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  • Oxford University Press  (36)
  • American Institute of Physics (AIP)
  • 2015-2019  (26)
  • 2010-2014  (19)
  • 1
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    Sex-Chromosome Homomorphy in Palearctic Tree Frogs Results from Both Turnovers and X-Y Recombination (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-20
    Description: Contrasting with birds and mammals, poikilothermic vertebrates often have homomorphic sex chromosomes, possibly resulting from high rates of sex-chromosome turnovers and/or occasional X–Y recombination. Strong support for the latter mechanism was provided by four species of European tree frogs, which inherited from a common ancestor (~5 Ma) the same pair of homomorphic sex chromosomes (linkage group 1, LG1), harboring the candidate sex-determining gene Dmrt1. Here, we test sex linkage of LG1 across six additional species of the Eurasian Hyla radiation with divergence times ranging from 6 to 40 Ma. LG1 turns out to be sex linked in six of nine resolved cases. Mapping the patterns of sex linkage to the Hyla phylogeny reveals several transitions in sex-determination systems within the last 10 My, including one switch in heterogamety. Phylogenetic trees of DNA sequences along LG1 are consistent with occasional X–Y recombination in all species where LG1 is sex linked. These patterns argue against one of the main potential causes for turnovers, namely the accumulation of deleterious mutations on nonrecombining chromosomes. Sibship analyses show that LG1 recombination is strongly reduced in males from most species investigated, including some in which it is autosomal. Intrinsically low male recombination might facilitate the evolution of male heterogamety, and the presence of important genes from the sex-determination cascade might predispose LG1 to become a sex chromosome.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 2
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    Building confidence in projections of the responses of living marine resources to climate change (2016)
    Oxford University Press
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    Publication Date: 2016-06-24
    Description: The Fifth Assessment Report of the Intergovernmental Panel on Climate Change highlights that climate change and ocean acidification are challenging the sustainable management of living marine resources (LMRs). Formal and systematic treatment of uncertainty in existing LMR projections, however, is lacking. We synthesize knowledge of how to address different sources of uncertainty by drawing from climate model intercomparison efforts. We suggest an ensemble of available models and projections, informed by observations, as a starting point to quantify uncertainties. Such an ensemble must be paired with analysis of the dominant uncertainties over different spatial scales, time horizons, and metrics. We use two examples: (i) global and regional projections of Sea Surface Temperature and (ii) projection of changes in potential catch of sablefish ( Anoplopoma fimbria ) in the 21st century, to illustrate this ensemble model approach to explore different types of uncertainties. Further effort should prioritize understanding dominant, undersampled dimensions of uncertainty, as well as the strategic collection of observations to quantify, and ultimately reduce, uncertainties. Our proposed framework will improve our understanding of future changes in LMR and the resulting risk of impacts to ecosystems and the societies under changing ocean conditions.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 3
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    Contact- and distance-based principal component analysis of protein dynamics (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-12-29
    Description: To interpret molecular dynamics simulations of complex systems, systematic dimensionality reduction methods such as principal component analysis (PCA) represent a well-established and popular approach. Apart from Cartesian coordinates, internal coordinates, e.g., backbone dihedral angles or various kinds of distances, may be used as input data in a PCA. Adopting two well-known model problems, folding of villin headpiece and the functional dynamics of BPTI, a systematic study of PCA using distance-based measures is presented which employs distances between C α -atoms as well as distances between inter-residue contacts including side chains. While this approach seems prohibitive for larger systems due to the quadratic scaling of the number of distances with the size of the molecule, it is shown that it is sufficient (and sometimes even better) to include only relatively few selected distances in the analysis. The quality of the PCA is assessed by considering the resolution of the resulting free energy landscape (to identify metastable conformational states and barriers) and the decay behavior of the corresponding autocorrelation functions (to test the time scale separation of the PCA). By comparing results obtained with distance-based, dihedral angle, and Cartesian coordinates, the study shows that the choice of input variables may drastically influence the outcome of a PCA.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Contact- and distance-based principal component analysis of protein dynamics (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-12-29
