multidomain FGFR originated in the last common ancestor of Placozoa, Cnidaria, and Bilateria. Additional domains were introduced mainly in the ancestor of triploblasts and in the Ecdysozoa. PMID:20016912

  4. Variation in effects of non-Hodgkin lymphoma risk factors according to the human leukocyte antigen (HLA-DRB1*01:01 allele and ancestral haplotype 8.1.

    Directory of Open Access Journals (Sweden)

    Sophia S Wang

    Full Text Available Genetic variations in human leukocyte antigens (HLA are critical in host responses to infections, transplantation, and immunological diseases. We previously identified associations with non-Hodgkin lymphoma (NHL and the HLA-DRB1*01:01 allele and extended ancestral haplotype (AH 8.1 (HLA-A*01-B*08-DR*03-TNF-308A. To illuminate how HLA alleles and haplotypes may influence NHL etiology, we examined potential interactions between HLA-DRB1*01:01 and AH 8.1, and a wide range of NHL risk factors among 685 NHL cases and 646 controls from a United States population-based case-control study. We calculated odds ratios and 95% confidence intervals by HLA allele or haplotype status, adjusted for sex, age, race and study center for NHL and two major subtypes using polychotomous unconditional logistic regression models. The previously reported elevation in NHL risk associated with exposures to termite treatment and polychlorinated biphenyls were restricted to individuals who did not possess HLA-DRB1*01:01. Previous associations for NHL and DLBCL with decreased sun exposure, higher BMI, and autoimmune conditions were statistically significant only among those with AH 8.1, and null among those without AH 8.1. Our results suggest that NHL risk factors vary in their association based on HLA-DRB1*01:01 and AH 8.1 status. Our results further suggest that certain NHL risk factors may act through a common mechanism to alter NHL risk. Finally, control participants with either HLA-DRB1*01:01 or AH 8.1 reported having a family history of NHL twice as likely as those who did not have either allele or haplotype, providing the first empirical evidence that HLA associations may explain some of the well-established relationship between family history and NHL risk.

  5. 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)

  6. 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...

  7. The Algebraic Reconstruction Technique (ART)

    International Nuclear Information System (INIS)

    Projections of charged particle beam current density (profiles) are frequently used as a measure of beam position and size. In conventional practice only two projections, usually horizontal and vertical, are measured. This puts a severe limit on the detail of information that can be achieved. A third projection provides a significant improvement. The Algebraic Reconstruction Technique (ART) uses three or more projections to reconstruct 3-dimensional density profiles. At the 200 MeV H-linac, we have used this technique to measure beam density, and it has proved very helpful, especially in helping determine if there is any coupling present in x-y phase space. We will present examples of measurements of current densities using this technique

  8. 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.

  9. 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

  10. Pediatric anterior cruciate ligament reconstruction

    OpenAIRE

    McConkey, Mark O.; Bonasia, Davide Edoardo; Amendola, Annunziato

    2011-01-01

    An increasing number of anterior cruciate ligament (ACL) injuries are seen in children now than in the past due to increased sports participation. The natural history of ACL deficient knees in active individuals, particularly in children is poor. Surgical management of ACL deficiency in children is complex due to the potential risk of injury to the physis and growth disturbance. Delaying ACL reconstruction until maturity is possible but risks instability episodes and intra-articular damage. S...

  11. Computed laminography and reconstruction algorithm

    Science.gov (United States)

    Que, Jie-Min; Cao, Da-Quan; Zhao, Wei; Tang, Xiao; Sun, Cui-Li; Wang, Yan-Fang; Wei, Cun-Feng; Shi, Rong-Jian; Wei, Long; Yu, Zhong-Qiang; Yan, Yong-Lian

    2012-08-01

    Computed laminography (CL) is an alternative to computed tomography if large objects are to be inspected with high resolution. This is especially true for planar objects. In this paper, we set up a new scanning geometry for CL, and study the algebraic reconstruction technique (ART) for CL imaging. We compare the results of ART with variant weighted functions by computer simulation with a digital phantom. It proves that ART algorithm is a good choice for the CL system.

