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.

WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States.

Science.gov (United States)

Gruenstaeudl, Michael

2016-02-01

Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. A set of command line-based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results. WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion.

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

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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.

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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.

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

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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

Structure versus time in the evolutionary diversification of avian carotenoid metabolic networks.

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Morrison, Erin S; Badyaev, Alexander V

2018-05-01

Historical associations of genes and proteins are thought to delineate pathways available to subsequent evolution; however, the effects of past functional involvements on contemporary evolution are rarely quantified. Here, we examined the extent to which the structure of a carotenoid enzymatic network persists in avian evolution. Specifically, we tested whether the evolution of carotenoid networks was most concordant with phylogenetically structured expansion from core reactions of common ancestors or with subsampling of biochemical pathway modules from an ancestral network. We compared structural and historical associations in 467 carotenoid networks of extant and ancestral species and uncovered the overwhelming effect of pre-existing metabolic network structure on carotenoid diversification over the last 50 million years of avian evolution. Over evolutionary time, birds repeatedly subsampled and recombined conserved biochemical modules, which likely maintained the overall structure of the carotenoid metabolic network during avian evolution. These findings explain the recurrent convergence of evolutionary distant species in carotenoid metabolism and weak phylogenetic signal in avian carotenoid evolution. Remarkable retention of an ancient metabolic structure throughout extensive and prolonged ecological diversification in avian carotenoid metabolism illustrates a fundamental requirement of organismal evolution - historical continuity of a deterministic network that links past and present functional associations of its components. © 2018 European Society For Evolutionary Biology. Journal of Evolutionary Biology © 2018 European Society For Evolutionary Biology.

Animal regeneration: ancestral character or evolutionary novelty?

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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.

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

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.

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.

Rapid maximum likelihood ancestral state reconstruction of continuous characters: A rerooting-free algorithm.

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Goolsby, Eric W

2017-04-01

Ancestral state reconstruction is a method used to study the evolutionary trajectories of quantitative characters on phylogenies. Although efficient methods for univariate ancestral state reconstruction under a Brownian motion model have been described for at least 25 years, to date no generalization has been described to allow more complex evolutionary models, such as multivariate trait evolution, non-Brownian models, missing data, and within-species variation. Furthermore, even for simple univariate Brownian motion models, most phylogenetic comparative R packages compute ancestral states via inefficient tree rerooting and full tree traversals at each tree node, making ancestral state reconstruction extremely time-consuming for large phylogenies. Here, a computationally efficient method for fast maximum likelihood ancestral state reconstruction of continuous characters is described. The algorithm has linear complexity relative to the number of species and outperforms the fastest existing R implementations by several orders of magnitude. The described algorithm is capable of performing ancestral state reconstruction on a 1,000,000-species phylogeny in fewer than 2 s using a standard laptop, whereas the next fastest R implementation would take several days to complete. The method is generalizable to more complex evolutionary models, such as phylogenetic regression, within-species variation, non-Brownian evolutionary models, and multivariate trait evolution. Because this method enables fast repeated computations on phylogenies of virtually any size, implementation of the described algorithm can drastically alleviate the computational burden of many otherwise prohibitively time-consuming tasks requiring reconstruction of ancestral states, such as phylogenetic imputation of missing data, bootstrapping procedures, Expectation-Maximization algorithms, and Bayesian estimation. The described ancestral state reconstruction algorithm is implemented in the Rphylopars

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

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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.

WARACS: Wrappers to Automate the Reconstruction of Ancestral Character States1

Science.gov (United States)

Gruenstaeudl, Michael

2016-01-01

Premise of the study: Reconstructions of ancestral character states are among the most widely used analyses for evaluating the morphological, cytological, or ecological evolution of an organismic lineage. The software application Mesquite remains the most popular application for such reconstructions among plant scientists, even though its support for automating complex analyses is limited. A software tool is needed that automates the reconstruction and visualization of ancestral character states with Mesquite and similar applications. Methods and Results: A set of command line–based Python scripts was developed that (a) communicates standardized input to and output from the software applications Mesquite, BayesTraits, and TreeGraph2; (b) automates the process of ancestral character state reconstruction; and (c) facilitates the visualization of reconstruction results. Conclusions: WARACS provides a simple tool that streamlines the reconstruction and visualization of ancestral character states over a wide array of parameters, including tree distribution, character state, and optimality criterion. PMID:26949580

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

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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.

Faciobrachial dystonic seizures result from fronto-temporo-basalganglial network involvement.

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Iyer, Rajesh Shankar; Ramakrishnan, T C R; Karunakaran; Shinto, Ajit; Kamaleshwaran, Koramadai Karuppuswamy

2017-01-01

•Faciobrachial dystonic seizures (FBDS) are caused by autoantibodies to leucine-rich glioma-inactivated1 proteins, a component of the voltage-gated potassium channel complex (VGKC-complex) and precede the clinical presentation of limbic encephalitis.•The exact pathophysiology of FBDS is not known and whether they are seizures or movement disorder is still debated.•We suggest the fronto-temporo-basal ganglia network involving the medial frontal and temporal regions along with the corpus striatum and substantia nigra being responsible for the clinical phenomenon of FBDS.•The varied clinical, electrical and imaging features of FBDS in our cases and in the literature are best explained by involvement of this network.•Entrainment from any part of this network will result in similar clinical expression of FBDS, whereas other electro-clinical associations and duration depends on the extent of involvement of the network.

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

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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.

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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.

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.

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.

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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.

A comparison of ancestral state reconstruction methods for quantitative characters.

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Royer-Carenzi, Manuela; Didier, Gilles

2016-09-07

Choosing an ancestral state reconstruction method among the alternatives available for quantitative characters may be puzzling. We present here a comparison of seven of them, namely the maximum likelihood, restricted maximum likelihood, generalized least squares under Brownian, Brownian-with-trend and Ornstein-Uhlenbeck models, phylogenetic independent contrasts and squared parsimony methods. A review of the relations between these methods shows that the maximum likelihood, the restricted maximum likelihood and the generalized least squares under Brownian model infer the same ancestral states and can only be distinguished by the distributions accounting for the reconstruction uncertainty which they provide. The respective accuracy of the methods is assessed over character evolution simulated under a Brownian motion with (and without) directional or stabilizing selection. We give the general form of ancestral state distributions conditioned on leaf states under the simulation models. Ancestral distributions are used first, to give a theoretical lower bound of the expected reconstruction error, and second, to develop an original evaluation scheme which is more efficient than comparing the reconstructed and the simulated states. Our simulations show that: (i) the distributions of the reconstruction uncertainty provided by the methods generally make sense (some more than others); (ii) it is essential to detect the presence of an evolutionary trend and to choose a reconstruction method accordingly; (iii) all the methods show good performances on characters under stabilizing selection; (iv) without trend or stabilizing selection, the maximum likelihood method is generally the most accurate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Infant and juvenile growth in ancestral Pueblo Indians.

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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.

Choosing the best ancestral character state reconstruction method.

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Royer-Carenzi, Manuela; Pontarotti, Pierre; Didier, Gilles

2013-03-01

Despite its intrinsic difficulty, ancestral character state reconstruction is an essential tool for testing evolutionary hypothesis. Two major classes of approaches to this question can be distinguished: parsimony- or likelihood-based approaches. We focus here on the second class of methods, more specifically on approaches based on continuous-time Markov modeling of character evolution. Among them, we consider the most-likely-ancestor reconstruction, the posterior-probability reconstruction, the likelihood-ratio method, and the Bayesian approach. We discuss and compare the above-mentioned methods over several phylogenetic trees, adding the maximum-parsimony method performance in the comparison. Under the assumption that the character evolves according a continuous-time Markov process, we compute and compare the expectations of success of each method for a broad range of model parameter values. Moreover, we show how the knowledge of the evolution model parameters allows to compute upper bounds of reconstruction performances, which are provided as references. The results of all these reconstruction methods are quite close one to another, and the expectations of success are not so far from their theoretical upper bounds. But the performance ranking heavily depends on the topology of the studied tree, on the ancestral node that is to be inferred and on the parameter values. Consequently, we propose a protocol providing for each parameter value the best method in terms of expectation of success, with regard to the phylogenetic tree and the ancestral node to infer. Copyright © 2012 Elsevier Inc. All rights reserved.

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

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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.

Loop 7 of E2 enzymes: an ancestral conserved functional motif involved in the E2-mediated steps of the ubiquitination cascade.

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Elena Papaleo

Full Text Available The ubiquitin (Ub system controls almost every aspect of eukaryotic cell biology. Protein ubiquitination depends on the sequential action of three classes of enzymes (E1, E2 and E3. E2 Ub-conjugating enzymes have a central role in the ubiquitination pathway, interacting with both E1 and E3, and influencing the ultimate fate of the substrates. Several E2s are characterized by an extended acidic insertion in loop 7 (L7, which if mutated is known to impair the proper E2-related functions. In the present contribution, we show that acidic loop is a conserved ancestral motif in E2s, relying on the presence of alternate hydrophobic and acidic residues. Moreover, the dynamic properties of a subset of family 3 E2s, as well as their binary and ternary complexes with Ub and the cognate E3, have been investigated. Here we provide a model of L7 role in the different steps of the ubiquitination cascade of family 3 E2s. The L7 hydrophobic residues turned out to be the main determinant for the stabilization of the E2 inactive conformations by a tight network of interactions in the catalytic cleft. Moreover, phosphorylation is known from previous studies to promote E2 competent conformations for Ub charging, inducing electrostatic repulsion and acting on the L7 acidic residues. Here we show that these active conformations are stabilized by a network of hydrophobic interactions between L7 and L4, the latter being a conserved interface for E3-recruitment in several E2s. In the successive steps, L7 conserved acidic residues also provide an interaction interface for both Ub and the Rbx1 RING subdomain of the cognate E3. Our data therefore suggest a crucial role for L7 of family 3 E2s in all the E2-mediated steps of the ubiquitination cascade. Its different functions are exploited thank to its conserved hydrophobic and acidic residues in a finely orchestrate mechanism.

Online social networks for crowdsourced multimedia-involved behavioral testing: An empirical study

Directory of Open Access Journals (Sweden)

Jun-Ho eChoi

2016-01-01

Full Text Available Online social networks have emerged as effective crowdsourcing media to recruit participants in recent days. However, issues regarding how to effectively exploit them have not been adequately addressed yet. In this paper, we investigate the reliability and effectiveness of multimedia-involved behavioral testing via social network-based crowdsourcing, especially focused on Facebook as a medium to recruit participants. We conduct a crowdsourcing-based experiment for a music recommendation problem. It is shown that different advertisement methods yield different degrees of efficiency and there exist significant differences in behavioral patterns across different genders and different age groups. In addition, we perform a comparison of our experiment with other multimedia-involved crowdsourcing experiments built on Amazon Mechanical Turk (MTurk, which suggests that crowdsourcing-based experiments using social networks for recruitment can achieve comparable efficiency. Based on the analysis results, advantages and disadvantages of social network-based crowdsourcing and suggestions for successful experiments are also discussed. We conclude that social networks have the potential to support multimedia-involved behavioral tests to gather in-depth data even for long-term periods.

Online Social Networks for Crowdsourced Multimedia-Involved Behavioral Testing: An Empirical Study

Science.gov (United States)

Choi, Jun-Ho; Lee, Jong-Seok

2016-01-01

Online social networks have emerged as effective crowdsourcing media to recruit participants in recent days. However, issues regarding how to effectively exploit them have not been adequately addressed yet. In this paper, we investigate the reliability and effectiveness of multimedia-involved behavioral testing via social network-based crowdsourcing, especially focused on Facebook as a medium to recruit participants. We conduct a crowdsourcing-based experiment for a music recommendation problem. It is shown that different advertisement methods yield different degrees of efficiency and there exist significant differences in behavioral patterns across different genders and different age groups. In addition, we perform a comparison of our experiment with other multimedia-involved crowdsourcing experiments built on Amazon Mechanical Turk (MTurk), which suggests that crowdsourcing-based experiments using social networks for recruitment can achieve comparable efficiency. Based on the analysis results, advantages and disadvantages of social network-based crowdsourcing and suggestions for successful experiments are also discussed. We conclude that social networks have the potential to support multimedia-involved behavioral tests to gather in-depth data even for long-term periods. PMID:26793137

Online Social Networks for Crowdsourced Multimedia-Involved Behavioral Testing: An Empirical Study.

Science.gov (United States)

Choi, Jun-Ho; Lee, Jong-Seok

2015-01-01

Online social networks have emerged as effective crowdsourcing media to recruit participants in recent days. However, issues regarding how to effectively exploit them have not been adequately addressed yet. In this paper, we investigate the reliability and effectiveness of multimedia-involved behavioral testing via social network-based crowdsourcing, especially focused on Facebook as a medium to recruit participants. We conduct a crowdsourcing-based experiment for a music recommendation problem. It is shown that different advertisement methods yield different degrees of efficiency and there exist significant differences in behavioral patterns across different genders and different age groups. In addition, we perform a comparison of our experiment with other multimedia-involved crowdsourcing experiments built on Amazon Mechanical Turk (MTurk), which suggests that crowdsourcing-based experiments using social networks for recruitment can achieve comparable efficiency. Based on the analysis results, advantages and disadvantages of social network-based crowdsourcing and suggestions for successful experiments are also discussed. We conclude that social networks have the potential to support multimedia-involved behavioral tests to gather in-depth data even for long-term periods.

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

On the Accuracy of Ancestral Sequence Reconstruction for Ultrametric Trees with Parsimony.

Science.gov (United States)

Herbst, Lina; Fischer, Mareike

2018-04-01

We examine a mathematical question concerning the reconstruction accuracy of the Fitch algorithm for reconstructing the ancestral sequence of the most recent common ancestor given a phylogenetic tree and sequence data for all taxa under consideration. In particular, for the symmetric four-state substitution model which is also known as Jukes-Cantor model, we answer affirmatively a conjecture of Li, Steel and Zhang which states that for any ultrametric phylogenetic tree and a symmetric model, the Fitch parsimony method using all terminal taxa is more accurate, or at least as accurate, for ancestral state reconstruction than using any particular terminal taxon or any particular pair of taxa. This conjecture had so far only been answered for two-state data by Fischer and Thatte. Here, we focus on answering the biologically more relevant case with four states, which corresponds to ancestral sequence reconstruction from DNA or RNA data.

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

Science.gov (United States)

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

2015-09-01

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

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.

Historian: accurate reconstruction of ancestral sequences and evolutionary rates.

Science.gov (United States)

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

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.

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 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.

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.

The Interaction between Personality, Social Network Position and Involvement in Innovation Process

NARCIS (Netherlands)

E. Dolgova (Evgenia); W. van Olffen (Woody); F.A.J. van den Bosch (Frans); H.W. Volberda (Henk)

2010-01-01

textabstractAbstract This dissertation proposal investigates how personality and individuals’ social network position affect individuals’ involvement into the innovation process. It posits that people would feel inclined to become involved into the different phases of the innovation process

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

Science.gov (United States)

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.

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

Science.gov (United States)

King, Benedict; Lee, Michael S Y

2015-05-01

Virtually all models for reconstructing ancestral states for discrete characters make the crucial assumption that the trait of interest evolves at a uniform rate across the entire tree. However, this assumption is unlikely to hold in many situations, particularly as ancestral state reconstructions are being performed on increasingly large phylogenies. Here, we show how failure to account for such variable evolutionary rates can cause highly anomalous (and likely incorrect) results, while three methods that accommodate rate variability yield the opposite, more plausible, and more robust reconstructions. The random local clock method, implemented in BEAST, estimates the position and magnitude of rate changes on the tree; split BiSSE estimates separate rate parameters for pre-specified clades; and the hidden rates model partitions each character state into a number of rate categories. Simulations show the inadequacy of traditional models when characters evolve with both asymmetry (different rates of change between states within a character) and heterotachy (different rates of character evolution across different clades). The importance of accounting for rate heterogeneity in ancestral state reconstruction is highlighted empirically with a new analysis of the evolution of viviparity in squamate reptiles, which reveal a predominance of forward (oviparous-viviparous) transitions and very few reversals. © The Author(s) 2015. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

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

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.

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.

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.

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.

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

DEFF Research Database (Denmark)

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

2015-01-01

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....

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

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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 �

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.

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

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Roxane Chiori

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

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 .

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...

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

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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.

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

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

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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.

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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.

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.

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 .

IcyTree: rapid browser-based visualization for phylogenetic trees and networks.

Science.gov (United States)

Vaughan, Timothy G

2017-08-01

IcyTree is an easy-to-use application which can be used to visualize a wide variety of phylogenetic trees and networks. While numerous phylogenetic tree viewers exist already, IcyTree distinguishes itself by being a purely online tool, having a responsive user interface, supporting phylogenetic networks (ancestral recombination graphs in particular), and efficiently drawing trees that include information such as ancestral locations or trait values. IcyTree also provides intuitive panning and zooming utilities that make exploring large phylogenetic trees of many thousands of taxa feasible. IcyTree is a web application and can be accessed directly at http://tgvaughan.github.com/icytree . Currently supported web browsers include Mozilla Firefox and Google Chrome. IcyTree is written entirely in client-side JavaScript (no plugin required) and, once loaded, does not require network access to run. IcyTree is free software, and the source code is made available at http://github.com/tgvaughan/icytree under version 3 of the GNU General Public License. tgvaughan@gmail.com. © The Author(s) 2017. Published by Oxford University Press.

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...

Integrative analysis for finding genes and networks involved in diabetes and other complex diseases

DEFF Research Database (Denmark)

Bergholdt, R.; Størling, Zenia, Marian; Hansen, Kasper Lage

2007-01-01

We have developed an integrative analysis method combining genetic interactions, identified using type 1 diabetes genome scan data, and a high-confidence human protein interaction network. Resulting networks were ranked by the significance of the enrichment of proteins from interacting regions. We...... identified a number of new protein network modules and novel candidate genes/proteins for type 1 diabetes. We propose this type of integrative analysis as a general method for the elucidation of genes and networks involved in diabetes and other complex diseases....

Temperature-dependent respiration-growth relations in ancestral maize cultivars

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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...

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.

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...

Functional brain networks involved in decision-making under certain and uncertain conditions

Energy Technology Data Exchange (ETDEWEB)

Farrar, Danielle C.; Moss, Mark B.; Killiany, Ronald J. [Boston University School of Medicine, Department of Anatomy and Neurobiology, Boston, MA (United States); Mian, Asim Z. [Boston University School of Medicine, Department of Radiology, Boston, MA (United States); Budson, Andrew E. [VA Boston Healthcare System, Boston, MA (United States)

2018-01-15

The aim of this study was to describe imaging markers of decision-making under uncertain conditions in normal individuals, in order to provide baseline activity to compare to impaired decision-making in pathological states. In this cross-sectional study, 19 healthy subjects ages 18-35 completed a novel decision-making card-matching task using a Phillips T3 Scanner and a 32-channel head coil. Functional data were collected in six functional runs. In one condition of the task, the participant was certain of the rule to apply to match the cards; in the other condition, the participant was uncertain. We performed cluster-based comparison of the two conditions using FSL fMRI Expert Analysis Tool and network-based analysis using MATLAB. The uncertain > certain comparison yielded three clusters - a midline cluster that extended through the midbrain, the thalamus, bilateral prefrontal cortex, the striatum, and bilateral parietal/occipital clusters. The certain > uncertain comparison yielded bilateral clusters in the insula, parietal and temporal lobe, as well as a medial frontal cluster. A larger, more connected functional network was found in the uncertain condition. The involvement of the insula, parietal cortex, temporal cortex, ventromedial prefrontal cortex, and orbitofrontal cortex of the certain condition reinforces the notion that certainty is inherently rewarding. For the uncertain condition, the involvement of the prefrontal cortex, parietal cortex, striatum, thalamus, amygdala, and hippocampal involvement was expected, as these are areas involved in resolving uncertainty and rule updating. The involvement of occipital cortical involvement and midbrain involvement may be attributed to increased visual attention and increased motor control. (orig.)

Functional brain networks involved in decision-making under certain and uncertain conditions

International Nuclear Information System (INIS)

Farrar, Danielle C.; Moss, Mark B.; Killiany, Ronald J.; Mian, Asim Z.; Budson, Andrew E.

2018-01-01

The aim of this study was to describe imaging markers of decision-making under uncertain conditions in normal individuals, in order to provide baseline activity to compare to impaired decision-making in pathological states. In this cross-sectional study, 19 healthy subjects ages 18-35 completed a novel decision-making card-matching task using a Phillips T3 Scanner and a 32-channel head coil. Functional data were collected in six functional runs. In one condition of the task, the participant was certain of the rule to apply to match the cards; in the other condition, the participant was uncertain. We performed cluster-based comparison of the two conditions using FSL fMRI Expert Analysis Tool and network-based analysis using MATLAB. The uncertain > certain comparison yielded three clusters - a midline cluster that extended through the midbrain, the thalamus, bilateral prefrontal cortex, the striatum, and bilateral parietal/occipital clusters. The certain > uncertain comparison yielded bilateral clusters in the insula, parietal and temporal lobe, as well as a medial frontal cluster. A larger, more connected functional network was found in the uncertain condition. The involvement of the insula, parietal cortex, temporal cortex, ventromedial prefrontal cortex, and orbitofrontal cortex of the certain condition reinforces the notion that certainty is inherently rewarding. For the uncertain condition, the involvement of the prefrontal cortex, parietal cortex, striatum, thalamus, amygdala, and hippocampal involvement was expected, as these are areas involved in resolving uncertainty and rule updating. The involvement of occipital cortical involvement and midbrain involvement may be attributed to increased visual attention and increased motor control. (orig.)

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

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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.

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...

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

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

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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.

Informatic parcellation of the network involved in the computation of subjective value

Science.gov (United States)

Rangel, Antonio

2014-01-01

Understanding how the brain computes value is a basic question in neuroscience. Although individual studies have driven this progress, meta-analyses provide an opportunity to test hypotheses that require large collections of data. We carry out a meta-analysis of a large set of functional magnetic resonance imaging studies of value computation to address several key questions. First, what is the full set of brain areas that reliably correlate with stimulus values when they need to be computed? Second, is this set of areas organized into dissociable functional networks? Third, is a distinct network of regions involved in the computation of stimulus values at decision and outcome? Finally, are different brain areas involved in the computation of stimulus values for different reward modalities? Our results demonstrate the centrality of ventromedial prefrontal cortex (VMPFC), ventral striatum and posterior cingulate cortex (PCC) in the computation of value across tasks, reward modalities and stages of the decision-making process. We also find evidence of distinct subnetworks of co-activation within VMPFC, one involving central VMPFC and dorsal PCC and another involving more anterior VMPFC, left angular gyrus and ventral PCC. Finally, we identify a posterior-to-anterior gradient of value representations corresponding to concrete-to-abstract rewards. PMID:23887811

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

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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

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.

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

Science.gov (United States)

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.

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

Mitochondrial introgression suggests extensive ancestral hybridization events among Saccharomyces species.

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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.

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.

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.

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

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)

Cambodian Parental Involvement: The Role of Parental Beliefs, Social Networks, and Trust

Science.gov (United States)

Eng, Sothy; Szmodis, Whitney; Mulsow, Miriam

2014-01-01

The role of social capital (parental beliefs, social networks, and trust) as a predictor of parental involvement in Cambodian children's education was examined, controlling for human capital (family socioeconomic status). Parents of elementary students (n = 273) were interviewed face to face in Cambodia. Teacher contact scored highest, followed by…

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.

Predicting Genes Involved in Human Cancer Using Network Contextual Information

Directory of Open Access Journals (Sweden)

Rahmani Hossein

2012-03-01

Full Text Available Protein-Protein Interaction (PPI networks have been widely used for the task of predicting proteins involved in cancer. Previous research has shown that functional information about the protein for which a prediction is made, proximity to specific other proteins in the PPI network, as well as local network structure are informative features in this respect. In this work, we introduce two new types of input features, reflecting additional information: (1 Functional Context: the functions of proteins interacting with the target protein (rather than the protein itself; and (2 Structural Context: the relative position of the target protein with respect to specific other proteins selected according to a novel ANOVA (analysis of variance based measure. We also introduce a selection strategy to pinpoint the most informative features. Results show that the proposed feature types and feature selection strategy yield informative features. A standard machine learning method (Naive Bayes that uses the features proposed here outperforms the current state-of-the-art methods by more than 5% with respect to F-measure. In addition, manual inspection confirms the biological relevance of the top-ranked features.

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,...

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

Directory of Open Access Journals (Sweden)

Katherine Belov

2006-03-01

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

Are palaeoscolecids ancestral ecdysozoans?

Science.gov (United States)

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

2010-01-01

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

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, ...

Students' Involvement in Social Networking and Attitudes towards Its Integration into Teaching

Science.gov (United States)

Umoh, Ukeme Ekpedeme; Etuk, Etuk Nssien

2016-01-01

The study examined Students' Involvement in Social Networking and attitudes towards its Integration into Teaching. The study was carried out in the University of Uyo, Akwa Ibom State, Nigeria. The population of the study consisted of 17,618 undergraduate students enrolled into full time degree programmes in the University of Uyo for 2014/2015…

Analysis of the enzyme network involved in cattle milk production using graph theory.

Science.gov (United States)

Ghorbani, Sholeh; Tahmoorespur, Mojtaba; Masoudi Nejad, Ali; Nasiri, Mohammad; Asgari, Yazdan

2015-06-01

Understanding cattle metabolism and its relationship with milk products is important in bovine breeding. A systemic view could lead to consequences that will result in a better understanding of existing concepts. Topological indices and quantitative characterizations mostly result from the application of graph theory on biological data. In the present work, the enzyme network involved in cattle milk production was reconstructed and analyzed based on available bovine genome information using several public datasets (NCBI, Uniprot, KEGG, and Brenda). The reconstructed network consisted of 3605 reactions named by KEGG compound numbers and 646 enzymes that catalyzed the corresponding reactions. The characteristics of the directed and undirected network were analyzed using Graph Theory. The mean path length was calculated to be4.39 and 5.41 for directed and undirected networks, respectively. The top 11 hub enzymes whose abnormality could harm bovine health and reduce milk production were determined. Therefore, the aim of constructing the enzyme centric network was twofold; first to find out whether such network followed the same properties of other biological networks, and second, to find the key enzymes. The results of the present study can improve our understanding of milk production in cattle. Also, analysis of the enzyme network can help improve the modeling and simulation of biological systems and help design desired phenotypes to increase milk production quality or quantity.

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...

Decreasing Risky Behavior on Social Network Sites: The Impact of Parental Involvement in Secondary Education Interventions.

Science.gov (United States)

Vanderhoven, Ellen; Schellens, Tammy; Valcke, Martin

2016-06-01

Teenagers face significant risks when using increasingly popular social network sites. Prevention and intervention efforts to raise awareness about these risks and to change risky behavior (so-called "e-safety" interventions) are essential for the wellbeing of these minors. However, several studies have revealed that while school interventions often affect awareness, they have only a limited impact on pupils' unsafe behavior. Utilizing the Theory of Planned Behavior and theories about parental involvement, we hypothesized that involving parents in an e-safety intervention would positively influence pupils' intentions and behavior. In a quasi-experimental study with pre- and post-test measures involving 207 pupils in secondary education, we compared the impact of an intervention without parental involvement with one that included active parental involvement by means of a homework task. We found that whereas parental involvement was not necessary to improve the intervention's impact on risk awareness, it did change intentions to engage in certain unsafe behavior, such as posting personal and sexual information on the profile page of a social network site, and in reducing existing problematic behavior. This beneficial impact was particularly evident for boys. These findings suggest that developing prevention campaigns with active parental involvement is well worth the effort. Researchers and developers should therefore focus on other efficient strategies to involve parents.

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

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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.

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...

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

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

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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.

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…

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

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.

Musical Imagery Involves Wernicke's Area in Bilateral and Anti-Correlated Network Interactions in Musicians.

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Zhang, Yizhen; Chen, Gang; Wen, Haiguang; Lu, Kun-Han; Liu, Zhongming

2017-12-06

Musical imagery is the human experience of imagining music without actually hearing it. The neural basis of this mental ability is unclear, especially for musicians capable of engaging in accurate and vivid musical imagery. Here, we created a visualization of an 8-minute symphony as a silent movie and used it as real-time cue for musicians to continuously imagine the music for repeated and synchronized sessions during functional magnetic resonance imaging (fMRI). The activations and networks evoked by musical imagery were compared with those elicited by the subjects directly listening to the same music. Musical imagery and musical perception resulted in overlapping activations at the anterolateral belt and Wernicke's area, where the responses were correlated with the auditory features of the music. Whereas Wernicke's area interacted within the intrinsic auditory network during musical perception, it was involved in much more complex networks during musical imagery, showing positive correlations with the dorsal attention network and the motor-control network and negative correlations with the default-mode network. Our results highlight the important role of Wernicke's area in forming vivid musical imagery through bilateral and anti-correlated network interactions, challenging the conventional view of segregated and lateralized processing of music versus language.

Palaeohistological Evidence for Ancestral High Metabolic Rate in Archosaurs.

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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.

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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.

An Atomic Force Microscopy Study of the Interactions Involving Polymers and Silane Networks

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Rodrigo L. Oréfice

1998-12-01

Full Text Available ABSTRACT: Silane coupling agents have been frequently used as interfacial agents in polymer composites to improve interfacial strength and resistance to fluid migration. Although the capability of these agents in improving properties and performance of composites has been reported, there are still many uncertainties regarding the processing-structure-property relationships and the mechanisms of coupling developed by silane agents. In this work, an Atomic Force Microscope (AFM was used to measure interactions between polymers and silica substrates, where silane networks with a series of different structures were processed. The influence of the structure of silane networks on the interactions with polymers was studied and used to determine the mechanisms involved in the coupling phenomenon. The AFM results showed that phenomena such as chain penetration, entanglements, intersegment bonding, chain conformation in the vicinities of rigid surfaces were identified as being relevant for the overall processes of adhesion and adsorption of polymeric chains within a silane network. AFM adhesion curves showed that penetration of polymeric chains through a more open silane network can lead to higher levels of interactions between polymer and silane agents.

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.

Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria

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Hou Jing

2006-04-01

Full Text Available Abstract Background Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event. Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear genome by horizontal gene transfer. However, a selective set of metabolism pathways is maintained in chloroplasts using both chloroplast genome encoded and nuclear genome encoded enzymes. As an organelle specialized for carrying out photosynthesis, does the chloroplast metabolic network have properties adapted for higher efficiency of photosynthesis? We compared metabolic network properties of chloroplasts and prokaryotic photosynthetic organisms, mostly cyanobacteria, based on metabolic maps derived from genome data to identify features of chloroplast network properties that are different from cyanobacteria and to analyze possible functional significance of those features. Results The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the Calvin Cycle have been analyzed using hypergraph representation. Results showed that the whole metabolic networks in chloroplast and cyanobacteria both possess small-world network properties. Although the number of compounds and reactions in chloroplasts is less than that in cyanobacteria, the chloroplast's metabolic network has longer average path length, a larger diameter, and is Calvin Cycle -centered, indicating an overall less-dense network structure with specific and local high density areas in chloroplasts. Moreover, chloroplast metabolic network exhibits a better modular organization than cyanobacterial ones. Enzymes involved in the same metabolic processes tend to cluster into the same module in chloroplasts. Conclusion In summary, the differences in metabolic network properties may reflect the evolutionary changes during endosymbiosis that led to the improvement of the photosynthesis efficiency in higher plants. Our

[High frequency of ancestral allele of the TJP1 polymorphism rs2291166 in Mexican population, conformational effect and applications in surgery and medicine].

Science.gov (United States)

Ramirez-Garcia, Sergio Alberto; Flores-Alvarado, Luis Javier; Topete-González, Luz Rosalba; Charles-Niño, Claudia; Mazariegos-Rubi, Manuel; Dávalos-Rodríguez, Nory Omayra

2016-01-01

TJP1 gene encodes a ZO-1 protein that is required for the recruitment of occludins and claudins in tight junction, and is involved in cell polarisation. It has different variations, the frequency of which has been studied in different populations. In Mexico there are no studies of this gene. These are required because their polymorphisms can be used in studies associated with medicine and surgery. Therefore, the aim of this study was to estimate the frequency of alleles and genotypes of rs2291166 gene polymorphism TJP1 in Mexico Mestizos population, and to estimate the conformational effect of an amino acid change. A total of 473 individuals were included. The rs2291166 polymorphism was identified PASA PCR-7% PAGE, and stained with silver nitrate. The conformational effect of amino acid change was performed in silico, and was carried out with servers ProtPraram Tool and Search Database with Fasta. The most frequent allele in the two populations is the ancestral allele (T). A genotype distribution similar to other populations was found. The polymorphism is in Hardy-Weinberg, p>0.05. Changing aspartate to alanine produced a conformational change. The study reveals a high frequency of the ancestral allele at rs2291166 polymorphism in the Mexican population. Copyright © 2015 Academia Mexicana de Cirugía A.C. Published by Masson Doyma México S.A. All rights reserved.

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.

Systematics and morphological evolution within the moss family Bryaceae: a comparison between parsimony and Bayesian methods for reconstruction of ancestral character states.

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Pedersen, Niklas; Holyoak, David T; Newton, Angela E

2007-06-01

The Bryaceae are a large cosmopolitan moss family including genera of significant morphological and taxonomic complexity. Phylogenetic relationships within the Bryaceae were reconstructed based on DNA sequence data from all three genomic compartments. In addition, maximum parsimony and Bayesian inference were employed to reconstruct ancestral character states of 38 morphological plus four habitat characters and eight insertion/deletion events. The recovered phylogenetic patterns are generally in accord with previous phylogenies based on chloroplast DNA sequence data and three major clades are identified. The first clade comprises Bryum bornholmense, B. rubens, B. caespiticium, and Plagiobryum. This corroborates the hypothesis suggested by previous studies that several Bryum species are more closely related to Plagiobryum than to the core Bryum species. The second clade includes Acidodontium, Anomobryum, and Haplodontium, while the third clade contains the core Bryum species plus Imbribryum. Within the latter clade, B. subapiculatum and B. tenuisetum form the sister clade to Imbribryum. Reconstructions of ancestral character states under maximum parsimony and Bayesian inference suggest fourteen morphological synapomorphies for the ingroup and synapomorphies are detected for most clades within the ingroup. Maximum parsimony and Bayesian reconstructions of ancestral character states are mostly congruent although Bayesian inference shows that the posterior probability of ancestral character states may decrease dramatically when node support is taken into account. Bayesian inference also indicates that reconstructions may be ambiguous at internal nodes for highly polymorphic characters.

Phylogenetic comparative methods on phylogenetic networks with reticulations.

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Bastide, Paul; Solís-Lemus, Claudia; Kriebel, Ricardo; Sparks, K William; Ané, Cécile

2018-04-25

The goal of Phylogenetic Comparative Methods (PCMs) is to study the distribution of quantitative traits among related species. The observed traits are often seen as the result of a Brownian Motion (BM) along the branches of a phylogenetic tree. Reticulation events such as hybridization, gene flow or horizontal gene transfer, can substantially affect a species' traits, but are not modeled by a tree. Phylogenetic networks have been designed to represent reticulate evolution. As they become available for downstream analyses, new models of trait evolution are needed, applicable to networks. One natural extension of the BM is to use a weighted average model for the trait of a hybrid, at a reticulation point. We develop here an efficient recursive algorithm to compute the phylogenetic variance matrix of a trait on a network, in only one preorder traversal of the network. We then extend the standard PCM tools to this new framework, including phylogenetic regression with covariates (or phylogenetic ANOVA), ancestral trait reconstruction, and Pagel's λ test of phylogenetic signal. The trait of a hybrid is sometimes outside of the range of its two parents, for instance because of hybrid vigor or hybrid depression. These two phenomena are rather commonly observed in present-day hybrids. Transgressive evolution can be modeled as a shift in the trait value following a reticulation point. We develop a general framework to handle such shifts, and take advantage of the phylogenetic regression view of the problem to design statistical tests for ancestral transgressive evolution in the evolutionary history of a group of species. We study the power of these tests in several scenarios, and show that recent events have indeed the strongest impact on the trait distribution of present-day taxa. We apply those methods to a dataset of Xiphophorus fishes, to confirm and complete previous analysis in this group. All the methods developed here are available in the Julia package PhyloNetworks.

Identification of Resting State Networks Involved in Executive Function.

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Connolly, Joanna; McNulty, Jonathan P; Boran, Lorraine; Roche, Richard A P; Delany, David; Bokde, Arun L W

2016-06-01

The structural networks in the human brain are consistent across subjects, and this is reflected also in that functional networks across subjects are relatively consistent. These findings are not only present during performance of a goal oriented task but there are also consistent functional networks during resting state. It suggests that goal oriented activation patterns may be a function of component networks identified using resting state. The current study examines the relationship between resting state networks measured and patterns of neural activation elicited during a Stroop task. The association between the Stroop-activated networks and the resting state networks was quantified using spatial linear regression. In addition, we investigated if the degree of spatial association of resting state networks with the Stroop task may predict performance on the Stroop task. The results of this investigation demonstrated that the Stroop activated network can be decomposed into a number of resting state networks, which were primarily associated with attention, executive function, visual perception, and the default mode network. The close spatial correspondence between the functional organization of the resting brain and task-evoked patterns supports the relevance of resting state networks in cognitive function.

DMPD: The involvement of the interleukin-1 receptor-associated kinases (IRAKs) incellular signaling networks controlling inflammation. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available ncellular signaling networks controlling inflammation. Ringwood L, Li L. Cytokine. 2008 Apr;42(1):1-7. Epub ...ases (IRAKs) incellular signaling networks controlling inflammation. PubmedID 182...49132 Title The involvement of the interleukin-1 receptor-associated kinases (IRAKs) incellular signaling networks controlling

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

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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.

