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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Natalia B. Fernandez; Natalia B. Fernandez; Patrik Vuilleumier; Patrik Vuilleumier; +4 Authors

    Congenital amusia in its most common form is a disorder characterized by a musical pitch processing deficit. Although pitch is involved in conveying emotion in music, the implications for pitch deficits on musical emotion judgements is still under debate. Relatedly, both limited and spared musical emotion recognition was reported in amusia in conditions where emotion cues were not determined by musical mode or dissonance. Additionally, assumed links between musical abilities and visuo-spatial attention processes need further investigation in congenital amusics. Hence, we here test to what extent musical emotions can influence attentional performance. Fifteen congenital amusic adults and fifteen healthy controls matched for age and education were assessed in three attentional conditions: executive control (distractor inhibition), alerting, and orienting (spatial shift) while music expressing either joy, tenderness, sadness, or tension was presented. Visual target detection was in the normal range for both accuracy and response times in the amusic relative to the control participants. Moreover, in both groups, music exposure produced facilitating effects on selective attention that appeared to be driven by the arousal dimension of musical emotional content, with faster correct target detection during joyful compared to sad music. These findings corroborate the idea that pitch processing deficits related to congenital amusia do not impede other cognitive domains, particularly visual attention. Furthermore, our study uncovers an intact influence of music and its emotional content on the attentional abilities of amusic individuals. The results highlight the domain-selectivity of the pitch disorder in congenital amusia, which largely spares the development of visual attention and affective systems.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Frontiers in Human N...arrow_drop_down
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    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DOAJ
    Article . 2021
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Frontiers in Human N...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DOAJ
      Article . 2021
      Data sources: DOAJ
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    Authors: Nieto, Michael Martin; Truax, D. Rodney;

    We attack the specific time-dependent Hamiltonian problem H=-{1/2} (t_o/t)^a \partial_{xx} + (1/2) \omega^2 (t/t_o)^b x^2. This corresponds to a time-dependent mass (TM) Schr\"odinger equation. We give the specific transformations to a different time-dependent quadratic Schr\"odinger equations (TQ) and to a different time-dependent oscillator (TO) equation. For each Schr\"odinger system, we give the Lie algebra of space-time symmetries, the number states, the squeezed-state and (with their classical motion), (\Delta x)^2, (\Delta p)^2, and the uncertainty product. Comment: LaTeX, 26 pages, including 3 figures and 13 tables. New title and format for journal. Conclusion added

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    arXiv.org e-Print Archive
    Other literature type . Preprint . 1999
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ arXiv.org e-Print Ar...arrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      arXiv.org e-Print Archive
      Other literature type . Preprint . 1999
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sánchez-Ramírez, Santiago; Weiss, Jörg G.; Thomas, Cristel G.; Cutter, Asher D.;

    Abstract When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that underlie the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Divergence in cis - and trans -acting regulatory controls evolve despite stabilizing selection on gene expression, being hastened by directional selection with adaptation, sexual selection, and inter-sexual conflict. Dysfunctional sex-biased gene expression, in particular, may provide an important source of genetic incompatibilities, with more severe misregulation expected for the heterogametic sex. Here, we characterize and compare male and female transcriptome profiles for sibling species of Caenorhabditis nematodes, C. briggsae and C. nigoni , and allele-specific expression in their F 1 hybrids to deconvolve features of expression divergence and regulatory dysfunction. Despite evidence of widespread stabilizing selection on gene expression, we find broad misregulation of sex-biased genes in F 1 hybrids that is most pronounced for the X-chromosome, supporting a “large-X” effect, and that counters expectations by disproportionately affecting hybrid females. Hybrid male misexpression, however, is greater in magnitude, with spermatogenesis genes especially prone to high divergence in both expression and coding sequences that may explain elevated sterility of hybrid males, consistent with “faster male” and “fragile male” models for Haldane’s rule. Regulatory and coding divergence overall correlate only weakly, however, and downregulation of male-biased genes in females implicates trans- acting modifiers in the evolutionary resolution of inter-sexual conflicts. This work identifies important differences between the sexes in how regulatory networks diverge that contributes to sex-biases in how genetic incompatibilities manifest during the speciation process. Author’s summary Many mutations that affect traits as species diverge do so by altering gene expression. Such gene regulatory changes also accumulate in the control of static traits, due to compensatory effects of mutation on multiple regulatory elements. Theory predicts many of these changes to cause inter-species hybrids to experience dysfunctional gene expression that leads to reduced fitness, disproportionately affecting the sex chromosomes and sex-biased gene expression. Our analyses of genome-wide expression data from Caenorhabditis nematode roundworms support these predictions. We find widespread rewiring of gene regulation despite extensive morphological stasis, and conserved overall expression profiles, that is a hallmark of these animals. Misregulation of expression in both sexes is most severe for genes linked to the X-chromosome, sperm genes show distinctive signatures of divergence, and differences between the sexes in regulatory evolution implicate resolved historical sexual conflicts over gene expression. This work clarifies how distinct components of regulatory networks evolve and contribute to sex differences in the manifestation of genetic incompatibilities in the speciation process.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bioRxivarrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ bioRxivarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Jonathan Z.L. Zhao; Eliseos J. Mucaki; Peter K. Rogan;