    Description: To interpret molecular dynamics simulations of complex systems, systematic dimensionality reduction methods such as principal component analysis (PCA) represent a well-established and popular approach. Apart from Cartesian coordinates, internal coordinates, e.g., backbone dihedral angles or various kinds of distances, may be used as input data in a PCA. Adopting two well-known model problems, folding of villin headpiece and the functional dynamics of BPTI, a systematic study of PCA using distance-based measures is presented which employs distances between C α -atoms as well as distances between inter-residue contacts including side chains. While this approach seems prohibitive for larger systems due to the quadratic scaling of the number of distances with the size of the molecule, it is shown that it is sufficient (and sometimes even better) to include only relatively few selected distances in the analysis. The quality of the PCA is assessed by considering the resolution of the resulting free energy landscape (to identify metastable conformational states and barriers) and the decay behavior of the corresponding autocorrelation functions (to test the time scale separation of the PCA). By comparing results obtained with distance-based, dihedral angle, and Cartesian coordinates, the study shows that the choice of input variables may drastically influence the outcome of a PCA.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 5
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    The probability distribution functions of emission line flux measurements and their ratios (2016)
    Oxford University Press
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    Publication Date: 2016-05-12
    Description: Many physical parameters in astrophysics are derived using the ratios of two observed quantities. If the relative uncertainties on measurements are small enough, uncertainties can be propagated analytically using simplifying assumptions, but for large normally distributed uncertainties, the probability distribution of the ratio become skewed, with a modal value offset from that expected in Gaussian uncertainty propagation. Furthermore, the most likely value of a ratio A/B is not equal to the reciprocal of the most likely value of B/A. The effect is most pronounced when the uncertainty on the denominator is larger than that on the numerator. We show that this effect is seen in an analysis of 12 126 spectra from the Sloan Digital Sky Survey (SDSS). The intrinsically fixed ratio of the [O iii ] lines at 4959 and 5007 Å is conventionally expressed as the ratio of the stronger line to the weaker line. Thus, the uncertainty on the denominator is larger, and non-Gaussian probability distributions result. By taking this effect into account, we derive an improved estimate of the intrinsic 5007/4959 ratio. We obtain a value of 3.012 ± 0.008, which is slightly but statistically significantly higher than the theoretical value of 2.98. We further investigate the suggestion that fluxes measured from emission lines in noisy spectra are strongly biased upwards. We were unable to detect this effect in the SDSS line flux measurements, and we could not reproduce the results of Rola and Pelat who first described this bias. We suggest that the magnitude of this effect may depend strongly on the specific fitting algorithm used.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Vibrational energy flow in the villin headpiece subdomain: Master equation simulations (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-02-18
    Description: We examine vibrational energy flow in dehydrated and hydrated villin headpiece subdomain HP36 by master equation simulations. Transition rates used in the simulations are obtained from communication maps calculated for HP36. In addition to energy flow along the main chain, we identify pathways for energy transport in HP36 via hydrogen bonding between residues quite far in sequence space. The results of the master equation simulations compare well with all-atom non-equilibrium simulations to about 1 ps following initial excitation of the protein, and quite well at long times, though for some residues we observe deviations between the master equation and all-atom simulations at intermediate times from about 1–10 ps. Those deviations are less noticeable for hydrated than dehydrated HP36 due to energy flow into the water.
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    Vibrational energy flow in the villin headpiece subdomain: Master equation simulations (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-02-18
    Description: We examine vibrational energy flow in dehydrated and hydrated villin headpiece subdomain HP36 by master equation simulations. Transition rates used in the simulations are obtained from communication maps calculated for HP36. In addition to energy flow along the main chain, we identify pathways for energy transport in HP36 via hydrogen bonding between residues quite far in sequence space. The results of the master equation simulations compare well with all-atom non-equilibrium simulations to about 1 ps following initial excitation of the protein, and quite well at long times, though for some residues we observe deviations between the master equation and all-atom simulations at intermediate times from about 1–10 ps. Those deviations are less noticeable for hydrated than dehydrated HP36 due to energy flow into the water.
