Resolution effects in reconstructing ancestral genomes.

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Zheng, Chunfang; Jeong, Yuji; Turcotte, Madisyn Gabrielle; Sankoff, David

2018-05-09

The reconstruction of ancestral genomes must deal with the problem of resolution, necessarily involving a trade-off between trying to identify genomic details and being overwhelmed by noise at higher resolutions. We use the median reconstruction at the synteny block level, of the ancestral genome of the order Gentianales, based on coffee, Rhazya stricta and grape, to exemplify the effects of resolution (granularity) on comparative genomic analyses. We show how decreased resolution blurs the differences between evolving genomes, with respect to rate, mutational process and other characteristics.

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

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

2016-01-01

Members of the sooty blotch and flyspeck (SBFS) complex are epiphytic fungi in the Ascomycota that cause economically damaging blemishes of apples worldwide. SBFS fungi are polyphyletic, but approx. 96% of SBFS species are in the Capnodiales. Evolutionary origins of SBFS fungi remain unclear, so we attempted to infer their origins by means of ancestral state reconstruction on a phylogenetic tree built utilizing genes for the nuc 28S rDNA (approx. 830 bp from near the 59 end) and the second largest subunit of RNA polymerase II (RPB2). The analyzed taxa included the well-known genera of SBFS as well as non-SBFS fungi from seven families within the Capnodiales. The non-SBFS taxa were selected based on their distinct ecological niches, including plant-parasitic and saprophytic species. The phylogenetic analyses revealed that most SBFS species in the Capnodiales are closely related to plant-parasitic fungi. Ancestral state reconstruction provided strong evidence that plant-parasitic fungi were the ancestors of the major SBFS lineages. Knowledge gained from this study may help to better understand the ecology and evolution of epiphytic fungi. © 2016 by The Mycological Society of America.

Reconstruction of Ancestral Genomes in Presence of Gene Gain and Loss.

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Avdeyev, Pavel; Jiang, Shuai; Aganezov, Sergey; Hu, Fei; Alekseyev, Max A

2016-03-01

Since most dramatic genomic changes are caused by genome rearrangements as well as gene duplications and gain/loss events, it becomes crucial to understand their mechanisms and reconstruct ancestral genomes of the given genomes. This problem was shown to be NP-complete even in the "simplest" case of three genomes, thus calling for heuristic rather than exact algorithmic solutions. At the same time, a larger number of input genomes may actually simplify the problem in practice as it was earlier illustrated with MGRA, a state-of-the-art software tool for reconstruction of ancestral genomes of multiple genomes. One of the key obstacles for MGRA and other similar tools is presence of breakpoint reuses when the same breakpoint region is broken by several different genome rearrangements in the course of evolution. Furthermore, such tools are often limited to genomes composed of the same genes with each gene present in a single copy in every genome. This limitation makes these tools inapplicable for many biological datasets and degrades the resolution of ancestral reconstructions in diverse datasets. We address these deficiencies by extending the MGRA algorithm to genomes with unequal gene contents. The developed next-generation tool MGRA2 can handle gene gain/loss events and shares the ability of MGRA to reconstruct ancestral genomes uniquely in the case of limited breakpoint reuse. Furthermore, MGRA2 employs a number of novel heuristics to cope with higher breakpoint reuse and process datasets inaccessible for MGRA. In practical experiments, MGRA2 shows superior performance for simulated and real genomes as compared to other ancestral genome reconstruction tools.

Ancestral sequence reconstruction in primate mitochondrial DNA: compositional bias and effect on functional inference.

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Krishnan, Neeraja M; Seligmann, Hervé; Stewart, Caro-Beth; De Koning, A P Jason; Pollock, David D

2004-10-01

Reconstruction of ancestral DNA and amino acid sequences is an important means of inferring information about past evolutionary events. Such reconstructions suggest changes in molecular function and evolutionary processes over the course of evolution and are used to infer adaptation and convergence. Maximum likelihood (ML) is generally thought to provide relatively accurate reconstructed sequences compared to parsimony, but both methods lead to the inference of multiple directional changes in nucleotide frequencies in primate mitochondrial DNA (mtDNA). To better understand this surprising result, as well as to better understand how parsimony and ML differ, we constructed a series of computationally simple "conditional pathway" methods that differed in the number of substitutions allowed per site along each branch, and we also evaluated the entire Bayesian posterior frequency distribution of reconstructed ancestral states. We analyzed primate mitochondrial cytochrome b (Cyt-b) and cytochrome oxidase subunit I (COI) genes and found that ML reconstructs ancestral frequencies that are often more different from tip sequences than are parsimony reconstructions. In contrast, frequency reconstructions based on the posterior ensemble more closely resemble extant nucleotide frequencies. Simulations indicate that these differences in ancestral sequence inference are probably due to deterministic bias caused by high uncertainty in the optimization-based ancestral reconstruction methods (parsimony, ML, Bayesian maximum a posteriori). In contrast, ancestral nucleotide frequencies based on an average of the Bayesian set of credible ancestral sequences are much less biased. The methods involving simpler conditional pathway calculations have slightly reduced likelihood values compared to full likelihood calculations, but they can provide fairly unbiased nucleotide reconstructions and may be useful in more complex phylogenetic analyses than considered here due to their speed and

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

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

2015-09-01

To understand evolutionary transformations it is necessary to identify the character states of extinct ancestors. Ancestral character state reconstruction is inherently difficult because it requires an accurate phylogeny, character state data, and a statistical model of transition rates and is fundamentally constrained by missing data such as extinct taxa. We argue that model based ancestral character state reconstruction should be used to generate hypotheses but should not be considered an analytical endpoint. Using the evolution of viviparity and reversals to oviparity in squamates as a case study, we show how anatomical, physiological, and ecological data can be used to evaluate hypotheses about evolutionary transitions. The evolution of squamate viviparity requires changes to the timing of reproductive events and the successive loss of features responsible for building an eggshell. A reversal to oviparity requires that those lost traits re-evolve. We argue that the re-evolution of oviparity is inherently more difficult than the reverse. We outline how the inviability of intermediate phenotypes might present physiological barriers to reversals from viviparity to oviparity. Finally, we show that ecological data supports an oviparous ancestral state for squamates and multiple transitions to viviparity. In summary, we conclude that the first squamates were oviparous, that frequent transitions to viviparity have occurred, and that reversals to oviparity in viviparous lineages either have not occurred or are exceedingly rare. As this evidence supports conclusions that differ from previous ancestral state reconstructions, our paper highlights the importance of incorporating biological evidence to evaluate model-generated hypotheses. © 2015 Wiley Periodicals, Inc.

Musculature in sipunculan worms: ontogeny and ancestral states.

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Schulze, Anja; Rice, Mary E

2009-01-01

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

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

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Daniel Magee

2017-02-01

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

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.

Historian: accurate reconstruction of ancestral sequences and evolutionary rates.

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Holmes, Ian H

2017-04-15

Reconstruction of ancestral sequence histories, and estimation of parameters like indel rates, are improved by using explicit evolutionary models and summing over uncertain alignments. The previous best tool for this purpose (according to simulation benchmarks) was ProtPal, but this tool was too slow for practical use. Historian combines an efficient reimplementation of the ProtPal algorithm with performance-improving heuristics from other alignment tools. Simulation results on fidelity of rate estimation via ancestral reconstruction, along with evaluations on the structurally informed alignment dataset BAliBase 3.0, recommend Historian over other alignment tools for evolutionary applications. Historian is available at https://github.com/evoldoers/historian under the Creative Commons Attribution 3.0 US license. ihholmes+historian@gmail.com. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Characterization of Reconstructed Ancestral Proteins Suggests a Change in Temperature of the Ancient Biosphere.

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Akanuma, Satoshi

2017-08-06

Understanding the evolution of ancestral life, and especially the ability of some organisms to flourish in the variable environments experienced in Earth's early biosphere, requires knowledge of the characteristics and the environment of these ancestral organisms. Information about early life and environmental conditions has been obtained from fossil records and geological surveys. Recent advances in phylogenetic analysis, and an increasing number of protein sequences available in public databases, have made it possible to infer ancestral protein sequences possessed by ancient organisms. However, the in silico studies that assess the ancestral base content of ribosomal RNAs, the frequency of each amino acid in ancestral proteins, and estimate the environmental temperatures of ancient organisms, show conflicting results. The characterization of ancestral proteins reconstructed in vitro suggests that ancient organisms had very thermally stable proteins, and therefore were thermophilic or hyperthermophilic. Experimental data supports the idea that only thermophilic ancestors survived the catastrophic increase in temperature of the biosphere that was likely associated with meteorite impacts during the early history of Earth. In addition, by expanding the timescale and including more ancestral proteins for reconstruction, it appears as though the Earth's surface temperature gradually decreased over time, from Archean to present.

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

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

2015-01-01

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. Viruses rescued from...... the reconstructed cDNAs were tested in cell culture and pigs. Both reconstructed ancestral genomes proved functional, and displayed distinct phenotypes in vitro and in vivo. We suggest that reconstruction of ancestral viruses is a useful tool for experimental and computational investigations of virulence and viral...... evolution. Importantly, ancestral reconstruction can be done even on the basis of a set of sequences that all correspond to non-functional variants....

A phylogenetic Kalman filter for ancestral trait reconstruction using molecular data.

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Lartillot, Nicolas

2014-02-15

Correlation between life history or ecological traits and genomic features such as nucleotide or amino acid composition can be used for reconstructing the evolutionary history of the traits of interest along phylogenies. Thus far, however, such ancestral reconstructions have been done using simple linear regression approaches that do not account for phylogenetic inertia. These reconstructions could instead be seen as a genuine comparative regression problem, such as formalized by classical generalized least-square comparative methods, in which the trait of interest and the molecular predictor are represented as correlated Brownian characters coevolving along the phylogeny. Here, a Bayesian sampler is introduced, representing an alternative and more efficient algorithmic solution to this comparative regression problem, compared with currently existing generalized least-square approaches. Technically, ancestral trait reconstruction based on a molecular predictor is shown to be formally equivalent to a phylogenetic Kalman filter problem, for which backward and forward recursions are developed and implemented in the context of a Markov chain Monte Carlo sampler. The comparative regression method results in more accurate reconstructions and a more faithful representation of uncertainty, compared with simple linear regression. Application to the reconstruction of the evolution of optimal growth temperature in Archaea, using GC composition in ribosomal RNA stems and amino acid composition of a sample of protein-coding genes, confirms previous findings, in particular, pointing to a hyperthermophilic ancestor for the kingdom. The program is freely available at www.phylobayes.org.

Reconstruction of ancestral RNA sequences under multiple structural constraints.

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Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldispühl, Jérôme

2016-11-11

Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

Reconstruction of ancestral RNA sequences under multiple structural constraints

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Olivier Tremblay-Savard

2016-11-01

Full Text Available Abstract Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given two alignments of homologous ncRNA families with consensus secondary structures and a phylogenetic tree, simultaneously calculates ancestral RNA sequences for these two families. Results We test our methodology on simulated data sets, and show that achARNement outperforms classical maximum parsimony approaches in terms of accuracy, but also reduces by several orders of magnitude the number of candidate sequences. To conclude this study, we apply our algorithms on the Glm clan and the FinP-traJ clan from the Rfam database. Conclusions Our results show that our methods reconstruct small sets of high-quality candidate ancestors with better agreement to the two target structures than with classical approaches. Our program is freely available at: http://csb.cs.mcgill.ca/acharnement .

Reconstruction of ancestral RNA sequences under multiple structural constraints

OpenAIRE

Tremblay-Savard, Olivier; Reinharz, Vladimir; Waldisp?hl, J?r?me

2016-01-01

Background Secondary structures form the scaffold of multiple sequence alignment of non-coding RNA (ncRNA) families. An accurate reconstruction of ancestral ncRNAs must use this structural signal. However, the inference of ancestors of a single ncRNA family with a single consensus structure may bias the results towards sequences with high affinity to this structure, which are far from the true ancestors. Methods In this paper, we introduce achARNement, a maximum parsimony approach that, given...

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

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Butzin, Nicholas C; Lapierre, Pascal; Green, Anna G; Swithers, Kristen S; Gogarten, J Peter; Noll, Kenneth M

2013-01-01

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

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

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Nicholas C Butzin

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

Phylogenetic uncertainty can bias the number of evolutionary transitions estimated from ancestral state reconstruction methods.

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Duchêne, Sebastian; Lanfear, Robert

2015-09-01

Ancestral state reconstruction (ASR) is a popular method for exploring the evolutionary history of traits that leave little or no trace in the fossil record. For example, it has been used to test hypotheses about the number of evolutionary origins of key life-history traits such as oviparity, or key morphological structures such as wings. Many studies that use ASR have suggested that the number of evolutionary origins of such traits is higher than was previously thought. The scope of such inferences is increasing rapidly, facilitated by the construction of very large phylogenies and life-history databases. In this paper, we use simulations to show that the number of evolutionary origins of a trait tends to be overestimated when the phylogeny is not perfect. In some cases, the estimated number of transitions can be several fold higher than the true value. Furthermore, we show that the bias is not always corrected by standard approaches to account for phylogenetic uncertainty, such as repeating the analysis on a large collection of possible trees. These findings have important implications for studies that seek to estimate the number of origins of a trait, particularly those that use large phylogenies that are associated with considerable uncertainty. We discuss the implications of this bias, and methods to ameliorate it. © 2015 Wiley Periodicals, Inc.

Reconstructed ancestral enzymes reveal that negative selection drove the evolution of substrate specificity in ADP-dependent kinases.

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Castro-Fernandez, Víctor; Herrera-Morande, Alejandra; Zamora, Ricardo; Merino, Felipe; Gonzalez-Ordenes, Felipe; Padilla-Salinas, Felipe; Pereira, Humberto M; Brandão-Neto, Jose; Garratt, Richard C; Guixe, Victoria

2017-09-22

One central goal in molecular evolution is to pinpoint the mechanisms and evolutionary forces that cause an enzyme to change its substrate specificity; however, these processes remain largely unexplored. Using the glycolytic ADP-dependent kinases of archaea, including the orders Thermococcales , Methanosarcinales , and Methanococcales , as a model and employing an approach involving paleoenzymology, evolutionary statistics, and protein structural analysis, we could track changes in substrate specificity during ADP-dependent kinase evolution along with the structural determinants of these changes. To do so, we studied five key resurrected ancestral enzymes as well as their extant counterparts. We found that a major shift in function from a bifunctional ancestor that could phosphorylate either glucose or fructose 6-phosphate (fructose-6-P) as a substrate to a fructose 6-P-specific enzyme was started by a single amino acid substitution resulting in negative selection with a ground-state mode against glucose and a subsequent 1,600-fold change in specificity of the ancestral protein. This change rendered the residual phosphorylation of glucose a promiscuous and physiologically irrelevant activity, highlighting how promiscuity may be an evolutionary vestige of ancestral enzyme activities, which have been eliminated over time. We also could reconstruct the evolutionary history of substrate utilization by using an evolutionary model of discrete binary characters, indicating that substrate uses can be discretely lost or acquired during enzyme evolution. These findings exemplify how negative selection and subtle enzyme changes can lead to major evolutionary shifts in function, which can subsequently generate important adaptive advantages, for example, in improving glycolytic efficiency in Thermococcales . © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

The evolution of brachiation in ateline primates, ancestral character states and history.

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Jones, Andrea L

2008-10-01

This study examines how brachiation locomotion evolved in ateline primates using recently-developed molecular phylogenies and character reconstruction algorithms, and a newly-collected dataset including the fossils Protopithecus, Caipora, and Cebupithecia. Fossils are added to two platyrrhine molecular phylogenies to create several phylogenetic scenarios. A generalized least squares algorithm reconstructs ateline and atelin ancestral character states for 17 characters that differentiate between ateline brachiators and nonbrachiators. Histories of these characters are mapped out on these phylogenies, producing two scenarios of ateline brachiation evolution that have four commonalities: First, many characters change towards the Ateles condition on the ateline stem lineage before Alouatta splits off from the atelins, suggesting that an ateline energy-maximizing strategy began before the atelines diversified. Second, the ateline last common ancestor is always reconstructed as an agile quadruped, usually with suspensory abilities. It is never exactly like Alouatta and many characters reverse and change towards the Alouatta condition after Alouatta separates from the atelins. Third, most characters undergo homoplastic change in all ateline lineages, especially on the Ateles and Brachyteles terminal branches. Fourth, ateline character evolution probably went through a hindlimb suspension with tail-bracing phase. The atelines most likely diversified via a quick adaptive radiation, with bursts of punctuated change occurring in their postcranial skeletons, due to changing climatic conditions, which may have caused competition among the atelines and between atelines and pitheciines.

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

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Victor Hanson-Smith

2016-07-01

Full Text Available 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.

Ancestral gene reconstruction and synthesis of ancient rhodopsins in the laboratory.

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Chang, Belinda S W

2003-08-01

Laboratory synthesis of ancestral proteins offers an intriguing opportunity to study the past directly. The development of Bayesian methods to infer ancestral sequences, combined with advances in models of molecular evolution, and synthetic gene technology make this an increasingly promising approach in evolutionary studies of molecular function. Visual pigments form the first step in the biochemical cascade of events in the retina in all animals known to possess visual capabilities. In vertebrates, the necessity of spanning a dynamic range of light intensities of many orders of magnitude has given rise to two different types of photoreceptors, rods specialized for dim-light conditions, and cones for daylight and color vision. These photoreceptors contain different types of visual pigment genes. Reviewed here are methods of inferring ancestral sequences, chemical synthesis of artificial ancestral genes in the laboratory, and applications to the evolution of vertebrate visual systems and the experimental recreation of an archosaur rod visual pigment. The ancestral archosaurs gave rise to several notable lineages of diapsid reptiles, including the birds and the dinosaurs, and would have existed over 200 MYA. What little is known of their physiology comes from fossil remains, and inference based on the biology of their living descendants. Despite its age, an ancestral archosaur pigment was successfully recreated in the lab, and showed interesting properties of its wavelength sensitivity that may have implications for the visual capabilities of the ancestral archosaurs in dim light.

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

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Carmel, Liran; Wolf, Yuri I; Rogozin, Igor B; Koonin, Eugene V

2010-01-01

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

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

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Liran Carmel

2010-01-01

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

Ancestral sequence alignment under optimal conditions

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Brown Daniel G

2005-11-01

Full Text Available Abstract Background Multiple genome alignment is an important problem in bioinformatics. An important subproblem used by many multiple alignment approaches is that of aligning two multiple alignments. Many popular alignment algorithms for DNA use the sum-of-pairs heuristic, where the score of a multiple alignment is the sum of its induced pairwise alignment scores. However, the biological meaning of the sum-of-pairs of pairs heuristic is not obvious. Additionally, many algorithms based on the sum-of-pairs heuristic are complicated and slow, compared to pairwise alignment algorithms. An alternative approach to aligning alignments is to first infer ancestral sequences for each alignment, and then align the two ancestral sequences. In addition to being fast, this method has a clear biological basis that takes into account the evolution implied by an underlying phylogenetic tree. In this study we explore the accuracy of aligning alignments by ancestral sequence alignment. We examine the use of both maximum likelihood and parsimony to infer ancestral sequences. Additionally, we investigate the effect on accuracy of allowing ambiguity in our ancestral sequences. Results We use synthetic sequence data that we generate by simulating evolution on a phylogenetic tree. We use two different types of phylogenetic trees: trees with a period of rapid growth followed by a period of slow growth, and trees with a period of slow growth followed by a period of rapid growth. We examine the alignment accuracy of four ancestral sequence reconstruction and alignment methods: parsimony, maximum likelihood, ambiguous parsimony, and ambiguous maximum likelihood. Additionally, we compare against the alignment accuracy of two sum-of-pairs algorithms: ClustalW and the heuristic of Ma, Zhang, and Wang. Conclusion We find that allowing ambiguity in ancestral sequences does not lead to better multiple alignments. Regardless of whether we use parsimony or maximum likelihood, the

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

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Illa, Eudald; Sargent, Daniel J; Lopez Girona, Elena; Bushakra, Jill; Cestaro, Alessandro; Crowhurst, Ross; Pindo, Massimo; Cabrera, Antonio; van der Knaap, Esther; Iezzoni, Amy; Gardiner, Susan; Velasco, Riccardo; Arús, Pere; Chagné, David; Troggio, Michela

2011-01-12

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. 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. 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.

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.

Resurrecting ancestral genes in bacteria to interpret ancient biosignatures

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Kacar, Betul; Guy, Lionel; Smith, Eric; Baross, John

2017-11-01

Two datasets, the geologic record and the genetic content of extant organisms, provide complementary insights into the history of how key molecular components have shaped or driven global environmental and macroevolutionary trends. Changes in global physico-chemical modes over time are thought to be a consistent feature of this relationship between Earth and life, as life is thought to have been optimizing protein functions for the entirety of its approximately 3.8 billion years of history on the Earth. Organismal survival depends on how well critical genetic and metabolic components can adapt to their environments, reflecting an ability to optimize efficiently to changing conditions. The geologic record provides an array of biologically independent indicators of macroscale atmospheric and oceanic composition, but provides little in the way of the exact behaviour of the molecular components that influenced the compositions of these reservoirs. By reconstructing sequences of proteins that might have been present in ancient organisms, we can downselect to a subset of possible sequences that may have been optimized to these ancient environmental conditions. How can one use modern life to reconstruct ancestral behaviours? Configurations of ancient sequences can be inferred from the diversity of extant sequences, and then resurrected in the laboratory to ascertain their biochemical attributes. One way to augment sequence-based, single-gene methods to obtain a richer and more reliable picture of the deep past, is to resurrect inferred ancestral protein sequences in living organisms, where their phenotypes can be exposed in a complex molecular-systems context, and then to link consequences of those phenotypes to biosignatures that were preserved in the independent historical repository of the geological record. As a first step beyond single-molecule reconstruction to the study of functional molecular systems, we present here the ancestral sequence reconstruction of the

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

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Sophie Nadot

2016-04-01

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

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...... optimization, which has clear advantages regarding speed, control and accuracy in comparison to commonly employed numerical routines. First prototype implementations easily allow reconstruction of a state of 20 qubits in a few minutes on a standard computer.......-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...

Molecular phylogenetic reconstruction and localization of the (TTAGG)n telomeric repeats in the chromosomes of Acromyrmex striatus (Roger, 1863) suggests a lower ancestral karyotype for leafcutter ants (Hymenoptera).

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Pereira, Tássia Tatiane Pontes; Dos Reis, Ana Caroline Coelho Corrêa; Cardoso, Danon Clemes; Cristiano, Maykon Passos

2018-01-01

Chromosome counts and karyotype characterization have proved to be important features of a genome. Chromosome changes during the diversification of ants might play an important role, given the diversity and success of Formicidae. Comparative karyotype analyses on ants have enriched and helped ant systematics. Among leafcutter ants, two major chromosome counts have been described, one frequent in Atta Fabricius, 1804 (2n = 22 in all Atta spp. whose karyotype is known) and the other frequent in Acromyrmex Mayr, 1865 (2n = 38 in the majority of species whose karyotype is known). The main exception is Acromyrmex striatus (Roger, 1863), which harbors a diploid chromosome set of 22. Here we describe the use of fluorescence in situ hybridization (FISH) with telomeric probes with (TTAGG) 6 repeats to describe the telomere composition of A. striatus and to recover potential interstitial non-telomeric signals that may reflect fusion events during the evolution of leafcutter lineage from 38 to 22 chromosomes. Further, we reconstruct the ancestral chromosome numbers of the leafcutter clade based on a recently proposed molecular phylogenetic hypothesis and phylogenomic tree. Distinct signals have been observed in both extremities on the telomere chromosomes of A. striatus . Non-telomeric signals have not been retrieved in our analysis. It could be supposed that the low-numbered karyotype indeed represents the ancestral chromosome number of leafcutters. The phylogenetic reconstruction also recovered a low chromosome number from the diverse approaches implemented, suggesting that n = 11 is the most likely ancestral karyotype of the leafcutter ants and is a plesiomorphic feature shared between A. striatus and Atta spp.

Molecular phylogenetic reconstruction and localization of the (TTAGGn telomeric repeats in the chromosomes of Acromyrmex striatus (Roger, 1863 suggests a lower ancestral karyotype for leafcutter ants (Hymenoptera

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Tássia Tatiane Pontes Pereira

2018-01-01

Full Text Available Chromosome counts and karyotype characterization have proved to be important features of a genome. Chromosome changes during the diversification of ants might play an important role, given the diversity and success of Formicidae. Comparative karyotype analyses on ants have enriched and helped ant systematics. Among leafcutter ants, two major chromosome counts have been described, one frequent in Atta Fabricius, 1804 (2n = 22 in all Atta spp. whose karyotype is known and the other frequent in Acromyrmex Mayr, 1865 (2n = 38 in the majority of species whose karyotype is known. The main exception is Acromyrmex striatus (Roger, 1863, which harbors a diploid chromosome set of 22. Here we describe the use of fluorescence in situ hybridization (FISH with telomeric probes with (TTAGG6 repeats to describe the telomere composition of A. striatus and to recover potential interstitial non-telomeric signals that may reflect fusion events during the evolution of leafcutter lineage from 38 to 22 chromosomes. Further, we reconstruct the ancestral chromosome numbers of the leafcutter clade based on a recently proposed molecular phylogenetic hypothesis and phylogenomic tree. Distinct signals have been observed in both extremities on the telomere chromosomes of A. striatus. Non-telomeric signals have not been retrieved in our analysis. It could be supposed that the low-numbered karyotype indeed represents the ancestral chromosome number of leafcutters. The phylogenetic reconstruction also recovered a low chromosome number from the diverse approaches implemented, suggesting that n = 11 is the most likely ancestral karyotype of the leafcutter ants and is a plesiomorphic feature shared between A. striatus and Atta spp.

Inference of the ancestral vertebrate phenotype through vestiges of the whole-genome duplications.

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Onimaru, Koh; Kuraku, Shigehiro

2018-03-16

Inferring the phenotype of the last common ancestor of living vertebrates is a challenging problem because of several unresolvable factors. They include the lack of reliable out-groups of living vertebrates, poor information about less fossilizable organs and specialized traits of phylogenetically important species, such as lampreys and hagfishes (e.g. secondary loss of vertebrae in adult hagfishes). These factors undermine the reliability of ancestral reconstruction by traditional character mapping approaches based on maximum parsimony. In this article, we formulate an approach to hypothesizing ancestral vertebrate phenotypes using information from the phylogenetic and functional properties of genes duplicated by genome expansions in early vertebrate evolution. We named the conjecture as 'chronological reconstruction of ohnolog functions (CHROF)'. This CHROF conjecture raises the possibility that the last common ancestor of living vertebrates may have had more complex traits than currently thought.

Approximate maximum parsimony and ancestral maximum likelihood.

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Alon, Noga; Chor, Benny; Pardi, Fabio; Rapoport, Anat

2010-01-01

We explore the maximum parsimony (MP) and ancestral maximum likelihood (AML) criteria in phylogenetic tree reconstruction. Both problems are NP-hard, so we seek approximate solutions. We formulate the two problems as Steiner tree problems under appropriate distances. The gist of our approach is the succinct characterization of Steiner trees for a small number of leaves for the two distances. This enables the use of known Steiner tree approximation algorithms. The approach leads to a 16/9 approximation ratio for AML and asymptotically to a 1.55 approximation ratio for MP.

Phylogenetic reconstruction and shell evolution of the Diplommatinidae (Gastropoda: Caenogastropoda).

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Webster, Nicole B; Van Dooren, Tom J M; Schilthuizen, Menno

2012-06-01

The fascinating and often unlikely shell shapes in the terrestrial micromollusc family Diplommatinidae (Gastropoda: Caenogastropoda) provide a particularly attractive set of multiple morphological traits to investigate evolutionary patterns of shape variation. Here, a molecular phylogenetic reconstruction, based on five genes and 2700 bp, was undertaken for this family, integrated with ancestral state reconstruction and phylogenetic PCA of discrete and quantitative traits, respectively. We found strong support for the Diplommatininae as a monophyletic group, separating the Cochlostomatidae into a separate family. Five main clades appear within the Diplommatininae, corresponding with both coiling direction and biogeographic patterns. A Belau clade (A) with highly diverse (but always sinistral) morphology comprised Hungerfordia, Palaina, and some Diplommatina. Arinia (dextral) and Opisthostoma (sinistroid) are sister groups in clade B. Clade C and D solely contain sinistral Diplommatina that are robust and little ornamented (clade C) or slender and sculptured (clade D). Clade E is dextral but biogeographically diverse with species from all sampled regions save the Caroline Islands. Adelopoma, Diplommatina, Palaina, and Hungerfordia require revision to allow taxonomy to reflect phylogeny, whereas Opisthostoma is clearly monophyletic. Ancestral state reconstruction suggests a sinistral origin for the Diplommatinidae, with three reversals to dextrality. Copyright © 2012 Elsevier Inc. All rights reserved.

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

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Katherine Belov

2006-03-01

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

Ancestrality and evolution of trait syndromes in finches (Fringillidae).

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Ponge, Jean-François; Zuccon, Dario; Elias, Marianne; Pavoine, Sandrine; Henry, Pierre-Yves; Théry, Marc; Guilbert, Éric

2017-12-01

Species traits have been hypothesized by one of us (Ponge, 2013) to evolve in a correlated manner as species colonize stable, undisturbed habitats, shifting from "ancestral" to "derived" strategies. We predicted that generalism, r-selection, sexual monomorphism, and migration/gregariousness are the ancestral states (collectively called strategy A) and evolved correlatively toward specialism, K-selection, sexual dimorphism, and residence/territoriality as habitat stabilized (collectively called B strategy). We analyzed the correlated evolution of four syndromes, summarizing the covariation between 53 traits, respectively, involved in ecological specialization, r-K gradient, sexual selection, and dispersal/social behaviors in 81 species representative of Fringillidae, a bird family with available natural history information and that shows variability for all these traits. The ancestrality of strategy A was supported for three of the four syndromes, the ancestrality of generalism having a weaker support, except for the core group Carduelinae (69 species). It appeared that two different B-strategies evolved from the ancestral state A, both associated with highly predictable environments: one in poorly seasonal environments, called B1, with species living permanently in lowland tropics, with "slow pace of life" and weak sexual dimorphism, and one in highly seasonal environments, called B2, with species breeding out-of-the-tropics, migratory, with a "fast pace of life" and high sexual dimorphism.

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

OpenAIRE

McCann, Jamie; Schneeweiss, Gerald M.; Stuessy, Tod F.; Villase?or, Jose L.; Weiss-Schneeweiss, Hanna

2016-01-01

Chromosome number change (polyploidy and dysploidy) plays an important role in plant diversification and speciation. Investigating chromosome number evolution commonly entails ancestral state reconstruction performed within a phylogenetic framework, which is, however, prone to uncertainty, whose effects on evolutionary inferences are insufficiently understood. Using the chromosomally diverse plant genus Melampodium (Asteraceae) as model group, we assess the impact of reconstruction method (ma...

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.

The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials.

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Suárez-Villota, Elkin Y; Haro, Ronie E; Vargas, Rodrigo A; Gallardo, Milton H

2016-01-01

The low-numbered 14-chromosome karyotype of marsupials has falsified the fusion hypothesis claiming ancestrality from a 22-chromosome karyotype. Since the 14-chromosome condition of the relict Dromiciops gliroides is reminecent of ancestrality, its interstitial traces of past putative fusions and heterochromatin banding patterns were studied and added to available marsupials' cytogenetic data. Fluorescent in situ hybridization (FISH) and self-genomic in situ hybridization (self-GISH) were used to detect telomeric and repetitive sequences, respectively. These were complemented with C-, fluorescent banding, and centromere immunodetection over mitotic spreads. The presence of interstitial telomeric sequences (ITS) and diploid numbers were reconstructed and mapped onto the marsupial phylogenetic tree. No interstitial, fluorescent signals, but clearly stained telomeric regions were detected by FISH and self-GISH. Heterochromatin distribution was sparse in the telomeric/subtelomeric regions of large submetacentric chromosomes. Large AT-rich blocks were detected in the long arm of four submetacentrics and CG-rich block in the telomeric regions of all chromosomes. The ancestral reconstructions both ITS presence and diploid numbers suggested that ITS are unrelated to fusion events. Although the lack of interstitial signals in D. gliroides' karyotype does not prove absence of past fusions, our data suggests its non-rearranged plesiomorphic condition.

Ancestral Relationships Using Metafounders: Finite Ancestral Populations and Across Population Relationships.

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Legarra, Andres; Christensen, Ole F; Vitezica, Zulma G; Aguilar, Ignacio; Misztal, Ignacy

2015-06-01

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 which each population is considered as an infinite, unrelated pool. Several ancestral populations may be connected and therefore related. Each ancestral population can be represented as a "metafounder," a pseudo-individual included as founder of the pedigree and similar to an "unknown parent group." Metafounders have self- and across relationships according to a set of parameters, which measure ancestral relationships, i.e., homozygozities within populations and relationships across populations. These parameters can be estimated from existing pedigree and marker genotypes using maximum likelihood or a method based on summary statistics, for arbitrarily complex pedigrees. Equivalences of genetic variance and variance components between the classical and this new parameterization are shown. Segregation variance on crosses of populations is modeled. Efficient algorithms for computation of relationship matrices, their inverses, and inbreeding coefficients are presented. Use of metafounders leads to compatibility of genomic and pedigree relationship matrices and to simple computing algorithms. Examples and code are given. Copyright © 2015 by the Genetics Society of America.

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: 8.225, year: 2015

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

DEFF Research Database (Denmark)

Natarajan, Chandrasekhar; Kumar, Amit; Moriyama, Hideaki

2016-01-01

the functional effects of causative mutations on the genetic background in which they actually occurred during evolution (i.e., in the BHG ancestor). An alternative ‘vertical’ approach is to reconstruct and resurrect ancestral proteins to test the effects of historical mutations on the genetic background...

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...

The mitochondrial genomes of Nuttalliella namaqua (Ixodoidea: Nuttalliellidae and Argas africolumbae (Ixodoidae: Argasidae: estimation of divergence dates for the major tick lineages and reconstruction of ancestral blood-feeding characters.

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Ben J Mans

Full Text Available Ixodida are composed of hard (Ixodidae, soft (Argasidae and the monotypic Nuttalliellidae (Nuttalliella namaqua tick families. Nuclear 18S rRNA analysis suggested that N. namaqua was the closest extant relative to the last common ancestral tick lineage. The mitochondrial genomes of N. namaqua and Argas africolumbae were determined using next generation sequencing and de novo assembly to investigate this further. The latter was included since previous estimates on the divergence times of argasids lacked data for this major genus. Mitochondrial gene order for both was identical to that of the Argasidae and Prostriata. Bayesian analysis of the COI, Cytb, ND1, ND2 and ND4 genes confirmed the monophyly of ticks, the basal position of N. namaqua to the other tick families and the accepted systematic relationships of the other tick genera. Molecular clock estimates were derived for the divergence of the major tick lineages and supported previous estimates on the origins of ticks in the Carboniferous. N. namaqua larvae fed successfully on lizards and mice in a prolonged manner similar to many argasids and all ixodids. Excess blood meal-derived water was secreted via the salivary glands, similar to ixodids. We propose that this prolonged larval feeding style eventually gave rise to the long feeding periods that typify the single larval, nymphal and adult stages of ixodid ticks and the associated secretion of water via the salivary glands. Ancestral reconstruction of characters involved in blood-feeding indicates that most of the characteristics unique to either hard or soft tick families were present in the ancestral tick lineage.

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

The morphology of neoptile feathers: ancestral state reconstruction and its phylogenetic implications.

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Foth, Christian

2011-04-01

Avian neoptile feathers are defined as the first feather generation, which covers the chick after hatching, and usually described as simple structures consisting of numerous downy barbs which are radially symmetrically arranged and come together in a short calamus. In contrast, in some birds (e.g., Anas platyrhynchos, Dromaius novaehollandiae) the neoptile feathers have a prominent rhachis, and therefore display clear bilateral symmetry. Because the symmetrical variety found in neoptile feathers is poorly understood, their morphology was studied in a more comprehensive and phylogenetic approach. Neoptile body feathers from over 22 bird species were investigated using light microscopy, SEM, and MicroCT. Characters such as an anterior-posterior axis, a central rhachis, medullary cells, and structure of the calamus wall were defined and mapped onto recent phylogenetic hypotheses for extant birds. It can be shown that bilaterally symmetric neoptile feathers (with a solid calamus wall) were already present in the stem lineage of crown-group birds (Neornithes). In contrast, simple radially symmetric neoptile feathers (with a fragile calamus wall) are an apomorphic character complex for the clade Neoaves. The simple morphology of this feather type may be the result of a reduced period of development during embryogenesis. To date, embryogenesis of neoptile feathers from only a few bird species was used as a model to reconstruct feather evolution. Because this study shows that the morphology of neoptile feathers is more diverse and even shows a clear phylogenetic signal, it is necessary to expand the spectrum of "model organisms" to species with bilaterally symmetric neoptile feathers and compare differences in the frequency of feather development from a phylogenetic point of view. Copyright © 2011 Wiley-Liss, Inc.

Ancestral Variations in the Shape and Size of the Zygoma.

Science.gov (United States)

Oettlé, Anna C; Demeter, Fabrice P; L'abbé, Ericka N

2017-01-01

The variable development of the zygoma, dictating its shape and size variations among ancestral groups, has important clinical implications and valuable anthropological and evolutionary inferences. The purpose of the study was to review the literature regarding the variations in the zygoma with ancestry. Ancestral variation in the zygoma reflects genetic variations because of genetic drift as well as natural selection and epigenetic changes to adapt to diet and climate variations with possible intensification by isolation. Prominence of the zygoma, zygomaxillary tuberosity, and malar tubercle have been associated with Eastern Asian populations in whom these features intensified. Prominence of the zygoma is also associated with groups from Eastern Europe and the rest of Asia. Diffusion of these traits occurred across the Behring Sea to the Arctic areas and to North and South America. The greatest zygomatic projections are exhibited in Arctic groups as an adaptation to extreme cold conditions, while Native South American groups also present with other features of facial robusticity. Groups from Australia, Malaysia, and Oceania show prominence of the zygoma to a certain extent, possibly because of archaic occupations by undifferentiated Southeast Asian populations. More recent interactions with Chinese groups might explain the prominent cheekbones noted in certain South African groups. Many deductions regarding evolutionary processes and diversifications of early groups have been made. Cognisance of these ancestral variations also have implications for forensic anthropological assessments as well as plastic and reconstructive surgery. More studies are needed to improve accuracy of forensic anthropological identification techniques. Anat Rec, 300:196-208, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Cases in which ancestral maximum likelihood will be confusingly misleading.

Science.gov (United States)

Handelman, Tomer; Chor, Benny

2017-05-07

Ancestral maximum likelihood (AML) is a phylogenetic tree reconstruction criteria that "lies between" maximum parsimony (MP) and maximum likelihood (ML). ML has long been known to be statistically consistent. On the other hand, Felsenstein (1978) showed that MP is statistically inconsistent, and even positively misleading: There are cases where the parsimony criteria, applied to data generated according to one tree topology, will be optimized on a different tree topology. The question of weather AML is statistically consistent or not has been open for a long time. Mossel et al. (2009) have shown that AML can "shrink" short tree edges, resulting in a star tree with no internal resolution, which yields a better AML score than the original (resolved) model. This result implies that AML is statistically inconsistent, but not that it is positively misleading, because the star tree is compatible with any other topology. We show that AML is confusingly misleading: For some simple, four taxa (resolved) tree, the ancestral likelihood optimization criteria is maximized on an incorrect (resolved) tree topology, as well as on a star tree (both with specific edge lengths), while the tree with the original, correct topology, has strictly lower ancestral likelihood. Interestingly, the two short edges in the incorrect, resolved tree topology are of length zero, and are not adjacent, so this resolved tree is in fact a simple path. While for MP, the underlying phenomenon can be described as long edge attraction, it turns out that here we have long edge repulsion. Copyright © 2017. Published by Elsevier Ltd.

Reconstructing the ups and downs of primate brain evolution: implications for adaptive hypotheses and Homo floresiensis

Directory of Open Access Journals (Sweden)

Barton Robert A

2010-01-01

Full Text Available Abstract Background Brain size is a key adaptive trait. It is often assumed that increasing brain size was a general evolutionary trend in primates, yet recent fossil discoveries have documented brain size decreases in some lineages, raising the question of how general a trend there was for brains to increase in mass over evolutionary time. We present the first systematic phylogenetic analysis designed to answer this question. Results We performed ancestral state reconstructions of three traits (absolute brain mass, absolute body mass, relative brain mass using 37 extant and 23 extinct primate species and three approaches to ancestral state reconstruction: parsimony, maximum likelihood and Bayesian Markov-chain Monte Carlo. Both absolute and relative brain mass generally increased over evolutionary time, but body mass did not. Nevertheless both absolute and relative brain mass decreased along several branches. Applying these results to the contentious case of Homo floresiensis, we find a number of scenarios under which the proposed evolution of Homo floresiensis' small brain appears to be consistent with patterns observed along other lineages, dependent on body mass and phylogenetic position. Conclusions Our results confirm that brain expansion began early in primate evolution and show that increases occurred in all major clades. Only in terms of an increase in absolute mass does the human lineage appear particularly striking, with both the rate of proportional change in mass and relative brain size having episodes of greater expansion elsewhere on the primate phylogeny. However, decreases in brain mass also occurred along branches in all major clades, and we conclude that, while selection has acted to enlarge primate brains, in some lineages this trend has been reversed. Further analyses of the phylogenetic position of Homo floresiensis and better body mass estimates are required to confirm the plausibility of the evolution of its small brain

An Evaluation of Phylogenetic Methods for Reconstructing Transmitted HIV Variants using Longitudinal Clonal HIV Sequence Data

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McCloskey, Rosemary M.; Liang, Richard H.; Harrigan, P. Richard; Brumme, Zabrina L.

2014-01-01

ABSTRACT A population of human immunodeficiency virus (HIV) within a host often descends from a single transmitted/founder virus. The high mutation rate of HIV, coupled with long delays between infection and diagnosis, make isolating and characterizing this strain a challenge. In theory, ancestral reconstruction could be used to recover this strain from sequences sampled in chronic infection; however, the accuracy of phylogenetic techniques in this context is unknown. To evaluate the accuracy of these methods, we applied ancestral reconstruction to a large panel of published longitudinal clonal and/or single-genome-amplification HIV sequence data sets with at least one intrapatient sequence set sampled within 6 months of infection or seroconversion (n = 19,486 sequences, median [interquartile range] = 49 [20 to 86] sequences/set). The consensus of the earliest sequences was used as the best possible estimate of the transmitted/founder. These sequences were compared to ancestral reconstructions from sequences sampled at later time points using both phylogenetic and phylogeny-naive methods. Overall, phylogenetic methods conferred a 16% improvement in reproducing the consensus of early sequences, compared to phylogeny-naive methods. This relative advantage increased with intrapatient sequence diversity (P reconstructing ancestral indel variation, especially within indel-rich regions of the HIV genome. Although further improvements are needed, our results indicate that phylogenetic methods for ancestral reconstruction significantly outperform phylogeny-naive alternatives, and we identify experimental conditions and study designs that can enhance accuracy of transmitted/founder virus reconstruction. IMPORTANCE When HIV is transmitted into a new host, most of the viruses fail to infect host cells. Consequently, an HIV infection tends to be descended from a single “founder” virus. A priority target for the vaccine research, these transmitted/founder viruses are

Reconstruction of photon number conditioned states using phase randomized homodyne measurements

International Nuclear Information System (INIS)

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

2013-01-01

We experimentally demonstrate the reconstruction of a photon number conditioned state without using a photon number discriminating detector. By using only phase randomized homodyne measurements, we reconstruct up to the three photon subtracted squeezed vacuum state. The reconstructed Wigner functions of these states show regions of pronounced negativity, signifying the non-classical nature of the reconstructed states. The techniques presented allow for complete characterization of the role of a conditional measurement on an ensemble of states, and might prove useful in systems where photon counting still proves technically challenging. (paper)

Integrating Principles Underlying Ancestral Spirits Belief in ...

African Journals Online (AJOL)

, associated with ancestral spirits and its use as powerful therapeutic agent for influencing behavior or lifestyle changes. Explanatory models of attachment to ancestral spirits by living descendants are first discussed, followed by a discussion ...

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…

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

DEFF Research Database (Denmark)

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

2014-01-01

split within this family. The ancestral larval feeding habit is reconstructed to be saprophagy with more specialised coprophagous saprophagy, phytophagy, and carnivory evolving multiple times from saprophagous ancestors. The origins of carnivory in larvae are significantly correlated with a reduction...

Are palaeoscolecids ancestral ecdysozoans?

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

2010-01-01

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

Evolution of life history and behavior in Hominidae: towards phylogenetic reconstruction of the chimpanzee-human last common ancestor.

Science.gov (United States)

Duda, Pavel; Zrzavý, Jan

2013-10-01

The origin of the fundamental behavioral differences between humans and our closest living relatives is one of the central issues of evolutionary anthropology. The prominent, chimpanzee-based referential model of early hominin behavior has recently been challenged on the basis of broad multispecies comparisons and newly discovered fossil evidence. Here, we argue that while behavioral data on extant great apes are extremely relevant for reconstruction of ancestral behaviors, these behaviors should be reconstructed trait by trait using formal phylogenetic methods. Using the widely accepted hominoid phylogenetic tree, we perform a series of character optimization analyses using 65 selected life-history and behavioral characters for all extant hominid species. This analysis allows us to reconstruct the character states of the last common ancestors of Hominoidea, Hominidae, and the chimpanzee-human last common ancestor. Our analyses demonstrate that many fundamental behavioral and life-history attributes of hominids (including humans) are evidently ancient and likely inherited from the common ancestor of all hominids. However, numerous behaviors present in extant great apes represent their own terminal autapomorphies (both uniquely derived and homoplastic). Any evolutionary model that uses a single extant species to explain behavioral evolution of early hominins is therefore of limited use. In contrast, phylogenetic reconstruction of ancestral states is able to provide a detailed suite of behavioral, ecological and life-history characters for each hypothetical ancestor. The living great apes therefore play an important role for the confident identification of the traits found in the chimpanzee-human last common ancestor, some of which are likely to represent behaviors of the fossil hominins. Copyright © 2013 Elsevier Ltd. All rights reserved.

Why Meillassoux’s Speculative Materialism Struggles with Ancestrality

Directory of Open Access Journals (Sweden)

Ciprian Jeler

2014-12-01

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

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

Pathgroups, a dynamic data structure for genome reconstruction problems.

Science.gov (United States)

Zheng, Chunfang

2010-07-01

Ancestral gene order reconstruction problems, including the median problem, quartet construction, small phylogeny, guided genome halving and genome aliquoting, are NP hard. Available heuristics dedicated to each of these problems are computationally costly for even small instances. We present a data structure enabling rapid heuristic solution to all these ancestral genome reconstruction problems. A generic greedy algorithm with look-ahead based on an automatically generated priority system suffices for all the problems using this data structure. The efficiency of the algorithm is due to fast updating of the structure during run time and to the simplicity of the priority scheme. We illustrate with the first rapid algorithm for quartet construction and apply this to a set of yeast genomes to corroborate a recent gene sequence-based phylogeny. http://albuquerque.bioinformatics.uottawa.ca/pathgroup/Quartet.html chunfang313@gmail.com Supplementary data are available at Bioinformatics online.

Ancestrality and evolution of trait syndromes in finches (Fringillidae)

OpenAIRE

Ponge, Jean‐François; Zuccon, Dario; Elias, Marianne; Pavoine, Sandrine; Henry, Pierre‐Yves; Théry, Marc; Guilbert, Éric

2017-01-01

International audience; Species traits have been hypothesized by one of us (Ponge, 2013) to evolve in a correlated manner as species colonize stable, undisturbed habitats, shifting from “ancestral” to “derived” strategies. We predicted that generalism, r-selection, sexual monomorphism, and migration/gregariousness are the ancestral states (collectively called strategy A) and evolved correlatively toward specialism, K-selection, sexual dimorphism, and residence/territoriality as habitat stabil...

Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope.

Science.gov (United States)

Doria-Rose, N A; Learn, G H; Rodrigo, A G; Nickle, D C; Li, F; Mahalanabis, M; Hensel, M T; McLaughlin, S; Edmonson, P F; Montefiori, D; Barnett, S W; Haigwood, N L; Mullins, J I

2005-09-01

Human immunodeficiency virus type 1 (HIV-1) is a difficult target for vaccine development, in part because of its ever-expanding genetic diversity and attendant capacity to escape immunologic recognition. Vaccine efficacy might be improved by maximizing immunogen antigenic similarity to viruses likely to be encountered by vaccinees. To this end, we designed a prototype HIV-1 envelope vaccine using a deduced ancestral state for the env gene. The ancestral state reconstruction method was shown to be >95% accurate by computer simulation and 99.8% accurate when estimating the known inoculum used in an experimental infection study in rhesus macaques. Furthermore, the deduced ancestor gene differed from the set of sequences used to derive the ancestor by an average of 12.3%, while these latter sequences were an average of 17.3% different from each other. A full-length ancestral subtype B HIV-1 env gene was constructed and shown to produce a glycoprotein of 160 kDa that bound and fused with cells expressing the HIV-1 coreceptor CCR5. This Env was also functional in a virus pseudotype assay. When either gp160- or gp140-expressing plasmids and recombinant gp120 were used to immunize rabbits in a DNA prime-protein boost regimen, the artificial gene induced immunoglobulin G antibodies capable of weakly neutralizing heterologous primary HIV-1 strains. The results were similar for rabbits immunized in parallel with a natural isolate, HIV-1 SF162. Further design efforts to better present conserved neutralization determinants are warranted.

Inference of Ancestral Recombination Graphs through Topological Data Analysis

Science.gov (United States)

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

2016-01-01

The recent explosion of genomic data has underscored the need for interpretable and comprehensive analyses that can capture complex phylogenetic relationships within and across species. Recombination, reassortment and horizontal gene transfer constitute examples of pervasive biological phenomena that cannot be captured by tree-like representations. Starting from hundreds of genomes, we are interested in the reconstruction of potential evolutionary histories leading to the observed data. Ancestral recombination graphs represent potential histories that explicitly accommodate recombination and mutation events across orthologous genomes. However, they are computationally costly to reconstruct, usually being infeasible for more than few tens of genomes. Recently, Topological Data Analysis (TDA) methods have been proposed as robust and scalable methods that can capture the genetic scale and frequency of recombination. We build upon previous TDA developments for detecting and quantifying recombination, and present a novel framework that can be applied to hundreds of genomes and can be interpreted in terms of minimal histories of mutation and recombination events, quantifying the scales and identifying the genomic locations of recombinations. We implement this framework in a software package, called TARGet, and apply it to several examples, including small migration between different populations, human recombination, and horizontal evolution in finches inhabiting the Galápagos Islands. PMID:27532298

Haplotype Diversity and Reconstruction of Ancestral Haplotype Associated with the c.35delG Mutation in the GJB2 (Cx26) Gene among the Volgo-Ural Populations of Russia.

Science.gov (United States)

Dzhemileva, L U; Posukh, O L; Barashkov, N A; Fedorova, S A; Teryutin, F M; Akhmetova, V L; Khidiyatova, I M; Khusainova, R I; Lobov, S L; Khusnutdinova, E K

2011-07-01

The mutations in theGJB2(Сх26) gene make the biggest contribution to hereditary hearing loss. The spectrum and prevalence of theGJB2gene mutations are specific to populations of different ethnic origins. For severalGJB2 mutations, their origin from appropriate ancestral founder chromosome was shown, approximate estimations of "age" obtained, and presumable regions of their origin outlined. This work presents the results of the carrier frequencies' analysis of the major (for European countries) mutation c.35delG (GJB2gene) among 2,308 healthy individuals from 18 Eurasian populations of different ethnic origins: Bashkirs, Tatars, Chuvashs, Udmurts, Komi-Permyaks, Mordvins, and Russians (the Volga-Ural region of Russia); Byelorussians, Ukrainians (Eastern Europe); Abkhazians, Avars, Cherkessians, and Ingushes (Caucasus); Kazakhs, Uzbeks, Uighurs (Central Asia); and Yakuts, and Altaians (Siberia). The prevalence of the c.35delG mutation in the studied ethnic groups may act as additional evidence for a prospective role of the founder effect in the origin and distribution of this mutation in various populations worldwide. The haplotype analysis of chromosomes with the c.35delG mutation in patients with nonsyndromic sensorineural hearing loss (N=112) and in population samples (N =358) permitted the reconstruction of an ancestral haplotype with this mutation, established the common origin of the majority of the studied mutant chromosomes, and provided the estimated time of the c.35delG mutation carriers expansion (11,800 years) on the territory of the Volga-Ural region.

Maximum parsimony on subsets of taxa.

Science.gov (United States)

Fischer, Mareike; Thatte, Bhalchandra D

2009-09-21

In this paper we investigate mathematical questions concerning the reliability (reconstruction accuracy) of Fitch's maximum parsimony algorithm for reconstructing the ancestral state given a phylogenetic tree and a character. In particular, we consider the question whether the maximum parsimony method applied to a subset of taxa can reconstruct the ancestral state of the root more accurately than when applied to all taxa, and we give an example showing that this indeed is possible. A surprising feature of our example is that ignoring a taxon closer to the root improves the reliability of the method. On the other hand, in the case of the two-state symmetric substitution model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that under a molecular clock the probability that the state at a single taxon is a correct guess of the ancestral state is a lower bound on the reconstruction accuracy of Fitch's method applied to all taxa.

A dynamic state observer for real-time reconstruction of the tokamak plasma profile state and disturbances

NARCIS (Netherlands)

Felici, F.; De Baar, M.; Steinbuch, M.

2014-01-01

A dynamic observer is presented which can reconstruct the internal state of a tokamak fusion plasma, consisting of the spatial distribution of current and temperature, from measurements. Today, the internal plasma state is usually reconstructed by solving an ill-conditioned inversion problem using a

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

Science.gov (United States)

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

2016-01-01

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

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

Directory of Open Access Journals (Sweden)

Jamie McCann

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

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

Directory of Open Access Journals (Sweden)

Jesse Robert Zaneveld

2014-08-01

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

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

Science.gov (United States)

Zaneveld, Jesse R R; Thurber, Rebecca L V

2014-01-01

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

Random unitary maps for quantum state reconstruction

International Nuclear Information System (INIS)

Merkel, Seth T.; Riofrio, Carlos A.; Deutsch, Ivan H.; Flammia, Steven T.

