Electron capture rates in a plasma

A new general expression is derived for nuclear electron capture rates within dense plasmas. Its qualitative nature leads us to question some widely accepted assumptions about how to calculate the effects of the plasma on the rates. A perturbative evaluation, though not directly applicable to the strongly interacting case, appears to bear out these suspicions.Comment: 9 page

A model of the near-earth plasma environment and application to the ISEE-A and -B orbit

A model of the near-earth environment to obtain a best estimate of the average flux of protons and electrons in the energy range from 0.1 to 100 keV for the International Sun-Earth Explorer (ISEE)-A and -B spacecraft. The possible radiation damage to the thermal coating on these spinning spacecraft is also studied. Applications of the model to other high-altitude satellites can be obtained with the appropriate orbit averaging. This study is the first attempt to synthesize an overall quantitative environment of low-energy particles for high altitude spacecraft, using data from in situ measurements

AP-8 trapped proton environment for solar maximum and solar minimum

Data sets from Ov-3 and Azur indicate a need for improvement in models of the stably trapped proton flux with energies between 0.1 and 400 MeV. Two computer accessible models are described: AP8MAX and AP8MIN. The models are presented in the form of nomographs, B-L plots, R-lambda plots, and equatorial radial profiles. Nomographs of the orbit-integrated fluxes are also discussed. The models are compared with each other, with the data, and with previous AP models. Requirements for future improvements include more complete data coverage and periodic comparisons with new data sets as they become available. The machine-sensible format in which the models are available are described

Identification of a Genomic Reservoir for New TRIM Genes in Primate Genomes

Tripartite Motif (TRIM) ubiquitin ligases act in the innate immune response against viruses. One of the best characterized members of this family, TRIM5α, serves as a potent retroviral restriction factor with activity against HIV. Here, we characterize what are likely to be the youngest TRIM genes in the human genome. For instance, we have identified 11 TRIM genes that are specific to humans and African apes (chimpanzees, bonobos, and gorillas) and another 7 that are human-specific. Many of these young genes have never been described, and their identification brings the total number of known human TRIM genes to approximately 100. These genes were acquired through segmental duplications, most of which originated from a single locus on chromosome 11. Another polymorphic duplication of this locus has resulted in these genes being copy number variable within the human population, with a Han Chinese woman identified as having 12 additional copies of these TRIM genes compared to other individuals screened in this study. Recently, this locus was annotated as one of 34 “hotspot” regions that are also copy number variable in the genomes of chimpanzees and rhesus macaques. Most of the young TRIM genes originating from this locus are expressed, spliced, and contain signatures of positive natural selection in regions known to determine virus recognition in TRIM5α. However, we find that they do not restrict the same retroviruses as TRIM5α, consistent with the high degree of divergence observed in the regions that control target specificity. We propose that this recombinationally volatile locus serves as a reservoir from which new TRIM genes arise through segmental duplication, allowing primates to continually acquire new antiviral genes that can be selected to target new and evolving pathogens

Rapid Evolution of BRCA1 and BRCA2 in Humans and Other Primates

The maintenance of chromosomal integrity is an essential task of every living organism and cellular repair mechanisms exist to guard against insults to DNA. Given the importance of this process, it is expected that DNA repair proteins would be evolutionarily conserved, exhibiting very minimal sequence change over time. However, BRCA1, an essential gene involved in DNA repair, has been reported to be evolving rapidly despite the fact that many protein-altering mutations within this gene convey a significantly elevated risk for breast and ovarian cancers. Results: To obtain a deeper understanding of the evolutionary trajectory of BRCA1, we analyzed complete BRCA1 gene sequences from 23 primate species. We show that specific amino acid sites have experienced repeated selection for amino acid replacement over primate evolution. This selection has been focused specifically on humans and our closest living relatives, chimpanzees (Pan troglodytes) and bonobos (Pan paniscus). After examining BRCA1 polymorphisms in 7 bonobo, 44 chimpanzee, and 44 rhesus macaque (Macaca mulatta) individuals, we find considerable variation within each of these species and evidence for recent selection in chimpanzee populations. Finally, we also sequenced and analyzed BRCA2 from 24 primate species and find that this gene has also evolved under positive selection. Conclusions: While mutations leading to truncated forms of BRCA1 are clearly linked to cancer phenotypes in humans, there is also an underlying selective pressure in favor of amino acid-altering substitutions in this gene. A hypothesis where viruses are the drivers of this natural selection is discussed.National Institutes of Health R01-GM-093086, 8U42OD011197-13National Science Foundation BCS-07115972Burroughs Wellcome FundMolecular Bioscience

