Empirical relation between angular momentum transport and thermal-to-magnetic pressure ratio in shearing box simulations

By combining data from different published 3-D simulations of Keplerian shearing boxes unstable to the magnetorotational instability (MRI), we highlight tight anti-correlations between the total effective inferred angular momentum transport parameter, $\alpha_{tot}$, its separate Maxwell and Reynolds contributions $\alpha_{mag}$ and $\alpha_{kin}$, and the kinetic to magnetic pressure ratio $\beta$, defined with the initial or saturated (when available) thermal pressure. Plots of $Log (\alpha_{kin}), Log (\alpha_{mag})$, and $Log (\alpha_{tot})$ vs $Log (\beta)$ are well fit by straight lines even as $\alpha_{kin}$, $\alpha_{mag}$,and $\alpha_{tot}$ vary by four orders of magnitude over the simulations included. The ratio $\alpha_{kin}/\alpha_{mag}$ and the product $\alpha_{tot}\beta$ are quite constant and largely independent of the presence or absence of weak mean fields, the choice of initial and boundary conditions, and the resolution. In short, simulations have more strongly constrained the product $\alpha_{tot}\beta$ than $\alpha_{tot}$ itself.Comment: 22 pages (includes 10 tables and 3 figs.), accepted by New Astronom

The contribution of statistical physics to evolutionary biology

Evolutionary biology shares many concepts with statistical physics: both deal with populations, whether of molecules or organisms, and both seek to simplify evolution in very many dimensions. Often, methodologies have undergone parallel and independent development, as with stochastic methods in population genetics. We discuss aspects of population genetics that have embraced methods from physics: amongst others, non-equilibrium statistical mechanics, travelling waves, and Monte-Carlo methods have been used to study polygenic evolution, rates of adaptation, and range expansions. These applications indicate that evolutionary biology can further benefit from interactions with other areas of statistical physics, for example, by following the distribution of paths taken by a population through time.Comment: 18 pages, 3 figures, glossary. Accepted in Trend in Ecology and Evolution (to appear in print in August 2011

Vitamin D, FOXO3a, and Sirtuin1 in Hashimoto's Thyroiditis and Differentiated Thyroid Cancer

Background: Protective effects of vitamin D have been reported in autoimmune and malignant thyroid diseases, though little is known about the underlying mechanism. Sirtuin 1 histon deacethylase (SIRT1) links the vitamin D pathway with regulation of transcription factor FOXO3a, a key player in cell cycle regulation and apoptosis. Aim of the present study was to investigate common single nucleotide polymorphisms (SNP's) in FOXO3a gene in respect to thyroid diseases, as well as to evaluate the hypothesis of Sirtuin1-FOXO3a interaction being a mediator of anti-proliferative vitamin D effects.Methods: The SNP's FOXO3a rs4946936/rs4945816/rs9400239 were genotyped in 257 patients with differentiated thyroid carcinoma (DTC), 139 patients with Hashimoto thyroiditis (HT) and 463 healthy controls (HC). Moreover, T-helper cells of HC and papillary thyroid cancer cell line BCPAP were incubated with 1,25(OH)2D3 and/or SIRT1 inhibitor Ex-527 in order to elucidate SIRT1- dependent vitamin D effects on cell proliferation and FOXO3a gene expression in vitro.Results: Patients with DTC tended to carry more often allele C in FOXO3a rs4946936 in comparison to HC (pcorrected = pc = 0.08). FOXO3a rs9400239T and rs4945816C was more frequent in HT in comparison to HC (pc = 0.02 and pc = 0.01, respectively). In both DTC and HT, we could not find a correlation of FOXO3a SNP's with vitamin D status. However, on in vitro level, 1,25(OH)2D3 showed an anti-proliferative effect in both T-helper cells and BCPAP, that was blocked by SIRT1 inhibition (T-helper cells: p = 0.0059, BCPAP: p = 0.04) and accompanied by elevated FOXO3a gene expression in T-helper cells (p = 0.05).Conclusions:FOXO3a rs9400239T and rs4945816C may constitute risk factors for HT, independent of the vitamin D status.This indicates the implication of FOXO3a in pathogenesis of autoimmune thyroid diseases. The dependency of anti-proliferative vitamin D effects on SIRT1 activity further suggests a key role of vitamin D-SIRT1-FOXO3a axis for protective vitamin D effects

Retelling the recent evolution of genetic diversity for Guzerá: Inferences from LD decay, runs of homozygosity and Ne over the generations

[EN] Genetic diversity is the one of the most important issues in conservation studies of livestock breeds or endangered species. In the present study, we tested the feasibility of describing the recent evolution in genetic diversity through genome-wide SNP genotyping and estimates of linkage disequilibrium decay patterns, effective population size, inbreeding coefficient based on runs of homozygosity and population structure. We choose the bovine indicine breed Guzerá because it has suffered recent bottlenecks which have been registered historically. A sample of 1036 females was genotyped using Illumina BovineSNP50. A resampling strategy was applied to correct for sampling biases caused by the population structure in herds, and by the extensive use of some sires for artificial reproduction. A subsample of 210 animals and 32,806 markers with MAF > 0.01 was used. Very low linkage disequilibrium was detected for distances greater than 120 Kb between two markers. Furthermore, three points of decrease in effective population size between generations were detected, which coincide with the historically registered bottlenecks. The inbreeding coefficient, based on runs of homozygosity, confirmed a strong contribution of the last 20–30 generations to current inbreeding. In the population structure analysis, the most probable number of sub-populations is 2, reflecting selection purpose (beef or dual-purpose). Taken together, these results allow a retelling of the recent evolution of this breed. The strategy described here will be useful for other breeds or even species for which a careful historical registry is not available for conservation proposals.SIWe thank to the farmers, who allowed the development of this project in their farms. We thank to Mr. Peter Laspina for reviewing language review and valuable comments. This study was supported by Fundação de Amparo a Pesquisa de Minas Gerais (FAPEMIG), Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) and Empresa Brasileira de Pesquisa Agropecuária (Embrapa). Marcos V. B. Silva was supported by the Embrapa – SEG 02.09.07.008.00.00 “Genomic Selection in Dairy Cattle in Brazil”, CNPq PVE 407246/2013-4 “Genomic Selection in Dairy Gyr and Girolando Breeds”, and FAPEMIG CVZ PPM 00395/14 “Genomic Selection in Brazilian Dairy Breeds” appropriated projects. MRSC has a fellowship from the CNPq – 307975/2010-0 and was supported by CNPq – 505338/2008-A and 481018/2008-5 projects. MGCDP, RVV, MAM have fellowships from FAPEMIG. PASF, FCS and ICR have CAPES fellowships

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

Foundations of Black Hole Accretion Disk Theory

This review covers the main aspects of black hole accretion disk theory. We begin with the view that one of the main goals of the theory is to better understand the nature of black holes themselves. In this light we discuss how accretion disks might reveal some of the unique signatures of strong gravity: the event horizon, the innermost stable circular orbit, and the ergosphere. We then review, from a first-principles perspective, the physical processes at play in accretion disks. This leads us to the four primary accretion disk models that we review: Polish doughnuts (thick disks), Shakura-Sunyaev (thin) disks, slim disks, and advection-dominated accretion flows (ADAFs). After presenting the models we discuss issues of stability, oscillations, and jets. Following our review of the analytic work, we take a parallel approach in reviewing numerical studies of black hole accretion disks. We finish with a few select applications that highlight particular astrophysical applications: measurements of black hole mass and spin, black hole vs. neutron star accretion disks, black hole accretion disk spectral states, and quasi-periodic oscillations (QPOs).Comment: 91 pages, 23 figures, final published version available at http://www.livingreviews.org/lrr-2013-

Gas pile-up, gap overflow, and Type 1.5 migration in circumbinary disks: general theory

Many astrophysical binaries, from planets to black holes, exert strong torques on their circumbinary accretion disks, and are expected to significantly modify the disk structure. Despite the several decade long history of the subject, the joint evolution of the binary + disk system has not been modeled with self-consistent assumptions for arbitrary mass ratios and accretion rates. Here we solve the coupled binary-disk evolution equations analytically in the strongly perturbed limit, treating the azimuthally-averaged angular momentum exchange between the disk and the binary and the modifications to the density, scale-height, and viscosity self-consistently, including viscous and tidal heating, diffusion limited cooling, radiation pressure, and the orbital decay of the binary. We find a solution with a central cavity and a migration rate similar to those previously obtained for Type-II migration, applicable for large masses and binary separations, and near-equal mass ratios. However, we identify a distinct new regime, applicable at smaller separations and masses, and mass ratio in the range 0.001< q < 0.1. For these systems, gas piles up outside the binary's orbit, but rather than creating a cavity, it continuously overflows as in a porous dam. The disk profile is intermediate between a weakly perturbed disk (producing Type-I migration) and a disk with a gap (with Type-II migration). However, the migration rate of the secondary is typically slower than both Type-I and Type-II rates. We term this new regime "Type-1.5" migration.Comment: 21 pages, 3 figures, accepted for publication in MNRA