2010-01-01

We study the possibility of performing quantum state reconstruction from a measurement record that is obtained as a sequence of expectation values of a Hermitian operator evolving under repeated application of a single random unitary map, U 0 . We show that while this single-parameter orbit in operator space is not informationally complete, it can be used to yield surprisingly high-fidelity reconstruction. For a d-dimensional Hilbert space with the initial observable in su(d), the measurement record lacks information about a matrix subspace of dimension ≥d-2 out of the total dimension d 2 -1. We determine the conditions on U 0 such that the bound is saturated, and show they are achieved by almost all pseudorandom unitary matrices. When we further impose the constraint that the physical density matrix must be positive, we obtain even higher fidelity than that predicted from the missing subspace. With prior knowledge that the state is pure, the reconstruction will be perfect (in the limit of vanishing noise) and for arbitrary mixed states, the fidelity is over 0.96, even for small d, and reaching F>0.99 for d>9. We also study the implementation of this protocol based on the relationship between random matrices and quantum chaos. We show that the Floquet operator of the quantum kicked top provides a means of generating the required type of measurement record, with implications on the relationship between quantum chaos and information gain.

Multilocus phylogeny reconstruction: new insights into the evolutionary history of the genus Petunia.

Science.gov (United States)

Reck-Kortmann, Maikel; Silva-Arias, Gustavo Adolfo; Segatto, Ana Lúcia Anversa; Mäder, Geraldo; Bonatto, Sandro Luis; de Freitas, Loreta Brandão

2014-12-01

The phylogeny of Petunia species has been difficult to resolve, primarily due to the recent diversification of the genus. Several studies have included molecular data in phylogenetic reconstructions of this genus, but all of them have failed to include all taxa and/or analyzed few genetic markers. In the present study, we employed the most inclusive genetic and taxonomic datasets for the genus, aiming to reconstruct the evolutionary history of Petunia based on molecular phylogeny, biogeographic distribution, and character evolution. We included all 20 Petunia morphological species or subspecies in these analyses. Based on nine nuclear and five plastid DNA markers, our phylogenetic analysis reinforces the monophyly of the genus Petunia and supports the hypothesis that the basal divergence is more related to the differentiation of corolla tube length, whereas the geographic distribution of species is more related to divergences within these main clades. Ancestral area reconstructions suggest the Pampas region as the area of origin and earliest divergence in Petunia. The state reconstructions suggest that the ancestor of Petunia might have had a short corolla tube and a bee pollination floral syndrome. Copyright © 2014 Elsevier Inc. All rights reserved.

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

International Nuclear Information System (INIS)

Tong, S; Alessio, A M; Kinahan, P E; Liu, H; Shi, P

2011-01-01

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.

Why Meillassoux’s Speculative Materialism Struggles with Ancestrality

OpenAIRE

Ciprian Jeler

2014-01-01

This paper shows that Quentin Meillassoux’s speculative materialism doesn’t offer us the means to account for the ancestral statements that the modern sciences produce, i.e. for the scientific statements about events preceding all forms of life. An analysis of the reasons why Meillassoux thinks that the problem of ancestrality problematizes the contemporary self-evidence of correlationism is first offered. The results of this analysis are then applied to speculative materialism itself and the...

Enzyme functional evolution through improved catalysis of ancestrally nonpreferred substrates

Science.gov (United States)

Huang, Ruiqi; Hippauf, Frank; Rohrbeck, Diana; Haustein, Maria; Wenke, Katrin; Feike, Janie; Sorrelle, Noah; Piechulla, Birgit; Barkman, Todd J.

2012-01-01

In this study, we investigated the role for ancestral functional variation that may be selected upon to generate protein functional shifts using ancestral protein resurrection, statistical tests for positive selection, forward and reverse evolutionary genetics, and enzyme functional assays. Data are presented for three instances of protein functional change in the salicylic acid/benzoic acid/theobromine (SABATH) lineage of plant secondary metabolite-producing enzymes. In each case, we demonstrate that ancestral nonpreferred activities were improved upon in a daughter enzyme after gene duplication, and that these functional shifts were likely coincident with positive selection. Both forward and reverse mutagenesis studies validate the impact of one or a few sites toward increasing activity with ancestrally nonpreferred substrates. In one case, we document the occurrence of an evolutionary reversal of an active site residue that reversed enzyme properties. Furthermore, these studies show that functionally important amino acid replacements result in substrate discrimination as reflected in evolutionary changes in the specificity constant (kcat/KM) for competing substrates, even though adaptive substitutions may affect KM and kcat separately. In total, these results indicate that nonpreferred, or even latent, ancestral protein activities may be coopted at later times to become the primary or preferred protein activities. PMID:22315396

Dynamical reconstruction of the global ocean state during the Last Glacial Maximum

Science.gov (United States)

Kurahashi-Nakamura, Takasumi; Paul, André; Losch, Martin

2017-04-01

The global ocean state for the modern age and for the Last Glacial Maximum (LGM) was dynamically reconstructed with a sophisticated data assimilation technique. A substantial amount of data including global seawater temperature, salinity (only for the modern estimate), and the isotopic composition of oxygen and carbon (only in the Atlantic for the LGM) were integrated into an ocean general circulation model with the help of the adjoint method, thereby the model was optimized to reconstruct plausible continuous fields of tracers, overturning circulation and water mass distribution. The adjoint-based LGM state estimation of this study represents the state of the art in terms of the length of forward model runs, the number of observations assimilated, and the model domain. Compared to the modern state, the reconstructed continuous sea-surface temperature field for the LGM shows a global-mean cooling of 2.2 K, and the reconstructed LGM ocean has a more vigorous Atlantic meridional overturning circulation, shallower North Atlantic Deep Water (NADW) equivalent, stronger stratification, and more saline deep water.

Animal regeneration: ancestral character or evolutionary novelty?

Science.gov (United States)

Slack, Jonathan Mw

2017-09-01

An old question about regeneration is whether it is an ancestral character which is a general property of living matter, or whether it represents a set of specific adaptations to the different circumstances faced by different types of animal. In this review, some recent results on regeneration are assessed to see if they can throw any new light on this question. Evidence in favour of an ancestral character comes from the role of Wnt and bone morphogenetic protein signalling in controlling the pattern of whole-body regeneration in acoels, which are a basal group of bilaterian animals. On the other hand, there is some evidence for adaptive acquisition or maintenance of the regeneration of appendages based on the occurrence of severe non-lethal predation, the existence of some novel genes in regenerating organisms, and differences at the molecular level between apparently similar forms of regeneration. It is tentatively concluded that whole-body regeneration is an ancestral character although has been lost from most animal lineages. Appendage regeneration is more likely to represent a derived character resulting from many specific adaptations. © 2017 The Author.

State reconstruction of one-dimensional wave packets

Science.gov (United States)

Krähmer, D. S.; Leonhardt, U.

1997-12-01

We review and analyze the method [U. Leonhardt, M.G. Raymer: Phys. Rev. Lett. 76, 1985 (1996)] for quantum-state reconstruction of one-dimensional non-relativistic wave packets from position observations. We illuminate the theoretical background of the technique and show how to extend the procedure to the continuous part of the spectrum.

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

A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences.

Science.gov (United States)

Groussin, M; Boussau, B; Gouy, M

2013-07-01

Most models of nucleotide or amino acid substitution used in phylogenetic studies assume that the evolutionary process has been homogeneous across lineages and that composition of nucleotides or amino acids has remained the same throughout the tree. These oversimplified assumptions are refuted by the observation that compositional variability characterizes extant biological sequences. Branch-heterogeneous models of protein evolution that account for compositional variability have been developed, but are not yet in common use because of the large number of parameters required, leading to high computational costs and potential overparameterization. Here, we present a new branch-nonhomogeneous and nonstationary model of protein evolution that captures more accurately the high complexity of sequence evolution. This model, henceforth called Correspondence and likelihood analysis (COaLA), makes use of a correspondence analysis to reduce the number of parameters to be optimized through maximum likelihood, focusing on most of the compositional variation observed in the data. The model was thoroughly tested on both simulated and biological data sets to show its high performance in terms of data fitting and CPU time. COaLA efficiently estimates ancestral amino acid frequencies and sequences, making it relevant for studies aiming at reconstructing and resurrecting ancestral amino acid sequences. Finally, we applied COaLA on a concatenate of universal amino acid sequences to confirm previous results obtained with a nonhomogeneous Bayesian model regarding the early pattern of adaptation to optimal growth temperature, supporting the mesophilic nature of the Last Universal Common Ancestor.

Reproductive function in mice exposed to ancestral and direct irradiation

International Nuclear Information System (INIS)

Nash, D.J.; Sprackling, L.S.

1978-01-01

Reproduction was studied in 13 inbred strains of mice that had been exposed continuously to 60 Co gamma radiation for varying numbers of generations. At weaning the mice were removed from the irradiation chamber and were tested for reproductive performance. Ancestral and direct levels of irradiation were determined for each animal. Each irradiated or control female was scored as fertile or sterile, and in utero litter counts were made in pregnant females that were dissected past the 10th day of pregnancy. The number of resorptions, dead embryos, and live embryos were counted, and the ratio of living embryos to the total number of embryos was determined for each litter. The overall fertility curves were sigmoid in the range of doses below those which caused complete sterility, which indicated some sort of cumulative damage. In 11 of the 13 strains studied, an increase in ancestral and/or direct irradiation led to significant decreases in fertility. The means of the number alive in the litters for the control and irradiated mice in each strain showed a definite trend toward fewer live mice in utero after irradiation. Least-squares analyses of variance were made to detect possible effects of any of six irradiation variables (ancestral linear, ancestral quadratic, ancestral cubic, direct linear, direct quadratic, or direct cubic) or of strain differences on total litter size and on ratio. Strain effects were significant in each instance. Litter size was more likely to be affected by radiation variables than ratios were

Additions, losses, and rearrangements on the evolutionary route from a reconstructed ancestor to the modern Saccharomyces cerevisiae genome.

Directory of Open Access Journals (Sweden)

Jonathan L Gordon

2009-05-01

Full Text Available Comparative genomics can be used to infer the history of genomic rearrangements that occurred during the evolution of a species. We used the principle of parsimony, applied to aligned synteny blocks from 11 yeast species, to infer the gene content and gene order that existed in the genome of an extinct ancestral yeast about 100 Mya, immediately before it underwent whole-genome duplication (WGD. The reconstructed ancestral genome contains 4,703 ordered loci on eight chromosomes. The reconstruction is complete except for the subtelomeric regions. We then inferred the series of rearrangement steps that led from this ancestor to the current Saccharomyces cerevisiae genome; relative to the ancestral genome we observe 73 inversions, 66 reciprocal translocations, and five translocations involving telomeres. Some fragile chromosomal sites were reused as evolutionary breakpoints multiple times. We identified 124 genes that have been gained by S. cerevisiae in the time since the WGD, including one that is derived from a hAT family transposon, and 88 ancestral loci at which S. cerevisiae did not retain either of the gene copies that were formed by WGD. Sites of gene gain and evolutionary breakpoints both tend to be associated with tRNA genes and, to a lesser extent, with origins of replication. Many of the gained genes in S. cerevisiae have functions associated with ethanol production, growth in hypoxic environments, or the uptake of alternative nutrient sources.

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

Science.gov (United States)

Schrago, Carlos G

2014-08-01

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

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

National Research Council Canada - National Science Library

Bowen, Jr, Stuart W

2007-01-01

.... relief and reconstruction program in Iraq. Two notable developments frame this Report. First, total relief and reconstruction investment for Iraq from all sources the United States, Iraq, and other donors passed...

State reconstruction and irregular wavefunctions for the hydrogen atom

Science.gov (United States)

Krähmer, D. S.; Leonhardt, U.

1997-07-01

Inspired by a recently proposed procedure by Leonhardt and Raymer for wavepacket reconstruction, we calculate the irregular wavefunctions for the bound states of the Coulomb potential. We select the irregular solutions which have the simplest semiclassical limit.

Time-dependent problems in quantum-mechanical state reconstruction

International Nuclear Information System (INIS)

Leonhardt, U.; Bardroff, P. J.

1997-01-01

We study the state reconstruction of wave packets that travel in time-dependent potentials. We solve the problem for explicitly time-dependent potentials. We solve the problem for explicitly time-dependent harmonic oscillators and sketch a general adaptive technique for finding the wave function that matches and observed evolution. (authors)

Invasion of Ancestral Mammals into Dim-light Environments Inferred from Adaptive Evolution of the Phototransduction Genes.

Science.gov (United States)

Wu, Yonghua; Wang, Haifeng; Hadly, Elizabeth A

2017-04-20

Nocturnality is a key evolutionary innovation of mammals that enables mammals to occupy relatively empty nocturnal niches. Invasion of ancestral mammals into nocturnality has long been inferred from the phylogenetic relationships of crown Mammalia, which is primarily nocturnal, and crown Reptilia, which is primarily diurnal, although molecular evidence for this is lacking. Here we used phylogenetic analyses of the vision genes involved in the phototransduction pathway to predict the diel activity patterns of ancestral mammals and reptiles. Our results demonstrated that the common ancestor of the extant Mammalia was dominated by positive selection for dim-light vision, supporting the predominate nocturnality of the ancestral mammals. Further analyses showed that the nocturnality of the ancestral mammals was probably derived from the predominate diurnality of the ancestral amniotes, which featured strong positive selection for bright-light vision. Like the ancestral amniotes, the common ancestor of the extant reptiles and various taxa in Squamata, one of the main competitors of the temporal niches of the ancestral mammals, were found to be predominate diurnality as well. Despite this relatively apparent temporal niche partitioning between ancestral mammals and the relevant reptiles, our results suggested partial overlap of their temporal niches during crepuscular periods.

Ancestral effect on HOMA-IR levels quantitated in an American population of Mexican origin.

Science.gov (United States)

Qu, Hui-Qi; Li, Quan; Lu, Yang; Hanis, Craig L; Fisher-Hoch, Susan P; McCormick, Joseph B

2012-12-01

An elevated insulin resistance index (homeostasis model assessment of insulin resistance [HOMA-IR]) is more commonly seen in the Mexican American population than in European populations. We report quantitative ancestral effects within a Mexican American population, and we correlate ancestral components with HOMA-IR. We performed ancestral analysis in 1,551 participants of the Cameron County Hispanic Cohort by genotyping 103 ancestry-informative markers (AIMs). These AIMs allow determination of the percentage (0-100%) ancestry from three major continental populations, i.e., European, African, and Amerindian. We observed that predominantly Amerindian ancestral components were associated with increased HOMA-IR (β = 0.124, P = 1.64 × 10(-7)). The correlation was more significant in males (Amerindian β = 0.165, P = 5.08 × 10(-7)) than in females (Amerindian β = 0.079, P = 0.019). This unique study design demonstrates how genomic markers for quantitative ancestral information can be used in admixed populations to predict phenotypic traits such as insulin resistance.

The structured ancestral selection graph and the many-demes limit.

Science.gov (United States)

Slade, Paul F; Wakeley, John

2005-02-01

We show that the unstructured ancestral selection graph applies to part of the history of a sample from a population structured by restricted migration among subpopulations, or demes. The result holds in the limit as the number of demes tends to infinity with proportionately weak selection, and we have also made the assumptions of island-type migration and that demes are equivalent in size. After an instantaneous sample-size adjustment, this structured ancestral selection graph converges to an unstructured ancestral selection graph with a mutation parameter that depends inversely on the migration rate. In contrast, the selection parameter for the population is independent of the migration rate and is identical to the selection parameter in an unstructured population. We show analytically that estimators of the migration rate, based on pairwise sequence differences, derived under the assumption of neutrality should perform equally well in the presence of weak selection. We also modify an algorithm for simulating genealogies conditional on the frequencies of two selected alleles in a sample. This permits efficient simulation of stronger selection than was previously possible. Using this new algorithm, we simulate gene genealogies under the many-demes ancestral selection graph and identify some situations in which migration has a strong effect on the time to the most recent common ancestor of the sample. We find that a similar effect also increases the sensitivity of the genealogy to selection.

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

Science.gov (United States)

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

2015-01-01

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

Phylogenetic signal from rearrangements in 18 Anopheles species by joint scaffolding extant and ancestral genomes.

Science.gov (United States)

Anselmetti, Yoann; Duchemin, Wandrille; Tannier, Eric; Chauve, Cedric; Bérard, Sèverine

2018-05-09

Genomes rearrangements carry valuable information for phylogenetic inference or the elucidation of molecular mechanisms of adaptation. However, the detection of genome rearrangements is often hampered by current deficiencies in data and methods: Genomes obtained from short sequence reads have generally very fragmented assemblies, and comparing multiple gene orders generally leads to computationally intractable algorithmic questions. We present a computational method, ADSEQ, which, by combining ancestral gene order reconstruction, comparative scaffolding and de novo scaffolding methods, overcomes these two caveats. ADSEQ provides simultaneously improved assemblies and ancestral genomes, with statistical supports on all local features. Compared to previous comparative methods, it runs in polynomial time, it samples solutions in a probabilistic space, and it can handle a significantly larger gene complement from the considered extant genomes, with complex histories including gene duplications and losses. We use ADSEQ to provide improved assemblies and a genome history made of duplications, losses, gene translocations, rearrangements, of 18 complete Anopheles genomes, including several important malaria vectors. We also provide additional support for a differentiated mode of evolution of the sex chromosome and of the autosomes in these mosquito genomes. We demonstrate the method's ability to improve extant assemblies accurately through a procedure simulating realistic assembly fragmentation. We study a debated issue regarding the phylogeny of the Gambiae complex group of Anopheles genomes in the light of the evolution of chromosomal rearrangements, suggesting that the phylogenetic signal they carry can differ from the phylogenetic signal carried by gene sequences, more prone to introgression.

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

Science.gov (United States)

Lehmann, Tobias; Hess, Martin; Melzer, Roland R

2012-01-01

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

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

Directory of Open Access Journals (Sweden)

Tobias Lehmann

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

Statistical dynamic image reconstruction in state-of-the-art high-resolution PET

International Nuclear Information System (INIS)

Rahmim, Arman; Cheng, J-C; Blinder, Stephan; Camborde, Maurie-Laure; Sossi, Vesna

2005-01-01

Modern high-resolution PET is now more than ever in need of scrutiny into the nature and limitations of the imaging modality itself as well as image reconstruction techniques. In this work, we have reviewed, analysed and addressed the following three considerations within the particular context of state-of-the-art dynamic PET imaging: (i) the typical average numbers of events per line-of-response (LOR) are now (much) less than unity (ii) due to the physical and biological decay of the activity distribution, one requires robust and efficient reconstruction algorithms applicable to a wide range of statistics and (iii) the computational considerations in dynamic imaging are much enhanced (i.e., more frames to be stored and reconstructed). Within the framework of statistical image reconstruction, we have argued theoretically and shown experimentally that the sinogram non-negativity constraint (when using the delayed-coincidence and/or scatter-subtraction techniques) is especially expected to result in an overestimation bias. Subsequently, two schemes are considered: (a) subtraction techniques in which an image non-negativity constraint has been imposed and (b) implementation of random and scatter estimates inside the reconstruction algorithms, thus enabling direct processing of Poisson-distributed prompts. Both techniques are able to remove the aforementioned bias, while the latter, being better conditioned theoretically, is able to exhibit superior noise characteristics. We have also elaborated upon and verified the applicability of the accelerated list-mode image reconstruction method as a powerful solution for accurate, robust and efficient dynamic reconstructions of high-resolution data (as well as a number of additional benefits in the context of state-of-the-art PET)

Prenatal effects of ancestral irradiation in inbred mice

International Nuclear Information System (INIS)

Sprackling, L.E.S.

1975-01-01

Mice from 13 inbred strains (S, Z, E, Bab, BaB, BrR, C, K, N, Q, G, CFW, CF1) received continuous cobalt 60 irradiation at low dose rates for varying numbers of consecutive generations. Some Bab and BaB mice had received continuous irradiation for from 24 to 31 generations and the other mice had up to six generations of continuous irradiation in their ancestry. At weaning, the mice were removed from the irradiation room and were mated within strains either to sibs or nonsibs. Ancestral and direct irradiation doses were calculated. The ancestral dose was the effective accumulated dose to the progeny of the mated mice. The direct dose was the amount of irradiation received by any mated female from her conception to her weaning. Each irradiated or control female was scored as fertile or sterile and in utero litter counts were made in pregnant females that were dissected past the tenth day of pregnancy; the sum of moles, dead embryos, and live embryos was the total in utero litter size. A ratio of the living embryos to the total number of embryos in utero was determined for each litter. An increase in ancestral or direct irradiation dose significantly decreased fertility in 11 of the 13 strains. The fertility curves for the pooled data were sigmoid in the area of the doses below those that caused complete sterility. Among the controls, there were significant strain differences in total litter size and in the ratio. Strain X--Y plots, with ancestral or direct doses plotted against total litter size or ratio, revealed the tendency for litter size to decrease as dose increased. The only trend shown for ratio was for the litters with ratios of 0.50 or less to appear more frequently among the irradiated mice. The few corpora lutea counts revealed nothing of significance. Generally, there was a definite trend toward fewer mice alive in utero among the irradiated mice

The ancestral selection graph under strong directional selection.

Science.gov (United States)

Pokalyuk, Cornelia; Pfaffelhuber, Peter

2013-08-01

The ancestral selection graph (ASG) was introduced by  Neuhauser and Krone (1997) in order to study populations of constant size which evolve under selection. Coalescence events, which occur at rate 1 for every pair of lines, lead to joint ancestry. In addition, splitting events in the ASG at rate α, the scaled selection coefficient, produce possible ancestors, such that the real ancestor depends on the ancestral alleles. Here, we use the ASG in the case without mutation in order to study fixation of a beneficial mutant. Using our main tool, a reversibility property of the ASG, we provide a new proof of the fact that a beneficial allele fixes roughly in time (2logα)/α if α is large. Copyright © 2012 Elsevier Inc. All rights reserved.

Infant and juvenile growth in ancestral Pueblo Indians.

Science.gov (United States)

Schillaci, Michael A; Nikitovic, Dejana; Akins, Nancy J; Tripp, Lianne; Palkovich, Ann M

2011-06-01

The present study examines patterns of infant and juvenile growth in a diachronic sample of ancestral Pueblo Indians (AD 1300-1680) from the American Southwest. An assessment of growth patterns is accompanied by an evaluation of pathological conditions often considered to be indicators of nutritional deficiencies and/or gastrointestinal infections. Growth patterns and the distribution of pathological conditions are interpreted relative to culturally relevant age categories defined by Puebloan rites of passage described in the ethnographic literature. A visual comparison of growth distance curves revealed that relative to a modern comparative group our sample of ancestral Pueblo infant and juveniles exhibited faltering growth beginning soon after birth to about 5 years of age. A comparison of curves describing growth relative to adult femoral length, however, indicated reduced growth occurring later, by around 2 years of age. Similar to previous studies, we observed a high proportion of nonsurvivors exhibiting porotic cranial lesions during the first 2 years of life. Contrary to expectations, infants and juveniles without evidence of porotic cranial lesions exhibited a higher degree of stunting. Our study is generally consistent with previous research reporting poor health and high mortality for ancestral Pueblo Indian infants and juveniles. Through use of a culturally relevant context defining childhood, we argue that the observed poor health and high mortality in our sample occur before the important transition from young to older child and the concomitant initial incorporation into tribal ritual organization. Copyright © 2011 Wiley-Liss, Inc.

Reconstructing Northeastern United States temperatures using Atlantic white cedar tree rings

Science.gov (United States)

Pearl, Jessie K.; Anchukaitis, Kevin J.; Pederson, Neil; Donnelly, Jeffrey P.

2017-11-01

Our knowledge of climate variability in the densely populated Northeastern United States is limited to instrumental data of the last century. Most regional paleoclimate proxies reflect a mix of climate responses, which makes reconstructing historical climate a challenge. Here we analyze tree-ring chronologies from Atlantic white cedar (Chamaecyparis thyoides) as a potential regional paleotemperature proxy. We evaluate our tree-ring network for spatiotemporal climate signal strength and reconstruction skill across New England. Atlantic white cedar sites in the northern section of the species’ range exhibit positive significant annual growth relationships with local and regional temperatures. Chronologies constructed from northern sites yield skillful reconstructions of temperature that reproduce centennial, multidecadal, and interannual variability in the instrumental record, providing a novel paleotemperature record for New England.

Wiring a Periscope – Ocelli, Retinula Axons, Visual Neuropils and the Ancestrality of Sea Spiders

Science.gov (United States)

Lehmann, Tobias; Heß, Martin; Melzer, Roland R.

2012-01-01

The Pycnogonida or sea spiders are cryptic, eight-legged arthropods with four median ocelli in a ‘periscope’ or eye tubercle. In older attempts at reconstructing phylogeny they were Arthropoda incertae sedis, but recent molecular trees placed them as the sister group either to all other euchelicerates or even to all euarthropods. Thus, pycnogonids are among the oldest extant arthropods and hold a key position for the understanding of arthropod evolution. This has stimulated studies of new sets of characters conductive to cladistic analyses, e.g. of the chelifores and of the hox gene expression pattern. In contrast knowledge of the architecture of the visual system is cursory. A few studies have analysed the ocelli and the uncommon “pseudoinverted” retinula cells. Moreover, analyses of visual neuropils are still at the stage of Hanström's early comprehensive works. We have therefore used various techniques to analyse the visual fibre pathways and the structure of their interrelated neuropils in several species. We found that pycnogonid ocelli are innervated to first and second visual neuropils in close vicinity to an unpaired midline neuropil, i.e. possibly the arcuate body, in a way very similar to ancestral euarthropods like Euperipatoides rowelli (Onychophora) and Limulus polyphemus (Xiphosura). This supports the ancestrality of pycnogonids and sheds light on what eyes in the pycnogonid ground plan might have ‘looked’ like. Recently it was suggested that arthropod eyes originated from simple ocelli similar to larval eyes. Hence, pycnogonid eyes would be one of the early offshoots among the wealth of more sophisticated arthropod eyes. PMID:22279594

State Space Reduction of Linear Processes using Control Flow Reconstruction

NARCIS (Netherlands)

van de Pol, Jan Cornelis; Timmer, Mark

2009-01-01

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

State Space Reduction of Linear Processes Using Control Flow Reconstruction

NARCIS (Netherlands)

van de Pol, Jan Cornelis; Timmer, Mark; Liu, Zhiming; Ravn, Anders P.

2009-01-01

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

Fast reconstruction of high-qubit-number quantum states via low-rate measurements

Science.gov (United States)

Li, K.; Zhang, J.; Cong, S.

2017-07-01

Due to the exponential complexity of the resources required by quantum state tomography (QST), people are interested in approaches towards identifying quantum states which require less effort and time. In this paper, we provide a tailored and efficient method for reconstructing mixed quantum states up to 12 (or even more) qubits from an incomplete set of observables subject to noises. Our method is applicable to any pure or nearly pure state ρ and can be extended to many states of interest in quantum information processing, such as a multiparticle entangled W state, Greenberger-Horne-Zeilinger states, and cluster states that are matrix product operators of low dimensions. The method applies the quantum density matrix constraints to a quantum compressive sensing optimization problem and exploits a modified quantum alternating direction multiplier method (quantum-ADMM) to accelerate the convergence. Our algorithm takes 8 ,35 , and 226 seconds, respectively, to reconstruct superposition state density matrices of 10 ,11 ,and12 qubits with acceptable fidelity using less than 1 % of measurements of expectation. To our knowledge it is the fastest realization that people can achieve using a normal desktop. We further discuss applications of this method using experimental data of mixed states obtained in an ion trap experiment of up to 8 qubits.

Tree-ring temperature reconstructions for the northeastern United States from Chamaecyparis thyoides

Science.gov (United States)

Anchukaitis, K. J.; Pederson, N.; Pearl, J. K.; Donnelly, J. P.

2014-12-01

Over the last century, the northeastern United States has warmed by over 1C, with the region of strongest warming found in coastal Massachusetts, Connecticut, and Rhode Island. These states are amongst the fastest warming in the entire country and the region as a whole is also warming faster than the national average. While these records all appear exceptional in the context of the last century, it is not known how these compare on longer time scales, to potential preindustrial late Holocene warm epochs, and in the context of decadal-scale variability in regional climate. Here, we develop a January through August temperature reconstruction using three Chamaecyparis thyoides (Atlantic White Cedar) chronologies in Massachusetts and Maine. The chronologies show a strong winter-spring-summer temperature signal representative of temperature variability from southern New York to northeastern Maine. The reconstruction is skillful and tracks upwards temperature trends since the early 19th century, reproducing decadal scale variability associated with warming from the 1920s through 1940s, cooling in the region from the 1940s until the 1960s, and warming since that time. No year since at least the middle of the 19th century is as warm as the Janaury through August temperatures seen in the exceptionally warm 2012. Recent modeling experiments simulate a range of decadal warming trends for the northeastern United States that is slightly higher than the reconstructed and instrumental trends. Atlantic White Cedar holds the potential to develop multicentury temperature reconstructions from this heavily-populated region.

Indigenous ancestral sayings contribute to modern conservation partnerships: examples using Phormium tenax.

Science.gov (United States)

Wehi, Priscilla M

2009-01-01

Traditional ecological knowledge (TEK) is central to indigenous worldviews and practices and is one of the most important contributions that indigenous people can bring to conservation management partnerships. However, researchers and managers may have difficulty accessing such knowledge, particularly where knowledge transmission has been damaged. A new methodological approach analyzes ancestral sayings from Maori oral traditions for ecological information about Phormium tenax, a plant with high cultural value that is a dominant component in many threatened wetland systems, and frequently used in restoration plantings in New Zealand. Maori ancestral sayings record an association with nectar-feeding native parrots that has only rarely been reported, as well as indications of important environmental parameters (rainfall and drought) for this species. These sayings provide evidence of indigenous management that has not been reported from interviews with elders, including evidence of fire use to create Phormium cultivations. TEK in Maori ancestral sayings imply landscape-scale processes in comparison to intensive, small-scale management methods often reported in interviews. TEK in ancestral sayings can be used to generate new scientific hypotheses, negotiate collaborative pathways, and identify ecological management strategies that support biodiversity retention. TEK can inform restoration ecology, historical ecology, and conservation management of species and ecosystems, especially where data from pollen records and archaeological artifacts are incomplete.

Reconstruction of chromosome rearrangements between the two most ancestral duckweed species Spirodela polyrhiza and S. intermedia.

Science.gov (United States)

Hoang, Phuong T N; Schubert, Ingo

2017-12-01

The monophyletic duckweeds comprising five genera within the monocot order Alismatales are neotenic, free-floating, aquatic organisms with fast vegetative propagation. Some species are considered for efficient biomass production, for life stock feeding, and for (simultaneous) wastewater phytoremediation. The ancestral genus Spirodela consists of only two species, Spirodela polyrhiza and Spirodela intermedia, both with a similar small genome (~160 Mbp/1C). Reference genome drafts and a physical map of 96 BACs on the 20 chromosome pairs of S. polyrhiza strain 7498 are available and provide useful tools for further evolutionary studies within and between duckweed genera. Here we applied sequential comparative multicolor fluorescence in situ hybridization (mcFISH) to address homeologous chromosomes in S. intermedia (2n = 36), to detect chromosome rearrangements between both species and to elucidate the mechanisms which may have led to the chromosome number alteration after their evolutionary separation. Ten chromosome pairs proved to be conserved between S. polyrhiza and S. intermedia, the remaining ones experienced, depending on the assumed direction of evolution, translocations, inversion, and fissions, respectively. These results represent a first step to unravel karyotype evolution among duckweeds and are anchor points for future genome assembly of S. intermedia.

Modeling X-linked ancestral origins in multiparental populations

NARCIS (Netherlands)

Zheng, Chaozhi

2015-01-01

The models for the mosaic structure of an individual's genome from multiparental populations have been developed primarily for autosomes, whereas X chromosomes receive very little attention. In this paper, we extend our previous approach to model ancestral origin processes along two X chromosomes

Nonparametric reconstruction of the dark energy equation of state

Energy Technology Data Exchange (ETDEWEB)

Heitmann, Katrin [Los Alamos National Laboratory; Holsclaw, Tracy [Los Alamos National Laboratory; Alam, Ujjaini [Los Alamos National Laboratory; Habib, Salman [Los Alamos National Laboratory; Higdon, David [Los Alamos National Laboratory; Sanso, Bruno [UC SANTA CRUZ; Lee, Herbie [UC SANTA CRUZ

2009-01-01

The major aim of ongoing and upcoming cosmological surveys is to unravel the nature of dark energy. In the absence of a compelling theory to test, a natural approach is to first attempt to characterize the nature of dark energy in detail, the hope being that this will lead to clues about the underlying fundamental theory. A major target in this characterization is the determination of the dynamical properties of the dark energy equation of state w. The discovery of a time variation in w(z) could then lead to insights about the dynamical origin of dark energy. This approach requires a robust and bias-free method for reconstructing w(z) from data, which does not rely on restrictive expansion schemes or assumed functional forms for w(z). We present a new non parametric reconstruction method for the dark energy equation of state based on Gaussian Process models. This method reliably captures nontrivial behavior of w(z) and provides controlled error bounds. We demollstrate the power of the method on different sets of simulated supernova data. The GP model approach is very easily extended to include diverse cosmological probes.

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

International Nuclear Information System (INIS)

Lougovski, P.

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 ''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

The complete sequence of marine bacteriophage VpV262 infecting vibrio parahaemolyticus indicates that an ancestral component of a T7 viral supergroup is widespread in the marine environment

International Nuclear Information System (INIS)

Hardies, Stephen C.; Comeau, Andre M.; Serwer, Philip; Suttle, Curtis A.

2003-01-01

The 46,012-bp sequence of the marine bacteriophage VpV262 infecting the bacterium Vibrio parahaemolyticus is reported. The VpV262 sequence reveals that it is a distant relative of marine Roseophage SIO1, and an even more distant relative of coliphage T7. VpV262 and SIO1 appear to represent a widespread marine phage group that lacks an RNA polymerase gene and is ancestral to the T7-like phages. We propose that this group together with the T7-like phages be designated as the T7 supergroup. The ancestral head structure gene module for the T7 supergroup was reconstructed by using sensitive biased Psi-blast searches supplemented by statistical support derived from gene order. In the early and replicative segments, these phages have participated in extensive interchange with the viral gene pool. VpV262 carries a different replicative module than SIO1 and the T7-like phages

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.

Environmental enrichment mitigates the impact of ancestral stress on motor skill and corticospinal tract plasticity.

Science.gov (United States)

McCreary, J Keiko; Erickson, Zachary T; Metz, Gerlinde A S

2016-10-06

An adverse fetal environment in utero has been associated with long-term alterations in brain structure and function, and a higher risk of neurological disorders in later life. A common consequence of early adverse experience is impaired motor system function. A causal relationship for stress-associated impairments and a suitable therapy, however, have not been determined yet. To investigate the impact of ancestral stress on corticospinal tract (CST) morphology and fine motor performance in rats, and to determine if adverse programming by ancestral stress can be mitigated by environmental enrichment therapy in rats. The study examined F3 offspring generated by three lineages; one with prenatal stress only in the F1 generation, one with compounding effects of multigenerational prenatal stress, and a non-stress control lineage. F3 offspring from each lineage were injected with biotinylated dextran amine (BDA) into the motor cortex for anterograde tracing of the CST. Examination of the CST revealed reduced axonal density in the ancestrally stressed lineages. These anatomical changes were associated with significant impairments in skilled walking, as indicated by reduced foot placement accuracy and disturbed inter-limb coordination. Therapeutic intervention by environmental enrichment reduced the neuromorphological consequences of ancestral stress and restored skilled walking ability. The data suggest a causal relationship between stress-induced abnormal CST function and loss of fine motor performance. Thus, ancestral stress may be a determinant of motor system development and motor skill. Environmental enrichment may represent an effective intervention for the adverse programming by ancestral stress and trauma. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Petz recovery versus matrix reconstruction

Science.gov (United States)

Holzäpfel, Milan; Cramer, Marcus; Datta, Nilanjana; Plenio, Martin B.

2018-04-01

The reconstruction of the state of a multipartite quantum mechanical system represents a fundamental task in quantum information science. At its most basic, it concerns a state of a bipartite quantum system whose subsystems are subjected to local operations. We compare two different methods for obtaining the original state from the state resulting from the action of these operations. The first method involves quantum operations called Petz recovery maps, acting locally on the two subsystems. The second method is called matrix (or state) reconstruction and involves local, linear maps that are not necessarily completely positive. Moreover, we compare the quantities on which the maps employed in the two methods depend. We show that any state that admits Petz recovery also admits state reconstruction. However, the latter is successful for a strictly larger set of states. We also compare these methods in the context of a finite spin chain. Here, the state of a finite spin chain is reconstructed from the reduced states of a few neighbouring spins. In this setting, state reconstruction is the same as the matrix product operator reconstruction proposed by Baumgratz et al. [Phys. Rev. Lett. 111, 020401 (2013)]. Finally, we generalize both these methods so that they employ long-range measurements instead of relying solely on short-range correlations embodied in such local reduced states. Long-range measurements enable the reconstruction of states which cannot be reconstructed from measurements of local few-body observables alone and hereby we improve existing methods for quantum state tomography of quantum many-body systems.

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

Science.gov (United States)

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

2015-12-01

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

Reconstruction of high-dimensional states entangled in orbital angular momentum using mutually unbiased measurements

CSIR Research Space (South Africa)

Giovannini, D

2013-06-01

Full Text Available : QELS_Fundamental Science, San Jose, California United States, 9-14 June 2013 Reconstruction of High-Dimensional States Entangled in Orbital Angular Momentum Using Mutually Unbiased Measurements D. Giovannini1, ⇤, J. Romero1, 2, J. Leach3, A...

Molecular phylogeny of Pompilinae (Hymenoptera: Pompilidae): Evidence for rapid diversification and host shifts in spider wasps.

Science.gov (United States)

Rodriguez, Juanita; Pitts, James P; Florez, Jaime A; Bond, Jason E; von Dohlen, Carol D

2016-01-01

Pompilinae is one of the largest subfamilies of spider wasps (Pompilidae). Most pompilines are generalist spider predators at the family level, but some taxa exhibit ecological specificity (i.e., to spider-host guild). Here we present the first molecular phylogenetic analysis of Pompilinae, toward the aim of evaluating the monophyly of tribes and genera. We further test whether changes in the rate of diversification are associated with host-guild shifts. Molecular data were collected from five nuclear loci (28S, EF1-F2, LWRh, Wg, Pol2) for 76 taxa in 39 genera. Data were analyzed using maximum likelihood (ML) and Bayesian inference (BI). The phylogenetic results were compared with previous hypotheses of subfamilial and tribal classification, as well as generic relationships in the subfamily. The classification of Pompilus and Agenioideus is also discussed. A Bayesian relaxed molecular clock analysis was used to examine divergence times. Diversification rate-shift tests accounted for taxon-sampling bias using ML and BI approaches. Ancestral host family and host guild were reconstructed using MP and ML methods. Ancestral host guild for all Pompilinae, for the ancestor at the node where a diversification rate-shift was detected, and two more nodes back in time was inferred using BI. In the resulting phylogenies, Aporini was the only previously proposed monophyletic tribe. Several genera (e.g., Pompilus, Microphadnus and Schistonyx) are also not monophyletic. Dating analyses produced a well-supported chronogram consistent with topologies from BI and ML results. The BI ancestral host-use reconstruction inferred the use of spiders belonging to the guild "other hunters" (frequenting the ground and vegetation) as the ancestral state for Pompilinae. This guild had the highest probability for the ML reconstruction and was equivocal for the MP reconstruction; various switching events to other guilds occurred throughout the evolution of the group. The diversification of

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

International Nuclear Information System (INIS)

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

2015-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

Ma, Jing; Chen, Xi; Liu, Yanan [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China); Xie, Qunhui [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Sun, Yawen; Chen, Jingshan; Leng, Ling; Yan, Huan [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China); Zhao, Bin, E-mail: binzhao@rcees.ac.cn [State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Tang, Naijun, E-mail: tangnaijun@tijmu.edu.cn [Department of Occupational and Environmental Health, School of Public Health, Tianjin Medical University, Tianjin 300070 (China)

2015-12-01

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

Asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size.

Science.gov (United States)

Chen, Hua; Chen, Kun

2013-07-01

The distributions of coalescence times and ancestral lineage numbers play an essential role in coalescent modeling and ancestral inference. Both exact distributions of coalescence times and ancestral lineage numbers are expressed as the sum of alternating series, and the terms in the series become numerically intractable for large samples. More computationally attractive are their asymptotic distributions, which were derived in Griffiths (1984) for populations with constant size. In this article, we derive the asymptotic distributions of coalescence times and ancestral lineage numbers for populations with temporally varying size. For a sample of size n, denote by Tm the mth coalescent time, when m + 1 lineages coalesce into m lineages, and An(t) the number of ancestral lineages at time t back from the current generation. Similar to the results in Griffiths (1984), the number of ancestral lineages, An(t), and the coalescence times, Tm, are asymptotically normal, with the mean and variance of these distributions depending on the population size function, N(t). At the very early stage of the coalescent, when t → 0, the number of coalesced lineages n - An(t) follows a Poisson distribution, and as m → n, $$n\\left(n-1\\right){T}_{m}/2N\\left(0\\right)$$ follows a gamma distribution. We demonstrate the accuracy of the asymptotic approximations by comparing to both exact distributions and coalescent simulations. Several applications of the theoretical results are also shown: deriving statistics related to the properties of gene genealogies, such as the time to the most recent common ancestor (TMRCA) and the total branch length (TBL) of the genealogy, and deriving the allele frequency spectrum for large genealogies. With the advent of genomic-level sequencing data for large samples, the asymptotic distributions are expected to have wide applications in theoretical and methodological development for population genetic inference.

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.

An assessment of particle filtering methods and nudging for climate state reconstructions

NARCIS (Netherlands)

S. Dubinkina (Svetlana); H. Goosse

2013-01-01

htmlabstractUsing the climate model of intermediate complexity LOVECLIM in an idealized framework, we assess three data-assimilation methods for reconstructing the climate state. The methods are a nudging, a particle filter with sequential importance resampling, and a nudging proposal particle

An Epistemological Analysis of the African Ontology of `Ancestral ...

African Journals Online (AJOL)

The paper explores the contemporary debate surrounding the idea of ancestral reincarnation in African society and philosophy. It analyzes various problem areas having to do with the physical and spiritual status of ancestors, their relationship with their societies of orientation, the philosophical contexts of their existence, ...

Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance

Directory of Open Access Journals (Sweden)

Asunción Delgado

2017-05-01

Full Text Available Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli. Unlike E. coli thioredoxin, however, these ancestral thioredoxins are not efficiently recruited by the bacteriophage T7 for its replisome and therefore prevent phage propagation in E. coli. These results suggest an approach to the engineering of virus resistance. Diseases caused by viruses may have a devastating effect in agriculture. We discuss how the suggested approach could be applied to the engineering of plant virus resistance.

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

Directory of Open Access Journals (Sweden)

Ulrike Loch

2008-01-01

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

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

Energy Technology Data Exchange (ETDEWEB)

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

1995-08-01

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

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.

Progressive Reconstruction: A Methodology for Stabilization and Reconstruction Operations

National Research Council Canada - National Science Library

Rohr, Karl C

2006-01-01

... these nations in accordance with stated United States' goals. The argument follows closely current and developing United States military doctrine on stabilization, reconstruction, and counterinsurgency operations...

Rescaling Education: Reconstructions of Scale in President Reagan's 1983 State of the Union Address

Science.gov (United States)

Collin, Ross; Ferrare, Joseph J.

2015-01-01

This article presents a discourse analysis of President Ronald Reagan's 1983 State of the Union Address. Focusing on questions of scale, the article considers how and with what effects Reagan reconstructs education as a local, state, national and global endeavour. It is argued that by situating education in a competitive global economy, Reagan…

Isolation of Ancestral Sylvatic Dengue Virus Type 1, Malaysia

Science.gov (United States)

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

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. PMID:21029545

Partially incorrect fossil data augment analyses of discrete trait evolution in living species.

Science.gov (United States)

Puttick, Mark N

2016-08-01

Ancestral state reconstruction of discrete character traits is often vital when attempting to understand the origins and homology of traits in living species. The addition of fossils has been shown to alter our understanding of trait evolution in extant taxa, but researchers may avoid using fossils alongside extant species if only few are known, or if the designation of the trait of interest is uncertain. Here, I investigate the impacts of fossils and incorrectly coded fossils in the ancestral state reconstruction of discrete morphological characters under a likelihood model. Under simulated phylogenies and data, likelihood-based models are generally accurate when estimating ancestral node values. Analyses with combined fossil and extant data always outperform analyses with extant species alone, even when around one quarter of the fossil information is incorrect. These results are especially pronounced when model assumptions are violated, such as when there is a trend away from the root value. Fossil data are of particular importance when attempting to estimate the root node character state. Attempts should be made to include fossils in analysis of discrete traits under likelihood, even if there is uncertainty in the fossil trait data. © 2016 The Authors.

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

Science.gov (United States)

Johnson Pokorná, Martina; Kratochvíl, Lukáš

2016-02-01

Amniote vertebrates, the group consisting of mammals and reptiles including birds, possess various mechanisms of sex determination. Under environmental sex determination (ESD), the sex of individuals depends on the environmental conditions occurring during their development and therefore there are no sexual differences present in their genotypes. Alternatively, through the mode of genotypic sex determination (GSD), sex is determined by a sex-specific genotype, i.e. by the combination of sex chromosomes at various stages of differentiation at conception. As well as influencing sex determination, sex-specific parts of genomes may, and often do, develop specific reproductive or ecological roles in their bearers. Accordingly, an individual with a mismatch between phenotypic (gonadal) and genotypic sex, for example an individual sex-reversed by environmental effects, should have a lower fitness due to the lack of specialized, sex-specific parts of their genome. In this case, evolutionary transitions from GSD to ESD should be less likely than transitions in the opposite direction. This prediction contrasts with the view that GSD was the ancestral sex-determining mechanism for amniote vertebrates. Ancestral GSD would require several transitions from GSD to ESD associated with an independent dedifferentiation of sex chromosomes, at least in the ancestors of crocodiles, turtles, and lepidosaurs (tuataras and squamate reptiles). In this review, we argue that the alternative theory postulating ESD as ancestral in amniotes is more parsimonious and is largely concordant with the theoretical expectations and current knowledge of the phylogenetic distribution and homology of sex-determining mechanisms. © 2014 Cambridge Philosophical Society.

Using Resurrected Ancestral Proviral Proteins to Engineer Virus Resistance.

Science.gov (United States)

Delgado, Asunción; Arco, Rocio; Ibarra-Molero, Beatriz; Sanchez-Ruiz, Jose M

2017-05-09

Proviral factors are host proteins hijacked by viruses for processes essential for virus propagation such as cellular entry and replication. Pathogens and their hosts co-evolve. It follows that replacing a proviral factor with a functional ancestral form of the same protein could prevent viral propagation without fatally compromising organismal fitness. Here, we provide proof of concept of this notion. Thioredoxins serve as general oxidoreductases in all known cells. We report that several laboratory resurrections of Precambrian thioredoxins display substantial levels of functionality within Escherichia coli. Unlike E. coli thioredoxin, however, these ancestral thioredoxins are not efficiently recruited by the bacteriophage T7 for its replisome and therefore prevent phage propagation in E. coli. These results suggest an approach to the engineering of virus resistance. Diseases caused by viruses may have a devastating effect in agriculture. We discuss how the suggested approach could be applied to the engineering of plant virus resistance. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

XD-GRASP: Golden-angle radial MRI with reconstruction of extra motion-state dimensions using compressed sensing.

Science.gov (United States)

Feng, Li; Axel, Leon; Chandarana, Hersh; Block, Kai Tobias; Sodickson, Daniel K; Otazo, Ricardo

2016-02-01

To develop a novel framework for free-breathing MRI called XD-GRASP, which sorts dynamic data into extra motion-state dimensions using the self-navigation properties of radial imaging and reconstructs the multidimensional dataset using compressed sensing. Radial k-space data are continuously acquired using the golden-angle sampling scheme and sorted into multiple motion-states based on respiratory and/or cardiac motion signals derived directly from the data. The resulting undersampled multidimensional dataset is reconstructed using a compressed sensing approach that exploits sparsity along the new dynamic dimensions. The performance of XD-GRASP is demonstrated for free-breathing three-dimensional (3D) abdominal imaging, two-dimensional (2D) cardiac cine imaging and 3D dynamic contrast-enhanced (DCE) MRI of the liver, comparing against reconstructions without motion sorting in both healthy volunteers and patients. XD-GRASP separates respiratory motion from cardiac motion in cardiac imaging, and respiratory motion from contrast enhancement in liver DCE-MRI, which improves image quality and reduces motion-blurring artifacts. XD-GRASP represents a new use of sparsity for motion compensation and a novel way to handle motions in the context of a continuous acquisition paradigm. Instead of removing or correcting motion, extra motion-state dimensions are reconstructed, which improves image quality and also offers new physiological information of potential clinical value. © 2015 Wiley Periodicals, Inc.

Wave packet interferometry and quantum state reconstruction by acousto-optic phase modulation

International Nuclear Information System (INIS)

Tekavec, Patrick F.; Dyke, Thomas R.; Marcus, Andrew H.

2006-01-01

Studies of wave packet dynamics often involve phase-selective measurements of coherent optical signals generated from sequences of ultrashort laser pulses. In wave packet interferometry (WPI), the separation between the temporal envelopes of the pulses must be precisely monitored or maintained. Here we introduce a new (and easy to implement) experimental scheme for phase-selective measurements that combines acousto-optic phase modulation with ultrashort laser excitation to produce an intensity-modulated fluorescence signal. Synchronous detection, with respect to an appropriately constructed reference, allows the signal to be simultaneously measured at two phases differing by 90 deg. Our method effectively decouples the relative temporal phase from the pulse envelopes of a collinear train of optical pulse pairs. We thus achieve a robust and high signal-to-noise scheme for WPI applications, such as quantum state reconstruction and electronic spectroscopy. The validity of the method is demonstrated, and state reconstruction is performed, on a model quantum system - atomic Rb vapor. Moreover, we show that our measurements recover the correct separation between the absorptive and dispersive contributions to the system susceptibility

A high order compact least-squares reconstructed discontinuous Galerkin method for the steady-state compressible flows on hybrid grids

Science.gov (United States)

Cheng, Jian; Zhang, Fan; Liu, Tiegang

2018-06-01

In this paper, a class of new high order reconstructed DG (rDG) methods based on the compact least-squares (CLS) reconstruction [23,24] is developed for simulating the two dimensional steady-state compressible flows on hybrid grids. The proposed method combines the advantages of the DG discretization with the flexibility of the compact least-squares reconstruction, which exhibits its superior potential in enhancing the level of accuracy and reducing the computational cost compared to the underlying DG methods with respect to the same number of degrees of freedom. To be specific, a third-order compact least-squares rDG(p1p2) method and a fourth-order compact least-squares rDG(p2p3) method are developed and investigated in this work. In this compact least-squares rDG method, the low order degrees of freedom are evolved through the underlying DG(p1) method and DG(p2) method, respectively, while the high order degrees of freedom are reconstructed through the compact least-squares reconstruction, in which the constitutive relations are built by requiring the reconstructed polynomial and its spatial derivatives on the target cell to conserve the cell averages and the corresponding spatial derivatives on the face-neighboring cells. The large sparse linear system resulted by the compact least-squares reconstruction can be solved relatively efficient when it is coupled with the temporal discretization in the steady-state simulations. A number of test cases are presented to assess the performance of the high order compact least-squares rDG methods, which demonstrates their potential to be an alternative approach for the high order numerical simulations of steady-state compressible flows.

Lack of Social Support Raises Stress Vulnerability in Rats with a History of Ancestral Stress.

Science.gov (United States)

Faraji, Jamshid; Soltanpour, Nabiollah; Lotfi, Hamid; Moeeini, Reza; Moharreri, Ali-Reza; Roudaki, Shabnam; Hosseini, S Abedin; Olson, David M; Abdollahi, Ali-Akbar; Soltanpour, Nasrin; Mohajerani, Majid H; Metz, Gerlinde A S

2017-07-13

Stress is a primary risk factor for psychiatric disorders. However, it is not fully understood why some stressed individuals are more vulnerable to psychiatric disorders than others. Here, we investigated whether multigenerational ancestral stress produces phenotypes that are sensitive to depression-like symptoms in rats. We also examined whether social isolation reveals potentially latent sensitivity to depression-like behaviours. F4 female rats born to a lineage of stressed mothers (F0-F3) received stress in adulthood while housed in pairs or alone. Social isolation during stress induced cognitive and psychomotor retardation only in rats exposed to ancestral stress. Social isolation also hampered the resilience of the hypothalamic-pituitary-adrenal axis to chronic stress and reduced hippocampal volume and brain-derived neurotrophic factor (BDNF) expression. Thus, synergy between social isolation and stress may unmask a latent history of ancestral stress, and raises vulnerability to mental health conditions. The findings support the notion that social support critically promotes stress coping and resilience.

Expression, purification and crystallization of the ancestral androgen receptor-DHT complex.

Science.gov (United States)

Colucci, Jennifer K; Ortlund, Eric A

2013-09-01

Steroid receptors (SRs) are a closely related family of ligand-dependent nuclear receptors that mediate the transcription of genes critical for development, reproduction and immunity. SR dysregulation has been implicated in cancer, inflammatory diseases and metabolic disorders. SRs bind their cognate hormone ligand with exquisite specificity, offering a unique system to study the evolution of molecular recognition. The SR family evolved from an estrogen-sensitive ancestor and diverged to become sensitive to progestagens, corticoids and, most recently, androgens. To understand the structural mechanisms driving the evolution of androgen responsiveness, the ancestral androgen receptor (ancAR1) was crystallized in complex with 5α-dihydrotestosterone (DHT) and a fragment of the transcriptional mediator/intermediary factor 2 (Tif2). Crystals diffracted to 2.1 Å resolution and the resulting structure will permit a direct comparison with its progestagen-sensitive ancestor, ancestral steroid receptor 2 (AncSR2).

Visual system evolution and the nature of the ancestral snake.

