Spectral optical monitoring of 3C390.3 in 1995-2007: I. Light curves and flux variation of the continuum and broad lines

Here we present the results of the long-term (1995-2007) spectral monitoring of the broad line radio galaxy \object{3C~390.3}, a well known AGN with the double peaked broad emission lines, usually assumed to be emitted from an accretion disk. To explore dimensions and structure of the BLR, we analyze the light curves of the broad H$\alpha$ and H$\beta$ line fluxes and the continuum flux. In order to find changes in the BLR, we analyze the H$\alpha$ and H$\beta$ line profiles, as well as the change in the line profiles during the monitoring period. First we try to find a periodicity in the continuum and H$\beta$ light curves, finding that there is a good chance for quasi-periodical oscillations. Using the line shapes and their characteristics (as e.g. peaks separation and their intensity ratio, or FWHM) of broad H$\beta$ and H$\alpha$ lines, we discuss the structure of the BLR. Also, we cross-correlate the continuum flux with H$\beta$ and H$\alpha$ lines to find dimensions of the BLR. We found that during the monitoring period the broad emission component of the H$\alpha$ and H$\beta$ lines, and the continuum flux varied by a factor of $\approx$4-5. Also, we detected different structure in the line profiles of H$\alpha$ and H$\beta$. It seems that an additional central component is present and superposed to the disk emission. In the period of high activity (after 2002), H$\beta$ became broader than H$\alpha$ and red wing of H$\beta$ was higher than the one of H$\alpha$. We found time lags of $\sim$95 days between the continuum and H$\beta$ flux, and about 120 days between the continuum and H$\alpha$ flux. Variation in the line profiles, as well as correlation between the line and continuum flux during the monitoring period is in the favor of the disk origin of the broad lines with the possible contribution of some additional region and/or some kind of perturbation in the disk.Comment: 32 pages, accepted to A&A, typos correcte

Molecular Adaptations for Sensing and Securing Prey and Insight into Amniote Genome Diversity from the Garter Snake Genome

Colubridae represents the most phenotypically diverse and speciose family of snakes, yet no well-assembled and annotated genome exists for this lineage. Here, we report and analyze the genome of the garter snake, Thamnophis sirtalis, a colubrid snake that is an important model species for research in evolutionary biology, physiology, genomics, behavior, and the evolution of toxin resistance. Using the garter snake genome, we show how snakes have evolved numerous adaptations for sensing and securing prey, and identify features of snake genome structure that provide insight into the evolution of amniote genomes. Analyses of the garter snake and other squamate reptile genomes highlight shifts in repeat element abundance and expansion within snakes, uncover evidence of genes under positive selection, and provide revised neutral substitution rate estimates for squamates. Our identification of Z and W sex chromosome-specific scaffolds provides evidence for multiple origins of sex chromosome systems in snakes and demonstrates the value of this genome for studying sex chromosome evolution. Analysis of gene duplication and loss in visual and olfactory gene families supports a dim-light ancestral condition in snakes and indicates that olfactory receptor repertoires underwent an expansion early in snake evolution. Additionally, we provide some of the first links between secreted venom proteins, the genes that encode them, and their evolutionary origins in a rear-fanged colubrid snake, together with new genomic insight into the coevolutionary arms race between garter snakes and highly toxic newt prey that led to toxin resistance in garter snakes

Precisión de los estudiantes de psicología en la estimación de la asociación

Las tablas de contingencia son un recurso frecuente para presentar información estadística en prensa e Internet, así como en documentos técnicos usados en el trabajo profesional, aunque la enseñanza actual no presta mucha importancia a este tema, suponiendo que su interpretación es sencilla. En este trabajo analizamos la percepción de la asociación y estimación de su intensidad en tablas de contingencia en una muestra de 414 estudiantes de psicología de tres universidades españolas. Se observan respuesta similares en las tres universidades, alta consistencia entre percepción subjetiva de la asociación y precisión de la estimación y mejores resultados que los obtenidos en un estudio previo de Estepa (1994) con estudiantes de Bachillerato. Sin embargo, las estrategias al realizar el juicio de asociación son mayoritariamente incorrectas y sólo influyen en la precisión del juicio en el caso de independencia en los datos. Estos problemas podrían presentarse en otros estudiantes, por lo que los profesores debieran conocerlos para tenerlos en cuenta en la enseñanza