    Background: Gene signatures derived from transcriptomic data using machine learning methods have shown promise for biodosimetry testing. These signatures may not be sufficiently robust for large scale testing, as their performance has not been adequately validated on external, independent datasets. The present study develops human and murine signatures with biochemically-inspired machine learning that are strictly validated using k-fold and traditional approaches. Methods: Gene Expression Omnibus (GEO) datasets of exposed human and murine lymphocytes were preprocessed via nearest neighbor imputation and expression of genes implicated in the literature to be responsive to radiation exposure (n=998) were then ranked by Minimum Redundancy Maximum Relevance (mRMR). Optimal signatures were derived by backward, complete, and forward sequential feature selection using Support Vector Machines (SVM), and validated using k-fold or traditional validation on independent datasets. Results: The best human signatures we derived exhibit k-fold validation accuracies of up to 98% (DDB2, PRKDC, TPP2, PTPRE, and GADD45A) when validated over 209 samples and traditional validation accuracies of up to 92% (DDB2, CD8A, TALDO1, PCNA, EIF4G2, LCN2, CDKN1A, PRKCH, ENO1, and PPM1D) when validated over 85 samples. Some human signatures are specific enough to differentiate between chemotherapy and radiotherapy. Certain multi-class murine signatures have sufficient granularity in dose estimation to inform eligibility for cytokine therapy (assuming these signatures could be translated to humans). We compiled a list of the most frequently appearing genes in the top 20 human and mouse signatures. More frequently appearing genes among an ensemble of signatures may indicate greater impact of these genes on the performance of individual signatures. Several genes in the signatures we derived are present in previously proposed signatures. Conclusions: Gene signatures for ionizing radiation exposure derived by machine learning have low error rates in externally validated, independent datasets, and exhibit high specificity and granularity for dose estimation.

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    DOAJ
    Article . 2018
    Data sources: DOAJ
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    F1000Research
    Article . 2018 . Peer-reviewed
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      DOAJ
      Article . 2018
      Data sources: DOAJ
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      F1000Research
      Article . 2018 . Peer-reviewed
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    Authors: Villaverde, Tamara; Global Carex Group;

