Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data

Summary: Here we present the open-source R/Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors. Availability and implementation: BEAT is freely available as part of Bioconductor at www.bioconductor.org/packages/devel/bioc/html/BEAT.html. The package is distributed under the GNU Lesser General Public License 3.0. Contact: [email protected] Supplementary information: Supplementary data are available at Bioinformatics online

An agent-based signal processing in-node environment for real-time human activity monitoring based on wireless body sensor networks

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Transthoracic echocardiography provides important long-term prognostic information in selected patients undergoing endovascular abdominal aortic repair

BACKGROUND: The value of performing transthoracic echocardiography (TTE) as part of the clinical assessment of patients awaiting endovascular repair of the abdominal aorta is little evaluated. We aimed to estimate the prognostic importance of information derived from TTE on long-term all-cause mortality in a selected group of patients undergoing endovascular aneurysm repair. METHODS AND RESULTS: This was a retrospective cohort study of 273 consecutive patients selected for endovascular aneurysm repair. All patients included in the analysis underwent TTE before their procedure. Multivariable Cox regression analysis was used to estimate the effect of TTE measures on all-cause mortality. Over a mean follow-up of 3.2±1.5 years, there were 78 deaths with a mean time to death of 1.28±1.16 years. A greater tubular ascending aorta (hazard ratio [HR] 5.6, 95% confidence interval [CI] 2.77-11.33), presence of mitral regurgitation (HR 8.13, 95% CI 4.09-12.16), lower left ventricular ejection fraction (HR 0.96, 95% CI 0.93-0.98), younger age (HR 0.97, 95% CI 0.95-0.99), and presence of diabetes mellitus (HR 1.46, 95% CI 1.24-1.89) were predictors of all-cause mortality. CONCLUSIONS: Echocardiography provides important long-term prognostic information in patients undergoing endovascular aneurysm repair. These TTE indices were more important at predicting outcome than standard conventional risk factors in this patient group. A greater tubular ascending aorta, presence of mitral regurgitation, reduced left ventricular ejection fraction, younger age, and diabetes mellitus were independently associated with long-term mortality

Ghost-gluon coupling, power corrections and ΛMS‾\Lambda_{\overline {\rm MS}} from twisted-mass lattice QCD at Nf=2

We present results concerning the non-perturbative evaluation of the ghost-gluon running QCD coupling constant from $N_f=2$ twisted-mass lattice calculations. A novel method for calibrating the lattice spacing, independent of the string tension and hadron spectrum is presented with results in agreement with previous estimates. The value of $\Lambda_{\overline{MS}}$ is computed from the running of the QCD coupling only after extrapolating to zero dynamical quark mass and after removing a non-perturbative OPE contribution that is assumed to be dominated by the dimension-two \VEV{A^2} gluon condensate. The effect due to the dynamical quark mass in the determination of \Lams is discussed.Comment: 33 pages, 6 fig

Oral platelet gel supernatant plus supportive medical treatment versus supportive medical treatment in the management of radiation-induced oral mucositis: a matched explorative active control trial by propensity analysis

OBJECTIVES:: In this active control trial, the rate of radio-induced WHO grade 3/4 oral mucositis and the change in quality of life, assessed by OMWQ-HN, were measured in subjects with head and neck cancer treated by platelet gel supernatant (PGS) and supportive medical treatment versus subjects treated by supportive medical treatment alone. MATERIALS AND METHODS:: Eighty patients with nonmetastatic head and neck cancer underwent curative or adjuvant radiotherapy. All patients underwent supportive medical treatment and/or PGS at the beginning and during radiotherapy. Sixteen patients received PGS in association with supportive medical treatment. To obtain 2 groups virtually randomized for important clinical characteristics subjects were matched, by propensity analysis, with a group of subjects (64 patients) treated with supportive medical treatment alone. RESULTS:: Subjects treated with standard supportive treatment experienced significant higher WHO grade 3/4 toxicity (55%; 35/64) than subjects treated by PGS (13%; 3/16). The reduced toxicity found in PGS group paralleled with the evidence that they developed later symptoms with respect to controls. The Cox proportional hazard model indicated that patients treated with standard supportive medical treatment experienced 2.7-fold increase (hazard ratio=2.7; 95% confidence interval, 1.3-5.7) in the occurrence of WHO grade 3/4 toxicity. PGS group significantly experienced higher quality of life than control groups as measured by OMWQ-HN. A significant decrease in the opioid analgesics usage was found in the PGS group. CONCLUSIONS:: These preliminary data should be interpreted with caution and could serve as a framework around which to design future trials