On a scalable nonparametric denoising of time series signals

Denoising and filtering of time series signals is a problem emerging in many areas of computational science. Here we demonstrate how the nonparametric computational methodology of the finite element method of time series analysis with H1 regularization can be extended for denoising of very long and noisy time series signals. The main computational bottleneck is the inner quadratic programming problem. Analyzing the solvability and utilizing the problem structure, we suggest an adapted version of the spectral projected gradient method (SPG-QP) to resolve the problem. This approach increases the granularity of parallelization, making the proposed methodology highly suitable for graphics processing unit (GPU) computing. We demonstrate the scalability of our open-source implementation based on PETSc for the Piz Daint supercomputer of the Swiss Supercomputing Centre (CSCS) by solving large-scale data denoising problems and comparing their computational scaling and performance to the performance of the standard denoising methods

The Krzyż conjecture revisited

The Krzyz conjecture concerns the largest values of the Taylor coefficients of a non-vanishing analytic function bounded by one in modulus in the unit disk. It has been open since 1968 even though information on the structure of extremal functions is available. The purpose of this paper is to collect various conditions that the coefficients of an extremal function (and various other quantities associated with it) should satisfy if the conjecture is true and to show that each one of these properties is equivalent to the conjecture itself. This may provide several possible starting points for future attempts at solving the problemThe first, third and fourth authors thankfully acknowledge partial support from MINECO grant MTM2012-37436-C02-02, Spain. Starting in 2014 the first author was supported by Academy of Finland grant 268009. The second author was supported by NSERC, Canada. The third author was also supported by NSF grant DMS-0901524, by NSF CAREER, Award No. DMS-1056965, and Sloan Research Fellowship, USA. The fourth author was partially supported by the European ESF Network HCAA (“Harmonic and Complex Analysis and Its Applications”) during the period November 2009 - April 201

RR Lyrae Variables in the Globular Cluster M55. The First Evidence for Non Radial Pulsations in RR Lyr Stars

We present the results of a photometric study of RR Lyrae variables in the field of the globular cluster M55. We have discovered nine new RR Lyrae stars, increasing the number of known variables in this cluster to 15 objects. Five of the newly discovered variables belong to Bailey type RRc and two to type RRab. Two background RRab stars are probable members of the Sagittarius dwarf galaxy. Fourier decomposition of the light curves was used to derive basic properties of the present sample of RR Lyrae variables. From an analysis of the RRc variables we obtain a mean mass of $M=0.53\pm0.03 M_\odot$, luminosity $\log L=1.75\pm0.01$, effective temperature $T_{eff}=7193\pm27$ K, and helium abundance $Y=0.27\pm0.01$. Based on the $B-V$ colors, periods and metallicities of the RRab stars we estimate the value of the color excess for M55 to be equal to $E(B-V)=0.11\pm0.03$. Using this value we derive the colors of the blue and red edges of the instability strip in M55. The blue edge lies at $(B-V)_0=0.20$ mag and the red edge lies at $(B-V)_0=0.38$ mag. We estimate the values of the visual apparent and dereddened distance moduli to be $13.65\pm0.11$ and $13.31\pm0.11$, respectively. The light curves of three of the RRc variables exhibit changes in amplitude of over 0.1 mag on the time scale of less than a week, rather short for the Blazhko effect, but with no evidence for another radial pulsational frequency. However we do detect other periodicities which are clearly visible in the light curve after removing variations with the first overtone radial frequency. This is strong evidence for the presence of non-radial pulsations, a behavior common for $\delta$ Scuti stars but not yet observed among RR Lyr variables.Comment: submitted to Astronomical Journal, 33 pages with 11 figure

Releases of Asian houbara must respect genetic and geographic origin to preserve inherited migration behaviour:evidence from a translocation experiment

Maintaining appropriate migratory strategies is important in conservation; however, translocations of migratory animals may alter locally-evolved migration behaviours of recipient populations if these are different and heritable. We used satellite telemetry and experimental translocation to quantify differences and assess heritability in migration behaviours between three migratory Asian houbara (Chlamydotis macqueenii) breeding populations (640 km range across eastern, central and western Uzbekistan). Adults from the eastern population migrated twice as far (mean = 1,184 km ± 44 s.e.) as the western population (656 km ± 183 s.e.) and showed significantly less variation in migration distance than the central population (1,030 km ± 127 s.e.). The western and central populations wintered significantly further north (mean: +8.32°N ± 1.70 s.e. and +4.19°N ± 1.16 s.e., respectively) and the central population further west (-3.47°E ± 1.46 s.e.) than individuals from the eastern population.These differences could arise from differing innate drive, or through learnt facultative responses to topography, filtered by survival. Translocated birds from the eastern population (wild laid and captive-reared, n= 5) migrated further than adults from either western or central recipient populations, particularly in their second migration year. Translocated birds continued migrating south past suitable wintering grounds used by the recipient populations despite having to negotiate mountain obstacles. Together, this suggests a considerable conserved heritable migratory component with local adaptation at a fine geographic scale. Surviving translocated individuals returned to their release site, suggesting continued translocations would lead to introgression of the heritable component and risk altering recipient migration patterns. Conservation biologists considering translocation interventions for migratory populations should evaluate potential genetic components of migratory behaviour