AMES, NESC and ENIQ: European networks in the field of structural integrity involving NDE and inspection effectiveness assessment

International Nuclear Information System (INIS)

Crutzen, S.; Hurst, R.; Debarberis, L.; Lemaitre, P.; Eriksen, B.

1999-01-01

Three European networks on structural integrity aspects of ageing nuclear components are presently managed by the Institute for Advanced Materials of the Joint Research Centre of the European Commission: AMES (Ageing Materials Evaluation and Studies), ENIQ (European Network for Inspection Qualification) and NESC (Network for Evaluating Steel Components). All three networks involve actions, which aim at the effectiveness and reliability assessment of NDE techniques and of inspection procedures: Either for materials damage detection and characterisation or for defect detection and evaluation. This paper is describing very generally the objectives of the three networks and is then concentrating on the results obtained in ENIQ, which are relevant with ISI and regulatory issues. (orig./DGE)

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

Science.gov (United States)

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.

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

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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.

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

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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

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.

Evolution and functional insights of different ancestral orthologous clades of chitin synthase genes in the fungal tree of life

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Mu eLi

2016-02-01

Full Text Available Chitin synthases (CHSs are key enzymes in the biosynthesis of chitin, an important structural component of fungal cell walls that can trigger innate immune responses in host plants and animals. Members of CHS gene family perform various functions in fungal cellular processes. Previous studies focused primarily on classifying diverse CHSs into different classes, regardless of their functional diversification, or on characterizing their functions in individual fungal species. A complete and systematic comparative analysis of CHS genes based on their orthologous relationships will be valuable for elucidating the evolution and functions of different CHS genes in fungi. Here, we identified and compared members of the CHS gene family across the fungal tree of life, including 18 divergent fungal lineages. Phylogenetic analysis revealed that the fungal CHS gene family is comprised of at least 10 ancestral orthologous clades, which have undergone multiple independent duplications and losses in different fungal lineages during evolution. Interestingly, one of these CHS clades (class III was expanded in plant or animal pathogenic fungi belonging to different fungal lineages. Two clades (classes VIb and VIc identified for the first time in this study occurred mainly in plant pathogenic fungi from Sordariomycetes and Dothideomycetes. Moreover, members of classes III and VIb were specifically up-regulated during plant infection, suggesting important roles in pathogenesis. In addition, CHS-associated networks conserved among plant pathogenic fungi are involved in various biological processes, including sexual reproduction and plant infection. We also identified specificity-determining sites, many of which are located at or adjacent to important structural and functional sites that are potentially responsible for functional divergence of different CHS classes. Overall, our results provide new insights into the evolution and function of members of CHS gene

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

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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.

Dynamic functional brain networks involved in simple visual discrimination learning.

Science.gov (United States)

Fidalgo, Camino; Conejo, Nélida María; González-Pardo, Héctor; Arias, Jorge Luis

2014-10-01

Visual discrimination tasks have been widely used to evaluate many types of learning and memory processes. However, little is known about the brain regions involved at different stages of visual discrimination learning. We used cytochrome c oxidase histochemistry to evaluate changes in regional brain oxidative metabolism during visual discrimination learning in a water-T maze at different time points during training. As compared with control groups, the results of the present study reveal the gradual activation of cortical (prefrontal and temporal cortices) and subcortical brain regions (including the striatum and the hippocampus) associated to the mastery of a simple visual discrimination task. On the other hand, the brain regions involved and their functional interactions changed progressively over days of training. Regions associated with novelty, emotion, visuo-spatial orientation and motor aspects of the behavioral task seem to be relevant during the earlier phase of training, whereas a brain network comprising the prefrontal cortex was found along the whole learning process. This study highlights the relevance of functional interactions among brain regions to investigate learning and memory processes. Copyright © 2014 Elsevier Inc. All rights reserved.

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.

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

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.

Occipital and occipital "plus" epilepsies: A study of involved epileptogenic networks through SEEG quantification.

Science.gov (United States)

Marchi, Angela; Bonini, Francesca; Lagarde, Stanislas; McGonigal, Aileen; Gavaret, Martine; Scavarda, Didier; Carron, Romain; Aubert, Sandrine; Villeneuve, Nathalie; Médina Villalon, Samuel; Bénar, Christian; Trebuchon, Agnes; Bartolomei, Fabrice

2016-09-01

Compared with temporal or frontal lobe epilepsies, the occipital lobe epilepsies (OLE) remain poorly characterized. In this study, we aimed at classifying the ictal networks involving OLE and investigated clinical features of the OLE network subtypes. We studied 194 seizures from 29 consecutive patients presenting with OLE and investigated by stereoelectroencephalography (SEEG). Epileptogenicity of occipital and extraoccipital regions was quantified according to the 'epileptogenicity index' (EI) method. We found that 79% of patients showed widespread epileptogenic zone organization, involving parietal or temporal regions in addition to the occipital lobe. Two main groups of epileptogenic zone organization within occipital lobe seizures were identified: a pure occipital group and an occipital "plus" group, the latter including two further subgroups, occipitotemporal and occipitoparietal. In 29% of patients, the epileptogenic zone was found to have a bilateral organization. The most epileptogenic structure was the fusiform gyrus (mean EI: 0.53). Surgery was proposed in 18/29 patients, leading to seizure freedom in 55% (Engel Class I). Results suggest that, in patient candidates for surgery, the majority of cases are characterized by complex organization of the EZ, corresponding to the occipital plus group. Copyright © 2016 Elsevier Inc. All rights reserved.

Are Adolescents Engaged in the Problematic Use of Social Networking Sites More Involved in Peer Aggression and Victimization?

Science.gov (United States)

Martínez-Ferrer, Belén; Moreno, David; Musitu, Gonzalo

2018-01-01

The problematic use of social networking sites is becoming a major public health concern. Previous research has found that adolescents who engage in a problematic use of social networking sites are likely to show maladjustment problems. However, little is known about its links with peer aggression and victimization. The main goal of this study was to analyze the relationship between problematic use of online social networking sites, peer aggression -overt vs. relational and reactive vs. instrumental-, and peer victimization -overt physical and verbal, and relational-, taking into account gender and age (in early and mid-adolescence). Participants were selected using randomized cluster sampling considering school and class as clusters. A battery of instruments was applied to 1,952 adolescents' secondary students from Spain (Andalusia) (50.4% boys), aged 11 to 16 ( M = 14.07, SD = 1.39). Results showed that girls and 14-16 adolescents were more involved in a problematic use of online social networking sites. Furthermore, adolescents with high problematic use of online social networking sites were more involved in overt-reactive and instrumental-and relational-reactive and instrumental-aggressive behaviors, and self-reported higher levels of overt-physical and verbal-and relational victimization. Even though boys indicated higher levels of all types of victimization, girls with high problematic use of online social networking sites scored the highest on relational victimization. Relating to age, early adolescents (aged 11-14) with higher problematic use of online social networking sites reported the highest levels of overt verbal and relational victimization. Overall, results suggested the co-occurrence of problematic use of online social networking sites, peer aggression and victimization. In addition, results showed the influence that gender and age had on peer victimization. This study highlights the continuity between offline and online domains with regard to

Are Adolescents Engaged in the Problematic Use of Social Networking Sites More Involved in Peer Aggression and Victimization?

Directory of Open Access Journals (Sweden)

Belén Martínez-Ferrer

2018-05-01

Full Text Available The problematic use of social networking sites is becoming a major public health concern. Previous research has found that adolescents who engage in a problematic use of social networking sites are likely to show maladjustment problems. However, little is known about its links with peer aggression and victimization. The main goal of this study was to analyze the relationship between problematic use of online social networking sites, peer aggression –overt vs. relational and reactive vs. instrumental–, and peer victimization –overt physical and verbal, and relational–, taking into account gender and age (in early and mid-adolescence. Participants were selected using randomized cluster sampling considering school and class as clusters. A battery of instruments was applied to 1,952 adolescents' secondary students from Spain (Andalusia (50.4% boys, aged 11 to 16 (M = 14.07, SD = 1.39. Results showed that girls and 14–16 adolescents were more involved in a problematic use of online social networking sites. Furthermore, adolescents with high problematic use of online social networking sites were more involved in overt—reactive and instrumental—and relational—reactive and instrumental—aggressive behaviors, and self-reported higher levels of overt—physical and verbal—and relational victimization. Even though boys indicated higher levels of all types of victimization, girls with high problematic use of online social networking sites scored the highest on relational victimization. Relating to age, early adolescents (aged 11–14 with higher problematic use of online social networking sites reported the highest levels of overt verbal and relational victimization. Overall, results suggested the co-occurrence of problematic use of online social networking sites, peer aggression and victimization. In addition, results showed the influence that gender and age had on peer victimization. This study highlights the continuity between offline

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.

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Jia-Yu Chen

2015-07-01

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

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

Science.gov (United States)

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.

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...

Community (in) Colleges: The Relationship Between Online Network Involvement and Academic Outcomes at a Community College

Science.gov (United States)

Evans, Eliza D.; McFarland, Daniel A.; Rios-Aguilar, Cecilia; Deil-Amen, Regina

2016-01-01

Objective: This study explores the relationship between online social network involvement and academic outcomes among community college students. Prior theory hypothesizes that socio-academic moments are especially important for the integration of students into community colleges and that integration is related to academic outcomes. Online social…

Local stakeholder involvement in the perspective of nuclear waste management: lessons form the Cowam network

International Nuclear Information System (INIS)

Heriard Dubreuil, G.; Gadbois, S.

2004-01-01

The management of high level radioactive waste is nowadays recognised as a complex decision-making process entailing technical, environmental, ethical, social, political and economic dimensions where no solution can be reached solely on the basis of technical considerations. While this issue is acknowledged as a problem for the community as a whole, waste management remains a global problem looking for a local solution. Starting from this view, COWAM network (Community Waste Management), developed under the Fifth Framework Programme of the European Commission, addressed the following objectives: 1) To empower local actors through a networking process; 2) To gather and discuss the available experiences of decision-making processes at the local level within their national context in Europe; 3) To set up an arena for balanced exchanges between local actors, NGOs, regulators and implementers; 4) To promote new approaches to decision-making in national contexts in Europe. COWAM network comprises 230 delegates from 10 European countries, involving in priority local communities and NGOs. The emphasis put on the local participation enabled members of COWAM network to overcome distrust and to build common lessons and views beyond usual stakeholder positions. Through the analysis of case studies different issues were identified, among them two relate more specifically to: 1) Expertise what is the purpose of expertise on environmental impact in the decision-making process? How is this expertise linked with other scientific and non scientific issues? What is the role of stakeholders in expertise? 2) Environmental quality in the long term and sustainable development how is the impact of radioactive waste management facilities on the environment in the long term taken into account? how is this associated with the sustainable development of the hosting community? How are local stakeholders involved in these issues and what is the expected benefit from their participation? (author)

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.

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.

School, Friends, and Substance Use: Gender Differences on the Influence of Attitudes Toward School and Close Friend Networks on Cannabis Involvement.

Science.gov (United States)

Zaharakis, Nikola; Mason, Michael J; Mennis, Jeremy; Light, John; Rusby, Julie C; Westling, Erika; Crewe, Stephanie; Flay, Brian R; Way, Thomas

2018-02-01

The school environment is extremely salient in young adolescents' lives. Adolescents who have unfavorable attitudes toward school and teachers are at elevated risk for dropping out of school and engaging in behavioral health risks. Peer network health-a summation of the positive and negative behaviors in which one's close friend group engages-may be one way by which attitudes toward school exert influence on youth substance use. Utilizing a sample of 248 primarily African-American young urban adolescents, we tested a moderated mediation model to determine if the indirect effect of attitude to school on cannabis involvement through peer network health was conditioned on gender. Attitude toward school measured at baseline was the predictor (X), peer network health measured at 6 months was the mediator (M), cannabis involvement (including use, offers to use, and refusals to use) measured at 24 months was the outcome (Y), and gender was the moderator (W). Results indicated that negative attitudes toward school were indirectly associated with increased cannabis involvement through peer network health. This relationship was not moderated by gender. Adolescents in our sample with negative attitudes toward school were more likely to receive more offers to use cannabis and to use cannabis more frequently through the perceived health behaviors of their close friends. Implications from these results point to opportunities to leverage the dynamic associations among school experiences, friends, and cannabis involvement, such as offers and use.

Time-Dependent-Asymmetric-Linear-Parsimonious Ancestral State Reconstruction.

Science.gov (United States)

Didier, Gilles

2017-10-01

The time-dependent-asymmetric-linear parsimony is an ancestral state reconstruction method which extends the standard linear parsimony (a.k.a. Wagner parsimony) approach by taking into account both branch lengths and asymmetric evolutionary costs for reconstructing quantitative characters (asymmetric costs amount to assuming an evolutionary trend toward the direction with the lowest cost). A formal study of the influence of the asymmetry parameter shows that the time-dependent-asymmetric-linear parsimony infers states which are all taken among the known states, except for some degenerate cases corresponding to special values of the asymmetry parameter. This remarkable property holds in particular for the Wagner parsimony. This study leads to a polynomial algorithm which determines, and provides a compact representation of, the parametric reconstruction of a phylogenetic tree, that is for all the unknown nodes, the set of all the possible reconstructed states associated with the asymmetry parameters leading to them. The time-dependent-asymmetric-linear parsimony is finally illustrated with the parametric reconstruction of the body size of cetaceans.

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.

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

Stakeholder involvement in the management of rural areas following a nuclear accident: the farming network

International Nuclear Information System (INIS)

Mercer, J.; Nisbet, A.F.

2002-01-01

The importance of the participation of stakeholders in the formulation of strategies for maintaining agricultural production and food safety following a nuclear accident, has been successfully demonstrated by the Agriculture and Food Countermeasures Working Group (AFCWG). This group was set up in the UK by the National Radiological Protection Board (NRPB) and the then Ministry of Agriculture, Fisheries and Food in 1997 (Nisbet and Mondon, 2001). Before this time stakeholder organisations had not collectively considered the implications of contamination of the foodchain in the event of an accidental release of radioactivity. With funding from the European Commission (EC) the UK approach to stakeholder engagement is being taken forward on a European basis during the period 2000-2004 through a project given the acronym FARMING (Food and Agriculture Restoration Management Involving Networked Groups). The overall objective of this project is to create a network of stakeholder working groups in 5 member states (UK, Belgium, Finland, France and Greece) to assist in the development of robust and practicable strategies for restoring and managing contaminated agricultural land and food products in a sustainable way. The initial intention was to involve at least 50 individual stakeholders

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...

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.

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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.

Mechanisms and neuronal networks involved in reactive and proactive cognitive control of interference in working memory.

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Irlbacher, Kerstin; Kraft, Antje; Kehrer, Stefanie; Brandt, Stephan A

2014-10-01

Cognitive control can be reactive or proactive in nature. Reactive control mechanisms, which support the resolution of interference, start after its onset. Conversely, proactive control involves the anticipation and prevention of interference prior to its occurrence. The interrelation of both types of cognitive control is currently under debate: Are they mediated by different neuronal networks? Or are there neuronal structures that have the potential to act in a proactive as well as in a reactive manner? This review illustrates the way in which integrating knowledge gathered from behavioral studies, functional imaging, and human electroencephalography proves useful in answering these questions. We focus on studies that investigate interference resolution at the level of working memory representations. In summary, different mechanisms are instrumental in supporting reactive and proactive control. Distinct neuronal networks are involved, though some brain regions, especially pre-SMA, possess functions that are relevant to both control modes. Therefore, activation of these brain areas could be observed in reactive, as well as proactive control, but at different times during information processing. Copyright © 2014 Elsevier Ltd. All rights reserved.

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

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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.

Functional connectivity profile of the human inferior frontal junction: involvement in a cognitive control network

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Sundermann Benedikt

2012-10-01

Full Text Available Abstract Background The human inferior frontal junction area (IFJ is critically involved in three main component processes of cognitive control (working memory, task switching and inhibitory control. As it overlaps with several areas in established anatomical labeling schemes, it is considered to be underreported as a functionally distinct location in the neuroimaging literature. While recent studies explicitly focused on the IFJ's anatomical organization and functional role as a single brain area, it is usually not explicitly denominated in studies on cognitive networks. However based on few analyses in small datasets constrained by specific a priori assumptions on its functional specialization, the IFJ has been postulated to be part of a cognitive control network. Goal of this meta-analysis was to establish the IFJ’s connectivity profile on a high formal level of evidence by aggregating published implicit knowledge about its co-activations. We applied meta-analytical connectivity modeling (MACM based on the activation likelihood estimation (ALE method without specific assumptions regarding functional specialization on 180 (reporting left IFJ activity and 131 (right IFJ published functional neuroimaging experiments derived from the BrainMap database. This method is based on coordinates in stereotaxic space, not on anatomical descriptors. Results The IFJ is significantly co-activated with areas in the dorsolateral and ventrolateral prefrontal cortex, anterior insula, medial frontal gyrus / pre-SMA, posterior parietal cortex, occipitotemporal junction / cerebellum, thalamus and putamen as well as language and motor areas. Results are corroborated by an independent resting-state fMRI analysis. Conclusions These results support the assumption that the IFJ is part of a previously described cognitive control network. They also highlight the involvement of subcortical structures in this system. A direct line is drawn from works on the functional

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

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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.

The neural network involved in a bimanual tactile-tactile matching discrimination task: a functional imaging study at 3 T

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Habas, Christophe; Cabanis, Emmanuel A. [UPMC Paris 6, Service de NeuroImagerie, Hopital des Quinze-Vingts, Paris (France)

2007-08-15

The cerebral and cerebellar network involved in a bimanual object recognition was studied in blood oxygenation dependent level functional magnetic resonance imaging (fMRI). Nine healthy right-handed volunteers were scanned (1) while performing bilateral finger movements (nondiscrimination motor task), and (2) while performing a bimanual tactile-tactile matching discrimination task using small chess pieces (tactile discrimination task). Extensive activations were specifically observed in the parietal (SII, superior lateral lobule), insular, prefrontal, cingulate and neocerebellar cortices (HVIII), with a left predominance in motor areas, during the tactile discrimination task in contrast to the findings during the nondiscrimination motor task. Bimanual tactile-tactile matching discrimination recruits multiple sensorimotor and associative cerebral and neocerebellar networks (including the cerebellar second homunculus, HVIII), comparable to the neural circuits involved in unimanual tactile object recognition. (orig.)

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.

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.

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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.

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

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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.

When Sharing Is a Bad Idea: The Effects of Online Social Network Engagement and Sharing Passwords with Friends on Cyberbullying Involvement.

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Meter, Diana J; Bauman, Sheri

2015-08-01

Every day, children and adolescents communicate online via social networking sites (SNSs). They also report sharing passwords with peers and friends, a potentially risky behavior in regard to cyber safety. This longitudinal study tested the hypotheses that social network engagement in multiple settings would predict more cyberbullying involvement over time, and that youth who reported sharing passwords would also experience an increase in cyberbullying involvement. Data were collected at two time points one year apart from 1,272 third through eighth grade students. In line with the first study hypothesis, participating in more online SNSs was associated with increased cyberbullying involvement over time, as well as sharing passwords over time. Cyberbullying involvement at T1 predicted decreases in sharing passwords over time, suggesting that youth become aware of the dangers of sharing passwords as a result of their experience. Sharing passwords at T1 was unrelated to cyberbullying involvement at T2. Although it seems that youth may be learning from their previous mistakes, due to the widespread use of social media and normality of sharing passwords among young people, it is important to continue to educate youth about cyber safety and risky online behavior.

Heat exchanger network retrofit optimization involving heat transfer enhancement

International Nuclear Information System (INIS)

Wang Yufei; Smith, Robin; Kim, Jin-Kuk

2012-01-01

Heat exchanger network retrofit plays an important role in energy saving in process industry. Many design methods for the retrofit of heat exchanger networks have been proposed during the last three decades. Conventional retrofit methods rely heavily on topology modifications which often result in a long retrofit duration and high initial costs. Moreover, the addition of extra surface area to the heat exchanger can prove difficult due to topology, safety and downtime constraints. Both of these problems can be avoided through the use of heat transfer enhancement in heat exchanger network retrofit. This paper presents a novel design approach to solve heat exchanger network retrofit problems based on heat transfer enhancement. An optimisation method based on simulated annealing has been developed to find the appropriate heat exchangers to be enhanced and to calculate the level of enhancement required. The physical insight of enhanced exchangers is also analysed. The new methodology allows several possible retrofit strategies using different retrofit methods be determined. Comparison of these retrofit strategies demonstrates that retrofit modification duration and payback time are reduced when heat transfer enhancement is utilised. Heat transfer enhancement can be also used as a substitute for increased heat exchanger network surface area to reduce retrofit investment costs.

The vertebrate Hox gene regulatory network for hindbrain segmentation: Evolution and diversification: Coupling of a Hox gene regulatory network to hindbrain segmentation is an ancient trait originating at the base of vertebrates.

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Parker, Hugo J; Bronner, Marianne E; Krumlauf, Robb

2016-06-01

Hindbrain development is orchestrated by a vertebrate gene regulatory network that generates segmental patterning along the anterior-posterior axis via Hox genes. Here, we review analyses of vertebrate and invertebrate chordate models that inform upon the evolutionary origin and diversification of this network. Evidence from the sea lamprey reveals that the hindbrain regulatory network generates rhombomeric compartments with segmental Hox expression and an underlying Hox code. We infer that this basal feature was present in ancestral vertebrates and, as an evolutionarily constrained developmental state, is fundamentally important for patterning of the vertebrate hindbrain across diverse lineages. Despite the common ground plan, vertebrates exhibit neuroanatomical diversity in lineage-specific patterns, with different vertebrates revealing variations of Hox expression in the hindbrain that could underlie this diversification. Invertebrate chordates lack hindbrain segmentation but exhibit some conserved aspects of this network, with retinoic acid signaling playing a role in establishing nested domains of Hox expression. © 2016 WILEY Periodicals, Inc.

Structuring an integrated care system: interpreted through the enacted diversity of the actors involved – the case of a French healthcare network

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Corinne Grenier

2011-02-01

Full Text Available Research question: We are looking at the process of structuring an integrated care system as an innovative process that swings back and forth between the diversity of the actors involved, local aspirations and national and regional regulations. We believe that innovation is enriched by the variety of the actors involved, but may also be blocked or disrupted by that diversity. Our research aims to add to other research, which, when questioning these integrated systems, analyses how the actors involved deal with diversity without really questioning it. Case study: The empirical basis of the paper is provided by case study analysis. The studied integrated care system is a French healthcare network that brings together healthcare professionals and various organisations in order to improve the way in which interventions are coordinated and formalised, in order to promote better detection and diagnosis procedures and the implementation of a care protocol. We consider this case as instrumental in developing theoretical proposals for structuring an integrated care system in light of the diversity of the actors involved. Results and discussion: We are proposing a model for structuring an integrated care system in light of the enacted diversity of the actors involved. This model is based on three factors: the diversity enacted by the leaders, three stances for considering the contribution made by diversity in the structuring process and the specific leading role played by those in charge of the structuring process.  Through this process, they determined how the actors involved in the project were differentiated, and on what basis those actors were involved. By mobilizing enacted diversity, the leaders are seeking to channel the emergence of a network in light of their own representation of that network. This model adds to published research on the structuring of integrated care systems.

Structuring an integrated care system: interpreted through the enacted diversity of the actors involved – the case of a French healthcare network

Directory of Open Access Journals (Sweden)

Corinne Grenier

2011-02-01

Full Text Available Research question: We are looking at the process of structuring an integrated care system as an innovative process that swings back and forth between the diversity of the actors involved, local aspirations and national and regional regulations. We believe that innovation is enriched by the variety of the actors involved, but may also be blocked or disrupted by that diversity. Our research aims to add to other research, which, when questioning these integrated systems, analyses how the actors involved deal with diversity without really questioning it.Case study: The empirical basis of the paper is provided by case study analysis. The studied integrated care system is a French healthcare network that brings together healthcare professionals and various organisations in order to improve the way in which interventions are coordinated and formalised, in order to promote better detection and diagnosis procedures and the implementation of a care protocol. We consider this case as instrumental in developing theoretical proposals for structuring an integrated care system in light of the diversity of the actors involved.Results and discussion: We are proposing a model for structuring an integrated care system in light of the enacted diversity of the actors involved. This model is based on three factors: the diversity enacted by the leaders, three stances for considering the contribution made by diversity in the structuring process and the specific leading role played by those in charge of the structuring process.  Through this process, they determined how the actors involved in the project were differentiated, and on what basis those actors were involved. By mobilizing enacted diversity, the leaders are seeking to channel the emergence of a network in light of their own representation of that network. This model adds to published research on the structuring of integrated care systems.

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

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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

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

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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.

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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.

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...

In silico transcriptional regulatory networks involved in tomato fruit ripening

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Stilianos Arhondakis

2016-08-01

Full Text Available ABSTRACTTomato fruit ripening is a complex developmental programme partly mediated by transcriptional regulatory networks. Several transcription factors (TFs which are members of gene families such as MADS-box and ERF were shown to play a significant role in ripening through interconnections into an intricate network. The accumulation of large datasets of expression profiles corresponding to different stages of tomato fruit ripening and the availability of bioinformatics tools for their analysis provide an opportunity to identify TFs which might regulate gene clusters with similar co-expression patterns. We identified two TFs, a SlWRKY22-like and a SlER24 transcriptional activator which were shown to regulate modules by using the LeMoNe algorithm for the analysis of our microarray datasets representing four stages of fruit ripening, breaker, turning, pink and red ripe. The WRKY22-like module comprised a subgroup of six various calcium sensing transcripts with similar to the TF expression patterns according to real time PCR validation. A promoter motif search identified a cis acting element, the W-box, recognized by WRKY TFs that was present in the promoter region of all six calcium sensing genes. Moreover, publicly available microarray datasets of similar ripening stages were also analyzed with LeMoNe resulting in TFs such as SlERF.E1, SlERF.C1, SlERF.B2, SLERF.A2, SlWRKY24, SLWRKY37 and MADS-box/TM29 which might also play an important role in regulation of ripening. These results suggest that the SlWRKY22-like might be involved in the coordinated regulation of expression of the six calcium sensing genes. Conclusively the LeMoNe tool might lead to the identification of putative TF targets for further physiological analysis as regulators of tomato fruit ripening.

Obesity is marked by distinct functional connectivity in brain networks involved in food reward and salience.

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Wijngaarden, M A; Veer, I M; Rombouts, S A R B; van Buchem, M A; Willems van Dijk, K; Pijl, H; van der Grond, J

2015-01-01

We hypothesized that brain circuits involved in reward and salience respond differently to fasting in obese versus lean individuals. We compared functional connectivity networks related to food reward and saliency after an overnight fast (baseline) and after a prolonged fast of 48 h in lean versus obese subjects. We included 13 obese (2 males, 11 females, BMI 35.4 ± 1.2 kg/m(2), age 31 ± 3 years) and 11 lean subjects (2 males, 9 females, BMI 23.2 ± 0.5 kg/m(2), age 28 ± 3 years). Resting-state functional magnetic resonance imaging scans were made after an overnight fast (baseline) and after a prolonged 48 h fast. Functional connectivity of the amygdala, hypothalamus and posterior cingulate cortex (default-mode) networks was assessed using seed-based correlations. At baseline, we found a stronger connectivity between hypothalamus and left insula in the obese subjects. This effect diminished upon the prolonged fast. After prolonged fasting, connectivity of the hypothalamus with the dorsal anterior cingulate cortex (dACC) increased in lean subjects and decreased in obese subjects. Amygdala connectivity with the ventromedial prefrontal cortex was stronger in lean subjects at baseline, which did not change upon the prolonged fast. No differences in posterior cingulate cortex connectivity were observed. In conclusion, obesity is marked by alterations in functional connectivity networks involved in food reward and salience. Prolonged fasting differentially affected hypothalamic connections with the dACC and the insula between obese and lean subjects. Our data support the idea that food reward and nutrient deprivation are differently perceived and/or processed in obesity. Copyright © 2015 Elsevier B.V. All rights reserved.

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.

Trauma histories among justice-involved youth: findings from the National Child Traumatic Stress Network

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Carly B. Dierkhising

2013-07-01

Full Text Available Background: Up to 90% of justice-involved youth report exposure to some type of traumatic event. On average, 70% of youth meet criteria for a mental health disorder with approximately 30% of youth meeting criteria for post-traumatic stress disorder (PTSD. Justice-involved youth are also at risk for substance use and academic problems, and child welfare involvement. Yet, less is known about the details of their trauma histories, and associations among trauma details, mental health problems, and associated risk factors. Objective: This study describes detailed trauma histories, mental health problems, and associated risk factors (i.e., academic problems, substance/alcohol use, and concurrent child welfare involvement among adolescents with recent involvement in the juvenile justice system. Method: The National Child Traumatic Stress Network Core Data Set (NCTSN-CDS is used to address these aims, among which 658 adolescents report recent involvement in the juvenile justice system as indexed by being detained or under community supervision by the juvenile court. Results: Age of onset of trauma exposure was within the first 5 years of life for 62% of youth and approximately one-third of youth report exposure to multiple or co-occurring trauma types each year into adolescence. Mental health problems are prevalent with 23.6% of youth meeting criteria for PTSD, 66.1% in the clinical range for externalizing problems, and 45.5% in the clinical range for internalizing problems. Early age of onset of trauma exposure was differentially associated with mental health problems and related risk factors among males and females. Conclusions: The results indicate that justice-involved youth report high rates of trauma exposure and that this trauma typically begins early in life, is often in multiple contexts, and persists over time. Findings provide support for establishing trauma-informed juvenile justice systems that can respond to the needs of traumatized youth.

Industrial Networks

DEFF Research Database (Denmark)

Karlsson, Christer

2015-01-01

Companies organize in a way that involves many activities that are external to the traditional organizational boundaries. This presents challenges to operations management and managing operations involves many issues and actions dealing with external networks. Taking a network perspective changes...

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.

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.

Brain network involved in visual processing of movement stimuli used in upper limb robotic training: an fMRI study.

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Nocchi, Federico; Gazzellini, Simone; Grisolia, Carmela; Petrarca, Maurizio; Cannatà, Vittorio; Cappa, Paolo; D'Alessio, Tommaso; Castelli, Enrico

2012-07-24

The potential of robot-mediated therapy and virtual reality in neurorehabilitation is becoming of increasing importance. However, there is limited information, using neuroimaging, on the neural networks involved in training with these technologies. This study was intended to detect the brain network involved in the visual processing of movement during robotic training. The main aim was to investigate the existence of a common cerebral network able to assimilate biological (human upper limb) and non-biological (abstract object) movements, hence testing the suitability of the visual non-biological feedback provided by the InMotion2 Robot. A visual functional Magnetic Resonance Imaging (fMRI) task was administered to 22 healthy subjects. The task required observation and retrieval of motor gestures and of the visual feedback used in robotic training. Functional activations of both biological and non-biological movements were examined to identify areas activated in both conditions, along with differential activity in upper limb vs. abstract object trials. Control of response was also tested by administering trials with congruent and incongruent reaching movements. The observation of upper limb and abstract object movements elicited similar patterns of activations according to a caudo-rostral pathway for the visual processing of movements (including specific areas of the occipital, temporal, parietal, and frontal lobes). Similarly, overlapping activations were found for the subsequent retrieval of the observed movement. Furthermore, activations of frontal cortical areas were associated with congruent trials more than with the incongruent ones. This study identified the neural pathway associated with visual processing of movement stimuli used in upper limb robot-mediated training and investigated the brain's ability to assimilate abstract object movements with human motor gestures. In both conditions, activations were elicited in cerebral areas involved in visual

Brain network involved in visual processing of movement stimuli used in upper limb robotic training: an fMRI study

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Nocchi Federico

2012-07-01

Full Text Available Abstract Background The potential of robot-mediated therapy and virtual reality in neurorehabilitation is becoming of increasing importance. However, there is limited information, using neuroimaging, on the neural networks involved in training with these technologies. This study was intended to detect the brain network involved in the visual processing of movement during robotic training. The main aim was to investigate the existence of a common cerebral network able to assimilate biological (human upper limb and non-biological (abstract object movements, hence testing the suitability of the visual non-biological feedback provided by the InMotion2 Robot. Methods A visual functional Magnetic Resonance Imaging (fMRI task was administered to 22 healthy subjects. The task required observation and retrieval of motor gestures and of the visual feedback used in robotic training. Functional activations of both biological and non-biological movements were examined to identify areas activated in both conditions, along with differential activity in upper limb vs. abstract object trials. Control of response was also tested by administering trials with congruent and incongruent reaching movements. Results The observation of upper limb and abstract object movements elicited similar patterns of activations according to a caudo-rostral pathway for the visual processing of movements (including specific areas of the occipital, temporal, parietal, and frontal lobes. Similarly, overlapping activations were found for the subsequent retrieval of the observed movement. Furthermore, activations of frontal cortical areas were associated with congruent trials more than with the incongruent ones. Conclusions This study identified the neural pathway associated with visual processing of movement stimuli used in upper limb robot-mediated training and investigated the brain’s ability to assimilate abstract object movements with human motor gestures. In both conditions

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

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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

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

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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.

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...

Identification and analysis of signaling networks potentially involved in breast carcinoma metastasis to the brain.

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Feng Li

Full Text Available Brain is a common site of breast cancer metastasis associated with significant neurologic morbidity, decreased quality of life, and greatly shortened survival. However, the molecular and cellular mechanisms underpinning brain colonization by breast carcinoma cells are poorly understood. Here, we used 2D-DIGE (Difference in Gel Electrophoresis proteomic analysis followed by LC-tandem mass spectrometry to identify the proteins differentially expressed in brain-targeting breast carcinoma cells (MB231-Br compared with parental MDA-MB-231 cell line. Between the two cell lines, we identified 12 proteins consistently exhibiting greater than 2-fold (p<0.05 difference in expression, which were associated by the Ingenuity Pathway Analysis (IPA with two major signaling networks involving TNFα/TGFβ-, NFκB-, HSP-70-, TP53-, and IFNγ-associated pathways. Remarkably, highly related networks were revealed by the IPA analysis of a list of 19 brain-metastasis-associated proteins identified recently by the group of Dr. A. Sierra using MDA-MB-435-based experimental system (Martin et al., J Proteome Res 2008 7:908-20, or a 17-gene classifier associated with breast cancer brain relapse reported by the group of Dr. J. Massague based on a microarray analysis of clinically annotated breast tumors from 368 patients (Bos et al., Nature 2009 459: 1005-9. These findings, showing that different experimental systems and approaches (2D-DIGE proteomics used on brain targeting cell lines or gene expression analysis of patient samples with documented brain relapse yield highly related signaling networks, suggest strongly that these signaling networks could be essential for a successful colonization of the brain by metastatic breast carcinoma cells.

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

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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

Inference of Ancestral Recombination Graphs through Topological Data Analysis

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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

Online social networks for patient involvement and recruitment in clinical research.

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Ryan, Gemma Sinead

2013-01-01

To review current literature and discuss the potential of online social networking to engage patients and the public and recruit and retain participants in clinical research. Online social networking is becoming a large influence on people's daily lives. Clinical research faces several challenges, with an increasing need to engage with patients and the public and for studies to recruit and retain increasing numbers of participants, particularly in under-served, under-represented and hard to reach groups and communities. Searches were conducted using EMBASE, BNI, ERIC, CINAHL, PSYCHinfo online databases and Google Scholar to identify any grey or unpublished literature that may be available. Review methods This is a methodology paper. Online social networking is a successful, cost-effective and efficient method by which to target and recruit a wide range of communities, adolescents, young people and underserved populations into quantitative and qualitative research. Retention of participants in longitudinal studies could be improved using social networks such as Facebook. Evidence indicates that a mixed approach to recruitment using social networking and traditional methods is most effective. Further research is required to strengthen the evidence available, especially in dissemination of research through online social networks. Researchers should consider using online social networking as a method of engaging the public, and also for the recruitment and follow up of participants.

A Bayesian approach to the evolution of metabolic networks on a phylogeny.

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Aziz Mithani

2010-08-01

Full Text Available The availability of genomes of many closely related bacteria with diverse metabolic capabilities offers the possibility of tracing metabolic evolution on a phylogeny relating the genomes to understand the evolutionary processes and constraints that affect the evolution of metabolic networks. Using simple (independent loss/gain of reactions or complex (incorporating dependencies among reactions stochastic models of metabolic evolution, it is possible to study how metabolic networks evolve over time. Here, we describe a model that takes the reaction neighborhood into account when modeling metabolic evolution. The model also allows estimation of the strength of the neighborhood effect during the course of evolution. We present Gibbs samplers for sampling networks at the internal node of a phylogeny and for estimating the parameters of evolution over a phylogeny without exploring the whole search space by iteratively sampling from the conditional distributions of the internal networks and parameters. The samplers are used to estimate the parameters of evolution of metabolic networks of bacteria in the genus Pseudomonas and to infer the metabolic networks of the ancestral pseudomonads. The results suggest that pathway maps that are conserved across the Pseudomonas phylogeny have a stronger neighborhood structure than those which have a variable distribution of reactions across the phylogeny, and that some Pseudomonas lineages are going through genome reduction resulting in the loss of a number of reactions from their metabolic networks.

