Characterization of Prostate Cancer with Gleason Score of at Least 7 by Using Quantitative Multiparametric MR Imaging: Validation of a Computer-aided Diagnosis System in Patients Referred for Prostate Biopsy.

Purpose To determine the performance of a computer-aided diagnosis (CAD) system trained at characterizing cancers in the peripheral zone (PZ) with a Gleason score of at least 7 in patients referred for multiparametric magnetic resonance (MR) imaging before prostate biopsy. Materials and Methods Two institutional review board-approved prospective databases of patients who underwent multiparametric MR imaging before prostatectomy (database 1) or systematic and targeted biopsy (database 2) were retrospectively used. All patients gave informed consent for inclusion in the databases.

Stiffness of benign and malignant prostate tissue measured by shear-wave elastography: a preliminary study.

Objectives: To measure benign and malignant prostate tissue stiffness using shear-wave elastography (SWE).

Methods: Thirty consecutive patients underwent transrectal SWE in the axial and sagittal planes before prostatectomy. After reviewing prostatectomy specimens, two radiologists measured stiffness in regions corresponding to cancers, lateral and median benign peripheral zone (PZ) and benign transition zone (TZ).

Quantitative Analysis of Prostate Multiparametric MR Images for Detection of Aggressive Prostate Cancer in the Peripheral Zone: A Multiple Imager Study.

Purpose To assess the intermanufacturer variability of quantitative models in discriminating cancers with a Gleason score of at least 7 among peripheral zone (PZ) lesions seen at 3-T multiparametric magnetic resonance (MR) imaging. Materials and Methods An institutional review board-approved prospective database of 257 patients who gave written consent and underwent T2-weighted, diffusion-weighted, and dynamic contrast material-enhanced imaging before prostatectomy was retrospectively reviewed. It contained outlined lesions found to be suspicious for malignancy by two independent radiologists and classified as malignant or benign after correlation with prostatectomy whole-mount specimens.

Complete Arabis alpina chloroplast genome sequence and insight into its polymorphism.

The alpine plant Arabis alpina (alpine rock-cress) is a thoroughly studied species in the fields of perennial plant flowering regulation, phylogeography, and adaptation to harsh alpine climatic conditions. We report the complete A. alpina chloroplast genome sequence obtained through de novo assembly of Illumina paired-end reads produced by total DNA sequencing.

Detection of genomic loci associated with environmental variables using generalized linear mixed models.

We tested the use of Generalized Linear Mixed Models to detect associations between genetic loci and environmental variables, taking into account the population structure of sampled individuals. We used a simulation approach to generate datasets under demographically and selectively explicit models. These datasets were used to analyze and optimize GLMM capacity to detect the association between markers and selective coefficients as environmental data in terms of false and true positive rates.

How accurate is multiparametric MR imaging in evaluation of prostate cancer volume?

Purpose: To assess the factors influencing multiparametric (MP) magnetic resonance (MR) imaging accuracy in estimating prostate cancer histologic volume (Vh).

Materials And Methods: A prospective database of 202 patients who underwent MP MR imaging before radical prostatectomy was retrospectively used. Institutional review board approval and informed consent were obtained.

Impaired liver function in Xenopus tropicalis exposed to benzo[a]pyrene: transcriptomic and metabolic evidence.

Background: Despite numerous studies suggesting that amphibians are highly sensitive to cumulative anthropogenic stresses, the role pollutants play in the decline of amphibian populations remains unclear. Amongst the most common aquatic contaminants, polycyclic aromatic hydrocarbons (PAHs) have been shown to induce several adverse effects on amphibian species in the larval stages. Conversely, adults exposed to high concentrations of the ubiquitous PAH, benzo[a]pyrene (BaP), tolerate the compound thanks to their highly efficient hepatic detoxification mechanisms.

Development of an Arabis alpina genomic contig sequence data set and application to single nucleotide polymorphisms discovery.

The alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This study presents the assembly of a pool of A. alpina genomic fragments using next-generation sequencing technologies.

Meeting review. Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics.

A workshop recently held at the École Polytechnique Fédérale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and landscape genomics and bringing together knowledge accumulated in both research fields. Indeed, an important challenge in theoretical population genetics is to incorporate effects of demographic history and population structure. But important design problems (e.

Influence of imaging and histological factors on prostate cancer detection and localisation on multiparametric MRI: a prospective study.

Objectives: To assess factors influencing prostate cancer detection on multiparametric (T2-weighted, diffusion-weighted, and dynamic contrast-enhanced) MRI.

Methods: One hundred and seventy-five patients who underwent radical prostatectomy were included. Pre-operative MRI performed at 1.

Effects of season and experimental warming on the bacterial community in a temperate mountain forest soil assessed by 16S rRNA gene pyrosequencing.

Climate warming may induce shifts in soil microbial communities possibly altering the long-term carbon mineralization potential of soils. We assessed the response of the bacterial community in a forest soil to experimental soil warming (+4 °C) in the context of seasonal fluctuations. Three experimental plots were sampled in the fourth year of warming in summer and winter and compared to control plots by 16S rRNA gene pyrosequencing.

Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies.

DNA metabarcoding refers to the DNA-based identification of multiple species from a single complex and degraded environmental sample. We developed new sampling and extraction protocols suitable for DNA metabarcoding analyses targeting soil extracellular DNA. The proposed sampling protocol has been designed to reduce, as much as possible, the influence of local heterogeneity by processing a large amount of soil resulting from the mixing of many different cores.

Transcription profiling of resistance to Bti toxins in the mosquito Aedes aegypti using next-generation sequencing.

The control of mosquitoes transmitting infectious diseases relies mainly on the use of chemical insecticides. However, resistance to most chemical insecticides threatens mosquito control programs. In this context, the spraying of toxins produced by the bacteria Bacillus thuringiensis subsp.

Transcriptome response to pollutants and insecticides in the dengue vector Aedes aegypti using next-generation sequencing technology.

Background: The control of mosquitoes transmitting infectious diseases relies mainly on the use of chemical insecticides. However, mosquito control programs are now threatened by the emergence of insecticide resistance. Hitherto, most research efforts have been focused on elucidating the molecular basis of inherited resistance.

The GC-heterogeneity of teleost fishes.

Background: One of the most striking features of mammalian and birds chromosomes is the variation in the guanine-cytosine (GC) content that occurs over scales of hundreds of kilobases to megabases; this is known as the "isochore" structure. Among other vertebrates the presence of isochores depends upon the taxon; isochore are clearly present in Crocodiles and turtles but fish genome seems very homogeneous on GC content. This has suggested a unique isochore origin after the divergence between Sarcopterygii and Actinopterygii, but before that between Sauropsida and mammals.

A markovian approach for the prediction of mouse isochores.

Hidden Markov models (HMMs) are effective tools to detect series of statistically homogeneous structures, but they are not well suited to analyse complex structures. For example, the duration of stay in a state of a HMM must follow a geometric law. Numerous other methodological difficulties are encountered when using HMMs to segregate genes from transposons or retroviruses, or to determine the isochore classes of genes.

A computational prediction of isochores based on hidden Markov models.

Mammalian genomes are organised into a mosaic of regions (in general more than 300 kb in length), with differing, relatively homogeneous G+C contents. The G+C content is the basic characteristic of isochores, but they have also been associated with many other biological properties. For instance, the genes are more compact and their density is highest in G+C rich isochores.