Science.gov (United States)

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

2015-07-01

The dominant hypothesis for the evolutionary origin of snakes from 'lizards' (non-snake squamates) is that stem snakes acquired many snake features while passing through a profound burrowing (fossorial) phase. To investigate this, we examined the visual pigments and their encoding opsin genes in a range of squamate reptiles, focusing on fossorial lizards and snakes. We sequenced opsin transcripts isolated from retinal cDNA and used microspectrophotometry to measure directly the spectral absorbance of the photoreceptor visual pigments in a subset of samples. In snakes, but not lizards, dedicated fossoriality (as in Scolecophidia and the alethinophidian Anilius scytale) corresponds with loss of all visual opsins other than RH1 (λmax 490-497 nm); all other snakes (including less dedicated burrowers) also have functional sws1 and lws opsin genes. In contrast, the retinas of all lizards sampled, even highly fossorial amphisbaenians with reduced eyes, express functional lws, sws1, sws2 and rh1 genes, and most also express rh2 (i.e. they express all five of the visual opsin genes present in the ancestral vertebrate). Our evidence of visual pigment complements suggests that the visual system of stem snakes was partly reduced, with two (RH2 and SWS2) of the ancestral vertebrate visual pigments being eliminated, but that this did not extend to the extreme additional loss of SWS1 and LWS that subsequently occurred (probably independently) in highly fossorial extant scolecophidians and A. scytale. We therefore consider it unlikely that the ancestral snake was as fossorial as extant scolecophidians, whether or not the latter are para- or monophyletic. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

The feasibility study of reconstructing a Y(4260)-like state with the ATLAS detector at the LHC

CERN Document Server

Jyotishmati, Susmita

2008-01-01

A Monte Carlo simulation study of the feasibility of reconstructing a Y(4260)-like state within the mass range 3.7-6.0 GeV/ c 2 decaying into J / ψhh , where h is a charged pion or a charged kaon, is carried out with the Atlas detector using the default event trigger conditions. The variations in the Y(4260)-like state detection efficiency resulting from possible p T trigger are presented. The criterion on the reconstructed proper time of the J / ψhh , where h system is proposed to reject backgrounds from B -meson decays. Additional studies needed to fully determine the Y(4260)-like state detection efficiency and the rejection of all backgrounds is summarized for future study.

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

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H Deborah Chen

2011-07-01

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

Deep Venous Thrombosis Prophylaxis in Anterior Cruciate Ligament Reconstructive Surgery: What Is the Current State of Practice?

Science.gov (United States)

Keller, Robert A; Moutzouros, Vasilios; Dines, Joshua S; Bush-Joseph, Charles A; Limpisvasti, Orr

Venous thromboembolism (VTE) is a significant perioperative risk with many common orthopaedic procedures. Currently, there is no standardized recommendation for the use of VTE prophylaxis during anterior cruciate ligament (ACL) reconstruction. This study sought to evaluate the current prophylactic practices of fellowship-trained sports medicine orthopaedic surgeons in the United States. Very few surgeons use perioperative VTE prophylaxis for ACL reconstructive surgery. Survey. Surveys were emailed to the alumni networks of 4 large ACGME-accredited sports medicine fellowship programs. Questions were focused on their current use of chemical and nonchemical VTE prophylaxis. Surveys were completed by 142 surgeons in the United States, yielding a response rate of 32%. Of those who responded, 50.7% stated that they routinely use chemical prophylaxis, with 95.5% of those using aspirin (acetylsalicylic acid [ASA]). There was no standardized dosing protocol, with respondents using ASA 325 mg once (46%) or twice daily (26%) or ASA 81 mg once (18%) or twice (10%) daily. The most common reason for not including chemical prophylaxis within the reconstruction procedure was that it is unnecessary given the low risk of VTE. Physicians also based their prophylaxis regimen more on their own clinical experience than concern for litigation. Half of all sports medicine fellowship-trained surgeons surveyed routinely use chemical VTE prophylaxis after ACL reconstruction, with more than 90% of those using ASA. Of those using ASA, there was no prevailing dosing protocol. For those not using chemical prophylaxis, the most important reason was that it was felt to be unnecessary due to the risks outweighing the benefits. Those who do not regularly use chemical prophylaxis would be willing to, however, if a patient had a personal or family history of clotting disorder or is currently on birth control. Additionally, clinical experience was the primary driver for a current prophylaxis protocol

The ancestral chromosomes of Dromiciops gliroides (Microbiotheridae), and its bearings on the karyotypic evolution of American marsupials

OpenAIRE

Su?rez-Villota, Elkin Y.; Haro, Ronie E.; Vargas, Rodrigo A.; Gallardo, Milton H.

2016-01-01

Background The low-numbered 14-chromosome karyotype of marsupials has falsified the fusion hypothesis claiming ancestrality from a 22-chromosome karyotype. Since the 14-chromosome condition of the relict Dromiciops gliroides is reminecent of ancestrality, its interstitial traces of past putative fusions and heterochromatin banding patterns were studied and added to available marsupials? cytogenetic data. Fluorescent in situ hybridization (FISH) and self-genomic in situ hybridization (self-GIS...

Temperature-dependent respiration-growth relations in ancestral maize cultivars

Science.gov (United States)

Bruce N. Smith; Jillian L. Walker; Rebekka L. Stone; Angela R. Jones; Lee D. Hansen

2001-01-01

Shoots from 4- to 6-day old seedlings of seven ancestral or old cultivars of Zea mays L. were placed in a calorimeter. Dark metabolic heat rate (q) and CO2 production rate (RCO2) were measured at nine temperatures (5, 10, 15, 20, 25, 30, 35, 40, and 45 °C). Temperature dependencies of q and RCO2 were used to model response of both growth and substrate carbon conversion...

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

DEFF Research Database (Denmark)

Caspeta, Luis; Nielsen, Jens

2015-01-01

adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40°C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses...... in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures....... In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance...

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

DEFF Research Database (Denmark)

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

2016-01-01

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

The phylogenetic significance of leaf anatomical traits of southern African Oxalis

Czech Academy of Sciences Publication Activity Database

Jooste, M.; Dreyer, L. L.; Oberlander, Kenneth

2016-01-01

Roč. 16, č. 1 (2016), s. 1-19, č. článku 225. ISSN 1471-2148 Institutional support: RVO:67985939 Keywords : ancestral state reconstruction * eEpistomaty * leaf anatomy * stomatal position * phylogenetics Subject RIV: EF - Botanics Impact factor: 3.221, year: 2016

Preserving half-metallic surface states in Cr O2 : Insights into surface reconstruction rules

Science.gov (United States)

Deng, Bei; Shi, X. Q.; Chen, L.; Tong, S. Y.

2018-04-01

The issue of whether the half-metallic (HM) nature of Cr O2 could be retained at its surface has been a standing problem under debate for a few decades, but until now is still controversial. Here, based on the density functional theory calculations we show, in startling contrast to the previous theoretical understandings, that the surfaces of Cr O2 favorably exhibit a half-metallic-semiconducting (SmC) transition driven by means of a surface electronic reconstruction largely attributed to the participation of the unexpected local charge carriers (LCCs), which convert the HM double exchange surface state into a SmC superexchange state and in turn, stabilize the surface as well. On the basis of the LCCs model, a new insight into the surface reconstruction rules is attained. Our novel finding not only provided an evident interpretation for the widely observed SmC character of Cr O2 surface, but also offered a novel means to improve the HM surface states for a variety of applications in spintronics and superconductors, and promote the experimental realization of the quantum anomalous Hall effect in half-metal based systems.

Accuracy of Genomic Prediction in Synthetic Populations Depending on the Number of Parents, Relatedness, and Ancestral Linkage Disequilibrium.

Science.gov (United States)

Schopp, Pascal; Müller, Dominik; Technow, Frank; Melchinger, Albrecht E

2017-01-01

Synthetics play an important role in quantitative genetic research and plant breeding, but few studies have investigated the application of genomic prediction (GP) to these populations. Synthetics are generated by intermating a small number of parents ([Formula: see text] and thereby possess unique genetic properties, which make them especially suited for systematic investigations of factors contributing to the accuracy of GP. We generated synthetics in silico from [Formula: see text]2 to 32 maize (Zea mays L.) lines taken from an ancestral population with either short- or long-range linkage disequilibrium (LD). In eight scenarios differing in relatedness of the training and prediction sets and in the types of data used to calculate the relationship matrix (QTL, SNPs, tag markers, and pedigree), we investigated the prediction accuracy (PA) of Genomic best linear unbiased prediction (GBLUP) and analyzed contributions from pedigree relationships captured by SNP markers, as well as from cosegregation and ancestral LD between QTL and SNPs. The effects of training set size [Formula: see text] and marker density were also studied. Sampling few parents ([Formula: see text]) generates substantial sample LD that carries over into synthetics through cosegregation of alleles at linked loci. For fixed [Formula: see text], [Formula: see text] influences PA most strongly. If the training and prediction set are related, using [Formula: see text] parents yields high PA regardless of ancestral LD because SNPs capture pedigree relationships and Mendelian sampling through cosegregation. As [Formula: see text] increases, ancestral LD contributes more information, while other factors contribute less due to lower frequencies of closely related individuals. For unrelated prediction sets, only ancestral LD contributes information and accuracies were poor and highly variable for [Formula: see text] due to large sample LD. For large [Formula: see text], achieving moderate accuracy requires

Higgs Boson in Multi-b-Jets Final States Reconstruction with Full Simulation of Atlas Detector

International Nuclear Information System (INIS)

Sapinski, M.; Cavalli, D.

2001-01-01

Channels with multi-b-jet final states are very important in the discovery strategies for the Higgs boson search in ATLAS experiment at LHC. Excellent jets reconstruction efficiencies and mass resolution capability of the di-jet system are crucial aspects of the detector performance for the signal observability in these channels. Full simulation and reconstruction of the four representative channels with b-jets in final states is discussed: WH, t(anti)tH with H → b(anti)b and A → Zh, H → hh with h → b(anti)b. These channels are used as benchmark ones to study the different complexity of events, level of combinatorial background from signal itself and universality of the algorithms used for jets reconstruction and energy calibration at the wide range of energy/mass scales. Equivalently important aspect of this study is to verify applicability of the fast detector simulation, based on parametrisation of main features of the detector, for studying signal and background rates for the above channels. For that reason the detailed comparisons of the expected efficiencies and acceptances in full (based on GEANT 3) and fast simulations are shown at the different stages of the selection procedures. In general good agreement is found between results obtained in both approaches. (author)

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.

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

Directory of Open Access Journals (Sweden)

Sa Geng

2014-07-01

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

Full reconstruction of a 14-qubit state within four hours

International Nuclear Information System (INIS)

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

2016-01-01

Full quantum state tomography (FQST) plays a unique role in the estimation of the state of a quantum system without a priori knowledge or assumptions. Unfortunately, since FQST requires informationally (over)complete measurements, both the number of measurement bases and the computational complexity of data processing suffer an exponential growth with the size of the quantum system. A 14-qubit entangled state has already been experimentally prepared in an ion trap, and the data processing capability for FQST of a 14-qubit state seems to be far away from practical applications. In this paper, the computational capability of FQST is pushed forward to reconstruct a 14-qubit state with a run time of only 3.35 hours using the linear regression estimation (LRE) algorithm, even when informationally overcomplete Pauli measurements are employed. The computational complexity of the LRE algorithm is first reduced from ∼10 19 to ∼10 15 for a 14-qubit state, by dropping all the zero elements, and its computational efficiency is further sped up by fully exploiting the parallelism of the LRE algorithm with parallel Graphic Processing Unit (GPU) programming. Our result demonstrates the effectiveness of using parallel computation to speed up the postprocessing for FQST, and can play an important role in quantum information technologies with large quantum systems. (paper)

Do Père David's deer lose memories of their ancestral predators?

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Chunwang Li

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

Pollination and reproduction of an invasive plant inside and outside its ancestral range

Science.gov (United States)

Petanidou, Theodora; Price, Mary V.; Bronstein, Judith L.; Kantsa, Aphrodite; Tscheulin, Thomas; Kariyat, Rupesh; Krigas, Nikos; Mescher, Mark C.; De Moraes, Consuelo M.; Waser, Nickolas M.

2018-05-01

Comparing traits of invasive species within and beyond their ancestral range may improve our understanding of processes that promote aggressive spread. Solanum elaeagnifolium (silverleaf nightshade) is a noxious weed in its ancestral range in North America and is invasive on other continents. We compared investment in flowers and ovules, pollination success, and fruit and seed set in populations from Arizona, USA ("AZ") and Greece ("GR"). In both countries, the populations we sampled varied in size and types of present-day disturbance. Stature of plants increased with population size in AZ samples whereas GR plants were uniformly tall. Taller plants produced more flowers, and GR plants produced more flowers for a given stature and allocated more ovules per flower. Similar functional groups of native bees pollinated in AZ and GR populations, but visits to flowers decreased with population size and we observed no visits in the largest GR populations. As a result, plants in large GR populations were pollen-limited, and estimates of fecundity were lower on average in GR populations despite the larger allocation to flowers and ovules. These differences between plants in our AZ and GR populations suggest promising directions for further study. It would be useful to sample S. elaeagnifolium in Mediterranean climates within the ancestral range (e.g., in California, USA), to study asexual spread via rhizomes, and to use common gardens and genetic studies to explore the basis of variation in allocation patterns and of relationships between visitation and fruit set.

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

Science.gov (United States)

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

2001-11-12

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

Dynamic dual-tracer PET reconstruction.

Science.gov (United States)

Gao, Fei; Liu, Huafeng; Jian, Yiqiang; Shi, Pengcheng

2009-01-01

Although of important medical implications, simultaneous dual-tracer positron emission tomography reconstruction remains a challenging problem, primarily because the photon measurements from dual tracers are overlapped. In this paper, we propose a simultaneous dynamic dual-tracer reconstruction of tissue activity maps based on guidance from tracer kinetics. The dual-tracer reconstruction problem is formulated in a state-space representation, where parallel compartment models serve as continuous-time system equation describing the tracer kinetic processes of dual tracers, and the imaging data is expressed as discrete sampling of the system states in measurement equation. The image reconstruction problem has therefore become a state estimation problem in a continuous-discrete hybrid paradigm, and H infinity filtering is adopted as the estimation strategy. As H infinity filtering makes no assumptions on the system and measurement statistics, robust reconstruction results can be obtained for the dual-tracer PET imaging system where the statistical properties of measurement data and system uncertainty are not available a priori, even when there are disturbances in the kinetic parameters. Experimental results on digital phantoms, Monte Carlo simulations and physical phantoms have demonstrated the superior performance.

An allele of an ancestral transcription factor dependent on a horizontally acquired gene product.

Science.gov (United States)

Chen, H Deborah; Jewett, Mollie W; Groisman, Eduardo A

2012-01-01

Changes in gene regulatory circuits often give rise to phenotypic differences among closely related organisms. In bacteria, these changes can result from alterations in the ancestral genome and/or be brought about by genes acquired by horizontal transfer. Here, we identify an allele of the ancestral transcription factor PmrA that requires the horizontally acquired pmrD gene product to promote gene expression. We determined that a single amino acid difference between the PmrA proteins from the human adapted Salmonella enterica serovar Paratyphi B and the broad host range S. enterica serovar Typhimurium rendered transcription of PmrA-activated genes dependent on the PmrD protein in the former but not the latter serovar. Bacteria harboring the serovar Typhimurium allele exhibited polymyxin B resistance under PmrA- or under PmrA- and PmrD-inducing conditions. By contrast, isogenic strains with the serovar Paratyphi B allele displayed PmrA-regulated polymyxin B resistance only when experiencing activating conditions for both PmrA and PmrD. We establish that the two PmrA orthologs display quantitative differences in several biochemical properties. Strains harboring the serovar Paratyphi B allele showed enhanced biofilm formation, a property that might promote serovar Paratyphi B's chronic infection of the gallbladder. Our findings illustrate how subtle differences in ancestral genes can impact the ability of horizontally acquired genes to confer new properties.

Preliminary appraisal of ground water in and near the ancestral Missouri River Valley, northeastern Montana

Science.gov (United States)

Levings, G.W.

1986-01-01

A preliminary appraisal was conducted in and near the ancestral Missouri River valley in northeastern Montana to describe the groundwater resources and to establish a data base for the area. The data base then could be used for future evaluation of possible changes in water levels or water quality. In this area, consolidated aquifers are the Upper Cretaceous Fox Hills-lower Hell Creek aquifer and the overlying Paleocene Fort Union Formation. Unconsolidated aquifers are Pleistocene terrace gravel and glacial deposits and Holocene alluvial deposits. Aquifers are recharged by precipitation, infiltration of streamflow, and possibly leakage from lakes and potholes. Groundwater moves from topographically higher areas to the ancestral valley, then along the ancestral valley to the southwest. Water is discharged from aquifers by evapotranspiration, springs and seeps, movement directly into streams and lakes, and from pumping wells. Average well yields are greatest for irrigation wells completed in outwash gravel (886 gallons/min). Eighteen wells were completed in various aquifers to monitor potential long-term changes in water levels and water quality. Measured water levels declined about 2 ft. or less during the study (1982-85). Chemical analysis of groundwater samples indicated that concentrations of some dissolved constituents exceeded U.S. Environmental Protection Agency standards for drinking water. (USGS)

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

Science.gov (United States)

Kradin, Richard L

2012-04-01

The ancestral claims on an individual can evoke mental conflict when they involve separating from an ethnic group whose beliefs and customs are devalued by the dominant culture. However, these claims are engraved on the psyche early in development by caretakers to the level of pre-object relatedness, where contents and affect tones are implicit and may be unavailable for later psychoanalytical interventions. In addition, as the anthropologist Clifford Geertz notes, one's culture of origin precedes the development of psyche and creates its own set of claims that must be renegotiated when one encounters a different domain of cultural symbols, a confrontation that can produce psychological dissonance and self-alienation. In this paper, three cases are examined in which mental conflicts were evoked by attempts at divesting ancestral claims in response to conscious efforts to assimilate into the dominant culture. These patients suffered from separation guilt and unstable self-esteem and reported dream imagery suggesting psychological imbalance. The requirement to carefully delineate the ancestral claims on psyche as well as those contents and affects that may not be accessible to therapeutic intervention is emphasized, and the importance of compromise and acceptance with respect to the psychological demands of the unconscious are considered. 2012, The Society of Analytical Psychology.

Chromosome evolution in kangaroos (Marsupialia: Macropodidae): cross species chromosome painting between the tammar wallaby and rock wallaby spp. with the 2n = 22 ancestral macropodid karyotype.

Science.gov (United States)

O'Neill, R J; Eldridge, M D; Toder, R; Ferguson-Smith, M A; O'Brien, P C; Graves, J A

1999-06-01

Marsupial mammals show extraordinary karyotype stability, with 2n = 14 considered ancestral. However, macropodid marsupials (kangaroos and wallabies) exhibit a considerable variety of karyotypes, with a hypothesised ancestral karyotype of 2n = 22. Speciation and karyotypic diversity in rock wallabies (Petrogale) is exceptional. We used cross species chromosome painting to examine the chromosome evolution between the tammar wallaby (2n = 16) and three 2n = 22 rock wallaby species groups with the putative ancestral karyotype. Hybridization of chromosome paints prepared from flow sorted chromosomes of the tammar wallaby to Petrogale spp., showed that this ancestral karyotype is largely conserved among 2n = 22 rock wallaby species, and confirmed the identity of ancestral chromosomes which fused to produce the bi-armed chromosomes of the 2n = 16 tammar wallaby. These results illustrate the fission-fusion process of karyotype evolution characteristic of the kangaroo group.

Breast reconstruction and post-mastectomy radiation practice

International Nuclear Information System (INIS)

Chen, Susie A; Hiley, Crispin; Nickleach, Dana; Petsuksiri, Janjira; Andic, Fundagul; Riesterer, Oliver; Switchenko, Jeffrey M; Torres, Mylin A

2013-01-01

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

Inferring ancestral distribution area and survival vegetation of Caragana (Fabaceae) in Tertiary

Science.gov (United States)

Mingli Zhang; Juanjuan Xue; Qiang Zhang; Stewart C. Sanderson

2015-01-01

Caragana, a leguminous genus mainly restricted to temperate Central and East Asia, occurs in arid, semiarid, and humid belts, and has forest, grassland, and desert ecotypes. Based on the previous molecular phylogenetic tree and dating, biogeographical analyses of extant species area and ecotype were conducted by means of four ancestral optimization approaches: S-DIVA,...

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

NARCIS (Netherlands)

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

2016-01-01

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

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

NARCIS (Netherlands)

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

2016-01-01

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

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.)

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

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.

Science.gov (United States)

Kang, Ji Hyoun; Schartl, Manfred; Walter, Ronald B; Meyer, Axel

2013-01-29

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. 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 selected sword trait is shown to be the most likely

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

OpenAIRE

Crawford, D H; Powell, L W; Leggett, B A; Francis, J S; Fletcher, L M; Webb, S I; Halliday, J W; Jazwinska, E C

1995-01-01

Hemochromatosis (HC) is a common inherited disorder of iron metabolism for which neither the gene nor biochemical defect have yet been identified. The aim of this study was to look for clinical evidence that the predominant ancestral haplotype in Australian patients is associated with a common mutation in the gene. We compared indices of iron metabolism and storage in three groups of HC patients categorized according to the presence of the ancestral haplotype (i.e., patients with two copies, ...

Paleoclimate Signals and Temperature Reconstructions for the Northeastern United States using Atlantic White Cedar Tree-Rings

Science.gov (United States)

Pearl, J. K.; Anchukaitis, K. J.; Pederson, N.; Donnelly, J. P.

2016-12-01

High-resolution paleoclimate records of the Common Era are essential for improving detection and attribution of internal and forced climate system responses. The densely populated northeastern United States is at risk from impending climate shifts as well as sea level rise. Here we present a new network of annually resolved proxy data from Atlantic white cedar trees throughout the northeastern United States. Ring width variability reflects winter through summer temperatures at inland sites north of New Jersey. Climate signals embedded in the full network are evaluated for their potential to provide reconstructions of both temperature and drought variability. We demonstrate skillful climate reconstructions for the last several centuries and the potential to use subfossil samples to extend these records over the Common Era. Our tree-ring network provides the long-term context at multidecadal and centennial time scales for the large-scale ocean-atmospheric processes that influence the climate of the region.

Potential pitfalls of reconstructing deep time evolutionary history with only extant data, a case study using the canidae (mammalia, carnivora).

Science.gov (United States)

Finarelli, John A; Goswami, Anjali

2013-12-01

Reconstructing evolutionary patterns and their underlying processes is a central goal in biology. Yet many analyses of deep evolutionary histories assume that data from the fossil record is too incomplete to include, and rely solely on databases of extant taxa. Excluding fossil taxa assumes that character state distributions across living taxa are faithful representations of a clade's entire evolutionary history. Many factors can make this assumption problematic. Fossil taxa do not simply lead-up to extant taxa; they represent now-extinct lineages that can substantially impact interpretations of character evolution for extant groups. Here, we analyze body mass data for extant and fossil canids (dogs, foxes, and relatives) for changes in mean and variance through time. AIC-based model selection recovered distinct models for each of eight canid subgroups. We compared model fit of parameter estimates for (1) extant data alone and (2) extant and fossil data, demonstrating that the latter performs significantly better. Moreover, extant-only analyses result in unrealistically low estimates of ancestral mass. Although fossil data are not always available, reconstructions of deep-time organismal evolution in the absence of deep-time data can be highly inaccurate, and we argue that every effort should be made to include fossil data in macroevolutionary studies. © 2013 The Authors. Evolution published by Wiley Periodicals, Inc. on behalf of The Society for the Study of Evolution.

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.

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

International Nuclear Information System (INIS)

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

2011-01-01

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.

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.

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

Science.gov (United States)

Gillette, Ross; Miller-Crews, Isaac; Skinner, Michael K; Crews, David

2015-01-01

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 (mPOA), lateral hypothalamus (LH), 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 mPOA. Epigenetic related genes were affected by stress in the ventromedial nucleus and by both ancestral exposure and stress during adolescence independently in the central amygdala. It is noteworthy that the LH showed no effects of either manipulation. Gene expression is discussed in the context of behavioral and physiological measures previously published.

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

OpenAIRE

Nadot S.; Sauquet H.; Damerval C.; Jabbour F.; Domenech B.

2016-01-01

Progress has been made recently towards the elucidation of phylogenetic relationships among subfamilies and tribes of the Ranunculaceae – the most recent hypothesis was published in 2016 by our team. Although relationships among the 10 tribes of the subfamily Ranunculoideae remain incompletely supported, this hypothesis provides an interesting framework to address the key issue of the ancestral vs. derived nature of a differentiated perianth within the family, and at the level of Ranunculales...

Analysis of ancestral and functionally relevant CD5 variants in systemic lupus erythematosus patients.

Directory of Open Access Journals (Sweden)

Maria Carmen Cenit

Full Text Available 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 role of CD5 on the development of SLE and/or SLE nephritis.The CD5 SNPs rs2241002 (C/T; Pro224Leu and rs2229177 (C/T; Ala471Val were genotyped using TaqMan allelic discrimination assays in a total of 1,324 controls and 681 SLE patients of Spanish origin. In vitro analysis of CD3-mediated T cell proliferative and cytokine response profiles of healthy volunteers homozygous for the above mentioned CD5 haplotypes were also analyzed.T-cell proliferation and cytokine release were significantly increased showing a bias towards to a Th2 profile after CD3 cross-linking of peripheral mononuclear cells from healthy individuals homozygous for the ancestral Pro224-Ala471 (CC haplotype, compared to the more recently derived Pro224-Val471 (CT. The same allelic combination was statistically associated with Lupus nephritis.The ancestral Ala471 CD5 allele confers lymphocyte hyper-responsiveness to TCR/CD3 cross-linking and is associated with nephritis in SLE patients.

Evaluation of proxy-based millennial reconstruction methods

Energy Technology Data Exchange (ETDEWEB)

Lee, Terry C.K.; Tsao, Min [University of Victoria, Department of Mathematics and Statistics, Victoria, BC (Canada); Zwiers, Francis W. [Environment Canada, Climate Research Division, Toronto, ON (Canada)

2008-08-15

A range of existing statistical approaches for reconstructing historical temperature variations from proxy data are compared using both climate model data and real-world paleoclimate proxy data. We also propose a new method for reconstruction that is based on a state-space time series model and Kalman filter algorithm. The state-space modelling approach and the recently developed RegEM method generally perform better than their competitors when reconstructing interannual variations in Northern Hemispheric mean surface air temperature. On the other hand, a variety of methods are seen to perform well when reconstructing surface air temperature variability on decadal time scales. An advantage of the new method is that it can incorporate additional, non-temperature, information into the reconstruction, such as the estimated response to external forcing, thereby permitting a simultaneous reconstruction and detection analysis as well as future projection. An application of these extensions is also demonstrated in the paper. (orig.)

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

DEFF Research Database (Denmark)

Mailund, Thomas; Dutheil, Julien; Hobolth, Asger

2011-01-01

event has occurred to split them apart. The size of these segments of constant divergence depends on the recombination rate, but also on the speciation time, the effective population size of the ancestral population, as well as demographic effects and selection. Thus, inference of these parameters may......, and the ancestral effective population size. The model is efficient enough to allow inference on whole-genome data sets. We first investigate the power and consistency of the model with coalescent simulations and then apply it to the whole-genome sequences of the two orangutan sub-species, Bornean (P. p. pygmaeus......) and Sumatran (P. p. abelii) orangutans from the Orangutan Genome Project. We estimate the speciation time between the two sub-species to be thousand years ago and the effective population size of the ancestral orangutan species to be , consistent with recent results based on smaller data sets. We also report...

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.

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.

Effectiveness of ancestral irradiation on the direct and correlated responses to selection for body weight in rats

International Nuclear Information System (INIS)

Gianola, D.

1975-01-01

The effects of ancestral irradiation of rat spermatogonia (a cumulative total of 4050 r of x-rays) were studied in a highly inbred line of rats to explore the feasibility of using irradiation to enhance the effectiveness of selection. Six generations after irradiation was terminated, a selection experiment for body weight at six weeks of age was started in both ancestrally irradiated and non-irradiated populations. There were two non-contemporaneous replicates in each of the populations. Within each of the ancestral treatment-replicate combinations one line was selected for high, one for low body weight at six weeks of age, and a third line was maintained by random selection. In each line, avoidance of mating of animals with grandparents in common was attempted. Data on the first ten progeny generations of selection were included in this study. Five types of covariances among relatives were used to estimate causal components of variance for five different genetic models within the ''non-irradiated'' and ''irradiated'' randomly selected models. The parameters in the genetic models were estimated by generalized least-squares. This analysis suggested that a genetic model including direct genetic and maternal genetic effects was adequate to describe the body weights at 3, 6 and 10 weeks of age and the weight gains between these ages. Ancestral irradiation seemed to have enhanced the maternal genetic variance and the covariance between the direct genetic and the maternal genetic effects. On the basis of the above analysis, it was deduced that mass selection should have been more effective in the descendants of irradiated males than in those of the non-irradiated males as a consequence of greater phenotypic variability in their progeny and an enhancement in the regression of the genetic value on the selection criterion

Evolutionary and biogeographical history of an ancient and global group of arachnids (Arachnida: Opiliones: Cyphophthalmi) with a new taxonomic arrangement

DEFF Research Database (Denmark)

Giribet, Gonzalo; Sharma, Prashant P.; Benavides, Ligia R.

2012-01-01

We investigate the phylogeny, biogeography, time of origin and diversification, ancestral area reconstruction and large-scale distributional patterns of an ancient group of arachnids, the harvestman suborder Cyphophthalmi. Analysis of molecular and morphological data allow us to propose a new......; Boreophthalmi includes Stylocellidae and Sironidae, the latter family of questionable monophyly. The internal resolution of each family is discussed and traced back to its geological time origin, as well as to its original landmass, using methods for estimating divergence times and ancestral area reconstruction....... The origin of Cyphophthalmi can be traced back to the Carboniferous, whereas the diversification time of most families ranges between the Carboniferous and the Jurassic, with the exception of Troglosironidae, whose current diversity originates in the Cretaceous/Tertiary. Ancestral area reconstruction...

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

Science.gov (United States)

Bissoonauth, Anu

2011-01-01

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

Evolution of developmental sequences in lepidosaurs

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Tomasz Skawiński

2017-04-01

Full Text Available Background Lepidosaurs, a group including rhynchocephalians and squamates, are one of the major clades of extant vertebrates. Although there has been extensive phylogenetic work on this clade, its interrelationships are a matter of debate. Morphological and molecular data suggest very different relationships within squamates. Despite this, relatively few studies have assessed the utility of other types of data for inferring squamate phylogeny. Methods We used developmental sequences of 20 events in 29 species of lepidosaurs. These sequences were analysed using event-pairing and continuous analysis. They were transformed into cladistic characters and analysed in TNT. Ancestral state reconstructions were performed on two main phylogenetic hypotheses of squamates (morphological and molecular. Results Cladistic analyses conducted using characters generated by these methods do not resemble any previously published phylogeny. Ancestral state reconstructions are equally consistent with both morphological and molecular hypotheses of squamate phylogeny. Only several inferred heterochronic events are common to all methods and phylogenies. Discussion Results of the cladistic analyses, and the fact that reconstructions of heterochronic events show more similarities between certain methods rather than phylogenetic hypotheses, suggest that phylogenetic signal is at best weak in the studied developmental events. Possibly the developmental sequences analysed here evolve too quickly to recover deep divergences within Squamata.

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.

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)

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

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 haplotype is likely to be applicable to many other genes

Can state-of-the-art HVS-based objective image quality criteria be used for image reconstruction techniques based on ROI analysis?

Science.gov (United States)

Dostal, P.; Krasula, L.; Klima, M.

2012-06-01

Various image processing techniques in multimedia technology are optimized using visual attention feature of the human visual system. Spatial non-uniformity causes that different locations in an image are of different importance in terms of perception of the image. In other words, the perceived image quality depends mainly on the quality of important locations known as regions of interest. The performance of such techniques is measured by subjective evaluation or objective image quality criteria. Many state-of-the-art objective metrics are based on HVS properties; SSIM, MS-SSIM based on image structural information, VIF based on the information that human brain can ideally gain from the reference image or FSIM utilizing the low-level features to assign the different importance to each location in the image. But still none of these objective metrics utilize the analysis of regions of interest. We solve the question if these objective metrics can be used for effective evaluation of images reconstructed by processing techniques based on ROI analysis utilizing high-level features. In this paper authors show that the state-of-the-art objective metrics do not correlate well with subjective evaluation while the demosaicing based on ROI analysis is used for reconstruction. The ROI were computed from "ground truth" visual attention data. The algorithm combining two known demosaicing techniques on the basis of ROI location is proposed to reconstruct the ROI in fine quality while the rest of image is reconstructed with low quality. The color image reconstructed by this ROI approach was compared with selected demosaicing techniques by objective criteria and subjective testing. The qualitative comparison of the objective and subjective results indicates that the state-of-the-art objective metrics are still not suitable for evaluation image processing techniques based on ROI analysis and new criteria is demanded.

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. Copyright © 2013 Wiley Periodicals, Inc.

Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica.

Science.gov (United States)

Sosa, Victoria; Ornelas, Juan Francisco; Ramírez-Barahona, Santiago; Gándara, Etelvina

2016-01-01

Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space) for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from hypothesized ancestors for the most significant

Historical reconstruction of climatic and elevation preferences and the evolution of cloud forest-adapted tree ferns in Mesoamerica

Directory of Open Access Journals (Sweden)

Victoria Sosa

2016-11-01

Full Text Available Background Cloud forests, characterized by a persistent, frequent or seasonal low-level cloud cover and fragmented distribution, are one of the most threatened habitats, especially in the Neotropics. Tree ferns are among the most conspicuous elements in these forests, and ferns are restricted to regions in which minimum temperatures rarely drop below freezing and rainfall is high and evenly distributed around the year. Current phylogeographic data suggest that some of the cloud forest-adapted species remained in situ or expanded to the lowlands during glacial cycles and contracted allopatrically during the interglacials. Although the observed genetic signals of population size changes of cloud forest-adapted species including tree ferns correspond to predicted changes by Pleistocene climate change dynamics, the observed patterns of intraspecific lineage divergence showed temporal incongruence. Methods Here we combined phylogenetic analyses, ancestral area reconstruction, and divergence time estimates with climatic and altitudinal data (environmental space for phenotypic traits of tree fern species to make inferences about evolutionary processes in deep time. We used phylogenetic Bayesian inference and geographic and altitudinal distribution of tree ferns to investigate ancestral area and elevation and environmental preferences of Mesoamerican tree ferns. The phylogeny was then used to estimate divergence times and ask whether the ancestral area and elevation and environmental shifts were linked to climatic events and historical climatic preferences. Results Bayesian trees retrieved Cyathea, Alsophyla, Gymnosphaera and Sphaeropteris in monophyletic clades. Splits for species in these genera found in Mesoamerican cloud forests are recent, from the Neogene to the Quaternary, Australia was identified as the ancestral area for the clades of these genera, except for Gymnosphaera that was Mesoamerica. Climate tolerance was not divergent from

Influence of iterative reconstruction on coronary calcium scores at multiple heart rates: a multivendor phantom study on state-of-the-art CT systems.

Science.gov (United States)

van der Werf, N R; Willemink, M J; Willems, T P; Greuter, M J W; Leiner, T

2017-12-28

The objective of this study was to evaluate the influence of iterative reconstruction on coronary calcium scores (CCS) at different heart rates for four state-of-the-art CT systems. Within an anthropomorphic chest phantom, artificial coronary arteries were translated in a water-filled compartment. The arteries contained three different calcifications with low (38 mg), medium (80 mg) and high (157 mg) mass. Linear velocities were applied, corresponding to heart rates of 0,  75 bpm. Data were acquired on four state-of-the-art CT systems (CT1-CT4) with routinely used CCS protocols. Filtered back projection (FBP) and three increasing levels of iterative reconstruction (L1-L3) were used for reconstruction. CCS were quantified as Agatston score and mass score. An iterative reconstruction susceptibility (IRS) index was used to assess susceptibility of Agatston score (IRS AS ) and mass score (IRS MS ) to iterative reconstruction. IRS values were compared between CT systems and between calcification masses. For each heart rate, differences in CCS of iterative reconstructed images were evaluated with CCS of FBP images as reference, and indicated as small ( 10%). Statistical analysis was performed with repeated measures ANOVA tests. While subtle differences were found for Agatston scores of low mass calcification, medium and high mass calcifications showed increased CCS up to 77% with increasing heart rates. IRS AS of CT1-T4 were 17, 41, 130 and 22% higher than IRS MS . Not only were IRS significantly different between all CT systems, but also between calcification masses. Up to a fourfold increase in IRS was found for the low mass calcification in comparison with the high mass calcification. With increasing iterative reconstruction strength, maximum decreases of 21 and 13% for Agatston and mass score were found. In total, 21 large differences between Agatston scores from FBP and iterative reconstruction were found, while only five large differences were found between

Palaeohistological Evidence for Ancestral High Metabolic Rate in Archosaurs.

Science.gov (United States)

Legendre, Lucas J; Guénard, Guillaume; Botha-Brink, Jennifer; Cubo, Jorge

2016-11-01

Metabolic heat production in archosaurs has played an important role in their evolutionary radiation during the Mesozoic, and their ancestral metabolic condition has long been a matter of debate in systematics and palaeontology. The study of fossil bone histology provides crucial information on bone growth rate, which has been used to indirectly investigate the evolution of thermometabolism in archosaurs. However, no quantitative estimation of metabolic rate has ever been performed on fossils using bone histological features. Moreover, to date, no inference model has included phylogenetic information in the form of predictive variables. Here we performed statistical predictive modeling using the new method of phylogenetic eigenvector maps on a set of bone histological features for a sample of extant and extinct vertebrates, to estimate metabolic rates of fossil archosauromorphs. This modeling procedure serves as a case study for eigenvector-based predictive modeling in a phylogenetic context, as well as an investigation of the poorly known evolutionary patterns of metabolic rate in archosaurs. Our results show that Mesozoic theropod dinosaurs exhibit metabolic rates very close to those found in modern birds, that archosaurs share a higher ancestral metabolic rate than that of extant ectotherms, and that this derived high metabolic rate was acquired at a much more inclusive level of the phylogenetic tree, among non-archosaurian archosauromorphs. These results also highlight the difficulties of assigning a given heat production strategy (i.e., endothermy, ectothermy) to an estimated metabolic rate value, and confirm findings of previous studies that the definition of the endotherm/ectotherm dichotomy may be ambiguous. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Ancestral diet leads to dynamic transgenerational plasticity for five generations in Drosophila melanogaster

OpenAIRE

Mikheyev, Alexander; Emborski, Carmen

2018-01-01

Ancestral exposures can influence phenotypic expression in subsequent generations, which influence diverse biological processes ranging from phenotypic plasticity to obesity. Currently, most transgenerational studies work under the assumption of transgenerational response stability and reproducibility through time and across exposure differences, relying on short-term (i.e. 2-3 generations) single-exposure experiments. Yet, little evidence exists in the literature to validate this assumption,...

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

Science.gov (United States)

Pharo, Elizabeth A; De Leo, Alison A; Renfree, Marilyn B; Thomson, Peter C; Lefèvre, Christophe M; Nicholas, Kevin R

2012-06-08

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

Inferred L/M cone opsin polymorphism of ancestral tarsiers sheds dim light on the origin of anthropoid primates.

Science.gov (United States)

Melin, Amanda D; Matsushita, Yuka; Moritz, Gillian L; Dominy, Nathaniel J; Kawamura, Shoji

2013-05-22

Tarsiers are small nocturnal primates with a long history of fuelling debate on the origin and evolution of anthropoid primates. Recently, the discovery of M and L opsin genes in two sister species, Tarsius bancanus (Bornean tarsier) and Tarsius syrichta (Philippine tarsier), respectively, was interpreted as evidence of an ancestral long-to-middle (L/M) opsin polymorphism, which, in turn, suggested a diurnal or cathemeral (arrhythmic) activity pattern. This view is compatible with the hypothesis that stem tarsiers were diurnal; however, a reversion to nocturnality during the Middle Eocene, as evidenced by hyper-enlarged orbits, predates the divergence of T. bancanus and T. syrichta in the Late Miocene. Taken together, these findings suggest that some nocturnal tarsiers possessed high-acuity trichromatic vision, a concept that challenges prevailing views on the adaptive origins of the anthropoid visual system. It is, therefore, important to explore the plausibility and antiquity of trichromatic vision in the genus Tarsius. Here, we show that Sulawesi tarsiers (Tarsius tarsier), a phylogenetic out-group of Philippine and Bornean tarsiers, have an L opsin gene that is more similar to the L opsin gene of T. syrichta than to the M opsin gene of T. bancanus in non-synonymous nucleotide sequence. This result suggests that an L/M opsin polymorphism is the ancestral character state of crown tarsiers and raises the possibility that many hallmarks of the anthropoid visual system evolved under dim (mesopic) light conditions. This interpretation challenges the persistent nocturnal-diurnal dichotomy that has long informed debate on the origin of anthropoid primates.

Reconstructing pectoral appendicular muscle anatomy in fossil fish and tetrapods over the fins-to-limbs transition.

Science.gov (United States)

Molnar, Julia L; Diogo, Rui; Hutchinson, John R; Pierce, Stephanie E

2018-05-01

The question of how tetrapod limbs evolved from fins is one of the great puzzles of evolutionary biology. While palaeontologists, developmental biologists, and geneticists have made great strides in explaining the origin and early evolution of limb skeletal structures, that of the muscles remains largely unknown. The main reason is the lack of consensus about appendicular muscle homology between the closest living relatives of early tetrapods: lobe-finned fish and crown tetrapods. In the light of a recent study of these homologies, we re-examined osteological correlates of muscle attachment in the pectoral girdle, humerus, radius, and ulna of early tetrapods and their close relatives. Twenty-nine extinct and six extant sarcopterygians were included in a meta-analysis using information from the literature and from original specimens, when possible. We analysed these osteological correlates using parsimony-based character optimization in order to reconstruct muscle anatomy in ancestral lobe-finned fish, tetrapodomorph fish, stem tetrapods, and crown tetrapods. Our synthesis revealed that many tetrapod shoulder muscles probably were already present in tetrapodomorph fish, while most of the more-distal appendicular muscles either arose later from largely undifferentiated dorsal and ventral muscle masses or did not leave clear correlates of attachment in these taxa. Based on this review and meta-analysis, we postulate a stepwise sequence of specific appendicular muscle acquisitions, splits, and fusions that led from the ancestral sarcopterygian pectoral fin to the ancestral tetrapod forelimb. This sequence largely agrees with previous hypotheses based on palaeontological and comparative work, but it is much more comprehensive in terms of both muscles and taxa. Combined with existing information about the skeletal system, our new synthesis helps to illuminate the genetic, developmental, morphological, functional, and ecological changes that were key components of the

Reconstruction of structural evolution in the trnL intron P6b loop of symbiotic Nostoc (Cyanobacteria).

Science.gov (United States)

Olsson, Sanna; Kaasalainen, Ulla; Rikkinen, Jouko

2012-02-01

In this study we reconstruct the structural evolution of the hyper-variable P6b region of the group I trnLeu intron in a monophyletic group of lichen-symbiotic Nostoc strains and establish it as a useful marker in the phylogenetic analysis of these organisms. The studied cyanobacteria occur as photosynthetic and/or nitrogen-fixing symbionts in lichen species of the diverse Nephroma guild. Phylogenetic analyses and secondary structure reconstructions are used to improve the understanding of the replication mechanisms in the P6b stem-loop and to explain the observed distribution patterns of indels. The variants of the P6b region in the Nostoc clade studied consist of different combinations of five sequence modules. The distribution of indels together with the ancestral character reconstruction performed enables the interpretation of the evolution of each sequence module. Our results indicate that the indel events are usually associated with single nucleotide changes in the P6b region and have occurred several times independently. In spite of their homoplasy, they provide phylogenetic information for closely related taxa. Thus we recognize that features of the P6b region can be used as molecular markers for species identification and phylogenetic studies involving symbiotic Nostoc cyanobacteria.

Discrete Wigner Function Reconstruction and Compressed Sensing

OpenAIRE

Zhang, Jia-Ning; Fang, Lei; Ge, Mo-Lin

2011-01-01

A new reconstruction method for Wigner function is reported for quantum tomography based on compressed sensing. By analogy with computed tomography, Wigner functions for some quantum states can be reconstructed with less measurements utilizing this compressed sensing based method.

Phylogeny, character evolution, and biogeography of Cuscuta (dodders; Convolvulaceae) inferred from coding plastid and nuclear sequences.

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García, Miguel A; Costea, Mihai; Kuzmina, Maria; Stefanović, Saša

2014-04-01

The parasitic genus Cuscuta, containing some 200 species circumscribed traditionally in three subgenera, is nearly cosmopolitan, occurring in a wide range of habitats and hosts. Previous molecular studies, on subgenera Grammica and Cuscuta, delimited major clades within these groups. However, the sequences used were unalignable among subgenera, preventing the phylogenetic comparison across the genus. We conducted a broad phylogenetic study using rbcL and nrLSU sequences covering the morphological, physiological, and geographical diversity of Cuscuta. We used parsimony methods to reconstruct ancestral states for taxonomically important characters. Biogeographical inferences were obtained using statistical and Bayesian approaches. Four well-supported major clades are resolved. Two of them correspond to subgenera Monogynella and Grammica. Subgenus Cuscuta is paraphyletic, with section Pachystigma sister to subgenus Grammica. Previously described cases of strongly supported discordance between plastid and nuclear phylogenies, interpreted as reticulation events, are confirmed here and three new cases are detected. Dehiscent fruits and globose stigmas are inferred as ancestral character states, whereas the ancestral style number is ambiguous. Biogeographical reconstructions suggest an Old World origin for the genus and subsequent spread to the Americas as a consequence of one long-distance dispersal. Hybridization may play an important yet underestimated role in the evolution of Cuscuta. Our results disagree with scenarios of evolution (polarity) previously proposed for several taxonomically important morphological characters, and with their usage and significance. While several cases of long-distance dispersal are inferred, vicariance or dispersal to adjacent areas emerges as the dominant biogeographical pattern.

Sexually dimorphic effects of ancestral exposure to vinclozolin on stress reactivity in rats.

Science.gov (United States)

Gillette, Ross; Miller-Crews, Isaac; Nilsson, Eric E; Skinner, Michael K; Gore, Andrea C; Crews, David

2014-10-01

How an individual responds to the environment depends upon both personal life history as well as inherited genetic and epigenetic factors from ancestors. Using a 2-hit, 3 generations apart model, we tested how F3 descendants of rats given in utero exposure to the environmental endocrine-disrupting chemical (EDC) vinclozolin reacted to stress during adolescence in their own lives, focusing on sexually dimorphic phenotypic outcomes. In adulthood, male and female F3 vinclozolin- or vehicle-lineage rats, stressed or nonstressed, were behaviorally characterized on a battery of tests and then euthanized. Serum was used for hormone assays, and brains were used for quantitative PCR and transcriptome analyses. Results showed that the effects of ancestral exposure to vinclozolin converged with stress experienced during adolescence in a sexually dimorphic manner. Debilitating effects were seen at all levels of the phenotype, including physiology, behavior, brain metabolism, gene expression, and genome-wide transcriptome modifications in specific brain nuclei. Additionally, females were significantly more vulnerable than males to transgenerational effects of vinclozolin on anxiety but not sociality tests. This fundamental transformation occurs in a manner not predicted by the ancestral exposure or the proximate effects of stress during adolescence, an interaction we refer to as synchronicity.

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. © 2012, The Society of Analytical Psychology.

Wigner Function Reconstruction in Levitated Optomechanics

Science.gov (United States)

Rashid, Muddassar; Toroš, Marko; Ulbricht, Hendrik

2017-10-01

We demonstrate the reconstruction of theWigner function from marginal distributions of the motion of a single trapped particle using homodyne detection. We show that it is possible to generate quantum states of levitated optomechanical systems even under the efect of continuous measurement by the trapping laser light. We describe the opto-mechanical coupling for the case of the particle trapped by a free-space focused laser beam, explicitly for the case without an optical cavity. We use the scheme to reconstruct the Wigner function of experimental data in perfect agreement with the expected Gaussian distribution of a thermal state of motion. This opens a route for quantum state preparation in levitated optomechanics.

Rapid changes in the gut microbiome during human evolution.

Science.gov (United States)

Moeller, Andrew H; Li, Yingying; Mpoudi Ngole, Eitel; Ahuka-Mundeke, Steve; Lonsdorf, Elizabeth V; Pusey, Anne E; Peeters, Martine; Hahn, Beatrice H; Ochman, Howard

2014-11-18

Humans are ecosystems containing trillions of microorganisms, but the evolutionary history of this microbiome is obscured by a lack of knowledge about microbiomes of African apes. We sequenced the gut communities of hundreds of chimpanzees, bonobos, and gorillas and developed a phylogenetic approach to reconstruct how present-day human microbiomes have diverged from those of ancestral populations. Compositional change in the microbiome was slow and clock-like during African ape diversification, but human microbiomes have deviated from the ancestral state at an accelerated rate. Relative to the microbiomes of wild apes, human microbiomes have lost ancestral microbial diversity while becoming specialized for animal-based diets. Individual wild apes cultivate more phyla, classes, orders, families, genera, and species of bacteria than do individual humans across a range of societies. These results indicate that humanity has experienced a depletion of the gut flora since diverging from Pan.

Ancestral dichlorodiphenyltrichloroethane (DDT) exposure promotes epigenetic transgenerational inheritance of obesity

Science.gov (United States)

2013-01-01

Background Ancestral environmental exposures to a variety of environmental factors and toxicants have been shown to promote the epigenetic transgenerational inheritance of adult onset disease. The present work examined the potential transgenerational actions of the insecticide dichlorodiphenyltrichloroethane (DDT) on obesity and associated disease. Methods Outbred gestating female rats were transiently exposed to a vehicle control or DDT and the F1 generation offspring bred to generate the F2 generation and F2 generation bred to generate the F3 generation. The F1 and F3 generation control and DDT lineage rats were aged and various pathologies investigated. The F3 generation male sperm were collected to investigate methylation between the control and DDT lineage male sperm. Results The F1 generation offspring (directly exposed as a fetus) derived from the F0 generation exposed gestating female rats were not found to develop obesity. The F1 generation DDT lineage animals did develop kidney disease, prostate disease, ovary disease and tumor development as adults. Interestingly, the F3 generation (great grand-offspring) had over 50% of males and females develop obesity. Several transgenerational diseases previously shown to be associated with metabolic syndrome and obesity were observed in the testis, ovary and kidney. The transgenerational transmission of disease was through both female (egg) and male (sperm) germlines. F3 generation sperm epimutations, differential DNA methylation regions (DMR), induced by DDT were identified. A number of the genes associated with the DMR have previously been shown to be associated with obesity. Conclusions Observations indicate ancestral exposure to DDT can promote obesity and associated disease transgenerationally. The etiology of disease such as obesity may be in part due to environmentally induced epigenetic transgenerational inheritance. PMID:24228800

Cut from the same cloth: The convergent evolution of dwarf morphotypes of the Carex flava group (Cyperaceae) in Circum-Mediterranean mountains

Science.gov (United States)

Benítez-Benítez, Carmen; Fernández-Mazuecos, Mario; Martín-Bravo, Santiago

2017-01-01

Plants growing in high-mountain environments may share common morphological features through convergent evolution resulting from an adaptative response to similar ecological conditions. The Carex flava species complex (sect. Ceratocystis, Cyperaceae) includes four dwarf morphotypes from Circum-Mediterranean mountains whose taxonomic status has remained obscure due to their apparent morphological resemblance. In this study we investigate whether these dwarf mountain morphotypes result from convergent evolution or common ancestry, and whether there are ecological differences promoting differentiation between the dwarf morphotypes and their taxonomically related large, well-developed counterparts. We used phylogenetic analyses of nrDNA (ITS) and ptDNA (rps16 and 5’trnK) sequences, ancestral state reconstruction, multivariate analyses of macro- and micromorphological data, and species distribution modeling. Dwarf morphotype populations were found to belong to three different genetic lineages, and several morphotype shifts from well-developed to dwarf were suggested by ancestral state reconstructions. Distribution modeling supported differences in climatic niche at regional scale between the large forms, mainly from lowland, and the dwarf mountain morphotypes. Our results suggest that dwarf mountain morphotypes within this sedge group are small forms of different lineages that have recurrently adapted to mountain habitats through convergent evolution. PMID:29281689

Vertex reconstruction in CMS

International Nuclear Information System (INIS)

Chabanat, E.; D'Hondt, J.; Estre, N.; Fruehwirth, R.; Prokofiev, K.; Speer, T.; Vanlaer, P.; Waltenberger, W.

2005-01-01

Due to 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-squares methods, robustifications of the classical algorithms 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

Mandible reconstruction: History, state of the art and persistent problems.

Science.gov (United States)

Ferreira, José J; Zagalo, Carlos M; Oliveira, Marta L; Correia, André M; Reis, Ana R

2015-06-01

Mandibular reconstruction has been experiencing an amazing evolution. Several different approaches are used to reconstruct this bone and therefore have a fundamental role in the recovery of oral functions. This review aims to highlight the persistent problems associated with the approaches identified, whether bone grafts or prosthetic devices are used. A brief summary of the historical evolution of the surgical procedures is presented, as well as an insight into possible future pathways. A literature review was conducted from September to December 2012 using the PubMed database. The keyword used was "mandible reconstruction." Articles published in the last three years were included as well as the relevant references from those articles and the "historical articles" were referred. This research resulted in a monograph that this article aims to summarize. Titanium plates, bone grafts, pediculate flaps, free osteomyocutaneous flaps, rapid prototyping, and tissue engineering strategies are some of the identified possibilities. The classical approaches present considerable associated morbidity donor-site-related problems. Research that results in the development of new prosthetics devices is needed. A new prosthetic approach could minimize the identified problems and offer the patients more predictable, affordable, and comfortable solutions. This review, while affirming the evolution and the good results found with the actual approaches, emphasizes the negative aspects that still subsist. Thus, it shows that mandible reconstruction is not a closed issue. On the contrary, it remains as a research field where new findings could have a direct positive impact on patients' life quality. The identification of the persistent problems reveals the characteristics to be considered in a new prosthetic device. This could overcome the current difficulties and result in more comfortable solutions. Medical teams have the responsibility to keep patients informed about the predictable

A reconstruction of sexual modes throughout animal evolution.

Science.gov (United States)

Sasson, Daniel A; Ryan, Joseph F

2017-12-06

Although most extant animals have separate sexes, simultaneous hermaphrodites can be found in lineages throughout the animal kingdom. However, the sexual modes of key ancestral nodes including the last common ancestor (LCA) of all animals remain unclear. Without these data, it is difficult to infer the reproductive-state transitions that occurred early in animal evolution, and thus a broad understanding of the evolution of animal reproduction remains elusive. In this study, we use a composite phylogeny from four previously published studies, two alternative topologies (ctenophores or sponges as sister to the rest of animals), and multiple phylogenetic approaches to conduct the most extensive analysis to date of the evolution of animal sexual modes. Our analyses clarify the sexual mode of many ancestral animal nodes and allow for sound inferences of modal transitions that have occurred in animal history. Our results also indicate that the transition from separate sexes to hermaphroditism has been more common in animal history than the reverse. These results provide the most complete view of the evolution of animal sexual modes to date and provide a framework for future inquiries into the correlation of these transitions with genes, behaviors, and physiology. These results also suggest that mutations promoting hermaphroditism have historically been more likely to invade gonochoristic populations than vice versa.