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

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Michael B Walker

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

Neural Networks Involved in Adolescent Reward Processing: An Activation Likelihood Estimation Meta-Analysis of Functional Neuroimaging Studies

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Silverman, Merav H.; Jedd, Kelly; Luciana, Monica

2015-01-01

Behavioral responses to, and the neural processing of, rewards change dramatically during adolescence and may contribute to observed increases in risk-taking during this developmental period. Functional MRI (fMRI) studies suggest differences between adolescents and adults in neural activation during reward processing, but findings are contradictory, and effects have been found in non-predicted directions. The current study uses an activation likelihood estimation (ALE) approach for quantitative meta-analysis of functional neuroimaging studies to: 1) confirm the network of brain regions involved in adolescents’ reward processing, 2) identify regions involved in specific stages (anticipation, outcome) and valence (positive, negative) of reward processing, and 3) identify differences in activation likelihood between adolescent and adult reward-related brain activation. Results reveal a subcortical network of brain regions involved in adolescent reward processing similar to that found in adults with major hubs including the ventral and dorsal striatum, insula, and posterior cingulate cortex (PCC). Contrast analyses find that adolescents exhibit greater likelihood of activation in the insula while processing anticipation relative to outcome and greater likelihood of activation in the putamen and amygdala during outcome relative to anticipation. While processing positive compared to negative valence, adolescents show increased likelihood for activation in the posterior cingulate cortex (PCC) and ventral striatum. Contrasting adolescent reward processing with the existing ALE of adult reward processing (Liu et al., 2011) reveals increased likelihood for activation in limbic, frontolimbic, and striatal regions in adolescents compared with adults. Unlike adolescents, adults also activate executive control regions of the frontal and parietal lobes. These findings support hypothesized elevations in motivated activity during adolescence. PMID:26254587

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

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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.

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

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Tetsuya eTachibana

2014-11-01

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

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...

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

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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

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.

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

Structural networks involved in attention and executive functions in multiple sclerosis

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Sara Llufriu

2017-01-01

Full Text Available Attention and executive deficits are disabling symptoms in multiple sclerosis (MS that have been related to disconnection mechanisms. We aimed to investigate changes in structural connectivity in MS and their association with attention and executive performance applying an improved framework that combines high order probabilistic tractography and anatomical exclusion criteria postprocessing. We compared graph theory metrics of structural networks and fractional anisotropy (FA of white matter (WM connections or edges between 72 MS subjects and 38 healthy volunteers (HV and assessed their correlation with cognition. Patients displayed decreased network transitivity, global efficiency and increased path length compared with HV (p < 0.05, corrected. Also, nodal strength was decreased in 26 of 84 gray matter regions. The distribution of nodes with stronger connections or hubs of the network was similar among groups except for the right pallidum and left insula, which became hubs in patients. MS subjects presented reduced edge FA widespread in the network, while FA was increased in 24 connections (p < 0.05, corrected. Decreased integrity of frontoparietal networks, deep gray nuclei and insula correlated with worse attention and executive performance (r between 0.38 and 0.55, p < 0.05, corrected. Contrarily, higher strength in the right transverse temporal cortex and increased FA of several connections (mainly from cingulate, frontal and occipital cortices were associated with worse functioning (r between −0.40 and −0.47, p < 0.05 corrected. In conclusion, structural brain connectivity is disturbed in MS due to widespread impairment of WM connections and gray matter structures. The increased edge connectivity suggests the presence of reorganization mechanisms at the structural level. Importantly, attention and executive performance relates to frontoparietal networks, deep gray nuclei and insula. These results support the relevance of

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

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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.

The Transmission of Gun and Other Weapon-Involved Violence Within Social Networks.

Science.gov (United States)

Tracy, Melissa; Braga, Anthony A; Papachristos, Andrew V

2016-01-01

Fatal and nonfatal injuries resulting from gun violence remain a persistent problem in the United States. The available research suggests that gun violence diffuses among people and across places through social relationships. Understanding the relationship between gun violence within social networks and individual gun violence risk is critical in preventing the spread of gun violence within populations. This systematic review examines the existing scientific evidence on the transmission of gun and other weapon-related violence in household, intimate partner, peer, and co-offending networks. Our review identified 16 studies published between 1996 and 2015 that suggest that exposure to a victim or perpetrator of violence in one's interpersonal relationships and social networks increases the risk of individual victimization and perpetration. Formal network analyses find high concentrations of gun violence in small networks and that exposure to gun violence in one's networks is highly correlated with one's own probability of being a gunshot victim. Physical violence by parents and weapon use by intimate partners also increase risk for victimization and perpetration. Additional work is needed to better characterize the mechanisms through which network exposures increase individual risk for violence and to evaluate interventions aimed at disrupting the spread of gun and other weapon violence in high-risk social networks. © The Author 2016. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

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...

Linear network theory

CERN Document Server

Sander, K F

1964-01-01

Linear Network Theory covers the significant algebraic aspect of network theory, with minimal reference to practical circuits. The book begins the presentation of network analysis with the exposition of networks containing resistances only, and follows it up with a discussion of networks involving inductance and capacity by way of the differential equations. Classification and description of certain networks, equivalent networks, filter circuits, and network functions are also covered. Electrical engineers, technicians, electronics engineers, electricians, and students learning the intricacies

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

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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

Mechanistically Distinct Pathways of Divergent Regulatory DNA Creation Contribute to Evolution of Human-Specific Genomic Regulatory Networks Driving Phenotypic Divergence of Homo sapiens.

Science.gov (United States)

Glinsky, Gennadi V

2016-09-19

Thousands of candidate human-specific regulatory sequences (HSRS) have been identified, supporting the hypothesis that unique to human phenotypes result from human-specific alterations of genomic regulatory networks. Collectively, a compendium of multiple diverse families of HSRS that are functionally and structurally divergent from Great Apes could be defined as the backbone of human-specific genomic regulatory networks. Here, the conservation patterns analysis of 18,364 candidate HSRS was carried out requiring that 100% of bases must remap during the alignments of human, chimpanzee, and bonobo sequences. A total of 5,535 candidate HSRS were identified that are: (i) highly conserved in Great Apes; (ii) evolved by the exaptation of highly conserved ancestral DNA; (iii) defined by either the acceleration of mutation rates on the human lineage or the functional divergence from non-human primates. The exaptation of highly conserved ancestral DNA pathway seems mechanistically distinct from the evolution of regulatory DNA segments driven by the species-specific expansion of transposable elements. Genome-wide proximity placement analysis of HSRS revealed that a small fraction of topologically associating domains (TADs) contain more than half of HSRS from four distinct families. TADs that are enriched for HSRS and termed rapidly evolving in humans TADs (revTADs) comprise 0.8-10.3% of 3,127 TADs in the hESC genome. RevTADs manifest distinct correlation patterns between placements of human accelerated regions, human-specific transcription factor-binding sites, and recombination rates. There is a significant enrichment within revTAD boundaries of hESC-enhancers, primate-specific CTCF-binding sites, human-specific RNAPII-binding sites, hCONDELs, and H3K4me3 peaks with human-specific enrichment at TSS in prefrontal cortex neurons (P sapiens is driven by the evolution of human-specific genomic regulatory networks via at least two mechanistically distinct pathways of creation of

The Prediction of Key Cytoskeleton Components Involved in Glomerular Diseases Based on a Protein-Protein Interaction Network.

Science.gov (United States)

Ding, Fangrui; Tan, Aidi; Ju, Wenjun; Li, Xuejuan; Li, Shao; Ding, Jie

2016-01-01

Maintenance of the physiological morphologies of different types of cells and tissues is essential for the normal functioning of each system in the human body. Dynamic variations in cell and tissue morphologies depend on accurate adjustments of the cytoskeletal system. The cytoskeletal system in the glomerulus plays a key role in the normal process of kidney filtration. To enhance the understanding of the possible roles of the cytoskeleton in glomerular diseases, we constructed the Glomerular Cytoskeleton Network (GCNet), which shows the protein-protein interaction network in the glomerulus, and identified several possible key cytoskeletal components involved in glomerular diseases. In this study, genes/proteins annotated to the cytoskeleton were detected by Gene Ontology analysis, and glomerulus-enriched genes were selected from nine available glomerular expression datasets. Then, the GCNet was generated by combining these two sets of information. To predict the possible key cytoskeleton components in glomerular diseases, we then examined the common regulation of the genes in GCNet in the context of five glomerular diseases based on their transcriptomic data. As a result, twenty-one cytoskeleton components as potential candidate were highlighted for consistently down- or up-regulating in all five glomerular diseases. And then, these candidates were examined in relation to existing known glomerular diseases and genes to determine their possible functions and interactions. In addition, the mRNA levels of these candidates were also validated in a puromycin aminonucleoside(PAN) induced rat nephropathy model and were also matched with existing Diabetic Nephropathy (DN) transcriptomic data. As a result, there are 15 of 21 candidates in PAN induced nephropathy model were consistent with our predication and also 12 of 21 candidates were matched with differentially expressed genes in the DN transcriptomic data. By providing a novel interaction network and prediction, GCNet

Perceived Conventionality in Co-speech Gestures Involves the Fronto-Temporal Language Network

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Dhana Wolf

2017-11-01

Full Text Available Face-to-face communication is multimodal; it encompasses spoken words, facial expressions, gaze, and co-speech gestures. In contrast to linguistic symbols (e.g., spoken words or signs in sign language relying on mostly explicit conventions, gestures vary in their degree of conventionality. Bodily signs may have a general accepted or conventionalized meaning (e.g., a head shake or less so (e.g., self-grooming. We hypothesized that subjective perception of conventionality in co-speech gestures relies on the classical language network, i.e., the left hemispheric inferior frontal gyrus (IFG, Broca's area and the posterior superior temporal gyrus (pSTG, Wernicke's area and studied 36 subjects watching video-recorded story retellings during a behavioral and an functional magnetic resonance imaging (fMRI experiment. It is well documented that neural correlates of such naturalistic videos emerge as intersubject covariance (ISC in fMRI even without involving a stimulus (model-free analysis. The subjects attended either to perceived conventionality or to a control condition (any hand movements or gesture-speech relations. Such tasks modulate ISC in contributing neural structures and thus we studied ISC changes to task demands in language networks. Indeed, the conventionality task significantly increased covariance of the button press time series and neuronal synchronization in the left IFG over the comparison with other tasks. In the left IFG, synchronous activity was observed during the conventionality task only. In contrast, the left pSTG exhibited correlated activation patterns during all conditions with an increase in the conventionality task at the trend level only. Conceivably, the left IFG can be considered a core region for the processing of perceived conventionality in co-speech gestures similar to spoken language. In general, the interpretation of conventionalized signs may rely on neural mechanisms that engage during language comprehension.

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

International Nuclear Information System (INIS)

Inui, Ken; Sagane, Yoshimasa; Miyata, Keita; Miyashita, Shin-Ichiro; Suzuki, Tomonori; Shikamori, Yasuyuki; Ohyama, Tohru; Niwa, Koichi; Watanabe, Toshihiro

2012-01-01

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

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...

Improving Patient Involvement in the Drug Development Process: Case Study of Potential Applications from an Online Peer Support Network.

Science.gov (United States)

Anand, Amrutha; Brandwood, Helen Jane; Jameson Evans, Matt

2017-11-01

To date, social media has been used predominantly by the pharmaceutical industry to market products and to gather feedback and comments on products from consumers, a process termed social listening. However, social media has only been used cautiously in the drug development cycle, mainly because of regulations, restrictions on engagement with patients, or a lack of guidelines for social media use from regulatory bodies. Despite this cautious approach, there is a clear drive, from both the industry and consumers, for increased patient participation in various stages of the drug development process. The authors use the example of HealthUnlocked, one of the world's largest health networks, to illustrate the potential applications of online health communities as a means of increasing patient involvement at various stages of the drug development process. Having identified the willingness of the user population to be involved in research, numerous ways to engage users on the platform have been identified and explored. This commentary describes some of these approaches and reports how online health networks that encourage people to share their experiences in managing their health can, in turn, enable rapid patient engagement for clinical research within the constraints of industry regulation. Copyright © 2017 Elsevier HS Journals, Inc. All rights reserved.

Introductory note on Emergent Unconscious Knowledge Networks (Asygnodic Networks

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Henry Bakis

2016-05-01

Full Text Available This note introduces the following paper on the concept of Emergent Unconscious Knowledge Networks (Asygnodic Networks created by E. Roche and M. Blaine. The concept of asyngnosis explains a large number of diverse phenomena involving organizations, groups and decision making. It will present the genesis and definition of Asygnodic Networks and will focus on how they raise challenges to traditional theories of decision making and emerging social networks.

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.

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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.

Regulatory network analysis of Epstein-Barr virus identifies functional modules and hub genes involved in infectious mononucleosis.

Science.gov (United States)

Poorebrahim, Mansour; Salarian, Ali; Najafi, Saeideh; Abazari, Mohammad Foad; Aleagha, Maryam Nouri; Dadras, Mohammad Nasr; Jazayeri, Seyed Mohammad; Ataei, Atousa; Poortahmasebi, Vahdat

2017-05-01

Epstein-Barr virus (EBV) is the most common cause of infectious mononucleosis (IM) and establishes lifetime infection associated with a variety of cancers and autoimmune diseases. The aim of this study was to develop an integrative gene regulatory network (GRN) approach and overlying gene expression data to identify the representative subnetworks for IM and EBV latent infection (LI). After identifying differentially expressed genes (DEGs) in both IM and LI gene expression profiles, functional annotations were applied using gene ontology (GO) and BiNGO tools, and construction of GRNs, topological analysis and identification of modules were carried out using several plugins of Cytoscape. In parallel, a human-EBV GRN was generated using the Hu-Vir database for further analyses. Our analysis revealed that the majority of DEGs in both IM and LI were involved in cell-cycle and DNA repair processes. However, these genes showed a significant negative correlation in the IM and LI states. Furthermore, cyclin-dependent kinase 2 (CDK2) - a hub gene with the highest centrality score - appeared to be the key player in cell cycle regulation in IM disease. The most significant functional modules in the IM and LI states were involved in the regulation of the cell cycle and apoptosis, respectively. Human-EBV network analysis revealed several direct targets of EBV proteins during IM disease. Our study provides an important first report on the response to IM/LI EBV infection in humans. An important aspect of our data was the upregulation of genes associated with cell cycle progression and proliferation.

Network methods to support user involvement in qualitative data analyses: an introduction to Participatory Theme Elicitation.

Science.gov (United States)

Best, Paul; Badham, Jennifer; Corepal, Rekesh; O'Neill, Roisin F; Tully, Mark A; Kee, Frank; Hunter, Ruth F

2017-11-23

While Patient and Public Involvement (PPI) is encouraged throughout the research process, engagement is typically limited to intervention design and post-analysis stages. There are few approaches to participatory data analyses within complex health interventions. Using qualitative data from a feasibility randomised controlled trial (RCT), this proof-of-concept study tests the value of a new approach to participatory data analysis called Participatory Theme Elicitation (PTE). Forty excerpts were given to eight members of a youth advisory PPI panel to sort into piles based on their perception of related thematic content. Using algorithms to detect communities in networks, excerpts were then assigned to a thematic cluster that combined the panel members' perspectives. Network analysis techniques were also used to identify key excerpts in each grouping that were then further explored qualitatively. While PTE analysis was, for the most part, consistent with the researcher-led analysis, young people also identified new emerging thematic content. PTE appears promising for encouraging user led identification of themes arising from qualitative data collected during complex interventions. Further work is required to validate and extend this method. ClinicalTrials.gov, ID: NCT02455986 . Retrospectively Registered on 21 May 2015.

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

Network coding at different layers in wireless networks

CERN Document Server

2016-01-01

This book focuses on how to apply network coding at different layers in wireless networks – including MAC, routing, and TCP – with special focus on cognitive radio networks. It discusses how to select parameters in network coding (e.g., coding field, number of packets involved, and redundant information ration) in order to be suitable for the varying wireless environments. The book explores how to deploy network coding in MAC to improve network performance and examines joint network coding with opportunistic routing to improve the successful rate of routing. In regards to TCP and network coding, the text considers transport layer protocol working with network coding to overcome the transmission error rate, particularly with how to use the ACK feedback of TCP to enhance the efficiency of network coding. The book pertains to researchers and postgraduate students, especially whose interests are in opportunistic routing and TCP in cognitive radio networks.

A novel strategy involved in [corrected] anti-oxidative defense: the conversion of NADH into NADPH by a metabolic network.

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Ranji Singh

Full Text Available The reduced nicotinamide adenine dinucleotide phosphate (NADPH is pivotal to the cellular anti-oxidative defence strategies in most organisms. Although its production mediated by different enzyme systems has been relatively well-studied, metabolic networks dedicated to the biogenesis of NADPH have not been fully characterized. In this report, a metabolic pathway that promotes the conversion of reduced nicotinamide adenine dinucleotide (NADH, a pro-oxidant into NADPH has been uncovered in Pseudomonas fluorescens exposed to oxidative stress. Enzymes such as pyruvate carboxylase (PC, malic enzyme (ME, malate dehydrogenase (MDH, malate synthase (MS, and isocitrate lyase (ICL that are involved in disparate metabolic modules, converged to create a metabolic network aimed at the transformation of NADH into NADPH. The downregulation of phosphoenol carboxykinase (PEPCK and the upregulation of pyruvate kinase (PK ensured that this metabolic cycle fixed NADH into NADPH to combat the oxidative stress triggered by the menadione insult. This is the first demonstration of a metabolic network invoked to generate NADPH from NADH, a process that may be very effective in combating oxidative stress as the increase of an anti-oxidant is coupled to the decrease of a pro-oxidant.

Retrofitting of heat exchanger networks involving streams with variable heat capacity: Application of single and multi-objective optimization

International Nuclear Information System (INIS)

Sreepathi, Bhargava Krishna; Rangaiah, G.P.

2015-01-01

Heat exchanger network (HEN) retrofitting improves the energy efficiency of the current process by reducing external utilities. In this work, HEN retrofitting involving streams having variable heat capacity is studied. For this, enthalpy values of a stream are fitted to a continuous cubic polynomial instead of a stepwise approach employed in the previous studies [1,2]. The former methodology is closer to reality as enthalpy or heat capacity changes gradually instead of step changes. Using the polynomial fitting formulation, single objective optimization (SOO) and multi-objective optimization (MOO) of a HEN retrofit problem are investigated. The results obtained show an improvement in the utility savings, and MOO provides many Pareto-optimal solutions to choose from. Also, Pareto-optimal solutions involving area addition in existing heat exchangers only (but no new exchangers and no structural modifications) are found and provided for comparison with those involving new exchangers and structural modifications as well. - Highlights: • HEN retrofitting involving streams with variable heat capacities is studied. • A continuous approach to handle variable heat capacity is proposed and tested. • Better and practical solutions are obtained for HEN retrofitting in process plants. • Pareto-optimal solutions provide many alternate choices for HEN retrofitting

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.

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

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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

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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.

Design alternatives for wavelength routing networks

Science.gov (United States)

Miliotis, K.; Papadimitriou, G. I.; Pomportsis, A. S.

2003-03-01

This paper attempts to provide a high level overview of many of the technologies employed in optical networks with a focus on wavelength-routing networks. Optical networks involve a number of technologies from the physics of light through protocols and networks architectures. In fact there is so much technology and know-how that most people involved with optical networks only have a full understanding of the narrow area they deal with. We start first examining the principles that govern light and its use as a wave guide, and then turn our focus to the various components that constitute an optical network and conclude with the description of all optical networks and wavelength-routed networks in greater detail.

Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway.

Science.gov (United States)

Sato, Yukuto; Hashiguchi, Yasuyuki; Nishida, Mutsumi

2009-02-20

Duplicate genes are considered to have evolved through the partitioning of ancestral functions among duplicates (subfunctionalization) and/or the acquisition of novel functions from a beneficial mutation (neofunctionalization). Additionally, an increase in gene dosage resulting from duplication may also confer an advantageous effect, as has been suggested for histone, tRNA, and rRNA genes. Currently, there is little understanding of the effect of increased gene dosage on subcellular networks like signal transduction pathways. Addressing this issue may provide further insights into the evolution by gene duplication. We analyzed the evolution of multiple stickleback phosphodiesterase (PDE, EC: 3.1.4.17) 1C genes involved in the cyclic nucleotide signaling pathway. Stickleback has 8-9 copies of this gene, whereas only one or two loci exist in other model vertebrates. Our phylogenetic and synteny analyses suggested that the multiple PDE1C genes in stickleback were generated by repeated duplications of >100-kbp chromosome segments. Sequence evolution analysis did not provide strong evidence for neofunctionalization in the coding sequences of stickleback PDE1C isoforms. On the other hand, gene expression analysis suggested that the derived isoforms acquired expression in new organs, implying their neofunctionalization in terms of expression patterns. In addition, at least seven isoforms of the stickleback PDE1C were co-expressed with olfactory-type G-proteins in the nose, suggesting that PDE1C dosage is increased in the stickleback olfactory transduction (OT) pathway. In silico simulations of OT implied that the increased PDE1C dosage extends the longevity of the depolarization signals of the olfactory receptor neuron. The predicted effect of the increase in PDE1C products on the OT pathway may play an important role in stickleback behavior and ecology. However, this possibility should be empirically examined. Our analyses imply that an increase in gene product sometimes

Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway

Directory of Open Access Journals (Sweden)

Nishida Mutsumi

2009-02-01

Full Text Available Abstract Background Duplicate genes are considered to have evolved through the partitioning of ancestral functions among duplicates (subfunctionalization and/or the acquisition of novel functions from a beneficial mutation (neofunctionalization. Additionally, an increase in gene dosage resulting from duplication may also confer an advantageous effect, as has been suggested for histone, tRNA, and rRNA genes. Currently, there is little understanding of the effect of increased gene dosage on subcellular networks like signal transduction pathways. Addressing this issue may provide further insights into the evolution by gene duplication. Results We analyzed the evolution of multiple stickleback phosphodiesterase (PDE, EC: 3.1.4.17 1C genes involved in the cyclic nucleotide signaling pathway. Stickleback has 8–9 copies of this gene, whereas only one or two loci exist in other model vertebrates. Our phylogenetic and synteny analyses suggested that the multiple PDE1C genes in stickleback were generated by repeated duplications of >100-kbp chromosome segments. Sequence evolution analysis did not provide strong evidence for neofunctionalization in the coding sequences of stickleback PDE1C isoforms. On the other hand, gene expression analysis suggested that the derived isoforms acquired expression in new organs, implying their neofunctionalization in terms of expression patterns. In addition, at least seven isoforms of the stickleback PDE1C were co-expressed with olfactory-type G-proteins in the nose, suggesting that PDE1C dosage is increased in the stickleback olfactory transduction (OT pathway. In silico simulations of OT implied that the increased PDE1C dosage extends the longevity of the depolarization signals of the olfactory receptor neuron. Conclusion The predicted effect of the increase in PDE1C products on the OT pathway may play an important role in stickleback behavior and ecology. However, this possibility should be empirically examined. Our

Social Network Sites, Friends, and Celebrities: The Roles of Social Comparison and Celebrity Involvement in Adolescents’ Body Image Dissatisfaction

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Shirley S. Ho

2016-08-01

Full Text Available This study applies the social comparison theory to examine the effects of adolescents’ engagement in comparison with friends and celebrities on social network sites (SNSs on (a their body image dissatisfaction (BID and (b their drive to be thin (DT or muscular (DM. The study also examines celebrity involvement as an antecedent of the outcome variables. Data were collected through a survey of 1,059 adolescents in Singapore. Regression analyses indicate that SNSs use was related to adolescents’ BID. Specifically, social comparison with friends on SNSs was significantly associated with adolescents’ BID, DT, and DM. Gender differences were also observed—social comparison with celebrities was significantly associated with BID and DT among female adolescents. Celebrity involvement was significantly associated with male BID. Theoretical and practical implications were discussed.

A lateralized functional auditory network is involved in anuran ...

Indian Academy of Sciences (India)

2016-10-05

Oct 5, 2016 ... menting a statistical, predictive notion of causality whereby causes precede to help ... GCCA methods provides a chance to investigate the brain networks ...... by the grants from the National Natural Science Foundation of China (No. .... vocal competition is dynamic and strongly affected by social contexts in ...

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

Energy Technology Data Exchange (ETDEWEB)

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

2012-03-16

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

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

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Grünewald Stefan

2011-01-01

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

Northern emporia and maritime networks. Modelling past communication using archaeological network analysis

DEFF Research Database (Denmark)

Sindbæk, Søren Michael

2015-01-01

preserve patterns of thisinteraction. Formal network analysis and modelling holds the potential to identify anddemonstrate such patterns, where traditional methods often prove inadequate. Thearchaeological study of communication networks in the past, however, calls for radically different analytical...... this is not a problem of network analysis, but network synthesis: theclassic problem of cracking codes or reconstructing black-box circuits. It is proposedthat archaeological approaches to network synthesis must involve a contextualreading of network data: observations arising from individual contexts, morphologies...

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

EXTERNALITIES IN EXCHANGE NETWORKS AN ADAPTATION OF EXISTING THEORIES OF EXCHANGE NETWORKS

NARCIS (Netherlands)

Dijkstra, Jacob

2009-01-01

The present paper extends the focus of network exchange research to externalities in exchange networks. Externalities of exchange are defined as direct effects on an actor's utility, of an exchange in which this actor is not involved. Existing theories in the field of network exchange do not inform

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.

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

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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.

Dominating biological networks.

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Tijana Milenković

Full Text Available Proteins are essential macromolecules of life that carry out most cellular processes. Since proteins aggregate to perform function, and since protein-protein interaction (PPI networks model these aggregations, one would expect to uncover new biology from PPI network topology. Hence, using PPI networks to predict protein function and role of protein pathways in disease has received attention. A debate remains open about whether network properties of "biologically central (BC" genes (i.e., their protein products, such as those involved in aging, cancer, infectious diseases, or signaling and drug-targeted pathways, exhibit some topological centrality compared to the rest of the proteins in the human PPI network.To help resolve this debate, we design new network-based approaches and apply them to get new insight into biological function and disease. We hypothesize that BC genes have a topologically central (TC role in the human PPI network. We propose two different concepts of topological centrality. We design a new centrality measure to capture complex wirings of proteins in the network that identifies as TC those proteins that reside in dense extended network neighborhoods. Also, we use the notion of domination and find dominating sets (DSs in the PPI network, i.e., sets of proteins such that every protein is either in the DS or is a neighbor of the DS. Clearly, a DS has a TC role, as it enables efficient communication between different network parts. We find statistically significant enrichment in BC genes of TC nodes and outperform the existing methods indicating that genes involved in key biological processes occupy topologically complex and dense regions of the network and correspond to its "spine" that connects all other network parts and can thus pass cellular signals efficiently throughout the network. To our knowledge, this is the first study that explores domination in the context of PPI networks.

Hierarchical Network Design

DEFF Research Database (Denmark)

Thomadsen, Tommy

2005-01-01

Communication networks are immensely important today, since both companies and individuals use numerous services that rely on them. This thesis considers the design of hierarchical (communication) networks. Hierarchical networks consist of layers of networks and are well-suited for coping...... with changing and increasing demands. Two-layer networks consist of one backbone network, which interconnects cluster networks. The clusters consist of nodes and links, which connect the nodes. One node in each cluster is a hub node, and the backbone interconnects the hub nodes of each cluster and thus...... the clusters. The design of hierarchical networks involves clustering of nodes, hub selection, and network design, i.e. selection of links and routing of ows. Hierarchical networks have been in use for decades, but integrated design of these networks has only been considered for very special types of networks...

Network Learning and Innovation in SME Formal Networks

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Jivka Deiters

2013-02-01

Full Text Available The driver for this paper is the need to better understand the potential for learning and innovation that networks canprovide especially for small and medium sized enterprises (SMEs which comprise by far the majority of enterprises in the food sector. With the challenges the food sector is facing in the near future, learning and innovation or more focused, as it is being discussed in the paper, ‘learning for innovation’ are not just opportunities but pre‐conditions for the sustainability of the sector. Network initiatives that could provide appropriate support involve social interaction and knowledge exchange, learning, competence development, and coordination (organization and management of implementation. The analysis identifies case studies in any of these orientations which serve different stages of the innovation process: invention and implementation. The variety of network case studies cover networks linked to a focus group for training, research, orconsulting, networks dealing with focused market oriented product or process development, promotional networks, and networks for open exchange and social networking.

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).

Science.gov (United States)

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.

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.

Cortical networks involved in visual awareness independent of visual attention.

Science.gov (United States)

Webb, Taylor W; Igelström, Kajsa M; Schurger, Aaron; Graziano, Michael S A

2016-11-29

It is now well established that visual attention, as measured with standard spatial attention tasks, and visual awareness, as measured by report, can be dissociated. It is possible to attend to a stimulus with no reported awareness of the stimulus. We used a behavioral paradigm in which people were aware of a stimulus in one condition and unaware of it in another condition, but the stimulus drew a similar amount of spatial attention in both conditions. The paradigm allowed us to test for brain regions active in association with awareness independent of level of attention. Participants performed the task in an MRI scanner. We looked for brain regions that were more active in the aware than the unaware trials. The largest cluster of activity was obtained in the temporoparietal junction (TPJ) bilaterally. Local independent component analysis (ICA) revealed that this activity contained three distinct, but overlapping, components: a bilateral, anterior component; a left dorsal component; and a right dorsal component. These components had brain-wide functional connectivity that partially overlapped the ventral attention network and the frontoparietal control network. In contrast, no significant activity in association with awareness was found in the banks of the intraparietal sulcus, a region connected to the dorsal attention network and traditionally associated with attention control. These results show the importance of separating awareness and attention when testing for cortical substrates. They are also consistent with a recent proposal that awareness is associated with ventral attention areas, especially in the TPJ.

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

Directory of Open Access Journals (Sweden)

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.

Abnormal binding and disruption in large scale networks involved in human partial seizures

Directory of Open Access Journals (Sweden)

Bartolomei Fabrice

2013-12-01

Full Text Available There is a marked increase in the amount of electrophysiological and neuroimaging works dealing with the study of large scale brain connectivity in the epileptic brain. Our view of the epileptogenic process in the brain has largely evolved over the last twenty years from the historical concept of “epileptic focus” to a more complex description of “Epileptogenic networks” involved in the genesis and “propagation” of epileptic activities. In particular, a large number of studies have been dedicated to the analysis of intracerebral EEG signals to characterize the dynamic of interactions between brain areas during temporal lobe seizures. These studies have reported that large scale functional connectivity is dramatically altered during seizures, particularly during temporal lobe seizure genesis and development. Dramatic changes in neural synchrony provoked by epileptic rhythms are also responsible for the production of ictal symptoms or changes in patient’s behaviour such as automatisms, emotional changes or consciousness alteration. Beside these studies dedicated to seizures, large-scale network connectivity during the interictal state has also been investigated not only to define biomarkers of epileptogenicity but also to better understand the cognitive impairments observed between seizures.

Bladder Cancer Advocacy Network

Science.gov (United States)

... Grants Bladder Cancer Think Tank Bladder Cancer Research Network Bladder Cancer Genomics Consortium Get Involved Ways to ... us? Who we are The Bladder Cancer Advocacy Network (BCAN) is a community of patients, caregivers, survivors, ...

An ancestral human genetic variant linked to an ancient disease: A novel association of FMO2 polymorphisms with tuberculosis (TB in Ethiopian populations provides new insight into the differential ethno-geographic distribution of FMO2*1.

Directory of Open Access Journals (Sweden)

Ephrem Mekonnen

Full Text Available The human FMO2 (flavin-containing monooxygenase 2 gene has been shown to be involved in innate immunity against microbial infections, including tuberculosis (TB, via the modulation of oxidative stress levels. It has also been found to possess a curious loss-of-function mutation (FMO2*1/FMO2*2 that demonstrates a distinctive differentiation in expression, function and ethno-geographic distribution. However, despite evidences of ethnic-specific genetic associations in the inflammatory profile of TB, no studies were done to investigate whether these patterns of variations correlate with evidences for the involvement of FMO2 in antimicrobial immune responses and ethnic differences in the distribution of FMO2 polymorphisms except for some pharmacogenetic data that suggest a potentially deleterious role for the functional variant (FMO2*1. This genetic epidemiological study was designed to investigate whether there is an association between FMO2 polymorphisms and TB, an ancient malady that remains a modern global health concern, in a sub-Saharan Africa setting where there is not only a relatively high co-prevalence of the disease and the ancestral FMO2*1 variant but also where both Mycobcaterium and Homo sapiens are considered to have originated and co-evolved. Blood samples and TB related clinical data were collected from ascertained TB cases and unrelated household controls (n = 292 from 3 different ethnic groups in Ethiopia. Latent Mtb infection was determined using Quantiferon to develop reliable TB progression phenotypes. We sequenced exonic regions of FMO2.We identified for the first time an association between FMO2 and TB both at the SNP and haplotype level. Two novel SNPs achieved a study-wide significance [chr1:171181877(A, p = 3.15E-07, OR = 4.644 and chr1:171165749(T, p = 3.32E-06, OR = 6.825] while multiple SNPs (22 showed nominal signals. The pattern of association suggested a protective effect of FMO2 against both active and latent TB

A flood-based information flow analysis and network minimization method for gene regulatory networks.

Science.gov (United States)

Pavlogiannis, Andreas; Mozhayskiy, Vadim; Tagkopoulos, Ilias

2013-04-24

Biological networks tend to have high interconnectivity, complex topologies and multiple types of interactions. This renders difficult the identification of sub-networks that are involved in condition- specific responses. In addition, we generally lack scalable methods that can reveal the information flow in gene regulatory and biochemical pathways. Doing so will help us to identify key participants and paths under specific environmental and cellular context. This paper introduces the theory of network flooding, which aims to address the problem of network minimization and regulatory information flow in gene regulatory networks. Given a regulatory biological network, a set of source (input) nodes and optionally a set of sink (output) nodes, our task is to find (a) the minimal sub-network that encodes the regulatory program involving all input and output nodes and (b) the information flow from the source to the sink nodes of the network. Here, we describe a novel, scalable, network traversal algorithm and we assess its potential to achieve significant network size reduction in both synthetic and E. coli networks. Scalability and sensitivity analysis show that the proposed method scales well with the size of the network, and is robust to noise and missing data. The method of network flooding proves to be a useful, practical approach towards information flow analysis in gene regulatory networks. Further extension of the proposed theory has the potential to lead in a unifying framework for the simultaneous network minimization and information flow analysis across various "omics" levels.

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

Fixed Access Network Sharing

Science.gov (United States)

Cornaglia, Bruno; Young, Gavin; Marchetta, Antonio

2015-12-01

Fixed broadband network deployments are moving inexorably to the use of Next Generation Access (NGA) technologies and architectures. These NGA deployments involve building fiber infrastructure increasingly closer to the customer in order to increase the proportion of fiber on the customer's access connection (Fibre-To-The-Home/Building/Door/Cabinet… i.e. FTTx). This increases the speed of services that can be sold and will be increasingly required to meet the demands of new generations of video services as we evolve from HDTV to "Ultra-HD TV" with 4k and 8k lines of video resolution. However, building fiber access networks is a costly endeavor. It requires significant capital in order to cover any significant geographic coverage. Hence many companies are forming partnerships and joint-ventures in order to share the NGA network construction costs. One form of such a partnership involves two companies agreeing to each build to cover a certain geographic area and then "cross-selling" NGA products to each other in order to access customers within their partner's footprint (NGA coverage area). This is tantamount to a bi-lateral wholesale partnership. The concept of Fixed Access Network Sharing (FANS) is to address the possibility of sharing infrastructure with a high degree of flexibility for all network operators involved. By providing greater configuration control over the NGA network infrastructure, the service provider has a greater ability to define the network and hence to define their product capabilities at the active layer. This gives the service provider partners greater product development autonomy plus the ability to differentiate from each other at the active network layer.

The corticotropin-releasing hormone network and the hypothalamic-pituitary-adrenal axis: molecular and cellular mechanisms involved.

Science.gov (United States)

Bonfiglio, Juan José; Inda, Carolina; Refojo, Damián; Holsboer, Florian; Arzt, Eduardo; Silberstein, Susana

2011-01-01

Corticotropin-releasing hormone (CRH) plays a key role in adjusting the basal and stress-activated hypothalamic-pituitary-adrenal axis (HPA). CRH is also widely distributed in extrahypothalamic circuits, where it acts as a neuroregulator to integrate the complex neuroendocrine, autonomic, and behavioral adaptive response to stress. Hyperactive and/or dysregulated CRH circuits are involved in neuroendocrinological disturbances and stress-related mood disorders such as anxiety and depression. This review describes the main physiological features of the CRH network and summarizes recent relevant information concerning the molecular mechanism of CRH action obtained from signal transduction studies using cells and wild-type and transgenic mice lines. Special focus is placed on the MAPK signaling pathways triggered by CRH through the CRH receptor 1 that plays an essential role in CRH action in pituitary corticotrophs and in specific brain structures. Recent findings underpin the concept of specific CRH-signaling pathways restricted to specific anatomical areas. Understanding CRH action at molecular levels will not only provide insight into the precise CRH mechanism of action, but will also be instrumental in identifying novel targets for pharmacological intervention in neuroendocrine tissues and specific brain areas involved in CRH-related disorders. Copyright © 2011 S. Karger AG, Basel.

Gross anatomy of network security

Science.gov (United States)

Siu, Thomas J.

2002-01-01

Information security involves many branches of effort, including information assurance, host level security, physical security, and network security. Computer network security methods and implementations are given a top-down description to permit a medically focused audience to anchor this information to their daily practice. The depth of detail of network functionality and security measures, like that of the study of human anatomy, can be highly involved. Presented at the level of major gross anatomical systems, this paper will focus on network backbone implementation and perimeter defenses, then diagnostic tools, and finally the user practices (the human element). Physical security measures, though significant, have been defined as beyond the scope of this presentation.