  12. Computed laminography and reconstruction algorithm

    International Nuclear Information System (INIS)

    Computed laminography (CL) is an alternative to computed tomography if large objects are to be inspected with high resolution. This is especially true for planar objects. In this paper, we set up a new scanning geometry for CL, and study the algebraic reconstruction technique (ART) for CL imaging. We compare the results of ART with variant weighted functions by computer simulation with a digital phantom. It proves that ART algorithm is a good choice for the CL system. (authors)

  13. A Reduction of the Graph Reconstruction Conjecture

    Directory of Open Access Journals (Sweden)

    Monikandan S.

    2014-08-01

    Full Text Available A graph is said to be reconstructible if it is determined up to isomor- phism from the collection of all its one-vertex deleted unlabeled subgraphs. Reconstruction Conjecture (RC asserts that all graphs on at least three vertices are reconstructible. In this paper, we prove that interval-regular graphs and some new classes of graphs are reconstructible and show that RC is true if and only if all non-geodetic and non-interval-regular blocks G with diam(G = 2 or diam(Ḡ = diam(G = 3 are reconstructible

  14. Minimonoka Stent for Canalicular Reconstruction

    Directory of Open Access Journals (Sweden)

    Sunil G Biradar,

    2015-04-01

    Full Text Available Objective: Canalicular injuries are relatively common and accounts for 16-26% of all lid tears. There are different techniques for reconstructing traumatic canalicular lacerations. The most favorable intervention would be one that is simple, less invasive with reduced postoperative complications/recovery time. The aim of this study is to report the surgical outcome with the Mini-Monoka monocanalicular stent. Material and Methods: Patients with traumatic canalicular lacerations who underwent surgical reconstruction using the Mini-Monoka monocanalicular stent were included. The surgical outcome was based on subjective (epiphora and objective (tear meniscus level, and lacrimal irrigation findings after stent removal. Result: Ten patients (mean age: 9.7 years of lower canaliculus injury were included. Successful stenting was accomplished in all cases. Postoperative eyelid position was satisfactory in most patients. The mean postoperative follow-up period was 6 months. There were no cases of premature stent extrusion. Functional drainage after stent removal was normal in all of patients. Syringing showed full patency. Conclusion:The MiniMonoka monocanalicular stent is an effective tool in reconstructing traumatic canalicular lacerations. Easy to use, carries a minimal risk of infection and injury to the non-lacerated canaliculus, and results in high anatomical and functional success rates.

  15. ANTARES alternative event reconstruction strategies

    CERN Document Server

    Becherini, Y

    2007-01-01

    The ANTARES Collaboration is building a high-energy neutrino telescope at 2500 m depth in the Mediterranean Sea. The experiment aims to search for high-energy cosmic neutrinos through the detection of Cerenkov light induced by muons and showers resulting from neutrino interactions with the surrounding medium. The detector will consist of a three-dimensional array of 900 optical modules housing photomultipliers. It will be composed of 12 strings, 5 of them being already in operation since January 2007. The muon track is reconstructed from the arrival time and the charge of the signals obtained from the photomultipliers, whose positions are known by means of an acoustic positioning system. The reconstruction strategies include several steps among which there are: optical background filtering, algorithms for first estimations of the track parameters, and a final fit aiming to reach an angular resolution better than 0.3 degree above 10 TeV in the full detector. Different reconstruction strategies will be presente...

  16. 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.

