On Statistical Modeling of Sequencing Noise in High Depth Data to Assess Tumor Evolution

© 2017, Springer Science+Business Media, LLC, part of Springer Nature. One cause of cancer mortality is tumor evolution to therapy-resistant disease. First line therapy often targets the dominant clone, and drug resistance can emerge from preexisting clones that gain fitness through therapy-induced natural selection. Such mutations may be identified using targeted sequencing assays by analysis of noise in high-depth data. Here, we develop a comprehensive, unbiased model for sequencing error background. We find that noise in sufficiently deep DNA sequencing data can be approximated by aggregating negative binomial distributions. Mutations with frequencies above noise may have prognostic value. We evaluate our model with simulated exponentially expanded populations as well as data from cell line and patient sample dilution experiments, demonstrating its utility in prognosticating tumor progression. Our results may have the potential to identify significant mutations that can cause recurrence. These results are relevant in the pretreatment clinical setting to determine appropriate therapy and prepare for potential recurrence pretreatment

On the prediction of reverberation time and strength in mosques

The present study focuses on the prediction of reverberation time and on the distribution of sound level with distance inside mosques. Four sets of measured data have been compared with theoretical predictions obtained by sound absorption data of materials typically found inside mosques. Some peculiarities of the sound field inside mosques are pointed out

On the effect of floor in mosques

In this paper the impact of typical floor inside mosques has been studied by the comparison of in situ acoustical measurements taken inside very similar environments, namely SS. Sergius and Baccus in Istanbul (Turkey) and S. Vitale in Ravenna (Italy). In the work typical layouts of floors have been rebuilt and tested for sound absorption with standard procedures. Finally, some theoretical formulas have been tested to predict the influence of the mosque floor

Is serum cystatin C a sensitive marker of glomerular filtration rate (GFR)? A preliminary study on renal transplant patients.

Human cystatin C is a basic low molecular mass protein (13,359 Dalton) freely filtered through the glomerulus and almost completely re-absorbed and catabolized by proximal tubular cells. We measured serum cystatin C in 38 kidney transplant patients (23 males, 15 females) aged between 6 and 32 years. To assess renal function, serum and urinary creatinine were also determined in all patients, and creatinine clearance was finally calculated. Cystatin C was determined by a particle-enhanced turbidimetric assay, and creatinine was measured by gas chromatography-mass spectrometry. To compare the diagnostic efficiency of cystatin C with that of creatinine, inulin clearance was performed on 12 renal transplant patients, and receiver operating characteristic (ROC) analysis was applied. The results of this study demonstrate that serum cystatin C significantly increases in renal transplant patients with reduced creatinine clearance (< 70 mL/min per 1.73 m2) and that the diagnostic accuracy of serum cystatin C is better than of serum creatinine. Cystatin C may be utilized as a very marker of reduced GFR

Indagine sulla diffusione delle nuove varianti del parvovirus canino tipo 2 in Abruzzo

Aim of the study - The diagnostic investigation results for canine parvovirus type 2 (CPV-2) infection in symptomatic dogs are reported, in order to evaluate the presence and the distribution of the viral variants in the canine population of Abruzzo region. Materials and methods - One hundred and four faecal samples were analyzed by conventional and real-time PCR with minor groove binder (MGB) probes. Results - CPV-2 DNA was detected in 55 (52,8%) samples and 31 (56,3%) CPV-2a, 1 (1,8%) CPV-2b and 23 (41,8%) CPV-2c strains were identified by real-time PCR with MGB probes.The distribution of CPV-2 over the sampling years appears different in relation to each variant. Conclusions - CPV-2 is an important causative agent of gastroenteritis in dogs of the Abruzzo region and the CPV-2a was the most prevalent variant. However, it appears that the CPV-2c occurrence is growing, while CPV-2b is poorly widespread. In conclusion, the monitoring of the parvovirus infection in dogs population is useful to verify the evolution of the geographic distribution of the CPV-2 variants and to evaluate the efficacy of the prophylactic measures performed to control the disease. [...