Biological Networks Entropies: Examples in Neural Memory Networks, Genetic Regulation Networks and Social Epidemic Networks

Directory of Open Access Journals (Sweden)

Jacques Demongeot

2018-01-01

Full Text Available Networks used in biological applications at different scales (molecule, cell and population are of different types: neuronal, genetic, and social, but they share the same dynamical concepts, in their continuous differential versions (e.g., non-linear Wilson-Cowan system as well as in their discrete Boolean versions (e.g., non-linear Hopfield system; in both cases, the notion of interaction graph G(J associated to its Jacobian matrix J, and also the concepts of frustrated nodes, positive or negative circuits of G(J, kinetic energy, entropy, attractors, structural stability, etc., are relevant and useful for studying the dynamics and the robustness of these systems. We will give some general results available for both continuous and discrete biological networks, and then study some specific applications of three new notions of entropy: (i attractor entropy, (ii isochronal entropy and (iii entropy centrality; in three domains: a neural network involved in the memory evocation, a genetic network responsible of the iron control and a social network accounting for the obesity spread in high school environment.

Managerial Challenges Within Networks - Emphasizing the Paradox of Network Participation

DEFF Research Database (Denmark)

Jakobsen, Morten

2003-01-01

Flexibility and access to numerous resources are essential benefits associated with network participation. An important aspect of managing the network participation of a company is to maintain a dynamic portfolio of partners, and thereby keep up the strategic opportunities for development. However......, maintaining the dynamics within a network seems to be a complex challenge. There is a risk that the network ends up in The Paradox of Network Participation. The desired renewal and flexibility are not utilised because the involved parties preserve the existing networks structure consisting of the same...... and thereby sort out the paradox of network participation. Trust and information are mechanisms employed to absorb uncertainty. The relationship between trust and the requirement for information depends on the maturity of the relationship. When trust becomes too important as uncertainty absorption mechanism...

Managerial challenges within networks: emphasizing the paradox of network participation

DEFF Research Database (Denmark)

Jakobsen, Morten

Flexibility and access to numerous resources are essential benefits associated with network participation. An important aspect of managing the network participation of a company is to maintain a dynamic portfolio of partners, and thereby keep up the strategic opportunities for development. However......, maintaining the dynamics within a network seems to be a complex challenge. There is a risk that the network ends up in The Paradox of Network Participation. The desired renewal and flexibility are not utilised because the involved parties preserve the existing networks structure consisting of the same...... and thereby sort out the paradox of network participation. Trust and information are mechanisms employed to absorb uncertainty. The relationship between trust and the requirement for information depends on the maturity of the relationship. When trust becomes too important as uncertainty absorption mechanism...

Network Security: What Non-Technical Administrators Must Know

Science.gov (United States)

Council, Chip

2005-01-01

Now it is increasingly critical that community college leaders become involved in network security and partner with their directors of information technology (IT). Network security involves more than just virus protection software and firewalls. It involves vigilance and requires top executive support. Leaders can help their IT directors to…

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.

Managing Interorganizational Networks

DEFF Research Database (Denmark)

Gustafsson, Jeppe

bold enough to predict that networks will become the dominant organisation form in future. Several authors maintain that the shift from traditional hierarchical structures to networks involves dramatic changes for managers and employees (Champy 2002, Rohlin 1994, Kanter 2002). This article seeks...... organisation theories and theories about strategic management....

The ghost of Afrikaner identity in Ancestral voices, Leap year and The long silence of Mario Salviati (Etienne van Heerden

Directory of Open Access Journals (Sweden)

Mariëtte van Graan

2017-04-01

Full Text Available Ghost characters are a characteristic of the novels of Etienne van Heerden, but little research has been done concerning the nature and function of these ghost characters. In this article I discuss Van Heerden’s use of ghost characters diachronically with reference to the novels Ancestral voices (1986, Leap year (1993 and The long silence of Mario Salviati (2000. In order to clarify the nature of these ghosts, I use the so-called science of the paranormal as a framework. The ghosts in the three novels will be classified accordingly, and then discussed within the context of the novels in which they appear. In this way, I shall show how the ghost characters in these novels can be read as a constantly changing embodiment of Afrikaner identity (a central theme in Van Heerden’s oeuvre. Van Heerden’s Afrikaner changes with the times: in Ancestral voices the ghost characters form a collective that represents a fragmented image of the stereotypical, archaic male Afrikaner identity; in Leap year a liminal character is written in a liminal time to embody a liminal Afrikaner identity; and in The long silence of Mario Salviati Van Heerden moves away from the exclusive Afrikaner identity to a broader South African identity by using ghost characters from very different backgrounds and origins. In conclusion I shall compare these identities and the historical contexts of these novels in order to show the function of Van Heerden’s ghost characters as constant rewritings of South African identities.

Temporal Databases in Network Management

National Research Council Canada - National Science Library

Gupta, Ajay

1998-01-01

.... This thesis discusses issues involved with performing network management, specifically with means of reducing and storing the large quantity of data that networks management tools and systems generate...

Not single brain areas but a network is involved in language: Applications in presurgical planning.

Science.gov (United States)

Alemi, Razieh; Batouli, Seyed Amir Hossein; Behzad, Ebrahim; Ebrahimpoor, Mitra; Oghabian, Mohammad Ali

2018-02-01

Language is an important human function, and is a determinant of the quality of life. In conditions such as brain lesions, disruption of the language function may occur, and lesion resection is a solution for that. Presurgical planning to determine the language-related brain areas would enhance the chances of language preservation after the operation; however, availability of a normative language template is essential. In this study, using data from 60 young individuals who were meticulously checked for mental and physical health, and using fMRI and robust imaging and data analysis methods, functional brain maps for the language production, perception and semantic were produced. The obtained templates showed that the language function should be considered as the product of the collaboration of a network of brain regions, instead of considering only few brain areas to be involved in that. This study has important clinical applications, and extends our knowledge on the neuroanatomy of the language function. Copyright © 2018 Elsevier B.V. All rights reserved.

Risk aversion and social networks

NARCIS (Netherlands)

Kovarik, J.; van der Leij, M.J.

2011-01-01

Agents involved in the formation of a social or economic network typically face uncertainty about the benefits of creating a link. However, the interplay of such uncertainty and risk attitudes has been neglected in the network formation literature. We propose a dynamic network formation model that

Risk aversion and social networks

NARCIS (Netherlands)

Kovářík, J.; van der Leij, M.J.

2012-01-01

Agents involved in the formation of a social or economic network typically face uncertainty about the benefits of creating a link. However, the interplay of such uncertainty and risk attitudes has been neglected in the network formation literature. We propose a dynamic network formation model that

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

Directory of Open Access Journals (Sweden)

Daniel Gonzalez

2014-01-01

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

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

Science.gov (United States)

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

2016-09-20

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

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

Cross-species chromosome painting in bats from Madagascar: the contribution of Myzopodidae to revealing ancestral syntenies in Chiroptera.

Science.gov (United States)

Richards, Leigh R; Rambau, Ramugondo V; Lamb, Jennifer M; Taylor, Peter J; Yang, Fengtang; Schoeman, M Corrie; Goodman, Steven M

2010-09-01

The chiropteran fauna of Madagascar comprises eight of the 19 recognized families of bats, including the endemic Myzopodidae. While recent systematic studies of Malagasy bats have contributed to our understanding of the morphological and genetic diversity of the island's fauna, little is known about their cytosystematics. Here we investigate karyotypic relationships among four species, representing four families of Chiroptera endemic to the Malagasy region using cross-species chromosome painting with painting probes of Myotis myotis: Myzopodidae (Myzopoda aurita, 2n = 26), Molossidae (Mormopterus jugularis, 2n = 48), Miniopteridae (Miniopterus griveaudi, 2n = 46), and Vespertilionidae (Myotis goudoti, 2n = 44). This study represents the first time a member of the family Myzopodidae has been investigated using chromosome painting. Painting probes of M. myotis were used to delimit 29, 24, 23, and 22 homologous chromosomal segments in the genomes of M. aurita, M. jugularis, M. griveaudi, and M. goudoti, respectively. Comparison of GTG-banded homologous chromosomes/chromosomal segments among the four species revealed the genome of M. aurita has been structured through 14 fusions of chromosomes and chromosomal segments of M. myotis chromosomes leading to a karyotype consisting solely of bi-armed chromosomes. In addition, chromosome painting revealed a novel X-autosome translocation in M. aurita. Comparison of our results with published chromosome maps provided further evidence for karyotypic conservatism within the genera Mormopterus, Miniopterus, and Myotis. Mapping of chromosomal rearrangements onto a molecular consensus phylogeny revealed ancestral syntenies shared between Myzopoda and other bat species of the infraorders Pteropodiformes and Vespertilioniformes. Our study provides further evidence for the involvement of Robertsonian (Rb) translocations and fusions/fissions in chromosomal evolution within Chiroptera.

Effective professional networking.

Science.gov (United States)

Goolsby, Mary Jo; Knestrick, Joyce M

2017-08-01

The reasons for nurse practitioners to develop a professional network are boundless and are likely to change over time. Networking opens doors and creates relationships that support new opportunities, personal development, collaborative research, policy activism, evidence-based practice, and more. Successful professional networking involves shared, mutually beneficial interactions between individuals and/or individuals and groups, regardless of whether it occurs face to face or electronically. This article combines nuggets from the literature with guidance based on the authors' combined experience in networking activities at the local, national, and international levels. ©2017 American Association of Nurse Practitioners.

Corporate-governmental networks in the Netherlands

NARCIS (Netherlands)

Mokken, R.J.; Stokman, F.N.

1979-01-01

Corporate networks studies have been restricted mainly to the private or business sectors. Network analyses involving both corporations and state or government agencies have been extremely rare. In this paper, the intercorporate network of interlocking directorates in the Netherlands, based on 86

Morphological neural networks

Energy Technology Data Exchange (ETDEWEB)

Ritter, G.X.; Sussner, P. [Univ. of Florida, Gainesville, FL (United States)

1996-12-31

The theory of artificial neural networks has been successfully applied to a wide variety of pattern recognition problems. In this theory, the first step in computing the next state of a neuron or in performing the next layer neural network computation involves the linear operation of multiplying neural values by their synaptic strengths and adding the results. Thresholding usually follows the linear operation in order to provide for nonlinearity of the network. In this paper we introduce a novel class of neural networks, called morphological neural networks, in which the operations of multiplication and addition are replaced by addition and maximum (or minimum), respectively. By taking the maximum (or minimum) of sums instead of the sum of products, morphological network computation is nonlinear before thresholding. As a consequence, the properties of morphological neural networks are drastically different than those of traditional neural network models. In this paper we consider some of these differences and provide some particular examples of morphological neural network.

Intelligent networked teleoperation control

CERN Document Server

Li, Zhijun; Su, Chun-Yi

2015-01-01

This book describes a unified framework for networked teleoperation systems involving multiple research fields: networked control systems for linear and nonlinear forms, bilateral teleoperation, trilateral teleoperation, multilateral teleoperation and cooperative teleoperation. It closely examines networked control as a field at the intersection of systems & control and robotics and presents a number of experimental case studies on testbeds for robotic systems, including networked haptic devices, robotic network systems and sensor network systems. The concepts and results outlined are easy to understand, even for readers fairly new to the subject. As such, the book offers a valuable reference work for researchers and engineers in the fields of systems & control and robotics.

Building Leadership Capacity in the Involving Network State

Science.gov (United States)

Pedersen, Dorthe; Tangkjaer, Christian

2013-01-01

New partnerships, cross-organisational collaborations and co-creation, digitalisation, involvement of citizens, public design and innovation stand out as new and emerging solutions in welfare delivery. However, New Public Management (NPM) seems to represent a historical repertoire of perspectives and tools that falls short of dealing with public…

New approach to ECG's features recognition involving neural network

International Nuclear Information System (INIS)

Babloyantz, A.; Ivanov, V.V.; Zrelov, P.V.

2001-01-01

A new approach for the detection of slight changes in the form of the ECG signal is proposed. It is based on the approximation of raw ECG data inside each RR-interval by the expansion in polynomials of special type and on the classification of samples represented by sets of expansion coefficients using a layered feed-forward neural network. The transformation applied provides significantly simpler data structure, stability to noise and to other accidental factors. A by-product of the method is the compression of ECG data with factor 5

Dual Headquarters Involvement in Multibusiness Firms

DEFF Research Database (Denmark)

Nell, Phillip Christopher; Kappen, Philip; Dellestrand, Henrik

The strategy literature has shown that headquarters involve themselves into subsidiary operations to add value. Yet, little is known about the extent to which multiple headquarters do so. Therefore, we investigate antecedents of corporate and divisional headquarters’ involvement in innovation...... development projects of subsidiaries. Analyses of 85 innovation development projects reveal that dual innovation importance (innovation that is important for the division and the rest of the firm), and dual dual embeddedness (innovating subsidiary is embedded both within the division and in the rest...... of the firm) lead to greater dual headquarters involvement, especially when the innovation development network is large. The results contribute to the literature on complex parenting and theory of selective headquarters involvement....

Joint Hub Network Development

NARCIS (Netherlands)

Cruijssen, F.C.A.M.; Borm, P.E.M.; Dullaert, W.; Hamers, H.J.M.

2007-01-01

This paper introduces a framework for joint hub network development. Building a joint physical hub for transhipment of goods is expensive and therefore involves considerable risks for the cooperating companies. In a practical setting, it is unlikely that an entire network will be built at once.

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

Science.gov (United States)

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.

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

Directory of Open Access Journals (Sweden)

Jairzinho Francisco Panqueba Cifuentes

2012-06-01

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

The impact of patient and public involvement in the work of the Dementias & Neurodegenerative Diseases Research Network (DeNDRoN): case studies.

Science.gov (United States)

Iliffe, Steve; McGrath, Terry; Mitchell, Douglas

2013-12-01

(i) To describe patient and public involvement (PPI) in a network promoting research in dementia and neurodegenerative diseases, in terms of activity at the different stages of the research cycle and within the different levels of the research network. (ii) To use case studies to try and answer the question: what benefits (if any) does PPI in research bring to the research process? PPI in health research is a central part of government policy, but the evidence base underpinning it needs strengthening. PPI allows exploration of feasibility, acceptability and relevance of hypotheses, assists in the precise definition of research questions and increases accrual to studies. However, the measurement of outcomes is methodologically difficult, because the impact of lay researchers may occur through team interactions and be difficult to untangle from the efforts of professional researchers. Opportunities for PPI in rapidly progressive diseases may be limited, and involvement of people with marked cognitive impairment is particularly challenging. (i) Description of PPI within the DeNDRoN network. (ii) Case studies of three research projects which asked for extra help from centrally organized PPI. PPI in research projects on the DeNDRoN portfolio may function at different levels, occurring at project, local research network and national level. Case studies of three research projects show different roles for PPI in research and different functions for centrally organized PPI, including contribution to remedial action in studies that are not recruiting to target, solving problems because of the complexity and sensitivity of the research topic, and linking researchers to PPI resources. The case studies suggest that centrally organized PPI can have 'diagnostic' and remedial functions in studies that are struggling to recruit and serve as reinforcement for study-level PPI in the complex and sensitive research topics that are typical in neurodegenerative diseases research. PPI may

MicroRNA-Mediated Positive Feedback Loop and Optimized Bistable Switch in a Cancer Network Involving miR-17-92

Science.gov (United States)

Li, Yichen; Li, Yumin; Zhang, Hui; Chen, Yong

2011-01-01

MicroRNAs (miRNAs) are small, noncoding RNAs that play an important role in many key biological processes, including development, cell differentiation, the cell cycle and apoptosis, as central post-transcriptional regulators of gene expression. Recent studies have shown that miRNAs can act as oncogenes and tumor suppressors depending on the context. The present work focuses on the physiological significance of miRNAs and their role in regulating the switching behavior. We illustrate an abstract model of the Myc/E2F/miR-17-92 network presented by Aguda et al. (2008), which is composed of coupling between the E2F/Myc positive feedback loops and the E2F/Myc/miR-17-92 negative feedback loop. By systematically analyzing the network in close association with plausible experimental parameters, we show that, in the presence of miRNAs, the system bistability emerges from the system, with a bistable switch and a one-way switch presented by Aguda et al. instead of a single one-way switch. Moreover, the miRNAs can optimize the switching process. The model produces a diverse array of response-signal behaviors in response to various potential regulating scenarios. The model predicts that this transition exists, one from cell death or the cancerous phenotype directly to cell quiescence, due to the existence of miRNAs. It was also found that the network involving miR-17-92 exhibits high noise sensitivity due to a positive feedback loop and also maintains resistance to noise from a negative feedback loop. PMID:22022595

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

Science.gov (United States)

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

2006-03-01

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

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

Directory of Open Access Journals (Sweden)

Shigeki Nakagome

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

Sensory biology. 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

2014-08-22

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. Copyright © 2014, American Association for the Advancement of Science.

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

Science.gov (United States)

Nakagome, Shigeki; Mano, Shuhei; Hasegawa, Masami

2013-01-01

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

Metropolitan Optical Networks 1995 Annual Report

DEFF Research Database (Denmark)

Kristensen, Martin; Jouanno, Jean-Marc; Malone, Kevin

1996-01-01

The annual report describes the research carried out in the ACTS-project METON (Metropolitan Optical Networks) in 1995. L.M. Ericsson is prime contractor and 12 partners including DTU is involved in the project.......The annual report describes the research carried out in the ACTS-project METON (Metropolitan Optical Networks) in 1995. L.M. Ericsson is prime contractor and 12 partners including DTU is involved in the project....

Using Long-Distance Scientist Involvement to Enhance NASA Volunteer Network Educational Activities

Science.gov (United States)

Ferrari, K.

2012-12-01

Since 1999, the NASA/JPL Solar System Ambassadors (SSA) and Solar System Educators (SSEP) programs have used specially-trained volunteers to expand education and public outreach beyond the immediate NASA center regions. Integrating nationwide volunteers in these highly effective programs has helped optimize agency funding set aside for education. Since these volunteers were trained by NASA scientists and engineers, they acted as "stand-ins" for the mission team members in communities across the country. Through the efforts of these enthusiastic volunteers, students gained an increased awareness of NASA's space exploration missions through Solar System Ambassador classroom visits, and teachers across the country became familiarized with NASA's STEM (Science, Technology, Engineering and Mathematics) educational materials through Solar System Educator workshops; however the scientist was still distant. In 2003, NASA started the Digital Learning Network (DLN) to bring scientists into the classroom via videoconferencing. The first equipment was expensive and only schools that could afford the expenditure were able to benefit; however, recent advancements in software allow classrooms to connect to the DLN via personal computers and an internet connection. Through collaboration with the DLN at NASA's Jet Propulsion Laboratory and the Goddard Spaceflight Center, Solar System Ambassadors and Solar System Educators in remote parts of the country are able to bring scientists into their classroom visits or workshops as guest speakers. The goals of this collaboration are to provide special elements to the volunteers' event, allow scientists opportunities for education involvement with minimal effort, acquaint teachers with DLN services and enrich student's classroom learning experience.;

Alcohol-induced histone acetylation reveals a gene network involved in alcohol tolerance.

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Alfredo Ghezzi

Full Text Available Sustained or repeated exposure to sedating drugs, such as alcohol, triggers homeostatic adaptations in the brain that lead to the development of drug tolerance and dependence. These adaptations involve long-term changes in the transcription of drug-responsive genes as well as an epigenetic restructuring of chromosomal regions that is thought to signal and maintain the altered transcriptional state. Alcohol-induced epigenetic changes have been shown to be important in the long-term adaptation that leads to alcohol tolerance and dependence endophenotypes. A major constraint impeding progress is that alcohol produces a surfeit of changes in gene expression, most of which may not make any meaningful contribution to the ethanol response under study. Here we used a novel genomic epigenetic approach to find genes relevant for functional alcohol tolerance by exploiting the commonalities of two chemically distinct alcohols. In Drosophila melanogaster, ethanol and benzyl alcohol induce mutual cross-tolerance, indicating that they share a common mechanism for producing tolerance. We surveyed the genome-wide changes in histone acetylation that occur in response to these drugs. Each drug induces modifications in a large number of genes. The genes that respond similarly to either treatment, however, represent a subgroup enriched for genes important for the common tolerance response. Genes were functionally tested for behavioral tolerance to the sedative effects of ethanol and benzyl alcohol using mutant and inducible RNAi stocks. We identified a network of genes that are essential for the development of tolerance to sedation by alcohol.

Dual-mode operation of neuronal networks involved in left-right alternation

DEFF Research Database (Denmark)

Talpalar, Adolfo E.; Bouvier, Julien; Borgius, Lotta

2013-01-01

All forms of locomotion are repetitive motor activities that require coordinated bilateral activation of muscles. The executive elements of locomotor control are networks of spinal neurons that determine gait pattern through the sequential activation of motor-neuron pools on either side of the bo...

Research network involving retired experts as a means to keep alive relevant knowledge - The case of IPEN in Brazil

International Nuclear Information System (INIS)

Barroso, A.C.O.; Imakuma, K.; Reis, J.S.B. Jr.

2007-01-01

courses within the USP grid. 3) The fact that the Brazilian Council for Scientific and Technological Development - CNPq has a range of research productivity fellowships for people who achieve a certain sustained level of publications. Depending on the researcher's classification, this mechanism includes a monthly income addition plus small funds for expenditures in traveling and laboratory consumables. Items a and b have caused many IPEN employees start to work towards graduate education at USP (IPEN). As they take most of the disciplines in subjects related to nuclear, which are taught by senior researchers / professors of IPEN, they end up performing their degree research work in fields that, most of the times, are related to the current work of their advisors at IPEN. Retired researchers usually keep the professor status and activities, probably because of their strong research group links, constructed over the years, but also because to have students is possibly the most important lever to keep up the indexes to maintain the CNPq productivity fellowship. This dynamic network is a powerful natural mechanism to transfer knowledge from retiring experts and also to disseminate nuclear knowledge, since IPEN has a diversified portfolio of disciplines that is also of interest to other students of the USP community. Based on the co-authorship of publications involving people from IPEN, collected annually from 2000 up to 2005, the social network evidenced by these data bases was analyzed. For the network 'photography' of each year a set of indicators were computed: a participation index of retirees in the publications of IPEN (no. of publications involving retirees / total no. of publications); a partnership index measuring the 'social capillarity' of the average collaborating retiree (no. of current workers that co-authored / no. of retired co-authors); a publication productivity index for the retired researchers; and some SN indexes, such as, diameter of the network

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

Science.gov (United States)

Griffin, Christopher T.; Nesbitt, Sterling J.

2016-12-01

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

Extensive copy number variations in admixed Indian population of African ancestry: potential involvement in adaptation.

Science.gov (United States)

Narang, Ankita; Jha, Pankaj; Kumar, Dhirendra; Kutum, Rintu; Mondal, Anupam Kumar; Dash, Debasis; Mukerji, Mitali

2014-11-13

Admixture mapping has been enormously resourceful in identifying genetic variations linked to phenotypes, adaptation, and diseases. In this study through analysis of copy number variable regions (CNVRs), we report extensive restructuring in the genomes of the recently admixed African-Indian population (OG-W-IP) that inhabits a highly saline environment in Western India. The study included subjects from OG-W-IP (OG), five different Indian and three HapMap populations that were genotyped using Affymetrix version 6.0 arrays. Copy number variations (CNVs) detected using Birdsuite were used to define CNVRs. Population structure with respect to CNVRs was delineated using random forest approach. OG genomes have a surprising excess of CNVs in comparison to other studied populations. Individual ancestry proportions computed using STRUCTURE also reveals a unique genetic component in OGs. Population structure analysis with CNV genotypes indicates OG to be distant from both the African and Indian ancestral populations. Interestingly, it shows genetic proximity with respect to CNVs to only one Indian population IE-W-LP4, which also happens to reside in the same geographical region. We also observe a significant enrichment of molecular processes related to ion binding and receptor activity in genes encompassing OG-specific CNVRs. Our results suggest that retention of CNVRs from ancestral natives and de novo acquisition of CNVRs could accelerate the process of adaptation especially in an extreme environment. Additionally, this population would be enormously useful for dissecting genes and delineating the involvement of CNVs in salt adaptation. © The Author(s) 2014. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Preservation of genes involved in sterol metabolism in cholesterol auxotrophs: facts and hypotheses.

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Giovanna Vinci

Full Text Available BACKGROUND: It is known that primary sequences of enzymes involved in sterol biosynthesis are well conserved in organisms that produce sterols de novo. However, we provide evidence for a preservation of the corresponding genes in two animals unable to synthesize cholesterol (auxotrophs: Drosophila melanogaster and Caenorhabditis elegans. PRINCIPAL FINDINGS: We have been able to detect bona fide orthologs of several ERG genes in both organisms using a series of complementary approaches. We have detected strong sequence divergence between the orthologs of the nematode and of the fruitfly; they are also very divergent with respect to the orthologs in organisms able to synthesize sterols de novo (prototrophs. Interestingly, the orthologs in both the nematode and the fruitfly are still under selective pressure. It is possible that these genes, which are not involved in cholesterol synthesis anymore, have been recruited to perform different new functions. We propose a more parsimonious way to explain their accelerated evolution and subsequent stabilization. The products of ERG genes in prototrophs might be involved in several biological roles, in addition to sterol synthesis. In the case of the nematode and the fruitfly, the relevant genes would have lost their ancestral function in cholesterogenesis but would have retained the other function(s, which keep them under pressure. CONCLUSIONS: By exploiting microarray data we have noticed a strong expressional correlation between the orthologs of ERG24 and ERG25 in D. melanogaster and genes encoding factors involved in intracellular protein trafficking and folding and with Start1 involved in ecdysteroid synthesis. These potential functional connections are worth being explored not only in Drosophila, but also in Caenorhabditis as well as in sterol prototrophs.

Reconstruction of the gene regulatory network involved in the sonic hedgehog pathway with a potential role in early development of the mouse brain.

Directory of Open Access Journals (Sweden)

Jinhua Liu

2014-10-01

Full Text Available The Sonic hedgehog (Shh signaling pathway is crucial for pattern formation in early central nervous system development. By systematically analyzing high-throughput in situ hybridization data of E11.5 mouse brain, we found that Shh and its receptor Ptch1 define two adjacent mutually exclusive gene expression domains: Shh+Ptch1- and Shh-Ptch1+. These two domains are associated respectively with Foxa2 and Gata3, two transcription factors that play key roles in specifying them. Gata3 ChIP-seq experiments and RNA-seq assays on Gata3-knockdown cells revealed that Gata3 up-regulates the genes that are enriched in the Shh-Ptch1+ domain. Important Gata3 targets include Slit2 and Slit3, which are involved in the process of axon guidance, as well as Slc18a1, Th and Qdpr, which are associated with neurotransmitter synthesis and release. By contrast, Foxa2 both up-regulates the genes expressed in the Shh+Ptch1- domain and down-regulates the genes characteristic of the Shh-Ptch1+ domain. From these and other data, we were able to reconstruct a gene regulatory network governing both domains. Our work provides the first genome-wide characterization of the gene regulatory network involved in the Shh pathway that underlies pattern formation in the early mouse brain.

Loss surface of XOR artificial neural networks

Science.gov (United States)

Mehta, Dhagash; Zhao, Xiaojun; Bernal, Edgar A.; Wales, David J.

2018-05-01

Training an artificial neural network involves an optimization process over the landscape defined by the cost (loss) as a function of the network parameters. We explore these landscapes using optimization tools developed for potential energy landscapes in molecular science. The number of local minima and transition states (saddle points of index one), as well as the ratio of transition states to minima, grow rapidly with the number of nodes in the network. There is also a strong dependence on the regularization parameter, with the landscape becoming more convex (fewer minima) as the regularization term increases. We demonstrate that in our formulation, stationary points for networks with Nh hidden nodes, including the minimal network required to fit the XOR data, are also stationary points for networks with Nh+1 hidden nodes when all the weights involving the additional node are zero. Hence, smaller networks trained on XOR data are embedded in the landscapes of larger networks. Our results clarify certain aspects of the classification and sensitivity (to perturbations in the input data) of minima and saddle points for this system, and may provide insight into dropout and network compression.

On Network Coded Filesystem Shim

DEFF Research Database (Denmark)

Sørensen, Chres Wiant; Roetter, Daniel Enrique Lucani; Médard, Muriel

2017-01-01

Although network coding has shown the potential to revolutionize networking and storage, its deployment has faced a number of challenges. Usual proposals involve two approaches. First, deploying a new protocol (e.g., Multipath Coded TCP), or retrofitting another one (e.g., TCP/NC) to deliver bene...

Building Leadership Capacity in the Involving Network State

DEFF Research Database (Denmark)

Pedersen, Dorthe; Tangkjær, Christian

2013-01-01

New partnerships, cross-organisational collaborations and co-creation, digitalisation, involvement of citizens, public design and innovation stand out as new and emerging solutions in welfare delivery. However, New Public Management (NPM) seems to represent a historical repertoire of perspectives...... communities in order to conduct the needed leadership capabilities and incorporate the impact of leadership education in a multi-contextual public sector. We argue that critical reflexivity needs to be a pivotal point in leadership programmes....

Metropolitan Optical Networks 1996 Annual Report

DEFF Research Database (Denmark)

Kristensen, Martin; Jouanno, Jean-Marc; Malone, Kevin

1997-01-01

The report desribes the reasearch carried out in the ACTS-project METON (Metropolitan Optical Networks) in 1996. L.M. Ericsson is prime contractor and 12 partners are involved in the project including DTU, i.e. EMI and MIC.......The report desribes the reasearch carried out in the ACTS-project METON (Metropolitan Optical Networks) in 1996. L.M. Ericsson is prime contractor and 12 partners are involved in the project including DTU, i.e. EMI and MIC....

Detecting Distributed Network Traffic Anomaly with Network-Wide Correlation Analysis

Directory of Open Access Journals (Sweden)

Yang Dan

2008-12-01

Full Text Available Distributed network traffic anomaly refers to a traffic abnormal behavior involving many links of a network and caused by the same source (e.g., DDoS attack, worm propagation. The anomaly transiting in a single link might be unnoticeable and hard to detect, while the anomalous aggregation from many links can be prevailing, and does more harm to the networks. Aiming at the similar features of distributed traffic anomaly on many links, this paper proposes a network-wide detection method by performing anomalous correlation analysis of traffic signals' instantaneous parameters. In our method, traffic signals' instantaneous parameters are firstly computed, and their network-wide anomalous space is then extracted via traffic prediction. Finally, an anomaly is detected by a global correlation coefficient of anomalous space. Our evaluation using Abilene traffic traces demonstrates the excellent performance of this approach for distributed traffic anomaly detection.

Evolution of the bHLH genes involved in stomatal development: implications for the expansion of developmental complexity of stomata in land plants.

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Jin-Hua Ran

Full Text Available Stomata play significant roles in plant evolution. A trio of closely related basic Helix-Loop-Helix (bHLH subgroup Ia genes, SPCH, MUTE and FAMA, mediate sequential steps of stomatal development, and their functions may be conserved in land plants. However, the evolutionary history of the putative SPCH/MUTE/FAMA genes is still greatly controversial, especially the phylogenetic positions of the bHLH Ia members from basal land plants. To better understand the evolutionary pattern and functional diversity of the bHLH genes involved in stomatal development, we made a comprehensive evolutionary analysis of the homologous genes from 54 species representing the major lineages of green plants. The phylogenetic analysis indicated: (1 All bHLH Ia genes from the two basal land plants Physcomitrella and Selaginella were closely related to the FAMA genes of seed plants; and (2 the gymnosperm 'SPCH' genes were sister to a clade comprising the angiosperm SPCH and MUTE genes, while the FAMA genes of gymnosperms and angiosperms had a sister relationship. The revealed phylogenetic relationships are also supported by the distribution of gene structures and previous functional studies. Therefore, we deduce that the function of FAMA might be ancestral in the bHLH Ia subgroup. In addition, the gymnosperm "SPCH" genes may represent an ancestral state and have a dual function of SPCH and MUTE, two genes that could have originated from a duplication event in the common ancestor of angiosperms. Moreover, in angiosperms, SPCHs have experienced more duplications and harbor more copies than MUTEs and FAMAs, which, together with variation of the stomatal development in the entry division, implies that SPCH might have contributed greatly to the diversity of stomatal development. Based on the above, we proposed a model for the correlation between the evolution of stomatal development and the genes involved in this developmental process in land plants.

Network coding for multi-resolution multicast

DEFF Research Database (Denmark)

2013-01-01

A method, apparatus and computer program product for utilizing network coding for multi-resolution multicast is presented. A network source partitions source content into a base layer and one or more refinement layers. The network source receives a respective one or more push-back messages from one...... or more network destination receivers, the push-back messages identifying the one or more refinement layers suited for each one of the one or more network destination receivers. The network source computes a network code involving the base layer and the one or more refinement layers for at least one...... of the one or more network destination receivers, and transmits the network code to the one or more network destination receivers in accordance with the push-back messages....

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

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Kyle S. McCommis

2016-08-01

Full Text Available Objective: Transport of pyruvate into the mitochondrial matrix by the Mitochondrial Pyruvate Carrier (MPC is an important and rate-limiting step in its metabolism. In pancreatic β-cells, mitochondrial pyruvate metabolism is thought to be important for glucose sensing and glucose-stimulated insulin secretion. Methods: To evaluate the role that the MPC plays in maintaining systemic glucose homeostasis, we used genetically-engineered Drosophila and mice with loss of MPC activity in insulin-producing cells. Results: In both species, MPC deficiency results in elevated blood sugar concentrations and glucose intolerance accompanied by impaired glucose-stimulated insulin secretion. In mouse islets, β-cell MPC-deficiency resulted in decreased respiration with glucose, ATP-sensitive potassium (KATP channel hyperactivity, and impaired insulin release. Moreover, treatment of pancreas-specific MPC knockout mice with glibenclamide, a sulfonylurea KATP channel inhibitor, improved defects in islet insulin secretion and abnormalities in glucose homeostasis in vivo. Finally, using a recently-developed biosensor for MPC activity, we show that the MPC is rapidly stimulated by glucose treatment in INS-1 insulinoma cells suggesting that glucose sensing is coupled to mitochondrial pyruvate carrier activity. Conclusions: Altogether, these studies suggest that the MPC plays an important and ancestral role in insulin-secreting cells in mediating glucose sensing, regulating insulin secretion, and controlling systemic glycemia. Keywords: Stimulus-coupled secretion, Insulin, β-Cell, Diabetes, Pyruvate, Mitochondria, Drosophila

A security architecture for 5G networks

OpenAIRE

Arfaoui, Ghada; Bisson, Pascal; Blom, Rolf; Borgaonkar, Ravishankar; Englund, Håkan; Félix, Edith; Klaedtke, Felix; Nakarmi, Prajwol Kumar; Näslund, Mats; O’Hanlon, Piers; Papay, Juri; Suomalainen, Jani; Surridge, Mike; Wary, Jean-Philippe; Zahariev, Alexander

2018-01-01

5G networks will provide opportunities for the creation of new services, for new business models, and for new players to enter the mobile market. The networks will support efficient and cost-effective launch of a multitude of services, tailored for different vertical markets having varying service and security requirements, and involving a large number of actors. Key technology concepts are network slicing and network softwarisation, including network function virtualisation and software-defi...

Qualitative exploration of centralities in municipal science education networks

DEFF Research Database (Denmark)

von der Fehr, Ane; Sølberg, Jan

2016-01-01

This article examines the social nature of educational change by conducting a social network analysis of social networks involving stakeholders of science education from teachers to political stakeholders. Social networks that comprise supportive structures for development of science education ar...... of science education, especially if they are aware of their own centrality and are able to use their position intentionally for the benefit of science education.......This article examines the social nature of educational change by conducting a social network analysis of social networks involving stakeholders of science education from teachers to political stakeholders. Social networks that comprise supportive structures for development of science education...... are diverse and in order to understand how municipal stakeholders may support such development, we explored four different municipal science education networks (MSE networks) using three different measures of centrality. The centrality measures differed in terms of what kind of stakeholder functions...

Online social networking for radiology.

Science.gov (United States)

Auffermann, William F; Chetlen, Alison L; Colucci, Andrew T; DeQuesada, Ivan M; Grajo, Joseph R; Heller, Matthew T; Nowitzki, Kristina M; Sherry, Steven J; Tillack, Allison A

2015-01-01

Online social networking services have changed the way we interact as a society and offer many opportunities to improve the way we practice radiology and medicine in general. This article begins with an introduction to social networking. Next, the latest advances in online social networking are reviewed, and areas where radiologists and clinicians may benefit from these new tools are discussed. This article concludes with several steps that the interested reader can take to become more involved in online social networking. Copyright © 2015 AUR. Published by Elsevier Inc. All rights reserved.

Network analysis of genes involved in the enhancement of hyperthermia sensitivity by the knockdown of BAG3 in human oral squamous cell carcinoma cells.

Science.gov (United States)

Yunoki, Tatsuya; Tabuchi, Yoshiaki; Hayashi, Atsushi; Kondo, Takashi

2016-07-01

BCL2-associated athanogene 3 (BAG3), a co-chaperone of the heat shock 70 kDa protein (HSPA) family of proteins, is a cytoprotective protein that acts against various stresses, including heat stress. The aim of the present study was to identify gene networks involved in the enhancement of hyperthermia (HT) sensitivity by the knockdown (KD) of BAG3 in human oral squamous cell carcinoma (OSCC) cells. Although a marked elevation in the protein expression of BAG3 was detected in human the OSCC HSC-3 cells exposed to HT at 44˚C for 90 min, its expression was almost completely suppressed in the cells transfected with small interfering RNA against BAG3 (siBAG) under normal and HT conditions. The silencing of BAG3 also enhanced the cell death that was increased in the HSC-3 cells by exposure to HT. Global gene expression analysis revealed many genes that were differentially expressed by >2-fold in the cells exposed to HT and transfected with siBAG. Moreover, Ingenuity® pathways analysis demonstrated two unique gene networks, designated as Pro-cell death and Anti-cell death, which were obtained from upregulated genes and were mainly associated with the biological functions of induction and the prevention of cell death, respectively. Of note, the expression levels of genes in the Pro-cell death and Anti-cell death gene networks were significantly elevated and reduced in the HT + BAG3-KD group compared to those in the HT control group, respectively. These results provide further insight into the molecular mechanisms involved in the enhancement of HT sensitivity by the silencing of BAG3 in human OSCC cells.