    Carex (Cyperaceae), with an estimated 2000 species, nearly cosmopolitan distribution and broad range of habitats, is one of the largest angiosperm genera and the largest in the temperate zone. In this article, we provide argument and evidence for a broader circumscription of Carex to add all species currently classified in Cymophyllus (monotypic), Kobresia (c. 60 species), Schoenoxiphium (c. 15 species) and Uncinia (c. 70 species) to those currently classified as Carex. Carex and these genera comprise tribe Cariceae (subfamily Cyperoideae, Cyperaceae) and form a wellsupported monophyletic group in all molecular phylogenetic studies to date. Carex as defined here in the broad sense currently comprises at least four clades. Three are strongly supported (Siderostictae, core Vignea and core Carex), whereas the caricoid clade, which includes all the segregate genera, receives only weak to moderate support. The caricoid clade is most commonly split into two clades, one including a monophyletic Schoenoxiphium and two small clades of species of Carex s.s., and the other comprising Kobresia, Uncinia and mostly unispicate species of Carex s.s. Morphological variation is high in all but the Vignea clade, making it extremely difficult to define consistent synapomorphies for most clades. However, Carex s.l. as newly circumscribed here is clearly differentiated from the sister groups in tribe Scirpeae by the transition from bisexual flowers with a bristle perianth in the sister group to unisexual flowers without a perianth in Carex. The naked female flowers of Carex s.l. are at least partially enclosed in a flask-shaped prophyll, termed a perigynium. Carex s.s. is not only by far the largest genus in the group, but also the earliest published name. As a result, only 72 new combinations and 58 replacement names are required to treat all of tribe Cariceae as a single genus Carex. We present the required transfers here, with synonymy, and we argue that this broader monophyletic circumscription of Carex reflects the close evolutionary relationships in the group and serves the goal of nomenclatural stability better than other possible treatments. We are grateful to the John D. and Catherine T. MacArthur Foundation for funding of the Biodiversity Synthesis Group of the Encyclopedia of Life (EOL) project, which funded our BioSynC Synthesis meeting at the Field Museum in Chicago in September 2011, when the Global Carex Group was formed. We also thank the US National Science Foundation (NSF) for funding our continuing international collaborative work on the phylogeny and classification of Carex under grants DEB 1255901 to ALH and MJW, and DEB 1256033 to EHR. We also acknowledge with thanks funding for nomenclatural research and for attendance at our second meeting during the Monocots V conference in New York in July, 2013, from the Natural Sciences and Engineering Research Council, Canada (NSERC) to MJW and JRS; University of Mainz to BG; JSPS KAKENHI Grant no. 25840136 to OY; Korea National Arboretum to SK; CGL2012- 38744 project from the Spanish Ministry of Economy and Competitiveness to ML; project 30870178 from the National Natural Science Foundation of China to SRZ, and a University of Wisconsin-Madison Raper Travel Grant to DS. The figures were prepared with invaluable technical advice from H. C. Rimmer. Peer reviewed

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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Recolector de Cienci...arrow_drop_down
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: The BABAR Collaboration; Aubert, B.;

    We present a measurement of the Cabibbo-Kobayashi-Maskawa CP-violating phase gamma with a Dalitz analysis of neutral D-meson decays to the K^0_s pi^- pi^+ final state from B^+/- -> D^{(*)}K^+/- decays, using a sample of 347 million B\bar{B} events collected by the BaBar detector. We measure gamma = (92 +/- 41 +/- 11 +/- 12)deg, where the first error is statistical, the second is the experimental systematic uncertainty and the third reflects the Dalitz model uncertainty. For the ratios r_B^{(*)} between the magnitudes of amplitudes A(B- -> D^{(*)0}K-) and A(B- ->\bar{D}^{(*)0} K-) we obtain the one-standard deviation intervals [0,0.14] and [0.02,0.20], respectively. All results presented here are preliminary. Comment: 21 pages, 6 figures. Contributed to the 33rd International Conference on High-Energy Physics, ICHEP 06, Moscow

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    arXiv.org e-Print Archive
    Other literature type . Preprint . 2006
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      arXiv.org e-Print Archive
      Other literature type . Preprint . 2006
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    Authors: J. W. Grayson; Y. Zhang; A. Mutzel; L. Renbaum-Wolff; +7 Authors

    Knowledge of the viscosity of particles containing secondary organic material (SOM) is useful for predicting reaction rates and diffusion in SOM particles. In this study we investigate the viscosity of SOM particles as a function of relative humidity and SOM particle mass concentration, during SOM synthesis. The SOM was generated via the ozonolysis of α-pinene at < 5 % relative humidity (RH). Experiments were carried out using the poke-and-flow technique, which measures the experimental flow time (τexp, flow) of SOM after poking the material with a needle. In the first set of experiments, we show that τexp, flow increased by a factor of 3600 as the RH increased from < 0.5 RH to 50 % RH, for SOM with a production mass concentration of 121 µg m−3. Based on simulations, the viscosities of the particles were between 6 × 105 and 5 × 107 Pa s at < 0.5 % RH and between 3 × 102 and 9 × 103 Pa s at 50 % RH. In the second set of experiments we show that under dry conditions τexp, flow decreased by a factor of 45 as the production mass concentration increased from 121 to 14 000 µg m−3. From simulations of the poke-and-flow experiments, the viscosity of SOM with a production mass concentration of 14 000 µg m−3 was determined to be between 4 × 104 and 1.5 × 106 Pa s compared to between 6 × 105 and 5 × 107 Pa s for SOM with a production mass concentration of 121 µg m−3. The results can be rationalized by a dependence of the chemical composition of SOM on production conditions. These results emphasize the shifting characteristics of SOM, not just with RH and precursor type, but also with the production conditions, and suggest that production mass concentration and the RH at which the viscosity was determined should be considered both when comparing laboratory results and when extrapolating these results to the atmosphere.