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

Directory of Open Access Journals (Sweden)

Pharo Elizabeth A

2012-06-01

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

Evidence for Ancestral Programming of Resilience in a Two-Hit Stress Model

Directory of Open Access Journals (Sweden)

Jamshid Faraji

2017-05-01

Full Text Available In a continuously stressful environment, the effects of recurrent prenatal stress (PS may accumulate across generations and alter stress vulnerability and resilience. Here, we report in female rats that a family history of recurrent ancestral PS facilitates certain aspects of movement performance, and that these benefits are abolished by the experience of a second hit, induced by a silent ischemia during adulthood. Female F4-generation rats with and without a family history of cumulative multigenerational PS (MPS were tested for skilled motor function before and after the induction of a minor ischemic insult by endothelin-1 infusion into the primary motor cortex. MPS resulted in improved skilled motor abilities and blunted hypothalamic-pituitary-adrenal (HPA axis function compared to non-stressed rats. Deep sequencing revealed downregulation of miR-708 in MPS rats along with upregulation of its predicted target genes Mapk10 and Rasd2. Through miR-708 stress may regulate mitogen-activated protein kinase (MAPK pathway activity. Hair trace elemental analysis revealed an increased Na/K ratio, which suggests a chronic shift in adrenal gland function. The ischemic lesion activated the HPA axis in MPS rats only; the lesion, however, abolished the advantage of MPS in skilled reaching. The findings indicate that MPS generates adaptive flexibility in movement, which is challenged by a second stressor, such as a neuropathological condition. Thus, a second “hit” by a stressor may limit behavioral flexibility and neural plasticity associated with ancestral stress.

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.

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

Science.gov (United States)

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

2015-01-01

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

Ancestral origins and invasion pathways in a globally invasive bird correlate with climate and influences from bird trade.

Science.gov (United States)

Jackson, Hazel; Strubbe, Diederik; Tollington, Simon; Prys-Jones, Robert; Matthysen, Erik; Groombridge, Jim J

2015-08-01

Invasive species present a major threat to global biodiversity. Understanding genetic patterns and evolutionary processes that reinforce successful establishment is paramount for elucidating mechanisms underlying biological invasions. Among birds, the ring-necked parakeet (Psittacula krameri) is one of the most successful invasive species, established in over 35 countries. However, little is known about the evolutionary genetic origins of this species and what population genetic signatures tell us about patterns of invasion. We reveal the ancestral origins of populations across the invasive range and explore the potential influence of climate and propagule pressure from the pet trade on observed genetic patterns. Ring-necked parakeet samples representing the ancestral native range (n = 96) were collected from museum specimens, and modern samples from the invasive range (n = 855) were gathered from across Europe, Mauritius and Seychelles, and sequenced for two mitochondrial DNA markers comprising 868 bp of cytochrome b and control region, and genotyped at 10 microsatellite loci. Invasive populations comprise birds that originate predominantly from Pakistan and northern areas of India. Haplotypes associated with more northerly distribution limits in the ancestral native range were more prevalent in invasive populations in Europe, and the predominance of Asian haplotypes in Europe is consistent with the higher number of Asian birds transported by the pet trade outside the native range. Successful establishment of invasive species is likely to be underpinned by a combination of environmental and anthropogenic influences. © 2015 John Wiley & Sons Ltd.

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

Directory of Open Access Journals (Sweden)

Jia-Yu Chen

2015-07-01

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

Photoacoustic image reconstruction via deep learning

Science.gov (United States)

Antholzer, Stephan; Haltmeier, Markus; Nuster, Robert; Schwab, Johannes

2018-02-01

Applying standard algorithms to sparse data problems in photoacoustic tomography (PAT) yields low-quality images containing severe under-sampling artifacts. To some extent, these artifacts can be reduced by iterative image reconstruction algorithms which allow to include prior knowledge such as smoothness, total variation (TV) or sparsity constraints. These algorithms tend to be time consuming as the forward and adjoint problems have to be solved repeatedly. Further, iterative algorithms have additional drawbacks. For example, the reconstruction quality strongly depends on a-priori model assumptions about the objects to be recovered, which are often not strictly satisfied in practical applications. To overcome these issues, in this paper, we develop direct and efficient reconstruction algorithms based on deep learning. As opposed to iterative algorithms, we apply a convolutional neural network, whose parameters are trained before the reconstruction process based on a set of training data. For actual image reconstruction, a single evaluation of the trained network yields the desired result. Our presented numerical results (using two different network architectures) demonstrate that the proposed deep learning approach reconstructs images with a quality comparable to state of the art iterative reconstruction methods.

Changes in exon–intron structure during vertebrate evolution affect the splicing pattern of exons

Science.gov (United States)

Gelfman, Sahar; Burstein, David; Penn, Osnat; Savchenko, Anna; Amit, Maayan; Schwartz, Schraga; Pupko, Tal; Ast, Gil

2012-01-01

Exon–intron architecture is one of the major features directing the splicing machinery to the short exons that are located within long flanking introns. However, the evolutionary dynamics of exon–intron architecture and its impact on splicing is largely unknown. Using a comparative genomic approach, we analyzed 17 vertebrate genomes and reconstructed the ancestral motifs of both 3′ and 5′ splice sites, as also the ancestral length of exons and introns. Our analyses suggest that vertebrate introns increased in length from the shortest ancestral introns to the longest primate introns. An evolutionary analysis of splice sites revealed that weak splice sites act as a restrictive force keeping introns short. In contrast, strong splice sites allow recognition of exons flanked by long introns. Reconstruction of the ancestral state suggests these phenomena were not prevalent in the vertebrate ancestor, but appeared during vertebrate evolution. By calculating evolutionary rate shifts in exons, we identified cis-acting regulatory sequences that became fixed during the transition from early vertebrates to mammals. Experimental validations performed on a selection of these hexamers confirmed their regulatory function. We additionally revealed many features of exons that can discriminate alternative from constitutive exons. These features were integrated into a machine-learning approach to predict whether an exon is alternative. Our algorithm obtains very high predictive power (AUC of 0.91), and using these predictions we have identified and successfully validated novel alternatively spliced exons. Overall, we provide novel insights regarding the evolutionary constraints acting upon exons and their recognition by the splicing machinery. PMID:21974994

Quantum process reconstruction based on mutually unbiased basis

International Nuclear Information System (INIS)

Fernandez-Perez, A.; Saavedra, C.; Klimov, A. B.

2011-01-01

We study a quantum process reconstruction based on the use of mutually unbiased projectors (MUB projectors) as input states for a D-dimensional quantum system, with D being a power of a prime number. This approach connects the results of quantum-state tomography using mutually unbiased bases with the coefficients of a quantum process, expanded in terms of MUB projectors. We also study the performance of the reconstruction scheme against random errors when measuring probabilities at the MUB projectors.

Species delimitation and phylogenetic reconstruction of the sinipercids (Perciformes: Sinipercidae) based on target enrichment of thousands of nuclear coding sequences.

Science.gov (United States)

Song, Shuli; Zhao, Jinliang; Li, Chenhong

2017-06-01

The sinipercids are freshwater fishes endemic to East Asia, mainly in China. Phylogenetic studies on the sinipercids have made great progress in the last decades, but interspecific relationships and evolutionary history of the sinipercids remain unresolved. Lack of distinctive morphological characters leads to problems in validating of some species, such as Siniperca loona. Moreover, genetic data are needed to delimitate species pairs with explicit hypothesis testing, such as in S. chuatsi vs. S. kneri and Coreoperca whiteheadi vs. C. liui. Here we reconstructed phylogeny of the sinipercids with an unprecedented scale of data, 16,943 loci of single-copy coding sequence data from nine sinipercid species, eight putative sister taxa and two outgroups. Targeted sequences were collected using gene enrichment and Illumina sequencing, yielding thousands of protein coding sequences and single nucleotide polymorphisms (SNPs) data. Maximum likelihood and coalescent species tree analyses resulted in identical and highly supported trees. We confirmed that the centrarchids are sister to the sinipercids. A monophyletic Sinipercidae with two genera, Siniperca and Coreoperca was also supported. Different from most previous studies, S. scherzeri was found as the most basal taxon to other species of Siniperca, which consists of two clades: a clade having S. roulei sister to S. chuatsi and S. kneri, and a clade consisting S. loona sister to S. obscura and S. undulata. We found that both S. loona and C. liui are valid species using Bayes factor delimitation (BFD ∗ ) based on SNPs data. Species delimitation also provided decisive support for S. chuatsi and S. kneri being two distinct species. We calibrated a chronogram of the sinipercids based on 100 loci and three fossil calibration points using BEAST, and reconstructed ancestral ranges of the sinipercids using Lagrange Analysis (DEC model) and Statistical Dispersal-Vicariance Analysis (S-DIVA) implemented in RASP. Divergence time

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

Directory of Open Access Journals (Sweden)

Nora Cardona-Castro

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

A discrete phase-space calculus for quantum spins based on a reconstruction method using coherent states

International Nuclear Information System (INIS)

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 e xpectation-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. (Author)

Quantum reconstruction of an intense polarization squeezed optical state

DEFF Research Database (Denmark)

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

2007-01-01

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

Founder haplotype analysis of Fanconi anemia in the Korean population finds common ancestral haplotypes for a FANCG variant.

Science.gov (United States)

Park, Joonhong; Kim, Myungshin; Jang, Woori; Chae, Hyojin; Kim, Yonggoo; Chung, Nack-Gyun; Lee, Jae-Wook; Cho, Bin; Jeong, Dae-Chul; Park, In Yang; Park, Mi Sun

2015-05-01

A common ancestral haplotype is strongly suggested in the Korean and Japanese patients with Fanconi anemia (FA), because common mutations have been frequently found: c.2546delC and c.3720_3724delAAACA of FANCA; c.307+1G>C, c.1066C>T, and c.1589_1591delATA of FANCG. Our aim in this study was to investigate the origin of these common mutations of FANCA and FANCG. We genotyped 13 FA patients consisting of five FA-A patients and eight FA-G patients from the Korean FA population. Microsatellite markers used for haplotype analysis included four CA repeat markers which are closely linked with FANCA and eight CA repeat markers which are contiguous with FANCG. As a result, Korean FA-A patients carrying c.2546delC or c.3720_3724delAAACA did not share the same haplotypes. However, three unique haplotypes carrying c.307+1G>C, c.1066C > T, or c.1589_1591delATA, that consisted of eight polymorphic loci covering a flanking region were strongly associated with Korean FA-G, consistent with founder haplotypes reported previously in the Japanese FA-G population. Our finding confirmed the common ancestral haplotypes on the origins of the East Asian FA-G patients, which will improve our understanding of the molecular population genetics of FA-G. To the best of our knowledge, this is the first report on the association between disease-linked mutations and common ancestral haplotypes in the Korean FA population. © 2015 John Wiley & Sons Ltd/University College London.

Estimation of the net acid load of the diet of ancestral preagricultural Homo sapiens and their hominid ancestors.

Science.gov (United States)

Sebastian, Anthony; Frassetto, Lynda A; Sellmeyer, Deborah E; Merriam, Renée L; Morris, R Curtis

2002-12-01

Natural selection has had diet resulting from the inventions of agriculture and animal husbandry. The objective was to estimate the net systemic load of acid (net endogenous acid production; NEAP) from retrojected ancestral preagricultural diets and to compare it with that of contemporary diets, which are characterized by an imbalance of nutrient precursors of hydrogen and bicarbonate ions that induces a lifelong, low-grade, pathogenically significant systemic metabolic acidosis. Using established computational methods, we computed NEAP for a large number of retrojected ancestral preagricultural diets and compared them with computed and measured values for typical American diets. The mean (+/- SD) NEAP for 159 retrojected preagricultural diets was -88 +/- 82 mEq/d; 87% were net base-producing. The computational model predicted NEAP for the average American diet (as recorded in the third National Health and Nutrition Examination Survey) as 48 mEq/d, within a few percentage points of published measured values for free-living Americans; the model, therefore, was not biased toward generating negative NEAP values. The historical shift from negative to positive NEAP was accounted for by the displacement of high-bicarbonate-yielding plant foods in the ancestral diet by cereal grains and energy-dense, nutrient-poor foods in the contemporary diet-neither of which are net base-producing. The findings suggest that diet-induced metabolic acidosis and its sequelae in humans eating contemporary diets reflect a mismatch between the nutrient composition of the diet and genetically determined nutritional requirements for optimal systemic acid-base status.

Reconstruction from scalar-tensor theory and the inhomogeneous equation of state in f(T) gravity

Energy Technology Data Exchange (ETDEWEB)

Said, Jackson Levi [University of Malta, Institute of Space Sciences and Astronomy, Msida (Malta); University of Malta, Department of Physics, Msida (Malta)

2017-12-15

General relativity (GR) characterizes gravity as a geometric properly exhibited as curvature on spacetime. Teleparallelism describes gravity through torsional properties, and can reproduce GR at the level of equations. Similar to f(R) gravity, on taking a generalization, f(T) gravity can produce various modifications its gravitational mechanism. The resulting field equations are inherently distinct to f(R) gravity in that they are second order. In the present work, f(T) gravity is examined in the cosmological context with a number of solutions reconstructed by means of an auxiliary scalar field. To do this, various forms of the Hubble parameter are considered with an f(T) Lagrangian emerging for each instance. In addition, the inhomogeneous equation of state (EoS) is investigated with a particular Hubble parameter model used to show how this can be used to reconstruct the f(T) Lagrangian. Observationally, the auxiliary scalar field and the exotic terms in the FRW field equations give the same results, meaning that the variation in the Hubble parameter may be interpreted as the need to reformulate gravity in some way, as in f(T) gravity. (orig.)

Reconstruction from scalar-tensor theory and the inhomogeneous equation of state in f(T) gravity

International Nuclear Information System (INIS)

Said, Jackson Levi

2017-01-01

General relativity (GR) characterizes gravity as a geometric properly exhibited as curvature on spacetime. Teleparallelism describes gravity through torsional properties, and can reproduce GR at the level of equations. Similar to f(R) gravity, on taking a generalization, f(T) gravity can produce various modifications its gravitational mechanism. The resulting field equations are inherently distinct to f(R) gravity in that they are second order. In the present work, f(T) gravity is examined in the cosmological context with a number of solutions reconstructed by means of an auxiliary scalar field. To do this, various forms of the Hubble parameter are considered with an f(T) Lagrangian emerging for each instance. In addition, the inhomogeneous equation of state (EoS) is investigated with a particular Hubble parameter model used to show how this can be used to reconstruct the f(T) Lagrangian. Observationally, the auxiliary scalar field and the exotic terms in the FRW field equations give the same results, meaning that the variation in the Hubble parameter may be interpreted as the need to reformulate gravity in some way, as in f(T) gravity. (orig.)

Reconstructed tree fern Alethopteris zeilleri (Carboniferous, Medullosales)

Energy Technology Data Exchange (ETDEWEB)

Zodrow, Erwin L. [Department of Earth Sciences, University College of Cape Breton, Sydney, Nova, Scotia (Canada B1P 6L2)

2007-01-02

From a smaller open-pit area in the roof shale of the basal Cantabrian coal seam in Sydney Coalfield, Cape Breton Island, Nova Scotia, Canada, large amounts of the pteridosperm foliage Alethopteris zeilleri (Ragot) were found. This foliage is associated with abundant, naked medullosalean axes and dichotomies of varying sizes, up to 0.80-m long, cauline structures 0.90 m and 1.3 m long, detached ovules assigned to Pachytesta incrassata Brongniart, rare male-pollen organs of the type Dolerotheca Halle, rooted tree ferns in life position, and one specimen each of a juvenile medullosalean frond and root mantle. The fossils are compression/impression-preserved, and the foliage yielded thickly cutinized cuticles with unoriented cells (57-103 by 27-57 {mu}m) in intercostal fields. Ultimate rachises, and abaxial surfaces (excluding costal fields) show a mixture of simple and complexly-branched trichomes, and two different structural bases. These, together with fractal dimensionality of curvatures of anticlinal walls in intercostal fields, have taxonomic potential for alethopterids. The finds suggest reconstructing A. zeilleri (Ragot) as a tree, 5-7 m high, that bore both P. incrassata Brongniart and Dolerotheca-type fructifications. Its habitat was low-land coastal plains in the Pennsylvanian coal swamps of ancestral Sydney Coalfield. (author)

Reconstruction techniques in supersymmetry searches in the ATLAS experiment

CERN Document Server

Gramstad, Eirik; The ATLAS collaboration

2018-01-01

Many supersymmetric scenarios feature final states with non-standard final state objects. The production of massive sparticles can lead to the production of boosted top quarks or vector bosons, high-pt b-jets. At the same time, transitions between nearly mass-degenerate sparticles can challenge the standard reconstruction because of the presence of very soft leptons or jets. The talk will review the application of innovative reconstruction techniques to supersymmetry searches in ATLAS.

Reconstructions of the sulfur-passivated InSb (100) surface

Energy Technology Data Exchange (ETDEWEB)

Ciochoń, Piotr, E-mail: piotr.ciochon@doctoral.uj.edu.pl; Olszowska, Natalia; Wróbel, Sonia; Kołodziej, Jacek

2017-04-01

Highlights: • Two new surface reconstructions of a S-passivated InSb (001) surface are reported. • The reconstructions are obtained through partial loss of surface sulfur. • They are characterized by the thickness of ∼4 Å and good crystallographic ordering. • The reconstructions provide adequate electronic passivation of the surface. - Abstract: We have studied the properties of the InSb (100) surface passivated with sulfur dimers emitted by the solid-state electrochemical cell in ultra-high vacuum. Annealing the passivated surface in the temperature equal to T = 326 °C led to the formation of the c(4 × 8) surface reconstruction, while increasing the temperature to T = 348 °C resulted in the transition to c(4 × 12) reconstruction. To the best of our knowledge these reconstructions have not been reported to date and are characterized by the exceptionally good crystallographic order. XPS studies revealed that there are at least 4 different chemical species of sulfur present on the surface and the estimated thickness of the sulfur layers is equal to around 4 Å. The surface reconstructions are characterized by the lowered intensity of the surface electronic states and resonances near the Fermi level, compared to the clean InSb surface, making them potentially very useful for the fabrication of InSb-based electronic and optoelectronic devices.

Preparation and tomographic reconstruction of an arbitrary single-photon path qubit

International Nuclear Information System (INIS)

Baek, So-Young; Kim, Yoon-Ho

2011-01-01

We report methods for preparation and tomographic reconstruction of an arbitrary single-photon path qubit. The arbitrary single-photon path qubit is prepared losslessly by passing the heralded single-photon state from spontaneous parametric down-conversion through variable beam splitter. Quantum state tomography of the single-photon path qubit is implemented by introducing path-projection measurements based on the first-order single-photon quantum interference. Using the state preparation and path-projection measurements methods for the single-photon path qubit, we demonstrate preparation and complete tomographic reconstruction of the single-photon path qubit with arbitrary purity. -- Highlights: → We report methods for preparation and tomographic reconstruction of an arbitrary single-photon path qubit. → We implement path-projection measurements based on the first-order single-photon quantum interference. → We demonstrate preparation and complete tomographic reconstruction of the single-photon path qubit with arbitrary purity.

Reestablishment of the Ancestral Cascades Arc in Western Nevada and Eastern California by Rollback of the Shallow Farallon Slab

Science.gov (United States)

Henry, C. D.; Cousens, B.; John, D. A.; Colgan, J. P.

2009-12-01

The character and even existence of an ancestral Tertiary Cascades arc in western Nevada and eastern California south of the modern arc are controversial. Based on extensive published and new data on the regional distribution, timing, style, and composition of magmatism, we conclude that an ancestral arc was established by WSW migration of magmatism into western NV and the northeastern Sierra Nevada in the Oligocene and Miocene as a result of progressive rollback of the shallow subducted slab. Magma migration started with the well-known southward sweep through NE NV and NW UT between ~46 and 36 Ma. By ~30 Ma, migration of the leading edge and central belt of activity was much more WSW, especially after removing younger ~E-W extension. Locally sourced, initially dispersed and small volume, intermediate to mafic lavas erupted in western NV and northeastern CA by ~30 Ma and the eastern Sierra Nevada by ~28 Ma, contemporaneous with the much more voluminous ignimbrite flare-up in central NV. As migration continued, the ignimbrite flare-up tapered off. A voluminous, NNW-trending, dominantly effusive volcanic belt developed by ~22-18 Ma in western NV and was continuous from the Bodie Hills (CA/NV) to the Warner Range (northeast CA) by ~16-15 Ma. The volcanic belt was dominated by intermediate to mafic magmas compositionally similar to those of the modern south Cascades arc but reflecting melting of an old, subduction-modified lithosphere (Cousens et al. 2008; Geosphere). Extensive middle Miocene bimodal rocks related to the Yellowstone hotspot cover these rocks in NW NV, NE CA, and SE OR, but 30-23 Ma, intermediate to mafic and lesser silicic rocks are voluminous wherever older rocks are exposed below the middle Miocene rocks. Between ~25 Ma and the present, magmatism migrated WSW at an average rate of ~8 km/Ma but was at least partly stepwise, as exemplified by an ~50 km westward step at 2 Ma in the Lassen area (Guffanti et al. 1990, JGR). The magmatic belt was as much

Computational analysis and functional expression of ancestral copepod luciferase.

Science.gov (United States)

Takenaka, Yasuhiro; Noda-Ogura, Akiko; Imanishi, Tadashi; Yamaguchi, Atsushi; Gojobori, Takashi; Shigeri, Yasushi

2013-10-10

We recently reported the cDNA sequences of 11 copepod luciferases from the superfamily Augaptiloidea in the order Calanoida. They were classified into two groups, Metridinidae and Heterorhabdidae/Lucicutiidae families, by phylogenetic analyses. To elucidate the evolutionary processes, we have now further isolated 12 copepod luciferases from Augaptiloidea species (Metridia asymmetrica, Metridia curticauda, Pleuromamma scutullata, Pleuromamma xiphias, Lucicutia ovaliformis and Heterorhabdus tanneri). Codon-based synonymous/nonsynonymous tests of positive selection for 25 identified copepod luciferases suggested that positive Darwinian selection operated in the evolution of Heterorhabdidae luciferases, whereas two types of Metridinidae luciferases had diversified via neutral mechanism. By in silico analysis of the decoded amino acid sequences of 25 copepod luciferases, we inferred two protein sequences as ancestral copepod luciferases. They were expressed in HEK293 cells where they exhibited notable luciferase activity both in intracellular lysates and cultured media, indicating that the luciferase activity was established before evolutionary diversification of these copepod species. © 2013.

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).

Relating appendicular skeletal variation of sigmodontine rodents to locomotion modes in a phylogenetic context.

Science.gov (United States)

Carvalho Coutinho, Ludmilla; Alves de Oliveira, João

2017-10-01

Sigmodontinae rodents constitute the second-largest subfamily among mammals. Alongside the taxonomic diversity, they are also ecologically diverse, exhibiting a wide array of locomotion modes, with semifossorial, terrestrial, semiaquatic, scansorial, arboreal, and saltatorial forms. To understand the ecomorphologic aspects that allow these rodents to display such locomotion diversity, we analyzed 35 qualitative characters of the appendicular skeleton (humerus, ulna, radius, scapula, femur, tibia, ilium, ischium and pubis) in 795 specimens belonging to 64 species, 34 genera and 10 tribes, representing all locomotion modes assigned to this subfamily. We performed a statistical analysis based upon the coefficient of trait differentiation to test the congruence of character states and the different locomotion modes. We also mapped characters states in a molecular phylogeny in order to reconstruct ancestral states and to evaluate how appendicular characters evolved within main lineages of Sigmodontinae radiation under a phylogenetic framework. The statistical analyses revealed six characters related to specific locomotion modes, except terrestrial. The mapping and parsimony ancestral states reconstruction identified two characters with phylogenetical signal and eight characters that are exclusively or more frequently recorded in certain modes of locomotion, four of them also detected by the statistical analysis. Notwithstanding the documented morphological variation, few changes characterize the transition to each of the locomotion modes, at least regarding the appendicular skeleton. This finding corroborates previous results that showed that sigmodontines exhibit an all-purpose appendicular morphology that allows them to use and explore a great variety of habitats. © 2017 Anatomical Society.

Reconstruction of the Dark Energy Equation of State from the Latest Observations

Science.gov (United States)

Dai, Ji-Ping; Yang, Yang; Xia, Jun-Qing

2018-04-01

Since the discovery of the accelerating expansion of our universe in 1998, studying the features of dark energy has remained a hot topic in modern cosmology. In the literature, dark energy is usually described by w ≡ P/ρ, where P and ρ denote its pressure and energy density. Therefore, exploring the evolution of w is the key approach to understanding dark energy. In this work, we adopt three different methods, polynomial expansion, principal component analysis, and the correlated prior method, to reconstruct w with a collection of the latest observations, including the type-Ia supernova, cosmic microwave background, large-scale structure, Hubble measurements, and baryon acoustic oscillations (BAOs), and find that the concordance cosmological constant model (w = ‑1) is still safely consistent with these observational data at the 68% confidence level. However, when we add the high-redshift BAO measurement from the Lyα forest (Lyα FB) of BOSS DR11 quasars into the calculation, there is a significant impact on the reconstruction result. In the standard ΛCDM model, since the Lyα FB data slightly prefer a negative dark energy density, in order to avoid this problem, a dark energy model with a w significantly smaller than ‑1 is needed to explain this Lyα FB data. In this work, we find the consistent conclusion that there is a strong preference for the time-evolving behavior of dark energy w at high redshifts, when including the Lyα FB data. Therefore, we think that this Lyα FB data needs to be watched carefully attention when studying the evolution of the dark energy equation of state.

Explosive diversification following a benthic to pelagic shift in freshwater fishes

OpenAIRE

Hollingsworth, Phillip R; Simons, Andrew M; Fordyce, James A; Hulsey, C Darrin

2013-01-01

Background Interspecific divergence along a benthic to pelagic habitat axis is ubiquitous in freshwater fishes inhabiting lentic environments. In this study, we examined the influence of this habitat axis on the macroevolution of a diverse, lotic radiation using mtDNA and nDNA phylogenies for eastern North America’s most species-rich freshwater fish clade, the open posterior myodome (OPM) cyprinids. We used ancestral state reconstruction to identify the earliest benthic to pelagic transition ...

Edge reconstruction effect in pristine and H-passivated zigzag silicon carbide nanoribbons.

Science.gov (United States)

Lou, Ping

2011-10-14

The edge reconstruction effect of the zigzag silicon carbide nanoribbons (zz SiC NRs) to a stable line of alternatively fused seven and five membered rings without and with H passivation have been studied using first principles density functional theory (DFT). The both side's edges of the pristine SiC are respectively terminated by Si and C atoms and are called the Si-edge and the C-edge, respectively. In the un-passivated systems, the C-edge reconstructed (Crc) could effectively lower the edge energy of the system, while the Si-edge reconstructed (Sirc) could raise the edge energy of the system. Thus, the Crc edge is the best edge for the edge reconstruction of the system, while the both edge reconstructed (brc) system is the metastability. Moreover, the brc system has a nonmagnetic metallic state, whereas the Crc system, as well as Sirc system, has a ferromagnetic metallic state. The edge reconstructed destroys the magnetic moment of the corresponding edge atoms. The magnetic moment arises from the unreconstructed zigzag edges. The pristine zz edge system has a ferrimagnetic metallic state. However, in the H-passivated systems, the unreconstructed zigzag edge (zz-H) is the best edge. The Crc-H system is the metastability. The Sirc-H system has only slightly higher energy than the Crc-H system, whereas the brc-H system of the pristine SiC NR has the highest edge energy. Thus, the H passivation would prevent the occurrence of edge reconstruction. Moreover, H passivation induces a metal-semiconductor transition in the zz and brc SiC NRs. Additionally, except for brc-H system which has non-magnetic semiconducting state, the zz-H, Crc-H, and Sirc-H systems have the magnetic state.

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

Directory of Open Access Journals (Sweden)

Omberg Larsson

2012-06-01

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

Reconstructing the Evolutionary History of Paralogous APETALA1/FRUITFULL-Like Genes in Grasses (Poaceae)

Science.gov (United States)

Preston, Jill C.; Kellogg, Elizabeth A.

2006-01-01

Gene duplication is an important mechanism for the generation of evolutionary novelty. Paralogous genes that are not silenced may evolve new functions (neofunctionalization) that will alter the developmental outcome of preexisting genetic pathways, partition ancestral functions (subfunctionalization) into divergent developmental modules, or function redundantly. Functional divergence can occur by changes in the spatio-temporal patterns of gene expression and/or by changes in the activities of their protein products. We reconstructed the evolutionary history of two paralogous monocot MADS-box transcription factors, FUL1 and FUL2, and determined the evolution of sequence and gene expression in grass AP1/FUL-like genes. Monocot AP1/FUL-like genes duplicated at the base of Poaceae and codon substitutions occurred under relaxed selection mostly along the branch leading to FUL2. Following the duplication, FUL1 was apparently lost from early diverging taxa, a pattern consistent with major changes in grass floral morphology. Overlapping gene expression patterns in leaves and spikelets indicate that FUL1 and FUL2 probably share some redundant functions, but that FUL2 may have become temporally restricted under partial subfunctionalization to particular stages of floret development. These data have allowed us to reconstruct the history of AP1/FUL-like genes in Poaceae and to hypothesize a role for this gene duplication in the evolution of the grass spikelet. PMID:16816429

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

Directory of Open Access Journals (Sweden)

Dani Eduardo Vargas Huanca

2016-09-01

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

United States-assisted studies on dose reconstruction in the former Soviet Union

International Nuclear Information System (INIS)

Anspaugh, L.R.; Bouville, A.

1995-12-01

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

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record.

Science.gov (United States)

Hsiang, Allison Y; Field, Daniel J; Webster, Timothy H; Behlke, Adam D B; Davis, Matthew B; Racicot, Rachel A; Gauthier, Jacques A

2015-05-20

The highly derived morphology and astounding diversity of snakes has long inspired debate regarding the ecological and evolutionary origin of both the snake total-group (Pan-Serpentes) and crown snakes (Serpentes). Although speculation abounds on the ecology, behavior, and provenance of the earliest snakes, a rigorous, clade-wide analysis of snake origins has yet to be attempted, in part due to a dearth of adequate paleontological data on early stem snakes. Here, we present the first comprehensive analytical reconstruction of the ancestor of crown snakes and the ancestor of the snake total-group, as inferred using multiple methods of ancestral state reconstruction. We use a combined-data approach that includes new information from the fossil record on extinct crown snakes, new data on the anatomy of the stem snakes Najash rionegrina, Dinilysia patagonica, and Coniophis precedens, and a deeper understanding of the distribution of phenotypic apomorphies among the major clades of fossil and Recent snakes. Additionally, we infer time-calibrated phylogenies using both new 'tip-dating' and traditional node-based approaches, providing new insights on temporal patterns in the early evolutionary history of snakes. Comprehensive ancestral state reconstructions reveal that both the ancestor of crown snakes and the ancestor of total-group snakes were nocturnal, widely foraging, non-constricting stealth hunters. They likely consumed soft-bodied vertebrate and invertebrate prey that was subequal to head size, and occupied terrestrial settings in warm, well-watered, and well-vegetated environments. The snake total-group - approximated by the Coniophis node - is inferred to have originated on land during the middle Early Cretaceous (~128.5 Ma), with the crown-group following about 20 million years later, during the Albian stage. Our inferred divergence dates provide strong evidence for a major radiation of henophidian snake diversity in the wake of the Cretaceous-Paleogene (K

Full characterization of a three-photon Greenberger-Horne-Zeilinger state using quantum state tomography.

Science.gov (United States)

Resch, K J; Walther, P; Zeilinger, A

2005-02-25

We have performed the first experimental tomographic reconstruction of a three-photon polarization state. Quantum state tomography is a powerful tool for fully describing the density matrix of a quantum system. We measured 64 three-photon polarization correlations and used a "maximum-likelihood" reconstruction method to reconstruct the Greenberger-Horne-Zeilinger state. The entanglement class has been characterized using an entanglement witness operator and the maximum predicted values for the Mermin inequality were extracted.

3-D image reconstruction in radiology

International Nuclear Information System (INIS)

Grangeat, P.

1999-01-01

In this course, we present highlights on fully 3-D image reconstruction algorithms used in 3-D X-ray Computed Tomography (3-D-CT) and 3-D Rotational Radiography (3-D-RR). We first consider the case of spiral CT with a one-row detector. Starting from the 2-D fan-beam inversion formula for a circular trajectory, we introduce spiral CT 3-D image reconstruction algorithm using axial interpolation for each transverse slice. In order to improve the X-ray detection efficiency and to speed the acquisition process, the future is to use multi-row detectors associated with small angle cone-beam geometry. The generalization of the 2-D fan-beam image reconstruction algorithm to cone beam defined direct inversion formula referred as Feldkamp's algorithm for a circular trajectory and Wang's algorithm for a spiral trajectory. However, large area detectors does exist such as Radiological Image Intensifiers or in a near future solid state detectors. To get a larger zoom effect, it defines a cone-beam geometry associated with a large aperture angle. For this case, we introduce indirect image reconstruction algorithm by plane re-binning in the Radon domain. We will present some results from a prototype MORPHOMETER device using the RADON reconstruction software. Lastly, we consider the special case of 3-D Rotational Digital Subtraction Angiography with a restricted number of views. We introduce constraint optimization algorithm using quadratic, entropic or half-quadratic constraints. Generalized ART (Algebraic Reconstruction Technique) iterative reconstruction algorithm can be derived from the Bregman algorithm. We present reconstructed vascular trees from a prototype MORPHOMETER device. (author)

Sensation Following Immediate Breast Reconstruction with Implants.

Science.gov (United States)

Lagergren, Jakob; Wickman, Marie; Hansson, Per

2010-01-01

Sensation is a neglected aspect of the outcome of breast reconstructions with implants. The aim of this prospective study was to evaluate the cutaneous somatosensory status in breasts following mastectomy and immediate reconstruction with permanent adjustable prostheses and to analyze the patients' subjective experience of the sensation. Twenty-four consecutive patients diagnosed with invasive or in situ breast carcinoma were examined preoperatively and 2 years after mastectomy and reconstruction, for assessment of perception thresholds for touch, cold, warmth, and heat pain above and below the areola. Von Frey filaments and a Peltier element-based thermode were used. The patients completed a questionnaire concerning their experienced sensation in the reconstructed breast. Using quantitative somato-sensory testing, the sensation to all the examined modalities was significantly impaired compared to preoperatively. Most affected was the area above the areola. Patients given postoperative radiotherapy (n = 9) did not differ from those without radiotherapy (n = 15) regarding any of the modalities. All patients reported reduced sensation in the reconstructed breast compared to that preoperatively. Twenty-three patients stated that the reconstructed breast felt different from the other breast; nevertheless 16 reported that the reconstructed breast felt like a real breast. The study revealed sensation impairment following mastectomy and immediate reconstruction with implants. Patients should be informed about this effect preoperatively to allow adequate expectations regarding the sensation outcome. However, two-thirds of the study patients considered that the reconstructed breast felt like a real breast, which must be one of the main purposes of a breast reconstruction.

Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat

Directory of Open Access Journals (Sweden)

Reem Joukhadar

2017-12-01

Full Text Available Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to

Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat.

Science.gov (United States)

Joukhadar, Reem; Daetwyler, Hans D; Bansal, Urmil K; Gendall, Anthony R; Hayden, Matthew J

2017-01-01

Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with

Game theory and the warrior diplomat interagency cooperation in stability and reconstruction operations

OpenAIRE

Irmischer, Drew M.

2010-01-01

Approved for public release; distribution is unlimited The U.S. has become increasingly involved with failed and failing states since the end of the Cold War in the 1990s. Further, failed and failing states are forecast to remain a national security issue well into the future. United States involvement with failed and failing states has primarily focused around reconstruction and stability operations, and crisis management efforts. Previous reconstruction and stability efforts have ...

Reconstructing Neutrino Mass Spectrum

OpenAIRE

Smirnov, A. Yu.

1999-01-01

Reconstruction of the neutrino mass spectrum and lepton mixing is one of the fundamental problems of particle physics. In this connection we consider two central topics: (i) the origin of large lepton mixing, (ii) possible existence of new (sterile) neutrino states. We discuss also possible relation between large mixing and existence of sterile neutrinos.

Imperatives for Effective Post-Conflict Reconstruction Contracting

National Research Council Canada - National Science Library

Pease, Gary D

2007-01-01

The successful conduct of post-conflict reconstruction operations has strategic significance because it enhances United States vital interests by setting the stage for stable and effective governments...

Derived (mutated)-types of TRPV6 channels elicit greater Ca²+ influx into the cells than ancestral-types of TRPV6: evidence from Xenopus oocytes and mammalian cell expression system.

Science.gov (United States)

Sudo, Yuka; Matsuo, Kiyotaka; Tetsuo, Tomoyuki; Tsutsumi, Satoshi; Ohkura, Masamichi; Nakai, Junichi; Uezono, Yasuhito

2010-01-01

The frequency of the allele containing three derived nonsynonymous SNPs (157C, 378M, 681M) of the gene encoding calcium permeable TRPV6 channels expressed in the intestine has been increased by positive selection in non-African populations. To understand the nature of these SNPs, we compared the properties of Ca²+ influx of ancestral (in African populations) and derived-TRPV6 (in non-African populations) channels with electrophysiological, Ca²+-imaging, and morphological methods using both the Xenopus oocyte and mammalian cell expression systems. Functional electrophysiological and Ca²+-imaging analyses indicated that the derived-TRPV6 elicited more Ca²+ influx than the ancestral one in TRPV6-expressing cells where both channels were equally expressed in the cells. Ca²+-inactivation properties in the ancestral- and derived-TRPV6 were almost the same. Furthermore, fluorescence resonance energy transfer (FRET) analysis showed that both channels have similar multimeric formation properties, suggesting that derived-TRPV6 itself could cause higher Ca²+ influx. These findings suggest that populations having derived-TRPV6 in non-African areas may absorb higher Ca²+ from the intestine than ancestral-TRPV6 in the African area.

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

Science.gov (United States)

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

2013-08-01

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

Variability in "1"8F-FDG PET/CT methodology of acquisition, reconstruction and analysis for oncologic imaging: state survey

International Nuclear Information System (INIS)

Fischer, Andreia C.F. da S.; Druzian, Aline C.; Bacelar, Alexandre; Pianta, Diego B.; Silva, Ana M. Marques da

2016-01-01

The SUV in "1"8F-FDG PET/CT oncological imaging is useful for cancer diagnosis, staging and treatment assessment. There are, however, several factors that can give rise to bias in SUV measurements. When using SUV as a diagnostic tool, one needs to minimize the variability in this measurement by standardization of patient preparation, acquisition and reconstruction parameters. The aim of this study is to evaluate the methodological variability in PET/CT acquisition in Rio Grande do Sul State. For that, in each department, a questionnaire was applied to survey technical information from PET/CT systems and about the acquisitions and analysis methods utilized. All departments implement quality assurance programs consistent with (inter)national recommendations. However, the acquisition and reconstruction methods of acquired PET data differ. The implementation of a harmonized strategy for quantifying the SUV is suggested, in order to obtain greater reproducibility and repeatability. (author)

Metamorphosis Is Ancestral for Crown Euarthropods, and Evolved in the Cambrian or Earlier.

Science.gov (United States)

Wolfe, Joanna M

2017-09-01

Macroevolutionary developmental biology employs fossilized ontogenetic data and phylogenetic comparative methods to probe the evolution of development at ancient nodes. Despite the prevalence of ecologically differentiated larval forms in marine invertebrates, it has been frequently presumed that the ancestors of arthropods were direct developers, and that metamorphosis may not have evolved until the Ordovician or later. Using fossils and new dated phylogenies, I infer that metamorphosis was likely ancestral for crown arthropods, contradicting this assumption. Based on a published morphological dataset encompassing 217 exceptionally preserved fossil and 96 extant taxa, fossils were directly incorporated into both the topology and age estimates, as in "tip dating" analyses. Using data from post-embryonic fossils representing 25 species throughout stem and crown arthropod lineages (as well as most of the 96 extant taxa), characters for metamorphosis were assigned based on inferred ecological changes in development (e.g., changes in habitat and adaptive landscape). Under all phylogenetic hypotheses, metamorphosis was supported as most likely ancestral to both ecdysozoans and euarthropods. Care must be taken to account for potential drastic post-embryonic morphological changes in evolutionary analyses. Many stem group euarthrpods may have had ecologically differentiated larval stages that did not preserve in the fossil record. Moreover, a complex life cycle and planktonic ecology may have evolved in the Ediacaran or earlier, and may have typified the pre-Cambrian explosion "wormworld" prior to the origin of crown group euarthropods. © The Author 2017. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology. All rights reserved. For permissions please email: journals.permissions@oup.com.

Resolution of deep nodes yields an improved backbone phylogeny and a new basal lineage to study early evolution of Asteraceae.

Science.gov (United States)

Panero, Jose L; Freire, Susana E; Ariza Espinar, Luis; Crozier, Bonnie S; Barboza, Gloria E; Cantero, Juan J

2014-11-01

A backbone phylogeny that fully resolves all subfamily and deeper nodes of Asteraceae was constructed using 14 chloroplast DNA loci. The recently named genus Famatinanthus was found to be sister to the Mutisioideae-Asteroideae clade that represents more than 99% of Asteraceae and was found to have the two chloroplast inversions present in all Asteraceae except the nine genera of Barnadesioideae. A monotypic subfamily Famatinanthoideae and tribe Famatinantheae are named herein as new. Relationships among the basal lineages of the family were resolved with strong support in the Bayesian analysis as (Barnadesioideae (Famatinanthoideae (Mutisioideae (Stifftioideae (Wunderlichioideae-Asteroideae))))). Ancestral state reconstruction of ten morphological characters at the root node of the Asteraceae showed that the ancestral sunflower would have had a woody habit, alternate leaves, solitary capitulescences, epaleate receptacles, smooth styles, smooth to microechinate pollen surface sculpturing, white to yellow corollas, and insect-mediated pollination. Herbaceous habit, echinate pollen surface, pubescent styles, and cymose capitulescences were reconstructed for backbone nodes of the phylogeny corresponding to clades that evolved shortly after Asteraceae dispersed out of South America. No support was found for discoid capitula, multiseriate involucres or bird pollination as the ancestral character condition for any node. Using this more resolved phylogenetic tree, the recently described Raiguenrayun cura+Mutisiapollis telleriae fossil should be associated to a more derived node than previously suggested when time calibrating phylogenies of Asteraceae. Copyright © 2014 Elsevier Inc. All rights reserved.

The evolution of Cayaponia (Cucurbitaceae): Repeated shifts from bat to bee pollination and long-distance dispersal to Africa 2-5 million years ago.

Science.gov (United States)

Duchen, Pablo; Renner, Susanne S

2010-07-01

The Cucurbitaceae genus Cayaponia comprises ∼60 species that occur from Uruguay to the southern United States and the Caribbean; C. africana occurs in West Africa and on Madagascar. Pollination is by bees or bats, raising the question of the evolutionary direction and frequency of pollinator shifts. Studies that investigated such shifts in other clades have suggested that bat pollination might be an evolutionary end point. • Plastid and nuclear DNA sequences were obtained for 50 accessions representing 30 species of Cayaponia and close relatives, and analyses were carried out to test monophyly, infer divergence times, and reconstruct ancestral states for habitat preferences and pollination modes. • The phylogeny shows that Cayaponia is monophyletic as long as Selysia (a genus with four species from Central and South America) is included. The required nomenclatural transfers are made in this paper. African and Madagascan accessions of C. africana form a clade that is part of a polytomy with Caribbean and South American species, and the inferred divergence time of 2-5 Ma implies a transoceanic dispersal event from the New World to Africa. The ancestral state reconstructions suggest that Cayaponia originated in tropical forests from where open savannas were reached several times and that bee pollination arose from bat pollination, roughly concomitant with the shifts from forests to savanna habitats. • Cayaponia provides the first example of evolutionary transitions from bat to bee pollination as well as another instance of transoceanic dispersal from the New World to Africa.

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

Science.gov (United States)

Caspeta, Luis; Nielsen, Jens

2015-07-21

A major challenge for the production of ethanol from biomass-derived feedstocks is to develop yeasts that can sustain growth under the variety of inhibitory conditions present in the production process, e.g., high osmolality, high ethanol titers, and/or elevated temperatures (≥ 40 °C). Using 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. Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3 °C, whereas they showed a growth trade-off at temperatures below 34 °C. Computational analysis of the physical properties of 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 in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures. In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance to inhibitory conditions found in industrial ethanol production processes. Yeast thermotolerance can significantly reduce the production costs of biomass

A Hybrid Model Based on Wavelet Decomposition-Reconstruction in Track Irregularity State Forecasting

Directory of Open Access Journals (Sweden)

Chaolong Jia

2015-01-01

Full Text Available Wavelet is able to adapt to the requirements of time-frequency signal analysis automatically and can focus on any details of the signal and then decompose the function into the representation of a series of simple basis functions. It is of theoretical and practical significance. Therefore, this paper does subdivision on track irregularity time series based on the idea of wavelet decomposition-reconstruction and tries to find the best fitting forecast model of detail signal and approximate signal obtained through track irregularity time series wavelet decomposition, respectively. On this ideology, piecewise gray-ARMA recursive based on wavelet decomposition and reconstruction (PG-ARMARWDR and piecewise ANN-ARMA recursive based on wavelet decomposition and reconstruction (PANN-ARMARWDR models are proposed. Comparison and analysis of two models have shown that both these models can achieve higher accuracy.

Optimization of reconstruction algorithms using Monte Carlo simulation

International Nuclear Information System (INIS)

Hanson, K.M.

1989-01-01

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

Optimization of reconstruction algorithms using Monte Carlo simulation

International Nuclear Information System (INIS)

Hanson, K.M.

1989-01-01

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 an 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 non-negativity 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. (author)

Online evolution reconstruction from a single measurement record with random time intervals for quantum communication

Science.gov (United States)

Zhou, Hua; Su, Yang; Wang, Rong; Zhu, Yong; Shen, Huiping; Pu, Tao; Wu, Chuanxin; Zhao, Jiyong; Zhang, Baofu; Xu, Zhiyong

2017-10-01

Online reconstruction of a time-variant quantum state from the encoding/decoding results of quantum communication is addressed by developing a method of evolution reconstruction from a single measurement record with random time intervals. A time-variant two-dimensional state is reconstructed on the basis of recovering its expectation value functions of three nonorthogonal projectors from a random single measurement record, which is composed from the discarded qubits of the six-state protocol. The simulated results prove that our method is robust to typical metro quantum channels. Our work extends the Fourier-based method of evolution reconstruction from the version for a regular single measurement record with equal time intervals to a unified one, which can be applied to arbitrary single measurement records. The proposed protocol of evolution reconstruction runs concurrently with the one of quantum communication, which can facilitate the online quantum tomography.

Mastectomy Skin Necrosis After Breast Reconstruction: A Comparative Analysis Between Autologous Reconstruction and Implant-Based Reconstruction.

Science.gov (United States)

Sue, Gloria R; Lee, Gordon K

2018-05-01

Mastectomy skin necrosis is a significant problem after breast reconstruction. We sought to perform a comparative analysis on this complication between patients undergoing autologous breast reconstruction and patients undergoing 2-stage expander implant breast reconstruction. A retrospective review was performed on consecutive patients undergoing autologous breast reconstruction or 2-stage expander implant breast reconstruction by the senior author from 2006 through 2015. Patient demographic factors including age, body mass index, history of diabetes, history of smoking, and history of radiation to the breast were collected. Our primary outcome measure was mastectomy skin necrosis. Fisher exact test was used for statistical analysis between the 2 patient cohorts. The treatment patterns of mastectomy skin necrosis were then analyzed. We identified 204 patients who underwent autologous breast reconstruction and 293 patients who underwent 2-stage expander implant breast reconstruction. Patients undergoing autologous breast reconstruction were older, heavier, more likely to have diabetes, and more likely to have had prior radiation to the breast compared with patients undergoing implant-based reconstruction. The incidence of mastectomy skin necrosis was 30.4% of patients in the autologous group compared with only 10.6% of patients in the tissue expander group (P care in the autologous group, only 3.2% were treated with local wound care in the tissue expander group (P skin necrosis is significantly more likely to occur after autologous breast reconstruction compared with 2-stage expander implant-based breast reconstruction. Patients with autologous reconstructions are more readily treated with local wound care compared with patients with tissue expanders, who tended to require operative treatment of this complication. Patients considering breast reconstruction should be counseled appropriately regarding the differences in incidence and management of mastectomy skin

Colour pattern homology and evolution in Vanessa butterflies (Nymphalidae: Nymphalini): eyespot characters.

Science.gov (United States)

Abbasi, R; Marcus, J M

2015-11-01

Ocelli are serially repeated colour patterns on the wings of many butterflies. Eyespots are elaborate ocelli that function in predator avoidance and deterrence as well as in mate choice. A phylogenetic approach was used to study ocelli and eyespot evolution in Vanessa butterflies, a genus exhibiting diverse phenotypes among these serial homologs. Forty-four morphological characters based on eyespot number, arrangement, shape and the number of elements in each eyespot were defined and scored. Ocelli from eight wing cells on the dorsal and ventral surfaces of the forewing and hindwing were evaluated. The evolution of these characters was traced over a phylogeny of Vanessa based on 7750 DNA base pairs from 10 genes. Our reconstruction predicts that the ancestral Vanessa had 5 serially arranged ocelli on all four wing surfaces. The ancestral state on the dorsal forewing and ventral hindwing was ocelli arranged in two heterogeneous groups. On the dorsal hindwing, the ancestral state was either homogenous or ocelli arranged in two heterogeneous groups. On the ventral forewing, we determined that the ancestral state was organized into three heterogeneous groups. In Vanessa, almost all ocelli are individuated and capable of independent evolution relative to other colour patterns except for the ocelli in cells -1 and 0 on the dorsal and ventral forewings, which appear to be constrained to evolve in parallel. The genus Vanessa is a good model system for the study of serial homology and the interaction of selective forces with developmental architecture to produce diversity in butterfly colour patterns. © 2015 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2015 European Society For Evolutionary Biology.

Origin of amphibian and avian chromosomes by fission, fusion, and retention of ancestral chromosomes

Science.gov (United States)

Voss, Stephen R.; Kump, D. Kevin; Putta, Srikrishna; Pauly, Nathan; Reynolds, Anna; Henry, Rema J.; Basa, Saritha; Walker, John A.; Smith, Jeramiah J.

2011-01-01

Amphibian genomes differ greatly in DNA content and chromosome size, morphology, and number. Investigations of this diversity are needed to identify mechanisms that have shaped the evolution of vertebrate genomes. We used comparative mapping to investigate the organization of genes in the Mexican axolotl (Ambystoma mexicanum), a species that presents relatively few chromosomes (n = 14) and a gigantic genome (>20 pg/N). We show extensive conservation of synteny between Ambystoma, chicken, and human, and a positive correlation between the length of conserved segments and genome size. Ambystoma segments are estimated to be four to 51 times longer than homologous human and chicken segments. Strikingly, genes demarking the structures of 28 chicken chromosomes are ordered among linkage groups defining the Ambystoma genome, and we show that these same chromosomal segments are also conserved in a distantly related anuran amphibian (Xenopus tropicalis). Using linkage relationships from the amphibian maps, we predict that three chicken chromosomes originated by fusion, nine to 14 originated by fission, and 12–17 evolved directly from ancestral tetrapod chromosomes. We further show that some ancestral segments were fused prior to the divergence of salamanders and anurans, while others fused independently and randomly as chromosome numbers were reduced in lineages leading to Ambystoma and Xenopus. The maintenance of gene order relationships between chromosomal segments that have greatly expanded and contracted in salamander and chicken genomes, respectively, suggests selection to maintain synteny relationships and/or extremely low rates of chromosomal rearrangement. Overall, the results demonstrate the value of data from diverse, amphibian genomes in studies of vertebrate genome evolution. PMID:21482624

Effects of ancestral populations on entrepreneurial founding and failure: private liquor stores in Alberta, 1994--2003

OpenAIRE

Glen Dowell; Robert J. David

2011-01-01

Until 1993, all liquor stores in the Canadian province of Alberta were government owned and run. In the fall of 1993, the provincial government exited liquor retailing, all government stores were shut down, and entrepreneurs were allowed to open private liquor stores. In this article, we take advantage of this abrupt regulatory change in the Alberta liquor-retailing industry to address two related issues that have received little empirical attention. First, we investigate how an ancestral pop...

Floral evolution of Philodendron subgenus Meconostigma (Araceae.

Directory of Open Access Journals (Sweden)

Letícia Loss de Oliveira

Full Text Available Elucidating the evolutionary patterns of flower and inflorescence structure is pivotal to understanding the phylogenetic relationships of Angiosperms as a whole. The inflorescence morphology and anatomy of Philodendron subgenus Meconostigma, belonging to the monocot family Araceae, has been widely studied but the evolutionary relationships of subgenus Meconostigma and the evolution of its flower characters have hitherto remained unclear. This study examines gynoecium evolution in subgenus Meconostigma in the context of an estimated molecular phylogeny for all extant species of subgenus Meconostigma and analysis of ancestral character reconstructions of some gynoecial structures. The phylogenetic reconstructions of all extant Meconostigma species were conducted under a maximum likelihood approach based on the sequences of two chloroplast (trnk and matK and two nuclear (ETS and 18S markers. This topology was used to reconstruct the ancestral states of seven floral characters and to elucidate their evolutionary pattern in the Meconostigma lineage. Our phylogeny shows that Meconostigma is composed of two major clades, one comprising two Amazonian species and the other all the species from the Atlantic Forest and Cerrado biomes with one Amazonian species. The common ancestor of the species of subgenus Meconostigma probably possessed short stylar lobes, long stylar canals, a stylar body, a vascular plexus in the gynoecium and druses in the stylar parenchyma but it is uncertain whether raphide inclusions were present in the parenchyma. The ancestral lineage also probably possessed up to 10 ovary locules. The evolution of these characters seems to have occurred independently in some lineages. We propose that the morphological and anatomical diversity observed in the gynoecial structures of subgenus Meconostigma is the result of an ongoing process of fusion of floral structures leading to a reduction of energy wastage and increase in stigmatic surface.

Floral evolution of Philodendron subgenus Meconostigma (Araceae).