Brain circuitries involved in semantic interference by demands of emotional and non-emotional distractors.

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Natalia Chechko

Full Text Available BACKGROUND: Previous studies have indicated that the processes leading to the resolution of emotional and non-emotional interference conflicts are unrelated, involving separate networks. It is also known that conflict resolution itself suggests a considerable overlap of the networks. Our study is an attempt to examine how these findings may be related. METHODOLOGY/PRINCIPAL FINDINGS: We used functional magnetic resonance imaging (fMRI to study neural responses of 24 healthy subjects to emotional and non-emotional conflict paradigms involving the presentation of congruent and incongruent word-face pairs based on semantic incompatibility between targets and distractors. In the emotional task, the behavioral interference conflict was greater (compared to the non-emotional task and was paralleled by involvement of the extrastriate visual and posterodorsal medial frontal cortices. In both tasks, we also observed a common network including the dorsal anterior cingulate, the supplemental motor area, the anterior insula and the inferior prefrontal cortex, indicating that these brain structures are markers of experienced conflict. However, the emotional task involved conflict-triggered networks to a considerably higher degree. CONCLUSIONS/SIGNIFICANCE: Our findings indicate that responses to emotional and non-emotional distractors involve the same systems, which are capable of flexible adjustments based on conflict demands. The function of systems related to conflict resolution is likely to be adjusted on the basis of an evaluation process that primarily involves the extrastriate visual cortex, with target playing a significant role.

Social anxiety disorder exhibit impaired networks involved in self and theory of mind processing.

Science.gov (United States)

Cui, Qian; Vanman, Eric J; Long, Zhiliang; Pang, Yajing; Chen, Yuyan; Wang, Yifeng; Duan, Xujun; Chen, Heng; Gong, Qiyong; Zhang, Wei; Chen, Huafu

2017-08-01

Most previous studies regarding social anxiety disorder (SAD) have focused on the role of emotional dysfunction, while impairments in self- and theory of mind (ToM)-processing have relatively been neglected. This study utilised functional connectivity density (FCD), resting-state functional connectivity (RSFC) and discriminant analyses to investigate impairments in self- and ToM-related networks in patients with SAD. Patients with SAD exhibited decreased long-range FCD in the right rostral anterior cingulate cortex (rACC) and decreased short-range FCD in the right superior temporal gyrus (STG)-key nodes involved in self- and ToM-processing, respectively. Decreased RSFC of the right rACC and STG with widespread frontal, temporal, posteromedial, sensorimotor, and somatosensory, regions was also observed in patients with SAD. Altered RSFC between the right rACC and bilateral superior frontal gyrus, between the right rACC and right middle frontal gyrus, and within the right STG itself provided the greatest contribution to individual diagnoses of SAD, with an accuracy of 84.5%. These results suggest that a lack of cognitive inhibition on emotional self-referential processing as well as impairments in social information integration may play critical roles in the pathomechanism of SAD and highlight the importance of recognising such features in the diagnosis and treatment of SAD. © The Author (2017). Published by Oxford University Press.

Asymmetric Modulation Gains in Network Coded Relay Networks

DEFF Research Database (Denmark)

Roetter, Daniel Enrique Lucani; Fitzek, Frank

2015-01-01

Wireless relays have usually been considered in two ways. On the one hand, a physical layer approach focused on per-packet reliability and involving the relay on each packet transmission. On the other, recent approaches have relied on the judicious activation of the relay at the network level to ...

Scalable Approaches to Control Network Dynamics: Prospects for City Networks

Science.gov (United States)

Motter, Adilson E.; Gray, Kimberly A.

2014-07-01

A city is a complex, emergent system and as such can be conveniently represented as a network of interacting components. A fundamental aspect of networks is that the systemic properties can depend as much on the interactions as they depend on the properties of the individual components themselves. Another fundamental aspect is that changes to one component can affect other components, in a process that may cause the entire or a substantial part of the system to change behavior. Over the past 2 decades, much research has been done on the modeling of large and complex networks involved in communication and transportation, disease propagation, and supply chains, as well as emergent phenomena, robustness and optimization in such systems...

Artificial Astrocytes Improve Neural Network Performance

Science.gov (United States)

Porto-Pazos, Ana B.; Veiguela, Noha; Mesejo, Pablo; Navarrete, Marta; Alvarellos, Alberto; Ibáñez, Oscar; Pazos, Alejandro; Araque, Alfonso

2011-01-01

Compelling evidence indicates the existence of bidirectional communication between astrocytes and neurons. Astrocytes, a type of glial cells classically considered to be passive supportive cells, have been recently demonstrated to be actively involved in the processing and regulation of synaptic information, suggesting that brain function arises from the activity of neuron-glia networks. However, the actual impact of astrocytes in neural network function is largely unknown and its application in artificial intelligence remains untested. We have investigated the consequences of including artificial astrocytes, which present the biologically defined properties involved in astrocyte-neuron communication, on artificial neural network performance. Using connectionist systems and evolutionary algorithms, we have compared the performance of artificial neural networks (NN) and artificial neuron-glia networks (NGN) to solve classification problems. We show that the degree of success of NGN is superior to NN. Analysis of performances of NN with different number of neurons or different architectures indicate that the effects of NGN cannot be accounted for an increased number of network elements, but rather they are specifically due to astrocytes. Furthermore, the relative efficacy of NGN vs. NN increases as the complexity of the network increases. These results indicate that artificial astrocytes improve neural network performance, and established the concept of Artificial Neuron-Glia Networks, which represents a novel concept in Artificial Intelligence with implications in computational science as well as in the understanding of brain function. PMID:21526157

Artificial astrocytes improve neural network performance.

Directory of Open Access Journals (Sweden)

Ana B Porto-Pazos

Full Text Available Compelling evidence indicates the existence of bidirectional communication between astrocytes and neurons. Astrocytes, a type of glial cells classically considered to be passive supportive cells, have been recently demonstrated to be actively involved in the processing and regulation of synaptic information, suggesting that brain function arises from the activity of neuron-glia networks. However, the actual impact of astrocytes in neural network function is largely unknown and its application in artificial intelligence remains untested. We have investigated the consequences of including artificial astrocytes, which present the biologically defined properties involved in astrocyte-neuron communication, on artificial neural network performance. Using connectionist systems and evolutionary algorithms, we have compared the performance of artificial neural networks (NN and artificial neuron-glia networks (NGN to solve classification problems. We show that the degree of success of NGN is superior to NN. Analysis of performances of NN with different number of neurons or different architectures indicate that the effects of NGN cannot be accounted for an increased number of network elements, but rather they are specifically due to astrocytes. Furthermore, the relative efficacy of NGN vs. NN increases as the complexity of the network increases. These results indicate that artificial astrocytes improve neural network performance, and established the concept of Artificial Neuron-Glia Networks, which represents a novel concept in Artificial Intelligence with implications in computational science as well as in the understanding of brain function.

Artificial astrocytes improve neural network performance.

Science.gov (United States)

Porto-Pazos, Ana B; Veiguela, Noha; Mesejo, Pablo; Navarrete, Marta; Alvarellos, Alberto; Ibáñez, Oscar; Pazos, Alejandro; Araque, Alfonso

2011-04-19

Compelling evidence indicates the existence of bidirectional communication between astrocytes and neurons. Astrocytes, a type of glial cells classically considered to be passive supportive cells, have been recently demonstrated to be actively involved in the processing and regulation of synaptic information, suggesting that brain function arises from the activity of neuron-glia networks. However, the actual impact of astrocytes in neural network function is largely unknown and its application in artificial intelligence remains untested. We have investigated the consequences of including artificial astrocytes, which present the biologically defined properties involved in astrocyte-neuron communication, on artificial neural network performance. Using connectionist systems and evolutionary algorithms, we have compared the performance of artificial neural networks (NN) and artificial neuron-glia networks (NGN) to solve classification problems. We show that the degree of success of NGN is superior to NN. Analysis of performances of NN with different number of neurons or different architectures indicate that the effects of NGN cannot be accounted for an increased number of network elements, but rather they are specifically due to astrocytes. Furthermore, the relative efficacy of NGN vs. NN increases as the complexity of the network increases. These results indicate that artificial astrocytes improve neural network performance, and established the concept of Artificial Neuron-Glia Networks, which represents a novel concept in Artificial Intelligence with implications in computational science as well as in the understanding of brain function.

The Networked Principal: Examining Principals' Social Relationships and Transformational Leadership in School and District Networks

Science.gov (United States)

Moolenaar, Nienke M.; Sleegers, Peter J. C.

2015-01-01

Purpose: While in everyday practice, school leaders are often involved in social relationships with a variety of stakeholders both within and outside their own schools, studies on school leaders' networks often focus either on networks within or outside schools. The purpose of this paper is to investigate the extent to which principals occupy…

Development of brain networks involved in spoken word processing of Mandarin Chinese.

Science.gov (United States)

Cao, Fan; Khalid, Kainat; Lee, Rebecca; Brennan, Christine; Yang, Yanhui; Li, Kuncheng; Bolger, Donald J; Booth, James R

2011-08-01

Developmental differences in phonological and orthographic processing of Chinese spoken words were examined in 9-year-olds, 11-year-olds and adults using functional magnetic resonance imaging (fMRI). Rhyming and spelling judgments were made to two-character words presented sequentially in the auditory modality. Developmental comparisons between adults and both groups of children combined showed that age-related changes in activation in visuo-orthographic regions depended on a task. There were developmental increases in the left inferior temporal gyrus and the right inferior occipital gyrus in the spelling task, suggesting more extensive visuo-orthographic processing in a task that required access to these representations. Conversely, there were developmental decreases in activation in the left fusiform gyrus and left middle occipital gyrus in the rhyming task, suggesting that the development of reading is marked by reduced involvement of orthography in a spoken language task that does not require access to these orthographic representations. Developmental decreases may arise from the existence of extensive homophony (auditory words that have multiple spellings) in Chinese. In addition, we found that 11-year-olds and adults showed similar activation in the left superior temporal gyrus across tasks, with both groups showing greater activation than 9-year-olds. This pattern suggests early development of perceptual representations of phonology. In contrast, 11-year-olds and 9-year-olds showed similar activation in the left inferior frontal gyrus across tasks, with both groups showing weaker activation than adults. This pattern suggests late development of controlled retrieval and selection of lexical representations. Altogether, this study suggests differential effects of character acquisition on development of components of the language network in Chinese as compared to previous reports on alphabetic languages. Published by Elsevier Inc.

First field trial of Virtual Network Operator oriented network on demand (NoD) service provisioning over software defined multi-vendor OTN networks

Science.gov (United States)

Li, Yajie; Zhao, Yongli; Zhang, Jie; Yu, Xiaosong; Chen, Haoran; Zhu, Ruijie; Zhou, Quanwei; Yu, Chenbei; Cui, Rui

2017-01-01

A Virtual Network Operator (VNO) is a provider and reseller of network services from other telecommunications suppliers. These network providers are categorized as virtual because they do not own the underlying telecommunication infrastructure. In terms of business operation, VNO can provide customers with personalized services by leasing network infrastructure from traditional network providers. The unique business modes of VNO lead to the emergence of network on demand (NoD) services. The conventional network provisioning involves a series of manual operation and configuration, which leads to high cost in time. Considering the advantages of Software Defined Networking (SDN), this paper proposes a novel NoD service provisioning solution to satisfy the private network need of VNOs. The solution is first verified in the real software defined multi-domain optical networks with multi-vendor OTN equipment. With the proposed solution, NoD service can be deployed via online web portals in near-real time. It reinvents the customer experience and redefines how network services are delivered to customers via an online self-service portal. Ultimately, this means a customer will be able to simply go online, click a few buttons and have new services almost instantaneously.

Modified Small Business Network Security

OpenAIRE

Md. Belayet Ali; Oveget Das; Md. Shamim Hossain

2012-01-01

This paper covers some likely threats and effectivesteps for a secure small business. It also involves a flowchart tocomprehend the overall small business network security easilyand we identify a set of security issues and applyappropriate techniques to satisfy the correspondingsecurity requirements. In respect of all, this document isstrong enough for any small business network security.

Connexin-Dependent Neuroglial Networking as a New Therapeutic Target

Directory of Open Access Journals (Sweden)

Mathieu Charvériat

2017-06-01

Full Text Available Astrocytes and neurons dynamically interact during physiological processes, and it is now widely accepted that they are both organized in plastic and tightly regulated networks. Astrocytes are connected through connexin-based gap junction channels, with brain region specificities, and those networks modulate neuronal activities, such as those involved in sleep-wake cycle, cognitive, or sensory functions. Additionally, astrocyte domains have been involved in neurogenesis and neuronal differentiation during development; they participate in the “tripartite synapse” with both pre-synaptic and post-synaptic neurons by tuning down or up neuronal activities through the control of neuronal synaptic strength. Connexin-based hemichannels are also involved in those regulations of neuronal activities, however, this feature will not be considered in the present review. Furthermore, neuronal processes, transmitting electrical signals to chemical synapses, stringently control astroglial connexin expression, and channel functions. Long-range energy trafficking toward neurons through connexin-coupled astrocytes and plasticity of those networks are hence largely dependent on neuronal activity. Such reciprocal interactions between neurons and astrocyte networks involve neurotransmitters, cytokines, endogenous lipids, and peptides released by neurons but also other brain cell types, including microglial and endothelial cells. Over the past 10 years, knowledge about neuroglial interactions has widened and now includes effects of CNS-targeting drugs such as antidepressants, antipsychotics, psychostimulants, or sedatives drugs as potential modulators of connexin function and thus astrocyte networking activity. In physiological situations, neuroglial networking is consequently resulting from a two-way interaction between astrocyte gap junction-mediated networks and those made by neurons. As both cell types are modulated by CNS drugs we postulate that neuroglial

Connexin-Dependent Neuroglial Networking as a New Therapeutic Target.

Science.gov (United States)

Charvériat, Mathieu; Naus, Christian C; Leybaert, Luc; Sáez, Juan C; Giaume, Christian

2017-01-01

Astrocytes and neurons dynamically interact during physiological processes, and it is now widely accepted that they are both organized in plastic and tightly regulated networks. Astrocytes are connected through connexin-based gap junction channels, with brain region specificities, and those networks modulate neuronal activities, such as those involved in sleep-wake cycle, cognitive, or sensory functions. Additionally, astrocyte domains have been involved in neurogenesis and neuronal differentiation during development; they participate in the "tripartite synapse" with both pre-synaptic and post-synaptic neurons by tuning down or up neuronal activities through the control of neuronal synaptic strength. Connexin-based hemichannels are also involved in those regulations of neuronal activities, however, this feature will not be considered in the present review. Furthermore, neuronal processes, transmitting electrical signals to chemical synapses, stringently control astroglial connexin expression, and channel functions. Long-range energy trafficking toward neurons through connexin-coupled astrocytes and plasticity of those networks are hence largely dependent on neuronal activity. Such reciprocal interactions between neurons and astrocyte networks involve neurotransmitters, cytokines, endogenous lipids, and peptides released by neurons but also other brain cell types, including microglial and endothelial cells. Over the past 10 years, knowledge about neuroglial interactions has widened and now includes effects of CNS-targeting drugs such as antidepressants, antipsychotics, psychostimulants, or sedatives drugs as potential modulators of connexin function and thus astrocyte networking activity. In physiological situations, neuroglial networking is consequently resulting from a two-way interaction between astrocyte gap junction-mediated networks and those made by neurons. As both cell types are modulated by CNS drugs we postulate that neuroglial networking may emerge as

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

Science.gov (United States)

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).

Network meta-analyses could be improved by searching more sources and by involving a librarian.

Science.gov (United States)

Li, Lun; Tian, Jinhui; Tian, Hongliang; Moher, David; Liang, Fuxiang; Jiang, Tongxiao; Yao, Liang; Yang, Kehu

2014-09-01

Network meta-analyses (NMAs) aim to rank the benefits (or harms) of interventions, based on all available randomized controlled trials. Thus, the identification of relevant data is critical. We assessed the conduct of the literature searches in NMAs. Published NMAs were retrieved by searching electronic bibliographic databases and other sources. Two independent reviewers selected studies and five trained reviewers abstracted data regarding literature searches, in duplicate. Search method details were examined using descriptive statistics. Two hundred forty-nine NMAs were included. Eight used previous systematic reviews to identify primary studies without further searching, and five did not report any literature searches. In the 236 studies that used electronic databases to identify primary studies, the median number of databases was 3 (interquartile range: 3-5). MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were the most commonly used databases. The most common supplemental search methods included reference lists of included studies (48%), reference lists of previous systematic reviews (40%), and clinical trial registries (32%). None of these supplemental methods was conducted in more than 50% of the NMAs. Literature searches in NMAs could be improved by searching more sources, and by involving a librarian or information specialist. Copyright © 2014 Elsevier Inc. All rights reserved.

Design Considerations for Multi-Channel Picture Communication Networks

OpenAIRE

Scheibe, Paul O.

1983-01-01

Design of networks intended for communication of digitally-encoded pictures involves considerations different from those used in the design of text or voice communication networks. This paper provides an overview of the elements useful in the design of picture communication networks by relation and contrast with other communication networks. Particular emphasis is given to picture communication systems useful in medical applications.

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

Science.gov (United States)

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

2009-10-01

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

How to Identify Success Among Networks That Promote Active Living.

Science.gov (United States)

Litt, Jill; Varda, Danielle; Reed, Hannah; Retrum, Jessica; Tabak, Rachel; Gustat, Jeanette; O'Hara Tompkins, Nancy

2015-11-01

We evaluated organization- and network-level factors that influence organizations' perceived success. This is important for managing interorganizational networks, which can mobilize communities to address complex health issues such as physical activity, and for achieving change. In 2011, we used structured interview and network survey data from 22 states in the United States to estimate multilevel random-intercept models to understand organization- and network-level factors that explain perceived network success. A total of 53 of 59 "whole networks" met the criteria for inclusion in the analysis (89.8%). Coordinators identified 559 organizations, with 3 to 12 organizations from each network taking the online survey (response rate = 69.7%; range = 33%-100%). Occupying a leadership position (P Organizations' perceptions of success can influence decisions about continuing involvement and investment in networks designed to promote environment and policy change for active living. Understanding these factors can help leaders manage complex networks that involve diverse memberships, varied interests, and competing community-level priorities.

Emotion Regulation and Complex Brain Networks: Association Between Expressive Suppression and Efficiency in the Fronto-Parietal Network and Default-Mode Network

Directory of Open Access Journals (Sweden)

Junhao Pan

2018-03-01

Full Text Available Emotion regulation (ER refers to the “implementation of a conscious or non-conscious goal to start, stop or otherwise modulate the trajectory of an emotion” (Etkin et al., 2015. Whereas multiple brain areas have been found to be involved in ER, relatively little is known about whether and how ER is associated with the global functioning of brain networks. Recent advances in brain connectivity research using graph-theory based analysis have shown that the brain can be organized into complex networks composed of functionally or structurally connected brain areas. Global efficiency is one graphic metric indicating the efficiency of information exchange among brain areas and is utilized to measure global functioning of brain networks. The present study examined the relationship between trait measures of ER (expressive suppression (ES and cognitive reappraisal (CR and global efficiency in resting-state functional brain networks (the whole brain network and ten predefined networks using structural equation modeling (SEM. The results showed that ES was reliably associated with efficiency in the fronto-parietal network and default-mode network. The finding advances the understanding of neural substrates of ER, revealing the relationship between ES and efficient organization of brain networks.

A Quantitative Risk Assessment Model Involving Frequency and Threat Degree under Line-of-Business Services for Infrastructure of Emerging Sensor Networks.

Science.gov (United States)

Jing, Xu; Hu, Hanwen; Yang, Huijun; Au, Man Ho; Li, Shuqin; Xiong, Naixue; Imran, Muhammad; Vasilakos, Athanasios V

2017-03-21

The prospect of Line-of-Business Services (LoBSs) for infrastructure of Emerging Sensor Networks (ESNs) is exciting. Access control remains a top challenge in this scenario as the service provider's server contains a lot of valuable resources. LoBSs' users are very diverse as they may come from a wide range of locations with vastly different characteristics. Cost of joining could be low and in many cases, intruders are eligible users conducting malicious actions. As a result, user access should be adjusted dynamically. Assessing LoBSs' risk dynamically based on both frequency and threat degree of malicious operations is therefore necessary. In this paper, we proposed a Quantitative Risk Assessment Model (QRAM) involving frequency and threat degree based on value at risk. To quantify the threat degree as an elementary intrusion effort, we amend the influence coefficient of risk indexes in the network security situation assessment model. To quantify threat frequency as intrusion trace effort, we make use of multiple behavior information fusion. Under the influence of intrusion trace, we adapt the historical simulation method of value at risk to dynamically access LoBSs' risk. Simulation based on existing data is used to select appropriate parameters for QRAM. Our simulation results show that the duration influence on elementary intrusion effort is reasonable when the normalized parameter is 1000. Likewise, the time window of intrusion trace and the weight between objective risk and subjective risk can be set to 10 s and 0.5, respectively. While our focus is to develop QRAM for assessing the risk of LoBSs for infrastructure of ESNs dynamically involving frequency and threat degree, we believe it is also appropriate for other scenarios in cloud computing.

A Quantitative Risk Assessment Model Involving Frequency and Threat Degree under Line-of-Business Services for Infrastructure of Emerging Sensor Networks

Science.gov (United States)

Jing, Xu; Hu, Hanwen; Yang, Huijun; Au, Man Ho; Li, Shuqin; Xiong, Naixue; Imran, Muhammad; Vasilakos, Athanasios V.

2017-01-01

The prospect of Line-of-Business Services (LoBSs) for infrastructure of Emerging Sensor Networks (ESNs) is exciting. Access control remains a top challenge in this scenario as the service provider’s server contains a lot of valuable resources. LoBSs’ users are very diverse as they may come from a wide range of locations with vastly different characteristics. Cost of joining could be low and in many cases, intruders are eligible users conducting malicious actions. As a result, user access should be adjusted dynamically. Assessing LoBSs’ risk dynamically based on both frequency and threat degree of malicious operations is therefore necessary. In this paper, we proposed a Quantitative Risk Assessment Model (QRAM) involving frequency and threat degree based on value at risk. To quantify the threat degree as an elementary intrusion effort, we amend the influence coefficient of risk indexes in the network security situation assessment model. To quantify threat frequency as intrusion trace effort, we make use of multiple behavior information fusion. Under the influence of intrusion trace, we adapt the historical simulation method of value at risk to dynamically access LoBSs’ risk. Simulation based on existing data is used to select appropriate parameters for QRAM. Our simulation results show that the duration influence on elementary intrusion effort is reasonable when the normalized parameter is 1000. Likewise, the time window of intrusion trace and the weight between objective risk and subjective risk can be set to 10 s and 0.5, respectively. While our focus is to develop QRAM for assessing the risk of LoBSs for infrastructure of ESNs dynamically involving frequency and threat degree, we believe it is also appropriate for other scenarios in cloud computing. PMID:28335569

Functional classification of the Gauteng provincial road network ...

African Journals Online (AJOL)

The built environment consists of various land uses and activities connected by a road network. The efficiency and effectiveness of the road network directly impacts economic growth and societal movement. This study involved the functional classification of the Gauteng provincial road network using the South African Road ...

Global Optimization for Transport Network Expansion and Signal Setting

OpenAIRE

Liu, Haoxiang; Wang, David Z. W.; Yue, Hao

2015-01-01

This paper proposes a model to address an urban transport planning problem involving combined network design and signal setting in a saturated network. Conventional transport planning models usually deal with the network design problem and signal setting problem separately. However, the fact that network capacity design and capacity allocation determined by network signal setting combine to govern the transport network performance requires the optimal transport planning to consider the two pr...

Brain networks underlying mental imagery of auditory and visual information.

Science.gov (United States)

Zvyagintsev, Mikhail; Clemens, Benjamin; Chechko, Natalya; Mathiak, Krystyna A; Sack, Alexander T; Mathiak, Klaus

2013-05-01

Mental imagery is a complex cognitive process that resembles the experience of perceiving an object when this object is not physically present to the senses. It has been shown that, depending on the sensory nature of the object, mental imagery also involves correspondent sensory neural mechanisms. However, it remains unclear which areas of the brain subserve supramodal imagery processes that are independent of the object modality, and which brain areas are involved in modality-specific imagery processes. Here, we conducted a functional magnetic resonance imaging study to reveal supramodal and modality-specific networks of mental imagery for auditory and visual information. A common supramodal brain network independent of imagery modality, two separate modality-specific networks for imagery of auditory and visual information, and a common deactivation network were identified. The supramodal network included brain areas related to attention, memory retrieval, motor preparation and semantic processing, as well as areas considered to be part of the default-mode network and multisensory integration areas. The modality-specific networks comprised brain areas involved in processing of respective modality-specific sensory information. Interestingly, we found that imagery of auditory information led to a relative deactivation within the modality-specific areas for visual imagery, and vice versa. In addition, mental imagery of both auditory and visual information widely suppressed the activity of primary sensory and motor areas, for example deactivation network. These findings have important implications for understanding the mechanisms that are involved in generation of mental imagery. © 2013 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Unraveling the WRKY transcription factors network in Arabidopsis Thaliana by integrative approach

Directory of Open Access Journals (Sweden)

Mouna Choura

2015-06-01

Full Text Available The WRKY transcription factors superfamily are involved in diverse biological processes in plants including response to biotic and abiotic stresses and plant immunity. Protein-protein interaction network is a useful approach for understanding these complex processes. The availability of Arabidopsis Thaliana interactome offers a good opportunity to do get a global view of protein network. In this work, we have constructed the WRKY transcription factor network by combining different sources of evidence and we characterized its topological features using computational tools. We found that WRKY network is a hub-based network involving multifunctional proteins denoted as hubs such as WRKY 70, WRKY40, WRKY 53, WRKY 60, WRKY 33 and WRKY 51. Functional annotation showed seven functional modules particularly involved in biotic stress and defense responses. Furthermore, the gene ontology and pathway enrichment analysis revealed that WRKY proteins are mainly involved in plant-pathogen interaction pathways and their functions are directly related to the stress response and immune system process.

Formal Food-related Networks in Ireland: A Case Study Analysis

Directory of Open Access Journals (Sweden)

Maeve Henchion

2012-03-01

Full Text Available  Strategic networking is of crucial importance for innovation in small and medium sized enterprises (SMEs as it enables these companies access external resources and overcome internal constraints. However, SMEs often lack the skills and competencies to engage in and benefit from networks. Consequently SMEs often fail in establishing strategic and efficient networks. To date, there is limited guidance available on the optimal design of such networks. Furthermore, limited guidance is available on the number of networks, and level of engagement therein, that companies should be involved with. Using case studies across a range of formal networks within the food sector in Ireland, insights into the success factors and barriers to network learning are presented, which provide a foundation for such guidelines. Three case studies were selected for analysis in Ireland. Up to ten in-depth interviews were scheduled with the network managers and key informants from the triple helix (i.e. policy, research and industry sectors within each formal network. Initially, interviewees were identified as a result of a review of secondary sources and personal knowledge of the authors. The snowball sampling technique was then employed to identify additional interviewees within each network. The findings from this study revealed that some formal networks had a strong institutional influence, including significant financial inputs, whilst others had bottom-up origins. Many networks had strong levels of interaction prior to formalisation, which provided solid trust-based foundations. Innovation and/or learning were not the expressed objectives of all networks at the outset. However, interviewees across all three networks felt that positive impacts had been achieved in these areas. Whilst being involved in a broad network can provide access to a wider range of ideas, these case studies suggest that being involved in a smaller, dense network, with high levels of IP

Fixation Probability in a Two-Locus Model by the Ancestral Recombination–Selection Graph

Science.gov (United States)

Lessard, Sabin; Kermany, Amir R.

2012-01-01

We use the ancestral influence graph (AIG) for a two-locus, two-allele selection model in the limit of a large population size to obtain an analytic approximation for the probability of ultimate fixation of a single mutant allele A. We assume that this new mutant is introduced at a given locus into a finite population in which a previous mutant allele B is already segregating with a wild type at another linked locus. We deduce that the fixation probability increases as the recombination rate increases if allele A is either in positive epistatic interaction with B and allele B is beneficial or in no epistatic interaction with B and then allele A itself is beneficial. This holds at least as long as the recombination fraction and the selection intensity are small enough and the population size is large enough. In particular this confirms the Hill–Robertson effect, which predicts that recombination renders more likely the ultimate fixation of beneficial mutants at different loci in a population in the presence of random genetic drift even in the absence of epistasis. More importantly, we show that this is true from weak negative epistasis to positive epistasis, at least under weak selection. In the case of deleterious mutants, the fixation probability decreases as the recombination rate increases. This supports Muller’s ratchet mechanism to explain the accumulation of deleterious mutants in a population lacking recombination. PMID:22095080

Detecting groups of similar components in complex networks

International Nuclear Information System (INIS)

Wang Jiao; Lai, C-H

2008-01-01

We study how to detect groups in a complex network each of which consists of component nodes sharing a similar connection pattern. Based on the mixture models and the exploratory analysis set up by Newman and Leicht (2007 Proc. Natl. Acad. Sci. USA 104 9564), we develop an algorithm that is applicable to a network with any degree distribution. The partition of a network suggested by this algorithm also applies to its complementary network. In general, groups of similar components are not necessarily identical with the communities in a community network; thus partitioning a network into groups of similar components provides additional information of the network structure. The proposed algorithm can also be used for community detection when the groups and the communities overlap. By introducing a tunable parameter that controls the involved effects of the heterogeneity, we can also investigate conveniently how the group structure can be coupled with the heterogeneity characteristics. In particular, an interesting example shows a group partition can evolve into a community partition in some situations when the involved heterogeneity effects are tuned. The extension of this algorithm to weighted networks is discussed as well.

Hybrid-Lambda: simulation of multiple merger and Kingman gene genealogies in species networks and species trees.

Science.gov (United States)

Zhu, Sha; Degnan, James H; Goldstien, Sharyn J; Eldon, Bjarki

2015-09-15

There has been increasing interest in coalescent models which admit multiple mergers of ancestral lineages; and to model hybridization and coalescence simultaneously. Hybrid-Lambda is a software package that simulates gene genealogies under multiple merger and Kingman's coalescent processes within species networks or species trees. Hybrid-Lambda allows different coalescent processes to be specified for different populations, and allows for time to be converted between generations and coalescent units, by specifying a population size for each population. In addition, Hybrid-Lambda can generate simulated datasets, assuming the infinitely many sites mutation model, and compute the F ST statistic. As an illustration, we apply Hybrid-Lambda to infer the time of subdivision of certain marine invertebrates under different coalescent processes. Hybrid-Lambda makes it possible to investigate biogeographic concordance among high fecundity species exhibiting skewed offspring distribution.

Custom Ontologies for Expanded Network Analysis

Science.gov (United States)

2006-12-01

for Expanded Network Analysis. In Visualising Network Information (pp. 6-1 – 6-10). Meeting Proceedings RTO-MP-IST-063, Paper 6. Neuilly-sur-Seine...Even to this day, current research groups are working to develop an approach that involves taking all available text, video, imagery and audio and

BRAND COMMUNICATION ON SOCIAL NETWORKS

Directory of Open Access Journals (Sweden)

Otilia-Elena PLATON

2015-07-01

Full Text Available The communication represents a basic element for the marketing activity that helps companies to achieve their objectives. Building long-term relationships between brands and consumers is one of the most important objectives pursued by marketers. This involves brand communication and creating multiple connections with consumers, even in the online environment. From this point of view, social networks proved to be an effective way of linking brands and consumers online. This paper aims to present some aspects involved by the usage of social networks in brand communication by analyzing several examples of online marketing campaigns implemented on Facebook on the occasion of Valentine's Day by six different brands.

International Regional Patterns of R&D Networks Involving Low Tech SMEs

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Aurora A.C. Teixeira

2013-03-01

Full Text Available A large number of studies have emphasized the spatial proximity of economic activity and its relation to the spatiality of knowledge creation in various types of connections. Far less attention has been paid to the understanding of the determinants of ‘cultural’ and geographical proximity in international R&D cooperation projects involving SMEs and the role of the quality of the Regional Innovation System (RIS. Using a database of completed European Cooperative Research projects, we conclude that: 1 technologically more complex projects are more likely to involve ‘culturally’ and geographically distant partners; 2 RIS related variables determine ‘cultural’ proximity but not geographical proximity; 3 at first sight surprisingly, international cooperation projects involving the 1st promoters of innovation-led regions (high patent propensity and high human capital levels are culturally more distant.

Canada-Africa grants spur novel ideas, networks | IDRC ...

International Development Research Centre (IDRC) Digital Library (Canada)

2016-06-22

Jun 22, 2016 ... Canada-Africa grants spur novel ideas, networks ... networks involving African and Canadian academic researchers. ... Remarkable new research into HIV prevention among the "choice disabled" — vulnerable groups less ...

Smart business networks: architectural aspects and risks

NARCIS (Netherlands)

L-F. Pau (Louis-François)

2004-01-01

textabstractThis paper summarizes key attributes and the uniqueness of smart business networks [1], to propose thereafter an operational implementation architecture. It involves, amongst others, the embedding of business logic specific to a network of business partners, inside the communications

Default mode network connectivity during task execution.

Science.gov (United States)

Vatansever, D; Menon, D K; Manktelow, A E; Sahakian, B J; Stamatakis, E A

2015-11-15

Initially described as task-induced deactivations during goal-directed paradigms of high attentional load, the unresolved functionality of default mode regions has long been assumed to interfere with task performance. However, recent evidence suggests a potential default mode network involvement in fulfilling cognitive demands. We tested this hypothesis in a finger opposition paradigm with task and fixation periods which we compared with an independent resting state scan using functional magnetic resonance imaging and a comprehensive analysis pipeline including activation, functional connectivity, behavioural and graph theoretical assessments. The results indicate task specific changes in the default mode network topography. Behaviourally, we show that increased connectivity of the posterior cingulate cortex with the left superior frontal gyrus predicts faster reaction times. Moreover, interactive and dynamic reconfiguration of the default mode network regions' functional connections illustrates their involvement with the task at hand with higher-level global parallel processing power, yet preserved small-world architecture in comparison with rest. These findings demonstrate that the default mode network does not disengage during this paradigm, but instead may be involved in task relevant processing. Copyright © 2015 Elsevier Inc. All rights reserved.

Conceptual and methodological biases in network models.

Science.gov (United States)

Lamm, Ehud

2009-10-01

Many natural and biological phenomena can be depicted as networks. Theoretical and empirical analyses of networks have become prevalent. I discuss theoretical biases involved in the delineation of biological networks. The network perspective is shown to dissolve the distinction between regulatory architecture and regulatory state, consistent with the theoretical impossibility of distinguishing a priori between "program" and "data." The evolutionary significance of the dynamics of trans-generational and interorganism regulatory networks is explored and implications are presented for understanding the evolution of the biological categories development-heredity, plasticity-evolvability, and epigenetic-genetic.

Convergence of Networks

DEFF Research Database (Denmark)

Prasad, Ramjee; Ruggieri, Marina

2008-01-01

The paper focuses on the revolutionary changes that could characterise the future of networks. Those changes involve many aspects in the conceivement and exploitation of networks: architecture, services, technologies and modeling. The convergence of wired and wireless technologies along...... with the integration of system componennts and the convergence of services (e.g. communications and navigation) are only some of the elements that shape the perpsected mosaic. Authors delineate this vision, highlighting the presence of the space and stratospheric components and the related services as building block...

Single-cell Transcriptional Analysis Reveals Novel Neuronal Phenotypes and Interaction Networks involved In the Central Circadian Clock

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James Park

2016-10-01

Full Text Available Single-cell heterogeneity confounds efforts to understand how a population of cells organizes into cellular networks that underlie tissue-level function. This complexity is prominent in the mammalian suprachiasmatic nucleus (SCN. Here, individual neurons exhibit a remarkable amount of asynchronous behavior and transcriptional heterogeneity. However, SCN neurons are able to generate precisely coordinated synaptic and molecular outputs that synchronize the body to a common circadian cycle by organizing into cellular networks. To understand this emergent cellular network property, it is important to reconcile single-neuron heterogeneity with network organization. In light of recent studies suggesting that transcriptionally heterogeneous cells organize into distinct cellular phenotypes, we characterized the transcriptional, spatial, and functional organization of 352 SCN neurons from mice experiencing phase-shifts in their circadian cycle. Using the community structure detection method and multivariate analytical techniques, we identified previously undescribed neuronal phenotypes that are likely to participate in regulatory networks with known SCN cell types. Based on the newly discovered neuronal phenotypes, we developed a data-driven neuronal network structure in which multiple cell types interact through known synaptic and paracrine signaling mechanisms. These results provide a basis from which to interpret the functional variability of SCN neurons and describe methodologies towards understanding how a population of heterogeneous single cells organizes into cellular networks that underlie tissue-level function.

Feasibility of a Friendship Network-Based Pediatric Obesity Intervention.