  17. War And Reconstruction: Four Comparative Case Studies

    Directory of Open Access Journals (Sweden)

    Pieter Kapp

    2012-02-01

    Full Text Available Traditionally defeated nations or peoples were regarded as at the mercy of the victorious powers. They were either incorporated into the power structure of the dominant power as a vassal or annexed by the victorious state, or were subjected to a humiliating peace treaty that did not provide for full restoration of their sovereignty. Very little attention was given to society at large; they were simply left at the mercy of whoever represented the new power. War as an instrument to reconstruct an entire society as a fully independent and sovereign state based on a new set of principles and an economic system in harmony with that of the triumphant party, is more closely associated with a revolution than with war in the traditional sense of the word. War as a means to create new states either through unification or separation is well known in history. But war to change the hearts and minds of entire society were less known before the twentieth century.

  18. 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.

  19. 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

  20. Understanding phenotypical character evolution in parmelioid lichenized fungi (Parmeliaceae, Ascomycota).

    Science.gov (United States)

    Divakar, Pradeep K; Kauff, Frank; Crespo, Ana; Leavitt, Steven D; Lumbsch, H Thorsten

    2013-01-01

    Parmelioid lichens form a species-rich group of predominantly foliose and fruticose lichenized fungi encompassing a broad range of morphological and chemical diversity. Using a multilocus approach, we reconstructed a phylogeny including 323 OTUs of parmelioid lichens and employed ancestral character reconstruction methods to understand the phenotypical evolution within this speciose group of lichen-forming fungi. Specifically, we were interested in the evolution of growth form, epicortex structure, and cortical chemistry. Since previous studies have shown that results may differ depending on the reconstruction method used, here we employed both maximum-parsimony and maximum-likelihood approaches to reconstruct ancestral character states. We have also implemented binary and multistate coding of characters and performed parallel analyses with both coding types to assess for potential coding-based biases. We reconstructed the ancestral states for nine well-supported major clades in the parmelioid group, two higher-level sister groups and the ancestral character state for all parmelioid lichens. We found that different methods for coding phenotypical characters and different ancestral character state reconstruction methods mostly resulted in identical reconstructions but yield conflicting inferences of ancestral states, in some cases. However, we found support for the ancestor of parmelioid lichens having been a foliose lichen with a non-pored epicortex and pseudocyphellae. Our data suggest that some traits exhibit patterns of evolution consistent with adaptive radiation. PMID:24312438

  1. Understanding phenotypical character evolution in parmelioid lichenized fungi (Parmeliaceae, Ascomycota.

    Directory of Open Access Journals (Sweden)

    Pradeep K Divakar

    Full Text Available Parmelioid lichens form a species-rich group of predominantly foliose and fruticose lichenized fungi encompassing a broad range of morphological and chemical diversity. Using a multilocus approach, we reconstructed a phylogeny including 323 OTUs of parmelioid lichens and employed ancestral character reconstruction methods to understand the phenotypical evolution within this speciose group of lichen-forming fungi. Specifically, we were interested in the evolution of growth form, epicortex structure, and cortical chemistry. Since previous studies have shown that results may differ depending on the reconstruction method used, here we employed both maximum-parsimony and maximum-likelihood approaches to reconstruct ancestral character states. We have also implemented binary and multistate coding of characters and performed parallel analyses with both coding types to assess for potential coding-based biases. We reconstructed the ancestral states for nine well-supported major clades in the parmelioid group, two higher-level sister groups and the ancestral character state for all parmelioid lichens. We found that different methods for coding phenotypical characters and different ancestral character state reconstruction methods mostly resulted in identical reconstructions but yield conflicting inferences of ancestral states, in some cases. However, we found support for the ancestor of parmelioid lichens having been a foliose lichen with a non-pored epicortex and pseudocyphellae. Our data suggest that some traits exhibit patterns of evolution consistent with adaptive radiation.

  2. 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

  3. 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...

  4. 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...

  5. Causality principle in reconstruction of sparse NMR spectra

    CERN Document Server

    Mayzel, Maxim; Orekhov, Vladislav Yu

    2014-01-01

    Rapid development of sparse sampling methodology offers dramatic increase in power and efficiency of magnetic resonance techniques in medicine, chemistry, molecular structural biology, and other fields. We show that harnessing causality of the sparsely detected NMR signal is a general approach for a major improvement of the spectra quality. The work gives a theoretical framework of the method and demonstrates notable improvement of the spectra reconstructed with two state-of-the-art signal processing algorithms, compressed sensing and SIFT.