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    DOAJ
    Article . 2016
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    Authors: Dunietz, Isard; Soares, Joao M.;

    We investigate the possibility of observing direct CP violation in self-tagging B-meson decays of the type b -> d J/\psi. The CP asymmetry can be generated due to strong or electromagnetic scattering in the final state, or due to long distance effects. The first two contributions give asymmetries of a few 10^(-3), in the standard model. The long distance effects are hard to estimate, but it cannot be excluded that they yield asymmetries of about 1%. Comment: 10 pages, Fermilab-pub-93/307-T

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      Other literature type . Preprint . 1993
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    Authors: Christian, G.; Hutcheon, D.; Akers, C.; Connolly, D.; +2 Authors

    The $^{20}$Ne$(p, \gamma)^{21}$Na reaction is the starting point of the NeNa cycle, which is an important process for the production of intermediate mass elements. The $E_{\text{cm}} = 1113$ keV resonance plays an important role in the determination of stellar rates for this reaction since it is used to normalize experimental direct capture yields at lower energies. The commonly accepted strength of this resonance, $\omega \gamma = 1.13 \pm 0.07$ eV, has been misinterpreted as the strength in the center-of-mass frame when it is actually the strength in the laboratory frame. This has motivated a new measurement of the $E_{\text{cm}} = 1113$ keV resonance strength in $^{20}$Ne$(p, \gamma)^{21}$Na using the DRAGON recoil mass spectrometer. The DRAGON result, $0.972 \pm 0.11$ eV, is in good agreement with the accepted value when both are calculated in the same frame of reference. Comment: 4 pages, 2 figures, recommended for publication in Phys. Rev. C, Brief Reports

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    Authors: Combes, Joshua; Ferrie, Christopher; Cesare, Chris; Tiersch, Markus; +3 Authors

    Syndrome measurements made in quantum error correction contain more information than is typically used. We show that the statistics of data from syndrome measurements can be used to do the following: (i) estimation of parameters of an error channel, including the ability correct away the invertible part of the error channel, once it is estimated; (ii) hypothesis testing (or model selection) to distinguish error channels, e.g., to determine if the errors are correlated. The unifying theme is to make use of all of the information in the statistics of the data collected from syndrome measurements using machine learning and control algorithms. Comment: 16 pages, 6 figures

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    arXiv.org e-Print Archive
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    Authors: Natalia B. Fernandez; Natalia B. Fernandez; Patrik Vuilleumier; Patrik Vuilleumier; +4 Authors

    Congenital amusia in its most common form is a disorder characterized by a musical pitch processing deficit. Although pitch is involved in conveying emotion in music, the implications for pitch deficits on musical emotion judgements is still under debate. Relatedly, both limited and spared musical emotion recognition was reported in amusia in conditions where emotion cues were not determined by musical mode or dissonance. Additionally, assumed links between musical abilities and visuo-spatial attention processes need further investigation in congenital amusics. Hence, we here test to what extent musical emotions can influence attentional performance. Fifteen congenital amusic adults and fifteen healthy controls matched for age and education were assessed in three attentional conditions: executive control (distractor inhibition), alerting, and orienting (spatial shift) while music expressing either joy, tenderness, sadness, or tension was presented. Visual target detection was in the normal range for both accuracy and response times in the amusic relative to the control participants. Moreover, in both groups, music exposure produced facilitating effects on selective attention that appeared to be driven by the arousal dimension of musical emotional content, with faster correct target detection during joyful compared to sad music. These findings corroborate the idea that pitch processing deficits related to congenital amusia do not impede other cognitive domains, particularly visual attention. Furthermore, our study uncovers an intact influence of music and its emotional content on the attentional abilities of amusic individuals. The results highlight the domain-selectivity of the pitch disorder in congenital amusia, which largely spares the development of visual attention and affective systems.