Science.gov (United States)

de Oliveira, Letícia Loss; Calazans, Luana Silva Braucks; de Morais, Érica Barroso; Mayo, Simon Joseph; Schrago, Carlos Guerra; Sakuragui, Cassia Mônica

2014-01-01

Elucidating the evolutionary patterns of flower and inflorescence structure is pivotal to understanding the phylogenetic relationships of Angiosperms as a whole. The inflorescence morphology and anatomy of Philodendron subgenus Meconostigma, belonging to the monocot family Araceae, has been widely studied but the evolutionary relationships of subgenus Meconostigma and the evolution of its flower characters have hitherto remained unclear. This study examines gynoecium evolution in subgenus Meconostigma in the context of an estimated molecular phylogeny for all extant species of subgenus Meconostigma and analysis of ancestral character reconstructions of some gynoecial structures. The phylogenetic reconstructions of all extant Meconostigma species were conducted under a maximum likelihood approach based on the sequences of two chloroplast (trnk and matK) and two nuclear (ETS and 18S) markers. This topology was used to reconstruct the ancestral states of seven floral characters and to elucidate their evolutionary pattern in the Meconostigma lineage. Our phylogeny shows that Meconostigma is composed of two major clades, one comprising two Amazonian species and the other all the species from the Atlantic Forest and Cerrado biomes with one Amazonian species. The common ancestor of the species of subgenus Meconostigma probably possessed short stylar lobes, long stylar canals, a stylar body, a vascular plexus in the gynoecium and druses in the stylar parenchyma but it is uncertain whether raphide inclusions were present in the parenchyma. The ancestral lineage also probably possessed up to 10 ovary locules. The evolution of these characters seems to have occurred independently in some lineages. We propose that the morphological and anatomical diversity observed in the gynoecial structures of subgenus Meconostigma is the result of an ongoing process of fusion of floral structures leading to a reduction of energy wastage and increase in stigmatic surface.

Functional evolution in the plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL gene family

Directory of Open Access Journals (Sweden)

Jill Christine Preston

2013-04-01

Full Text Available The SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL family of transcription factors is functionally diverse, controlling a number of fundamental aspects of plant growth and development, including vegetative phase change, flowering time, branching, and leaf initiation rate. In natural plant populations, variation in flowering time and shoot architecture have major consequences for fitness. Likewise, in crop species, variation in branching and developmental rate impact biomass and yield. Thus, studies aimed at dissecting how the various functions are partitioned among different SPL genes in diverse plant lineages are key to providing insight into the genetic basis of local adaptation and have already garnered attention by crop breeders. Here we use phylogenetic reconstruction to reveal nine major SPL gene lineages, each of which is described in terms of function and diversification. To assess evidence for ancestral and derived functions within each SPL gene lineage, we use ancestral character state reconstructions. Our analyses suggest an emerging pattern of sub-functionalization, neo-functionalization, and possible convergent evolution following both ancient and recent gene duplication. Based on these analyses we suggest future avenues of research that may prove fruitful for elucidating the importance of SPL gene evolution in plant growth and development.

Explosive diversification following a benthic to pelagic shift in freshwater fishes.

Science.gov (United States)

Hollingsworth, Phillip R; Simons, Andrew M; Fordyce, James A; Hulsey, C Darrin

2013-12-17

Interspecific divergence along a benthic to pelagic habitat axis is ubiquitous in freshwater fishes inhabiting lentic environments. In this study, we examined the influence of this habitat axis on the macroevolution of a diverse, lotic radiation using mtDNA and nDNA phylogenies for eastern North America's most species-rich freshwater fish clade, the open posterior myodome (OPM) cyprinids. We used ancestral state reconstruction to identify the earliest benthic to pelagic transition in this group and generated fossil-calibrated estimates of when this shift occurred. This transition could have represented evolution into a novel adaptive zone, and therefore, we tested for a period of accelerated lineage accumulation after this historical habitat shift. Ancestral state reconstructions inferred a similar and concordant region of our mtDNA and nDNA based gene trees as representing the shift from benthic to pelagic habitats in the OPM clade. Two independent tests conducted on each gene tree suggested an increased diversification rate after this inferred habitat transition. Furthermore, lineage through time analyses indicated rapid early cladogenesis in the clade arising after the benthic to pelagic shift. A burst of diversification followed the earliest benthic to pelagic transition during the radiation of OPM cyprinids in eastern North America. As such, the benthic/pelagic habitat axis has likely influenced the generation of biodiversity across disparate freshwater ecosystems.

Crossing statistic: reconstructing the expansion history of the universe

International Nuclear Information System (INIS)

Shafieloo, Arman

2012-01-01

We present that by combining Crossing Statistic [1,2] and Smoothing method [3-5] one can reconstruct the expansion history of the universe with a very high precision without considering any prior on the cosmological quantities such as the equation of state of dark energy. We show that the presented method performs very well in reconstruction of the expansion history of the universe independent of the underlying models and it works well even for non-trivial dark energy models with fast or slow changes in the equation of state of dark energy. Accuracy of the reconstructed quantities along with independence of the method to any prior or assumption gives the proposed method advantages to the other non-parametric methods proposed before in the literature. Applying on the Union 2.1 supernovae combined with WiggleZ BAO data we present the reconstructed results and test the consistency of the two data sets in a model independent manner. Results show that latest available supernovae and BAO data are in good agreement with each other and spatially flat ΛCDM model is in concordance with the current data

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 the same as that of dense YSZ, but the effective creep rate increases by a factor of 8–10 due to porosity. The relationship of creep rate and volume fraction of YSZ computed by numerical homogenization is underestimated by most existing analytical models. The Ramakrishnan–Arunchalam creep model provides...

A fast sparse reconstruction algorithm for electrical tomography

International Nuclear Information System (INIS)

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

2014-01-01

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 L 1 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 L 2 −L 1 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)

Hanford environmental dose reconstruction project - an overview

International Nuclear Information System (INIS)

Shipler, D.B.; Napier, B.A.; Farris, W.T.

1996-01-01

The Hanford Environmental Dose Reconstruction Project was initiated because of public interest in the historical releases of radioactive materials from the Hanford Site, located in southcentral Washington State. By 1986, over 38,000 pages of environmental monitoring documentation from the early years of Hanford operations had been released. Special committees reviewing the documents recommended initiation of the Hanford Environmental Dose Reconstruction Project, which began in October 1987, and is conducted by Battelle, Pacific Northwest Laboratories. The technical approach taken was to reconstruct releases of radioactive materials based on facility operating information; develop and/or adapt transport, pathway, and dose models and computer codes; reconstruct environmental, meterological, and hydrological monitoring information; reconstruct demographic, agricultural, and lifestyle characteristics; apply statistical methods to all forms of uncertainty in the information, parameters, and models; and perform scientific investigation that were technically defensible. The geographic area for the study includes ∼2 x 10 5 km 2 (75,000 mi 2 ) in eastern Washington, western Idaho, and northeastern Oregon (essentially the Mid-columbia Basin of the Pacific Northwest). Three exposure pathways were considered: the atmosphere, the Columbia River, and ground water

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

International Nuclear Information System (INIS)

Delageniere-Guillot, S.

1993-02-01

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)

Allo-allo-triploid Sphagnum × falcatulum: single individuals contain most of the Holantarctic diversity for ancestrally indicative markers.

Science.gov (United States)

Karlin, Eric F; Smouse, Peter E

2017-08-01

Allopolyploids exhibit both different levels and different patterns of genetic variation than are typical of diploids. However, scant attention has been given to the partitioning of allelic information and diversity in allopolyploids, particularly that among homeologous monoploid components of the hologenome. Sphagnum × falcatulum is a double allopolyploid peat moss that spans a considerable portion of the Holantarctic. With monoploid genomes from three ancestral species, this organism exhibits a complex evolutionary history involving serial inter-subgeneric allopolyploidizations. Studying populations from three disjunct regions [South Island (New Zealand); Tierra de Fuego archipelago (Chile, Argentina); Tasmania (Australia)], allelic information for five highly stable microsatellite markers that differed among the three (ancestral) monoploid genomes was examined. Using Shannon information and diversity measures, the holoploid information, as well as the information within and among the three component monoploid genomes, was partitioned into separate components for individuals within and among populations and regions, and those information components were then converted into corresponding diversity measures. The majority (76 %) of alleles detected across these five markers are most likely to have been captured by hybridization, but the information within each of the three monoploid genomes varied, suggesting a history of recurrent allopolyploidization between ancestral species containing different levels of genetic diversity. Information within individuals, equivalent to the information among monoploid genomes (for this dataset), was relatively stable, and represented 83 % of the grand total information across the Holantarctic, with both inter-regional and inter-population diversification each accounting for about 5 % of the total information. Sphagnum × falcatulum probably inherited the great majority of its genetic diversity at these markers by reticulation

Trends in Materials Science for Ligament Reconstruction.

Science.gov (United States)

Sava, Oana Roxana; Sava, Daniel Florin; Radulescu, Marius; Albu, Madalina Georgiana; Ficai, Denisa; Veloz-Castillo, Maria Fernanda; Mendez-Rojas, Miguel Angel; Ficai, Anton

2017-01-01

The number of ligament injuries increases every year and concomitantly the need for materials or systems that can reconstruct the ligament. Limitations imposed by autografts and allografts in ligament reconstruction together with the advances in materials science and biology have attracted a lot of interest for developing systems and materials for ligament replacement or reconstruction. This review intends to synthesize the major steps taken in the development of polymer-based materials for anterior cruciate ligament, their advantages and drawbacks and the results of different in vitro and in vivo tests. Until present, there is no successful polymer system for ligament reconstruction implanted in humans. The developing field of synthetic polymers for ligament reconstruction still has a lot of potential. In addition, several nano-structured materials, made of nanofibers or in the form of ceramic/polymeric nanocomposites, are attracting the interest of several groups due to their potential use as engineered scaffolds that mimic the native environment of cells, increasing the chances for tissue regeneration. Here, we review the last 15 years of literature in order to obtain a better understanding on the state-of-the-art that includes the usage of nano- and poly-meric materials for ligament reconstruction, and to draw perspectives on the future development of the field. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Ulysses S. Grant and Reconstruction.

Science.gov (United States)

Wilson, David L.

1989-01-01

Discusses the role played by Ulysses S. Grant during the four years of Reconstruction before he became President of the United States. Describes the dynamics of the relationship between Grant and Andrew Johnson. Points out that Grant's attitude of service to the laws created by Congress submerged his desire to create a new South. (KO)

Reconstruction of dynamical systems from interspike intervals

International Nuclear Information System (INIS)

Sauer, T.

1994-01-01

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

Ancestral Variations of the PCDHG Gene Cluster Predispose to Dyslexia in a Multiplex Family

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Teesta Naskar

2018-02-01

Full Text Available Dyslexia is a heritable neurodevelopmental disorder characterized by difficulties in reading and writing. In this study, we describe the identification of a set of 17 polymorphisms located across 1.9 Mb region on chromosome 5q31.3, encompassing genes of the PCDHG cluster, TAF7, PCDH1 and ARHGAP26, dominantly inherited with dyslexia in a multi-incident family. Strikingly, the non-risk form of seven variations of the PCDHG cluster, are preponderant in the human lineage, while risk alleles are ancestral and conserved across Neanderthals to non-human primates. Four of these seven ancestral variations (c.460A > C [p.Ile154Leu], c.541G > A [p.Ala181Thr], c.2036G > C [p.Arg679Pro] and c.2059A > G [p.Lys687Glu] result in amino acid alterations. p.Ile154Leu and p.Ala181Thr are present at EC2: EC3 interacting interface of γA3-PCDH and γA4-PCDH respectively might affect trans-homophilic interaction and hence neuronal connectivity. p.Arg679Pro and p.Lys687Glu are present within the linker region connecting trans-membrane to extracellular domain. Sequence analysis indicated the importance of p.Ile154, p.Arg679 and p.Lys687 in maintaining class specificity. Thus the observed association of PCDHG genes encoding neural adhesion proteins reinforces the hypothesis of aberrant neuronal connectivity in the pathophysiology of dyslexia. Additionally, the striking conservation of the identified variants indicates a role of PCDHG in the evolution of highly specialized cognitive skills critical to reading.

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.

The structure of reconstructed chalcopyrite surfaces

Science.gov (United States)

Thinius, Sascha; Islam, Mazharul M.; Bredow, Thomas

2018-03-01

Chalcopyrite (CuFeS2) surfaces are of major interest for copper exploitation in aqueous solution, called leaching. Since leaching is a surface process knowledge of the surface structure, bonding pattern and oxidation states is important for improving the efficiency. At present such information is not available from experimental studies. Therefore a detailed computational study of chalcopyrite surfaces is performed. The structures of low-index stoichiometric chalcopyrite surfaces {hkl} h, k, l ∈ {0, 1, 2} have been studied with density functional theory (DFT) and global optimization strategies. We have applied ab initio molecular dynamics (MD) in combination with simulated annealing (SA) in order to explore possible reconstructions via a minima hopping (MH) algorithm. In almost all cases reconstruction involving substantial rearrangement has occurred accompanied by reduction of the surface energy. The analysis of the change in the coordination sphere and migration during reconstruction reveals that S-S dimers are formed on the surface. Further it was observed that metal atoms near the surface move toward the bulk forming metal alloys passivated by sulfur. The obtained surface energies of reconstructed surfaces are in the range of 0.53-0.95 J/m2.

Error Evaluation in a Stereovision-Based 3D Reconstruction System

Directory of Open Access Journals (Sweden)

Kohler Sophie

2010-01-01

Full Text Available The work presented in this paper deals with the performance analysis of the whole 3D reconstruction process of imaged objects, specifically of the set of geometric primitives describing their outline and extracted from a pair of images knowing their associated camera models. The proposed analysis focuses on error estimation for the edge detection process, the starting step for the whole reconstruction procedure. The fitting parameters describing the geometric features composing the workpiece to be evaluated are used as quality measures to determine error bounds and finally to estimate the edge detection errors. These error estimates are then propagated up to the final 3D reconstruction step. The suggested error analysis procedure for stereovision-based reconstruction tasks further allows evaluating the quality of the 3D reconstruction. The resulting final error estimates enable lastly to state if the reconstruction results fulfill a priori defined criteria, for example, fulfill dimensional constraints including tolerance information, for vision-based quality control applications for example.

The pig story (tiboi sakkoko Storytelling of kinship, memories of the past, and rights to plots of ancestral land in Mentawai

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Juniator Tulius

2016-07-01

Full Text Available This paper examines some significant elements of the pig story (tiboi sakkoko. This tale contains crucial information about the collective identity, ancestors and historical events affecting particular Mentawai kin-groups. As families do not preserve their culture and traditions in written form, storytellers of kin-groups have narrated the pig story from generation to generation so as to preserve it carefully. In the course of time, storytellers establish particular ways of telling their stories so as to remember the content and plot of the stories easily. Through the pig story, members of kin groups also recollect their ancestral place of origin and plots of ancestral lands. The role of human memory is indispensable to recalling all these important elements. Therefore, this paper analyses memories of the past of different family generations. To achieve its aims, this paper also evaluates the roles of family stories in the culture and traditions of Mentawai society.

The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification.

Science.gov (United States)

Desroches, M; Royer, G; Roche, D; Mercier-Darty, M; Vallenet, D; Médigue, C; Bastard, K; Rodriguez, C; Clermont, O; Denamur, E; Decousser, J-W

2018-01-01

More than a century ago, Theodor Escherich isolated the bacterium that was to become Escherichia coli , one of the most studied organisms. Not long after, the strain began an odyssey and landed in many laboratories across the world. As laboratory culture conditions could be responsible for major changes in bacterial strains, we conducted a genome analysis of isolates of this emblematic strain from different culture collections (England, France, the United States, Germany). Strikingly, many discrepancies between the isolates were observed, as revealed by multilocus sequence typing (MLST), the presence of virulence-associated genes, core genome MLST, and single nucleotide polymorphism/indel analyses. These differences are correlated with the phylogeographic history of the strain and were due to an unprecedented number of mutations in coding DNA repair functions such as mismatch repair (MutL) and oxidized guanine nucleotide pool cleaning (MutT), conferring a specific mutational spectrum and leading to a mutator phenotype. The mutator phenotype was probably acquired during subculturing and corresponded to second-order selection. Furthermore, all of the isolates exhibited hypersusceptibility to antibiotics due to mutations in efflux pump- and porin-encoding genes, as well as a specific mutation in the sigma factor-encoding gene rpoS . These defects reflect a self-preservation and nutritional competence tradeoff allowing survival under the starvation conditions imposed by storage. From a clinical point of view, dealing with such mutator strains can lead microbiologists to draw false conclusions about isolate relatedness and may impact therapeutic effectiveness. IMPORTANCE Mutator phenotypes have been described in laboratory-evolved bacteria, as well as in natural isolates. Several genes can be impacted, each of them being associated with a typical mutational spectrum. By studying one of the oldest strains available, the ancestral Escherich strain, we were able to

Architectural and town-planning reconstruction problems of the city of Voronezh

Science.gov (United States)

Mikhaylova, TTatyana; Parshin, Dmitriy; Shoshinov, Vitaly; Trebukhin, Anatoliy

2018-03-01

The analysis of the state of the historically developed urban district of the city of Voronezh is made. The ways of solving the identified architectural and urban problems of reconstruction of historically developed buildings are proposed. The concept of reconstruction of a territory with historical buildings along Vaytsekhovsky Street is presented.

Phylogenetic reconstruction by cross-species chromosome painting and G-banding in four species of Phyllostomini tribe (Chiroptera, Phyllostomidae) in the Brazilian Amazon: an independent evidence for monophyly.

Science.gov (United States)

Ribas, Talita Fernanda Augusto; Rodrigues, Luis Reginaldo Ribeiro; Nagamachi, Cleusa Yoshiko; Gomes, Anderson José Baia; Rissino, Jorge das Dores; O'Brien, Patricia Caroline Mary; Yang, Fengtang; Ferguson-Smith, Malcolm Andrew; Pieczarka, Julio Cesar

2015-01-01

The subfamily Phyllostominae comprises taxa with a variety of feeding strategies. From the cytogenetic point of view, Phyllostominae shows different rates of chromosomal evolution between genera, with Phyllostomus hastatus probably retaining the ancestral karyotype for the subfamily. Since chromosomal rearrangements occur rarely in the genome and have great value as phylogenetic markers and in taxonomic characterization, we analyzed three species: Lophostoma silvicola (LSI), Phyllostomus discolor (PDI) and Tonatia saurophila (TSA), representing the tribe Phyllostomini, collected in the Amazon region, by classic and molecular cytogenetic techniques in order to reconstruct the phylogenetic relationships within this tribe. LSA has a karyotype of 2n=34 and FN=60, PDI has 2n=32 and FN=60 and TSA has 2n=16 and FN=20. Comparative analysis using G-banding and chromosome painting show that the karyotypic complement of TSA is highly rearranged relative to LSI and PHA, while LSI, PHA and PDI have similar karyotypes, differing by only three chromosome pairs. Nearly all chromosomes of PDI and PHA were conserved in toto, except for chromosome 15 that was changed by a pericentric inversion. A strongly supported phylogeny (bootstrap=100 and Bremer=10 steps), confirms the monophyly of Phyllostomini. In agreement with molecular topologies, TSA was in the basal position, while PHA and LSI formed sister taxa. A few ancestral syntenies are conserved without rearrangements and most associations are autapomorphic traits for Tonatia or plesiomorphic for the three genera analyzed here. The karyotype of TSA is highly derived in relation to that of other phyllostomid bats, differing from the supposed ancestral karyotype of Phyllostomidae by multiple rearrangements. Phylogenies based on chromosomal data are independent evidence for the monophyly of tribe Phyllostomini as determined by molecular topologies and provide additional support for the paraphyly of the genus Tonatia by the exclusion

Phylogenetic reconstruction by cross-species chromosome painting and G-banding in four species of Phyllostomini tribe (Chiroptera, Phyllostomidae in the Brazilian Amazon: an independent evidence for monophyly.

Directory of Open Access Journals (Sweden)

Talita Fernanda Augusto Ribas

Full Text Available The subfamily Phyllostominae comprises taxa with a variety of feeding strategies. From the cytogenetic point of view, Phyllostominae shows different rates of chromosomal evolution between genera, with Phyllostomus hastatus probably retaining the ancestral karyotype for the subfamily. Since chromosomal rearrangements occur rarely in the genome and have great value as phylogenetic markers and in taxonomic characterization, we analyzed three species: Lophostoma silvicola (LSI, Phyllostomus discolor (PDI and Tonatia saurophila (TSA, representing the tribe Phyllostomini, collected in the Amazon region, by classic and molecular cytogenetic techniques in order to reconstruct the phylogenetic relationships within this tribe. LSA has a karyotype of 2n=34 and FN=60, PDI has 2n=32 and FN=60 and TSA has 2n=16 and FN=20. Comparative analysis using G-banding and chromosome painting show that the karyotypic complement of TSA is highly rearranged relative to LSI and PHA, while LSI, PHA and PDI have similar karyotypes, differing by only three chromosome pairs. Nearly all chromosomes of PDI and PHA were conserved in toto, except for chromosome 15 that was changed by a pericentric inversion. A strongly supported phylogeny (bootstrap=100 and Bremer=10 steps, confirms the monophyly of Phyllostomini. In agreement with molecular topologies, TSA was in the basal position, while PHA and LSI formed sister taxa. A few ancestral syntenies are conserved without rearrangements and most associations are autapomorphic traits for Tonatia or plesiomorphic for the three genera analyzed here. The karyotype of TSA is highly derived in relation to that of other phyllostomid bats, differing from the supposed ancestral karyotype of Phyllostomidae by multiple rearrangements. Phylogenies based on chromosomal data are independent evidence for the monophyly of tribe Phyllostomini as determined by molecular topologies and provide additional support for the paraphyly of the genus Tonatia by

Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae

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Chen Ling-Yun

2012-03-01

Full Text Available Abstract Background Hydrocharitaceae is a fully aquatic monocot family, consists of 18 genera with approximately 120 species. The family includes both fresh and marine aquatics and exhibits great diversity in form and habit including annual and perennial life histories; submersed, partially submersed and floating leaf habits and linear to orbicular leaf shapes. The family has a cosmopolitan distribution and is well represented in the Tertiary fossil record in Europe. At present, the historical biogeography of the family is not well understood and the generic relationships remain controversial. In this study we investigated the phylogeny and biogeography of Hydrocharitaceae by integrating fossils and DNA sequences from eight genes. We also conducted ancestral state reconstruction for three morphological characters. Results Phylogenetic analyses produced a phylogeny with most branches strongly supported by bootstrap values greater than 95 and Bayesian posterior probability values of 1.0. Stratiotes is the first diverging lineage with the remaining genera in two clades, one clade consists of Lagarosiphon, Ottelia, Blyxa, Apalanthe, Elodea and Egeria; and the other consists of Hydrocharis-Limnobium, Thalassia, Enhalus, Halophila, Najas, Hydrilla, Vallisneria, Nechamandra and Maidenia. Biogeographic analyses (DIVA, Mesquite and divergence time estimates (BEAST resolved the most recent common ancestor of Hydrocharitaceae as being in Asia during the Late Cretaceous and Palaeocene (54.7-72.6 Ma. Dispersals (including long-distance dispersal and migrations through Tethys seaway and land bridges probably played major roles in the intercontinental distribution of this family. Ancestral state reconstruction suggested that in Hydrocharitaceae evolution of dioecy is bidirectional, viz., from dioecy to hermaphroditism, and from hermaphroditism to dioecy, and that the aerial-submerged leaf habit and short-linear leaf shape are the ancestral states. Conclusions

Generic phylogeny, historical biogeography and character evolution of the cosmopolitan aquatic plant family Hydrocharitaceae.

Science.gov (United States)

Chen, Ling-Yun; Chen, Jin-Ming; Gituru, Robert Wahiti; Wang, Qing-Feng

2012-03-10

Hydrocharitaceae is a fully aquatic monocot family, consists of 18 genera with approximately 120 species. The family includes both fresh and marine aquatics and exhibits great diversity in form and habit including annual and perennial life histories; submersed, partially submersed and floating leaf habits and linear to orbicular leaf shapes. The family has a cosmopolitan distribution and is well represented in the Tertiary fossil record in Europe. At present, the historical biogeography of the family is not well understood and the generic relationships remain controversial. In this study we investigated the phylogeny and biogeography of Hydrocharitaceae by integrating fossils and DNA sequences from eight genes. We also conducted ancestral state reconstruction for three morphological characters. Phylogenetic analyses produced a phylogeny with most branches strongly supported by bootstrap values greater than 95 and Bayesian posterior probability values of 1.0. Stratiotes is the first diverging lineage with the remaining genera in two clades, one clade consists of Lagarosiphon, Ottelia, Blyxa, Apalanthe, Elodea and Egeria; and the other consists of Hydrocharis-Limnobium, Thalassia, Enhalus, Halophila, Najas, Hydrilla, Vallisneria, Nechamandra and Maidenia. Biogeographic analyses (DIVA, Mesquite) and divergence time estimates (BEAST) resolved the most recent common ancestor of Hydrocharitaceae as being in Asia during the Late Cretaceous and Palaeocene (54.7-72.6 Ma). Dispersals (including long-distance dispersal and migrations through Tethys seaway and land bridges) probably played major roles in the intercontinental distribution of this family. Ancestral state reconstruction suggested that in Hydrocharitaceae evolution of dioecy is bidirectional, viz., from dioecy to hermaphroditism, and from hermaphroditism to dioecy, and that the aerial-submerged leaf habit and short-linear leaf shape are the ancestral states. Our study has shed light on the previously controversial

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.

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

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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.

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.

Industrial dynamic tomographic reconstruction

International Nuclear Information System (INIS)

Oliveira, Eric Ferreira de

2016-01-01

The state of the art methods applied to industrial processes is currently based on the principles of classical tomographic reconstructions developed for tomographic patterns of static distributions, or is limited to cases of low variability of the density distribution function of the tomographed object. Noise and motion artifacts are the main problems caused by a mismatch in the data from views acquired in different instants. All of these add to the known fact that using a limited amount of data can result in the presence of noise, artifacts and some inconsistencies with the distribution under study. One of the objectives of the present work is to discuss the difficulties that arise from implementing reconstruction algorithms in dynamic tomography that were originally developed for static distributions. Another objective is to propose solutions that aim at reducing a temporal type of information loss caused by employing regular acquisition systems to dynamic processes. With respect to dynamic image reconstruction it was conducted a comparison between different static reconstruction methods, like MART and FBP, when used for dynamic scenarios. This comparison was based on a MCNPx simulation as well as an analytical setup of an aluminum cylinder that moves along the section of a riser during the process of acquisition, and also based on cross section images from CFD techniques. As for the adaptation of current tomographic acquisition systems for dynamic processes, this work established a sequence of tomographic views in a just-in-time fashion for visualization purposes, a form of visually disposing density information as soon as it becomes amenable to image reconstruction. A third contribution was to take advantage of the triple color channel necessary to display colored images in most displays, so that, by appropriately scaling the acquired values of each view in the linear system of the reconstruction, it was possible to imprint a temporal trace into the regularly

Visual image reconstruction from human brain activity: A modular decoding approach

International Nuclear Information System (INIS)

Miyawaki, Yoichi; Uchida, Hajime; Yamashita, Okito; Sato, Masa-aki; Kamitani, Yukiyasu; Morito, Yusuke; Tanabe, Hiroki C; Sadato, Norihiro

2009-01-01

Brain activity represents our perceptual experience. But the potential for reading out perceptual contents from human brain activity has not been fully explored. In this study, we demonstrate constraint-free reconstruction of visual images perceived by a subject, from the brain activity pattern. We reconstructed visual images by combining local image bases with multiple scales, whose contrasts were independently decoded from fMRI activity by automatically selecting relevant voxels and exploiting their correlated patterns. Binary-contrast, 10 x 10-patch images (2 100 possible states), were accurately reconstructed without any image prior by measuring brain activity only for several hundred random images. The results suggest that our approach provides an effective means to read out complex perceptual states from brain activity while discovering information representation in multi-voxel patterns.

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; 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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; 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Krolikowski, Jan; Frueboes, Tomasz; Gokieli, Ryszard; Górski, Maciej; Kazana, Malgorzata; Nawrocki, Krzysztof; Romanowska-Rybinska, Katarzyna; Szleper, Michal; Wrochna, Grzegorz; Zalewski, Piotr; Almeida, Nuno; Bargassa, Pedrame; David Tinoco Mendes, Andre; Faccioli, Pietro; Ferreira Parracho, Pedro Guilherme; Gallinaro, Michele; Musella, Pasquale; Nayak, Aruna; Pela, Joao; Ribeiro, Pedro Quinaz; Seixas, Joao; Varela, Joao; Afanasiev, Serguei; Belotelov, Ivan; Bunin, Pavel; Gavrilenko, Mikhail; Golutvin, Igor; Kamenev, Alexey; Karjavin, Vladimir; Kozlov, Guennady; Lanev, Alexander; Moisenz, Petr; Palichik, Vladimir; Perelygin, Victor; Shmatov, Sergey; Smirnov, Vitaly; Volodko, Anton; Zarubin, Anatoli; Golovtsov, Victor; Ivanov, Yury; Kim, Victor; Levchenko, Petr; Murzin, Victor; Oreshkin, Vadim; Smirnov, Igor; Sulimov, Valentin; Uvarov, Lev; Vavilov, Sergey; Vorobyev, Alexey; Vorobyev, Andrey; Andreev, Yuri; Dermenev, Alexander; Gninenko, Sergei; Golubev, Nikolai; Kirsanov, Mikhail; Krasnikov, Nikolai; Matveev, Viktor; Pashenkov, Anatoli; Toropin, Alexander; Troitsky, Sergey; Epshteyn, Vladimir; Erofeeva, Maria; Gavrilov, Vladimir; Kaftanov, Vitali; Kossov, Mikhail; Krokhotin, Andrey; Lychkovskaya, Natalia; Popov, Vladimir; Safronov, Grigory; Semenov, Sergey; Stolin, Viatcheslav; Vlasov, Evgueni; Zhokin, Alexander; Belyaev, Andrey; Boos, Edouard; Dubinin, Mikhail; Dudko, Lev; Ershov, Alexander; Gribushin, Andrey; Kodolova, Olga; Lokhtin, Igor; Markina, Anastasia; Obraztsov, Stepan; Perfilov, Maxim; Petrushanko, Sergey; Sarycheva, Ludmila; Savrin, Viktor; Snigirev, Alexander; Andreev, Vladimir; Azarkin, Maksim; Dremin, Igor; Kirakosyan, Martin; Leonidov, Andrey; Mesyats, Gennady; Rusakov, Sergey V; Vinogradov, Alexey; Azhgirey, Igor; Bayshev, Igor; Bitioukov, Sergei; Grishin, Viatcheslav; Kachanov, Vassili; Konstantinov, Dmitri; Korablev, Andrey; Krychkine, Victor; Petrov, Vladimir; Ryutin, Roman; Sobol, Andrei; Tourtchanovitch, Leonid; Troshin, Sergey; Tyurin, Nikolay; Uzunian, Andrey; Volkov, Alexey; Adzic, Petar; Djordjevic, Milos; Krpic, Dragomir; Milosevic, Jovan; Aguilar-Benitez, Manuel; Alcaraz Maestre, Juan; Arce, Pedro; Battilana, Carlo; Calvo, Enrique; Cerrada, Marcos; Chamizo Llatas, Maria; Colino, Nicanor; De La Cruz, Begona; Delgado Peris, Antonio; Diez Pardos, Carmen; Domínguez Vázquez, Daniel; Fernandez Bedoya, Cristina; Fernández Ramos, Juan Pablo; Ferrando, Antonio; Flix, Jose; Fouz, Maria Cruz; Garcia-Abia, Pablo; Gonzalez Lopez, Oscar; Goy Lopez, Silvia; Hernandez, Jose M; Josa, Maria Isabel; Merino, Gonzalo; Puerta Pelayo, Jesus; Redondo, Ignacio; Romero, Luciano; Santaolalla, Javier; Soares, Mara Senghi; Willmott, Carlos; Albajar, Carmen; Codispoti, Giuseppe; de Trocóniz, Jorge F; Cuevas, Javier; Fernandez Menendez, Javier; Folgueras, Santiago; Gonzalez Caballero, Isidro; Lloret Iglesias, Lara; Vizan Garcia, Jesus Manuel; Brochero Cifuentes, Javier Andres; Cabrillo, Iban Jose; Calderon, Alicia; Chuang, Shan-Huei; Duarte Campderros, Jordi; Felcini, Marta; Fernandez, Marcos; Gomez, Gervasio; Gonzalez Sanchez, Javier; Jorda, Clara; Lobelle Pardo, Patricia; Lopez Virto, Amparo; Marco, Jesus; Marco, Rafael; Martinez Rivero, Celso; Matorras, Francisco; Munoz Sanchez, Francisca Javiela; Piedra Gomez, Jonatan; Rodrigo, Teresa; Rodríguez-Marrero, Ana Yaiza; Ruiz-Jimeno, Alberto; Scodellaro, Luca; Sobron Sanudo, Mar; Vila, Ivan; Vilar Cortabitarte, Rocio; Abbaneo, Duccio; Auffray, Etiennette; Auzinger, Georg; Baillon, Paul; Ball, Austin; Barney, David; Bell, Alan James; Benedetti, Daniele; Bernet, Colin; Bialas, Wojciech; Bloch, Philippe; Bocci, Andrea; Bolognesi, Sara; Bona, Marcella; Breuker, Horst; Bunkowski, Karol; Camporesi, Tiziano; Cerminara, Gianluca; Christiansen, Tim; Coarasa Perez, Jose Antonio; Curé, Benoît; D'Enterria, David; De Roeck, Albert; Di Guida, Salvatore; Dupont-Sagorin, Niels; Elliott-Peisert, Anna; Frisch, Benjamin; Funk, Wolfgang; Gaddi, Andrea; Georgiou, Georgios; Gerwig, Hubert; Gigi, Dominique; Gill, Karl; Giordano, Domenico; Glege, Frank; Gomez-Reino Garrido, Robert; Gouzevitch, Maxime; Govoni, Pietro; Gowdy, Stephen; Guida, Roberto; Guiducci, Luigi; Hansen, Magnus; Hartl, Christian; Harvey, John; Hegeman, Jeroen; Hegner, Benedikt; Hoffmann, Hans Falk; Innocente, Vincenzo; Janot, Patrick; Kaadze, Ketino; Karavakis, Edward; Lecoq, Paul; Lenzi, Piergiulio; Lourenco, Carlos; Maki, Tuula; Malberti, Martina; Malgeri, Luca; Mannelli, Marcello; Masetti, Lorenzo; Maurisset, Aurelie; Mavromanolakis, Georgios; Meijers, Frans; Mersi, Stefano; Meschi, Emilio; Moser, Roland; Mozer, Matthias Ulrich; Mulders, Martijn; Nesvold, Erik; Nguyen, Matthew; Orimoto, Toyoko; Orsini, Luciano; Palencia Cortezon, Enrique; Perez, Emmanuelle; Petrilli, Achille; Pfeiffer, Andreas; Pierini, Maurizio; Pimiä, Martti; Piparo, Danilo; Polese, Giovanni; Quertenmont, Loic; Racz, Attila; Reece, William; Rodrigues Antunes, Joao; Rolandi, Gigi; Rommerskirchen, Tanja; Rovelli, Chiara; Rovere, Marco; Sakulin, Hannes; Schäfer, Christoph; Schwick, Christoph; Segoni, Ilaria; Sharma, Archana; Siegrist, Patrice; Silva, Pedro; Simon, Michal; Sphicas, Paraskevas; Spiga, Daniele; Spiropulu, Maria; Stoye, Markus; Tsirou, Andromachi; Vichoudis, Paschalis; Wöhri, Hermine Katharina; Worm, Steven; Zeuner, Wolfram Dietrich; Bertl, Willi; Deiters, Konrad; Erdmann, Wolfram; Gabathuler, Kurt; Horisberger, Roland; Ingram, Quentin; Kaestli, Hans-Christian; König, Stefan; Kotlinski, Danek; Langenegger, Urs; Meier, Frank; Renker, Dieter; Rohe, Tilman; Sibille, Jennifer; Bäni, Lukas; Bortignon, Pierluigi; Caminada, Lea; Casal, Bruno; Chanon, Nicolas; Chen, Zhiling; Cittolin, Sergio; Dissertori, Günther; Dittmar, Michael; Eugster, Jürg; Freudenreich, Klaus; Grab, Christoph; Hintz, Wieland; Lecomte, Pierre; Lustermann, Werner; Marchica, Carmelo; Martinez Ruiz del Arbol, Pablo; Milenovic, Predrag; Moortgat, Filip; Nägeli, Christoph; Nef, Pascal; Nessi-Tedaldi, Francesca; Pape, Luc; Pauss, Felicitas; Punz, Thomas; Rizzi, Andrea; Ronga, Frederic Jean; Rossini, Marco; Sala, Leonardo; Sanchez, Ann - Karin; Sawley, Marie-Christine; Starodumov, Andrei; Stieger, Benjamin; Takahashi, Maiko; Tauscher, Ludwig; Thea, Alessandro; Theofilatos, Konstantinos; Treille, Daniel; Urscheler, Christina; Wallny, Rainer; Weber, Matthias; Wehrli, Lukas; Weng, Joanna; Aguilo, Ernest; Amsler, Claude; Chiochia, Vincenzo; De Visscher, Simon; Favaro, Carlotta; Ivova Rikova, Mirena; Jaeger, Andreas; Millan Mejias, Barbara; Otiougova, Polina; Robmann, Peter; Schmidt, Alexander; Snoek, Hella; Chang, Yuan-Hann; Chen, Kuan-Hsin; Kuo, Chia-Ming; Li, Syue-Wei; Lin, Willis; Liu, Zong-Kai; Lu, Yun-Ju; Mekterovic, Darko; Volpe, Roberta; Yu, Shin-Shan; Bartalini, Paolo; Chang, Paoti; Chang, You-Hao; Chang, Yu-Wei; Chao, Yuan; Chen, Kai-Feng; Dietz, Charles; Grundler, Ulysses; Hou, George Wei-Shu; Hsiung, Yee; Kao, Kai-Yi; Lei, Yeong-Jyi; Lu, Rong-Shyang; Shiu, Jing-Ge; Tzeng, Yeng-Ming; Wan, Xia; Wang, Minzu; Adiguzel, Aytul; Bakirci, Mustafa Numan; Cerci, Salim; Dozen, Candan; Dumanoglu, Isa; Eskut, Eda; Girgis, Semiray; Gokbulut, Gul; Hos, Ilknur; Kangal, Evrim Ersin; Kayis Topaksu, Aysel; Onengut, Gulsen; Ozdemir, Kadri; Ozturk, Sertac; Polatoz, Ayse; Sogut, Kenan; Sunar Cerci, Deniz; Tali, Bayram; Topakli, Huseyin; Uzun, Dilber; Vergili, Latife Nukhet; Vergili, Mehmet; Akin, Ilina Vasileva; Aliev, Takhmasib; Bilin, Bugra; Bilmis, Selcuk; Deniz, Muhammed; Gamsizkan, Halil; Guler, Ali Murat; Ocalan, Kadir; Ozpineci, Altug; Serin, Meltem; Sever, Ramazan; Surat, Ugur Emrah; Yalvac, Metin; Yildirim, Eda; Zeyrek, Mehmet; Deliomeroglu, Mehmet; Demir, Durmus; Gülmez, Erhan; Isildak, Bora; Kaya, Mithat; Kaya, Ozlem; Özbek, Melih; Ozkorucuklu, Suat; Sonmez, Nasuf; Levchuk, Leonid; Bostock, Francis; Brooke, James John; Cheng, Teh Lee; Clement, Emyr; Cussans, David; Frazier, Robert; Goldstein, Joel; Grimes, Mark; Heath, Greg P; Heath, Helen F; Kreczko, Lukasz; Metson, Simon; Newbold, Dave M; Nirunpong, Kachanon; Poll, Anthony; Senkin, Sergey; Smith, Vincent J; Basso, Lorenzo; Bell, Ken W; Belyaev, Alexander; Brew, Christopher; Brown, Robert M; Camanzi, Barbara; Cockerill, David JA; Coughlan, John A; Harder, Kristian; Harper, Sam; Jackson, James; Kennedy, Bruce W; Olaiya, Emmanuel; Petyt, David; Radburn-Smith, Benjamin Charles; Shepherd-Themistocleous, Claire; Tomalin, Ian R; Womersley, William John; Bainbridge, Robert; Ball, Gordon; Ballin, Jamie; Beuselinck, Raymond; Buchmuller, Oliver; Colling, David; Cripps, Nicholas; Cutajar, Michael; Davies, Gavin; Della Negra, Michel; Ferguson, William; Fulcher, Jonathan; Futyan, David; Gilbert, Andrew; Guneratne Bryer, Arlo; Hall, Geoffrey; Hatherell, Zoe; Hays, Jonathan; Iles, Gregory; Jarvis, Martyn; Karapostoli, Georgia; Lyons, Louis; Magnan, Anne-Marie; Marrouche, Jad; Mathias, Bryn; Nandi, Robin; Nash, Jordan; Nikitenko, Alexander; Papageorgiou, Anastasios; Pesaresi, Mark; Petridis, Konstantinos; Pioppi, Michele; Raymond, David Mark; Rogerson, Samuel; Rompotis, Nikolaos; Rose, Andrew; Ryan, Matthew John; Seez, Christopher; Sharp, Peter; Sparrow, Alex; Tapper, Alexander; Tourneur, Stephane; Vazquez Acosta, Monica; Virdee, Tejinder; Wakefield, Stuart; Wardle, Nicholas; Wardrope, David; Whyntie, Tom; Barrett, Matthew; Chadwick, Matthew; Cole, Joanne; Hobson, Peter R; Khan, Akram; Kyberd, Paul; Leslie, Dawn; Martin, William; Reid, Ivan; Teodorescu, Liliana; Hatakeyama, Kenichi; Liu, Hongxuan; Henderson, Conor; Bose, Tulika; Carrera Jarrin, Edgar; Fantasia, Cory; Heister, Arno; St John, Jason; Lawson, Philip; Lazic, Dragoslav; Rohlf, James; Sperka, David; Sulak, Lawrence; Avetisyan, Aram; Bhattacharya, Saptaparna; Chou, John Paul; Cutts, David; Ferapontov, Alexey; Heintz, Ulrich; Jabeen, Shabnam; Kukartsev, Gennadiy; Landsberg, Greg; Luk, Michael; Narain, Meenakshi; Nguyen, Duong; Segala, Michael; Sinthuprasith, Tutanon; Speer, Thomas; Tsang, Ka Vang; Breedon, Richard; Breto, Guillermo; Calderon De La Barca Sanchez, Manuel; Chauhan, Sushil; Chertok, Maxwell; Conway, John; Conway, Rylan; Cox, Peter Timothy; Dolen, James; Erbacher, Robin; Houtz, Rachel; Ko, Winston; Kopecky, Alexandra; Lander, Richard; Liu, Haidong; Mall, Orpheus; Maruyama, Sho; Miceli, Tia; Nikolic, Milan; Pellett, Dave; Robles, Jorge; Rutherford, Britney; Salur, Sevil; Searle, Matthew; Smith, John; Squires, Michael; Tripathi, Mani; Vasquez Sierra, Ricardo; Andreev, Valeri; Arisaka, Katsushi; Cline, David; Cousins, Robert; Deisher, Amanda; Duris, Joseph; Erhan, Samim; Farrell, Chris; Hauser, Jay; Ignatenko, Mikhail; Jarvis, Chad; Plager, Charles; Rakness, Gregory; Schlein, Peter; Tucker, Jordan; Valuev, Vyacheslav; Babb, John; Clare, Robert; Ellison, John Anthony; Gary, J William; Giordano, Ferdinando; Hanson, Gail; Jeng, Geng-Yuan; Kao, Shih-Chuan; Liu, Hongliang; Long, Owen Rosser; Luthra, Arun; Nguyen, Harold; Paramesvaran, Sudarshan; Sturdy, Jared; Sumowidagdo, Suharyo; Wilken, Rachel; Wimpenny, Stephen; Andrews, Warren; Branson, James G; Cerati, Giuseppe Benedetto; Evans, David; Golf, Frank; Holzner, André; Kelley, Ryan; Lebourgeois, Matthew; Letts, James; Mangano, Boris; Padhi, Sanjay; Palmer, Christopher; Petrucciani, Giovanni; Pi, Haifeng; Pieri, Marco; Ranieri, Riccardo; Sani, Matteo; Sharma, Vivek; Simon, Sean; Sudano, Elizabeth; Tadel, Matevz; Tu, Yanjun; Vartak, Adish; Wasserbaech, Steven; Würthwein, Frank; Yagil, Avraham; Yoo, Jaehyeok; Barge, Derek; Bellan, Riccardo; Campagnari, Claudio; D'Alfonso, Mariarosaria; Danielson, Thomas; Flowers, Kristen; Geffert, Paul; Incandela, Joe; Justus, Christopher; Kalavase, Puneeth; Koay, Sue Ann; Kovalskyi, Dmytro; Krutelyov, Vyacheslav; Lowette, Steven; Mccoll, Nickolas; Mullin, Sam Daniel; Pavlunin, Viktor; Rebassoo, Finn; Ribnik, Jacob; Richman, Jeffrey; Rossin, Roberto; Stuart, David; To, Wing; Vlimant, Jean-Roch; West, Christopher; Apresyan, Artur; Bornheim, Adolf; Bunn, Julian; Chen, Yi; Duarte, Javier; Gataullin, Marat; Ma, Yousi; Mott, Alexander; Newman, Harvey B; Rogan, Christopher; Shin, Kyoungha; Timciuc, Vladlen; Traczyk, Piotr; Veverka, Jan; Wilkinson, Richard; Yang, Yong; Zhu, Ren-Yuan; Akgun, Bora; Carroll, Ryan; Ferguson, Thomas; Iiyama, Yutaro; Jang, Dong Wook; Jun, Soon Yung; Liu, Yueh-Feng; Paulini, Manfred; Russ, James; Vogel, Helmut; Vorobiev, Igor; Cumalat, John Perry; Dinardo, Mauro Emanuele; Drell, Brian Robert; Edelmaier, Christopher; Ford, William T; Gaz, Alessandro; Heyburn, Bernadette; Luiggi Lopez, Eduardo; Nauenberg, Uriel; Smith, James; Stenson, Kevin; Ulmer, Keith; Wagner, Stephen Robert; Zang, Shi-Lei; Agostino, Lorenzo; Alexander, James; Chatterjee, Avishek; Eggert, Nicholas; Gibbons, Lawrence Kent; Heltsley, Brian; Hopkins, Walter; Khukhunaishvili, Aleko; Kreis, Benjamin; Nicolas Kaufman, Gala; Patterson, Juliet Ritchie; Puigh, Darren; Ryd, Anders; Salvati, Emmanuele; Shi, Xin; Sun, Werner; Teo, Wee Don; Thom, Julia; Thompson, Joshua; Vaughan, Jennifer; Weng, Yao; Winstrom, Lucas; Wittich, Peter; Biselli, Angela; Cirino, Guy; Winn, Dave; Abdullin, Salavat; Albrow, Michael; Anderson, Jacob; Apollinari, Giorgio; Atac, Muzaffer; Bakken, Jon Alan; Bauerdick, Lothar AT; Beretvas, Andrew; Berryhill, Jeffrey; Bhat, Pushpalatha C; Bloch, Ingo; Burkett, Kevin; Butler, Joel Nathan; Chetluru, Vasundhara; Cheung, Harry; Chlebana, Frank; Cihangir, Selcuk; Cooper, William; Eartly, David P; Elvira, Victor Daniel; Esen, Selda; Fisk, Ian; Freeman, Jim; Gao, Yanyan; Gottschalk, Erik; Green, Dan; Gutsche, Oliver; Hanlon, Jim; Harris, Robert M; Hirschauer, James; Hooberman, Benjamin; Jensen, Hans; Jindariani, Sergo; Johnson, Marvin; Joshi, Umesh; Klima, Boaz; Kousouris, Konstantinos; Kunori, Shuichi; Kwan, Simon; Leonidopoulos, Christos; Limon, Peter; Lincoln, Don; Lipton, Ron; Lykken, Joseph; Maeshima, Kaori; Marraffino, John Michael; Mason, David; McBride, Patricia; Miao, Ting; Mishra, Kalanand; Mrenna, Stephen; Musienko, Yuri; Newman-Holmes, Catherine; O'Dell, Vivian; Pivarski, James; Pordes, Ruth; Prokofyev, Oleg; Schwarz, Thomas; Sexton-Kennedy, Elizabeth; Sharma, Seema; Spalding, William J; Spiegel, Leonard; Tan, Ping; Taylor, Lucas; Tkaczyk, Slawek; Uplegger, Lorenzo; Vaandering, Eric Wayne; Vidal, Richard; Whitmore, Juliana; Wu, Weimin; Yang, Fan; Yumiceva, Francisco; Yun, Jae Chul; Acosta, Darin; Avery, Paul; Bourilkov, Dimitri; Chen, Mingshui; Das, Souvik; De Gruttola, Michele; Di Giovanni, Gian Piero; Dobur, Didar; Drozdetskiy, Alexey; Field, Richard D; Fisher, Matthew; Fu, Yu; Furic, Ivan-Kresimir; Gartner, Joseph; Goldberg, Sean; Hugon, Justin; Kim, Bockjoo; Konigsberg, Jacobo; Korytov, Andrey; Kropivnitskaya, Anna; Kypreos, Theodore; Low, Jia Fu; Matchev, Konstantin; Mitselmakher, Guenakh; Muniz, Lana; Myeonghun, Park; Remington, Ronald; Rinkevicius, Aurelijus; Schmitt, Michael; Scurlock, Bobby; Sellers, Paul; Skhirtladze, Nikoloz; Snowball, Matthew; Wang, Dayong; Yelton, John; Zakaria, Mohammed; Gaultney, Vanessa; Lebolo, Luis Miguel; Linn, Stephan; Markowitz, Pete; Martinez, German; Rodriguez, Jorge Luis; Adams, Todd; Askew, Andrew; Bochenek, Joseph; Chen, Jie; Diamond, Brendan; Gleyzer, Sergei V; Haas, Jeff; Hagopian, Sharon; Hagopian, Vasken; Jenkins, Merrill; Johnson, Kurtis F; Prosper, Harrison; Sekmen, Sezen; Veeraraghavan, Venkatesh; Baarmand, Marc M; Dorney, Brian; Hohlmann, Marcus; Kalakhety, Himali; Vodopiyanov, Igor; Adams, Mark Raymond; Anghel, Ioana Maria; Apanasevich, Leonard; Bai, Yuting; Bazterra, Victor Eduardo; Betts, Russell Richard; Callner, Jeremy; Cavanaugh, Richard; Dragoiu, Cosmin; Gauthier, Lucie; Gerber, Cecilia Elena; Hofman, David Jonathan; Khalatyan, Samvel; Kunde, Gerd J; Lacroix, Florent; Malek, Magdalena; O'Brien, Christine; Silkworth, Christopher; Silvestre, Catherine; Smoron, Agata; Strom, Derek; Varelas, Nikos; Akgun, Ugur; Albayrak, Elif Asli; Bilki, Burak; Clarida, Warren; Duru, Firdevs; Lae, Chung Khim; McCliment, Edward; Merlo, Jean-Pierre; Mermerkaya, Hamit; Mestvirishvili, Alexi; Moeller, Anthony; Nachtman, Jane; Newsom, Charles Ray; Norbeck, Edwin; Olson, Jonathan; Onel, Yasar; Ozok, Ferhat; Sen, Sercan; Wetzel, James; Yetkin, Taylan; Yi, Kai; Barnett, Bruce Arnold; Blumenfeld, Barry; Bonato, Alessio; Eskew, Christopher; Fehling, David; Giurgiu, Gavril; Gritsan, Andrei; Guo, Zijin; Hu, Guofan; Maksimovic, Petar; Rappoccio, Salvatore; Swartz, Morris; Tran, Nhan Viet; Whitbeck, Andrew; Baringer, Philip; Bean, Alice; Benelli, Gabriele; Grachov, Oleg; Kenny Iii, Raymond Patrick; Murray, Michael; Noonan, Daniel; Sanders, Stephen; Stringer, Robert; Wood, Jeffrey Scott; Zhukova, Victoria; Barfuss, Anne-Fleur; Bolton, Tim; Chakaberia, Irakli; Ivanov, Andrew; Khalil, Sadia; Makouski, Mikhail; Maravin, Yurii; Shrestha, Shruti; Svintradze, Irakli; Gronberg, Jeffrey; Lange, David; Wright, Douglas; Baden, Drew; Boutemeur, Madjid; Eno, Sarah Catherine; Ferencek, Dinko; Gomez, Jaime; Hadley, Nicholas John; Kellogg, Richard G; Kirn, Malina; Lu, Ying; Mignerey, Alice; Rossato, Kenneth; Rumerio, Paolo; Santanastasio, Francesco; Skuja, Andris; Temple, Jeffrey; Tonjes, Marguerite; Tonwar, Suresh C; Twedt, Elizabeth; Alver, Burak; Bauer, Gerry; Bendavid, Joshua; Busza, Wit; Butz, Erik; Cali, Ivan Amos; Chan, Matthew; Dutta, Valentina; Everaerts, Pieter; Gomez Ceballos, Guillelmo; Goncharov, Maxim; Hahn, Kristan Allan; Harris, Philip; Kim, Yongsun; Klute, Markus; Lee, Yen-Jie; Li, Wei; Loizides, Constantinos; Luckey, Paul David; Ma, Teng; Nahn, Steve; Paus, Christoph; Ralph, Duncan; Roland, Christof; Roland, Gunther; Rudolph, Matthew; Stephans, George; Stöckli, Fabian; Sumorok, Konstanty; Sung, Kevin; Velicanu, Dragos; Wenger, Edward Allen; Wolf, Roger; Wyslouch, Bolek; Xie, Si; Yang, Mingming; Yilmaz, Yetkin; Yoon, Sungho; Zanetti, Marco; Cooper, Seth; Cushman, Priscilla; Dahmes, Bryan; De Benedetti, Abraham; Franzoni, Giovanni; Gude, Alexander; Haupt, Jason; Klapoetke, Kevin; Kubota, Yuichi; Mans, Jeremy; Pastika, Nathaniel; Rekovic, Vladimir; Rusack, Roger; Sasseville, Michael; Singovsky, Alexander; Tambe, Norbert; Turkewitz, Jared; Cremaldi, Lucien Marcus; Godang, Romulus; Kroeger, Rob; Perera, Lalith; Rahmat, Rahmat; Sanders, David A; Summers, Don; Bloom, Kenneth; Bose, Suvadeep; Butt, Jamila; Claes, Daniel R; Dominguez, Aaron; Eads, Michael; Jindal, Pratima; Keller, Jason; Kelly, Tony; Kravchenko, Ilya; Lazo-Flores, Jose; Malbouisson, Helena; Malik, Sudhir; Snow, Gregory R; Baur, Ulrich; Godshalk, Andrew; Iashvili, Ia; Jain, Supriya; Kharchilava, Avto; Kumar, Ashish; Smith, Kenneth; Wan, Zongru; Alverson, George; Barberis, Emanuela; Baumgartel, Darin; Boeriu, Oana; Chasco, Matthew; Reucroft, Steve; Swain, John; Trocino, Daniele; Wood, Darien; Zhang, Jinzhong; Anastassov, Anton; Kubik, Andrew; Mucia, Nicholas; Odell, Nathaniel; Ofierzynski, Radoslaw Adrian; Pollack, Brian; Pozdnyakov, Andrey; Schmitt, Michael; Stoynev, Stoyan; Velasco, Mayda; Won, Steven; Antonelli, Louis; Berry, Douglas; Brinkerhoff, Andrew; Hildreth, Michael; Jessop, Colin; Karmgard, Daniel John; Kolb, Jeff; Kolberg, Ted; Lannon, Kevin; Luo, Wuming; Lynch, Sean; Marinelli, Nancy; Morse, David Michael; Pearson, Tessa; Ruchti, Randy; Slaunwhite, Jason; Valls, Nil; Wayne, Mitchell; Ziegler, Jill; Bylsma, Ben; Durkin, Lloyd Stanley; Hill, Christopher; Killewald, Phillip; Kotov, Khristian; Ling, Ta-Yung; Rodenburg, Marissa; Vuosalo, Carl; Williams, Grayson; Adam, Nadia; Berry, Edmund; Elmer, Peter; Gerbaudo, Davide; Halyo, Valerie; Hebda, Philip; Hunt, Adam; Laird, Edward; Lopes Pegna, David; Marlow, Daniel; Medvedeva, Tatiana; Mooney, Michael; Olsen, James; Piroué, Pierre; Quan, Xiaohang; Safdi, Ben; Saka, Halil; Stickland, David; Tully, Christopher; Werner, Jeremy Scott; Zuranski, Andrzej; Acosta, Jhon Gabriel; Huang, Xing Tao; Lopez, Angel; Mendez, Hector; Oliveros, Sandra; Ramirez Vargas, Juan Eduardo; Zatserklyaniy, Andriy; Alagoz, Enver; Barnes, Virgil E; Bolla, Gino; Borrello, Laura; Bortoletto, Daniela; De Mattia, Marco; Everett, Adam; Gutay, Laszlo; Hu, Zhen; Jones, Matthew; Koybasi, Ozhan; Kress, Matthew; Laasanen, Alvin T; Leonardo, Nuno; Maroussov, Vassili; Merkel, Petra; Miller, David Harry; Neumeister, Norbert; Shipsey, Ian; Silvers, David; Svyatkovskiy, Alexey; Vidal Marono, Miguel; Yoo, Hwi Dong; Zablocki, Jakub; Zheng, Yu; Guragain, Samir; Parashar, Neeti; Adair, Antony; Boulahouache, Chaouki; Ecklund, Karl Matthew; Geurts, Frank JM; Padley, Brian Paul; Redjimi, Radia; Roberts, Jay; Zabel, James; Betchart, Burton; Bodek, Arie; Chung, Yeon Sei; Covarelli, Roberto; de Barbaro, Pawel; Demina, Regina; Eshaq, Yossof; Flacher, Henning; Garcia-Bellido, Aran; Goldenzweig, Pablo; Gotra, Yury; Han, Jiyeon; Harel, Amnon; Miner, Daniel Carl; Petrillo, Gianluca; Sakumoto, Willis; Vishnevskiy, Dmitry; Zielinski, Marek; Bhatti, Anwar; Ciesielski, Robert; Demortier, Luc; Goulianos, Konstantin; Lungu, Gheorghe; Malik, Sarah; Mesropian, Christina; Arora, Sanjay; Atramentov, Oleksiy; Barker, Anthony; Contreras-Campana, Christian; Contreras-Campana, Emmanuel; Duggan, Daniel; Gershtein, Yuri; Gray, Richard; Halkiadakis, Eva; Hidas, Dean; Hits, Dmitry; Lath, Amitabh; Panwalkar, Shruti; Park, Michael; Patel, Rishi; Richards, Alan; Rose, Keith; Schnetzer, Steve; Somalwar, Sunil; Stone, Robert; Thomas, Scott; Cerizza, Giordano; Hollingsworth, Matthew; Spanier, Stefan; Yang, Zong-Chang; York, Andrew; Eusebi, Ricardo; Flanagan, Will; Gilmore, Jason; Gurrola, Alfredo; Kamon, Teruki; Khotilovich, Vadim; Montalvo, Roy; Osipenkov, Ilya; Pakhotin, Yuriy; Perloff, Alexx; Roe, Jeffrey; Safonov, Alexei; Sengupta, Sinjini; Suarez, Indara; Tatarinov, Aysen; Toback, David; Akchurin, Nural; Bardak, Cemile; Damgov, Jordan; Dudero, Phillip Russell; Jeong, Chiyoung; Kovitanggoon, Kittikul; Lee, Sung Won; Libeiro, Terence; Mane, Poonam; Roh, Youn; Sill, Alan; Volobouev, Igor; Wigmans, Richard; Yazgan, Efe; Appelt, Eric; Brownson, Eric; Engh, Daniel; Florez, Carlos; Gabella, William; Issah, Michael; Johns, Willard; Johnston, Cody; Kurt, Pelin; Maguire, Charles; Melo, Andrew; Sheldon, Paul; Snook, Benjamin; Tuo, Shengquan; Velkovska, Julia; Arenton, Michael Wayne; Balazs, Michael; Boutle, Sarah; Cox, Bradley; Francis, Brian; Goadhouse, Stephen; Goodell, Joseph; Hirosky, Robert; Ledovskoy, Alexander; Lin, Chuanzhe; Neu, Christopher; Wood, John; Yohay, Rachel; Gollapinni, Sowjanya; Harr, Robert; Karchin, Paul Edmund; Kottachchi Kankanamge Don, Chamath; Lamichhane, Pramod; Mattson, Mark; Milstène, Caroline; Sakharov, Alexandre; Anderson, Michael; Bachtis, Michail; Belknap, Donald; Bellinger, James Nugent; Carlsmith, Duncan; Cepeda, Maria; Dasu, Sridhara; Efron, Jonathan; Friis, Evan; Gray, Lindsey; Grogg, Kira Suzanne; Grothe, Monika; Hall-Wilton, Richard; Herndon, Matthew; Hervé, Alain; Klabbers, Pamela; Klukas, Jeffrey; Lanaro, Armando; Lazaridis, Christos; Leonard, Jessica; Loveless, Richard; Mohapatra, Ajit; Ojalvo, Isabel; Parker, William; Ross, Ian; Savin, Alexander; Smith, Wesley H; Swanson, Joshua; Weinberg, Marc

2012-01-01

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

Reconstructing building mass models from UAV images

KAUST Repository

Li, Minglei; Nan, Liangliang; Smith, Neil; Wonka, Peter

2015-01-01

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

Amplification of an ancestral mammalian L1 family of long interspersed repeated DNA occurred just before the murine radiation

International Nuclear Information System (INIS)

Pascale, E.; Valle, E.; Furano, A.V.

