On the origin of black hole X-ray emission in quiescence: Chandra observations of XTE J1550-564 and H 1743-322

We report the results of observations of the black hole binaries XTE J1550-564 and H 1743-322 in their quiescent state using the Chandra X-ray Observatory. Both sources are detected at their faintest level of X-ray emission ever observed with a 0.5-10 keV unabsorbed luminosity of 2 $\times$ 10$^{32}$ (d/5 kpc)$^2$ erg s$^{-1}$ for XTE J1550-564 and 9 $\times$ 10$^{31}$ (d/8 kpc)$^2$ erg s$^{-1}$ for H 1743-322. These luminosities are in the upper range compared to the faintest levels observed in other black hole systems, possibly related to residual accretion for these sources with frequent outbursts. For XTE J1550-564, the Chandra observations also constrain the X-ray spectrum as a fit with an absorbed power-law model yields a photon index of 2.25 $\pm$ 0.08, clearly indicating a softening of the X-ray spectrum at lower luminosities compared to the standard hard state. Similar softening at low luminosity is seen for several black hole transients with orbital periods less than 60 hours. Most of the current models of accreting black holes are able to reproduce such softening in quiescence. In contrast, we find that systems with orbital periods longer than 60 hours appear to have hard spectra in quiescence and their behaviour may be consistent with hardening in quiescence.Comment: 23 pages, 6 figures. The Astrophysical Journal, accepted, in pres

P07-05. HIV and STI prevalence among men who have sex with men (MSM) recruited through respondent driven sampling (RDS) in Buenos Aires, Argentina

Fil: Pando, María A. Centro Nacional de Referencia para el SIDA; Argentina.Fil: Marone, Rubén. Nexo Asociación Civil; Argentina.Fil: Balán, Iván C. Columbia University. HIV Center for Clinical and Behavioral Studies; Estados Unidos.Fil: Dolezal, Curtis. Columbia University. HIV Center for Clinical and Behavioral Studies; Estados Unidos.Fil: Squiquera, Luis. Nexo Asociación Civil; Argentina. Fil: Balan, Iván C. Columbia University. HIV Center for Clinical and Behavioral Studies; Estados Unidos.Fil: Picconi, María Alejandra. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Servicio Virus Oncogénicos; Argentina.Fil: Gonzales, J. ANLIS Dr.C.G.Malbrán. Instituto Nacional de Enfermedades Infecciosas. Servicio Virus Oncogénicos; Argentina.Fil: Rey, Jorge. Hospital de Clínicas José de San Martín; Argentina.Fil: Fernandez Toscano, M. Hospital de Clínicas José de San Martín; Argentina.Fil: Rodriguez Fermepín, Marcelo. UBA. Laboratorio de Inmunología Clínica; Argentina.Fil: Gallo Vaulet, Lucia. UBA. Laboratorio de Inmunología Clínica; Argentina.Fil: Carballo Dieguez, Alex. Columbia University. HIV Center for Clinical and Behavioral Studies; Estados Unidos.Fil: Avila, María M. Centro Nacional de Referencia para el SIDA; Argentina.Background MSM constitute one of the populations most affected by HIV and other STIs in Argentina. Previous prevalence studies were based on convenience samples. RDS, a methodology designed to access hidden populations, is being used for the first time in Argentina to recruit MSM. Methods RDS recruitment started in November 2007 with 16 first generation participants (seeds) who were selected for their potential to tap in MSM networks. Recruitment is ongoing. Men must be 18 years of age or older, be residents of Buenos Aires, self-report having sex with men at least 10 times in their lives and at least once in the past six months. They must have a coupon indicating they have been referred by a study participant. Specimens are being collected for HIV and STI diagnosis. All data are weighted using the RDS Analysis Tool (RDSAT). Results To date, 333 MSM were recruited through RDS showing a prevalence of 11.3, 16.6, 7.9, 17.6, 4.0 and 88.3% for HIV, HBV, HCV, T. pallidum, Chlamydia and HPV, respectively. Chlamydia and HPV diagnoses were only performed in 73 and 79 participants, respectively. Among HPV positive individuals, 47.8% had almost one of these high risk types (16, 58, 33, 45, 18 and 31) and 32% had multiple infections with 2 or more types. Conclusion Compared with previous studies, these results show similar HIV, HBV and T. pallidum prevalences but higher HCV prevalence. For the first time, an elevated prevalence of HPV was detected on MSM, with high frequency of types associated with ano-genital cancer. Preliminary analyses of socio demographic data show that RDS helps recruit a diversity of MSM, particularly of lower socio-economic level usually missed with other recruitment methods. The high prevalence of coinfections in this population should be taken into account if MSM are part of vaccine trials given that STI may increase HIV sexual transmission

Efficient Behavior of Small-World Networks

We introduce the concept of efficiency of a network, measuring how efficiently it exchanges information. By using this simple measure small-world networks are seen as systems that are both globally and locally efficient. This allows to give a clear physical meaning to the concept of small-world, and also to perform a precise quantitative a nalysis of both weighted and unweighted networks. We study neural networks and man-made communication and transportation systems and we show that the underlying general principle of their construction is in fact a small-world principle of high efficiency.Comment: 1 figure, 2 tables. Revised version. Accepted for publication in Phys. Rev. Let

Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROHs and their length are indicators of the level and origin of inbreeding. Frequent common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler. plink software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP frequency. A functional overview of breed-specific ROH islands was obtained via over-representation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively), whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora Romagnola and Casertana. The largest number of ROH islands was identified in the Italian Landrace (n = 32), Cinta Senese (n = 26) and Lithuanian White Old Type (n = 22) breeds. Several ROH islands were in regions encompassing genes known to affect morphological traits. Comparative ROH structure analysis among breeds indicated the similar genetic structure of local breeds across Europe. This study contributed to understanding of the genetic history of the investigated pig breeds and provided information to manage these pig genetic resources

Genome‐wide detection of copy number variants in European autochthonous and commercial pig breeds by whole‐genome sequencing of DNA pools identified breed‐characterising copy number states

In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent important genetic resources for this species. The genome of 725 pigs was sequenced using a breed‐specific DNA pooling approach (30–35 animals per pool) obtaining an average depth per pool of 42×. This approach maximised CNV discovery as well as the related copy number states characterising, on average, the analysed breeds. By mining more than 17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710 CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per breed that were considered as private. A few CNVRs were analysed in more detail, together with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds, confirming the role of the multiple copies in determining breed‐specific coat colours. The CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome variability unravelled here can explain part of the genetic diversity among breeds and might contribute to explain their origin, history and adaptation to a variety of production systems.info:eu-repo/semantics/acceptedVersio

Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems

Background: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining wholegenome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. Conclusions: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources