The X-ray spectral evolution of Cyg X-2 in the framework of bulk Comptonization

We used the newly developed thermal plus bulk Comptonization model comptb to investigate the spectral evolution of the neutron star LMXB Cyg X-2 along its Z-track. We selected a single source in order to trace in a quantitative way the evolution of the physical parameters of the model. We analyzed archival broad-band BeppoSAX spectra of Cyg X-2. Five broad-band spectra have been newly extracted according to the source position in the Z-track described in the colour-colour and colour-intensity diagrams. We have fitted the spectra of the source with two comptb components. The first one, with bulk parameter delta=0, dominates the overall source broad-band spectrum and its origin is related to thermal upscattering (Comptonization) of cold seed photons off warm electrons in high-opacity enviroment. We attribute the origin of these seed photons to the part of the disk which illuminates the outer coronal region (transition layer) located between the accretion disk itself and the neutron star surface. This thermal component is roughly constant with time and with inferred mass accretion rate. The second comptb model describes the overall Comptonization (thermal plus bulk, delta > 0) of hotter seed photons which come from both the inner transition layer and from the neutron star surface. The appearance of this component in the colour-colour or hardness-intensity diagram is more pronounced in the horizontal branch and is progressively disappearing towards the normal branch, where a pure blackbody spectrum is observed. The spectral evolution of Cyg X-2 is studied and interpreted in terms of changes in the innermost environmental conditions of the system, leading to a variable thermal-bulk Comptonization efficiency.Comment: 10 pages, 7 figures, accepted for publication in A&

On the stability of the thermal Comptonization index in neutron star low-mass X-ray binaries in their different spectral states

Most of the spectra of neutron star low mass X-ray binaries (NS LMXBs), being them persistent or transient, are characterized by the presence of a strong thermal Comptonization bump, thought to originate in the transition layer (TL) between the accretion disk and the NS surface. The observable quantities which characterize this component dominating the emission below 30 keV, are the spectral index alpha and the rollover energy, both related to the electron temperature and optical depth of the plasma. Starting from observational results on a sample of NS LMXBs in different spectral states, we formulate the problem of X-ray spectral formation in the TL of these sources. We predict a stability of the thermal Comptonization spectral index in different spectral states if the energy release in the TL is much higher than the intercepted flux coming from the accretion disk. We use an equation for the energy balance and the radiative transfer diffusion equation for a slab geometry in the TL, to derive a formula for the thermal Comptonization index alpha. We show that in this approximation the TL electron temperature kTe and optical depth tau_0 can be written as a function of the energy flux from the disk intercepted by the corona (TL) and that in the corona itself Qdisk/Qcor, in turn leading to a relation alpha=f(Qdisk/Qcor), with alpha ~ 1 when Qdisk/Qcor <<1. We show that the observed spectral index alpha for the sample of sources here considered lies in a belt around 1 +/- 0.2 a part for the case of GX 354--0. Comparing our theoretical predictions with observations, we claim that this result, which is consistent with the condition Qdisk/Qcor <<1, can give us constraints on the accretion geometry of these systems, an issue that seems difficult to be solved using only the spectral analysis method.Comment: 7 pages, 3 figures, accepted for publication in A&

Spectral Index as a Function of Mass Accretion Rate in Black Hole Sources. Monte-Carlo Simulations and an Analytical Description

In this Paper, we present theoretical arguments that the observationally established index saturation effect vs mass accretion rate is a signature of the bulk (converging) flow onto the black hole. We demonstrate that the index saturation value depends on the plasma temperature of converging flow. We self-consistently calculate the Compton cloud (CC) plasma temperature as a function of mass accretion rate using the energy balance between energy dissipation and Compton cooling. We explain the observable phenomenon, index- mdot correlations using a Monte-Carlo simulation of radiative processes in the innermost part (CC) of a BH source and we account for the Comptonization processes in the presence of thermal and bulk motions, as basic types of plasma motion. We show that, when mdot increases, BH sources evolve to high and very soft states (HSS and VSS, respectively), in which the strong blackbody-like and steep power-law components are formed in the resulting X-ray spectrum. The simultaneous detections of these two components strongly depends on sensitivity of high energy instruments, given that the relative contribution of the hard power-law tail in the resulting VSS spectrum can be very low, which is why, to date {\it RXTE} observations of the VSS X-ray spectrum has been characterized by the presence of the strong BB-like component only. We also predict specific patterns for high-energy efold (cutoff) energy (E_{fold}) evolution with mdot for thermal and dynamical (bulk) Comptonization cases. For the former case, E_{fold} monotonically decreases with mdot, in the latter case, the E_{fold}-decrease is followed by its increase at high values of mdot. The observational evolution of E_{fold} vs mdot can be one more test for the presence of a converging flow effect in the formation of the resulting spectra in the close vicinity of BHs.Comment: 15 pages, 11 figures, accepted for the publication in the Astrophysical Journa

Probabilistic base calling of Solexa sequencing data

BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput data poses new challenges; currently a fair proportion of the tags are routinely discarded due to an inability to match them to a reference sequence, thereby reducing the effective throughput of the technology. RESULTS: We propose a novel base calling algorithm using model-based clustering and probability theory to identify ambiguous bases and code them with IUPAC symbols. We also select optimal sub-tags using a score based on information content to remove uncertain bases towards the ends of the reads. CONCLUSION: We show that the method improves genome coverage and number of usable tags as compared with Solexa's data processing pipeline by an average of 15%. An R package is provided which allows fast and accurate base calling of Solexa's fluorescence intensity files and the production of informative diagnostic plots