1990-01-01

Each mammalian genus examined so far contains 50,000-100,000 members of an L1 (LINE 1) family of long interspersed repeated DNA elements. Current knowledge on the evolution of L1 families presents a paradox because, although L1 families have been in mammalian genomes since before the mammalian radiation ∼80 million years ago, most members of the L1 families are only a few million years old. Accordingly it has been suggested either that the extensive amplification that characterizes present-day L1 families did not occur in the past or that old members were removed as new one were generated. However, the authors show here that an ancestral rodent L1 family was extensively amplified ∼10 million years ago and that the relics of this amplification have persisted in modern murine genomes. This amplification occurred just before the divergence of modern murine genera from their common ancestor and identifies the murine node in the lineage of modern muroid rodents The results suggest that repeated amplification of L1 elements is a feature of the evaluation of mammalian genomes and that ancestral amplification events could provide a useful tool for determining mammalian lineages

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

DEFF Research Database (Denmark)

Henryon, M; Berg, P; Sørensen, A C

2009-01-01

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

Algebraic reconstruction techniques for spectral reconstruction in diffuse optical tomography

International Nuclear Information System (INIS)

Brendel, Bernhard; Ziegler, Ronny; Nielsen, Tim

2008-01-01

Reconstruction in diffuse optical tomography (DOT) necessitates solving the diffusion equation, which is nonlinear with respect to the parameters that have to be reconstructed. Currently applied solving methods are based on the linearization of the equation. For spectral three-dimensional reconstruction, the emerging equation system is too large for direct inversion, but the application of iterative methods is feasible. Computational effort and speed of convergence of these iterative methods are crucial since they determine the computation time of the reconstruction. In this paper, the iterative methods algebraic reconstruction technique (ART) and conjugated gradients (CGs) as well as a new modified ART method are investigated for spectral DOT reconstruction. The aim of the modified ART scheme is to speed up the convergence by considering the specific conditions of spectral reconstruction. As a result, it converges much faster to favorable results than conventional ART and CG methods

Reconstruction after complex facial trauma: achieving optimal outcome through multiple contemporary surgeries.

Science.gov (United States)

Jaiswal, Rohit; Pu, Lee L Q

2013-04-01

Major facial trauma injuries often require complex repair. Traditionally, the reconstruction of such injuries has primarily utilized only free tissue transfer. However, the advent of newer, contemporary procedures may lead to potential reconstructive improvement through the use of complementary procedures after free flap reconstruction. An 18-year-old male patient suffered a major left facial degloving injury resulting in soft-tissue defect with exposed zygoma, and parietal bone. Multiple operations were undertaken in a staged manner for reconstruction. A state-of-the-art free anterolateral thigh (ALT) perforator flap and Medpor implant reconstruction of the midface were initially performed, followed by flap debulking, lateral canthopexy, midface lift with redo canthopexy, scalp tissue expansion for hairline reconstruction, and epidermal skin grafting for optimal skin color matching. Over a follow-up period of 2 years, a good and impressive reconstructive result was achieved through the use of multiple contemporary reconstructive procedures following an excellent free ALT flap reconstruction. Multiple staged reconstructions are essential in producing an optimal outcome in this complex facial injury that would likely not have been produced through a 1-stage traditional free flap reconstruction. Utilizing multiple, sequential contemporary surgeries may substantially improve outcome through the enhancement and refinement of results based on possibly the best initial soft-tissue reconstruction.

Sparse BLIP: BLind Iterative Parallel imaging reconstruction using compressed sensing.

Science.gov (United States)

She, Huajun; Chen, Rong-Rong; Liang, Dong; DiBella, Edward V R; Ying, Leslie

2014-02-01

To develop a sensitivity-based parallel imaging reconstruction method to reconstruct iteratively both the coil sensitivities and MR image simultaneously based on their prior information. Parallel magnetic resonance imaging reconstruction problem can be formulated as a multichannel sampling problem where solutions are sought analytically. However, the channel functions given by the coil sensitivities in parallel imaging are not known exactly and the estimation error usually leads to artifacts. In this study, we propose a new reconstruction algorithm, termed Sparse BLind Iterative Parallel, for blind iterative parallel imaging reconstruction using compressed sensing. The proposed algorithm reconstructs both the sensitivity functions and the image simultaneously from undersampled data. It enforces the sparseness constraint in the image as done in compressed sensing, but is different from compressed sensing in that the sensing matrix is unknown and additional constraint is enforced on the sensitivities as well. Both phantom and in vivo imaging experiments were carried out with retrospective undersampling to evaluate the performance of the proposed method. Experiments show improvement in Sparse BLind Iterative Parallel reconstruction when compared with Sparse SENSE, JSENSE, IRGN-TV, and L1-SPIRiT reconstructions with the same number of measurements. The proposed Sparse BLind Iterative Parallel algorithm reduces the reconstruction errors when compared to the state-of-the-art parallel imaging methods. Copyright © 2013 Wiley Periodicals, Inc.

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

International Nuclear Information System (INIS)

Hofmann, Christian; Sawall, Stefan; Knaup, Michael; Kachelrieß, Marc

2014-01-01

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

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

MR fingerprinting reconstruction with Kalman filter.

Science.gov (United States)

Zhang, Xiaodi; Zhou, Zechen; Chen, Shiyang; Chen, Shuo; Li, Rui; Hu, Xiaoping

2017-09-01

Magnetic resonance fingerprinting (MR fingerprinting or MRF) is a newly introduced quantitative magnetic resonance imaging technique, which enables simultaneous multi-parameter mapping in a single acquisition with improved time efficiency. The current MRF reconstruction method is based on dictionary matching, which may be limited by the discrete and finite nature of the dictionary and the computational cost associated with dictionary construction, storage and matching. In this paper, we describe a reconstruction method based on Kalman filter for MRF, which avoids the use of dictionary to obtain continuous MR parameter measurements. With this Kalman filter framework, the Bloch equation of inversion-recovery balanced steady state free-precession (IR-bSSFP) MRF sequence was derived to predict signal evolution, and acquired signal was entered to update the prediction. The algorithm can gradually estimate the accurate MR parameters during the recursive calculation. Single pixel and numeric brain phantom simulation were implemented with Kalman filter and the results were compared with those from dictionary matching reconstruction algorithm to demonstrate the feasibility and assess the performance of Kalman filter algorithm. The results demonstrated that Kalman filter algorithm is applicable for MRF reconstruction, eliminating the need for a pre-define dictionary and obtaining continuous MR parameter in contrast to the dictionary matching algorithm. Copyright © 2017 Elsevier Inc. All rights reserved.

New method for initial density reconstruction

Science.gov (United States)

Shi, Yanlong; Cautun, Marius; Li, Baojiu

2018-01-01

A theoretically interesting and practically important question in cosmology is the reconstruction of the initial density distribution provided a late-time density field. This is a long-standing question with a revived interest recently, especially in the context of optimally extracting the baryonic acoustic oscillation (BAO) signals from observed galaxy distributions. We present a new efficient method to carry out this reconstruction, which is based on numerical solutions to the nonlinear partial differential equation that governs the mapping between the initial Lagrangian and final Eulerian coordinates of particles in evolved density fields. This is motivated by numerical simulations of the quartic Galileon gravity model, which has similar equations that can be solved effectively by multigrid Gauss-Seidel relaxation. The method is based on mass conservation, and does not assume any specific cosmological model. Our test shows that it has a performance comparable to that of state-of-the-art algorithms that were very recently put forward in the literature, with the reconstructed density field over ˜80 % (50%) correlated with the initial condition at k ≲0.6 h /Mpc (1.0 h /Mpc ). With an example, we demonstrate that this method can significantly improve the accuracy of BAO reconstruction.

Direct reconstruction of dark energy.

Science.gov (United States)

Clarkson, Chris; Zunckel, Caroline

2010-05-28

An important issue in cosmology is reconstructing the effective dark energy equation of state directly from observations. With so few physically motivated models, future dark energy studies cannot only be based on constraining a dark energy parameter space. We present a new nonparametric method which can accurately reconstruct a wide variety of dark energy behavior with no prior assumptions about it. It is simple, quick and relatively accurate, and involves no expensive explorations of parameter space. The technique uses principal component analysis and a combination of information criteria to identify real features in the data, and tailors the fitting functions to pick up trends and smooth over noise. We find that we can constrain a large variety of w(z) models to within 10%-20% at redshifts z≲1 using just SNAP-quality data.

Reconciling phylogeography and ecological niche models for New Zealand beetles looking beyond glacial refugia

DEFF Research Database (Denmark)

Marske, Katharine Ann; Leschen, Richard; Buckley, Thomas

2011-01-01

stochastic search variable selection incorporated in BEAST to identify historical dispersal patterns via ancestral state reconstruction. Ecological niche models (ENMs) were incorporated to reconstruct the potential geographic distribution of each species during the Last Glacial Maximum (LGM). Coalescent...... analyses suggest a North Island origin for E. lawsoni, with gene flow predominately north–south between adjacent regions. ENMs for E. lawsoni indicated glacial refugia in coastal regions of both main islands, consistent with phylogenetic patterns but at odds with the coalescent dates, which implicate much...... on both main islands is evident. Divergence dates for both species are consistent with the topographic evolution of New Zealand over the last 10 Ma, whereas the signature of the LGM is less apparent in the time-scaled phylogeny....

A Review of Sex Determining Mechanisms in Geckos (Gekkota: Squamata)

Science.gov (United States)

Gamble, T.

2010-01-01

Geckos are a species-rich clade of reptiles possessing diverse sex determining mechanisms. Some species possess genetic sex determination, with both male and female heterogamety, while other species have temperature-dependent sex determination. I compiled information from the literature on the taxonomic distribution of these sex determining mechanisms in geckos. Using phylogenetic data from the literature, I reconstructed the minimum number of transitions among these sex determining mechanisms with parsimony-based ancestral state reconstruction. While only a small number of gecko species have been characterized, numerous changes among sex determining mechanisms were inferred. This diversity, coupled with the high frequency of transitions, makes geckos excellent candidates as a model clade for the study of vertebrate sex determination and evolution. PMID:20234154

Serotonin-immunoreactivity in the ventral nerve cord of Pycnogonida--support for individually identifiable neurons as ancestral feature of the arthropod nervous system.

Science.gov (United States)

Brenneis, Georg; Scholtz, Gerhard

2015-07-10

The arthropod ventral nerve cord features a comparably low number of serotonin-immunoreactive neurons, occurring in segmentally repeated arrays. In different crustaceans and hexapods, these neurons have been individually identified and even inter-specifically homologized, based on their soma positions and neurite morphologies. Stereotypic sets of serotonin-immunoreactive neurons are also present in myriapods, whereas in the investigated chelicerates segmental neuron clusters with higher and variable cell numbers have been reported. This led to the suggestion that individually identifiable serotonin-immunoreactive neurons are an apomorphic feature of the Mandibulata. To test the validity of this neurophylogenetic hypothesis, we studied serotonin-immunoreactivity in three species of Pycnogonida (sea spiders). This group of marine arthropods is nowadays most plausibly resolved as sister group to all other extant chelicerates, rendering its investigation crucial for a reliable reconstruction of arthropod nervous system evolution. In all three investigated pycnogonids, the ventral walking leg ganglia contain different types of serotonin-immunoreactive neurons, the somata of which occurring mostly singly or in pairs within the ganglionic cortex. Several of these neurons are readily and consistently identifiable due to their stereotypic soma position and characteristic neurite morphology. They can be clearly homologized across different ganglia and different specimens as well as across the three species. Based on these homologous neurons, we reconstruct for their last common ancestor (presumably the pycnogonid stem species) a minimal repertoire of at least seven identified serotonin-immunoreactive neurons per hemiganglion. Beyond that, each studied species features specific pattern variations, which include also some neurons that were not reliably labeled in all specimens. Our results unequivocally demonstrate the presence of individually identifiable serotonin

Molecular reconstruction of extinct LINE-1 elements and their interaction with nonautonomous elements.

Science.gov (United States)

Wagstaff, Bradley J; Kroutter, Emily N; Derbes, Rebecca S; Belancio, Victoria P; Roy-Engel, Astrid M

2013-01-01

Non-long terminal repeat retroelements continue to impact the human genome through cis-activity of long interspersed element-1 (LINE-1 or L1) and trans-mobilization of Alu. Current activity is dominated by modern subfamilies of these elements, leaving behind an evolutionary graveyard of extinct Alu and L1 subfamilies. Because Alu is a nonautonomous element that relies on L1 to retrotranspose, there is the possibility that competition between these elements has driven selection and antagonistic coevolution between Alu and L1. Through analysis of synonymous versus nonsynonymous codon evolution across L1 subfamilies, we find that the C-terminal ORF2 cys domain experienced a dramatic increase in amino acid substitution rate in the transition from L1PA5 to L1PA4 subfamilies. This observation coincides with the previously reported rapid evolution of ORF1 during the same transition period. Ancestral Alu sequences have been previously reconstructed, as their short size and ubiquity have made it relatively easy to retrieve consensus sequences from the human genome. In contrast, creating constructs of extinct L1 copies is a more laborious task. Here, we report our efforts to recreate and evaluate the retrotransposition capabilities of two ancestral L1 elements, L1PA4 and L1PA8 that were active ~18 and ~40 Ma, respectively. Relative to the modern L1PA1 subfamily, we find that both elements are similarly active in a cell culture retrotransposition assay in HeLa, and both are able to efficiently trans-mobilize Alu elements from several subfamilies. Although we observe some variation in Alu subfamily retrotransposition efficiency, any coevolution that may have occurred between LINEs and SINEs is not evident from these data. Population dynamics and stochastic variation in the number of active source elements likely play an important role in individual LINE or SINE subfamily amplification. If coevolution also contributes to changing retrotransposition rates and the progression of

Did warfare among ancestral hunter-gatherers affect the evolution of human social behaviors?

Science.gov (United States)

Bowles, Samuel

2009-06-05

Since Darwin, intergroup hostilities have figured prominently in explanations of the evolution of human social behavior. Yet whether ancestral humans were largely "peaceful" or "warlike" remains controversial. I ask a more precise question: If more cooperative groups were more likely to prevail in conflicts with other groups, was the level of intergroup violence sufficient to influence the evolution of human social behavior? Using a model of the evolutionary impact of between-group competition and a new data set that combines archaeological evidence on causes of death during the Late Pleistocene and early Holocene with ethnographic and historical reports on hunter-gatherer populations, I find that the estimated level of mortality in intergroup conflicts would have had substantial effects, allowing the proliferation of group-beneficial behaviors that were quite costly to the individual altruist.

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.

Bessel Fourier orientation reconstruction: an analytical EAP reconstruction using multiple shell acquisitions in diffusion MRI.

Science.gov (United States)

Hosseinbor, Ameer Pasha; Chung, Moo K; Wu, Yu-Chien; Alexander, Andrew L

2011-01-01

The estimation of the ensemble average propagator (EAP) directly from q-space DWI signals is an open problem in diffusion MRI. Diffusion spectrum imaging (DSI) is one common technique to compute the EAP directly from the diffusion signal, but it is burdened by the large sampling required. Recently, several analytical EAP reconstruction schemes for multiple q-shell acquisitions have been proposed. One, in particular, is Diffusion Propagator Imaging (DPI) which is based on the Laplace's equation estimation of diffusion signal for each shell acquisition. Viewed intuitively in terms of the heat equation, the DPI solution is obtained when the heat distribution between temperatuere measurements at each shell is at steady state. We propose a generalized extension of DPI, Bessel Fourier Orientation Reconstruction (BFOR), whose solution is based on heat equation estimation of the diffusion signal for each shell acquisition. That is, the heat distribution between shell measurements is no longer at steady state. In addition to being analytical, the BFOR solution also includes an intrinsic exponential smootheing term. We illustrate the effectiveness of the proposed method by showing results on both synthetic and real MR datasets.

Archaeology of the Afro-Ecuadorians in La Concepción, Ancestral Territory of the Chota-Mira Valley (Carchi-Ecuador)

OpenAIRE

Balanzategui , Daniela Catalina

2017-01-01

Historical Archaeology of the African Diaspora in the Americas urges for interdisciplinary, collaborative, and intercultural approaches to shed light on how the material culture reflects conditions of enslavement and racialization, but also process of resistance and historical reparation. This investigation is organized in five articles connected around the topic of the cultural construction of the African Diaspora identities in the Afro-Ecuadorian Ancestral Territory of the Chota-Mira Valley...

European bank for reconstruction and development

Directory of Open Access Journals (Sweden)

Kastratović Radovan

2015-01-01

Full Text Available European Bank for Reconstruction and Development - EBRD was established in the year 1991 and commenced operations in 1991. The objective of the Bank was to instigate market oriented approach to business in the countries of Central and Eastern Europe. This comprises support offered to structural reforms, privatisation, and development of entrepreneurship and legal system through financing of project conducive to the achievement of the aimed targets. The Bank approves loans both to the nation states and to the private sector. European Bank for Reconstruction and Development often appears in the role of investor. In addition, the Bank has also its consultative function. Owners of the European Bank for Reconstruction and Development are the developed countries and those that participate in the distribution of the Bank's profit. The Bank invests in the countries of Central, Eastern and South-East Europe, but also in those of Central Asia and Southern Mediterranean. The importance that the European Bank for Reconstruction and Development has for our country is best illustrated by the fact that this Bank is our largest institutional investor, with investments exceeding 3.5 billion EUR. This work begins with presentation of general information on the work of the European Bank for Reconstruction and Development, its objectives, activities, background history, ownership and organisational structure. It proceeds by giving relevant data on the Bank's business operations - the manner of project financing, the Bank's funds distribution per geographic criteria and activities, and the operative and financial results of the Bank's business activities. Brief description is also offered of the cooperation that the European Bank has with other international financial institutions. Finally, data is given bearing witness on the importance that the European Bank for Reconstruction and Development has for Serbia.

Escaping social-ecological traps through tribal stewardship on national forest lands in the Pacific Northwest, United States of America

Science.gov (United States)

Jonathan W. Long; Frank K. Lake

2018-01-01

Tribal communities in the Pacific Northwest of the United States of America (USA) have long-standing relationships to ancestral lands now managed by federal land management agencies. In recent decades, federal and state governments have increasingly recognized tribal rights to resources on public lands and to participate in their management. In support of a new...

Antiplasmodial activity is an ancient and conserved feature of tick defensins

Directory of Open Access Journals (Sweden)

Alejandro Cabezas-Cruz

2016-10-01

Full Text Available Ancestral sequence reconstruction has been widely used to test evolution-based hypotheses. The genome of the European tick vector, Ixodes ricinus, encodes for defensin peptides with diverse antimicrobial activities against distantly related pathogens. These pathogens include fungi, Gram-negative and Gram-positive bacteria, i.e., a wide antimicrobial spectrum. Ticks do not transmit these pathogens, suggesting that these defensins may act against a wide range of microbes encountered by ticks during blood feeding or off-host periods. As demonstrated here, these I. ricinus defensins are also effective against the apicomplexan parasite Plasmodium falciparum. To study the general evolution of antimicrobial activity in tick defensins, the ancestral amino acid sequence of chelicerate defensins, which existed approximately 444 million years ago, was reconstructed using publicly available scorpion and tick defensin sequences (named Scorpions-Ticks Defensins Ancestor, STiDA. The activity of STiDA was tested against P. falciparum and the same Gram-negative and Gram-positive bacteria that were used for the I. ricinus defensins. While some extant tick defensins exhibit a wide antimicrobial spectrum, the ancestral defensin showed moderate activity against one of the tested microbes, P. falciparum. This study suggests that amino acid variability and defensin family expansion increased the antimicrobial spectrum of ancestral tick defensins.

Latest Miocene-earliest Pliocene evolution of the ancestral Rio Grande at the Española-San Luis Basin boundary, northern New Mexico

Science.gov (United States)

Daniel J. Koning,; Aby, Scott B.; Grauch, V. J.; Matthew J. Zimmerer,

2016-01-01

We use stratigraphic relations, paleoflow data, and 40Ar/39Ar dating to interpret net aggradation, punctuated by at least two minor incisional events, along part of the upper ancestral Rio Grande fluvial system between 5.5 and 4.5 Ma (in northern New Mexico). The studied fluvial deposits, which we informally call the Sandlin unit of the Santa Fe Group, overlie a structural high between the San Luis and Española Basins. The Sandlin unit was deposited by two merging, west- to southwest-flowing, ancestral Rio Grande tributaries respectively sourced in the central Taos Mountains and southern Taos Mountains-northeastern Picuris Mountains. The river confluence progressively shifted southwestward (downstream) with time, and the integrated river (ancestral Rio Grande) flowed southwards into the Española Basin to merge with the ancestral Rio Chama. Just prior to the end of the Miocene, this fluvial system was incised in the southern part of the study area (resulting in an approximately 4–7 km wide paleovalley), and had sufficient competency to transport cobbles and boulders. Sometime between emplacement of two basalt flows dated at 5.54± 0.38 Ma and 4.82±0.20 Ma (groundmass 40Ar/39Ar ages), this fluvial system deposited 10–12 m of sandier sediment (lower Sandlin subunit) preserved in the northern part of this paleovalley. The fluvial system widened between 4.82±0.20 and 4.50±0.07 Ma, depositing coarse sand and fine gravel up to 14 km north of the present-day Rio Grande. This 10–25 m-thick sediment package (upper Sandlin unit) buried earlier south- to southeast-trending paleovalleys (500–800 m wide) inferred from aeromagnetic data. Two brief incisional events are recognized. The first was caused by the 4.82±0.20 Ma basalt flow impounding south-flowing paleodrainages, and the second occurred shortly after emplacement of a 4.69±0.09 Ma basalt flow in the northern study area. Drivers responsible for Sandlin unit aggradation may include climate

Recently evolved diversity and convergent radiations of rainforest mahoganies (Meliaceae) shed new light on the origins of rainforest hyperdiversity.

Science.gov (United States)

Koenen, Erik J M; Clarkson, James J; Pennington, Terence D; Chatrou, Lars W

2015-07-01

Tropical rainforest hyperdiversity is often suggested to have evolved over a long time-span (the 'museum' model), but there is also evidence for recent rainforest radiations. The mahoganies (Meliaceae) are a prominent plant group in lowland tropical rainforests world-wide but also occur in all other tropical ecosystems. We investigated whether rainforest diversity in Meliaceae has accumulated over a long time or has more recently evolved. We inferred the largest time-calibrated phylogeny for the family to date, reconstructed ancestral states for habitat and deciduousness, estimated diversification rates and modeled potential shifts in macro-evolutionary processes using a recently developed Bayesian method. The ancestral Meliaceae is reconstructed as a deciduous species that inhabited seasonal habitats. Rainforest clades have diversified from the Late Oligocene or Early Miocene onwards. Two contemporaneous Amazonian clades have converged on similar ecologies and high speciation rates. Most species-level diversity of Meliaceae in rainforest is recent. Other studies have found steady accumulation of lineages, but the large majority of plant species diversity in rainforests is recent, suggesting (episodic) species turnover. Rainforest hyperdiversity may best be explained by recent radiations from a large stock of higher level taxa. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

Performance of τq-lepton reconstruction and identification in CMS

Energy Technology Data Exchange (ETDEWEB)

Chatrchyan, Serguei; et al.

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.

The generalized back projection theorem for cone beam reconstruction

International Nuclear Information System (INIS)

Peyrin, F.C.

1985-01-01

The use of cone beam scanners raises the problem of three dimensional reconstruction from divergent projections. After a survey on bidimensional analytical reconstruction methods we examine their application to the 3D problem. Finally, it is shown that the back projection theorem can be generalized to cone beam projections. This allows to state a new inversion formula suitable for both the 4 π parallel and divergent geometries. It leads to the generalization of the ''rho-filtered back projection'' algorithm which is outlined

Validation of Magnetic Reconstruction Codes for Real-Time Applications

International Nuclear Information System (INIS)

Mazon, D.; Murari, A.; Boulbe, C.; Faugeras, B.; Blum, J.; Svensson, J.; Quilichini, T.; Gelfusa, M.

2010-01-01

The real-time reconstruction of the plasma magnetic equilibrium in a tokamak is a key point to access high-performance regimes. Indeed, the shape of the plasma current density profile is a direct output of the reconstruction and has a leading effect for reaching a steady-state high-performance regime of operation. The challenge is thus to develop real-time methods and algorithms that reconstruct the magnetic equilibrium from the perspective of using these outputs for feedback control purposes. In this paper the validation of the JET real-time equilibrium reconstruction codes using both a Bayesian approach and a full equilibrium solver named Equinox will be detailed, the comparison being performed with the off-line equilibrium code EFIT (equilibrium fitting) or the real-time boundary reconstruction code XLOC (X-point local expansion). In this way a significant database, a methodology, and a strategy for the validation are presented. The validation of the results has been performed using a validated database of 130 JET discharges with a large variety of magnetic configurations. Internal measurements like polarimetry and motional Stark effect have been also used for the Equinox validation including some magnetohydrodynamic signatures for the assessment of the reconstructed safety profile and current density. (authors)

MADS goes genomic in conifers: towards determining the ancestral set of MADS-box genes in seed plants.

Science.gov (United States)

Gramzow, Lydia; Weilandt, Lisa; Theißen, Günter

2014-11-01

MADS-box genes comprise a gene family coding for transcription factors. This gene family expanded greatly during land plant evolution such that the number of MADS-box genes ranges from one or two in green algae to around 100 in angiosperms. Given the crucial functions of MADS-box genes for nearly all aspects of plant development, the expansion of this gene family probably contributed to the increasing complexity of plants. However, the expansion of MADS-box genes during one important step of land plant evolution, namely the origin of seed plants, remains poorly understood due to the previous lack of whole-genome data for gymnosperms. The newly available genome sequences of Picea abies, Picea glauca and Pinus taeda were used to identify the complete set of MADS-box genes in these conifers. In addition, MADS-box genes were identified in the growing number of transcriptomes available for gymnosperms. With these datasets, phylogenies were constructed to determine the ancestral set of MADS-box genes of seed plants and to infer the ancestral functions of these genes. Type I MADS-box genes are under-represented in gymnosperms and only a minimum of two Type I MADS-box genes have been present in the most recent common ancestor (MRCA) of seed plants. In contrast, a large number of Type II MADS-box genes were found in gymnosperms. The MRCA of extant seed plants probably possessed at least 11-14 Type II MADS-box genes. In gymnosperms two duplications of Type II MADS-box genes were found, such that the MRCA of extant gymnosperms had at least 14-16 Type II MADS-box genes. The implied ancestral set of MADS-box genes for seed plants shows simplicity for Type I MADS-box genes and remarkable complexity for Type II MADS-box genes in terms of phylogeny and putative functions. The analysis of transcriptome data reveals that gymnosperm MADS-box genes are expressed in a great variety of tissues, indicating diverse roles of MADS-box genes for the development of gymnosperms. This study is

Reconstruction of initial pressure from limited view photoacoustic images using deep learning

Science.gov (United States)

Waibel, Dominik; Gröhl, Janek; Isensee, Fabian; Kirchner, Thomas; Maier-Hein, Klaus; Maier-Hein, Lena

2018-02-01

Quantification of tissue properties with photoacoustic (PA) imaging typically requires a highly accurate representation of the initial pressure distribution in tissue. Almost all PA scanners reconstruct the PA image only from a partial scan of the emitted sound waves. Especially handheld devices, which have become increasingly popular due to their versatility and ease of use, only provide limited view data because of their geometry. Owing to such limitations in hardware as well as to the acoustic attenuation in tissue, state-of-the-art reconstruction methods deliver only approximations of the initial pressure distribution. To overcome the limited view problem, we present a machine learning-based approach to the reconstruction of initial pressure from limited view PA data. Our method involves a fully convolutional deep neural network based on a U-Net-like architecture with pixel-wise regression loss on the acquired PA images. It is trained and validated on in silico data generated with Monte Carlo simulations. In an initial study we found an increase in accuracy over the state-of-the-art when reconstructing simulated linear-array scans of blood vessels.

Graph-cut based discrete-valued image reconstruction.

Science.gov (United States)

Tuysuzoglu, Ahmet; Karl, W Clem; Stojanovic, Ivana; Castañòn, David; Ünlü, M Selim

2015-05-01

Efficient graph-cut methods have been used with great success for labeling and denoising problems occurring in computer vision. Unfortunately, the presence of linear image mappings has prevented the use of these techniques in most discrete-amplitude image reconstruction problems. In this paper, we develop a graph-cut based framework for the direct solution of discrete amplitude linear image reconstruction problems cast as regularized energy function minimizations. We first analyze the structure of discrete linear inverse problem cost functions to show that the obstacle to the application of graph-cut methods to their solution is the variable mixing caused by the presence of the linear sensing operator. We then propose to use a surrogate energy functional that overcomes the challenges imposed by the sensing operator yet can be utilized efficiently in existing graph-cut frameworks. We use this surrogate energy functional to devise a monotonic iterative algorithm for the solution of discrete valued inverse problems. We first provide experiments using local convolutional operators and show the robustness of the proposed technique to noise and stability to changes in regularization parameter. Then we focus on nonlocal, tomographic examples where we consider limited-angle data problems. We compare our technique with state-of-the-art discrete and continuous image reconstruction techniques. Experiments show that the proposed method outperforms state-of-the-art techniques in challenging scenarios involving discrete valued unknowns.

Manhattan-World Urban Reconstruction from Point Clouds

KAUST Repository

Li, Minglei; Wonka, Peter; Nan, Liangliang

2016-01-01

Manhattan-world urban scenes are common in the real world. We propose a fully automatic approach for reconstructing such scenes from 3D point samples. Our key idea is to represent the geometry of the buildings in the scene using a set of well-aligned boxes. We first extract plane hypothesis from the points followed by an iterative refinement step. Then, candidate boxes are obtained by partitioning the space of the point cloud into a non-uniform grid. After that, we choose an optimal subset of the candidate boxes to approximate the geometry of the buildings. The contribution of our work is that we transform scene reconstruction into a labeling problem that is solved based on a novel Markov Random Field formulation. Unlike previous methods designed for particular types of input point clouds, our method can obtain faithful reconstructions from a variety of data sources. Experiments demonstrate that our method is superior to state-of-the-art methods. © Springer International Publishing AG 2016.

Manhattan-World Urban Reconstruction from Point Clouds

KAUST Repository

Li, Minglei

2016-09-16

Manhattan-world urban scenes are common in the real world. We propose a fully automatic approach for reconstructing such scenes from 3D point samples. Our key idea is to represent the geometry of the buildings in the scene using a set of well-aligned boxes. We first extract plane hypothesis from the points followed by an iterative refinement step. Then, candidate boxes are obtained by partitioning the space of the point cloud into a non-uniform grid. After that, we choose an optimal subset of the candidate boxes to approximate the geometry of the buildings. The contribution of our work is that we transform scene reconstruction into a labeling problem that is solved based on a novel Markov Random Field formulation. Unlike previous methods designed for particular types of input point clouds, our method can obtain faithful reconstructions from a variety of data sources. Experiments demonstrate that our method is superior to state-of-the-art methods. © Springer International Publishing AG 2016.

Breast reconstruction after mastectomy

Directory of Open Access Journals (Sweden)

Daniel eSchmauss

2016-01-01

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

Breast reconstruction - implants

Science.gov (United States)

Breast implants surgery; Mastectomy - breast reconstruction with implants; Breast cancer - breast reconstruction with implants ... harder to find a tumor if your breast cancer comes back. Getting breast implants does not take as long as breast reconstruction ...

A Linear Dynamical Systems Approach to Streamflow Reconstruction Reveals History of Regime Shifts in Northern Thailand

Science.gov (United States)

Nguyen, Hung T. T.; Galelli, Stefano

2018-03-01

Catchment dynamics is not often modeled in streamflow reconstruction studies; yet, the streamflow generation process depends on both catchment state and climatic inputs. To explicitly account for this interaction, we contribute a linear dynamic model, in which streamflow is a function of both catchment state (i.e., wet/dry) and paleoclimatic proxies. The model is learned using a novel variant of the Expectation-Maximization algorithm, and it is used with a paleo drought record—the Monsoon Asia Drought Atlas—to reconstruct 406 years of streamflow for the Ping River (northern Thailand). Results for the instrumental period show that the dynamic model has higher accuracy than conventional linear regression; all performance scores improve by 45-497%. Furthermore, the reconstructed trajectory of the state variable provides valuable insights about the catchment history—e.g., regime-like behavior—thereby complementing the information contained in the reconstructed streamflow time series. The proposed technique can replace linear regression, since it only requires information on streamflow and climatic proxies (e.g., tree-rings, drought indices); furthermore, it is capable of readily generating stochastic streamflow replicates. With a marginal increase in computational requirements, the dynamic model brings more desirable features and value to streamflow reconstructions.

Gene duplication and the evolution of hemoglobin isoform differentiation in birds.

Science.gov (United States)

Grispo, Michael T; Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Moriyama, Hideaki; Weber, Roy E; Storz, Jay F

2012-11-02

The majority of bird species co-express two functionally distinct hemoglobin (Hb) isoforms in definitive erythrocytes as follows: HbA (the major adult Hb isoform, with α-chain subunits encoded by the α(A)-globin gene) and HbD (the minor adult Hb isoform, with α-chain subunits encoded by the α(D)-globin gene). The α(D)-globin gene originated via tandem duplication of an embryonic α-like globin gene in the stem lineage of tetrapod vertebrates, which suggests the possibility that functional differentiation between the HbA and HbD isoforms may be attributable to a retained ancestral character state in HbD that harkens back to a primordial, embryonic function. To investigate this possibility, we conducted a combined analysis of protein biochemistry and sequence evolution to characterize the structural and functional basis of Hb isoform differentiation in birds. Functional experiments involving purified HbA and HbD isoforms from 11 different bird species revealed that HbD is characterized by a consistently higher O(2) affinity in the presence of allosteric effectors such as organic phosphates and Cl(-) ions. In the case of both HbA and HbD, analyses of oxygenation properties under the two-state Monod-Wyman-Changeux allosteric model revealed that the pH dependence of Hb-O(2) affinity stems primarily from changes in the O(2) association constant of deoxy (T-state)-Hb. Ancestral sequence reconstructions revealed that the amino acid substitutions that distinguish the adult-expressed Hb isoforms are not attributable to the retention of an ancestral (pre-duplication) character state in the α(D)-globin gene that is shared with the embryonic α-like globin gene.

Gene Duplication and the Evolution of Hemoglobin Isoform Differentiation in Birds*

Science.gov (United States)

Grispo, Michael T.; Natarajan, Chandrasekhar; Projecto-Garcia, Joana; Moriyama, Hideaki; Weber, Roy E.; Storz, Jay F.

2012-01-01

The majority of bird species co-express two functionally distinct hemoglobin (Hb) isoforms in definitive erythrocytes as follows: HbA (the major adult Hb isoform, with α-chain subunits encoded by the αA-globin gene) and HbD (the minor adult Hb isoform, with α-chain subunits encoded by the αD-globin gene). The αD-globin gene originated via tandem duplication of an embryonic α-like globin gene in the stem lineage of tetrapod vertebrates, which suggests the possibility that functional differentiation between the HbA and HbD isoforms may be attributable to a retained ancestral character state in HbD that harkens back to a primordial, embryonic function. To investigate this possibility, we conducted a combined analysis of protein biochemistry and sequence evolution to characterize the structural and functional basis of Hb isoform differentiation in birds. Functional experiments involving purified HbA and HbD isoforms from 11 different bird species revealed that HbD is characterized by a consistently higher O2 affinity in the presence of allosteric effectors such as organic phosphates and Cl− ions. In the case of both HbA and HbD, analyses of oxygenation properties under the two-state Monod-Wyman-Changeux allosteric model revealed that the pH dependence of Hb-O2 affinity stems primarily from changes in the O2 association constant of deoxy (T-state)-Hb. Ancestral sequence reconstructions revealed that the amino acid substitutions that distinguish the adult-expressed Hb isoforms are not attributable to the retention of an ancestral (pre-duplication) character state in the αD-globin gene that is shared with the embryonic α-like globin gene. PMID:22962007

Adaptive algebraic reconstruction technique

International Nuclear Information System (INIS)

Lu Wenkai; Yin Fangfang

2004-01-01

Algebraic reconstruction techniques (ART) are iterative procedures for reconstructing objects from their projections. It is proven that ART can be computationally efficient by carefully arranging the order in which the collected data are accessed during the reconstruction procedure and adaptively adjusting the relaxation parameters. In this paper, an adaptive algebraic reconstruction technique (AART), which adopts the same projection access scheme in multilevel scheme algebraic reconstruction technique (MLS-ART), is proposed. By introducing adaptive adjustment of the relaxation parameters during the reconstruction procedure, one-iteration AART can produce reconstructions with better quality, in comparison with one-iteration MLS-ART. Furthermore, AART outperforms MLS-ART with improved computational efficiency

Loop Replacement Enhances the Ancestral Antibacterial Function of a Bifunctional Scorpion Toxin

Directory of Open Access Journals (Sweden)

Shangfei Zhang

2018-06-01

Full Text Available On the basis of the evolutionary relationship between scorpion toxins targeting K+ channels (KTxs and antibacterial defensins (Zhu S., Peigneur S., Gao B., Umetsu Y., Ohki S., Tytgat J. Experimental conversion of a defensin into a neurotoxin: Implications for origin of toxic function. Mol. Biol. Evol. 2014, 31, 546–559, we performed protein engineering experiments to modify a bifunctional KTx (i.e., weak inhibitory activities on both K+ channels and bacteria via substituting its carboxyl loop with the structurally equivalent loop of contemporary defensins. As expected, the engineered peptide (named MeuTXKα3-KFGGI remarkably improved the antibacterial activity, particularly on some Gram-positive bacteria, including several antibiotic-resistant opportunistic pathogens. Compared with the unmodified toxin, its antibacterial spectrum also enlarged. Our work provides a new method to enhance the antibacterial activity of bifunctional scorpion venom peptides, which might be useful in engineering other proteins with an ancestral activity.

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

Energy Technology Data Exchange (ETDEWEB)

Randriamalala, Tsitohaina

2012-04-19

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

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.

A Qualitative Study of Breast Reconstruction Decision-Making among Asian Immigrant Women Living in the United States.

Science.gov (United States)

Fu, Rose; Chang, Michelle Milee; Chen, Margaret; Rohde, Christine Hsu

2017-02-01

Despite research supporting improved psychosocial well-being, quality of life, and survival for patients undergoing postmastectomy breast reconstruction, Asian patients remain one-fifth as likely as Caucasians to choose reconstruction. This study investigates cultural factors, values, and perceptions held by Asian women that might impact breast reconstruction rates. The authors conducted semistructured interviews of immigrant East Asian women treated for breast cancer in the New York metropolitan area, investigating social structure, culture, attitudes toward surgery, and body image. Three investigators independently coded transcribed interviews, and then collectively evaluated them through axial coding of recurring themes. Thirty-five immigrant East Asian women who underwent surgical treatment for breast cancer were interviewed. Emerging themes include functionality, age, perceptions of plastic surgery, inconvenience, community/family, fear of implants, language, and information. Patients spoke about breasts as a function of their roles as a wife or mother, eliminating the need for breasts when these roles were fulfilled. Many addressed the fear of multiple operations. Quality and quantity of information, and communication with practitioners, impacted perceptions about treatment. Reconstructive surgery was often viewed as cosmetic. Community and family played a significant role in decision-making. Asian women are statistically less likely than Caucasians to pursue breast reconstruction. This is the first study to investigate culture-specific perceptions of breast reconstruction. Results from this study can be used to improve cultural competency in addressing patient concerns. Improving access to information regarding treatment options and surgical outcomes may improve informed decision-making among immigrant Asian women.

On the Trails of the Proteasome Fold: Structural and Functional Analysis of the Ancestral β-Subunit Protein Anbu.

Science.gov (United States)

Vielberg, Marie-Theres; Bauer, Verena C; Groll, Michael

2018-03-02

The 20S proteasome is a key player in eukaryotic and archaeal protein degradation, but its progenitor in eubacteria is unknown. Recently, the ancestral β-subunit protein (Anbu) was predicted to be the evolutionary precursor of the proteasome. We crystallized Anbu from Hyphomicrobium sp. strain MC1 in four different space groups and solved the structures by SAD-phasing and Patterson search calculation techniques. Our data reveal that Anbu adopts the classical fold of Ntn-hydrolases, but its oligomeric state differs from that of barrel-shaped proteases. In contrast to their typical architecture, the Anbu protomer is a tightly interacting dimer that can assemble into a helical superstructure. Although Anbu features a catalytic triad of Thr1O γ , Asp17O δ1 and Lys32N ε , it is unable to hydrolyze standard protease substrates. The lack of activity might be caused by the incapacity of Thr1NH 2 to function as a Brønsted acid during substrate cleavage due to its missing activation via hydrogen bonding. Altogether, we demonstrate that the topology of the proteasomal fold is conserved in Anbu, but whether it acts as a protease still needs to be clarified. Copyright © 2018 Elsevier Ltd. All rights reserved.

Robust and accurate multi-view reconstruction by prioritized matching

DEFF Research Database (Denmark)

Ylimaki, Markus; Kannala, Juho; Holappa, Jukka

2012-01-01

a prioritized matching method which expands the most promising seeds first. The output of the method is a three-dimensional point cloud. Unlike previous correspondence growing approaches our method allows to use the best-first matching principle in the generic multi-view stereo setting with arbitrary number...... of input images. Our experiments show that matching the most promising seeds first provides very robust point cloud reconstructions efficiently with just a single expansion step. A comparison to the current state-of-the-art shows that our method produces reconstructions of similar quality but significantly...

First report of fossil "keratose" demosponges in Phanerozoic carbonates: preservation and 3-D reconstruction.

Science.gov (United States)

Luo, Cui; Reitner, Joachim

2014-06-01

Fossil record of Phanerozoic non-spicular sponges, beside of being important with respect to the lineage evolution per se, could provide valuable references for the investigation of Precambrian ancestral animal fossils. However, although modern phylogenomic studies resolve non-spicular demosponges as the sister group of the remaining spiculate demosponges, the fossil record of the former is extremely sparse or unexplored compared to that of the latter; the Middle Cambrian Vauxiidae Walcott 1920, is the only confirmed fossil taxon of non-spicular demosponges. Here, we describe carbonate materials from Devonian (Upper Givetian to Lower Frasnian) bioherms of northern France and Triassic (Anisian) microbialites of Poland that most likely represent fossil remnants of keratose demosponges. These putative fossils of keratose demosponges are preserved as automicritic clumps. They are morphologically distinguishable from microbial fabrics but similar to other spiculate sponge fossils, except that the skeletal elements consist of fibrous networks instead of assembled spicules. Consistent with the immunological behavior of sponges, these fibrous skeletons often form a rim at the edge of the automicritic aggregate, separating the inner part of the aggregate from foreign objects. To confirm the architecture of these fibrous networks, two fossil specimens and a modern thorectid sponge for comparison were processed for three-dimensional (3-D) reconstruction using serial grinding tomography. The resulting fossil reconstructions are three-dimensionally anastomosing, like modern keratose demosponges, but their irregular and nonhierarchical meshes indicate a likely verongid affinity, although a precise taxonomic conclusion cannot be made based on the skeletal architecture alone. This study is a preliminary effort, but an important start to identify fossil non-spicular demosponges in carbonates and to re-evaluate their fossilization potential.

Independent Innovation in the Evolution of Paddle-Shaped Tails in Viviparous Sea Snakes (Elapidae: Hydrophiinae)

DEFF Research Database (Denmark)

Sanders, Kate; Redsted Rasmussen, Arne; Elmberg, Johan

2012-01-01

Abstract The viviparous sea snakes (Hydrophiinae) comprise ∼90% of living marine reptiles and display many physical and behavioral adaptations for breathing, diving, and achieving osmotic balance in marine habitats. Among the most important innovations found in marine snakes are their paddle......-shaped (dorsoventrally expanded) tails, which provide propulsive thrust in the dense aquatic medium. Here, we reconstruct the evolution of caudal paddles in viviparous sea snakes using a dated molecular phylogeny for all major lineages and computed tomography of internal osteological structures. Bayesian ancestral state...... reconstructions show that extremely large caudal paddles supported by elongated vertebral processes are unlikely to have been present in the most recent common ancestor of extant sea snakes. Instead, these characters appear to have been acquired independently in two highly marine lineages of relatively recent...

Diffusion archeology for diffusion progression history reconstruction.

Science.gov (United States)

Sefer, Emre; Kingsford, Carl

2016-11-01

Diffusion through graphs can be used to model many real-world processes, such as the spread of diseases, social network memes, computer viruses, or water contaminants. Often, a real-world diffusion cannot be directly observed while it is occurring - perhaps it is not noticed until some time has passed, continuous monitoring is too costly, or privacy concerns limit data access. This leads to the need to reconstruct how the present state of the diffusion came to be from partial diffusion data. Here, we tackle the problem of reconstructing a diffusion history from one or more snapshots of the diffusion state. This ability can be invaluable to learn when certain computer nodes are infected or which people are the initial disease spreaders to control future diffusions. We formulate this problem over discrete-time SEIRS-type diffusion models in terms of maximum likelihood. We design methods that are based on submodularity and a novel prize-collecting dominating-set vertex cover (PCDSVC) relaxation that can identify likely diffusion steps with some provable performance guarantees. Our methods are the first to be able to reconstruct complete diffusion histories accurately in real and simulated situations. As a special case, they can also identify the initial spreaders better than the existing methods for that problem. Our results for both meme and contaminant diffusion show that the partial diffusion data problem can be overcome with proper modeling and methods, and that hidden temporal characteristics of diffusion can be predicted from limited data.

Parallel MR image reconstruction using augmented Lagrangian methods.

Science.gov (United States)

Ramani, Sathish; Fessler, Jeffrey A

2011-03-01

Magnetic resonance image (MRI) reconstruction using SENSitivity Encoding (SENSE) requires regularization to suppress noise and aliasing effects. Edge-preserving and sparsity-based regularization criteria can improve image quality, but they demand computation-intensive nonlinear optimization. In this paper, we present novel methods for regularized MRI reconstruction from undersampled sensitivity encoded data--SENSE-reconstruction--using the augmented Lagrangian (AL) framework for solving large-scale constrained optimization problems. We first formulate regularized SENSE-reconstruction as an unconstrained optimization task and then convert it to a set of (equivalent) constrained problems using variable splitting. We then attack these constrained versions in an AL framework using an alternating minimization method, leading to algorithms that can be implemented easily. The proposed methods are applicable to a general class of regularizers that includes popular edge-preserving (e.g., total-variation) and sparsity-promoting (e.g., l(1)-norm of wavelet coefficients) criteria and combinations thereof. Numerical experiments with synthetic and in vivo human data illustrate that the proposed AL algorithms converge faster than both general-purpose optimization algorithms such as nonlinear conjugate gradient (NCG) and state-of-the-art MFISTA.

Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.

Science.gov (United States)

Peris, David; Arias, Armando; Orlić, Sandi; Belloch, Carmela; Pérez-Través, Laura; Querol, Amparo; Barrio, Eladio

2017-03-01

Horizontal gene transfer (HGT) in eukaryotic plastids and mitochondrial genomes is common, and plays an important role in organism evolution. In yeasts, recent mitochondrial HGT has been suggested between S. cerevisiae and S. paradoxus. However, few strains have been explored given the lack of accurate mitochondrial genome annotations. Mitochondrial genome sequences are important to understand how frequent these introgressions occur, and their role in cytonuclear incompatibilities and fitness. Indeed, most of the Bateson-Dobzhansky-Muller genetic incompatibilities described in yeasts are driven by cytonuclear incompatibilities. We herein explored the mitochondrial inheritance of several worldwide distributed wild Saccharomyces species and their hybrids isolated from different sources and geographic origins. We demonstrated the existence of several recombination points in mitochondrial region COX2-ORF1, likely mediated by either the activity of the protein encoded by the ORF1 (F-SceIII) gene, a free-standing homing endonuclease, or mostly facilitated by A+T tandem repeats and regions of integration of GC clusters. These introgressions were shown to occur among strains of the same species and among strains of different species, which suggests a complex model of Saccharomyces evolution that involves several ancestral hybridization events in wild environments. Copyright © 2017 Elsevier Inc. All rights reserved.