  6. Rehabilitation and reconstruction of housing stock (nondestructive testing)

    International Nuclear Information System (INIS)

    Radiometry and radiography are used for nondestructive testing of the state of buildings which are to be reconstructed. The application is described of the radiometric method for controlling support elements of wooden structures of appartment buildings and the application is described of radiography for assessing wood quality and reinforced concrete structures. The use of radiometry is limited in view of the high costs of the measurement apparatus and the need of trained operators. (J.P.)

  7. 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...

  8. 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

  9. 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.

  10. 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。

  11. 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)

  12. A Comparison of Manual Neuronal Reconstruction from Biocytin Histology or 2-Photon Imaging: Morphometry and Computer Modeling

    Directory of Open Access Journals (Sweden)

    Arne Vladimir Blackman

    2014-07-01

    Full Text Available Accurate 3D reconstruction of neurons is vital for applications linking anatomy and physiology. Reconstructions are typically created using Neurolucida after biocytin histology (BH. An alternative inexpensive and fast method is to use freeware such as Neuromantic to reconstruct from fluorescence imaging (FI stacks acquired using 2-photon laser-scanning microscopy during physiological recording. We compare these two methods with respect to morphometry, cell classification, and multicompartmental modeling in the NEURON simulation environment. Quantitative morphological analysis of the same cells reconstructed using both methods reveals that whilst biocytin reconstructions facilitate tracing of more distal collaterals, both methods are comparable in representing the overall morphology: automated clustering of reconstructions from both methods successfully separates neocortical basket cells from pyramidal cells but not BH from FI reconstructions. BH reconstructions suffer more from tissue shrinkage and compression artifacts than FI reconstructions do. FI reconstructions, on the other hand, consistently have larger process diameters. Consequently, significant differences in NEURON modeling of excitatory post-synaptic potential (EPSP forward propagation are seen between the two methods, with FI reconstructions exhibiting smaller depolarizations. Simulated action potential backpropagation (bAP, however, is indistinguishable between reconstructions obtained with the two methods. In our hands, BH reconstructions are necessary for NEURON modeling and detailed morphological tracing, and thus remain state of the art, although they are more labor intensive, more expensive, and suffer from a higher failure rate. However, for a subset of anatomical applications such as cell type identification, FI reconstructions are superior, because of indistinguishable classification performance with greater ease of use, essentially 100% success rate, and lower cost.

  13. Results of large scale thyroid dose reconstruction in Ukraine

    International Nuclear Information System (INIS)

    In 1993, the Ukrainian Ministry on Chernobyl Affairs initiated a large scale reconstruction of thyroid exposures to radioiodine after the Chernobyl accident. The objective was to provide the state policy on social compensations with a scientific background. About 7000 settlements from five contaminated regions have gotten certificates of thyroid exposure since then. Certificates contain estimates of the average thyroid dose from 131I for seven age groups. The primary dose estimates used about 150000 direct measurements of the 131I activity in the thyroid glands of inhabitants from Chernigiv, Kiev, Zhytomyr, and also Vinnytsa regions. Parameters of the assumed intake function were related to environmental and questionnaire data. The dose reconstruction for the remaining territory was based on empirical relations between intake function parameters and the 137Cs deposition. The relationship was specified by the distance and the direction to the Chernobyl Nuclear Power Plant. The relations were first derived for territories with direct measurements and then they were spread on other areas using daily iodine releases and atmospheric transportation routes. The results of the dose reconstruction allowed to mark zones on the territory of Ukraine according to the average levels of thyroid exposures. These zones underlay a policy of post-accidental health care and social compensations. Another important application of the thyroid dose reconstruction is the radiation risk assessment of thyroid cancer among people exposed during childhood due to the Chernobyl accident

  14. Nonlinear dual reconstruction of SPECT activity and attenuation images.

    Science.gov (United States)

    Liu, Huafeng; Guo, Min; Hu, Zhenghui; Shi, Pengcheng; Hu, Hongjie

    2014-01-01

    In single photon emission computed tomography (SPECT), accurate attenuation maps are needed to perform essential attenuation compensation for high quality radioactivity estimation. Formulating the SPECT activity and attenuation reconstruction tasks as coupled signal estimation and system parameter identification problems, where the activity distribution and the attenuation parameter are treated as random variables with known prior statistics, we present a nonlinear dual reconstruction scheme based on the unscented Kalman filtering (UKF) principles. In this effort, the dynamic changes of the organ radioactivity distribution are described through state space evolution equations, while the photon-counting SPECT projection data are measured through the observation equations. Activity distribution is then estimated with sub-optimal fixed attenuation parameters, followed by attenuation map reconstruction given these activity estimates. Such coupled estimation processes are iteratively repeated as necessary until convergence. The results obtained from Monte Carlo simulated data, physical phantom, and real SPECT scans demonstrate the improved performance of the proposed method both from visual inspection of the images and a quantitative evaluation, compared to the widely used EM-ML algorithms. The dual estimation framework has the potential to be useful for estimating the attenuation map from emission data only and thus benefit the radioactivity reconstruction. PMID:25225796

  15. Advances in dose reconstruction at Oak Ridge

    International Nuclear Information System (INIS)

    The Oak Ridge Dose Reconstruction has seven tasks: (1) releases of radionuclides from X-10 radiolanthanum processing, (2) atmospheric and aquatic discharges of mercury from Y-12, (3) releases of PCB's from all facilities, (4) aquatic releases of radionuclides from X-10 into the Clinch River, (5) a systematic search for classified and unclassified records of past releases (6) releases of uranium from all facilities, and (7) screening of contaminants and release events not previously evaluated in the study. The contaminants, exposure pathways, and release events requiring the most intensive analysis are identified first through screening level calculations and then through an iterative assessment approach based on a preliminary uncertainty analysis of more realistic sets of models and assumptions. Subjective probability distributions are developed for uncertain model components, reflecting the present state of knowledge about true but unknown values, and these uncertainties are propagated through to estimates of dose and health risk using Monte Carlo simulation. This procedure is effective in identifying the components of the dose reconstruction model of dominant importance. Efforts are focused on the review and improvement of the set of preliminary assumptions that may significantly impact the overall uncertainty in the final result. The results of the screening calculations and the preliminary uncertainty analysis are compared against established decision criteria to identify the need for resource re-allocation among tasks. To date, a 10-4 life-time incidence of cancer incidence and a hazard index of one have been proposed as a decision criterion. Decisions about reallocation of resources among Tasks will be made by the Oak Ridge Health Agreement Steering Panel and the Tennessee Department of Health, which actively seek public involvement and participation

  16. Immediate Debridement and Reconstruction with

    Directory of Open Access Journals (Sweden)

    Hyoseob Lim

    2012-01-01

    Full Text Available Background Poststernotomy mediastinitis is a rare, but life-threatening complication,thus early diagnosis and proper management is essential for poststernotomy mediastinitis.The main treatment for mediastinitis is aggressive debridement. Several options exist forreconstruction of defects after debridement. The efficacy of immediate debridement andreconstruction with a pectoralis major muscle flap designed for the defect immediately afterthe diagnosis of poststernotomy mediastinitis is demonstrated.Methods Between September 2009 and June 2011, 6 patients were referred to the Departmentof Plastic and Reconstructive Surgery and the Department of Thoracic and CardiovascularSurgery of Ajou University Hospital for poststernotomy mediastinitis. All of the patientsunderwent extensive debridement and reconstruction with pectoralis major muscle flaps,advanced based on the pedicle of the thoracoacromial artery as soon as possible followingdiagnosis. A retrospective review of the 6 cases was performed to evaluate infection control,postoperative morbidity, and mortality.Results All patients had complete wound closures and reduced severity of infections basedon the erythrocyte sedimentation rate and C-reactive protein levels and a reduction inpoststernal fluid collection on computed tomography an average of 6 days postoperatively.A lack of growth of organisms in the wound culture was demonstrated after 3 weeks. Therewere no major wound morbidities, such as hematomas, but one minor complication requireda skin graft caused by skin flap necrosis. No patient expired after definitive surgery.Conclusions Immediate debridement and reconstruction using a pectoralis major muscle flapis a safe technique for managing infections associated with poststernotomy mediastinitis,and is associated with minimal morbidity and mortality.