Science.gov (United States)

Giannini, Courtney M; Irby, Megan B; Skelton, Joseph A; Gesell, Sabina B

2017-02-01

There is growing evidence supporting social network-based interventions for adolescents with obesity. This study's aim was to determine the feasibility of a social network-based intervention by assessing adolescents' friendship networks, willingness to involve friends in treatment, and how these factors influence enjoyment. Adolescents (N = 42) were recruited from a tertiary care obesity clinic. Participants gave a list of closest friends, friendship characteristics, and which of their friends they would involve in treatment. A subset (N = 14) participated in group treatment, were encouraged to bring friends, and invited to a second interview. Participants nominated a mean of 4.0 (standard deviation [SD] = 1.6) friends and were more likely to nominate closer friends (p = 0.003). Friends who attended group sessions were more likely to have multiple friendships in common with the participant's own network (p = 0.04). Involving friends in treatment is feasible and desired by adolescents and may be a novel approach for augmenting obesity treatment outcomes.

Breadth-First Search-Based Single-Phase Algorithms for Bridge Detection in Wireless Sensor Networks

Science.gov (United States)

Akram, Vahid Khalilpour; Dagdeviren, Orhan

2013-01-01

Wireless sensor networks (WSNs) are promising technologies for exploring harsh environments, such as oceans, wild forests, volcanic regions and outer space. Since sensor nodes may have limited transmission range, application packets may be transmitted by multi-hop communication. Thus, connectivity is a very important issue. A bridge is a critical edge whose removal breaks the connectivity of the network. Hence, it is crucial to detect bridges and take preventions. Since sensor nodes are battery-powered, services running on nodes should consume low energy. In this paper, we propose energy-efficient and distributed bridge detection algorithms for WSNs. Our algorithms run single phase and they are integrated with the Breadth-First Search (BFS) algorithm, which is a popular routing algorithm. Our first algorithm is an extended version of Milic's algorithm, which is designed to reduce the message length. Our second algorithm is novel and uses ancestral knowledge to detect bridges. We explain the operation of the algorithms, analyze their proof of correctness, message, time, space and computational complexities. To evaluate practical importance, we provide testbed experiments and extensive simulations. We show that our proposed algorithms provide less resource consumption, and the energy savings of our algorithms are up by 5.5-times. PMID:23845930

Parallel consensual neural networks.

Science.gov (United States)

Benediktsson, J A; Sveinsson, J R; Ersoy, O K; Swain, P H

1997-01-01

A new type of a neural-network architecture, the parallel consensual neural network (PCNN), is introduced and applied in classification/data fusion of multisource remote sensing and geographic data. The PCNN architecture is based on statistical consensus theory and involves using stage neural networks with transformed input data. The input data are transformed several times and the different transformed data are used as if they were independent inputs. The independent inputs are first classified using the stage neural networks. The output responses from the stage networks are then weighted and combined to make a consensual decision. In this paper, optimization methods are used in order to weight the outputs from the stage networks. Two approaches are proposed to compute the data transforms for the PCNN, one for binary data and another for analog data. The analog approach uses wavelet packets. The experimental results obtained with the proposed approach show that the PCNN outperforms both a conjugate-gradient backpropagation neural network and conventional statistical methods in terms of overall classification accuracy of test data.

Networks as Tools for Urban Sustainability

DEFF Research Database (Denmark)

Jensen, Jesper Ole; Tollin, Nicola

2004-01-01

Due to the increasing number of networks related to sustainable development (SUD) the paper focuses on understanding in which way networks can be considered useful tools for sustainable urban development, taking particularly into consideration the networks potential of spreading innovative policies...... will be discussed through a case study of a Danish municipal network on Sustainable Development, Dogme 2000 . This network has become quite successful in terms of learning and innovation, committing actors, and influencing local policies, to a larger extent than other SUD-networks the municipalities are involved in....... By applying the GREMI -theories of “innovative milieux” (Aydalot, 1986; Camagni, 1991) to the case study, we will suggest some reasons for the benefits achieved by the Dogme-network, compared to other networks. This analysis will point to the existence of an “innovative milieu” on sustainability within...

Evidence for an Ancestral Association of Human Coronavirus 229E with Bats.

Science.gov (United States)

Corman, Victor Max; Baldwin, Heather J; Tateno, Adriana Fumie; Zerbinati, Rodrigo Melim; Annan, Augustina; Owusu, Michael; Nkrumah, Evans Ewald; Maganga, Gael Darren; Oppong, Samuel; Adu-Sarkodie, Yaw; Vallo, Peter; da Silva Filho, Luiz Vicente Ribeiro Ferreira; Leroy, Eric M; Thiel, Volker; van der Hoek, Lia; Poon, Leo L M; Tschapka, Marco; Drosten, Christian; Drexler, Jan Felix

2015-12-01

We previously showed that close relatives of human coronavirus 229E (HCoV-229E) exist in African bats. The small sample and limited genomic characterizations have prevented further analyses so far. Here, we tested 2,087 fecal specimens from 11 bat species sampled in Ghana for HCoV-229E-related viruses by reverse transcription-PCR (RT-PCR). Only hipposiderid bats tested positive. To compare the genetic diversity of bat viruses and HCoV-229E, we tested historical isolates and diagnostic specimens sampled globally over 10 years. Bat viruses were 5- and 6-fold more diversified than HCoV-229E in the RNA-dependent RNA polymerase (RdRp) and spike genes. In phylogenetic analyses, HCoV-229E strains were monophyletic and not intermixed with animal viruses. Bat viruses formed three large clades in close and more distant sister relationships. A recently described 229E-related alpaca virus occupied an intermediate phylogenetic position between bat and human viruses. According to taxonomic criteria, human, alpaca, and bat viruses form a single CoV species showing evidence for multiple recombination events. HCoV-229E and the alpaca virus showed a major deletion in the spike S1 region compared to all bat viruses. Analyses of four full genomes from 229E-related bat CoVs revealed an eighth open reading frame (ORF8) located at the genomic 3' end. ORF8 also existed in the 229E-related alpaca virus. Reanalysis of HCoV-229E sequences showed a conserved transcription regulatory sequence preceding remnants of this ORF, suggesting its loss after acquisition of a 229E-related CoV by humans. These data suggested an evolutionary origin of 229E-related CoVs in hipposiderid bats, hypothetically with camelids as intermediate hosts preceding the establishment of HCoV-229E. The ancestral origins of major human coronaviruses (HCoVs) likely involve bat hosts. Here, we provide conclusive genetic evidence for an evolutionary origin of the common cold virus HCoV-229E in hipposiderid bats by analyzing a

Reinterpretation of Halokinetic Features in the Ancestral Rocky Mountains Paradox Salt Basin, Utah and Colorado

Science.gov (United States)

Thompson, J. A.; Giles, K. A.; Rowan, M. G.; Hearon, T. E., IV

2016-12-01

The Paradox Basin in southeastern Utah and southwestern Colorado is a foreland basin formed in response to flexural loading by the Pennsylvanian-aged Uncompaghre uplift during the Ancestral Rocky Mountain orogen. Thick sequences of evaporites (Paradox Formation) were deposited within the foreland basin, which interfinger with clastic sediments in the foredeep and carbonates around the basin margin. Differential loading of the Pennsylvanian-Jurassic sediments onto the evaporites drove synsedimentary halokinesis, creating a series of salt walls and adjacent minibasins within the larger foreland basin. The growing salt walls within the basin influenced patterns of sediment deposition from the Pennsylvanian through the Cretaceous. By integrating previously published mapping with recent field observations, mapping, and subsurface interpretations of well logs and 2D seismic lines, we present interpretations of the timing, geometry, and nature of halokinesis within the Paradox Basin, which record the complex salt tectonic history in the basin. Furthermore, we present recent work on the relationships between the local passive salt history and the formation of syndepositional counter-regional extensional fault systems within the foreland. These results will be integrated into a new regional salt-tectonic and stratigraphic framework of the Paradox Basin, and have broader implications for interpreting sedimentary records in other basins with a mobile substrate.

Mastication dyspraxia: a neurodevelopmental disorder reflecting disruption of the cerebellocerebral network involved in planned actions.

Science.gov (United States)

Mariën, Peter; Vidts, Annelies; Van Hecke, Wim; De Surgeloose, Didier; De Belder, Frank; Parizel, Paul M; Engelborghs, Sebastiaan; De Deyn, Peter P; Verhoeven, Jo

2013-04-01

cerebellocerebral network is crucially important in the planning and execution of skilled actions, but also seem to show for the first time that mastication deficits may be of true apraxic origin. As a result, it is hypothesized that "mastication dyspraxia" may have to be considered as a distinct nosological entity within the group of the developmental dyspraxias following a disruption of the cerebellocerebral network involved in planned actions.

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

Directory of Open Access Journals (Sweden)

Liran Carmel

2010-01-01

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

Global value chains: Building blocks and network dynamics

Science.gov (United States)

Tsekeris, Theodore

2017-12-01

The paper employs measures and tools from complex network analysis to enhance the understanding and interpretation of structural characteristics pertaining to the Global Value Chains (GVCs) during the period 1995-2011. The analysis involves the country, sector and country-sector value chain networks to identify main drivers of structural change. The results indicate significant intertemporal changes, mirroring the increased globalization in terms of network size, strength and connectivity. They also demonstrate higher clustering and increased concentration of the most influential countries and country-sectors relative to all others in the GVC network, with the geographical dimension to prevail over the sectoral dimension in the formation of value chains. The regionalization and less hierarchical organization drive country-sector production sharing, while the sectoral value chain network has become more integrated and more competitive over time. The findings suggest that the impact of country-sector policies and/or shocks may vary with the own-group and network-wide influence of each country, take place in multiple geographical scales, as GVCs have a block structure, and involve time dynamics.

Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

Directory of Open Access Journals (Sweden)

Xiaorui Chen

2017-10-01

Full Text Available Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.

Comparative Genomics of Facultative Bacterial Symbionts Isolated from European Orius Species Reveals an Ancestral Symbiotic Association

Science.gov (United States)

Chen, Xiaorui; Hitchings, Matthew D.; Mendoza, José E.; Balanza, Virginia; Facey, Paul D.; Dyson, Paul J.; Bielza, Pablo; Del Sol, Ricardo

2017-01-01

Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis) from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector–immunity proteins from the Tai4 sub-family to the symbiotic lifestyle. PMID:29067021

RESEARCH ON NON-DESTRUCTIVE TESTING TECHNOLOGY IN CONSERVATION REPAIR PROJECT OF ANCESTRAL TEMPLE IN MUKDEN PALACE

Directory of Open Access Journals (Sweden)

J. Yang

2017-08-01

Full Text Available Due to the use of wood and other non-permanent materials, traditional Chinese architecture is one of the most fragile constructions in various heritage objects today. With the increasing emphasis on the protection of cultural relics, the repair project of wooden structure has become more and more important. There are various kinds of destructions, which pose a hidden danger to the overall safety of the ancient buildings, caused not only by time and nature, but also by improper repairs in history or nowadays. Today, the use of digital technology is a basic requirement in the conservation of cultural heritage. Detection technology, especially non-destructive testing technology, could provide more accurate records in capturing detailed physical characteristics of structures such as geometric deformation and invisible damage, as well as prevent a man-made destruction in the process of repair project. This paper aims to interpret with a typical example, Ancestral Temple in Mukden Palace, along with a discussion of how to use the non-destructive testing technology with ground penetrating radar, stress wave, resistograph and so on, in addition to find an appropriate protection method in repair project of traditional Chinese wooden architecture.

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.

Research on Non-Destructive Testing Technology in Conservation Repair Project of Ancestral Temple in Mukden Palace

Science.gov (United States)

Yang, J.; Fu, M.

2017-08-01

Due to the use of wood and other non-permanent materials, traditional Chinese architecture is one of the most fragile constructions in various heritage objects today. With the increasing emphasis on the protection of cultural relics, the repair project of wooden structure has become more and more important. There are various kinds of destructions, which pose a hidden danger to the overall safety of the ancient buildings, caused not only by time and nature, but also by improper repairs in history or nowadays. Today, the use of digital technology is a basic requirement in the conservation of cultural heritage. Detection technology, especially non-destructive testing technology, could provide more accurate records in capturing detailed physical characteristics of structures such as geometric deformation and invisible damage, as well as prevent a man-made destruction in the process of repair project. This paper aims to interpret with a typical example, Ancestral Temple in Mukden Palace, along with a discussion of how to use the non-destructive testing technology with ground penetrating radar, stress wave, resistograph and so on, in addition to find an appropriate protection method in repair project of traditional Chinese wooden architecture.

Trends in Integrated Ship Control Networking

DEFF Research Database (Denmark)

Jørgensen, N.; Nielsen, Jens Frederik Dalsgaard

1997-01-01

Integrated Ship Control systems can be designed as robust, distributed, autonomous control systems. The EU funded ATOMOS and ATOMOS II projects involves both technical and non technical aspects of this process. A reference modelling concept giving an outline of a generic ISC system covering...... the network and the equipment connected to it, a framework for verification of network functionality and performance by simulation and a general distribution platform for ISC systems, The ATOMOS Network, are results of this work....

Brain Network Involved in the Recognition of Facial Expressions of Emotion in the Early Blind

Directory of Open Access Journals (Sweden)

Ryo Kitada

2011-10-01

Full Text Available Previous studies suggest that the brain network responsible for the recognition of facial expressions of emotion (FEEs begins to emerge early in life. However, it has been unclear whether visual experience of faces is necessary for the development of this network. Here, we conducted both psychophysical and functional magnetic-resonance imaging (fMRI experiments to test the hypothesis that the brain network underlying the recognition of FEEs is not dependent on visual experience of faces. Early-blind, late-blind and sighted subjects participated in the psychophysical experiment. Regardless of group, subjects haptically identified basic FEEs at above-chance levels, without any feedback training. In the subsequent fMRI experiment, the early-blind and sighted subjects haptically identified facemasks portraying three different FEEs and casts of three different shoe types. The sighted subjects also completed a visual task that compared the same stimuli. Within the brain regions activated by the visually-identified FEEs (relative to shoes, haptic identification of FEEs (relative to shoes by the early-blind and sighted individuals activated the posterior middle temporal gyrus adjacent to the superior temporal sulcus, the inferior frontal gyrus, and the fusiform gyrus. Collectively, these results suggest that the brain network responsible for FEE recognition can develop without any visual experience of faces.

Seeded Bayesian Networks: Constructing genetic networks from microarray data

Directory of Open Access Journals (Sweden)

Quackenbush John

2008-07-01

Full Text Available Abstract Background DNA microarrays and other genomics-inspired technologies provide large datasets that often include hidden patterns of correlation between genes reflecting the complex processes that underlie cellular metabolism and physiology. The challenge in analyzing large-scale expression data has been to extract biologically meaningful inferences regarding these processes – often represented as networks – in an environment where the datasets are often imperfect and biological noise can obscure the actual signal. Although many techniques have been developed in an attempt to address these issues, to date their ability to extract meaningful and predictive network relationships has been limited. Here we describe a method that draws on prior information about gene-gene interactions to infer biologically relevant pathways from microarray data. Our approach consists of using preliminary networks derived from the literature and/or protein-protein interaction data as seeds for a Bayesian network analysis of microarray results. Results Through a bootstrap analysis of gene expression data derived from a number of leukemia studies, we demonstrate that seeded Bayesian Networks have the ability to identify high-confidence gene-gene interactions which can then be validated by comparison to other sources of pathway data. Conclusion The use of network seeds greatly improves the ability of Bayesian Network analysis to learn gene interaction networks from gene expression data. We demonstrate that the use of seeds derived from the biomedical literature or high-throughput protein-protein interaction data, or the combination, provides improvement over a standard Bayesian Network analysis, allowing networks involving dynamic processes to be deduced from the static snapshots of biological systems that represent the most common source of microarray data. Software implementing these methods has been included in the widely used TM4 microarray analysis package.

Social Network Methods for the Educational and Psychological Sciences

Science.gov (United States)

Sweet, Tracy M.

2016-01-01

Social networks are especially applicable in educational and psychological studies involving social interactions. A social network is defined as a specific relationship among a group of individuals. Social networks arise in a variety of situations such as friendships among children, collaboration and advice seeking among teachers, and coauthorship…

The Zygosaccharomyces bailii transcription factor Haa1 is required for acetic acid and copper stress responses suggesting subfunctionalization of the ancestral bifunctional protein Haa1/Cup2.

Science.gov (United States)

Palma, Margarida; Dias, Paulo Jorge; Roque, Filipa de Canaveira; Luzia, Laura; Guerreiro, Joana Fernandes; Sá-Correia, Isabel

2017-01-13

The food spoilage yeast species Zygosaccharomyces bailii exhibits an extraordinary capacity to tolerate weak acids, in particular acetic acid. In Saccharomyces cerevisiae, the transcription factor Haa1 (ScHaa1) is considered the main player in genomic expression reprogramming in response to acetic acid stress, but the role of its homologue in Z. bailii (ZbHaa1) is unknown. In this study it is demonstrated that ZbHaa1 is a ScHaa1 functional homologue by rescuing the acetic acid susceptibility phenotype of S. cerevisiae haa1Δ. The disruption of ZbHAA1 in Z. bailii IST302 and the expression of an extra ZbHAA1 copy confirmed ZbHAA1 as a determinant of acetic acid tolerance. ZbHaa1 was found to be required for acetic acid stress-induced transcriptional activation of Z. bailii genes homologous to ScHaa1-target genes. An evolutionary analysis of the Haa1 homologues identified in 28 Saccharomycetaceae species genome sequences, including Z bailii, was carried out using phylogenetic and gene neighbourhood approaches. Consistent with previous studies, this analysis revealed a group containing pre-whole genome duplication species Haa1/Cup2 single orthologues, including ZbHaa1, and two groups containing either Haa1 or Cup2 orthologues from post-whole genome duplication species. S. cerevisiae Cup2 (alias Ace1) is a transcription factor involved in response and tolerance to copper stress. Taken together, these observations led us to hypothesize and demonstrate that ZbHaa1 is also involved in copper-induced transcriptional regulation and copper tolerance. The transcription factor ZbHaa1 is required for adaptive response and tolerance to both acetic acid and copper stresses. The subfunctionalization of the single ancestral Haa1/Cup2 orthologue that originated Haa1 and Cup2 paralogues after whole genome duplication is proposed.

Media in a Crisis Situation Involving National Interest:

DEFF Research Database (Denmark)

Xigen, Li; Lindsay, Laura; Mogensen, Kirsten

A content analysis of coverage of 9/11 incident during the first eight hours examined how five television networks framed the news coverage as events unfolded. Media performed their function in a crisis basically as they were expected and coverage and issues do not vary significantly among...... the networks. This study found that a variety of sources was used, and the influence of government officials was not as great as in the coverage of a crisis with less involvement of U.S. national interest. Media primarily serve as the sources of accurate information instead of guidance and consolation...

Alcances translocales de cultos ancestrales: El caso de las danzas rituales aztecas (Translocales reaches of ancestral cults: The case of the Aztec ritual dances

Directory of Open Access Journals (Sweden)

Renée de la Torre

2007-03-01

Full Text Available Este trabajo trata sobre las transformaciones de identidad que se gestan en los grupos de danza conocidos como aztecas o concheros en su intercambio cultural y encuentro con redes espirituales alternativas o conocidas como movimientos de espiritualidad Nueva Era (o New Age. El objetivo de este trabajo es dar cuenta de los procesos a partir de los cuales la tradición dancística conchera o azteca está siendo trasformada por las dinámicas de la globalización cultural, haciendo de esta tradición mexicana y ancestral, un eslabón de una amplia red New Age de alcances planetarios.

Networks in social policy problems

CERN Document Server

Scotti, marco

2012-01-01

Network science is the key to managing social communities, designing the structure of efficient organizations and planning for sustainable development. This book applies network science to contemporary social policy problems. In the first part, tools of diffusion and team design are deployed to challenges in adoption of ideas and the management of creativity. Ideas, unlike information, are generated and adopted in networks of personal ties. Chapters in the second part tackle problems of power and malfeasance in political and business organizations, where mechanisms in accessing and controlling informal networks often outweigh formal processes. The third part uses ideas from biology and physics to understand global economic and financial crises, ecological depletion and challenges to energy security. Ideal for researchers and policy makers involved in social network analysis, business strategy and economic policy, it deals with issues ranging from what makes public advisories effective to how networks influenc...

A linear mitochondrial genome of Cyclospora cayetanensis (Eimeriidae, Eucoccidiorida, Coccidiasina, Apicomplexa) suggests the ancestral start position within mitochondrial genomes of eimeriid coccidia.

Science.gov (United States)

Ogedengbe, Mosun E; Qvarnstrom, Yvonne; da Silva, Alexandre J; Arrowood, Michael J; Barta, John R

2015-05-01

The near complete mitochondrial genome for Cyclospora cayetanensis is 6184 bp in length with three protein-coding genes (Cox1, Cox3, CytB) and numerous lsrDNA and ssrDNA fragments. Gene arrangements were conserved with other coccidia in the Eimeriidae, but the C. cayetanensis mitochondrial genome is not circular-mapping. Terminal transferase tailing and nested PCR completed the 5'-terminus of the genome starting with a 21 bp A/T-only region that forms a potential stem-loop. Regions homologous to the C. cayetanensis mitochondrial genome 5'-terminus are found in all eimeriid mitochondrial genomes available and suggest this may be the ancestral start of eimeriid mitochondrial genomes. Copyright © 2015 Australian Society for Parasitology Inc. All rights reserved.

Field-trip guide to subaqueous volcaniclastic facies in the Ancestral Cascades arc in southern Washington State—The Ohanapecosh Formation and Wildcat Creek beds

Science.gov (United States)

Jutzeler, Martin; McPhie, Jocelyn

2017-06-27

Partly situated in the idyllic Mount Rainier National Park, this field trip visits exceptional examples of Oligocene subaqueous volcaniclastic successions in continental basins adjacent to the Ancestral Cascades arc. The >800-m-thick Ohanapecosh Formation (32–26 Ma) and the >300-m-thick Wildcat Creek (27 Ma) beds record similar sedimentation processes from various volcanic sources. Both show evidence of below-wave-base deposition, and voluminous accumulation of volcaniclastic facies from subaqueous density currents and suspension settling. Eruption-fed facies include deposits from pyroclastic flows that crossed the shoreline, from tephra fallout over water, and from probable Surtseyan eruptions, whereas re-sedimented facies comprise subaqueous density currents and debris flow deposits.

Analysis of pharmacy student motivators and deterrents for professional organization involvement.

Science.gov (United States)

Petersen, Erin; Wascher, Molly; Kier, Karen

2017-07-01

The purpose of this study was to determine motivators and deterrents impacting a student pharmacist's decision to join professional organizations. The goal was to create a list of meaningful factors that organizations can use for membership recruitment. This descriptive study utilized a blinded electronic survey sent to eight accredited pharmacy schools in Ohio, Michigan, Wisconsin, Indiana, Illinois, and Kentucky. The survey assessed motivating and hindering factors, as well as demographic data. Eight-hundred fifty-six students completed the survey, a 15.05% participation rate. Professional development and networking were the top two endorsed motivational factors, selected as significant by 88.0% and 87.5% respectively. Upon chi-square analysis, networking (pmotivating factors with which membership was found to be significantly influenced. Networking and involvement opportunities were more significant for members while scholarships were a greater motivator among nonmembers. Time required for involvement and cost were the most commonly selected hindrances with 78% and 76% respectively identifying these as significant barriers. The hindering factor found to be significantly different between active members and nonmembers was bylaws/rules of the organization (p=0.032), with non-members rating this as a greater consideration than current members. Multiple factors contribute to a student's decision to join a professional organization. Those active members find greater significance in networking involvement opportunities. Non-member students found scholarships more motivating and recognize bylaws as a consideration for membership more than current members. These results emphasize the multifactorial nature of membership and may direct future membership initiatives. Copyright © 2017 Elsevier Inc. All rights reserved.

Power laws and fragility in flow networks.

Science.gov (United States)

Shore, Jesse; Chu, Catherine J; Bianchi, Matt T

2013-01-01

What makes economic and ecological networks so unlike other highly skewed networks in their tendency toward turbulence and collapse? Here, we explore the consequences of a defining feature of these networks: their nodes are tied together by flow. We show that flow networks tend to the power law degree distribution (PLDD) due to a self-reinforcing process involving position within the global network structure, and thus present the first random graph model for PLDDs that does not depend on a rich-get-richer function of nodal degree. We also show that in contrast to non-flow networks, PLDD flow networks are dramatically more vulnerable to catastrophic failure than non-PLDD flow networks, a finding with potential explanatory power in our age of resource- and financial-interdependence and turbulence.

Joint Hub Network Development

OpenAIRE

Cruijssen, F.C.A.M.; Borm, P.E.M.; Dullaert, W.; Hamers, H.J.M.

2007-01-01

This paper introduces a framework for joint hub network development. Building a joint physical hub for transhipment of goods is expensive and therefore involves considerable risks for the cooperating companies. In a practical setting, it is unlikely that an entire network will be built at once. Rather, the partners will have a more cautious attitude and build the hub facilities one-by-one. In the proposed framework, every time a new hub is introduced, partners will have the opportunity to dec...

Bayesian Networks An Introduction

CERN Document Server

Koski, Timo

2009-01-01

Bayesian Networks: An Introduction provides a self-contained introduction to the theory and applications of Bayesian networks, a topic of interest and importance for statisticians, computer scientists and those involved in modelling complex data sets. The material has been extensively tested in classroom teaching and assumes a basic knowledge of probability, statistics and mathematics. All notions are carefully explained and feature exercises throughout. Features include:.: An introduction to Dirichlet Distribution, Exponential Families and their applications.; A detailed description of learni

Product Platform Development in Industrial Networks

DEFF Research Database (Denmark)

Karlsson, Christer; Skold, Martin

2011-01-01

The article examines the strategic issues involved in the deployment of product platform development in an industrial network. The move entails identifying the types and characteristics of generically different product platform strategies and clarifying strategic motives and differences. Number o...... of platforms and product brands serve as the key dimensions when distinguishing the different strategies. Each strategy has its own challenges and raises various issues to deal with.......The article examines the strategic issues involved in the deployment of product platform development in an industrial network. The move entails identifying the types and characteristics of generically different product platform strategies and clarifying strategic motives and differences. Number...

Infant joint attention, neural networks and social cognition.

Science.gov (United States)

Mundy, Peter; Jarrold, William

2010-01-01

Neural network models of attention can provide a unifying approach to the study of human cognitive and emotional development (Posner & Rothbart, 2007). In this paper we argue that a neural network approach to the infant development of joint attention can inform our understanding of the nature of human social learning, symbolic thought process and social cognition. At its most basic, joint attention involves the capacity to coordinate one's own visual attention with that of another person. We propose that joint attention development involves increments in the capacity to engage in simultaneous or parallel processing of information about one's own attention and the attention of other people. Infant practice with joint attention is both a consequence and an organizer of the development of a distributed and integrated brain network involving frontal and parietal cortical systems. This executive distributed network first serves to regulate the capacity of infants to respond to and direct the overt behavior of other people in order to share experience with others through the social coordination of visual attention. In this paper we describe this parallel and distributed neural network model of joint attention development and discuss two hypotheses that stem from this model. One is that activation of this distributed network during coordinated attention enhances the depth of information processing and encoding beginning in the first year of life. We also propose that with development, joint attention becomes internalized as the capacity to socially coordinate mental attention to internal representations. As this occurs the executive joint attention network makes vital contributions to the development of human symbolic thinking and social cognition. Copyright © 2010 Elsevier Ltd. All rights reserved.

A balanced memory network.

Directory of Open Access Journals (Sweden)

Yasser Roudi

2007-09-01

Full Text Available A fundamental problem in neuroscience is understanding how working memory--the ability to store information at intermediate timescales, like tens of seconds--is implemented in realistic neuronal networks. The most likely candidate mechanism is the attractor network, and a great deal of effort has gone toward investigating it theoretically. Yet, despite almost a quarter century of intense work, attractor networks are not fully understood. In particular, there are still two unanswered questions. First, how is it that attractor networks exhibit irregular firing, as is observed experimentally during working memory tasks? And second, how many memories can be stored under biologically realistic conditions? Here we answer both questions by studying an attractor neural network in which inhibition and excitation balance each other. Using mean-field analysis, we derive a three-variable description of attractor networks. From this description it follows that irregular firing can exist only if the number of neurons involved in a memory is large. The same mean-field analysis also shows that the number of memories that can be stored in a network scales with the number of excitatory connections, a result that has been suggested for simple models but never shown for realistic ones. Both of these predictions are verified using simulations with large networks of spiking neurons.

Computer Network Availability at Sandia National Laboratories, Albuquerque NM: Measurement and Perception; TOPICAL

International Nuclear Information System (INIS)

NELSON, SPENCER D.; TOLENDINO, LAWRENCE F.

1999-01-01

The desire to provide a measure of computer network availability at Sandia National Laboratories has existed for along time. Several attempts were made to build this measure by accurately recording network failures, identifying the type of network element involved, the root cause of the problem, and the time to repair the fault. Recognizing the limitations of available methods, it became obvious that another approach of determining network availability had to be defined. The chosen concept involved the periodic sampling of network services and applications from various network locations. A measure of ''network'' availability was then calculated based on the ratio of polling success to failure. The effort required to gather the information and produce a useful metric is not prohibitive and the information gained has verified long held feelings regarding network performance with real data

Solving Dynamic Battlespace Movement Problems Using Dynamic Distributed Computer Networks

National Research Council Canada - National Science Library

Bradford, Robert

2000-01-01

.... The thesis designs a system using this architecture that invokes operations research network optimization algorithms to solve problems involving movement of people and equipment over dynamic road networks...

Emergency Department Visits Involving Misuse and Abuse of the Antipsychotic Quetiapine: Results from the Drug Abuse Warning Network (DAWN

Directory of Open Access Journals (Sweden)

Margaret E. Mattson

2015-01-01

Full Text Available Case reports in medical literature suggest that the atypical antipsychotic quetiapine, a medication not previously considered to have abuse potential, is now being subject to misuse and abuse (MUA; ie, taken when not prescribed for them or used in a way other than instructed by their health professional. Here we present systematic, nationally representative data from the 2005 to 2011 Drug Abuse Warning Network (DAWN for prevalence of emergency department (ED visits among the U.S. general population involving quetiapine and related to MUA, suicide attempts, and adverse reactions. Nationally, quetiapine-related ED visits increased 90% between 2005 and 2011, from 35,581 ED visits to 67,497. DAWN data indicate that when used without medical supervision for recreational/self-medication purposes, quetiapine poses health risks for its users, especially among polydrug users and women. These findings suggest that the medical and public health communities should increase vigilance concerning this drug and its potential for MUA.

Reconstruction, visualization and explorative analysis of human pluripotency network

Directory of Open Access Journals (Sweden)

Priyanka Narad

2017-09-01

Full Text Available Identification of genes/proteins involved in pluripotency and their inter-relationships is important for understanding the induction/loss and maintenance of pluripotency. With the availability of large volume of data on interaction/regulation of pluripotency scattered across a large number of biological databases and hundreds of scientific journals, it is required a systematic integration of data which will create a complete view of pluripotency network. Describing and interpreting such a network of interaction and regulation (i.e., stimulation and inhibition links are essential tasks of computational biology, an important first step in systems-level understanding of the underlying mechanisms of pluripotency. To address this, we have assembled a network of 166 molecular interactions, stimulations and inhibitions, based on a collection of research data from 147 publications, involving 122 human genes/proteins, all in a standard electronic format, enabling analyses by readily available software such as Cytoscape and its Apps (formerly called "Plugins". The network includes the core circuit of OCT4 (POU5F1, SOX2 and NANOG, its periphery (such as STAT3, KLF4, UTF1, ZIC3, and c-MYC, connections to upstream signaling pathways (such as ACTIVIN, WNT, FGF, and BMP, and epigenetic regulators (such as L1TD1, LSD1 and PRC2. We describe the general properties of the network and compare it with other literature-based networks. Gene Ontology (GO analysis is being performed to find out the over-represented GO terms in the network. We use several expression datasets to condense the network to a set of network links that identify the key players (genes/proteins and the pathways involved in transition from one state of pluripotency to other state (i.e., native to primed state, primed to non-pluripotent state and pluripotent to non-pluripotent state.

Networks as Tools for Sustainable Urban Development

DEFF Research Database (Denmark)

Jensen, Jesper Ole; Tollin, Nicola

will be discussed through a case study of a Danish municipal network on Sustainable Development, Dogme 20001. This network has become quite successful in terms of learning and innovation, committing actors, and influencing local policies, to a larger extent than other SUD-networks the municipalities are involved in....... By applying the GREMI2-theories of “innovative milieux” (Aydalot, 1986; Camagni, 1991) to the case study, we will suggest some reasons for the benefits achieved by the Dogme-network, compared to other networks. This analysis will point to the existence of an “innovative milieu” on sustainability within......Due to the increasing number of networks related to sustainable development (SUD) the paper focuses on understanding in which way networks can be considered useful tools for sustainable urban development, taking particularly into consideration the networks potential of spreading innovative policies...

Ancestral association between HLA and HFE H63D and C282Y gene mutations from northwest Colombia.

Science.gov (United States)

Rodriguez, Libia M; Giraldo, Mabel C; Velasquez, Laura I; Alvarez, Cristiam M; Garcia, Luis F; Jimenez-Del-Rio, Marlene; Velez-Pardo, Carlos

2015-03-01

A significant association between HFE gene mutations and the HLA-A*03-B*07 and HLA-A*29-B*44 haplotypes has been reported in the Spanish population. It has been proposed that these mutations are probably connected with Celtic and North African ancestry, respectively. We aimed to find the possible ancestral association between HLA alleles and haplotypes associated with the HFE gene (C282Y and H63D) mutations in 214 subjects from Antioquia, Colombia. These were 18 individuals with presumed hereditary hemochromatosis ("HH") and 196 controls. The HLA-B*07 allele was in linkage disequilibrium (LD) with C282Y, while HLA-A*23, A*29, HLA-B*44, and B*49 were in LD with H63D. Altogether, our results show that, although the H63D mutation is more common in the Antioquia population, it is not associated with any particular HLA haplotype, whereas the C282Y mutation is associated with HLA-A*03-B*07, this supporting a northern Spaniard ancestry.

Ancestral association between HLA and HFE H63D and C282Y gene mutations from northwest Colombia

Directory of Open Access Journals (Sweden)

Libia M Rodriguez

2015-03-01

Full Text Available A significant association between HFE gene mutations and the HLA-A*03-B*07 and HLA-A*29-B*44 haplotypes has been reported in the Spanish population. It has been proposed that these mutations are probably connected with Celtic and North African ancestry, respectively. We aimed to find the possible ancestral association between HLA alleles and haplotypes associated with the HFE gene (C282Y and H63D mutations in 214 subjects from Antioquia, Colombia. These were 18 individuals with presumed hereditary hemochromatosis (“HH” and 196 controls. The HLA-B*07 allele was in linkage disequilibrium (LD with C282Y, while HLA-A*23, A*29, HLA-B*44, and B*49 were in LD with H63D. Altogether, our results show that, although the H63D mutation is more common in the Antioquia population, it is not associated with any particular HLA haplotype, whereas the C282Y mutation is associated with HLA-A*03-B*07, this supporting a northern Spaniard ancestry.

Parents, Friends, and Romantic Partners: Enmeshment in Deviant Networks and Adolescent Delinquency Involvement

Science.gov (United States)

Lonardo, Robert A.; Giordano, Peggy C.; Longmore, Monica A.; Manning, Wendy D.

2009-01-01

Adolescent networks include parents, friends, and romantic partners, but research on the social learning mechanisms related to delinquency has not typically examined the characteristics of all three domains simultaneously. Analyses draw on data from the Toledo Adolescent Relationships Study (n = 957), and our analytic sample contains 51% male and…

Coiled-Coil Proteins Facilitated the Functional Expansion of the Centrosome

Science.gov (United States)

Kuhn, Michael; Hyman, Anthony A.; Beyer, Andreas

2014-01-01

Repurposing existing proteins for new cellular functions is recognized as a main mechanism of evolutionary innovation, but its role in organelle evolution is unclear. Here, we explore the mechanisms that led to the evolution of the centrosome, an ancestral eukaryotic organelle that expanded its functional repertoire through the course of evolution. We developed a refined sequence alignment technique that is more sensitive to coiled coil proteins, which are abundant in the centrosome. For proteins with high coiled-coil content, our algorithm identified 17% more reciprocal best hits than BLAST. Analyzing 108 eukaryotic genomes, we traced the evolutionary history of centrosome proteins. In order to assess how these proteins formed the centrosome and adopted new functions, we computationally emulated evolution by iteratively removing the most recently evolved proteins from the centrosomal protein interaction network. Coiled-coil proteins that first appeared in the animal–fungi ancestor act as scaffolds and recruit ancestral eukaryotic proteins such as kinases and phosphatases to the centrosome. This process created a signaling hub that is crucial for multicellular development. Our results demonstrate how ancient proteins can be co-opted to different cellular localizations, thereby becoming involved in novel functions. PMID:24901223

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

Science.gov (United States)

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.

A versatile framework for cooperative hub network development

NARCIS (Netherlands)

Cruijssen, F.C.A.M.; Borm, P.; Dullaert, W.; Hamers, H.