    Electronic ISSN: 1931-9223
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 8
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    Projected ocean warming creates a conservation challenge for river herring populations (2015)
    Oxford University Press
    Details
    Publication Date: 2015-01-20
    Description: The term river herring collectively refers to alewife ( Alosa pseudoharengus ) and blueback herring ( A. aestivalis ), two anadromous fishes distributed along the east coast of North America. Historically, river herring spawning migrations supported important fisheries, and their spawning runs continue to be of cultural significance to many coastal communities. Recently, substantial declines in spawning run size prompted a petition to consider river herring for listing under the Endangered Species Act (ESA). The ESA status review process requires an evaluation of a species' response to multiple stressors, including climate change. For anadromous species that utilize a range of habitats throughout their life cycle, the response to a changing global climate is inherently complex and likely varies regionally. River herring occupy marine habitat for most of their lives, and we demonstrate that their relative abundance in the ocean has been increasing in recent years. We project potential effects of ocean warming along the US Atlantic coast on river herring in two seasons (spring and fall), and two future periods (2020–2060 and 2060–2100) by linking species distribution models to projected temperature changes from global climate models. Our analyses indicate that climate change will likely result in reductions in total suitable habitat across the study region, which will alter the marine distribution of river herring. We also project that density will likely decrease for both species in fall, but may increase in spring. Finally, we demonstrate that river herring may have increased sensitivity to climate change under a low abundance scenario. This result could be an important consideration for resource managers when planning for climate change because establishing effective conservation efforts in the near term may improve population resiliency and provide lasting benefits to river herring populations.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 9
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    The Correlation of the NA Measurements by Counting 28Si Atoms (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-07-15
    Description: An additional value of the Avogadro constant was obtained by counting the atoms in isotopically enriched Si spheres. With respect to the previous determination, the spheres were etched and repolished to eliminate metal contaminations and to improve the roundness. In addition, all the input quantities—molar mass, lattice parameter, mass, and volume—were remeasured aiming at a smaller uncertainty. In order to make the values given in Andreas et al. [Metrologia 48 , S1 (2011)] and Azuma et al. [Metrologia 52 , 360 (2015)] usable for a least squares adjustment, we report about the estimate of their correlation.
    Print ISSN: 0047-2689
    Electronic ISSN: 1529-7845
    Topics: Chemistry and Pharmacology , Physics
    Published by American Institute of Physics (AIP)
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  • 10
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    Cusk (Brosme brosme) and climate change: assessing the threat to a candidate marine fish species under the US Endangered Species Act (2012)
    Oxford University Press
    Details
    Publication Date: 2012-10-13
    Description: Hare, J.A., Manderson, J.P., Nye, J.A., Alexander, M.A., Auster, P.J., Borggaard, D.L., Capotondi, A.M., Damon-Randall, K.B., Heupel, E., Mateo, I., O'Brien, L., Richardson, D.E., Stock, C.A., and Biege, S.T. 2012. Cusk ( Brosme brosme ) and climate change: assessing the threat to a candidate marine fish species under the US Endangered Species Act. – ICES Journal of Marine Science, 69: 1753–1768. In the Northwest Atlantic Ocean cusk ( Brosme brosme ) has declined dramatically, primarily as a result of fishing activities. These declines have led to concern about its status, which has prompted reviews under the US Endangered Species Act and the Canadian Species at Risk Act. Changes in distribution and abundance of a number of marine fish in the Northwest Atlantic have been linked to climate variability and change, suggesting that both fishing and climate may affect the status of cusk. Our goal was to evaluate potential effects of climate change on Northwest Atlantic cusk distribution. Coupling a species niche model with the output from an ensemble of climate models, we projected cusk distribution in the future. Our results indicate cusk habitat in the region will shrink and fragment, which is a result of a spatial mismatch between high complexity seafloor habitat and suitable temperature. The importance of habitat patch connectivity for cusk is poorly understood, so the population-level consequences of climate-related habitat fragmentation are uncertain. More broadly, climate change may reduce appropriate thermal habitat and increase habitat fragmentation for other cold-water species in the region; thereby, increasing the potential for regional overexploitation and extirpation.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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