Solar causes of the long-term increase in geomagnetic activity

We analyze the causes of the century-long increase in geomagnetic activity, quantified by annual means of the aa index, using observations of interplanetary space, galactic cosmic rays, the ionosphere, and the auroral electrojet, made during the last three solar cycles. The effects of changes in ionospheric conductivity, the Earth's dipole tilt, and magnetic moment are shown to be small; only changes in near-Earth interplanetary space make a significant contribution to the long-term increase in activity. We study the effects of the interplanetary medium by applying dimensional analysis to generate the optimum solar wind-magnetosphere energy coupling function, having an unprecedentedly high correlation coefficient of 0.97. Analysis of the terms of the coupling function shows that the largest contributions to the drift in activity over solar cycles 20-22 originate from rises in the average interplanetary magnetic field (IMF) strength, solar wind concentration, and speed; average IMF orientation has grown somewhat less propitious for causing geomagnetic activity. The combination of these factors explains almost all of the 39% rise in aa observed over the last three solar cycles. Whereas the IMF strength varies approximately in phase with sunspot numbers, neither its orientation nor the solar wind density shows any coherent solar cycle variation. The solar wind speed peaks strongly in the declining phase of even-numbered cycles and can be identified as the chief cause of the phase shift between the sunspot numbers and the aa index. The rise in the IMF magnitude, the largest single contributor to the drift in geomagnetic activity, is shown to be caused by a rise in the solar coronal magnetic field, consistent with a rise in the coronal source field, modeled from photospheric observations, and an observed decay in cosmic ray fluxes

adult_worm_and_eight_miracidia_stringent_filter

vcf comprised of stringently filtered variants found from ddRADseq in S. japonicum adult worm and eight miracidia samples

Data from: Whole genome amplification and reduced-representation genome sequencing of Schistosoma japonicum miracidia

Background: In areas where schistosomiasis control programs have been implemented, morbidity and prevalence have been greatly reduced. However, to sustain these reductions and move towards interruption of transmission, new tools for disease surveillance are needed. Genomic methods have the potential to help trace the sources of new infections, and allow us to monitor drug resistance. Large-scale genotyping efforts for schistosome species have been hindered by cost, limited numbers of established target loci, and the small amount of DNA obtained from miracidia, the life stage most readily acquired from humans. Here, we present a method using next generation sequencing to provide high-resolution genomic data from S. japonicum for population-based studies. Methodology/Principal Findings: We applied whole genome amplification followed by double digest restriction site associated DNA sequencing (ddRADseq) to individual S. japonicum miracidia preserved on Whatman FTA cards. We found that we could effectively and consistently survey hundreds of thousands of variants from 10,000 to 30,000 loci from archived miracidia as old as six years. An analysis of variation from eight miracidia obtained from three hosts in two villages in Sichuan showed clear population structuring by village and host even within this limited sample. Conclusions/Significance: This high-resolution sequencing approach yields three orders of magnitude more information than microsatellite genotyping methods that have been employed over the last decade, creating the potential to answer detailed questions about the sources of human infections and to monitor drug resistance. Costs per sample range from $50-$200, depending on the amount of sequence information desired, and we expect these costs can be reduced further given continued reductions in sequencing costs, improvement of protocols, and parallelization. This approach provides new promise for using modern genome-scale sampling to S. japonicum surveillance, and could be applied to other schistosome species and other parasitic helminthe

Patterns of relatedness and genetic diversity inferred from whole genome sequencing of archival blood fluke miracidia (Schistosoma japonicum).

Genomic approaches hold great promise for resolving unanswered questions about transmission patterns and responses to control efforts for schistosomiasis and other neglected tropical diseases. However, the cost of generating genomic data and the challenges associated with obtaining sufficient DNA from individual schistosome larvae (miracidia) from mammalian hosts have limited the application of genomic data for studying schistosomes and other complex macroparasites. Here, we demonstrate the feasibility of utilizing whole genome amplification and sequencing (WGS) to analyze individual archival miracidia. As an example, we sequenced whole genomes of 22 miracidia from 11 human hosts representing two villages in rural Sichuan, China, and used these data to evaluate patterns of relatedness and genetic diversity. We also down-sampled our dataset to test how lower coverage sequencing could increase the cost effectiveness of WGS while maintaining power to accurately infer relatedness. Collectively, our results illustrate that population-level WGS datasets are attainable for individual miracidia and represent a powerful tool for ultimately providing insight into overall genetic diversity, parasite relatedness, and transmission patterns for better design and evaluation of disease control efforts

var_sharing_sampling

calculates pairwise similarity of genotypes between samples of a vc