2010-01-01

This paper introduces a framework for cooperative hub network development. Building a joint physical hub for the transshipment of goods is expensive and, therefore, involves considerable risks for cooperating companies. In a practical setting, it is unlikely that an entire network will be built at

A versatile framework for cooperative hub network development

NARCIS (Netherlands)

Cruijssen, Frans; Borm, Peter; Dullaert, Wout; Hamers, Herbert

This paper introduces a framework for cooperative hub network development. Building a joint physical hub for the transshipment of goods is expensive and, therefore, involves considerable risks for cooperating companies. In a practical setting, it is unlikely that an entire network will be built at

Optical slotted circuit switched network: a bandwidth efficient alternative to wavelength-routed network

Science.gov (United States)

Li, Yan; Collier, Martin

2007-11-01

Wavelength-routed networks have received enormous attention due to the fact that they are relatively simple to implement and implicitly offer Quality of Service (QoS) guarantees. However, they suffer from a bandwidth inefficiency problem and require complex Routing and Wavelength Assignment (RWA). Most attempts to address the above issues exploit the joint use of WDM and TDM technologies. The resultant TDM-based wavelength-routed networks partition the wavelength bandwidth into fixed-length time slots organized as a fixed-length frame. Multiple connections can thus time-share a wavelength and the grooming of their traffic leads to better bandwidth utilization. The capability of switching in both wavelength and time domains in such networks also mitigates the RWA problem. However, TMD-based wavelength-routed networks work in synchronous mode and strict synchronization among all network nodes is required. Global synchronization for all-optical networks which operate at extremely high speed is technically challenging, and deploying an optical synchronizer for each wavelength involves considerable cost. An Optical Slotted Circuit Switching (OSCS) architecture is proposed in this paper. In an OSCS network, slotted circuits are created to better utilize the wavelength bandwidth than in classic wavelength-routed networks. The operation of the protocol is such as to avoid the need for global synchronization required by TDM-based wavelength-routed networks.

Networking as an efficient, modern way of favouring stakeholders' involvement in implementing good radiological protection

International Nuclear Information System (INIS)

Lefaure, Ch.; Janssens, A.; Mrabit, K.; Ahier, B.

2006-01-01

Since the publication of ICRP 22 and ICRP 26 in 1973 and 1977 respectively, the understanding and practical implementation of the concept of Optimisation of Radiation Protection known as ALARA ('as low as reasonably achievable') has developed considerably globally and particularly in Europe. In the 1990 ICRP 60 publication, ALARA was re-emphasised as the cornerstone of the radiological protection system. This is also an explicit requirement of the International Basic Safety Standards for Protection against Ionizing Radiation and for the Safety of Radiation Sources (International BSS) and EC Directive laying down the Basic Safety Standards for radiological protection (EURATOM Directive 96/29), as well as of most of the national regulations. Throughout the 1980's and early 1990's ALARA was integrated into many organisations' radiation protection programmes, particularly in the nuclear industry and mainly for managing occupational exposure. One of the main lessons identified from that period was that it was not possible to implement good radiological protection by relying only on technical rules and procedures summarised in the three words: 'Time-Distance-Shielding'. A fourth word, 'Commitment', was to be added as no radiological protection programme would be successful without the commitment of all concerned stakeholders: regulatory bodies, managers, workers, etc. The scope of this presentation is, through different international feedback experiences, to demonstrate how networking is an efficient, modern way of fostering stakeholders involvement in implementing good radiological protection. (authors)

An Architectural Modelfor Intelligent Network Management

Institute of Scientific and Technical Information of China (English)

罗军舟; 顾冠群; 费翔

2000-01-01

Traditional network management approach involves the management of each vendor's equipment and network segment in isolation through its own proprietary element management system. It is necessary to set up a new network management architecture that calls for operation consolidation across vendor and technology boundaries. In this paper, an architectural model for Intelligent Network Management (INM) is presented. The INM system includes a manager system, which controls all subsystems and coordinates different management tasks; an expert system, which is responsible for handling particularly difficult problems, and intelligent agents, which bring the management closer to applications and user requirements by spreading intelligent agents through network segments or domain. In the expert system model proposed, especially an intelligent fault management system is given.The architectural model is to build the INM system to meet the need of managing modern network systems.

Growth Limits in Large Scale Networks

DEFF Research Database (Denmark)

Knudsen, Thomas Phillip

limitations. The rising complexity of network management with the convergence of communications platforms is shown as problematic for both automatic management feasibility and for manpower resource management. In the fourth step the scope is extended to include the present society with the DDN project as its......The Subject of large scale networks is approached from the perspective of the network planner. An analysis of the long term planning problems is presented with the main focus on the changing requirements for large scale networks and the potential problems in meeting these requirements. The problems...... the fundamental technological resources in network technologies are analysed for scalability. Here several technological limits to continued growth are presented. The third step involves a survey of major problems in managing large scale networks given the growth of user requirements and the technological...

Neural networks with discontinuous/impact activations

CERN Document Server

Akhmet, Marat

2014-01-01

This book presents as its main subject new models in mathematical neuroscience. A wide range of neural networks models with discontinuities are discussed, including impulsive differential equations, differential equations with piecewise constant arguments, and models of mixed type. These models involve discontinuities, which are natural because huge velocities and short distances are usually observed in devices modeling the networks. A discussion of the models, appropriate for the proposed applications, is also provided. This book also: Explores questions related to the biological underpinning for models of neural networks\\ Considers neural networks modeling using differential equations with impulsive and piecewise constant argument discontinuities Provides all necessary mathematical basics for application to the theory of neural networks Neural Networks with Discontinuous/Impact Activations is an ideal book for researchers and professionals in the field of engineering mathematics that have an interest in app...

Genomes of Helicobacter pylori from native Peruvians suggest admixture of ancestral and modern lineages and reveal a western type cag-pathogenicity island

Directory of Open Access Journals (Sweden)

Rahman Syed

2006-07-01

Full Text Available Abstract Background Helicobacter pylori is presumed to be co-evolved with its human host and is a highly diverse gastric pathogen at genetic levels. Ancient origins of H. pylori in the New World are still debatable. It is not clear how different waves of human migrations in South America contributed to the evolution of strain diversity of H. pylori. The objective of our 'phylogeographic' study was to gain fresh insights into these issues through mapping genetic origins of H. pylori of native Peruvians (of Amerindian ancestry and their genomic comparison with isolates from Spain, and Japan. Results For this purpose, we attempted to dissect genetic identity of strains by fluorescent amplified fragment length polymorphism (FAFLP analysis, multilocus sequence typing (MLST of the 7 housekeeping genes (atpA, efp, ureI, ppa, mutY, trpC, yphC and the sequence analyses of the babB adhesin and oipA genes. The whole cag pathogenicity-island (cagPAI from these strains was analyzed using PCR and the geographic type of cagA phosphorylation motif EPIYA was determined by gene sequencing. We observed that while European genotype (hp-Europe predominates in native Peruvian strains, approximately 20% of these strains represent a sub-population with an Amerindian ancestry (hsp-Amerind. All of these strains however, irrespective of their ancestral affiliation harbored a complete, 'western' type cagPAI and the motifs surrounding it. This indicates a possible acquisition of cagPAI by the hsp-Amerind strains from the European strains, during decades of co-colonization. Conclusion Our observations suggest presence of ancestral H. pylori (hsp-Amerind in Peruvian Amerindians which possibly managed to survive and compete against the Spanish strains that arrived to the New World about 500 years ago. We suggest that this might have happened after native Peruvian H. pylori strains acquired cagPAI sequences, either by new acquisition in cag-negative strains or by recombination

Intrinsic network connectivity and own body perception in gender dysphoria.

Science.gov (United States)

Feusner, Jamie D; Lidström, Andreas; Moody, Teena D; Dhejne, Cecilia; Bookheimer, Susan Y; Savic, Ivanka

2017-08-01

Gender dysphoria (GD) is characterized by incongruence between one's identity and gender assigned at birth. The biological mechanisms of GD are unclear. We investigated brain network connectivity patterns involved in own body perception in the context of self in GD. Twenty-seven female-to-male (FtM) individuals with GD, 27 male controls, and 27 female controls underwent resting state fMRI. We compared functional connections within intrinsic connectivity networks involved in self-referential processes and own body perception -default mode network (DMN) and salience network - and visual networks, using independent components analyses. Behavioral correlates of network connectivity were also tested using self-perception ratings while viewing own body images morphed to their sex assigned at birth, and to the sex of their gender identity. FtM exhibited decreased connectivity of anterior and posterior cingulate and precuneus within the DMN compared with controls. In FtM, higher "self" ratings for bodies morphed towards the sex of their gender identity were associated with greater connectivity of the anterior cingulate within the DMN, during long viewing times. In controls, higher ratings for bodies morphed towards their gender assigned at birth were associated with right insula connectivity within the salience network, during short viewing times. Within visual networks FtM showed weaker connectivity in occipital and temporal regions. Results suggest disconnectivity within networks involved in own body perception in the context of self in GD. Moreover, perception of bodies in relation to self may be reflective rather than reflexive, as a function of mesial prefrontal processes. These may represent neurobiological correlates to the subjective disconnection between perception of body and self-identification.

A class of dynamin-like GTPases involved in the generation of the tubular ER network

Science.gov (United States)

Hu, Junjie; Shibata, Yoko; Zhu, Peng-Peng; Voss, Christiane; Rismanchi, Neggy; Prinz, William A.; Rapoport, Tom A.; Blackstone, Craig

2009-01-01

The endoplasmic reticulum (ER) consists of tubules that are shaped by the reticulons and DP1/Yop1p, but how the tubules form an interconnected network is unknown. Here, we show that mammalian atlastins, which are dynamin-like, integral membrane GTPases, interact with the tubule-shaping proteins. The atlastins localize to the tubular ER and are required for proper network formation in vivo and in vitro. Depletion of the atlastins or overexpression of dominant-negative forms inhibits tubule interconnections. The Sey1p GTPase in S. cerevisiae is likely a functional ortholog of the atlastins; it shares the same signature motifs and membrane topology and interacts genetically and physically with the tubule-shaping proteins. Cells simultaneously lacking Sey1p and a tubule-shaping protein have ER morphology defects. These results indicate that formation of the tubular ER network depends on conserved dynamin-like GTPases. Since atlastin-1 mutations cause a common form of hereditary spastic paraplegia, we suggest ER shaping defects as a novel neuropathogenic mechanism. PMID:19665976

Anomaly detection in an automated safeguards system using neural networks

International Nuclear Information System (INIS)

Whiteson, R.; Howell, J.A.

1992-01-01

An automated safeguards system must be able to detect an anomalous event, identify the nature of the event, and recommend a corrective action. Neural networks represent a new way of thinking about basic computational mechanisms for intelligent information processing. In this paper, we discuss the issues involved in applying a neural network model to the first step of this process: anomaly detection in materials accounting systems. We extend our previous model to a 3-tank problem and compare different neural network architectures and algorithms. We evaluate the computational difficulties in training neural networks and explore how certain design principles affect the problems. The issues involved in building a neural network architecture include how the information flows, how the network is trained, how the neurons in a network are connected, how the neurons process information, and how the connections between neurons are modified. Our approach is based on the demonstrated ability of neural networks to model complex, nonlinear, real-time processes. By modeling the normal behavior of the processes, we can predict how a system should be behaving and, therefore, detect when an abnormality occurs

Physical Layer Network Coding

DEFF Research Database (Denmark)

Fukui, Hironori; Yomo, Hironori; Popovski, Petar

2013-01-01

of interfering nodes and usage of spatial reservation mechanisms. Specifically, we introduce a reserved area in order to protect the nodes involved in two-way relaying from the interference caused by neighboring nodes. We analytically derive the end-to-end rate achieved by PLNC considering the impact......Physical layer network coding (PLNC) has the potential to improve throughput of multi-hop networks. However, most of the works are focused on the simple, three-node model with two-way relaying, not taking into account the fact that there can be other neighboring nodes that can cause....../receive interference. The way to deal with this problem in distributed wireless networks is usage of MAC-layer mechanisms that make a spatial reservation of the shared wireless medium, similar to the well-known RTS/CTS in IEEE 802.11 wireless networks. In this paper, we investigate two-way relaying in presence...

Conflict and convention in dynamic networks.

Science.gov (United States)

Foley, Michael; Forber, Patrick; Smead, Rory; Riedl, Christoph

2018-03-01

An important way to resolve games of conflict (snowdrift, hawk-dove, chicken) involves adopting a convention: a correlated equilibrium that avoids any conflict between aggressive strategies. Dynamic networks allow individuals to resolve conflict via their network connections rather than changing their strategy. Exploring how behavioural strategies coevolve with social networks reveals new dynamics that can help explain the origins and robustness of conventions. Here, we model the emergence of conventions as correlated equilibria in dynamic networks. Our results show that networks have the tendency to break the symmetry between the two conventional solutions in a strongly biased way. Rather than the correlated equilibrium associated with ownership norms (play aggressive at home, not away), we usually see the opposite host-guest norm (play aggressive away, not at home) evolve on dynamic networks, a phenomenon common to human interaction. We also show that learning to avoid conflict can produce realistic network structures in a way different than preferential attachment models. © 2017 The Author(s).

Default network activation during episodic and semantic memory retrieval: A selective meta-analytic comparison.

Science.gov (United States)

Kim, Hongkeun

2016-01-08

It remains unclear whether and to what extent the default network subregions involved in episodic memory (EM) and semantic memory (SM) processes overlap or are separated from one another. This study addresses this issue through a controlled meta-analysis of functional neuroimaging studies involving healthy participants. Various EM and SM task paradigms differ widely in the extent of default network involvement. Therefore, the issue at hand cannot be properly addressed without some control for this factor. In this regard, this study employs a two-stage analysis: a preliminary meta-analysis to select EM and SM task paradigms that recruit relatively extensive default network regions and a main analysis to compare the selected task paradigms. Based on a within-EM comparison, the default network contributed more to recollection/familiarity effects than to old/new effects, and based on a within-SM comparison, it contributed more to word/pseudoword effects than to semantic/phonological effects. According to a direct comparison of recollection/familiarity and word/pseudoword effects, each involving a range of default network regions, there were more overlaps than separations in default network subregions involved in these two effects. More specifically, overlaps included the bilateral posterior cingulate/retrosplenial cortex, left inferior parietal lobule, and left anteromedial prefrontal regions, whereas separations included only the hippocampal formation and the parahippocampal cortex region, which was unique to recollection/familiarity effects. These results indicate that EM and SM retrieval processes involving strong memory signals recruit extensive and largely overlapping default network regions and differ mainly in distinct contributions of hippocampus and parahippocampal regions to EM retrieval. Copyright © 2015 Elsevier Ltd. All rights reserved.

Phylogenetic networks: A tool to display character conflict and ...

African Journals Online (AJOL)

Evolutionary trees have the assumption that evolution and phylogeny can be represented in a strictly bifurcating manner. Firmly speaking, from one ancestral taxon, two descendant taxa emerge. Nevertheless, hybridization, recombination and horizontal gene transfer is in conflict with this straightforward concept. In such ...

Competitive cluster growth in complex networks.

Science.gov (United States)

Moreira, André A; Paula, Demétrius R; Costa Filho, Raimundo N; Andrade, José S

2006-06-01

In this work we propose an idealized model for competitive cluster growth in complex networks. Each cluster can be thought of as a fraction of a community that shares some common opinion. Our results show that the cluster size distribution depends on the particular choice for the topology of the network of contacts among the agents. As an application, we show that the cluster size distributions obtained when the growth process is performed on hierarchical networks, e.g., the Apollonian network, have a scaling form similar to what has been observed for the distribution of a number of votes in an electoral process. We suggest that this similarity may be due to the fact that social networks involved in the electoral process may also possess an underlining hierarchical structure.

Integration of relational and hierarchical network information for protein function prediction

Directory of Open Access Journals (Sweden)

Jiang Xiaoyu

2008-08-01

Full Text Available Abstract Background In the current climate of high-throughput computational biology, the inference of a protein's function from related measurements, such as protein-protein interaction relations, has become a canonical task. Most existing technologies pursue this task as a classification problem, on a term-by-term basis, for each term in a database, such as the Gene Ontology (GO database, a popular rigorous vocabulary for biological functions. However, ontology structures are essentially hierarchies, with certain top to bottom annotation rules which protein function predictions should in principle follow. Currently, the most common approach to imposing these hierarchical constraints on network-based classifiers is through the use of transitive closure to predictions. Results We propose a probabilistic framework to integrate information in relational data, in the form of a protein-protein interaction network, and a hierarchically structured database of terms, in the form of the GO database, for the purpose of protein function prediction. At the heart of our framework is a factorization of local neighborhood information in the protein-protein interaction network across successive ancestral terms in the GO hierarchy. We introduce a classifier within this framework, with computationally efficient implementation, that produces GO-term predictions that naturally obey a hierarchical 'true-path' consistency from root to leaves, without the need for further post-processing. Conclusion A cross-validation study, using data from the yeast Saccharomyces cerevisiae, shows our method offers substantial improvements over both standard 'guilt-by-association' (i.e., Nearest-Neighbor and more refined Markov random field methods, whether in their original form or when post-processed to artificially impose 'true-path' consistency. Further analysis of the results indicates that these improvements are associated with increased predictive capabilities (i.e., increased

A fuzzy network module extraction technique for gene expression data

Indian Academy of Sciences (India)

2014-05-01

expression network from the distance matrix. The distance matrix is .... mental process, cellular component assembly involved in ..... the molecules are present in the network. User can ... hsa05213:Endometrial cancer. 24. 0.07.

WDM Network and Multicasting Protocol Strategies

Directory of Open Access Journals (Sweden)

Pinar Kirci

2014-01-01

Full Text Available Optical technology gains extensive attention and ever increasing improvement because of the huge amount of network traffic caused by the growing number of internet users and their rising demands. However, with wavelength division multiplexing (WDM, it is easier to take the advantage of optical networks and optical burst switching (OBS and to construct WDM networks with low delay rates and better data transparency these technologies are the best choices. Furthermore, multicasting in WDM is an urgent solution for bandwidth-intensive applications. In the paper, a new multicasting protocol with OBS is proposed. The protocol depends on a leaf initiated structure. The network is composed of source, ingress switches, intermediate switches, edge switches, and client nodes. The performance of the protocol is examined with Just Enough Time (JET and Just In Time (JIT reservation protocols. Also, the paper involves most of the recent advances about WDM multicasting in optical networks. WDM multicasting in optical networks is given as three common subtitles: Broadcast and-select networks, wavelength-routed networks, and OBS networks. Also, in the paper, multicast routing protocols are briefly summarized and optical burst switched WDM networks are investigated with the proposed multicast schemes.

Temporal node centrality in complex networks

Science.gov (United States)

Kim, Hyoungshick; Anderson, Ross

2012-02-01

Many networks are dynamic in that their topology changes rapidly—on the same time scale as the communications of interest between network nodes. Examples are the human contact networks involved in the transmission of disease, ad hoc radio networks between moving vehicles, and the transactions between principals in a market. While we have good models of static networks, so far these have been lacking for the dynamic case. In this paper we present a simple but powerful model, the time-ordered graph, which reduces a dynamic network to a static network with directed flows. This enables us to extend network properties such as vertex degree, closeness, and betweenness centrality metrics in a very natural way to the dynamic case. We then demonstrate how our model applies to a number of interesting edge cases, such as where the network connectivity depends on a small number of highly mobile vertices or edges, and show that our centrality definition allows us to track the evolution of connectivity. Finally we apply our model and techniques to two real-world dynamic graphs of human contact networks and then discuss the implication of temporal centrality metrics in the real world.

Recruitment of pre-existing networks during the evolution of C4 photosynthesis.

Science.gov (United States)

Reyna-Llorens, Ivan; Hibberd, Julian M

2017-09-26

During C 4 photosynthesis, CO 2 is concentrated around the enzyme RuBisCO. The net effect is to reduce photorespiration while increasing water and nitrogen use efficiencies. Species that use C 4 photosynthesis have evolved independently from their C 3 ancestors on more than 60 occasions. Along with mimicry and the camera-like eye, the C 4 pathway therefore represents a remarkable example of the repeated evolution of a highly complex trait. In this review, we provide evidence that the polyphyletic evolution of C 4 photosynthesis is built upon pre-existing metabolic and genetic networks. For example, cells around veins of C 3 species show similarities to those of the C 4 bundle sheath in terms of C 4 acid decarboxylase activity and also the photosynthetic electron transport chain. Enzymes of C 4 photosynthesis function together in gluconeogenesis during early seedling growth of C 3 Arabidopsis thaliana Furthermore, multiple C 4 genes appear to be under control of both light and chloroplast signals in the ancestral C 3 state. We, therefore, hypothesize that relatively minor rewiring of pre-existing genetic and metabolic networks has facilitated the recurrent evolution of this trait. Understanding how these changes are likely to have occurred could inform attempts to install C 4 traits into C 3 crops.This article is part of the themed issue 'Enhancing photosynthesis in crop plants: targets for improvement'. © 2017 The Author(s).

Centrality Robustness and Link Prediction in Complex Social Networks

DEFF Research Database (Denmark)

Davidsen, Søren Atmakuri; Ortiz-Arroyo, Daniel

2012-01-01

. Secondly, we present a method to predict edges in dynamic social networks. Our experimental results indicate that the robustness of the centrality measures applied to more realistic social networks follows a predictable pattern and that the use of temporal statistics could improve the accuracy achieved......This chapter addresses two important issues in social network analysis that involve uncertainty. Firstly, we present am analysis on the robustness of centrality measures that extend the work presented in Borgati et al. using three types of complex network structures and one real social network...

Partnership capacity for community health improvement plan implementation: findings from a social network analysis.

Science.gov (United States)

McCullough, J Mac; Eisen-Cohen, Eileen; Salas, S Bianca

2016-07-13

Many health departments collaborate with community organizations on community health improvement processes. While a number of resources exist to plan and implement a community health improvement plan (CHIP), little empirical evidence exists on how to leverage and expand partnerships when implementing a CHIP. The purpose of this study was to identify characteristics of the network involved in implementing the CHIP in one large community. The aims of this analysis are to: 1) identify essential network partners (and thereby highlight potential network gaps), 2) gauge current levels of partner involvement, 3) understand and effectively leverage network resources, and 4) enable a data-driven approach for future collaborative network improvements. We collected primary data via survey from n = 41 organizations involved in the Health Improvement Partnership of Maricopa County (HIPMC), in Arizona. Using the previously validated Program to Analyze, Record, and Track Networks to Enhance Relationships (PARTNER) tool, organizations provided information on existing ties with other coalition members, including frequency and depth of partnership and eight categories of perceived value/trust of each current partner organization. The coalition's overall network had a density score of 30 %, degree centralization score of 73 %, and trust score of 81 %. Network maps are presented to identify existing relationships between HIPMC members according to partnership frequency and intensity, duration of involvement in the coalition, and self-reported contributions to the coalition. Overall, number of ties and other partnership measures were positively correlated with an organization's perceived value and trustworthiness as rated by other coalition members. Our study presents a novel use of social network analysis methods to evaluate the coalition of organizations involved in implementing a CHIP in an urban community. The large coalition had relatively low network density but high

Independent functional connectivity networks underpin food and monetary reward sensitivity in excess weight.

Science.gov (United States)

Verdejo-Román, Juan; Fornito, Alex; Soriano-Mas, Carles; Vilar-López, Raquel; Verdejo-García, Antonio

2017-02-01

Overvaluation of palatable food is a primary driver of obesity, and is associated with brain regions of the reward system. However, it remains unclear if this network is specialized in food reward, or generally involved in reward processing. We used functional magnetic resonance imaging (fMRI) to characterize functional connectivity during processing of food and monetary rewards. Thirty-nine adults with excess weight and 37 adults with normal weight performed the Willingness to Pay for Food task and the Monetary Incentive Delay task in the fMRI scanner. A data-driven graph approach was applied to compare whole-brain, task-related functional connectivity between groups. Excess weight was associated with decreased functional connectivity during the processing of food rewards in a network involving primarily frontal and striatal areas, and increased functional connectivity during the processing of monetary rewards in a network involving principally frontal and parietal areas. These two networks were topologically and anatomically distinct, and were independently associated with BMI. The processing of food and monetary rewards involve segregated neural networks, and both are altered in individuals with excess weight. Copyright © 2016 Elsevier Inc. All rights reserved.

Adaptive Filtering Using Recurrent Neural Networks

Science.gov (United States)

Parlos, Alexander G.; Menon, Sunil K.; Atiya, Amir F.

2005-01-01

A method for adaptive (or, optionally, nonadaptive) filtering has been developed for estimating the states of complex process systems (e.g., chemical plants, factories, or manufacturing processes at some level of abstraction) from time series of measurements of system inputs and outputs. The method is based partly on the fundamental principles of the Kalman filter and partly on the use of recurrent neural networks. The standard Kalman filter involves an assumption of linearity of the mathematical model used to describe a process system. The extended Kalman filter accommodates a nonlinear process model but still requires linearization about the state estimate. Both the standard and extended Kalman filters involve the often unrealistic assumption that process and measurement noise are zero-mean, Gaussian, and white. In contrast, the present method does not involve any assumptions of linearity of process models or of the nature of process noise; on the contrary, few (if any) assumptions are made about process models, noise models, or the parameters of such models. In this regard, the method can be characterized as one of nonlinear, nonparametric filtering. The method exploits the unique ability of neural networks to approximate nonlinear functions. In a given case, the process model is limited mainly by limitations of the approximation ability of the neural networks chosen for that case. Moreover, despite the lack of assumptions regarding process noise, the method yields minimum- variance filters. In that they do not require statistical models of noise, the neural- network-based state filters of this method are comparable to conventional nonlinear least-squares estimators.

Reciprocal Family, Friendship and Church Support Networks of African Americans: Findings from the National Survey of American Life.

Science.gov (United States)

Taylor, Robert Joseph; Mouzon, Dawne M; Nguyen, Ann W; Chatters, Linda M

2016-12-01

This study examined reciprocal support networks involving extended family, friends and church members among African Americans. Our analysis examined specific patterns of reciprocal support (i.e., received only, gave only, both gave and received, neither gave or received), as well as network characteristics (i.e., contact and subjective closeness) as correlates of reciprocal support. The analysis is based on the African American sub-sample of the National Survey of American Life (NSAL). Overall, our findings indicate that African Americans are very involved in reciprocal support networks with their extended family, friends and church members. Respondents were most extensively involved in reciprocal supports with extended family members, followed closely by friends and church networks. Network characteristics (i.e., contact and subjective closeness) were significantly and consistently associated with involvement with reciprocal support exchanges for all three networks. These and other findings are discussed in detail. This study complements previous work on the complementary roles of family, friend and congregational support networks, as well as studies of racial differences in informal support networks.

Analysis of Collaboration and Co-Citation Networks between Researchers Studying Violence Involving Women

Science.gov (United States)

Muñoz-Muñoz, Ana M.; Mirón-Valdivieso, M. Dolores

2017-01-01

Introduction: We analyse the collaboration and co-citation networks at the international level in scientific articles about violence against women. The aim is to identify who are writing about this subject, if they are women and/or men, who the most influential authors are and which institutions they belong to, and finally which authors are cited…

Attacks on public telephone networks: technologies and challenges

Science.gov (United States)

Kosloff, T.; Moore, Tyler; Keller, J.; Manes, Gavin W.; Shenoi, Sujeet

2003-09-01

Signaling System 7 (SS7) is vital to signaling and control in America's public telephone networks. This paper describes a class of attacks on SS7 networks involving the insertion of malicious signaling messages via compromised SS7 network components. Three attacks are discussed in detail: IAM flood attacks, redirection attacks and point code spoofing attacks. Depending on their scale of execution, these attacks can produce effects ranging from network congestion to service disruption. Methods for detecting these denial-of-service attacks and mitigating their effects are also presented.

Antenna analysis using neural networks

Science.gov (United States)

Smith, William T.

1992-01-01

Conventional computing schemes have long been used to analyze problems in electromagnetics (EM). The vast majority of EM applications require computationally intensive algorithms involving numerical integration and solutions to large systems of equations. The feasibility of using neural network computing algorithms for antenna analysis is investigated. The ultimate goal is to use a trained neural network algorithm to reduce the computational demands of existing reflector surface error compensation techniques. Neural networks are computational algorithms based on neurobiological systems. Neural nets consist of massively parallel interconnected nonlinear computational elements. They are often employed in pattern recognition and image processing problems. Recently, neural network analysis has been applied in the electromagnetics area for the design of frequency selective surfaces and beam forming networks. The backpropagation training algorithm was employed to simulate classical antenna array synthesis techniques. The Woodward-Lawson (W-L) and Dolph-Chebyshev (D-C) array pattern synthesis techniques were used to train the neural network. The inputs to the network were samples of the desired synthesis pattern. The outputs are the array element excitations required to synthesize the desired pattern. Once trained, the network is used to simulate the W-L or D-C techniques. Various sector patterns and cosecant-type patterns (27 total) generated using W-L synthesis were used to train the network. Desired pattern samples were then fed to the neural network. The outputs of the network were the simulated W-L excitations. A 20 element linear array was used. There were 41 input pattern samples with 40 output excitations (20 real parts, 20 imaginary). A comparison between the simulated and actual W-L techniques is shown for a triangular-shaped pattern. Dolph-Chebyshev is a different class of synthesis technique in that D-C is used for side lobe control as opposed to pattern

Cloudified Mobility and Bandwidth Prediction in Virtualized LTE Networks

NARCIS (Netherlands)

Zhao, Zongliang; Karimzadeh Motallebi Azar, Morteza; Braun, Torsten; Pras, Aiko; van den Berg, Hans Leo

Network Function Virtualization involves implementing network functions (e.g., virtualized LTE component) in software that can run on a range of industry standard server hardware, and can be migrated or instantiated on demand. A prediction service hosted on cloud infrastructures enables consumers to

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.

Using actor-network theory to study an educational situation: an ...

African Journals Online (AJOL)

Actor-network theory allows a researcher to analyse a complex social setting involving both human and non-human actors. An actor network can be used to model a dynamic and complex set of relationships between these actors. This article describes actor-network theory and shows how it was applied to study and model ...

European network for health technology assessment, EUnetHTA: planning, development, and implementation of a sustainable European network for health technology assessment

DEFF Research Database (Denmark)

Kristensen, Finn Børlum; Mäkelä, Marjukka; Neikter, Susanna Allgurin

2009-01-01

OBJECTIVES: The European network on Health Technology Assessment (EUnetHTA) aimed to produce tangible and practical results to be used in the various phases of health technology assessment and to establish a framework and processes to support this. This article presents the background, objectives......, and organization of EUnetHTA, which involved a total of sixty-four partner organizations. METHODS: Establishing an effective and sustainable structure for a transnational network involved many managerial, policy, and methodological tools, according to the objective of each task or Work Package. Transparency...... the use of HTA at national and regional levels. Responsiveness to political developments in Europe should be balanced with maintaining a high level of ambition to promote independent, evidence-based information and well-tested tools for best practice based on a strong network of HTA institutions....

Conversation Analysis on Social Networking Sites

OpenAIRE

Belkaroui , Rami; Faiz , Rim; Elkhlifi , Aymen

2014-01-01

International audience; With the explosion of Web 2.0, people are becoming more communicative through expansion of services and multi-platform applications such as microblogs, forums and social networks which establishes social and collabora-tive backgrounds. These services can be seen as very large information repository containing millions of text messages usually organized into complex networks involving users interacting with each other at specific times. Several works focused only to ret...

Solving local problems through local involvement? Experiences from Danish Urban Regeneration

DEFF Research Database (Denmark)

Jensen, Jesper Ole

-down approaches or massive public subsidies, the public regeneration schemes from the last decade have increasingly emphasized the need for involving local actors in the urban regeneration e.g. through partnerships, network building, involvement and participation of local actors and institutions, and financially...... agenda, and what can be learned from the development so far. Although ‘local involvement’ is a commonly used term in various urban regeneration programs, it can have many different meanings and implications. Therefore, the paper will discuss local involvement in the urban regeneration based on four...

Networks for prevention of violence: from utopia to action

Directory of Open Access Journals (Sweden)

Kathie Njaine

2006-06-01

Full Text Available This article aims to discuss the experience of networks for the protection of people exposed to situations of violence or prevention networks. It is based on the concept created by Castells, who defines the information age. This study is part of the investigation "Successful experiences in the prevention of violence", carried out by the Latin-American Center for Studies on Violence Jorge Careli/ENSP-IFF/Fiocruz, in cooperation with the Secretariat for Health Survey of the Ministry of Health. The article analyzes the possibilities and limitations in the construction of networks for the prevention of violence, seeking to understand the sense of actions and movements carried out in networks. The method we used is a case study of two network initiatives in the Southern region of the country. In terms of results, in face of the difficulties of working in networks, we found it to be necessary: to break with sectorial and vertical actions; to promote constant communication and interchange of information; to permanently train the professionals and persons involved in the network, incorporating them into the protective and preventive actions; and to promote the participation of wide social sectors. In conclusion, one can affirm that the construction of a protection network involves complex steps, looking to the same problem with new eyes and a new vision for planting solutions.

Complex Networks in Psychological Models

Science.gov (United States)

Wedemann, R. S.; Carvalho, L. S. A. V. D.; Donangelo, R.

We develop schematic, self-organizing, neural-network models to describe mechanisms associated with mental processes, by a neurocomputational substrate. These models are examples of real world complex networks with interesting general topological structures. Considering dopaminergic signal-to-noise neuronal modulation in the central nervous system, we propose neural network models to explain development of cortical map structure and dynamics of memory access, and unify different mental processes into a single neurocomputational substrate. Based on our neural network models, neurotic behavior may be understood as an associative memory process in the brain, and the linguistic, symbolic associative process involved in psychoanalytic working-through can be mapped onto a corresponding process of reconfiguration of the neural network. The models are illustrated through computer simulations, where we varied dopaminergic modulation and observed the self-organizing emergent patterns at the resulting semantic map, interpreting them as different manifestations of mental functioning, from psychotic through to normal and neurotic behavior, and creativity.

Functional brain networks underlying detection and integration of disconfirmatory evidence.

Science.gov (United States)

Lavigne, Katie M; Metzak, Paul D; Woodward, Todd S

2015-05-15

Processing evidence that disconfirms a prior interpretation is a fundamental aspect of belief revision, and has clear social and clinical relevance. This complex cognitive process requires (at minimum) an alerting stage and an integration stage, and in the current functional magnetic resonance imaging (fMRI) study, we used multivariate analysis methodology on two datasets in an attempt to separate these sequentially-activated cognitive stages and link them to distinct functional brain networks. Thirty-nine healthy participants completed one of two versions of an evidence integration experiment involving rating two consecutive animal images, both of which consisted of two intact images of animal faces morphed together at different ratios (e.g., 70/30 bird/dolphin followed by 10/90 bird/dolphin). The two versions of the experiment differed primarily in terms of stimulus presentation and timing, which facilitated functional interpretation of brain networks based on differences in the hemodynamic response shapes between versions. The data were analyzed using constrained principal component analysis for fMRI (fMRI-CPCA), which allows distinct, simultaneously active task-based networks to be separated, and these were interpreted using both temporal (task-based hemodynamic response shapes) and spatial (dominant brain regions) information. Three networks showed increased activity during integration of disconfirmatory relative to confirmatory evidence: (1) a network involved in alerting to the requirement to revise an interpretation, identified as the salience network (dorsal anterior cingulate cortex and bilateral insula); (2) a sensorimotor response-related network (pre- and post-central gyri, supplementary motor area, and thalamus); and (3) an integration network involving rostral prefrontal, orbitofrontal and posterior parietal cortex. These three networks were staggered in their peak activity (alerting, responding, then integrating), but at certain time points (e

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

Directory of Open Access Journals (Sweden)

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.

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.

A reverse engineering algorithm for neural networks, applied to the subthalamopallidal network of basal ganglia.

Science.gov (United States)

Floares, Alexandru George

2008-01-01

Modeling neural networks with ordinary differential equations systems is a sensible approach, but also very difficult. This paper describes a new algorithm based on linear genetic programming which can be used to reverse engineer neural networks. The RODES algorithm automatically discovers the structure of the network, including neural connections, their signs and strengths, estimates its parameters, and can even be used to identify the biophysical mechanisms involved. The algorithm is tested on simulated time series data, generated using a realistic model of the subthalamopallidal network of basal ganglia. The resulting ODE system is highly accurate, and results are obtained in a matter of minutes. This is because the problem of reverse engineering a system of coupled differential equations is reduced to one of reverse engineering individual algebraic equations. The algorithm allows the incorporation of common domain knowledge to restrict the solution space. To our knowledge, this is the first time a realistic reverse engineering algorithm based on linear genetic programming has been applied to neural networks.

Family and Friends: Which Types of Personal Relationships Go Together in a Network?

Science.gov (United States)

Rözer, Jesper; Mollenhorst, Gerald; Poortman, Anne-Rigt

We examine the link between family and personal networks. Using arguments about meeting opportunities, competition and social influence, we hypothesise how the presence of specific types of family members (i.e., a partner, children, parents and siblings) and non-family members (i.e., friends, neighbours and colleagues) in the network mutually affect one another. In addition, we propose that-beyond their mere presence-the active role of family members in the network strongly affects the presence of non-family members in the network. Data from the third wave of the Survey on the Social Networks of the Dutch, collected in 2012 and 2013, show that active involvement is of key importance; more than merely having family members present in one's personal network, the active involvement of specific types of family members in the personal network is associated with having disproportionally more other family members and having somewhat fewer non-family members in the network.

Betweenness in time dependent networks

International Nuclear Information System (INIS)

Alsayed, Ahmad; Higham, Desmond J.