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads

Motivation: Paired-end sequencing allows circumventing the shortness of the reads produced by second generation sequencers and is essential for de novo assembly of genomes. However, obtaining a finished genome from short reads is still an open challenge. We present an algorithm that exploits the pairing information issued from inserts of potentially any length. The method determines paths through an overlaps graph by using a constrained search tree. We also present a method that automatically determines suited overlaps cutoffs according to the contextual coverage, reducing thus the need for manual parameterization. Finally, we introduce an interactive mode that allows querying an assembly at targeted regions. Results: We assess our methods by assembling two Staphylococcus aureus strains that were sequenced on the Illumina platform. Using 100 bp paired-end reads and minimal manual curation, we produce a finished genome sequence for the previously undescribed isolate SGH-10-168. Availability and implementation: The presented algorithms are implemented in the standalone Edena software, freely available under the General Public License (GPLv3) at www.genomic.ch/edena.php. Contact: [email protected] Supplementary Information: Supplementary data are available at Bioinformatics onlin

Cell-free DNA testing of an extended range of chromosomal anomalies: clinical experience with 6,388 consecutive cases

PURPOSE: Cell-free DNA (cfDNA) testing for fetal aneuploidies was broadly implemented for common trisomies and sex-chromosome anomalies (SCAs). However, such an approach identifies only 75 to 85% of clinically relevant aneuploidies. METHODS: We present a consecutive series of 6,388 cases, thus uncovering a broader array of aneuploidies, including the rare autosomal trisomies (RATs) and the maternally inherited deletion and duplication copy-number variations (CNVs), with complete and stratified follow-up by amniocentesis. Combined measurements of z-scores and the fetal fraction, in conjunction with fetal cfDNA enrichment, were used to stratify the likelihood of true and false results. RESULTS: We obtained an incremental diagnostic yield of 50%; RATs and CNVs were found to be significant causes of fetal pathology. Scrutinizing z-scores and the fetal fraction made it possible to distinguish the sources of false-negative results; predict the likelihood of false-positive results for major trisomies and SCAs; classify maternal mosaic SCAs and CNVs, preventing false-positive results; and robustly identify maternally inherited CNVs and detect recurrent genomic disorders as a standardized function of the fetal fraction. CONCLUSION: With the clinical pertinence of this broader detection scheme confirmed, we offer recommendations for its implementation. Genet Med 19 2, 169–175

Analysis of the salivary microbiome using culture-independent techniques

The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated

Analysis of the salivary microbiome using culture-independent techniques

The salivary microbiota is a potential diagnostic indicator of several diseases. Culture-independent techniques are required to study the salivary microbial community since many of its members have not been cultivated

Detection of Genomic Variation by Selection of a 9 Mb DNA Region and High Throughput Sequencing

Detection of the rare polymorphisms and causative mutations of genetic diseases in a targeted genomic area has become a major goal in order to understand genomic and phenotypic variability. We have interrogated repeat-masked regions of 8.9 Mb on human chromosomes 21 (7.8 Mb) and 7 (1.1 Mb) from an individual from the International HapMap Project (NA12872). We have optimized a method of genomic selection for high throughput sequencing. Microarray-based selection and sequencing resulted in 260-fold enrichment, with 41% of reads mapping to the target region. 83% of SNPs in the targeted region had at least 4-fold sequence coverage and 54% at least 15-fold. When assaying HapMap SNPs in NA12872, our sequence genotypes are 91.3% concordant in regions with coverage≥4-fold, and 97.9% concordant in regions with coverage≥15-fold. About 81% of the SNPs recovered with both thresholds are listed in dbSNP. We observed that regions with low sequence coverage occur in close proximity to low-complexity DNA. Validation experiments using Sanger sequencing were performed for 46 SNPs with 15-20 fold coverage, with a confirmation rate of 96%, suggesting that DNA selection provides an accurate and cost-effective method for identifying rare genomic variants

Massive production of small RNAs from a non-coding region of Cauliflower mosaic virus in plant defense and viral counter-defense

To successfully infect plants, viruses must counteract small RNA-based host defense responses. During infection of Arabidopsis, Cauliflower mosaic pararetrovirus (CaMV) is transcribed into pregenomic 35S and subgenomic 19S RNAs. The 35S RNA is both reverse transcribed and also used as an mRNA with highly structured 600 nt leader. We found that this leader region is transcribed into long sense- and antisense-RNAs and spawns a massive quantity of 21, 22 and 24 nt viral small RNAs (vsRNAs), comparable to the entire complement of host-encoded small-interfering RNAs and microRNAs. Leader-derived vsRNAs were detected bound to the Argonaute 1 (AGO1) effector protein, unlike vsRNAs from other viral regions. Only negligible amounts of leader-derived vsRNAs were bound to AGO4. Genetic evidence showed that all four Dicer-like (DCL) proteins mediate vsRNA biogenesis, whereas the RNA polymerases Pol IV, Pol V, RDR1, RDR2 and RDR6 are not required for this process. Surprisingly, CaMV titers were not increased in dcl1/2/3/4 quadruple mutants that accumulate only residual amounts of vsRNAs. Ectopic expression of CaMV leader vsRNAs from an attenuated geminivirus led to increased accumulation of this chimeric virus. Thus, massive production of leader-derived vsRNAs does not restrict viral replication but may serve as a decoy diverting the silencing machinery from viral promoter and coding region