  17. Unsupervised learning of spect reconstruction

    International Nuclear Information System (INIS)

    An approach of image reconstruction from projection in single-photon emission computed tomography (SPECT), based on an unsupervised learning artificial Kohonen neural network, is developed. A kind of random sampling technique is used to generate sensory input from tomographic projections. It is proved that an adequate interpretation and representation of the synaptic strengths of the network can be used to obtain the tomographic image. A relevant numerical experiment is reported. To validate the method tests were performed using a typical phantom (simulated object) used in limited data sets tomography. At the end of the self-organizing process the synaptic strengths can be shown on x-y plane as a map of points. The density of points gives the reconstructed image. In order to obtain a usual representation of the image a grid of 32 x 32 pixels was superimposed on the map and the number of points in each pixel was counted in order to form the image function. As the number of points in each pixel (especially for pixels corresponding to the background of the phantom) is relatively small, the image function is spoiled by noise. Noise filtering was used to improve the quality of the image. The final result is presented as a 3D-surface plot and as a corresponding 8-level gray map. It can be concluded that a good reconstruction of sizes and shapes was obtained. Some artifacts spoil the region located around the spikes. This artifact can be reduced if an increased number of external stimuli are presented to the network. The price paid for this improvement is the increase of computation time. (authors)

  18. Hanford Environmental Dose Reconstruction Project

    International Nuclear Information System (INIS)

    The objective of the Hanford Environmental Dose Reconstruction Project is to estimate the radiation doses that populations could have received from nuclear operations at Hanford since 1944. The project is being managed and conducted by the Pacific Northwest Laboratory (PNL) under the direction of an independent Technical Steering Panel (TSP). The project is divided into the following technical tasks. These tasks correspond to the path radionuclides followed, from released to impact on humans (dose estimates): source terms; environmental transport; environmental monitoring data; demographics, agriculture, food habits; and, environmental pathways and dose estimates

  19. Perforator Flaps for Perineal Reconstructions

    OpenAIRE

    Niranjan, Niri S.

    2006-01-01

    Whenever there is soft tissue loss from the perineum there are many options for reconstruction. These include allowing the wound to heal by secondary intention and the use of local random or axial pattern flaps, regional flaps, or free flaps. The axial skin flap can be defined as a flap based on known constant vessels of the subcutaneous tissue and its vena comitantes. The perforator flap on the other hand is a randomly selected perforator consisting of an artery with vena comitantes, which p...

  20. The Arthroscopic Superior Capsular Reconstruction.

    Science.gov (United States)

    Adams, Christopher R; Denard, Patrick J; Brady, Paul C; Hartzler, Robert U; Burkhart, Stephen S

    2016-01-01

    In a subset of patients with rotator cuff tears, the glenohumeral joint has minimal degenerative changes and the rotator cuff tendon is either irreparable or very poor quality and unlikely to heal. Reverse shoulder arthroplasty (RSA) is often considered for these patients despite the lack of glenohumeral arthritis. However, due to the permanent destruction of the glenohumeral articular surfaces, complication rates, and concerns about implant longevity with RSA, we believe the superior capsular reconstruction (SCR) is a viable alternative. In this article, we describe our technique for the SCR. PMID:27552457