2015-01-01

The concept of betweenness has given rise to a very useful class of network centrality measures. Loosely, betweenness quantifies the level of importance of a node in terms of its propensity to act as an intermediary when messages are passed around the network. In this work we generalize a walk-based betweenness measure to the case of time-dependent networks, such as those arising in telecommunications and on-line social media. We also introduce a new kind of betweenness measure, temporal betweenness, which quantifies the importance of a time-point. We illustrate the effectiveness of these new measures on synthetic examples, and also give results on real data sets involving voice call, email and Twitter

Triangular clustering in document networks

Energy Technology Data Exchange (ETDEWEB)

Cheng Xueqi; Ren Fuxin [Institute of Computing Technology, Chinese Academy of Sciences, Beijing 100190 (China); Zhou Shi [Department of Computer Science, University College London, Malet Place, London WC1E 6BT (United Kingdom); Hu Maobin [School of Engineering Science, University of Science and Technology of China, Hefei 230026 (China)], E-mail: cxq@ict.ac.cn, E-mail: renfuxin@software.ict.ac.cn, E-mail: s.zhou@adastral.ucl.ac.uk, E-mail: humaobin@ustc.edu.cn

2009-03-15

Document networks have the characteristic that a document node, e.g. a webpage or an article, carries meaningful content. Properties of document networks are not only affected by topological connectivity between nodes, but are also strongly influenced by the semantic relation between the content of the nodes. We observed that document networks have a large number of triangles and a high value clustering coefficient. Also there is a strong correlation between the probability of formation of a triangle and the content similarity among the three nodes involved. We propose the degree-similarity product (DSP) model, which well reproduces these properties. The model achieves this by using a preferential attachment mechanism that favours the linkage between nodes that are both popular and similar. This work is a step forward towards a better understanding of the structure and evolution of document networks.

SOCIAL NETWORKS AND INTERPERSONAL COMMUNICATION

Directory of Open Access Journals (Sweden)

Veronica GHEORGHIȚĂ

2014-11-01

Full Text Available Social networks visible influence people's ability to interact and communicate. Extending social circles by establishing virtual links involves a number of positive aspects such as: instant access to options for interaction, sharing of information to large communities of people, intensification of acts of communication, high levels of feedback and trust with people with whom we communicate. On the other hand, social networks adversely affects communication by decreasing the interaction face to face, by imposing superficial communications experiences, grammatical and spelling erosion of the language. Therefore, the study aims to capture the spread of social networks, their use and impact on interpersonal communication. More specifically, they look for the answer to the question: what is the nature of interpersonal communication that is found on social networking sites: personal, emotional, private or shared, informal, and public?

System-wide analysis reveals a complex network of tumor-fibroblast interactions involved in tumorigenicity.

Directory of Open Access Journals (Sweden)

Megha Rajaram

Full Text Available Many fibroblast-secreted proteins promote tumorigenicity, and several factors secreted by cancer cells have in turn been proposed to induce these proteins. It is not clear whether there are single dominant pathways underlying these interactions or whether they involve multiple pathways acting in parallel. Here, we identified 42 fibroblast-secreted factors induced by breast cancer cells using comparative genomic analysis. To determine what fraction was active in promoting tumorigenicity, we chose five representative fibroblast-secreted factors for in vivo analysis. We found that the majority (three out of five played equally major roles in promoting tumorigenicity, and intriguingly, each one had distinct effects on the tumor microenvironment. Specifically, fibroblast-secreted amphiregulin promoted breast cancer cell survival, whereas the chemokine CCL7 stimulated tumor cell proliferation while CCL2 promoted innate immune cell infiltration and angiogenesis. The other two factors tested had minor (CCL8 or minimally (STC1 significant effects on the ability of fibroblasts to promote tumor growth. The importance of parallel interactions between fibroblasts and cancer cells was tested by simultaneously targeting fibroblast-secreted amphiregulin and the CCL7 receptor on cancer cells, and this was significantly more efficacious than blocking either pathway alone. We further explored the concept of parallel interactions by testing the extent to which induction of critical fibroblast-secreted proteins could be achieved by single, previously identified, factors produced by breast cancer cells. We found that although single factors could induce a subset of genes, even combinations of factors failed to induce the full repertoire of functionally important fibroblast-secreted proteins. Together, these results delineate a complex network of tumor-fibroblast interactions that act in parallel to promote tumorigenicity and suggest that effective anti

Complex Network Theory Applied to the Growth of Kuala Lumpur's Public Urban Rail Transit Network.

Science.gov (United States)

Ding, Rui; Ujang, Norsidah; Hamid, Hussain Bin; Wu, Jianjun

2015-01-01

Recently, the number of studies involving complex network applications in transportation has increased steadily as scholars from various fields analyze traffic networks. Nonetheless, research on rail network growth is relatively rare. This research examines the evolution of the Public Urban Rail Transit Networks of Kuala Lumpur (PURTNoKL) based on complex network theory and covers both the topological structure of the rail system and future trends in network growth. In addition, network performance when facing different attack strategies is also assessed. Three topological network characteristics are considered: connections, clustering and centrality. In PURTNoKL, we found that the total number of nodes and edges exhibit a linear relationship and that the average degree stays within the interval [2.0488, 2.6774] with heavy-tailed distributions. The evolutionary process shows that the cumulative probability distribution (CPD) of degree and the average shortest path length show good fit with exponential distribution and normal distribution, respectively. Moreover, PURTNoKL exhibits clear cluster characteristics; most of the nodes have a 2-core value, and the CPDs of the centrality's closeness and betweenness follow a normal distribution function and an exponential distribution, respectively. Finally, we discuss four different types of network growth styles and the line extension process, which reveal that the rail network's growth is likely based on the nodes with the biggest lengths of the shortest path and that network protection should emphasize those nodes with the largest degrees and the highest betweenness values. This research may enhance the networkability of the rail system and better shape the future growth of public rail networks.

Comparative Analysis of Different Protocols to Manage Large Scale Networks

OpenAIRE

Anil Rao Pimplapure; Dr Jayant Dubey; Prashant Sen

2013-01-01

In recent year the numbers, complexity and size is increased in Large Scale Network. The best example of Large Scale Network is Internet, and recently once are Data-centers in Cloud Environment. In this process, involvement of several management tasks such as traffic monitoring, security and performance optimization is big task for Network Administrator. This research reports study the different protocols i.e. conventional protocols like Simple Network Management Protocol and newly Gossip bas...

Heat exchanger networks design with constraints

International Nuclear Information System (INIS)

Amidpur, M.; Zoghi, A.; Nasiri, N.

2000-01-01

So far there have been two approaches to the problem of heat recovery system design where stream matching constraints exist. The first approach involves mathematical techniques for solving the combinational problem taking due recognition of the constraints. These methodologies are now efficient, still suffer from the problem of taking a significant amount of control and direction away from the designer. The second approach based upon so called pinch technology and involves the use of adaptation of standard problem table algorithm. Unfortunately, the proposed methodologies are not very easy to understand, therefore they fail to provide the insight and generally associated with these approaches. Here, a new pinch based methodology is presented. In this method, we modified the traditional numerical targeting procedure-problem table algorithm which is stream cascade table. Unconstrained groups are established by using of artificial intelligence method such that they have minimum utility consumption among different alternatives. Each group is an individual network, therefore, traditional optimization, used in pinch technology, should be employed. By transferring energy between groups heat recovery can be maximized, then each group designs individually and finally networks combine together. One of the advantages of using this method is simple targeting and easy networks-design. Besides the approach has the potential using of new network design methods such as dual temperature approach, flexible pinch design, pseudo pinch design. It is hoped that this methodology provides insight easy network design

Border trees of complex networks

International Nuclear Information System (INIS)

Villas Boas, Paulino R; Rodrigues, Francisco A; Travieso, Gonzalo; Fontoura Costa, Luciano da

2008-01-01

The comprehensive characterization of the structure of complex networks is essential to understand the dynamical processes which guide their evolution. The discovery of the scale-free distribution and the small-world properties of real networks were fundamental to stimulate more realistic models and to understand important dynamical processes related to network growth. However, the properties of the network borders (nodes with degree equal to 1), one of its most fragile parts, remained little investigated and understood. The border nodes may be involved in the evolution of structures such as geographical networks. Here we analyze the border trees of complex networks, which are defined as the subgraphs without cycles connected to the remainder of the network (containing cycles) and terminating into border nodes. In addition to describing an algorithm for identification of such tree subgraphs, we also consider how their topological properties can be quantified in terms of their depth and number of leaves. We investigate the properties of border trees for several theoretical models as well as real-world networks. Among the obtained results, we found that more than half of the nodes of some real-world networks belong to the border trees. A power-law with cut-off was observed for the distribution of the depth and number of leaves of the border trees. An analysis of the local role of the nodes in the border trees was also performed

Networks and Fault Lines: Understanding the role of housing associations in neighbourhood regeneration: a network governance perspective

Directory of Open Access Journals (Sweden)

Gerard van Bortel

2016-03-01

Full Text Available The changing role of housing associations in neighbourhood regeneration This study aims to increase our understanding of the role of social housing organisations in neighbourhood regeneration governance networks, in order to enhance the performance and outcomes of these networks. Our understanding of how governance networks work is still limited, especially concerning the role of non-state actors like housing associations. Hierarchical government steering is increasingly mixed with market mechanisms and networked forms of decision-making. These shifts in governance often result in more complex decision-making that can easily lead to deadlocks, low-quality outcomes and ambiguous anchorage of democratic principles. Neighbourhood regeneration takes place in rather exceptional governance networks. The organisations involved, and the problems at hand, are place-based. Actors, like housing associations, local authorities and community organisations, are more or less ‘locked’ into the regeneration network and need to collaborate in order to solve the problems. The complexity of neighbourhood renewal processes is often very high, due to the large number of actors involved, and the combination of insufficient housing quality, lack of affordability and supply, along with social and economic problems that need to be addressed. Housing associations focus on the delivery of affordable decent quality housing; but, in many countries—like the Netherlands and England—these organisations also have an important role in neighbourhood regeneration. Housing associations are non-profit organisations that provide housing for low and moderate-income households. They operate largely autonomously from the government, although they are often strongly regulated and dependent on government subsidies. Housing associations in England and the Netherlands share many organisational characteristics and hybrid third-sector values emerging from the need to balance social and

Quantum-Mechanical Calculations on Molecular Substructures Involved in Nanosystems

Directory of Open Access Journals (Sweden)

Beata Szefler

2014-09-01

Full Text Available In this review article, four ideas are discussed: (a aromaticity of fullerenes patched with flowers of 6-and 8-membered rings, optimized at the HF and DFT levels of theory, in terms of HOMA and NICS criteria; (b polybenzene networks, from construction to energetic and vibrational spectra computations; (c quantum-mechanical calculations on the repeat units of various P-type crystal networks and (d construction and stability evaluation, at DFTB level of theory, of some exotic allotropes of diamond D5, involved in hyper-graphenes. The overall conclusion was that several of the yet hypothetical molecular nanostructures herein described are serious candidates to the status of real molecules.

Electronic Networking as an Avenue of Enhanced Professional Interchange.

Science.gov (United States)

Ratcliff, James L.

Electronic networking is communication between two or more people that involves one or more telecommunications media. There is electronic networking software available for most computers, including IBM, Apple, and Radio Shack personal computers. Depending upon the sophistication of the hardware and software used, individuals and groups can…

Ancestral trees for modeling stem cell lineages genetically rather than functionally: understanding mutation accumulation and distinguishing the restrictive cancer stem cell propagation theory and the unrestricted cell propagation theory of human tumorigenesis.

Science.gov (United States)

Shibata, Darryl K; Kern, Scott E

2008-01-01

Cancer stem cells either could be rare or common in tumors, constituting the major distinction between the two fundamentally opposed theoretical models of tumor progression: A newer and restrictive stem cell propagation model, in which the stem cells are a small and special minority of the tumor cells, and a standard older model, an unrestricted cell proliferation theory, in which many or most tumor cells are capable of indefinite generations of cell division. Stem cells of tumors are difficult to quantitate using functional assays, and the validity of the most common assays is seriously questioned. Nonetheless, stem cells are an essential component of any tumorigenesis model. Alternative approaches to studying tumor stem cells should be explored. Cell populations can be conceived of as having a genealogy, a relationship of cells to their ancestral lineage, from the zygote to the adult cells or neoplasms. Models using ancestral trees thus offer an anatomic and genetic means to "observe" stem cells independent of artificial conditions. Ancestral trees broaden our attention backward along a lineage, to the zygote stage, and thereby add insight into how the mutations of tumors accumulate. It is possible that a large fraction of mutations in a tumor originate from normal, endogenous, replication errors (nearly all being passenger mutations) occurring prior to the emergence of the first transformed cell. Trees can be constructed from experimental measurements - molecular clocks - of real human tissues and tumors. Detailed analysis of single-cell methylation patterns, heritable yet slightly plastic, now can provide this information in the necessary depth. Trees based on observations of molecular clocks may help us to distinguish between competing theories regarding the proliferative properties among cells of actual human tumors, to observe subtle and difficult phenomena such as the extinction of stem lineages, and to address the origins and rates of mutations in various

Comparison of crisp and fuzzy character networks in handwritten word recognition

Science.gov (United States)

Gader, Paul; Mohamed, Magdi; Chiang, Jung-Hsien

1992-01-01

Experiments involving handwritten word recognition on words taken from images of handwritten address blocks from the United States Postal Service mailstream are described. The word recognition algorithm relies on the use of neural networks at the character level. The neural networks are trained using crisp and fuzzy desired outputs. The fuzzy outputs were defined using a fuzzy k-nearest neighbor algorithm. The crisp networks slightly outperformed the fuzzy networks at the character level but the fuzzy networks outperformed the crisp networks at the word level.

Social network extraction based on Web: 1. Related superficial methods

Science.gov (United States)

Khairuddin Matyuso Nasution, Mahyuddin

2018-01-01

Often the nature of something affects methods to resolve the related issues about it. Likewise, methods to extract social networks from the Web, but involve the structured data types differently. This paper reveals several methods of social network extraction from the same sources that is Web: the basic superficial method, the underlying superficial method, the description superficial method, and the related superficial methods. In complexity we derive the inequalities between methods and so are their computations. In this case, we find that different results from the same tools make the difference from the more complex to the simpler: Extraction of social network by involving co-occurrence is more complex than using occurrences.

Network effects in environmental justice struggles: An investigation of conflicts between mining companies and civil society organizations from a network perspective.

Science.gov (United States)

Aydin, Cem Iskender; Ozkaynak, Begum; Rodríguez-Labajos, Beatriz; Yenilmez, Taylan

2017-01-01

This paper examines conflicts that occur between mining companies and civil society organizations (CSOs) around the world and offers an innovative analysis of mining conflicts from a social network perspective. The analysis showed that, as the number of CSOs involved in a conflict increased, its outcome was more likely to be perceived as a success in terms of environmental justice (EJ); if a CSO was connected to other central CSOs, the average perception of EJ success was likely to increase; and as network distance between two conflicts increased (or decreased), they were more likely to lead to different (or similar) EJ outcomes. Such network effects in mining conflicts have policy implications for EJ movements. It would be a strategic move on the part of successful CSOs to become involved in other major conflicts and disseminate information about how they achieved greater EJ success.

A framework for interpreting functional networks in schizophrenia

Directory of Open Access Journals (Sweden)

Peter eWilliamson

2012-06-01

Full Text Available Some promising genetic correlates of schizophrenia have emerged in recent years but none explain more than a small fraction of cases. The challenge of our time is to characterize the neuronal networks underlying schizophrenia and other neuropsychiatric illnesses. It has been proposed that schizophrenia arises from a uniquely human brain network associated with directed effort including the dorsal anterior and posterior cingulate cortex, auditory cortex, and hippocampus and while mood disorders arise from a different brain network associated with emotional encoding including the ventral anterior cingulate cortex, orbital frontal cortex, and amygdala. Both interact with a representation network including the frontal and temporal poles and the fronto-insular cortex, allowing the representation of the thoughts, feelings and actions of self and others. This paper reviews recent morphological and functional literature in light of the proposed networks underlying these disorders. It is suggested that there is considerable support for the involvement of the directed effort network in schizophrenia from studies of brain structure with voxel-based morphometry (VBM and diffusion tensor imaging (DTI. While early studies of resting brain networks are inconclusive, functional magnetic resonance imaging imaging (fMRI studies of task-related networks clearly implicate these regions. In keeping with the model, functional deficits in regions associated with directed effort and self-monitoring are associated with structural anomalies in action-related regions in schizophrenic patients. VBM, DTI, fMRI studies of mood disordered patients support the involvement of a different network associated with emotional encoding. The distinction between disorders is enhanced by combining structural and functional data. It is concluded that brain networks associated with directed effort are particularly vulnerable to failure in the human brain leading to the symptoms of

Network Analysis of Human Genes Influencing Susceptibility to Mycobacterial Infections

Science.gov (United States)

Lipner, Ettie M.; Garcia, Benjamin J.; Strong, Michael

2016-01-01

Tuberculosis and nontuberculous mycobacterial infections constitute a high burden of pulmonary disease in humans, resulting in over 1.5 million deaths per year. Building on the premise that genetic factors influence the instance, progression, and defense of infectious disease, we undertook a systems biology approach to investigate relationships among genetic factors that may play a role in increased susceptibility or control of mycobacterial infections. We combined literature and database mining with network analysis and pathway enrichment analysis to examine genes, pathways, and networks, involved in the human response to Mycobacterium tuberculosis and nontuberculous mycobacterial infections. This approach allowed us to examine functional relationships among reported genes, and to identify novel genes and enriched pathways that may play a role in mycobacterial susceptibility or control. Our findings suggest that the primary pathways and genes influencing mycobacterial infection control involve an interplay between innate and adaptive immune proteins and pathways. Signaling pathways involved in autoimmune disease were significantly enriched as revealed in our networks. Mycobacterial disease susceptibility networks were also examined within the context of gene-chemical relationships, in order to identify putative drugs and nutrients with potential beneficial immunomodulatory or anti-mycobacterial effects. PMID:26751573

Cortical networks involved in visual awareness independent of visual attention

OpenAIRE

Webb, Taylor W.; Igelström, Kajsa M.; Schurger, Aaron; Graziano, Michael S. A.

2016-01-01

Do specific areas of the brain participate in subjective visual experience? We measured brain activity in humans using fMRI. Participants were aware of a visual stimulus in one condition and unaware of it in another condition. The two conditions were balanced for their effect on visual attention. Specific brain areas were more active in the aware than in the unaware condition, suggesting they were involved in subjective awareness independent of attention. The largest cluster of activity was f...

From Isolated to Networked: A Paradigmatic Shift in Mitochondrial Physiology

OpenAIRE

Aon, Miguel A.

2010-01-01

A new paradigm of mitochondrial function in networks is emerging which includes, without undermining, the glorious and still useful paradigm of the isolated mitochondrion. The mitochondrial network paradigm introduces new concepts, tools, and analytical techniques. Among them is that mitochondrial function in networks exhibits interdependence and multiplicative effects based on synchronization mechanisms, which involve communication between mitochondrial neighbors. The collective dynamics of ...

Networked traffic state estimation involving mixed fixed-mobile sensor data using Hamilton-Jacobi equations

KAUST Repository

Canepa, Edward S.; Claudel, Christian G.

2017-01-01

Nowadays, traffic management has become a challenge for urban areas, which are covering larger geographic spaces and facing the generation of different kinds of traffic data. This article presents a robust traffic estimation framework for highways modeled by a system of Lighthill Whitham Richards equations that is able to assimilate different sensor data available. We first present an equivalent formulation of the problem using a Hamilton–Jacobi equation. Then, using a semi-analytic formula, we show that the model constraints resulting from the Hamilton–Jacobi equation are linear ones. We then pose the problem of estimating the traffic density given incomplete and inaccurate traffic data as a Mixed Integer Program. We then extend the density estimation framework to highway networks with any available data constraint and modeling junctions. Finally, we present a travel estimation application for a small network using real traffic measurements obtained obtained during Mobile Century traffic experiment, and comparing the results with ground truth data.

Neural networks involved in learning lexical-semantic and syntactic information in a second language.

Science.gov (United States)

Mueller, Jutta L; Rueschemeyer, Shirley-Ann; Ono, Kentaro; Sugiura, Motoaki; Sadato, Norihiro; Nakamura, Akinori

2014-01-01

The present study used functional magnetic resonance imaging (fMRI) to investigate the neural correlates of language acquisition in a realistic learning environment. Japanese native speakers were trained in a miniature version of German prior to fMRI scanning. During scanning they listened to (1) familiar sentences, (2) sentences including a novel sentence structure, and (3) sentences containing a novel word while visual context provided referential information. Learning-related decreases of brain activation over time were found in a mainly left-hemispheric network comprising classical frontal and temporal language areas as well as parietal and subcortical regions and were largely overlapping for novel words and the novel sentence structure in initial stages of learning. Differences occurred at later stages of learning during which content-specific activation patterns in prefrontal, parietal and temporal cortices emerged. The results are taken as evidence for a domain-general network supporting the initial stages of language learning which dynamically adapts as learners become proficient.

Networked traffic state estimation involving mixed fixed-mobile sensor data using Hamilton-Jacobi equations

KAUST Repository

Canepa, Edward S.

2017-06-19

Nowadays, traffic management has become a challenge for urban areas, which are covering larger geographic spaces and facing the generation of different kinds of traffic data. This article presents a robust traffic estimation framework for highways modeled by a system of Lighthill Whitham Richards equations that is able to assimilate different sensor data available. We first present an equivalent formulation of the problem using a Hamilton–Jacobi equation. Then, using a semi-analytic formula, we show that the model constraints resulting from the Hamilton–Jacobi equation are linear ones. We then pose the problem of estimating the traffic density given incomplete and inaccurate traffic data as a Mixed Integer Program. We then extend the density estimation framework to highway networks with any available data constraint and modeling junctions. Finally, we present a travel estimation application for a small network using real traffic measurements obtained obtained during Mobile Century traffic experiment, and comparing the results with ground truth data.

Adaptive nonlinear control using input normalized neural networks

International Nuclear Information System (INIS)

Leeghim, Henzeh; Seo, In Ho; Bang, Hyo Choong

2008-01-01

An adaptive feedback linearization technique combined with the neural network is addressed to control uncertain nonlinear systems. The neural network-based adaptive control theory has been widely studied. However, the stability analysis of the closed-loop system with the neural network is rather complicated and difficult to understand, and sometimes unnecessary assumptions are involved. As a result, unnecessary assumptions for stability analysis are avoided by using the neural network with input normalization technique. The ultimate boundedness of the tracking error is simply proved by the Lyapunov stability theory. A new simple update law as an adaptive nonlinear control is derived by the simplification of the input normalized neural network assuming the variation of the uncertain term is sufficiently small

A Network Thermodynamic Approach to Compartmental Analysis

Science.gov (United States)

Mikulecky, D. C.; Huf, E. G.; Thomas, S. R.

1979-01-01

We introduce a general network thermodynamic method for compartmental analysis which uses a compartmental model of sodium flows through frog skin as an illustrative example (Huf and Howell, 1974a). We use network thermodynamics (Mikulecky et al., 1977b) to formulate the problem, and a circuit simulation program (ASTEC 2, SPICE2, or PCAP) for computation. In this way, the compartment concentrations and net fluxes between compartments are readily obtained for a set of experimental conditions involving a square-wave pulse of labeled sodium at the outer surface of the skin. Qualitative features of the influx at the outer surface correlate very well with those observed for the short circuit current under another similar set of conditions by Morel and LeBlanc (1975). In related work, the compartmental model is used as a basis for simulation of the short circuit current and sodium flows simultaneously using a two-port network (Mikulecky et al., 1977a, and Mikulecky et al., A network thermodynamic model for short circuit current transients in frog skin. Manuscript in preparation; Gary-Bobo et al., 1978). The network approach lends itself to computation of classic compartmental problems in a simple manner using circuit simulation programs (Chua and Lin, 1975), and it further extends the compartmental models to more complicated situations involving coupled flows and non-linearities such as concentration dependencies, chemical reaction kinetics, etc. PMID:262387

Optical Access Networks

Science.gov (United States)

Zheng, Jun; Ansari, Nirwan

2005-06-01

are now underway this hot area. The purpose of this feature issue is to expose the networking community to the latest research breakthroughs and progresses in the area of optical access networks. This feature issue aims to present a collection of papers that focus on the state-of-the-art research in various networking aspects of optical access networks. Original papers are solicited from all researchers involved in area of optical access networks. Topics of interest include but not limited to: Optical access network architectures and protocols Passive optical networks (BPON, EPON, GPON, etc.) Active optical networks Multiple access control Multiservices and QoS provisioning Network survivability Field trials and standards Performance modeling and analysis

Proceedings of a Conference on Telecommunication Technologies, Networkings and Libraries

Science.gov (United States)

Knight, N. K.

1981-12-01

Current and developing technologies for digital transmission of image data likely to have an impact on the operations of libraries and information centers or provide support for information networking are reviewed. Technologies reviewed include slow scan television, teleconferencing, and videodisc technology and standards development for computer network interconnection through hardware and software, particularly packet switched networks computer network protocols for library and information service applications, the structure of a national bibliographic telecommunications network; and the major policy issues involved in the regulation or deregulation of the common communications carriers industry.

Genetic networks and soft computing.

Science.gov (United States)

Mitra, Sushmita; Das, Ranajit; Hayashi, Yoichi

2011-01-01

The analysis of gene regulatory networks provides enormous information on various fundamental cellular processes involving growth, development, hormone secretion, and cellular communication. Their extraction from available gene expression profiles is a challenging problem. Such reverse engineering of genetic networks offers insight into cellular activity toward prediction of adverse effects of new drugs or possible identification of new drug targets. Tasks such as classification, clustering, and feature selection enable efficient mining of knowledge about gene interactions in the form of networks. It is known that biological data is prone to different kinds of noise and ambiguity. Soft computing tools, such as fuzzy sets, evolutionary strategies, and neurocomputing, have been found to be helpful in providing low-cost, acceptable solutions in the presence of various types of uncertainties. In this paper, we survey the role of these soft methodologies and their hybridizations, for the purpose of generating genetic networks.

[Network structures in biological systems].

Science.gov (United States)

Oleskin, A V

2013-01-01

Network structures (networks) that have been extensively studied in the humanities are characterized by cohesion, a lack of a central control unit, and predominantly fractal properties. They are contrasted with structures that contain a single centre (hierarchies) as well as with those whose elements predominantly compete with one another (market-type structures). As far as biological systems are concerned, their network structures can be subdivided into a number of types involving different organizational mechanisms. Network organization is characteristic of various structural levels of biological systems ranging from single cells to integrated societies. These networks can be classified into two main subgroups: (i) flat (leaderless) network structures typical of systems that are composed of uniform elements and represent modular organisms or at least possess manifest integral properties and (ii) three-dimensional, partly hierarchical structures characterized by significant individual and/or intergroup (intercaste) differences between their elements. All network structures include an element that performs structural, protective, and communication-promoting functions. By analogy to cell structures, this element is denoted as the matrix of a network structure. The matrix includes a material and an immaterial component. The material component comprises various structures that belong to the whole structure and not to any of its elements per se. The immaterial (ideal) component of the matrix includes social norms and rules regulating network elements' behavior. These behavioral rules can be described in terms of algorithms. Algorithmization enables modeling the behavior of various network structures, particularly of neuron networks and their artificial analogs.

Dynamic hydro-climatic networks in pristine and regulated rivers

Science.gov (United States)

Botter, G.; Basso, S.; Lazzaro, G.; Doulatyari, B.; Biswal, B.; Schirmer, M.; Rinaldo, A.

2014-12-01

Flow patterns observed at-a-station are the dynamical byproduct of a cascade of processes involving different compartments of the hydro-climatic network (e.g., climate, rainfall, soil, vegetation) that regulates the transformation of rainfall into streamflows. In complex branching rivers, flow regimes result from the heterogeneous arrangement around the stream network of multiple hydrologic cascades that simultaneously occur within distinct contributing areas. As such, flow regimes are seen as the integrated output of a complex "network of networks", which can be properly characterized by its degree of temporal variability and spatial heterogeneity. Hydrologic networks that generate river flow regimes are dynamic in nature. In pristine rivers, the time-variance naturally emerges at multiple timescales from climate variability (namely, seasonality and inter-annual fluctuations), implying that the magnitude (and the features) of the water flow between two nodes may be highly variable across different seasons and years. Conversely, the spatial distribution of river flow regimes within pristine rivers involves scale-dependent transport features, as well as regional climatic and soil use gradients, which in small and meso-scale catchments (A guarantee quite uniform flow regimes and high spatial correlations. Human-impacted rivers, instead, constitute hybrid networks where observed spatio-temporal patterns are dominated by anthropogenic shifts, such as landscape alterations and river regulation. In regulated rivers, the magnitude and the features of water flows from node to node may change significantly through time due to damming and withdrawals. However, regulation may impact river regimes in a spatially heterogeneous manner (e.g. in localized river reaches), with a significant decrease of spatial correlations and network connectivity. Provided that the spatial and temporal dynamics of flow regimes in complex rivers may strongly impact important biotic processes

Inferring the gene network underlying the branching of tomato inflorescence.

Directory of Open Access Journals (Sweden)

Laura Astola

Full Text Available The architecture of tomato inflorescence strongly affects flower production and subsequent crop yield. To understand the genetic activities involved, insight into the underlying network of genes that initiate and control the sympodial growth in the tomato is essential. In this paper, we show how the structure of this network can be derived from available data of the expressions of the involved genes. Our approach starts from employing biological expert knowledge to select the most probable gene candidates behind branching behavior. To find how these genes interact, we develop a stepwise procedure for computational inference of the network structure. Our data consists of expression levels from primary shoot meristems, measured at different developmental stages on three different genotypes of tomato. With the network inferred by our algorithm, we can explain the dynamics corresponding to all three genotypes simultaneously, despite their apparent dissimilarities. We also correctly predict the chronological order of expression peaks for the main hubs in the network. Based on the inferred network, using optimal experimental design criteria, we are able to suggest an informative set of experiments for further investigation of the mechanisms underlying branching behavior.

Bridging humans via agent networks

International Nuclear Information System (INIS)

Ishida, Toru

1994-01-01

Recent drastic advance in telecommunication networks enabled the human organization of new class, teleorganization, which differ from any existing organization in that the organization which is easy to create by using telecommunication networks is virtual and remote, that people can join multiple organizations simultaneously, and that the organization can involve people who may not know each other. In order to enjoy the recent advance in telecommunication, the agent networks to help people organize themselves are needed. In this paper, an architecture of agent networks, in which each agent learns the preference or the utility functioin of the owner, and acts on behalf of the owner in maintaining the organization, is proposed. When an agent networks supports a human organization, the conventional human interface is divided into personal and social interfaces. The functionalities of the social interface in teleconferencing and telelearning were investigated. In both cases, the existence of B-ISDN is assumed, and the extension to the business meeting scheduling using personal handy phone (PHS) networks with personal digital assistant (PDA) terminals is expected. These circumstances are described. Mutual selection protocols (MSP) and their dynamic properties are explained. (K.I.)

Chinese immigrant entrepreneurs’ involvement in internationalization and innovation: Three Canadian cases

DEFF Research Database (Denmark)

Zhang, Xiaotian; Vissak, Tiia

2014-01-01

that these immigrants’ experience of doing business in China and Canada, their network relationships and knowledge of these markets quickened their firms’ internationalization considerably. Moreover, these firms became active in product or service innovation as the case immigrants also involved other immigrants...

Phase separation in living micellar networks

Science.gov (United States)

Cristobal, G.; Rouch, J.; Curély, J.; Panizza, P.

We present a lattice model based on two n→0 spin vectors, capable of treating the thermodynamics of living networks in micellar solutions at any surfactant concentration. We establish an isomorphism between the coupling constants in the two spin vector Hamiltonian and the surfactant energies involved in the micellar situation. Solving this Hamiltonian in the mean-field approximation allows one to calculate osmotic pressure, aggregation number, free end and cross-link densities at any surfactant concentration. We derive a phase diagram, including changes in topology such as the transition between spheres and rods and between saturated and unsaturated networks. A phase separation can be found between a saturated network and a dilute solution composed of long flexible micelles or a saturated network and a solution of spherical micelles.

Complex Network Theory Applied to the Growth of Kuala Lumpur's Public Urban Rail Transit Network.

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Rui Ding

Full Text Available Recently, the number of studies involving complex network applications in transportation has increased steadily as scholars from various fields analyze traffic networks. Nonetheless, research on rail network growth is relatively rare. This research examines the evolution of the Public Urban Rail Transit Networks of Kuala Lumpur (PURTNoKL based on complex network theory and covers both the topological structure of the rail system and future trends in network growth. In addition, network performance when facing different attack strategies is also assessed. Three topological network characteristics are considered: connections, clustering and centrality. In PURTNoKL, we found that the total number of nodes and edges exhibit a linear relationship and that the average degree stays within the interval [2.0488, 2.6774] with heavy-tailed distributions. The evolutionary process shows that the cumulative probability distribution (CPD of degree and the average shortest path length show good fit with exponential distribution and normal distribution, respectively. Moreover, PURTNoKL exhibits clear cluster characteristics; most of the nodes have a 2-core value, and the CPDs of the centrality's closeness and betweenness follow a normal distribution function and an exponential distribution, respectively. Finally, we discuss four different types of network growth styles and the line extension process, which reveal that the rail network's growth is likely based on the nodes with the biggest lengths of the shortest path and that network protection should emphasize those nodes with the largest degrees and the highest betweenness values. This research may enhance the networkability of the rail system and better shape the future growth of public rail networks.

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

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

2001-01-01

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

Evolutionary algorithms for mobile ad hoc networks

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Dorronsoro, Bernabé; Danoy, Grégoire; Pigné, Yoann; Bouvry, Pascal

2014-01-01

Describes how evolutionary algorithms (EAs) can be used to identify, model, and minimize day-to-day problems that arise for researchers in optimization and mobile networking. Mobile ad hoc networks (MANETs), vehicular networks (VANETs), sensor networks (SNs), and hybrid networks—each of these require a designer’s keen sense and knowledge of evolutionary algorithms in order to help with the common issues that plague professionals involved in optimization and mobile networking. This book introduces readers to both mobile ad hoc networks and evolutionary algorithms, presenting basic concepts as well as detailed descriptions of each. It demonstrates how metaheuristics and evolutionary algorithms (EAs) can be used to help provide low-cost operations in the optimization process—allowing designers to put some “intelligence” or sophistication into the design. It also offers efficient and accurate information on dissemination algorithms topology management, and mobility models to address challenges in the ...

Scottish Stroke Research Network: the first three years.

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McCormick, K; Langhorne, P; Graham, F E J; McFarlane, C

2010-08-01

Research networks were introduced in the UK to facilitate and improve clinical research and stroke was seen as a priority topic for local research network development. The Scottish Stroke Research Network (SSRN) is one of 11 stroke research networks in the UK. In this article we review the progress of the Scottish Stroke Research Network in the three years since inception. Between 2006-2009 the number of active hospital research sites has increased from 10 to 22 expanding to involve 20 stroke research nurses. There was a corresponding 58% increase in recruitment of participants into stroke studies, from 376 in 2006/07 to 594 in 2008/09. The majority (17/20) of our current studies are interventional. Data from one of these, the CLOTs trial (Clots in Legs Or sTocking after Stroke), demonstrates that the annual recruitment in Scotland increased from a median of 94 (range 6-122) patients per year in the six years before the SSRN, to 140 (135-158) patients per year after SSRN involvement. We currently screen about 50% of Scottish stroke patients and approximately 5% of Scottish stroke patients are participating in research studies that we support. The SSRN has made good progress in the first three years. Increasing the recruitment of screened patients remains a challenge.

Understanding emotion with brain networks.

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Pessoa, Luiz

2018-02-01

Emotional processing appears to be interlocked with perception, cognition, motivation, and action. These interactions are supported by the brain's large-scale non-modular anatomical and functional architectures. An important component of this organization involves characterizing the brain in terms of networks. Two aspects of brain networks are discussed: brain networks should be considered as inherently overlapping (not disjoint) and dynamic (not static). Recent work on multivariate pattern analysis shows that affective dimensions can be detected in the activity of distributed neural systems that span cortical and subcortical regions. More broadly, the paper considers how we should think of causation in complex systems like the brain, so as to inform the relationship between emotion and other mental aspects, such as cognition.

Acupuncture analgesia involves modulation of pain-induced gamma oscillations and cortical network connectivity.

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Hauck, Michael; Schröder, Sven; Meyer-Hamme, Gesa; Lorenz, Jürgen; Friedrichs, Sunja; Nolte, Guido; Gerloff, Christian; Engel, Andreas K

2017-11-24

Recent studies support the view that cortical sensory, limbic and executive networks and the autonomic nervous system might interact in distinct manners under the influence of acupuncture to modulate pain. We performed a double-blind crossover design study to investigate subjective ratings, EEG and ECG following experimental laser pain under the influence of sham and verum acupuncture in 26 healthy volunteers. We analyzed neuronal oscillations and inter-regional coherence in the gamma band of 128-channel-EEG recordings as well as heart rate variability (HRV) on two experimental days. Pain ratings and pain-induced gamma oscillations together with vagally-mediated power in the high-frequency bandwidth (vmHF) of HRV decreased significantly stronger during verum than sham acupuncture. Gamma oscillations were localized in the prefrontal cortex (PFC), mid-cingulate cortex (MCC), primary somatosensory cortex and insula. Reductions of pain ratings and vmHF-power were significantly correlated with increase of connectivity between the insula and MCC. In contrast, connectivity between left and right PFC and between PFC and insula correlated positively with vmHF-power without a relationship to acupuncture analgesia. Overall, these findings highlight the influence of the insula in integrating activity in limbic-saliency networks with vagally mediated homeostatic control to mediate antinociception under the influence of acupuncture.

Proteins Potentially Involved in Immune Evasion Strategies in Sporothrix brasiliensis Elucidated by Ultra-High-Resolution Mass Spectrometry.

Science.gov (United States)

Rossato, Luana; Moreno, Leandro Ferreira; Jamalian, Azadeh; Stielow, Benjamin; de Almeida, Sandro Rogério; de Hoog, Sybren; Freeke, Joanna

2018-06-27