AVALIAÇÃO DOS PARÂMETROS HEMATOLÓGICOS EM RATOS WISTAR DESCENDENTES DE MÃES OBESAS

O modelo de obesidade em ratos por meio de uma dieta hiperlipídica têm se consolidado, sendo relevante compreender os componentes da hereditariedade nesta enfermidade. Através do hemograma é possível avaliar os elementos sanguíneos e as células responsáveis pela defesa do organismo, incluindo a morfologia e interpretação das mesmas. Compreender estes fatores em ratos descendentes de mães obesas poderia contribuir na compreensão dos mecanismos imuno-hematológicos envolvidos na obesidade e na hereditariedade. Com isso o objetivo deste estudo é avaliar os parâmetros hematológicos e leucocitários de ratos alimentados com dieta hiperlipídica descendentes de mães obesas. Foram utilizadas 20 ratas Wistar (peso inicial 200g) alimentadas com dieta padrão (CT) ou com dieta hiperlipídica (HL). Posteriormente, alocou-se 3 fêmeas com 1 macho por 4 dias, certificando o cruzamento. Após 23 dias do nascimento da ninhada, foi feita a separação da prole em 4 grupos com 5 animais cada, e submetidos à dieta HL ou CT. Ficando então os grupos CT, CT+ HL, HL, HL + CT. Após 20 semanas de dieta, os animais foram anestesiados e tiveram peritônio exposto para coleta de sangue, que serviu para a realização e análise do hemograma, por diferenciação celular. Todos os procedimentos foram realizados de acordo com as diretrizes da utilização de animais para fins científicos (Lei 11.794/08), e protocolada no CEUA sob o n° 9062310117. As ratas HL tiveram um ganho de peso significativamente maior a partir da 10ª semana, comparando as ratas CT. Já em relação à prole, após 13 semanas, o grupo HL obteve um ganho de peso maior em relação aos demais grupos: CT: 144,8 ± 12,15 g; CT+HL (ratos descendentes de mães CT alimentados com ração HL): 138,6 ± 5,34 g; HL+CT (ratos descendentes de mães HL alimentados com ração CT): 152,2 ± 5,23 g; HL 161 ± 10,75 g. Nos parâmetros hematológicos da prole, foi observada diferença entre o grupo CT e experimental, os monócitos apresentaram uma redução significativa de 1,6± 0,89, hemoglobina 13,8 ± 1,07, hematócrito 37,9 ± 5,51 nos grupos que receberam dieta CT comparado à CT+HL, VCM apresentou aumento de 50,4 ± 0,55 no grupo CT e 53,5 ± 0,58 na dieta HL. Dentro das condições experimentais deste trabalho e com base nos resultados obtidos, conclui-se que a dieta hiperlipídica é capaz de induzir a obesidade, com capacidade de influenciar a proliferação e a diferenciação hematopoiética, porém a prole alimentada com ração padrão (CT) consegue adaptar a dieta independente do fator hereditário em relação à obesidade

Cherenkov radiation emitted by ultrafast laser pulses and the generation of coherent polaritons

We report on the generation of coherent phonon polaritons in ZnTe, GaP and LiTaO$_{3}$ using ultrafast optical pulses. These polaritons are coupled modes consisting of mostly far-infrared radiation and a small phonon component, which are excited through nonlinear optical processes involving the Raman and the second-order susceptibilities (difference frequency generation). We probe their associated hybrid vibrational-electric field, in the THz range, by electro-optic sampling methods. The measured field patterns agree very well with calculations for the field due to a distribution of dipoles that follows the shape and moves with the group velocity of the optical pulses. For a tightly focused pulse, the pattern is identical to that of classical Cherenkov radiation by a moving dipole. Results for other shapes and, in particular, for the planar and transient-grating geometries, are accounted for by a convolution of the Cherenkov field due to a point dipole with the function describing the slowly-varying intensity of the pulse. Hence, polariton fields resulting from pulses of arbitrary shape can be described quantitatively in terms of expressions for the Cherenkov radiation emitted by an extended source. Using the Cherenkov approach, we recover the phase-matching conditions that lead to the selection of specific polariton wavevectors in the planar and transient grating geometry as well as the Cherenkov angle itself. The formalism can be easily extended to media exhibiting dispersion in the THz range. Calculations and experimental data for point-like and planar sources reveal significant differences between the so-called superluminal and subluminal cases where the group velocity of the optical pulses is, respectively, above and below the highest phase velocity in the infrared.Comment: 13 pages, 11 figure

Response to Comment on “Estimating the reproducibility of psychological science”

Gilbert et al. conclude that evidence from the Open Science Collaboration's Reproducibility Project: Psychology indicates high reproducibility, given the study methodology. Their very optimistic assessment is limited by statistical misconceptions and by causal inferences from selectively interpreted, correlational data. Using the Reproducibility Project: Psychology data, both optimistic and pessimistic conclusions about reproducibility are possible, and neither are yet warranted.status: publishe