Bridging trees for posterior inference on ancestral recombination graphs.

We present a new Markov chain Monte Carlo algorithm, implemented in the software Arbores, for inferring the history of a sample of DNA sequences. Our principal innovation is a bridging procedure, previously applied only for simple stochastic processes, in which the local computations within a bridge can proceed independently of the rest of the DNA sequence, facilitating large-scale parallelization.

Metabolic profiling of polycystic ovary syndrome reveals interactions with abdominal obesity.

BACKGROUND: Polycystic ovary syndrome (PCOS) is a common reproductive disorder associated with metabolic disturbances including obesity, insulin resistance and diabetes mellitus. Here we investigate whether changes in the metabolic profile of PCOS women are driven by increased tendency to obesity or are specific features of PCOS related to increased testosterone levels. DESIGN AND METHODS: We conducted an NMR metabolomics association study of PCOS cases (n=145) and controls (n=687) nested in a population-based birth cohort (n=3127). Subjects were 31 years old at examination. The main analyses were adjusted for waist circumference (WC) as a proxy measure of central obesity. Subsequently, metabolite concentrations were compared between cases and controls within pre-defined WC strata. In each stratum, additional metabolomics association analyses with testosterone levels were conducted separately among cases and controls. RESULTS: Overall, women with PCOS showed more adverse metabolite profiles than the controls. Four lipid fractions in different subclasses of very low density lipoprotein (VLDL) were associated with PCOS, after adjusting for WC and correction for multiple testing (P<0.002). In stratified analysis the PCOS women within large WC strata (⩾98 cm) had significantly lower high density lipoprotein (HDL) levels, Apo A1 and albumin values compared with the controls. Testosterone levels were significantly associated with VLDL and serum lipids in PCOS cases with large WC but not in the controls. The higher testosterone levels, adjusted for WC, associated adversely with insulin levels and HOMA IR in cases but not in the controls. CONCLUSIONS: Our findings show that both abdominal obesity and hyperandrogenism contribute to the dyslipidaemia and other metabolic traits of PCOS which all may negatively contribute to the long-term health of women with PCOS.

Genome-wide data reveal novel genes for methotrexate response in a large cohort of juvenile idiopathic arthritis cases.

Clinical response to methotrexate (MTX) treatment for children with juvenile idiopathic arthritis (JIA) displays considerable heterogeneity. Currently, there are no reliable predictors to identify non-responders: earlier identification could lead to a targeted treatment. We genotyped 759 JIA cases from the UK, the Netherlands and Czech Republic. Clinical variables were measured at baseline and 6 months after start of the treatment. In Phase I analysis, samples were analysed for the association with MTX response using ordinal regression of ACR-pedi categories and linear regression of change in clinical variables, and identified 31 genetic regions (P<0.001). Phase II analysis increased SNP density in the most strongly associated regions, identifying 14 regions (P<1 × 10(-5)): three contain genes of particular biological interest (ZMIZ1, TGIF1 and CFTR). These data suggest a role for novel pathways in MTX response and further investigations within associated regions will help to reach our goal of predicting response to MTX in JIA.

Bionic ear imaging.

PURPOSE: The aim of this study was to illustrate the different imaging features of middle and inner ear implants, brainstem implants and inferior colliculus implants. MATERIALS AND METHODS: We retrospectively reviewed the computed tomography (CT) images of 468 patients with congenital or acquired transmissive or neurosensory hearing loss who underwent surgery. The implants examined were: 22 Vibrant Soundbridge implants, 5 at the long limb of the incus and 17 at the round window, 350 cochlear implants, 95 brainstem implants and 1 implant at the inferior colliculus. All patients underwent a postoperative CT scan (single or multislice scanner) and/or a Dentomaxillofacial cone-beam CT scan (CBCT) (axial and multiplanar reconstruction), and/or a plain-film radiography to visualise the correct position of the implant. RESULTS: The CBCT scan depicts Vibrant site of implant better than plain-film radiography, with a lower radiation dose compared to CT. For cochlear implants, a single plain radiograph in the Stenvers projection can directly visualise the electrodes in the cochlea. All patients with brainstem or inferior colliculus implants underwent postoperative CT to exclude complications and the assess correct implantation, but the follow-up of these implants can be performed by plain radiography alone. CONCLUSIONS: CT and CBCT scans are reliable and relatively fast methods for precisely determining the location of middle ear implants. CBCT is preferable to CT because of the lower radiation dose administered; a single plain-film radiograph is enough to visualise and follow-up cochlear, brainstem and inferior colliculus implants.

[Spontaneous splenorenal and splenocaval shunts studied by echotomography]. / Dérivations spléno-rénales et spléno-caves spontanées explorées par échotomographie.

Spontaneous spleno-renal and spleno-caval shunts may be anatomically and functionally important in portal hypertension syndromes, as demonstrated by the distinct opacification of the inferior vena cava observed after portal venography with iodine contrast media. Part of the course of these porto-caval anastomotic vessels can be visualized by ultrasonography opposite the left adrenal gland and in the space between the spleen and the left kidney. The images obtained are characteristic enough for the diagnosis of spleno-renal shunt to be suspected before it is confirmed by portal venography, as was the case in the four patients with hepatic cirrhosis reported by the authors.