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    Authors: Nieto, Michael Martin; Truax, D. Rodney;

    We attack the specific time-dependent Hamiltonian problem H=-{1/2} (t_o/t)^a \partial_{xx} + (1/2) \omega^2 (t/t_o)^b x^2. This corresponds to a time-dependent mass (TM) Schr\"odinger equation. We give the specific transformations to a different time-dependent quadratic Schr\"odinger equations (TQ) and to a different time-dependent oscillator (TO) equation. For each Schr\"odinger system, we give the Lie algebra of space-time symmetries, the number states, the squeezed-state and (with their classical motion), (\Delta x)^2, (\Delta p)^2, and the uncertainty product. Comment: LaTeX, 26 pages, including 3 figures and 13 tables. New title and format for journal. Conclusion added

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    arXiv.org e-Print Archive
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      Other literature type . Preprint . 1999
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    Authors: Sánchez-Ramírez, Santiago; Weiss, Jörg G.; Thomas, Cristel G.; Cutter, Asher D.;

    Abstract When gene regulatory networks diverge between species, their dysfunctional expression in inter-species hybrid individuals can create genetic incompatibilities that underlie the developmental defects responsible for intrinsic post-zygotic reproductive isolation. Divergence in cis - and trans -acting regulatory controls evolve despite stabilizing selection on gene expression, being hastened by directional selection with adaptation, sexual selection, and inter-sexual conflict. Dysfunctional sex-biased gene expression, in particular, may provide an important source of genetic incompatibilities, with more severe misregulation expected for the heterogametic sex. Here, we characterize and compare male and female transcriptome profiles for sibling species of Caenorhabditis nematodes, C. briggsae and C. nigoni , and allele-specific expression in their F 1 hybrids to deconvolve features of expression divergence and regulatory dysfunction. Despite evidence of widespread stabilizing selection on gene expression, we find broad misregulation of sex-biased genes in F 1 hybrids that is most pronounced for the X-chromosome, supporting a “large-X” effect, and that counters expectations by disproportionately affecting hybrid females. Hybrid male misexpression, however, is greater in magnitude, with spermatogenesis genes especially prone to high divergence in both expression and coding sequences that may explain elevated sterility of hybrid males, consistent with “faster male” and “fragile male” models for Haldane’s rule. Regulatory and coding divergence overall correlate only weakly, however, and downregulation of male-biased genes in females implicates trans- acting modifiers in the evolutionary resolution of inter-sexual conflicts. This work identifies important differences between the sexes in how regulatory networks diverge that contributes to sex-biases in how genetic incompatibilities manifest during the speciation process. Author’s summary Many mutations that affect traits as species diverge do so by altering gene expression. Such gene regulatory changes also accumulate in the control of static traits, due to compensatory effects of mutation on multiple regulatory elements. Theory predicts many of these changes to cause inter-species hybrids to experience dysfunctional gene expression that leads to reduced fitness, disproportionately affecting the sex chromosomes and sex-biased gene expression. Our analyses of genome-wide expression data from Caenorhabditis nematode roundworms support these predictions. We find widespread rewiring of gene regulation despite extensive morphological stasis, and conserved overall expression profiles, that is a hallmark of these animals. Misregulation of expression in both sexes is most severe for genes linked to the X-chromosome, sperm genes show distinctive signatures of divergence, and differences between the sexes in regulatory evolution implicate resolved historical sexual conflicts over gene expression. This work clarifies how distinct components of regulatory networks evolve and contribute to sex differences in the manifestation of genetic incompatibilities in the speciation process.

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    Authors: Jonathan Z.L. Zhao; Eliseos J. Mucaki; Peter K. Rogan;