Computed Tomography Image Quality Evaluation of a New Iterative Reconstruction Algorithm in the Abdomen (Adaptive Statistical Iterative Reconstruction-V) a Comparison With Model-Based Iterative Reconstruction, Adaptive Statistical Iterative Reconstruction, and Filtered Back Projection Reconstructions.

Science.gov (United States)

Goodenberger, Martin H; Wagner-Bartak, Nicolaus A; Gupta, Shiva; Liu, Xinming; Yap, Ramon Q; Sun, Jia; Tamm, Eric P; Jensen, Corey T

The purpose of this study was to compare abdominopelvic computed tomography images reconstructed with adaptive statistical iterative reconstruction-V (ASIR-V) with model-based iterative reconstruction (Veo 3.0), ASIR, and filtered back projection (FBP). Abdominopelvic computed tomography scans for 36 patients (26 males and 10 females) were reconstructed using FBP, ASIR (80%), Veo 3.0, and ASIR-V (30%, 60%, 90%). Mean ± SD patient age was 32 ± 10 years with mean ± SD body mass index of 26.9 ± 4.4 kg/m. Images were reviewed by 2 independent readers in a blinded, randomized fashion. Hounsfield unit, noise, and contrast-to-noise ratio (CNR) values were calculated for each reconstruction algorithm for further comparison. Phantom evaluation of low-contrast detectability (LCD) and high-contrast resolution was performed. Adaptive statistical iterative reconstruction-V 30%, ASIR-V 60%, and ASIR 80% were generally superior qualitatively compared with ASIR-V 90%, Veo 3.0, and FBP (P ASIR-V 60% with respective CNR values of 5.54 ± 2.39, 8.78 ± 3.15, and 3.49 ± 1.77 (P ASIR 80% had the best and worst spatial resolution, respectively. Adaptive statistical iterative reconstruction-V 30% and ASIR-V 60% provided the best combination of qualitative and quantitative performance. Adaptive statistical iterative reconstruction 80% was equivalent qualitatively, but demonstrated inferior spatial resolution and LCD.

Superfast maximum-likelihood reconstruction for quantum tomography

Science.gov (United States)

Shang, Jiangwei; Zhang, Zhengyun; Ng, Hui Khoon

2017-06-01

Conventional methods for computing maximum-likelihood estimators (MLE) often converge slowly in practical situations, leading to a search for simplifying methods that rely on additional assumptions for their validity. In this work, we provide a fast and reliable algorithm for maximum-likelihood reconstruction that avoids this slow convergence. Our method utilizes the state-of-the-art convex optimization scheme, an accelerated projected-gradient method, that allows one to accommodate the quantum nature of the problem in a different way than in the standard methods. We demonstrate the power of our approach by comparing its performance with other algorithms for n -qubit state tomography. In particular, an eight-qubit situation that purportedly took weeks of computation time in 2005 can now be completed in under a minute for a single set of data, with far higher accuracy than previously possible. This refutes the common claim that MLE reconstruction is slow and reduces the need for alternative methods that often come with difficult-to-verify assumptions. In fact, recent methods assuming Gaussian statistics or relying on compressed sensing ideas are demonstrably inapplicable for the situation under consideration here. Our algorithm can be applied to general optimization problems over the quantum state space; the philosophy of projected gradients can further be utilized for optimization contexts with general constraints.

Hadronic energy reconstruction in the CALICE combined calorimeter system

Energy Technology Data Exchange (ETDEWEB)

Israeli, Yasmine [Max-Planck-Institut fuer Physik, Foehringer Ring 6, 80805 Muenchen (Germany); Collaboration: CALICE-D-Collaboration

2016-07-01

Future linear electron-positron colliders, ILC and CLIC, aim for precision measurements and discoveries beyond and complementary to the program of the LHC. For this purpose, detectors with the capability for sophisticated reconstruction of final states with energy resolutions substantially beyond the current state of the art are being designed. The CALICE collaboration develops highly granular calorimeters for future colliders, among them silicon-tungsten electromagnetic calorimeters and hadronic calorimeters with scintillators read out by SiPMs. Such a combined system was tested with hadrons at CERN as well as at Fermilab. In this contribution, we report on the energy reconstruction in the combined setup, which requires different intercalibration factors to account for the varying longitudinal sampling of sub-detectors. Software compensation methods are applied to improve the energy resolution and to compensate for the different energy deposit of hadronic and electromagnetic showers.

Breadth of T cell responses after immunization with adenovirus vectors encoding ancestral antigens or polyvalent papillomavirus antigens

DEFF Research Database (Denmark)

Ragonnaud, Emeline; Pedersen, Anders Gorm; Holst, Peter Johannes

2017-01-01

to the other PV proteins. The PV sequences were fused to a T cell adjuvant, the murine invariant chain and encoded in a recombinant adenoviral vector which was administered to naïve outbred mice. By measuring T cell responses induced by these different vaccines and towards peptide pools representing 3...... circulating strains and a putative ancestor of oncogenic HPVs, we showed that the ancestral vaccine antigen has to be approximately 90% identical to the circulating PVs before a marked drop of ~90% mean CD8+ T cell responses ensues. Interestingly, the combination of two or three type-specific PV vaccines did...

An improved muon reconstruction algorithm for INO-ICAL experiment

International Nuclear Information System (INIS)

Bhattacharya, Kolahal; MandaI, Naba K.

2013-01-01

The charge current interaction of neutrino in INO-ICAL detector will be identified with a muon (μ ± ) in the detector whose kinematics is related with the kinematics of the neutrino. So, muon reconstruction is a very important step in achieving INO physics goals. The existing muon reconstruction package for INO-ICAL has poor performance in specific regimes of experimental interest: (a) for larger zenith angle (θ > 50°), (b) for lower energies (E < 1 GeV); mainly due to poor error propagation scheme insensitive to energy E, angle (θ, φ) and inhomogeneous magnetic field along the muon track. Since, a significant fraction of muons from atmospheric neutrino interactions will have initial energy < 1 GeV and almost uniform distribution in cosθ a robust package for muon reconstruction is essential. We have implemented higher order correction terms in the propagation of the state and error covariance matrices of the Kalman Iter. The algorithm ensures track element merging in most cases and also increases reconstruction efficiency. The performance of this package will be presented in comparison with the previous one. (author)

Anterior cruciate ligament reconstruction failure after tibial shaft malunion.

Science.gov (United States)

LaFrance, Russell M; Gorczyca, John T; Maloney, Michael D

2012-02-17

Anterior cruciate ligament (ACL) reconstruction is common, with >100,000 procedures performed each year in the United States. Several factors are associated with failure, including poor surgical technique, graft incorporation failure, overly aggressive rehabilitation, and trauma. Tibial shaft fracture is also common and frequently requires operative intervention. Failure to reestablish the anatomic alignment of the tibia may cause abnormal forces across adjacent joints, which can cause degenerative joint disease or attritional failure of the surrounding soft tissues. This article describes a case of ACL reconstruction failure after a tibial fracture that resulted in malunion. Excessive force across the graft from lower-extremity malalignment and improper tunnel placement likely contributed to the attritional failure of the graft. This patient required a staged procedure for corrective tibial osteotomy followed by revision ACL reconstruction. This article describes ACL reconstruction failure, tibial shaft malunions, their respective treatments, the technical details of each procedure, and the technical aspects that must be considered when these procedures are done in a staged manner by 2 surgeons. Copyright 2012, SLACK Incorporated.

Numerical analysis of residual stresses reconstruction for axisymmetric glass components

Science.gov (United States)

Tao, Bo; Xu, Shuang; Yao, Honghui

2018-01-01

A non-destructive measurement method for 3D stress state in a glass cylinder using photoelasticity has been analyzed by simulation in this research. Based on simulated stresses in a glass cylinder, intensity of the cylinder in a circular polariscope can be calculated by Jones calculus. Therefore, the isoclinic angle and optical retardation can be obtained by six steps phase shifting technique. Through the isoclinic angle and optical retardation, the magnitude and distribution of residual stresses inside the glass cylinder in cylindrical coordinate system can be reconstructed. Comparing the reconstructed stresses with numerical simulated stresses, the results verify this non-destructive method can be used to reconstruct the 3D stresses. However, there are some mismatches in axial stress, radial stress and circumferential stress.

Review of evolution of tunnel position in anterior cruciate ligament reconstruction.

Science.gov (United States)

Rayan, Faizal; Nanjayan, Shashi Kumar; Quah, Conal; Ramoutar, Darryl; Konan, Sujith; Haddad, Fares S

2015-03-18

Anterior cruciate ligament (ACL) rupture is one of the commonest knee sport injuries. The annual incidence of the ACL injury is between 100000-200000 in the United States. Worldwide around 400000 ACL reconstructions are performed in a year. The goal of ACL reconstruction is to restore the normal knee anatomy and kinesiology. The tibial and femoral tunnel placements are of primordial importance in achieving this outcome. Other factors that influence successful reconstruction are types of grafts, surgical techniques and rehabilitation programmes. A comprehensive understanding of ACL anatomy has led to the development of newer techniques supplemented by more robust biological and mechanical concepts. In this review we are mainly focussing on the evolution of tunnel placement in ACL reconstruction, focusing on three main categories, i.e., anatomical, biological and clinical outcomes. The importance of tunnel placement in the success of ACL reconstruction is well researched. Definite clinical and functional data is lacking to establish the superiority of the single or double bundle reconstruction technique. While there is a trend towards the use of anteromedial portals for femoral tunnel placement, their clinical superiority over trans-tibial tunnels is yet to be established.

Evolution of larval life mode of Oecophoridae (Lepidoptera: Gelechioidea) inferred from molecular phylogeny.

Science.gov (United States)

Kim, Sora; Kaila, Lauri; Lee, Seunghwan

2016-08-01

Phylogenetic relationships within family Oecophoridae have been poorly understood. Consequently the subfamily and genus level classifications with this family problematic. A comprehensive phylogenetic analysis of Oecophoridae, the concealer moths, was performed based on analysis of 4444 base pairs of mitochondrial COI, nuclear ribosomal RNA genes (18S and 28S) and nuclear protein coding genes (IDH, MDH, Rps5, EF1a and wingless) for 82 taxa. Data were analyzed using maximum likelihood (ML), parsimony (MP) and Bayesian (BP) phylogenetic frameworks. Phylogenetic analyses indicated that (i) genera Casmara, Tyrolimnas and Pseudodoxia did not belong to Oecophoridae, suggesting that Oecophoridae s. authors was not monophyletic; (ii) other oecophorids comprising two subfamilies, Pleurotinae and Oecophorinae, were nested within the same clade, and (iii) Martyringa, Acryptolechia and Periacmini were clustered with core Xyloryctidae. They appeared to be sister lineage with core Oecophoridae. BayesTraits were implemented to explore the ancestral character states to infer historical microhabitat patterns and sheltering strategy of larvae. Reconstruction of ancestral microhabitat of oecophorids indicated that oecophorids might have evolved from dried plant feeders and further convergently specialized. The ancestral larva sheltering strategy of oecophorids might have used a silk tube by making itself, shifting from mining leaves. Copyright © 2016 Elsevier Inc. All rights reserved.

Holographic images reconstructed from GMR-based fringe pattern

Directory of Open Access Journals (Sweden)

Kikuchi Hiroshi

2013-01-01

Full Text Available We have developed a magneto-optical spatial light modulator (MOSLM using giant magneto-resistance (GMR structures for realizing a holographic three-dimensional (3D display. For practical applications, reconstructed image of hologram consisting of GMR structures should be investigated in order to study the feasibility of the MOSLM. In this study, we fabricated a hologram with GMR based fringe-pattern and demonstrated a reconstructed image. A fringe-pattern convolving a crossshaped image was calculated by a conventional binary computer generated hologram (CGH technique. The CGH-pattern has 2,048 × 2,048 with 5 μm pixel pitch. The GMR stack consists of a Tb-Fe-Co/CoFe pinned layer, a Ag spacer, a Gd-Fe free layer for light modulation, and a Ru capping layer, was deposited by dc-magnetron sputtering. The GMR hologram was formed using photo-lithography and Krion milling processes, followed by the deposition of a Tb-Fe-Co reference layer with large coercivity and the same Kerr-rotation angle compared to the free layer, and a lift-off process. The reconstructed image of the ON-state was clearly observed and successfully distinguished from the OFF-state by switching the magnetization direction of the free-layer with an external magnetic field. These results indicate the possibility of realizing a holographic 3D display by the MOSLM using the GMR structures.

The Microcephalin Ancestral Allele in a Neanderthal Individual

Science.gov (United States)

Lari, Martina; Rizzi, Ermanno; Milani, Lucio; Corti, Giorgio; Balsamo, Carlotta; Vai, Stefania; Catalano, Giulio; Pilli, Elena; Longo, Laura; Condemi, Silvana; Giunti, Paolo; Hänni, Catherine; De Bellis, Gianluca; Orlando, Ludovic; Barbujani, Guido; Caramelli, David

2010-01-01

Background The high frequency (around 0.70 worlwide) and the relatively young age (between 14,000 and 62,000 years) of a derived group of haplotypes, haplogroup D, at the microcephalin (MCPH1) locus led to the proposal that haplogroup D originated in a human lineage that separated from modern humans >1 million years ago, evolved under strong positive selection, and passed into the human gene pool by an episode of admixture circa 37,000 years ago. The geographic distribution of haplogroup D, with marked differences between Africa and Eurasia, suggested that the archaic human form admixing with anatomically modern humans might have been Neanderthal. Methodology/Principal Findings Here we report the first PCR amplification and high- throughput sequencing of nuclear DNA at the microcephalin (MCPH1) locus from Neanderthal individual from Mezzena Rockshelter (Monti Lessini, Italy). We show that a well-preserved Neanderthal fossil dated at approximately 50,000 years B.P., was homozygous for the ancestral, non-D, allele. The high yield of Neanderthal mtDNA sequences of the studied specimen, the pattern of nucleotide misincorporation among sequences consistent with post-mortem DNA damage and an accurate control of the MCPH1 alleles in all personnel that manipulated the sample, make it extremely unlikely that this result might reflect modern DNA contamination. Conclusions/Significance The MCPH1 genotype of the Monti Lessini (MLS) Neanderthal does not prove that there was no interbreeding between anatomically archaic and modern humans in Europe, but certainly shows that speculations on a possible Neanderthal origin of what is now the most common MCPH1 haplogroup are not supported by empirical evidence from ancient DNA. PMID:20498832

The microcephalin ancestral allele in a Neanderthal individual.

Directory of Open Access Journals (Sweden)

Martina Lari

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

Image Reconstruction. Chapter 13

Energy Technology Data Exchange (ETDEWEB)

Nuyts, J. [Department of Nuclear Medicine and Medical Imaging Research Center, Katholieke Universiteit Leuven, Leuven (Belgium); Matej, S. [Medical Image Processing Group, Department of Radiology, University of Pennsylvania, Philadelphia, PA (United States)

2014-12-15

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.

Qualitative and quantitative improvements of PET reconstruction on GPU architecture

International Nuclear Information System (INIS)

Autret, Awen

2016-01-01

In positron emission tomography, reconstructed images suffer from a high noise level and a low resolution. Iterative reconstruction processes require an estimation of the system response (scanner and patient) and the quality of the images depends on the accuracy of this estimate. Accurate and fast to compute models already exists for the attenuation, scattering, random coincidences and dead times. Thus, this thesis focuses on modeling the system components associated with the detector response and the positron range. A new multi-GPU parallelization of the reconstruction based on a cutting of the volume is also proposed to speed up the reconstruction exploiting the computing power of such architectures. The proposed detector response model is based on a multi-ray approach that includes all the detector effects as the geometry and the scattering in the crystals. An evaluation study based on data obtained through Mote Carlo simulation (MCS) showed this model provides reconstructed images with a better contrast to noise ratio and resolution compared with those of the methods from the state of the art. The proposed positron range model is based on a simplified MCS, integrated into the forward projector during the reconstruction. A GPU implementation of this method allows running MCS three order of magnitude faster than the same simulation on GATE, while providing similar results. An evaluation study shows this model integrated in the reconstruction gives images with better contrast recovery and resolution while avoiding artifacts. (author)

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.

Coordinate reconstruction using box reconstruction and projection of X-ray photo

International Nuclear Information System (INIS)

Achmad Suntoro

2011-01-01

Some mathematical formula have been derived for a process of reconstruction to define the coordinate of any point relative to a pre set coordinate system. The process of reconstruction uses a reconstruction box in which each edge's length of the box is known, each top-bottom face and left-right face of the box having a cross marker, and the top face and the right face of the box as plane projections by X-ray source in perspective projection -system. Using the data of the two X-ray projection images, any point inside the reconstruction box, as long as its projection is recorded in the two photos, will be determined its coordinate relative to the midpoint of the reconstruction box as the central point coordinates. (author)

Single-resolution and multiresolution extended-Kalman-filter-based reconstruction approaches to optical refraction tomography.

Science.gov (United States)

Naik, Naren; Vasu, R M; Ananthasayanam, M R

2010-02-20

The problem of reconstruction of a refractive-index distribution (RID) in optical refraction tomography (ORT) with optical path-length difference (OPD) data is solved using two adaptive-estimation-based extended-Kalman-filter (EKF) approaches. First, a basic single-resolution EKF (SR-EKF) is applied to a state variable model describing the tomographic process, to estimate the RID of an optically transparent refracting object from noisy OPD data. The initialization of the biases and covariances corresponding to the state and measurement noise is discussed. The state and measurement noise biases and covariances are adaptively estimated. An EKF is then applied to the wavelet-transformed state variable model to yield a wavelet-based multiresolution EKF (MR-EKF) solution approach. To numerically validate the adaptive EKF approaches, we evaluate them with benchmark studies of standard stationary cases, where comparative results with commonly used efficient deterministic approaches can be obtained. Detailed reconstruction studies for the SR-EKF and two versions of the MR-EKF (with Haar and Daubechies-4 wavelets) compare well with those obtained from a typically used variant of the (deterministic) algebraic reconstruction technique, the average correction per projection method, thus establishing the capability of the EKF for ORT. To the best of our knowledge, the present work contains unique reconstruction studies encompassing the use of EKF for ORT in single-resolution and multiresolution formulations, and also in the use of adaptive estimation of the EKF's noise covariances.

Segmentation-DrivenTomographic Reconstruction

DEFF Research Database (Denmark)

Kongskov, Rasmus Dalgas

such that the segmentation subsequently can be carried out by use of a simple segmentation method, for instance just a thresholding method. We tested the advantages of going from a two-stage reconstruction method to a one stage segmentation-driven reconstruction method for the phase contrast tomography reconstruction......The tomographic reconstruction problem is concerned with creating a model of the interior of an object from some measured data, typically projections of the object. After reconstructing an object it is often desired to segment it, either automatically or manually. For computed tomography (CT...

Reconstruction of the interaction term between dark matter and dark energy using SNe Ia

Energy Technology Data Exchange (ETDEWEB)

Solano, Freddy Cueva; Nucamendi, Ulises, E-mail: freddy@ifm.umich.mx, E-mail: ulises@ifm.umich.mx [Instituto de Física y Matemáticas, Universidad Michoacana de San Nicolás de Hidalgo, Edificio C-3, Ciudad Universitaria, CP. 58040, Morelia, Michoacán (Mexico)

2012-04-01

We apply a parametric reconstruction method to a homogeneous, isotropic and spatially flat Friedmann-Robertson-Walker (FRW) cosmological model filled of a fluid of dark energy (DE) with constant equation of state (EOS) parameter interacting with dark matter (DM)\\@. The reconstruction method is based on expansions of the general interaction term and the relevant cosmological variables in terms of Chebyshev polynomials which form a complete set orthonormal functions. This interaction term describes an exchange of energy flow between the DE and DM within dark sector. To show how the method works we do the reconstruction of the interaction function expanding it in terms of only the first six Chebyshev polynomials and obtain the best estimation for the coefficients of the expansion assuming three models: (a) a DE equation of the state parameter w = −1 (an interacting cosmological Λ), (b) a DE equation of the state parameter w = constant with a dark matter density parameter fixed, (c) a DE equation of the state parameter w = constant with a free constant dark matter density parameter to be estimated, and using the Union2 SNe Ia data set from ''The Supernova Cosmology Project'' (SCP) composed by 557 type Ia supernovae. In both cases, the preliminary reconstruction shows that in the best scenario there exist the possibility of a crossing of the noninteracting line Q = 0 in the recent past within the 1σ and 2σ errors from positive values at early times to negative values at late times. This means that, in this reconstruction, there is an energy transfer from DE to DM at early times and an energy transfer from DM to DE at late times. We conclude that this fact is an indication of the possible existence of a crossing behavior in a general interaction coupling between dark components.

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

Science.gov (United States)

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

2011-05-01

Primary dysferlinopathies are a group of recessive heterogeneous muscular dystrophies. The most common clinical presentations are Miyoshi myopathy and LGMD2B. Additional presentations range from isolated hyperCKemia to severe functional disability. Symptomatology begins in the posterior muscle compartment of the calf and its clinical course progresses slowly in Miyoshi myopathy whereas LGMD2B involves predominantly the proximal muscles of the lower limbs. The age of onset ranges from 13 to 60years in Caucasians. We present five patients that carry a novel mutation in the exon12/intron12 boundary: c.1180_1180+7delAGTGCGTG (r.1054_1284del). We provide evidence of a founder effect due to a common ancestral origin of this mutation, detected in heterozygosity in four patients and in homozygosity in one patient. Copyright © 2011 Elsevier B.V. All rights reserved.

Effects of ancestral x irradiation followed by random mating on body weight of rats

International Nuclear Information System (INIS)

Gianola, D.; Chapman, A.B.; Rutledge, J.J.

1977-01-01

Effects of nine generations of 450R per generation of ancestral spermatogonial x irradiation of inbred rats on body weight were examined. After six generations of random mating (avoiding inbreeding) following the termination of irradiation, descendants of irradiated males (R) were significantly lighter than their controls (C) at 3 and 6 weeks, but not at 10 weeks of age. However, differences in growth between R and C populations were small. Among-litter and within-litter variance estimates were generally larger in the R lines than in the C lines, suggesting that selection responses would be greater in R than in C lines. In conjunction with previous evidence--obtained during the irradiation phase of the experiment--this suggested that more rapid response to selection for 6-week body weight, in particular, might accrue in the R lines

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

Science.gov (United States)

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

2014-04-01

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

An attempt to reconstruct phylogenetic relationships within Caribbean nummulitids: simulating relationships and tracing character evolution

Science.gov (United States)

Eder, Wolfgang; Ives Torres-Silva, Ana; Hohenegger, Johann

2017-04-01

Phylogenetic analysis and trees based on molecular data are broadly applied and used to infer genetical and biogeographic relationship in recent larger foraminifera. Molecular phylogenetic is intensively used within recent nummulitids, however for fossil representatives these trees are only of minor informational value. Hence, within paleontological studies a phylogenetic approach through morphometric analysis is of much higher value. To tackle phylogenetic relationships within the nummulitid family, a much higher number of morphological character must be measured than are commonly used in biometric studies, where mostly parameters describing embryonic size (e.g., proloculus diameter, deuteroloculus diameter) and/or the marginal spiral (e.g., spiral diagrams, spiral indices) are studied. For this purpose 11 growth-independent and/or growth-invariant characters have been used to describe the morphological variability of equatorial thin sections of seven Carribbean nummulitid taxa (Nummulites striatoreticulatus, N. macgillavry, Palaeonummulites willcoxi, P.floridensis, P. soldadensis, P.trinitatensis and P.ocalanus) and one outgroup taxon (Ranikothalia bermudezi). Using these characters, phylogenetic trees were calculated using a restricted maximum likelihood algorithm (REML), and results are cross-checked by ordination and cluster analysis. Square-change parsimony method has been run to reconstruct ancestral states, as well as to simulate the evolution of the chosen characters along the calculated phylogenetic tree and, independent - contrast analysis was used to estimate confidence intervals. Based on these simulations, phylogenetic tendencies of certain characters proposed for nummulitids (e.g., Cope's rule or nepionic acceleration) can be tested, whether these tendencies are valid for the whole family or only for certain clades. At least, within the Carribean nummulitids, phylogenetic trends along some growth-independent characters of the embryo (e.g., first

Residual motion compensation in ECG-gated interventional cardiac vasculature reconstruction

Science.gov (United States)

Schwemmer, C.; Rohkohl, C.; Lauritsch, G.; Müller, K.; Hornegger, J.

2013-06-01

Three-dimensional reconstruction of cardiac vasculature from angiographic C-arm CT (rotational angiography) data is a major challenge. Motion artefacts corrupt image quality, reducing usability for diagnosis and guidance. Many state-of-the-art approaches depend on retrospective ECG-gating of projection data for image reconstruction. A trade-off has to be made regarding the size of the ECG-gating window. A large temporal window is desirable to avoid undersampling. However, residual motion will occur in a large window, causing motion artefacts. We present an algorithm to correct for residual motion. Our approach is based on a deformable 2D-2D registration between the forward projection of an initial, ECG-gated reconstruction, and the original projection data. The approach is fully automatic and does not require any complex segmentation of vasculature, or landmarks. The estimated motion is compensated for during the backprojection step of a subsequent reconstruction. We evaluated the method using the publicly available CAVAREV platform and on six human clinical datasets. We found a better visibility of structure, reduced motion artefacts, and increased sharpness of the vessels in the compensated reconstructions compared to the initial reconstructions. At the time of writing, our algorithm outperforms the leading result of the CAVAREV ranking list. For the clinical datasets, we found an average reduction of motion artefacts by 13 ± 6%. Vessel sharpness was improved by 25 ± 12% on average.

Vaginal reconstruction

International Nuclear Information System (INIS)

Lesavoy, M.A.

1985-01-01

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

Deciphering the Origin, Evolution, and Physiological Function of the Subtelomeric Aryl-Alcohol Dehydrogenase Gene Family in the Yeast Saccharomyces cerevisiae.

Science.gov (United States)

Yang, Dong-Dong; de Billerbeck, Gustavo M; Zhang, Jin-Jing; Rosenzweig, Frank; Francois, Jean-Marie

2018-01-01

Homology searches indicate that Saccharomyces cerevisiae strain BY4741 contains seven redundant genes that encode putative aryl-alcohol dehydrogenases (AAD). Yeast AAD genes are located in subtelomeric regions of different chromosomes, and their functional role(s) remain enigmatic. Here, we show that two of these genes, AAD4 and AAD14 , encode functional enzymes that reduce aliphatic and aryl-aldehydes concomitant with the oxidation of cofactor NADPH, and that Aad4p and Aad14p exhibit different substrate preference patterns. Other yeast AAD genes are undergoing pseudogenization. The 5' sequence of AAD15 has been deleted from the genome. Repair of an AAD3 missense mutation at the catalytically essential Tyr 73 residue did not result in a functional enzyme. However, ancestral-state reconstruction by fusing Aad6 with Aad16 and by N-terminal repair of Aad10 restores NADPH-dependent aryl-alcohol dehydrogenase activities. Phylogenetic analysis indicates that AAD genes are narrowly distributed in wood-saprophyte fungi and in yeast that occupy lignocellulosic niches. Because yeast AAD genes exhibit activity on veratraldehyde, cinnamaldehyde, and vanillin, they could serve to detoxify aryl-aldehydes released during lignin degradation. However, none of these compounds induce yeast AAD gene expression, and Aad activities do not relieve aryl-aldehyde growth inhibition. Our data suggest an ancestral role for AAD genes in lignin degradation that is degenerating as a result of yeast's domestication and use in brewing, baking, and other industrial applications. IMPORTANCE Functional characterization of hypothetical genes remains one of the chief tasks of the postgenomic era. Although the first Saccharomyces cerevisiae genome sequence was published over 20 years ago, 22% of its estimated 6,603 open reading frames (ORFs) remain unverified. One outstanding example of this category of genes is the enigmatic seven-member AAD family. Here, we demonstrate that proteins encoded by two

Genetic variation in ecoraces of tropical tasar silkworm, Antheraea ...

Indian Academy of Sciences (India)

used to reconstruct more ancient evolutionary events (Meyer et al. 1995). ... the PCR amplified products. Formerly, 13 diverse strains of silkworm, Bombyx mori, were ... Phylogenetic studies on ancestral position of microsatel- lite sequences in ...

Insect form vision as one potential shaping force of spider web decoration design.

Science.gov (United States)

Cheng, R-C; Yang, E-C; Lin, C-P; Herberstein, M E; Tso, I-M

2010-03-01

Properties of prey sensory systems are important factors shaping the design of signals generated by organisms exploiting them. In this study we assessed how prey sensory preference affected the exploiter signal design by investigating the evolutionary relationship and relative attractiveness of linear and cruciate form web decorations built by Argiope spiders. Because insects have an innate preference for bilaterally symmetrical patterns, we hypothesized that cruciate form decorations were evolved from linear form due to their higher visual attractiveness to insects. We first reconstructed a molecular phylogeny of the Asian members of the genus Argiope using mitochondrial markers to infer the evolutionary relationship of two decoration forms. Results of ancestral character state reconstruction showed that the linear form was ancestral and the cruciate form derived. To evaluate the luring effectiveness of two decoration forms, we performed field experiments in which the number and orientation of decoration bands were manipulated. Decoration bands arranged in a cruciate form were significantly more attractive to insects than those arranged in a linear form, no matter whether they were composed of silks or dummies. Moreover, dummy decoration bands arranged in a cruciate form attracted significantly more insects than those arranged in a vertical/horizontal form. Such results suggest that pollinator insects' innate preference for certain bilateral or radial symmetrical patterns might be one of the driving forces shaping the arrangement pattern of spider web decorations.

Breast Reconstruction After Mastectomy

Science.gov (United States)

... Cancer Prevention Genetics of Breast & Gynecologic Cancers Breast Cancer Screening Research Breast Reconstruction After Mastectomy On This Page What is breast reconstruction? How do surgeons use implants to reconstruct a woman’s breast? How do surgeons ...

Reconstruction of neuronal input through modeling single-neuron dynamics and computations

International Nuclear Information System (INIS)

Qin, Qing; Wang, Jiang; Yu, Haitao; Deng, Bin; Chan, Wai-lok

2016-01-01

Mathematical models provide a mathematical description of neuron activity, which can better understand and quantify neural computations and corresponding biophysical mechanisms evoked by stimulus. In this paper, based on the output spike train evoked by the acupuncture mechanical stimulus, we present two different levels of models to describe the input-output system to achieve the reconstruction of neuronal input. The reconstruction process is divided into two steps: First, considering the neuronal spiking event as a Gamma stochastic process. The scale parameter and the shape parameter of Gamma process are, respectively, defined as two spiking characteristics, which are estimated by a state-space method. Then, leaky integrate-and-fire (LIF) model is used to mimic the response system and the estimated spiking characteristics are transformed into two temporal input parameters of LIF model, through two conversion formulas. We test this reconstruction method by three different groups of simulation data. All three groups of estimates reconstruct input parameters with fairly high accuracy. We then use this reconstruction method to estimate the non-measurable acupuncture input parameters. Results show that under three different frequencies of acupuncture stimulus conditions, estimated input parameters have an obvious difference. The higher the frequency of the acupuncture stimulus is, the higher the accuracy of reconstruction is.

Reconstruction of neuronal input through modeling single-neuron dynamics and computations

Energy Technology Data Exchange (ETDEWEB)

Qin, Qing; Wang, Jiang; Yu, Haitao; Deng, Bin, E-mail: dengbin@tju.edu.cn; Chan, Wai-lok [School of Electrical Engineering and Automation, Tianjin University, Tianjin 300072 (China)

2016-06-15

Mathematical models provide a mathematical description of neuron activity, which can better understand and quantify neural computations and corresponding biophysical mechanisms evoked by stimulus. In this paper, based on the output spike train evoked by the acupuncture mechanical stimulus, we present two different levels of models to describe the input-output system to achieve the reconstruction of neuronal input. The reconstruction process is divided into two steps: First, considering the neuronal spiking event as a Gamma stochastic process. The scale parameter and the shape parameter of Gamma process are, respectively, defined as two spiking characteristics, which are estimated by a state-space method. Then, leaky integrate-and-fire (LIF) model is used to mimic the response system and the estimated spiking characteristics are transformed into two temporal input parameters of LIF model, through two conversion formulas. We test this reconstruction method by three different groups of simulation data. All three groups of estimates reconstruct input parameters with fairly high accuracy. We then use this reconstruction method to estimate the non-measurable acupuncture input parameters. Results show that under three different frequencies of acupuncture stimulus conditions, estimated input parameters have an obvious difference. The higher the frequency of the acupuncture stimulus is, the higher the accuracy of reconstruction is.

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

Directory of Open Access Journals (Sweden)

Vincent J Lynch

2009-01-01

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

PRÁCTICAS SOSTENIBLES BASADAS EN EL CONOCIMIENTO ANCESTRAL Y LA TECNOLOGÍA. APLICACIÓN EN EL CULTIVO DE MAÍZ

Directory of Open Access Journals (Sweden)

Tony JinsopYangüés Pappa

2012-11-01

Full Text Available Este trabajo fue desarrollado en la microcuenca Membrillo del cantón Bolívar, provincia de Manabí, su objetivo fue incrementar la productividad del cultivo de maíz aplicando prácticas sostenibles basadas en el conocimiento ancestral y la tecnología. Para lograr el objetivo propuesto se realizó un Diagnóstico Rural Participativo (DRP y se aplicaron las Metodologías de Escuelas de Aprendizaje (ERAs. Entre los principales resultados obtenidos se destacan el incremento de la productividad promedio del cultivo del maíz a 120 qq/ha con prácticas alternativas sostenibles basadas en el conocimiento ancestral y la tecnología en las comunidades donde se aplicaron las experiencias, alcanzando estas mayores ingresos que satisfacen las necesidades de los productores y consecuentemente se logró reducir la presión hacia los bosques por la producción intensiva alcanzada. Se capacitaron a los agricultores involucrados en técnicas de elaboración de bioinsumos que se utilizaron para la producción de maíz, alternativas para el manejo técnico sostenible y amigable con el ambiente en este cultivo. También se demostró que las prácticas implementadas en el desarrollo de este trabajo contribuyen al desarrollo sostenible de la Microcuenca Membrillo.

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.

Discrepancies in the female pelvic medicine and reconstructive surgeon workforce.

Science.gov (United States)

Muffly, Tyler M; Weterings, Robbie; Barber, Mathew D; Steinberg, Adam C

2015-01-01

It is unclear whether the current distribution of surgeons practicing female pelvic medicine and reconstructive surgery in the United States is adequate to meet the needs of a growing and aging population. We assessed the geographic distribution of female pelvic surgeons as represented by members of the American Urogynecologic Society (AUGS) throughout the United States at the county, state, and American Congress of Obstetricians and Gynecologists district levels. County-level data from the AUGS, American Congress of Obstetricians and Gynecologists, and the United States Census were analyzed in this observational study. State and national patterns of female pelvic surgeon density were mapped graphically using ArcGIS software and 2010 US Census demographic data. In 2013, the 1058 AUGS practicing physicians represented 0.13% of the total physician workforce. There were 6.7 AUGS members available for every 1 million women and 20 AUGS members for every 1 million postreproductive-aged women in the United States. The density of female pelvic surgeons was highest in metropolitan areas. Overall, 88% of the counties in the United States lacked female pelvic surgeons. Nationwide, there was a mean of 1 AUGS member for every 31 practicing general obstetrician-gynecologists. These findings have implications for training, recruiting, and retaining female pelvic surgeons. The uneven distribution of female pelvic surgeons throughout the United States is likely to worsen as graduating female pelvic medicine and reconstructive surgery fellows continue to cluster in urban areas.

War and reconstruction in northern Mozambique

OpenAIRE

Tilman Bruck

2006-01-01

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

Reconstruction of the Proximal Humerus after Wide Resection of Tumors: Comparison of Three Reconstructive Options

International Nuclear Information System (INIS)

EL-SHERBINY, M.

2008-01-01

bone flaps were nonunion of one end in 2 cases of PLSCG and one case of FVFG. Limb shortening was seen in 32 cases with PLSCG. Conclusion: Summarizing our experience in this small study, we can state that, limb sparing surgical resection of tumors of the proximal humerus is effective in local tumor control and preserving hand and elbow movements. MSTS functional score of the limb after reconstruction and shoulder fusion with FVFG or PLSCG is nearly the same as mobile shoulder reconstruction with endo prosthesis. Shoulder range of movement was grossly limited with prosthesis replacement while a wider range of movement was obtained with shoulder fusion. Pedicled lateral scapular crest graft is able to bridge defects only up to 12 cm whereas the fibula can replace a longer defect. Selection between those reconstructive options should be individualized and is based on the age, the length of defect, the type of resection, intraarticular or extra articular, preservation of deltoid and axillary nerve, the prognosis of the tumor.

Tracing the rise of ants - out of the ground.

Directory of Open Access Journals (Sweden)

Andrea Lucky

Full Text Available The evolution of ants (Hymenoptera: Formicidae is increasingly well-understood due to recent phylogenetic analyses, along with estimates of divergence times and diversification rates. Yet, leading hypotheses regarding the ancestral habitat of ants conflict with new findings that early ant lineages are cryptic and subterranean. Where the ants evolved, in respect to habitat, and how habitat shifts took place over time have not been formally tested. Here, we reconstruct the habitat transitions of crown-group ants through time, focusing on where they nest and forage (in the canopy, litter, or soil. Based on ancestral character reconstructions, we show that in contrast to the current consensus based on verbal arguments that ants evolved in tropical leaf litter, the soil is supported as the ancestral stratum of all ants. We also find subsequent movements up into the litter and, in some cases, into the canopy. Given the global importance of ants, because of their diversity, ecological influence and status as the most successful eusocial lineage on Earth, understanding the early evolution of this lineage provides insight into the factors that made this group so successful today.

[Reconstructive methods after Fournier gangrene].

Science.gov (United States)

Wallner, C; Behr, B; Ring, A; Mikhail, B D; Lehnhardt, M; Daigeler, A

2016-04-01

Fournier's gangrene is a variant of the necrotizing fasciitis restricted to the perineal and genital region. It presents as an acute life-threatening disease and demands rapid surgical debridement, resulting in large soft tissue defects. Various reconstructive methods have to be applied to reconstitute functionality and aesthetics. The objective of this work is to identify different reconstructive methods in the literature and compare them to our current concepts for reconstructing defects caused by Fournier gangrene. Analysis of the current literature and our reconstructive methods on Fournier gangrene. The Fournier gangrene is an emergency requiring rapid, calculated antibiotic treatment and radical surgical debridement. After the acute phase of the disease, appropriate reconstructive methods are indicated. The planning of the reconstruction of the defect depends on many factors, especially functional and aesthetic demands. Scrotal reconstruction requires a higher aesthetic and functional reconstructive degree than perineal cutaneous wounds. In general, thorough wound hygiene, proper pre-operative planning, and careful consideration of the patient's demands are essential for successful reconstruction. In the literature, various methods for reconstruction after Fournier gangrene are described. Reconstruction with a flap is required for a good functional result in complex regions as the scrotum and penis, while cutaneous wounds can be managed through skin grafting. Patient compliance and tissue demand are crucial factors in the decision-making process.

Shaping the breast in secondary microsurgical breast reconstruction: single- vs. two-esthetic unit reconstruction.

Science.gov (United States)

Gravvanis, Andreas; Smith, Roger W

2010-10-01

The esthetic outcome is dictated essentially not only by the position, size, and shape of the reconstructed breast, but also by the extra scaring involved. In the present study, we conducted a visual analog scale survey to compare the esthetic outcome in delayed autologous breast reconstruction following two different abdominal flaps inset. Twenty-five patients had their reconstruction using the Single-esthetic Unit principle and were compared with 25 patients that their breast was reconstructed using the Two-Esthetic Unit principle. Photographic images were formulated to a PowerPoint presentation and cosmetic outcomes were assessed from 30 physicians, by means of a Questionnaire and a visual analog scale. Our data showed that the single-esthetic unit breast reconstruction presents significant advantages over the traditional two-esthetic units, due to inconspicuous flap reconstruction, better position of the inframammary fold, and more natural transition from native and reconstructed tissues. Moreover, patient self-evaluation of esthetic outcome and quality of life showed that single-esthetic unit reconstruction is associated with higher patient satisfaction, therefore should be considered the method of choice. © 2010 Wiley-Liss, Inc.

MR fingerprinting Deep RecOnstruction NEtwork (DRONE).

Science.gov (United States)

Cohen, Ouri; Zhu, Bo; Rosen, Matthew S

2018-09-01

Demonstrate a novel fast method for reconstruction of multi-dimensional MR fingerprinting (MRF) data using deep learning methods. A neural network (NN) is defined using the TensorFlow framework and trained on simulated MRF data computed with the extended phase graph formalism. The NN reconstruction accuracy for noiseless and noisy data is compared to conventional MRF template matching as a function of training data size and is quantified in simulated numerical brain phantom data and International Society for Magnetic Resonance in Medicine/National Institute of Standards and Technology phantom data measured on 1.5T and 3T scanners with an optimized MRF EPI and MRF fast imaging with steady state precession (FISP) sequences with spiral readout. The utility of the method is demonstrated in a healthy subject in vivo at 1.5T. Network training required 10 to 74 minutes; once trained, data reconstruction required approximately 10 ms for the MRF EPI and 76 ms for the MRF FISP sequence. Reconstruction of simulated, noiseless brain data using the NN resulted in a RMS error (RMSE) of 2.6 ms for T 1 and 1.9 ms for T 2 . The reconstruction error in the presence of noise was less than 10% for both T 1 and T 2 for SNR greater than 25 dB. Phantom measurements yielded good agreement (R 2  = 0.99/0.99 for MRF EPI T 1 /T 2 and 0.94/0.98 for MRF FISP T 1 /T 2 ) between the T 1 and T 2 estimated by the NN and reference values from the International Society for Magnetic Resonance in Medicine/National Institute of Standards and Technology phantom. Reconstruction of MRF data with a NN is accurate, 300- to 5000-fold faster, and more robust to noise and dictionary undersampling than conventional MRF dictionary-matching. © 2018 International Society for Magnetic Resonance in Medicine.

Our Clinical Experience in Lower Eyelid Reconstruction and Comparison of Reconstruction Techniques.

Directory of Open Access Journals (Sweden)

Erol Kesiktas

2011-03-01

Full Text Available Lower eyelid reconstruction after tumor resection or trauma is extremely important in order to obtain the protection of the globe and it requires extra care. The aim of this study is to evaluate the techniques that we use in lower eyelid reconstruction. Between the years of 1999-2009, a total of 23 patients who had lower eyelid defects due to tumor resection (21 patients or trauma (2 patients were reconstructed by the use of various flaps. Eleven of the patients were women and twelve of them were men. Average age was 60.7. For the reconstruction 13 Mustarde flap, 9 bipedicled Tripier flap, 1 Tenzel flap and 1 bipedicled infraorbital flaps were used. Average postoperative follow up interval was 35 months. (18-47 months. Flap necrosis, function loss in the lower lid were not experienced in any of the patients. Cosmetically satisfactory results were obtained. In lower eyelid reconstruction, the size of the defect and the amount of skin around must be carefully evaluated and should be considered while planning the reconstruction. [Cukurova Med J 2011; 36(1: 15-23

Track reconstruction for the P2 experiment

Energy Technology Data Exchange (ETDEWEB)

Tyukin, Alexey [JGU, Mainz (Germany); Collaboration: P2-Collaboration

2016-07-01

The P2 experiment at the future MESA accelerator in Mainz will measure elastically scattered electrons from a hydrogen or lead target in order to determine the parity violating asymmetry for different beam polarisations, which is created due to the weak charge of the target. The asymmetry can provide access to the Weinberg angle and the neutron skin of heavy nuclei. These quantities depend heavily on the momentum transfer Q{sup 2}, thus a reconstruction of single electron tracks in an inhomogeneous magnetic field is necessary. For this, the P2 detector will have four tracking planes of thin high voltage monolithic active pixel sensors (HV-MAPS). The scattered electrons propagate through a magnetic field and hit all four planes. In order to fit the hit positions the General Broken Lines method is used. As a fast propagator, a variation of the Runge-Kutta algorithm is applied, which solves the equation of motion in an inhomogeneous magnetic field numerically, such that the final state momentum and scattering angle can be reconstructed. The initial momentum and incident angle can vary strongly due to the thickness of the target, limiting the reconstruction quality. The average single track Q{sup 2} value of 0.006 GeV{sup 2}/c{sup 2} can be reconstructed with about 4 % uncertainty in a first analysis of the Geant4 simulation, leading to a high total precision due to large electron numbers in the experiment.

Butterflyfishes as a System for Investigating Pair Bonding

KAUST Repository

Nowicki, Jessica; O'Connell, Lauren; Cowman, Peter F; Walker, Stefan; Coker, Darren James; Pratchett, Morgan

2017-01-01

from the late Miocene to recent. In six sympatric and wide-spread species representing a clade with one ancestrally reconstructed transition from paired to solitary grouping, we then verified social systems at Lizard Island, Australia. In situ

Evolution of sweet taste perception in hummingbirds by transformation of the ancestral umami receptor

Science.gov (United States)

Baldwin, Maude W.; Toda, Yasuka; Nakagita, Tomoya; O'Connell, Mary J.; Klasing, Kirk C.; Misaka, Takumi; Edwards, Scott V.; Liberles, Stephen D.

2015-01-01

Sensory systems define an animal's capacity for perception and can evolve to promote survival in new environmental niches. We have uncovered a noncanonical mechanism for sweet taste perception that evolved in hummingbirds since their divergence from insectivorous swifts, their closest relatives. We observed the widespread absence in birds of an essential subunit (T1R2) of the only known vertebrate sweet receptor, raising questions about how specialized nectar feeders such as hummingbirds sense sugars. Receptor expression studies revealed that the ancestral umami receptor (the T1R1-T1R3 heterodimer) was repurposed in hummingbirds to function as a carbohydrate receptor. Furthermore, the molecular recognition properties of T1R1-T1R3 guided taste behavior in captive and wild hummingbirds. We propose that changing taste receptor function enabled hummingbirds to perceive and use nectar, facilitating the massive radiation of hummingbird species. PMID:25146290

State-of-the-art Machine Learning in event reconstruction and object identification

CERN Document Server

Kagan, Michael; The ATLAS collaboration

2017-01-01

Recent advances in deep learning have seen great success in the realms of computer vision, natural language processing, and broadly in data science. However, these new ideas are only just beginning to be applied to the analysis of High Energy Physics data. In this talk, I will discuss developments in the application of computer vision and deep learning techniques for event reconstruction and particle identification for the LHC .

Residual motion compensation in ECG-gated interventional cardiac vasculature reconstruction

International Nuclear Information System (INIS)

Schwemmer, C; Müller, K; Hornegger, J; Rohkohl, C; Lauritsch, G

2013-01-01

Three-dimensional reconstruction of cardiac vasculature from angiographic C-arm CT (rotational angiography) data is a major challenge. Motion artefacts corrupt image quality, reducing usability for diagnosis and guidance. Many state-of-the-art approaches depend on retrospective ECG-gating of projection data for image reconstruction. A trade-off has to be made regarding the size of the ECG-gating window. A large temporal window is desirable to avoid undersampling. However, residual motion will occur in a large window, causing motion artefacts. We present an algorithm to correct for residual motion. Our approach is based on a deformable 2D–2D registration between the forward projection of an initial, ECG-gated reconstruction, and the original projection data. The approach is fully automatic and does not require any complex segmentation of vasculature, or landmarks. The estimated motion is compensated for during the backprojection step of a subsequent reconstruction. We evaluated the method using the publicly available CAVAREV platform and on six human clinical datasets. We found a better visibility of structure, reduced motion artefacts, and increased sharpness of the vessels in the compensated reconstructions compared to the initial reconstructions. At the time of writing, our algorithm outperforms the leading result of the CAVAREV ranking list. For the clinical datasets, we found an average reduction of motion artefacts by 13 ± 6%. Vessel sharpness was improved by 25 ± 12% on average. (paper)

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

Breast Reconstruction Following Cancer Treatment.

Science.gov (United States)

Gerber, Bernd; Marx, Mario; Untch, Michael; Faridi, Andree

2015-08-31

About 8000 breast reconstructions after mastectomy are per - formed in Germany each year. It has become more difficult to advise patients because of the wide variety of heterologous and autologous techniques that are now available and because of changes in the recommendations about radiotherapy. This article is based on a review of pertinent articles (2005-2014) that were retrieved by a selective search employing the search terms "mastectomy" and "breast reconstruction." The goal of reconstruction is to achieve an oncologically safe and aestically satisfactory result for the patient over the long term. Heterologous, i.e., implant-based, breast reconstruction (IBR) and autologous breast reconstruction (ABR) are complementary techniques. Immediate reconstruction preserves the skin of the breast and its natural form and prevents the psychological trauma associated with mastectomy. If post-mastectomy radiotherapy (PMRT) is not indicated, implant-based reconstruction with or without a net/acellular dermal matrix (ADM) is a common option. Complications such as seroma formation, infection, and explantation are significantly more common when an ADM is used (15.3% vs. 5.4% ). If PMRT is performed, then the complication rate of implant-based breast reconstruction is 1 to 48% ; in particular, Baker grade III/IV capsular fibrosis occurs in 7 to 22% of patients, and the prosthesis must be explanted in 9 to 41% . Primary or, preferably, secondary autologous reconstruction is an alternative. The results of ABR are more stable over the long term, but the operation is markedly more complex. Autologous breast reconstruction after PMRT does not increase the risk of serious complications (20.5% vs. 17.9% without radiotherapy). No randomized controlled trials have yet been conducted to compare the reconstructive techniques with each other. If radiotherapy will not be performed, immediate reconstruction with an implant is recommended. On the other hand, if post-mastectomy radiotherapy

Oblique Photogrammetry Supporting 3d Urban Reconstruction of Complex Scenarios

Science.gov (United States)

Toschi, I.; Ramos, M. M.; Nocerino, E.; Menna, F.; Remondino, F.; Moe, K.; Poli, D.; Legat, K.; Fassi, F.

2017-05-01

Accurate 3D city models represent an important source of geospatial information to support various "smart city" applications, such as space management, energy assessment, 3D cartography, noise and pollution mapping as well as disaster management. Even though remarkable progress has been made in recent years, there are still many open issues, especially when it comes to the 3D modelling of complex urban scenarios like historical and densely-built city centres featuring narrow streets and non-conventional building shapes. Most approaches introduce strong building priors/constraints on symmetry and roof typology that penalize urban environments having high variations of roof shapes. Furthermore, although oblique photogrammetry is rapidly maturing, the use of slanted views for façade reconstruction is not completely included in the reconstruction pipeline of state-of-the-art software. This paper aims to investigate state-of-the-art methods for 3D building modelling in complex urban scenarios with the support of oblique airborne images. A reconstruction approach based on roof primitives fitting is tested. Oblique imagery is then exploited to support the manual editing of the generated building models. At the same time, mobile mapping data are collected at cm resolution and then integrated with the aerial ones. All approaches are tested on the historical city centre of Bergamo (Italy).

Centromere Destiny in Dicentric Chromosomes: New Insights from the Evolution of Human Chromosome 2 Ancestral Centromeric Region.

Science.gov (United States)

Chiatante, Giorgia; Giannuzzi, Giuliana; Calabrese, Francesco Maria; Eichler, Evan E; Ventura, Mario

2017-07-01

Dicentric chromosomes are products of genomic rearrangements that place two centromeres on the same chromosome. Due to the presence of two primary constrictions, they are inherently unstable and overcome their instability by epigenetically inactivating and/or deleting one of the two centromeres, thus resulting in functionally monocentric chromosomes that segregate normally during cell division. Our understanding to date of dicentric chromosome formation, behavior and fate has been largely inferred from observational studies in plants and humans as well as artificially produced de novo dicentrics in yeast and in human cells. We investigate the most recent product of a chromosome fusion event fixed in the human lineage, human chromosome 2, whose stability was acquired by the suppression of one centromere, resulting in a unique difference in chromosome number between humans (46 chromosomes) and our most closely related ape relatives (48 chromosomes). Using molecular cytogenetics, sequencing, and comparative sequence data, we deeply characterize the relicts of the chromosome 2q ancestral centromere and its flanking regions, gaining insight into the ancestral organization that can be easily broadened to all acrocentric chromosome centromeres. Moreover, our analyses offered the opportunity to trace the evolutionary history of rDNA and satellite III sequences among great apes, thus suggesting a new hypothesis for the preferential inactivation of some human centromeres, including IIq. Our results suggest two possible centromere inactivation models to explain the evolutionarily stabilization of human chromosome 2 over the last 5-6 million years. Our results strongly favor centromere excision through a one-step process. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Fast implementations of reconstruction-based scatter compensation in fully 3D SPECT image reconstruction

International Nuclear Information System (INIS)

Kadrmas, Dan J.; Karimi, Seemeen S.; Frey, Eric C.; Tsui, Benjamin M.W.

1998-01-01

Accurate scatter compensation in SPECT can be performed by modelling the scatter response function during the reconstruction process. This method is called reconstruction-based scatter compensation (RBSC). It has been shown that RBSC has a number of advantages over other methods of compensating for scatter, but using RBSC for fully 3D compensation has resulted in prohibitively long reconstruction times. In this work we propose two new methods that can be used in conjunction with existing methods to achieve marked reductions in RBSC reconstruction times. The first method, coarse-grid scatter modelling, significantly accelerates the scatter model by exploiting the fact that scatter is dominated by low-frequency information. The second method, intermittent RBSC, further accelerates the reconstruction process by limiting the number of iterations during which scatter is modelled. The fast implementations were evaluated using a Monte Carlo simulated experiment of the 3D MCAT phantom with 99m Tc tracer, and also using experimentally acquired data with 201 Tl tracer. Results indicated that these fast methods can reconstruct, with fully 3D compensation, images very similar to those obtained using standard RBSC methods, and in reconstruction times that are an order of magnitude shorter. Using these methods, fully 3D iterative reconstruction with RBSC can be performed well within the realm of clinically realistic times (under 10 minutes for 64x64x24 image reconstruction). (author)

Update on orbital reconstruction.

Science.gov (United States)

Chen, Chien-Tzung; Chen, Yu-Ray

2010-08-01

Orbital trauma is common and frequently complicated by ocular injuries. The recent literature on orbital fracture is analyzed with emphasis on epidemiological data assessment, surgical timing, method of approach and reconstruction materials. Computed tomographic (CT) scan has become a routine evaluation tool for orbital trauma, and mobile CT can be applied intraoperatively if necessary. Concomitant serious ocular injury should be carefully evaluated preoperatively. Patients presenting with nonresolving oculocardiac reflex, 'white-eyed' blowout fracture, or diplopia with a positive forced duction test and CT evidence of orbital tissue entrapment require early surgical repair. Otherwise, enophthalmos can be corrected by late surgery with a similar outcome to early surgery. The use of an endoscope-assisted approach for orbital reconstruction continues to grow, offering an alternative method. Advances in alloplastic materials have improved surgical outcome and shortened operating time. In this review of modern orbital reconstruction, several controversial issues such as surgical indication, surgical timing, method of approach and choice of reconstruction material are discussed. Preoperative fine-cut CT image and thorough ophthalmologic examination are key elements to determine surgical indications. The choice of surgical approach and reconstruction materials much depends on the surgeon's experience and the reconstruction area. Prefabricated alloplastic implants together with image software and stereolithographic models are significant advances that help to more accurately reconstruct the traumatized orbit. The recent evolution of orbit reconstruction improves functional and aesthetic results and minimizes surgical complications.

Reconstruction of missed critical frequency of F2-layer over Mexico using TEC

Science.gov (United States)

Sergeeva, M. A.; Maltseva, O. A.; Gonzalez-Esparza, A.; Romero Hernandez, E.; De la Luz, V.; Rodriguez-Martinez, M. R.

2016-12-01

The study of the Earth's ionosphere's state is one of the key issues within the Space Weather monitoring task. It is hard to overestimate the importance of diagnostics of its current state and forecasts of Space Weather conditions. There are different methods of short-time predictions for the ionosphere state change. The real-time monitoring of the ionospheric Total Electron Content (TEC) provides the opportunity to choose an appropriate technique for the particular observation point on the Earth. From September 2015 the continuous monitoring of TEC variations over the territory of Mexico is performed by the Mexican Space Weather Service (SCiESMEX). Regular patterns of the diurnal and seasonal TEC variations were revealed in base of past statistics and real-time observations which can be used to test the prediction method. Some specific features of the ionosphere behaviour are discussed. However, with all the merits of TEC as an ionospheric parameter, for the full picture of the processes in the ionosphere and for practical applications it is needed to identify the behaviour of other principal ionospheric parameters provided by ionosondes. Currently, SCiESMEX works on the project of the ionosonde installation in Mexico. This study was focused on the reconstruction of the critical frequency of F2-layer of the ionosphere (foF2) when this data is missing. For this purpose measurements of TEC and the median value of the equivalent slab thickness of the ionosphere were used. First, the foF2 values reconstruction was made for the case of the ionosonde data being absent during some hours or days. Second, the possibility of foF2 reconstruction was estimated for the Mexican region having no ionosonde using local TEC data and foF2 data obtained in the regions close to Mexico. Calculations were performed for quiet and disturbed periods. The results of reconstruction were compared to the foF2 obtained from the International Reference Model and to median foF2 values. Comparison

Biogeographic origins of the viviparous sea snake assemblage (Elapidae) of the Indian Ocean

DEFF Research Database (Denmark)

Ukuwela, D P; Lee, Michael S. Y.; Redsted Rasmussen, Arne

2017-01-01

Abstract: One of the primary goals in biogeography is to understand how different biotas have been assembled in different regions of the world. The presence of the viviparous sea snakes in the Indian Ocean (IO) poses a unique question in this regard due to their evolutionary origins in Australasia...... (Australia and New Guinea). Here, we examined the origins and patterns of colonization of the IO sea snake assemblage through time-calibrated molecular phylogenies and ancestral area reconstructions. We further evaluated how past and present barriers to dispersal affect genetic diversity of IO sea snakes...... by examining the population genetic structure of the widespread sea snake, Hydrophis curtus. Our phylogenetic analyses and ancestral area reconstructions strongly indicate that the majority of the IO sea snakes are derived from the Southeast Asian (SEA) sea snake fauna through dispersal and colonization...

Federal Health Coverage Mandates and Health Care Utilization: The Case of the Women's Health and Cancer Rights Act and Use of Breast Reconstruction Surgery.

Science.gov (United States)

Xie, Yang; Tang, Yuexin; Wehby, George L

2015-08-01

Utilization of breast reconstruction services remains low among women who underwent mastectomy despite the improvement in quality of life associated with this treatment. The objective of this study is to identify the effect of the Women's Health and Cancer Rights Act (WHCRA)-an understudied ongoing federal law that mandated insurance coverage of breast reconstruction following mastectomy beginning in 1999-on use of reconstructive surgery after mastectomy. We use a difference-in-differences (DD) approach to identify the change in breast reconstruction utilization induced by WHCRA by comparing the pre- and post-policy changes in utilization between states that did not have existing laws mandating coverage before the WHCRA (treatment group) and those that had such state laws (control group). The data are from the Surveillance, Epidemiology, and End Results program. The main sample includes 15,737 female patients who were under the age of 64 and underwent mastectomy within 4 months of diagnosis of early stage breast cancer during 1998 and 2000. Based on the DD model, the odds of using reconstruction services in the states without preexisting laws increased after the WHCRA by 31% in 1999 and 36% in 2000 (compared with 1998 before the WHCRA). These effects are masked in a simple pre/post model for change in reconstruction across all states. Additional analyses through 2007 indicate that the WHCRA had long-term effects on utilization. Furthermore, analyses by state indicate that most states in the treatment group experienced a significance increase in utilization. The use of breast reconstruction after mastectomy significantly increased after the WHCRA. At a minimum, our estimates may be considered the lower bound of the real policy effect.

Improving parallel imaging by jointly reconstructing multi-contrast data.

Science.gov (United States)

Bilgic, Berkin; Kim, Tae Hyung; Liao, Congyu; Manhard, Mary Kate; Wald, Lawrence L; Haldar, Justin P; Setsompop, Kawin

2018-08-01

To develop parallel imaging techniques that simultaneously exploit coil sensitivity encoding, image phase prior information, similarities across multiple images, and complementary k-space sampling for highly accelerated data acquisition. We introduce joint virtual coil (JVC)-generalized autocalibrating partially parallel acquisitions (GRAPPA) to jointly reconstruct data acquired with different contrast preparations, and show its application in 2D, 3D, and simultaneous multi-slice (SMS) acquisitions. We extend the joint parallel imaging concept to exploit limited support and smooth phase constraints through Joint (J-) LORAKS formulation. J-LORAKS allows joint parallel imaging from limited autocalibration signal region, as well as permitting partial Fourier sampling and calibrationless reconstruction. We demonstrate highly accelerated 2D balanced steady-state free precession with phase cycling, SMS multi-echo spin echo, 3D multi-echo magnetization-prepared rapid gradient echo, and multi-echo gradient recalled echo acquisitions in vivo. Compared to conventional GRAPPA, proposed joint acquisition/reconstruction techniques provide more than 2-fold reduction in reconstruction error. JVC-GRAPPA takes advantage of additional spatial encoding from phase information and image similarity, and employs different sampling patterns across acquisitions. J-LORAKS achieves a more parsimonious low-rank representation of local k-space by considering multiple images as additional coils. Both approaches provide dramatic improvement in artifact and noise mitigation over conventional single-contrast parallel imaging reconstruction. Magn Reson Med 80:619-632, 2018. © 2018 International Society for Magnetic Resonance in Medicine. © 2018 International Society for Magnetic Resonance in Medicine.

Precipitation Reconstructions and Periods of Drought in the Upper Green River Basin, Wyoming, USA

Science.gov (United States)

Follum, M.; Barnett, A.; Bellamy, J.; Gray, S.; Tootle, G.

2008-12-01

Due to recent drought and stress on water supplies in the Colorado River Compact States, more emphasis has been placed on the study of water resources in the Upper Green River Basin (UGRB) of Wyoming, Utah, and Colorado. The research described here focuses on the creation of long-duration precipitation records for the UGRB using tree-ring chronologies. When combined with existing proxy streamflow reconstructions and drought frequency analysis, these records offer a detailed look at hydrologic variability in the UGRB. Approximately thirty-three existing tree ring chronologies were analyzed for the UGRB area. Several new tree ring chronologies were also developed to enhance the accuracy and the geographical diversity of the resulting tree-ring reconstructions. In total, three new Douglas-fir (Pseudotsuga menziesii) and four new limber pine (Pinus flexilis) sites were added to the available tree-ring chronologies in this area. Tree-ring based reconstructions of annual (previous July through current June) precipitation were then created for each of the seventeen sub-watersheds in the UGRB. Reconstructed precipitation records extend back to at least 1654 AD, with reconstructions for some sub-basins beginning pre-1500. Variance explained (i.e. adjusted R2) ranged from 0.41 to 0.74, and the reconstructions performed well in a variety of verification tests. Additional analyses focused on stochastic estimation of drought frequency and return period, and detailed comparisons between reconstructed records and instrumental observations. Overall, this work points to the prevalence of severe, widespread drought in the UGRB. These analyses also highlight the relative wetness and lack of sustained dry periods during the instrumental period (1895-Present). Such long- term assessments are, in turn, vital tools as the Compact States contemplate the "Law of the River" in the face of climate change and ever-growing water demands.

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)

Accurate 3D reconstruction by a new PDS-OSEM algorithm for HRRT

International Nuclear Information System (INIS)

Chen, Tai-Been; Horng-Shing Lu, Henry; Kim, Hang-Keun; Son, Young-Don; Cho, Zang- Hee

2014-01-01

State-of-the-art high resolution research tomography (HRRT) provides high resolution PET images with full 3D human brain scanning. But, a short time frame in dynamic study causes many problems related to the low counts in the acquired data. The PDS-OSEM algorithm was proposed to reconstruct the HRRT image with a high signal-to-noise ratio that provides accurate information for dynamic data. The new algorithm was evaluated by simulated image, empirical phantoms, and real human brain data. Meanwhile, the time activity curve was adopted to validate a reconstructed performance of dynamic data between PDS-OSEM and OP-OSEM algorithms. According to simulated and empirical studies, the PDS-OSEM algorithm reconstructs images with higher quality, higher accuracy, less noise, and less average sum of square error than those of OP-OSEM. The presented algorithm is useful to provide quality images under the condition of low count rates in dynamic studies with a short scan time. - Highlights: • The PDS-OSEM reconstructs PET images with iteratively compensating random and scatter corrections from prompt sinogram. • The PDS-OSEM can reconstruct PET images with low count data and data contaminations. • The PDS-OSEM provides less noise and higher quality of reconstructed images than those of OP-OSEM algorithm in statistical sense

Phylogeny and evolution of pharmacophagy in tiger moths (Lepidoptera: Erebidae: Arctiinae.

Directory of Open Access Journals (Sweden)

Jennifer M Zaspel

Full Text Available The focus of this study was to reconstruct a phylogenetic hypothesis for the moth subfamily Arctiinae (tiger moths, woolly bears to investigate the evolution of larval and adult pharmacophagy of pyrrolizidine alkaloids (PAs and the pathway to PA chemical specialization in Arctiinae. Pharmacophagy, collection of chemicals for non-nutritive purposes, is well documented in many species, including the model species Utetheisa ornatrix L. A total of 86 exemplar ingroup species representing tiger moth tribes and subtribes (68 genera and nine outgroup species were selected. Ingroup species included the most species-rich generic groups to represent the diversity of host-plant associations and pharmacophagous behaviors found throughout Arctiinae. Up to nine genetic markers were sequenced: one mitochondrial (COI barcode region, one nuclear rRNA (D2 region, 28S rRNA, and seven nuclear protein-coding gene fragments: elongation factor 1-α protein, wingless, ribosomal protein subunit S5, carbamoylphosphate synthase domain regions, glyceraldehyde-3-phosphate dehydrogenase, isocitrate dehydrogenase and cytosolic malate dehydrogenase. A total of 6984 bp was obtained for most species. These data were analyzed using model-based phylogenetic methods: maximum likelihood (ML and Bayesian inference (BI. Ancestral pharmacophagous behaviors and obligate PA associations were reconstructed using the resulting Bayes topology and Reconstructing Ancestral States in Phylogenies (RASP software. Our results corroborate earlier studies on the evolution of adult pharmacophagous behaviors, suggesting that this behavior arose multiple times and is concentrated in the phaegopterine-euchromiine-ctenuchine clade (PEC. Our results suggest that PA specialization may have arisen early in the phylogeny of the subfamily and that facultative larval pharmacophagous behaviors are the derived condition.

Consistent reconstruction of 4D fetal heart ultrasound images to cope with fetal motion.

Science.gov (United States)

Tanner, Christine; Flach, Barbara; Eggenberger, Céline; Mattausch, Oliver; Bajka, Michael; Goksel, Orcun

2017-08-01

4D ultrasound imaging of the fetal heart relies on reconstructions from B-mode images. In the presence of fetal motion, current approaches suffer from artifacts, which are unrecoverable for single sweeps. We propose to use many sweeps and exploit the resulting redundancy to automatically recover from motion by reconstructing a 4D image which is consistent in phase, space, and time. An interactive visualization framework to view animated ultrasound slices from 4D reconstructions on arbitrary planes was developed using a magnetically tracked mock probe. We first quantified the performance of 10 4D reconstruction formulations on simulated data. Reconstructions of 14 in vivo sequences by a baseline, the current state-of-the-art, and the proposed approach were then visually ranked with respect to temporal quality on orthogonal views. Rankings from 5 observers showed that the proposed 4D reconstruction approach significantly improves temporal image quality in comparison with the baseline. The 4D reconstructions of the baseline and the proposed methods were then inspected interactively for accessibility to clinically important views and rated for their clinical usefulness by an ultrasound specialist in obstetrics and gynecology. The reconstructions by the proposed method were rated as 'very useful' in 71% and were statistically significantly more useful than the baseline reconstructions. Multi-sweep fetal heart ultrasound acquisitions in combination with consistent 4D image reconstruction improves quality as well as clinical usefulness of the resulting 4D images in the presence of fetal motion.

Incomplete projection reconstruction of computed tomography based on the modified discrete algebraic reconstruction technique

Science.gov (United States)

Yang, Fuqiang; Zhang, Dinghua; Huang, Kuidong; Gao, Zongzhao; Yang, YaFei

2018-02-01

Based on the discrete algebraic reconstruction technique (DART), this study aims to address and test a new improved algorithm applied to incomplete projection data to generate a high quality reconstruction image by reducing the artifacts and noise in computed tomography. For the incomplete projections, an augmented Lagrangian based on compressed sensing is first used in the initial reconstruction for segmentation of the DART to get higher contrast graphics for boundary and non-boundary pixels. Then, the block matching 3D filtering operator was used to suppress the noise and to improve the gray distribution of the reconstructed image. Finally, simulation studies on the polychromatic spectrum were performed to test the performance of the new algorithm. Study results show a significant improvement in the signal-to-noise ratios (SNRs) and average gradients (AGs) of the images reconstructed from incomplete data. The SNRs and AGs of the new images reconstructed by DART-ALBM were on average 30%-40% and 10% higher than the images reconstructed by DART algorithms. Since the improved DART-ALBM algorithm has a better robustness to limited-view reconstruction, which not only makes the edge of the image clear but also makes the gray distribution of non-boundary pixels better, it has the potential to improve image quality from incomplete projections or sparse projections.

Fetal brain volumetry through MRI volumetric reconstruction and segmentation

Science.gov (United States)

Estroff, Judy A.; Barnewolt, Carol E.; Connolly, Susan A.; Warfield, Simon K.

2013-01-01

Purpose Fetal MRI volumetry is a useful technique but it is limited by a dependency upon motion-free scans, tedious manual segmentation, and spatial inaccuracy due to thick-slice scans. An image processing pipeline that addresses these limitations was developed and tested. Materials and methods The principal sequences acquired in fetal MRI clinical practice are multiple orthogonal single-shot fast spin echo scans. State-of-the-art image processing techniques were used for inter-slice motion correction and super-resolution reconstruction of high-resolution volumetric images from these scans. The reconstructed volume images were processed with intensity non-uniformity correction and the fetal brain extracted by using supervised automated segmentation. Results Reconstruction, segmentation and volumetry of the fetal brains for a cohort of twenty-five clinically acquired fetal MRI scans was done. Performance metrics for volume reconstruction, segmentation and volumetry were determined by comparing to manual tracings in five randomly chosen cases. Finally, analysis of the fetal brain and parenchymal volumes was performed based on the gestational age of the fetuses. Conclusion The image processing pipeline developed in this study enables volume rendering and accurate fetal brain volumetry by addressing the limitations of current volumetry techniques, which include dependency on motion-free scans, manual segmentation, and inaccurate thick-slice interpolation. PMID:20625848

BES-II fast data reconstruction

International Nuclear Information System (INIS)

Rong Gang; Zhang Jiawen; Guo Yiqing; Zhang Shaoqiang; Zhao Dixin

2002-01-01

The BES-II fast data reconstruction is reported. Based on PC FARM and/or a 'Distributed Clustered Linux PC System', BES-II fast data reconstruction system is set up. With this system the BES-II data can be fully reconstructed in about 20 minutes after data collection. It takes only 12 minutes to fully reconstruct 30000 events, collected with BES-II detector at BEPC Collider, with a P III-800 PC. The detector performance can be examined based on fully reconstructed data in about 20 minutes after data taking in the BES-II experiment

Mitogenomics and phylogenomics reveal priapulid worms as extant models of the ancestral Ecdysozoan.

Science.gov (United States)

Webster, Bonnie L; Copley, Richard R; Jenner, Ronald A; Mackenzie-Dodds, Jacqueline A; Bourlat, Sarah J; Rota-Stabelli, Omar; Littlewood, D T J; Telford, Maximilian J

2006-01-01

Research into arthropod evolution is hampered by the derived nature and rapid evolution of the best-studied out-group: the nematodes. We consider priapulids as an alternative out-group. Priapulids are a small phylum of bottom-dwelling marine worms; their tubular body with spiny proboscis or introvert has changed little over 520 million years and recognizable priapulids are common among exceptionally preserved Cambrian fossils. Using the complete mitochondrial genome and 42 nuclear genes from Priapulus caudatus, we show that priapulids are slowly evolving ecdysozoans; almost all these priapulid genes have evolved more slowly than nematode orthologs and the priapulid mitochondrial gene order may be unchanged since the Cambrian. Considering their primitive bodyplan and embryology and the great conservation of both nuclear and mitochondrial genomes, priapulids may deserve the popular epithet of "living fossil." Their study is likely to yield significant new insights into the early evolution of the Ecdysozoa and the origins of the arthropods and their kin as well as aiding inference of the morphology of ancestral Ecdysozoa and Bilateria and their genomes.

Estimation of 3D reconstruction errors in a stereo-vision system

Science.gov (United States)

Belhaoua, A.; Kohler, S.; Hirsch, E.

2009-06-01

The paper presents an approach for error estimation for the various steps of an automated 3D vision-based reconstruction procedure of manufactured workpieces. The process is based on a priori planning of the task and built around a cognitive intelligent sensory system using so-called Situation Graph Trees (SGT) as a planning tool. Such an automated quality control system requires the coordination of a set of complex processes performing sequentially data acquisition, its quantitative evaluation and the comparison with a reference model (e.g., CAD object model) in order to evaluate quantitatively the object. To ensure efficient quality control, the aim is to be able to state if reconstruction results fulfill tolerance rules or not. Thus, the goal is to evaluate independently the error for each step of the stereo-vision based 3D reconstruction (e.g., for calibration, contour segmentation, matching and reconstruction) and then to estimate the error for the whole system. In this contribution, we analyze particularly the segmentation error due to localization errors for extracted edge points supposed to belong to lines and curves composing the outline of the workpiece under evaluation. The fitting parameters describing these geometric features are used as quality measure to determine confidence intervals and finally to estimate the segmentation errors. These errors are then propagated through the whole reconstruction procedure, enabling to evaluate their effect on the final 3D reconstruction result, specifically on position uncertainties. Lastly, analysis of these error estimates enables to evaluate the quality of the 3D reconstruction, as illustrated by the shown experimental results.

Robust sparse image reconstruction of radio interferometric observations with PURIFY

Science.gov (United States)

Pratley, Luke; McEwen, Jason D.; d'Avezac, Mayeul; Carrillo, Rafael E.; Onose, Alexandru; Wiaux, Yves

2018-01-01

Next-generation radio interferometers, such as the Square Kilometre Array, will revolutionize our understanding of the Universe through their unprecedented sensitivity and resolution. However, to realize these goals significant challenges in image and data processing need to be overcome. The standard methods in radio interferometry for reconstructing images, such as CLEAN, have served the community well over the last few decades and have survived largely because they are pragmatic. However, they produce reconstructed interferometric images that are limited in quality and scalability for big data. In this work, we apply and evaluate alternative interferometric reconstruction methods that make use of state-of-the-art sparse image reconstruction algorithms motivated by compressive sensing, which have been implemented in the PURIFY software package. In particular, we implement and apply the proximal alternating direction method of multipliers algorithm presented in a recent article. First, we assess the impact of the interpolation kernel used to perform gridding and degridding on sparse image reconstruction. We find that the Kaiser-Bessel interpolation kernel performs as well as prolate spheroidal wave functions while providing a computational saving and an analytic form. Secondly, we apply PURIFY to real interferometric observations from the Very Large Array and the Australia Telescope Compact Array and find that images recovered by PURIFY are of higher quality than those recovered by CLEAN. Thirdly, we discuss how PURIFY reconstructions exhibit additional advantages over those recovered by CLEAN. The latest version of PURIFY, with developments presented in this work, is made publicly available.

One step linear reconstruction method for continuous wave diffuse optical tomography

Science.gov (United States)

Ukhrowiyah, N.; Yasin, M.

2017-09-01

The method one step linear reconstruction method for continuous wave diffuse optical tomography is proposed and demonstrated for polyvinyl chloride based material and breast phantom. Approximation which used in this method is selecting regulation coefficient and evaluating the difference between two states that corresponding to the data acquired without and with a change in optical properties. This method is used to recovery of optical parameters from measured boundary data of light propagation in the object. The research is demonstrated by simulation and experimental data. Numerical object is used to produce simulation data. Chloride based material and breast phantom sample is used to produce experimental data. Comparisons of results between experiment and simulation data are conducted to validate the proposed method. The results of the reconstruction image which is produced by the one step linear reconstruction method show that the image reconstruction almost same as the original object. This approach provides a means of imaging that is sensitive to changes in optical properties, which may be particularly useful for functional imaging used continuous wave diffuse optical tomography of early diagnosis of breast cancer.

Particle-flow reconstruction and global event description with the CMS detector

Energy Technology Data Exchange (ETDEWEB)

Sirunyan, Albert M; et al.

2017-06-15

The CMS apparatus was identified, a few years before the start of the LHC operation at CERN, to feature properties well suited to particle-flow (PF) reconstruction: a highly-segmented tracker, a fine-grained electromagnetic calorimeter, a hermetic hadron calorimeter, a strong magnetic field, and an excellent muon spectrometer. A fully-fledged PF reconstruction algorithm tuned to the CMS detector was therefore developed and has been consistently used in physics analyses for the first time at a hadron collider. For each collision, the comprehensive list of final-state particles identified and reconstructed by the algorithm provides a global event description that leads to unprecedented CMS performance for jet and hadronic tau decay reconstruction, missing transverse momentum determination, and electron and muon identification. This approach also allows particles from pileup interactions to be identified and enables efficient pileup mitigation methods. The data collected by CMS at a centre-of-mass energy of 8 TeV show excellent agreement with the simulation and confirm the superior PF performance at least up to an average of 20 pileup interactions.

A multilocus molecular phylogeny of combtooth blennies (Percomorpha: Blennioidei: Blenniidae): Multiple invasions of intertidal habitats

KAUST Repository

Hundt, Peter J.

2014-01-01

The combtooth blennies (f. Blenniidae) is a diverse family of primarily marine fishes with approximately 387 species that inhabit subtidal, intertidal, supralittoral habitats in tropical and warm temperate regions throughout the world. The Blenniidae has typically been divided into six groups based on morphological characters: Blenniini, Nemophini, Omobranchini, Phenablenniini, Parablenniini, and Salariini. There is, however, considerable debate over the validity of these groups and their relationships. Since little is known about the relationships in this group, other aspects of their evolutionary history, such as habitat evolution and remain unexplored. Herein, we use Bayesian and maximum likelihood analyses of four nuclear loci (ENC1, myh6, ptr, and tbr1) from 102 species, representing 41 genera, to resolve the phylogeny of the Blenniidae, determine the validity of the previously recognized groupings, and explore the evolution of habitat association using ancestral state reconstruction. Bayesian and maximum likelihood analyses of the resulting 3100. bp of DNA sequence produced nearly identical topologies, and identified many well-supported clades. Of these clades, Nemophini was the only traditionally recognized group strongly supported as monophyletic. This highly resolved and thoroughly sampled blenniid phylogeny provides strong evidence that the traditional rank-based classification does not adequately delimit monophyletic groups with the Blenniidae. This phylogeny redefines the taxonomy of the group and supports the use of 13 unranked clades for the classification of blenniids. Ancestral state reconstructions identified four independent invasions of intertidal habitats within the Blenniidae, and subsequent invasions into supralittoral and freshwater habitats from these groups. The independent invasions of intertidal habitats are likely to have played an important role in the evolutionary history of blennies. © 2013 Elsevier Inc.

Depiction of lower limb venous anatomy in patients undergoing interventional deep venous reconstruction-the role of balanced steady state free precession MRI.

Science.gov (United States)

Helyar, Vincent G; Gupta, Yuri; Blakeway, Lyndall; Charles-Edwards, Geoff; Katsanos, Konstantinos; Karunanithy, Narayan

2018-02-01

This study evaluates the use of balanced steady-state free precession MRI (bSSFP-MRI) in the diagnostic work-up of patients undergoing interventional deep venous reconstruction (I-DVR). Intravenous digital subtraction angiography (IVDSA) was used as the gold-standard for comparison to assess disease extent and severity. A retrospective comparison of bSSFP-MRI to IVDSA was performed in all patients undergoing both examinations for treatment planning prior to I-DVR. The severity of disease in each venous segment was graded by two board-certified radiologists working independently, according to a predetermined classification system. In total, 44 patients (225 venous segments) fulfilled the inclusion criteria. A total of 156 abnormal venous segments were diagnosed using bSSFP-MRI compared with 151 using IVDSA. The prevalence of disease was higher in the iliac and femoral segments (range, 79.6-88.6%). Overall sensitivity, specificity, positive likelihood ratio, negative likelihood ratio and the diagnostic ratio for bSSFP-MRI were 99.3%, 91.9%, 12.3, 0.007 and 1700, respectively. This study supports the use of non-contrast balanced SSFP-MRI in the assessment of the deep veins of the lower limb prior to I-DVR. The technique offers an accurate, fast and non-invasive alternative to IVDSA. Advances in Knowledge: Although balanced SSFP-MRI is commonly used in cardiac imaging, its use elsewhere is limited and its use in evaluating the deep veins prior to interventional reconstruction is not described. Our study demonstrates the usefulness of this technique in the work-up of patients awaiting interventional venous reconstruction compared with the current gold standard.

Comprehensive Use of Curvature for Robust and Accurate Online Surface Reconstruction.

Science.gov (United States)

Lefloch, Damien; Kluge, Markus; Sarbolandi, Hamed; Weyrich, Tim; Kolb, Andreas

2017-12-01

Interactive real-time scene acquisition from hand-held depth cameras has recently developed much momentum, enabling applications in ad-hoc object acquisition, augmented reality and other fields. A key challenge to online reconstruction remains error accumulation in the reconstructed camera trajectory, due to drift-inducing instabilities in the range scan alignments of the underlying iterative-closest-point (ICP) algorithm. Various strategies have been proposed to mitigate that drift, including SIFT-based pre-alignment, color-based weighting of ICP pairs, stronger weighting of edge features, and so on. In our work, we focus on surface curvature as a feature that is detectable on range scans alone and hence does not depend on accurate multi-sensor alignment. In contrast to previous work that took curvature into consideration, however, we treat curvature as an independent quantity that we consistently incorporate into every stage of the real-time reconstruction pipeline, including densely curvature-weighted ICP, range image fusion, local surface reconstruction, and rendering. Using multiple benchmark sequences, and in direct comparison to other state-of-the-art online acquisition systems, we show that our approach significantly reduces drift, both when analyzing individual pipeline stages in isolation, as well as seen across the online reconstruction pipeline as a whole.

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

International Nuclear Information System (INIS)

Widner, Thomas E.; email = twidner@jajoneses.com

1999-01-01

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

New possibilities of three-dimensional reconstruction of computed tomography scans

International Nuclear Information System (INIS)

Herman, M.; Tarjan, Z.; Pozzi-Mucelli, R.S.

1996-01-01

Three-dimensional (3D) computed tomography (CT) scan reconstructions provide impressive and illustrative images of various parts of the human body. Such images are reconstructed from a series of basic CT scans by dedicated software. The state of the art in 3D computed tomography is demonstrated with emphasis on the imaging of soft tissues. Examples are presented of imaging the craniofacial and maxillofacial complex, central nervous system, cardiovascular system, musculoskeletal system, gastrointestinal and urogenital systems, and respiratory system, and their potential in clinical practice is discussed. Although contributing no new essential diagnostic information against conventional CT scans, 3D scans can help in spatial orientation. 11 figs., 25 refs

The Cost-Effectiveness of Anterior Cruciate Ligament Reconstruction in Competitive Athletes.

Science.gov (United States)

Stewart, Bruce A; Momaya, Amit M; Silverstein, Marc D; Lintner, David

2017-01-01

Competitive athletes value the ability to return to competitive play after the treatment of anterior cruciate ligament (ACL) injuries. ACL reconstruction has high success rates for return to play, but some studies indicate that patients may do well with nonoperative physical therapy treatment. To evaluate the cost-effectiveness of the treatment of acute ACL tears with either initial surgical reconstruction or physical therapy in competitive athletes. Economic and decision analysis; Level of evidence, 2. The incremental cost, incremental effectiveness, and incremental cost-effectiveness ratio (ICER) of ACL reconstruction compared with physical therapy were calculated from a cost-effectiveness analysis of ACL reconstruction compared with physical therapy for the initial management of acute ACL injuries in competitive athletes. The ACL reconstruction strategy and the physical therapy strategy were represented as Markov models. Costs and quality-adjusted life-years (QALYs) were evaluated over a 6-year time horizon and were analyzed from a societal perspective. Quality of life and probabilities of clinical outcomes were obtained from the peer-reviewed literature, and costs were compiled from a large academic hospital in the United States. One-way, 2-way, and probabilistic sensitivity analyses were used to assess the effect of uncertainty in variables on the ICER of ACL reconstruction. The ICER of ACL reconstruction compared with physical therapy was $22,702 per QALY gained. The ICER was most sensitive to the quality of life of returning to play or not returning to play, costs, and duration of follow-up but relatively insensitive to the rates and costs of complications, probabilities of return to play for both operative and nonoperative treatments, and discount rate. ACL reconstruction is a cost-effective strategy for competitive athletes with an ACL injury.

Hybrid spectral CT reconstruction.

Directory of Open Access Journals (Sweden)

Darin P Clark

Full Text Available Current photon counting x-ray detector (PCD technology faces limitations associated with spectral fidelity and photon starvation. One strategy for addressing these limitations is to supplement PCD data with high-resolution, low-noise data acquired with an energy-integrating detector (EID. In this work, we propose an iterative, hybrid reconstruction technique which combines the spectral properties of PCD data with the resolution and signal-to-noise characteristics of EID data. Our hybrid reconstruction technique is based on an algebraic model of data fidelity which substitutes the EID data into the data fidelity term associated with the PCD reconstruction, resulting in a joint reconstruction problem. Within the split Bregman framework, these data fidelity constraints are minimized subject to additional constraints on spectral rank and on joint intensity-gradient sparsity measured between the reconstructions of the EID and PCD data. Following a derivation of the proposed technique, we apply it to the reconstruction of a digital phantom which contains realistic concentrations of iodine, barium, and calcium encountered in small-animal micro-CT. The results of this experiment suggest reliable separation and detection of iodine at concentrations ≥ 5 mg/ml and barium at concentrations ≥ 10 mg/ml in 2-mm features for EID and PCD data reconstructed with inherent spatial resolutions of 176 μm and 254 μm, respectively (point spread function, FWHM. Furthermore, hybrid reconstruction is demonstrated to enhance spatial resolution within material decomposition results and to improve low-contrast detectability by as much as 2.6 times relative to reconstruction with PCD data only. The parameters of the simulation experiment are based on an in vivo micro-CT experiment conducted in a mouse model of soft-tissue sarcoma. Material decomposition results produced from this in vivo data demonstrate the feasibility of distinguishing two K-edge contrast agents with

Hybrid spectral CT reconstruction

Science.gov (United States)

Clark, Darin P.

2017-01-01

Current photon counting x-ray detector (PCD) technology faces limitations associated with spectral fidelity and photon starvation. One strategy for addressing these limitations is to supplement PCD data with high-resolution, low-noise data acquired with an energy-integrating detector (EID). In this work, we propose an iterative, hybrid reconstruction technique which combines the spectral properties of PCD data with the resolution and signal-to-noise characteristics of EID data. Our hybrid reconstruction technique is based on an algebraic model of data fidelity which substitutes the EID data into the data fidelity term associated with the PCD reconstruction, resulting in a joint reconstruction problem. Within the split Bregman framework, these data fidelity constraints are minimized subject to additional constraints on spectral rank and on joint intensity-gradient sparsity measured between the reconstructions of the EID and PCD data. Following a derivation of the proposed technique, we apply it to the reconstruction of a digital phantom which contains realistic concentrations of iodine, barium, and calcium encountered in small-animal micro-CT. The results of this experiment suggest reliable separation and detection of iodine at concentrations ≥ 5 mg/ml and barium at concentrations ≥ 10 mg/ml in 2-mm features for EID and PCD data reconstructed with inherent spatial resolutions of 176 μm and 254 μm, respectively (point spread function, FWHM). Furthermore, hybrid reconstruction is demonstrated to enhance spatial resolution within material decomposition results and to improve low-contrast detectability by as much as 2.6 times relative to reconstruction with PCD data only. The parameters of the simulation experiment are based on an in vivo micro-CT experiment conducted in a mouse model of soft-tissue sarcoma. Material decomposition results produced from this in vivo data demonstrate the feasibility of distinguishing two K-edge contrast agents with a spectral

A new approach of equilibrium reconstruction for ITER

International Nuclear Information System (INIS)

Imazawa, R.; Kawano, Y.; Kusama, Y.

2011-01-01

We have proposed a new approach for equilibrium reconstruction that can be applied to ITER-like burning plasmas. In this study, we have focused on carrying out equilibrium reconstruction using polarimetry, which is feasible for ITER-like burning plasmas. Polarimetry in burning plasmas is different from that in the existing tokamaks in two regards: (1) increased importance of the relativistic effects and (2) significant coupling with the Faraday and Cotton–Mouton effects. We found that when polarimetric data (orientation angle, θ, and ellipticity angle, ε, of a polarization state) are used as the constraints in the equilibrium reconstruction, the optimum weighting factors for θ and ε depend on the magnetic surfaces through which the viewing chord of polarimetry passes. We applied our approach to the operation scenarios II (S2) and IV (S4) in ITER. In the case where the viewing chords are via both the equatorial and upper ports, the measurement requirements for the accuracy of the q-profile in ITER (±10%) were satisfied in S2 and S4 when the measuring errors of θ and ε were less than 0.5° and 3°, respectively.

Evolution of the staminode in a representative sample of Scrophularia and its role as nectar safeguard in three widespread species

Science.gov (United States)

Rodríguez-Riaño, Tomás; Valtueña, Francisco J.; López, Josefa; Navarro-Pérez, María Luisa; Pérez-Bote, José Luis; Ortega-Olivencia, Ana

2015-06-01

Approximately 30 % of the genera of Scrophulariaceae s.str. have a staminode, which is the remnant of a sterile stamen. However, there are no studies of the functionality or evolutionary pattern of staminodes in that family. This paper investigates three Scrophularia species with different staminode sizes to determine if the staminode safeguards nectar from dilution by rainwater and if it influences pollinator behavior. We also study staminode evolution and ancestral state reconstruction onto a phylogeny containing 71 species and subspecies with four different staminode developmental stages: tiny, large, enormous, and absent. The results showed that large staminodes did not hinder nectar collection or modify pollinator-visiting time but acted as a barrier to reduce rainwater entry. The latter reduced the dilution of nectar, which did not occur with tiny staminodes. The phylogenetic study revealed that the ancestral state in the genus corresponds with the presence of a large staminode vs. the tiny and enormous staminodes that are considered as derived. The complete disappearance of the staminode has occurred independently at least twice. Events occurred that increased or reduced the staminode size in one of the clades (Clade II), which includes species of sect. Caninae; most of these events occurred during the Pleistocene (0.6-2.7 Ma).

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

Directory of Open Access Journals (Sweden)

Violetta R Beklemisheva

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

An integrative systematic framework helps to reconstruct skeletal evolution of glass sponges (Porifera, Hexactinellida).

Science.gov (United States)

Dohrmann, Martin; Kelley, Christopher; Kelly, Michelle; Pisera, Andrzej; Hooper, John N A; Reiswig, Henry M

2017-01-01

frameworks. We find that of these four approaches, total-evidence analysis using MP gave the most plausible results concerning congruence with existing phylogenetic and taxonomic hypotheses, whereas the other methods, especially ML and binning, performed more poorly. We use our total-evidence phylogeny of all extant glass sponge genera for ancestral state reconstruction of morphological characters in MP and ML frameworks, gaining new insights into the evolution of major hexactinellid body plans and other characters such as different spicule types. Our study demonstrates how a comprehensive, albeit in some parts provisional, phylogeny of a larger taxon can be achieved with an integrative approach utilizing molecular and morphological data, and how this can be used as a basis for understanding phenotypic evolution. The datasets and associated trees presented here are intended as a resource and starting point for future work on glass sponge evolution.

Multi-view Multi-sparsity Kernel Reconstruction for Multi-class Image Classification

KAUST Repository

Zhu, Xiaofeng

2015-05-28

This paper addresses the problem of multi-class image classification by proposing a novel multi-view multi-sparsity kernel reconstruction (MMKR for short) model. Given images (including test images and training images) representing with multiple visual features, the MMKR first maps them into a high-dimensional space, e.g., a reproducing kernel Hilbert space (RKHS), where test images are then linearly reconstructed by some representative training images, rather than all of them. Furthermore a classification rule is proposed to classify test images. Experimental results on real datasets show the effectiveness of the proposed MMKR while comparing to state-of-the-art algorithms.

Control-oriented modeling of the plasma particle density in tokamaks and application to real-time density profile reconstruction

NARCIS (Netherlands)

Blanken, T.C.; Felici, F.; Rapson, C.J.; de Baar, M.R.; Heemels, W.P.M.H.

2018-01-01

A model-based approach to real-time reconstruction of the particle density profile in tokamak plasmas is presented, based on a dynamic state estimator. Traditionally, the density profile is reconstructed in real-time by solving an ill-conditioned inversion problem using a measurement at a single

Miocene magmatism in the Bodie Hills volcanic field, California and Nevada: A long-lived eruptive center in the southern segment of the ancestral Cascades arc

Science.gov (United States)

John, David A.; du Bray, Edward A.; Blakely, Richard J.; Fleck, Robert J.; Vikre, Peter; Box, Stephen E.; Moring, Barry C.

2012-01-01

The Middle to Late Miocene Bodie Hills volcanic field is a >700 km2, long-lived (∼9 Ma) but episodic eruptive center in the southern segment of the ancestral Cascades arc north of Mono Lake (California, U.S.). It consists of ∼20 major eruptive units, including 4 trachyandesite stratovolcanoes emplaced along the margins of the field, and numerous, more centrally located silicic trachyandesite to rhyolite flow dome complexes. Bodie Hills volcanism was episodic with two peak periods of eruptive activity: an early period ca. 14.7–12.9 Ma that mostly formed trachyandesite stratovolcanoes and a later period between ca. 9.2 and 8.0 Ma dominated by large trachyandesite-dacite dome fields. A final period of small silicic dome emplacement occurred ca. 6 Ma. Aeromagnetic and gravity data suggest that many of the Miocene volcanoes have shallow plutonic roots that extend to depths ≥1–2 km below the surface, and much of the Bodie Hills may be underlain by low-density plutons presumably related to Miocene volcanism.Compositions of Bodie Hills volcanic rocks vary from ∼50 to 78 wt% SiO2, although rocks with Bodie Hills rocks are porphyritic, commonly containing 15–35 vol% phenocrysts of plagioclase, pyroxene, and hornblende ± biotite. The oldest eruptive units have the most mafic compositions, but volcanic rocks oscillated between mafic and intermediate to felsic compositions through time. Following a 2 Ma hiatus in volcanism, postsubduction rocks of the ca. 3.6–0.1 Ma, bimodal, high-K Aurora volcanic field erupted unconformably onto rocks of the Miocene Bodie Hills volcanic field.At the latitude of the Bodie Hills, subduction of the Farallon plate is inferred to have ended ca. 10 Ma, evolving to a transform plate margin. However, volcanism in the region continued until 8 Ma without an apparent change in rock composition or style of eruption. Equidimensional, polygenetic volcanoes and the absence of dike swarms suggest a low differential horizontal stress regime

Tomographic reconstruction by using FPSIRT (Fast Particle System Iterative Reconstruction Technique)

Energy Technology Data Exchange (ETDEWEB)

Moreira, Icaro Valgueiro M.; Melo, Silvio de Barros; Dantas, Carlos; Lima, Emerson Alexandre; Silva, Ricardo Martins; Cardoso, Halisson Alberdan C., E-mail: ivmm@cin.ufpe.br, E-mail: sbm@cin.ufpe.br, E-mail: rmas@cin.ufpe.br, E-mail: hacc@cin.ufpe.br, E-mail: ccd@ufpe.br, E-mail: eal@cin.ufpe.br [Universidade Federal de Pernambuco (UFPE), Recife, PE (Brazil)

2015-07-01

The PSIRT (Particle System Iterative Reconstruction Technique) is a method of tomographic image reconstruction primarily designed to work with configurations suitable for industrial applications. A particle system is an optimization technique inspired in real physical systems that associates to the reconstructing material a set of particles with certain physical features, subject to a force eld, which can produce movement. The system constantly updates the set of particles by repositioning them in such a way as to approach the equilibrium. The elastic potential along a trajectory is a function of the difference between the attenuation coefficient in the current configuration and the corresponding input data. PSIRT has been successfully used to reconstruct simulated and real objects subject to sets of parallel and fanbeam lines in different angles, representing typical gamma-ray tomographic arrangements. One of PSIRT's limitation was its performance, too slow for real time scenarios. In this work, it is presented a reformulation in PSIRT's computational model, which is able to grant the new algorithm, the FPSIRT - Fast System Iterative Reconstruction Technique, a performance up to 200-time faster than PSIRT's. In this work a comparison of their application to real and simulated data from the HSGT, High Speed Gamma Tomograph, is presented. (author)

Tomographic reconstruction by using FPSIRT (Fast Particle System Iterative Reconstruction Technique)

International Nuclear Information System (INIS)

Moreira, Icaro Valgueiro M.; Melo, Silvio de Barros; Dantas, Carlos; Lima, Emerson Alexandre; Silva, Ricardo Martins; Cardoso, Halisson Alberdan C.

2015-01-01

The PSIRT (Particle System Iterative Reconstruction Technique) is a method of tomographic image reconstruction primarily designed to work with configurations suitable for industrial applications. A particle system is an optimization technique inspired in real physical systems that associates to the reconstructing material a set of particles with certain physical features, subject to a force eld, which can produce movement. The system constantly updates the set of particles by repositioning them in such a way as to approach the equilibrium. The elastic potential along a trajectory is a function of the difference between the attenuation coefficient in the current configuration and the corresponding input data. PSIRT has been successfully used to reconstruct simulated and real objects subject to sets of parallel and fanbeam lines in different angles, representing typical gamma-ray tomographic arrangements. One of PSIRT's limitation was its performance, too slow for real time scenarios. In this work, it is presented a reformulation in PSIRT's computational model, which is able to grant the new algorithm, the FPSIRT - Fast System Iterative Reconstruction Technique, a performance up to 200-time faster than PSIRT's. In this work a comparison of their application to real and simulated data from the HSGT, High Speed Gamma Tomograph, is presented. (author)

From Endosymbiont to Host-Controlled Organelle: The Hijacking of Mitochondrial Protein Synthesis and Metabolism

NARCIS (Netherlands)

Gabaldon, T.; Huynen, M.A.

2007-01-01

Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the transition from a free-living cell to a specialized organelle, we compared a reconstructed ancestral

From endosymbiont to host-controlled organelle: the hijacking of mitochondrial protein synthesis and metabolism.

NARCIS (Netherlands)

Gabaldon, T.; Huynen, M.A.

2007-01-01

Mitochondria are eukaryotic organelles that originated from the endosymbiosis of an alpha-proteobacterium. To gain insight into the evolution of the mitochondrial proteome as it proceeded through the transition from a free-living cell to a specialized organelle, we compared a reconstructed ancestral

Constraints on mutational pathways of hemoglobin evolution

DEFF Research Database (Denmark)

Kumar, Amit; Natarajan, Chandrasekhar; Moriyama, Hideaki

2016-01-01

amino acid substitutions that occurred during an evolutionary reduction in hemoglobin (Hb)-O2 affinity in nightjars (nocturnal birds in the family Caprimulgidae).We selected nightjar Hbs for experimental study because ancestral sequence reconstructions indicated that the evolved reduction in Hb-O2...

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.

The evolving breast reconstruction

DEFF Research Database (Denmark)

Thomsen, Jørn Bo; Gunnarsson, Gudjon Leifur

2014-01-01

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

Reconstructing see-saw models

International Nuclear Information System (INIS)

Ibarra, Alejandro

2007-01-01

In this talk we discuss the prospects to reconstruct the high-energy see-saw Lagrangian from low energy experiments in supersymmetric scenarios. We show that the model with three right-handed neutrinos could be reconstructed in theory, but not in practice. Then, we discuss the prospects to reconstruct the model with two right-handed neutrinos, which is the minimal see-saw model able to accommodate neutrino observations. We identify the relevant processes to achieve this goal, and comment on the sensitivity of future experiments to them. We find the prospects much more promising and we emphasize in particular the importance of the observation of rare leptonic decays for the reconstruction of the right-handed neutrino masses

An ant genus-group (Prenolepis) illuminates the biogeography and drivers of insect diversification in the Indo-Pacific.

Science.gov (United States)

Matos-Maraví, Pável; Clouse, Ronald M; Sarnat, Eli M; Economo, Evan P; LaPolla, John S; Borovanska, Michaela; Rabeling, Christian; Czekanski-Moir, Jesse; Latumahina, Fransina; Wilson, Edward O; Janda, Milan

2018-06-01

The Malay Archipelago and the tropical South Pacific (hereafter the Indo-Pacific region) are considered biodiversity hotspots, yet a general understanding of the origins and diversification of species-rich groups in the region remains elusive. We aimed to test hypotheses for the evolutionary processes driving insect species diversity in the Indo-Pacific using a higher-level and comprehensive phylogenetic hypothesis for an ant clade consisting of seven genera. We estimated divergence times and reconstructed the biogeographical history of ant species in the Prenolepis genus-group (Formicidae: Formicinae: Lasiini). We used a fossil-calibrated phylogeny to infer ancestral geographical ranges utilizing a biogeographic model that includes founder-event speciation. Ancestral state reconstructions of the ants' ecological preferences, and diversification rates were estimated for selected Indo-Pacific clades. Overall, we report that faunal interchange between Asia and Australia has occurred since at least 20-25 Ma, and early dispersal to the Fijian Basin happened during the early and mid-Miocene (ca. 10-20 Ma). Differences in diversification rates across Indo-Pacific clades may be related to ecological preference breadth, which in turn may have facilitated geographical range expansions. Ancient dispersal routes suggested by our results agree with the palaeogeography of the region. For this particular group of ants, the rapid orogenesis in New Guinea and possibly subsequent ecological shifts may have promoted their rapid diversification and widespread distribution across the Indo-Pacific. Copyright © 2018 Elsevier Inc. All rights reserved.

The role of fusion in ant chromosome evolution: insights from cytogenetic analysis using a molecular phylogenetic approach in the genus mycetophylax.

Science.gov (United States)

Cardoso, Danon Clemes; das Graças Pompolo, Silvia; Cristiano, Maykon Passos; Tavares, Mara Garcia

2014-01-01

Among insect taxa, ants exhibit one of the most variable chromosome numbers ranging from n = 1 to n = 60. This high karyotype diversity is suggested to be correlated to ants diversification. The karyotype evolution of ants is usually understood in terms of Robertsonian rearrangements towards an increase in chromosome numbers. The ant genus Mycetophylax is a small monogynous basal Attini ant (Formicidae: Myrmicinae), endemic to sand dunes along the Brazilian coastlines. A recent taxonomic revision validates three species, Mycetophylax morschi, M. conformis and M. simplex. In this paper, we cytogenetically characterized all species that belongs to the genus and analyzed the karyotypic evolution of Mycetophylax in the context of a molecular phylogeny and ancestral character state reconstruction. M. morschi showed a polymorphic number of chromosomes, with colonies showing 2n = 26 and 2n = 30 chromosomes. M. conformis presented a diploid chromosome number of 30 chromosomes, while M. simplex showed 36 chromosomes. The probabilistic models suggest that the ancestral haploid chromosome number of Mycetophylax was 17 (Likelihood framework) or 18 (Bayesian framework). The analysis also suggested that fusions were responsible for the evolutionary reduction in chromosome numbers of M. conformis and M. morschi karyotypes whereas fission may determines the M. simplex karyotype. These results obtained show the importance of fusions in chromosome changes towards a chromosome number reduction in Formicidae and how a phylogenetic background can be used to reconstruct hypotheses about chromosomes evolution.

Femoral Condyle Fracture during Anterior Cruciate Ligament Reconstruction

Directory of Open Access Journals (Sweden)

Selahattin Ozyurek

2015-07-01

Full Text Available Dear Editor,We have greatly enjoyed reading the case report entitled “‘Femoral Condyle Fracture during Revision of Anterior Cruciate Ligament Reconstruction: Case Report and a Review of Literature in the issue of Arch Bone Jt Surg. 2015;3(2 with great interest. We would like to commend the authors for their detailed and valuable work. Although various case reports have described postoperative distal femur fracture at a range of time intervals (1,2 intraoperative intra-articular distal femur fracture is a unique entity.However, we believe that some important additional observations seem necessary to be contributed through this study. In this article, the authors stated that, to the best of their knowledge, there is no other case report in the literature introducing a femoral condyle fracture during arthroscopic ACL reconstruction or revision reconstruction. Nevertheless, we would like to call the attention of the readers to the fact that that the literature contains one additional case report re‌porting on intraoperative distal femoral coronal plane (Hoffa fracture during primary ACL reconstruction (2. Werner BC and Miller MD presented of case report of an intraoperative distal femoral coronal plane (Hoffa fracture that occurred during independent femoral tunnel drilling and dilation in a primary ACL reconstruction. As in the their case, this type of fracture can occur with appropriately placed femoral tunnels, but the risk can increase with larger graft diameters in patients with smaller lateral femoral condyles The patient was treated with open reduction and internal fixation, without compromise of graft stability and with good recovery of function. We believe that tailoring graft size to the size of the patient is important to prevent similar adverse events.

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.

Automatic Indoor Building Reconstruction from Mobile Laser Scanning Data

Science.gov (United States)

Xie, L.; Wang, R.

2017-09-01

Indoor reconstruction from point clouds is a hot topic in photogrammetry, computer vision and computer graphics. Reconstructing indoor scene from point clouds is challenging due to complex room floorplan and line-of-sight occlusions. Most of existing methods deal with stationary terrestrial laser scanning point clouds or RGB-D point clouds. In this paper, we propose an automatic method for reconstructing indoor 3D building models from mobile laser scanning point clouds. The method includes 2D floorplan generation, 3D building modeling, door detection and room segmentation. The main idea behind our approach is to separate wall structure into two different types as the inner wall and the outer wall based on the observation of point distribution. Then we utilize a graph cut based optimization method to solve the labeling problem and generate the 2D floorplan based on the optimization result. Subsequently, we leverage an ?-shape based method to detect the doors on the 2D projected point clouds and utilize the floorplan to segment the individual room. The experiments show that this door detection method can achieve a recognition rate at 97% and the room segmentation method can attain the correct segmentation results. We also evaluate the reconstruction accuracy on the synthetic data, which indicates the accuracy of our method is comparable to the state-of-the art.

SART-Type Half-Threshold Filtering Approach for CT Reconstruction.

Science.gov (United States)

Yu, Hengyong; Wang, Ge

2014-01-01

The [Formula: see text] regularization problem has been widely used to solve the sparsity constrained problems. To enhance the sparsity constraint for better imaging performance, a promising direction is to use the [Formula: see text] norm (0 < p < 1) and solve the [Formula: see text] minimization problem. Very recently, Xu et al. developed an analytic solution for the [Formula: see text] regularization via an iterative thresholding operation, which is also referred to as half-threshold filtering. In this paper, we design a simultaneous algebraic reconstruction technique (SART)-type half-threshold filtering framework to solve the computed tomography (CT) reconstruction problem. In the medical imaging filed, the discrete gradient transform (DGT) is widely used to define the sparsity. However, the DGT is noninvertible and it cannot be applied to half-threshold filtering for CT reconstruction. To demonstrate the utility of the proposed SART-type half-threshold filtering framework, an emphasis of this paper is to construct a pseudoinverse transforms for DGT. The proposed algorithms are evaluated with numerical and physical phantom data sets. Our results show that the SART-type half-threshold filtering algorithms have great potential to improve the reconstructed image quality from few and noisy projections. They are complementary to the counterparts of the state-of-the-art soft-threshold filtering and hard-threshold filtering.

Current Limitations of Surgical Robotics in Reconstructive Plastic Microsurgery

Directory of Open Access Journals (Sweden)

Youri P. A. Tan

2018-03-01

Full Text Available Surgical robots have the potential to provide surgeons with increased capabilities, such as removing physiologic tremor, scaling motion and increasing manual dexterity. Several surgical specialties have subsequently integrated robotic surgery into common clinical practice. Plastic and reconstructive microsurgical procedures have not yet  benefitted significantly from technical developments observed over the last two decades. Several studies have successfully demonstrated the feasibility of utilising surgical robots in plastic surgery procedures, yet limited work has been done to identify and analyse current barriers that have prevented wide-scale adaptation of surgical robots for microsurgery. Therefore, a systematic review using PubMed, MEDLINE, Embase and Web of Science databases was performed, in order to evaluate current state of surgical robotics within the field of reconstructive microsurgery and their limitations. Despite the theoretical potential of surgical robots, current commercially available robotic systems are suboptimal for plastic or reconstructive microsurgery. Absence of bespoke microsurgical instruments, increases in operating time, and high costs associated with robotic-assisted provide a barrier to using such systems effectively for reconstructive microsurgery. Consequently, surgical robots provide currently little overall advantage over conventional microsurgery. Nevertheless, if current barriers can be addressed and systems are specifically designed for microsurgery, surgical robots may have the potential of meaningful impact on clinical outcomes within  this surgical subspeciality.