    Background: Gene signatures derived from transcriptomic data using machine learning methods have shown promise for biodosimetry testing. These signatures may not be sufficiently robust for large scale testing, as their performance has not been adequately validated on external, independent datasets. The present study develops human and murine signatures with biochemically-inspired machine learning that are strictly validated using k-fold and traditional approaches. Methods: Gene Expression Omnibus (GEO) datasets of exposed human and murine lymphocytes were preprocessed via nearest neighbor imputation and expression of genes implicated in the literature to be responsive to radiation exposure (n=998) were then ranked by Minimum Redundancy Maximum Relevance (mRMR). Optimal signatures were derived by backward, complete, and forward sequential feature selection using Support Vector Machines (SVM), and validated using k-fold or traditional validation on independent datasets. Results: The best human signatures we derived exhibit k-fold validation accuracies of up to 98% (DDB2, PRKDC, TPP2, PTPRE, and GADD45A) when validated over 209 samples and traditional validation accuracies of up to 92% (DDB2, CD8A, TALDO1, PCNA, EIF4G2, LCN2, CDKN1A, PRKCH, ENO1, and PPM1D) when validated over 85 samples. Some human signatures are specific enough to differentiate between chemotherapy and radiotherapy. Certain multi-class murine signatures have sufficient granularity in dose estimation to inform eligibility for cytokine therapy (assuming these signatures could be translated to humans). We compiled a list of the most frequently appearing genes in the top 20 human and mouse signatures. More frequently appearing genes among an ensemble of signatures may indicate greater impact of these genes on the performance of individual signatures. Several genes in the signatures we derived are present in previously proposed signatures. Conclusions: Gene signatures for ionizing radiation exposure derived by machine learning have low error rates in externally validated, independent datasets, and exhibit high specificity and granularity for dose estimation.

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    Authors: Villaverde, Tamara; Global Carex Group;

    Carex (Cyperaceae), with an estimated 2000 species, nearly cosmopolitan distribution and broad range of habitats, is one of the largest angiosperm genera and the largest in the temperate zone. In this article, we provide argument and evidence for a broader circumscription of Carex to add all species currently classified in Cymophyllus (monotypic), Kobresia (c. 60 species), Schoenoxiphium (c. 15 species) and Uncinia (c. 70 species) to those currently classified as Carex. Carex and these genera comprise tribe Cariceae (subfamily Cyperoideae, Cyperaceae) and form a wellsupported monophyletic group in all molecular phylogenetic studies to date. Carex as defined here in the broad sense currently comprises at least four clades. Three are strongly supported (Siderostictae, core Vignea and core Carex), whereas the caricoid clade, which includes all the segregate genera, receives only weak to moderate support. The caricoid clade is most commonly split into two clades, one including a monophyletic Schoenoxiphium and two small clades of species of Carex s.s., and the other comprising Kobresia, Uncinia and mostly unispicate species of Carex s.s. Morphological variation is high in all but the Vignea clade, making it extremely difficult to define consistent synapomorphies for most clades. However, Carex s.l. as newly circumscribed here is clearly differentiated from the sister groups in tribe Scirpeae by the transition from bisexual flowers with a bristle perianth in the sister group to unisexual flowers without a perianth in Carex. The naked female flowers of Carex s.l. are at least partially enclosed in a flask-shaped prophyll, termed a perigynium. Carex s.s. is not only by far the largest genus in the group, but also the earliest published name. As a result, only 72 new combinations and 58 replacement names are required to treat all of tribe Cariceae as a single genus Carex. We present the required transfers here, with synonymy, and we argue that this broader monophyletic circumscription of Carex reflects the close evolutionary relationships in the group and serves the goal of nomenclatural stability better than other possible treatments. We are grateful to the John D. and Catherine T. MacArthur Foundation for funding of the Biodiversity Synthesis Group of the Encyclopedia of Life (EOL) project, which funded our BioSynC Synthesis meeting at the Field Museum in Chicago in September 2011, when the Global Carex Group was formed. We also thank the US National Science Foundation (NSF) for funding our continuing international collaborative work on the phylogeny and classification of Carex under grants DEB 1255901 to ALH and MJW, and DEB 1256033 to EHR. We also acknowledge with thanks funding for nomenclatural research and for attendance at our second meeting during the Monocots V conference in New York in July, 2013, from the Natural Sciences and Engineering Research Council, Canada (NSERC) to MJW and JRS; University of Mainz to BG; JSPS KAKENHI Grant no. 25840136 to OY; Korea National Arboretum to SK; CGL2012- 38744 project from the Spanish Ministry of Economy and Competitiveness to ML; project 30870178 from the National Natural Science Foundation of China to SRZ, and a University of Wisconsin-Madison Raper Travel Grant to DS. The figures were prepared with invaluable technical advice from H. C. Rimmer. Peer reviewed

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    Authors: The BABAR Collaboration; Aubert, B.;

    We present a measurement of the Cabibbo-Kobayashi-Maskawa CP-violating phase gamma with a Dalitz analysis of neutral D-meson decays to the K^0_s pi^- pi^+ final state from B^+/- -> D^{(*)}K^+/- decays, using a sample of 347 million B\bar{B} events collected by the BaBar detector. We measure gamma = (92 +/- 41 +/- 11 +/- 12)deg, where the first error is statistical, the second is the experimental systematic uncertainty and the third reflects the Dalitz model uncertainty. For the ratios r_B^{(*)} between the magnitudes of amplitudes A(B- -> D^{(*)0}K-) and A(B- ->\bar{D}^{(*)0} K-) we obtain the one-standard deviation intervals [0,0.14] and [0.02,0.20], respectively. All results presented here are preliminary. Comment: 21 pages, 6 figures. Contributed to the 33rd International Conference on High-Energy Physics, ICHEP 06, Moscow

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    Authors: J. W. Grayson; Y. Zhang; A. Mutzel; L. Renbaum-Wolff; +7 Authors

    Knowledge of the viscosity of particles containing secondary organic material (SOM) is useful for predicting reaction rates and diffusion in SOM particles. In this study we investigate the viscosity of SOM particles as a function of relative humidity and SOM particle mass concentration, during SOM synthesis. The SOM was generated via the ozonolysis of α-pinene at < 5 % relative humidity (RH). Experiments were carried out using the poke-and-flow technique, which measures the experimental flow time (τexp, flow) of SOM after poking the material with a needle. In the first set of experiments, we show that τexp, flow increased by a factor of 3600 as the RH increased from < 0.5 RH to 50 % RH, for SOM with a production mass concentration of 121 µg m−3. Based on simulations, the viscosities of the particles were between 6 × 105 and 5 × 107 Pa s at < 0.5 % RH and between 3 × 102 and 9 × 103 Pa s at 50 % RH. In the second set of experiments we show that under dry conditions τexp, flow decreased by a factor of 45 as the production mass concentration increased from 121 to 14 000 µg m−3. From simulations of the poke-and-flow experiments, the viscosity of SOM with a production mass concentration of 14 000 µg m−3 was determined to be between 4 × 104 and 1.5 × 106 Pa s compared to between 6 × 105 and 5 × 107 Pa s for SOM with a production mass concentration of 121 µg m−3. The results can be rationalized by a dependence of the chemical composition of SOM on production conditions. These results emphasize the shifting characteristics of SOM, not just with RH and precursor type, but also with the production conditions, and suggest that production mass concentration and the RH at which the viscosity was determined should be considered both when comparing laboratory results and when extrapolating these results to the atmosphere.

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    Authors: Dunietz, Isard; Soares, Joao M.;

    We investigate the possibility of observing direct CP violation in self-tagging B-meson decays of the type b -> d J/\psi. The CP asymmetry can be generated due to strong or electromagnetic scattering in the final state, or due to long distance effects. The first two contributions give asymmetries of a few 10^(-3), in the standard model. The long distance effects are hard to estimate, but it cannot be excluded that they yield asymmetries of about 1%. Comment: 10 pages, Fermilab-pub-93/307-T

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    Authors: Christian, G.; Hutcheon, D.; Akers, C.; Connolly, D.; +2 Authors

    The $^{20}$Ne$(p, \gamma)^{21}$Na reaction is the starting point of the NeNa cycle, which is an important process for the production of intermediate mass elements. The $E_{\text{cm}} = 1113$ keV resonance plays an important role in the determination of stellar rates for this reaction since it is used to normalize experimental direct capture yields at lower energies. The commonly accepted strength of this resonance, $\omega \gamma = 1.13 \pm 0.07$ eV, has been misinterpreted as the strength in the center-of-mass frame when it is actually the strength in the laboratory frame. This has motivated a new measurement of the $E_{\text{cm}} = 1113$ keV resonance strength in $^{20}$Ne$(p, \gamma)^{21}$Na using the DRAGON recoil mass spectrometer. The DRAGON result, $0.972 \pm 0.11$ eV, is in good agreement with the accepted value when both are calculated in the same frame of reference. Comment: 4 pages, 2 figures, recommended for publication in Phys. Rev. C, Brief Reports

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