A New Pipeline for the Normalization and Pooling of Metabolomics Data

Pooling metabolomics data across studies is often desirable to increase the statistical power of the analysis. However, this can raise methodological challenges as several preanalytical and analytical factors could introduce differences in measured concentrations and variability between datasets. Specifically, different studies may use variable sample types (e.g., serum versus plasma) collected, treated, and stored according to different protocols, and assayed in different laboratories using different instruments. To address these issues, a new pipeline was developed to normalize and pool metabolomics data through a set of sequential steps: (i) exclusions of the least informative observations and metabolites and removal of outliers; imputation of missing data; (ii) identification of the main sources of variability through principal component partial R-square (PC-PR2) analysis; (iii) application of linear mixed models to remove unwanted variability, including samples' originating study and batch, and preserve biological variations while accounting for potential differences in the residual variances across studies. This pipeline was applied to targeted metabolomics data acquired using Biocrates AbsoluteIDQ kits in eight case-control studies nested within the European Prospective Investigation into Cancer and Nutrition (EPIC) cohort. Comprehensive examination of metabolomics measurements indicated that the pipeline improved the comparability of data across the studies. Our pipeline can be adapted to normalize other molecular data, including biomarkers as well as proteomics data, and could be used for pooling molecular datasets, for example in international consortia, to limit biases introduced by inter-study variability. This versatility of the pipeline makes our work of potential interest to molecular epidemiologists

Numerical Analysis of a Tubular Phononic Crystal Sensor

International audienceWe present a theoretical investigation of the dispersion and transmission properties of a tubular phononic crystal for sensing application. We show the existence of modes confined in a cavity with displacement field spreading over both the solid and fluid parts. Therefore, the frequency of the transmission peak associated to this mode should be sensitive to the sound velocity of the fluid filling the tube

Unsupervised generation of synthetic CT from CBCT using 3D GAN in head and neck cancer radiotherapy

International audienc

Evaluation of synthetic CTs by 3D Cycle-GAN from prostate MR images

International audienc

3D patch cycle- GAN-based MR-to-CT synthesis from monocenter and multicenter training

International audienc

Evaluation of prostate synthetic CTs from MRI using 2D cycle-GAN with multicentric learning

International audienc

Parental smoking, maternal alcohol, coffee and tea consumption during pregnancy, and childhood acute leukemia: the ESTELLE study

International audiencePurpose To investigate the role of parental smoking during pre-conception and pregnancy, maternal beverage consumption (alcohol, coffee and tea) during pregnancy and their possible interactions, in the etiology of childhood acute leukemia (CL). Methods The ESTELLE study included 747 cases of CL [636 cases of acute lymphoblastic leukemia (ALL) and 100 cases of acute myeloblastic leukemia (AML)] diagnosed in France in 2010–2011 and 1,421 population controls frequency-matched with the cases on age and gender. Data were obtained from structured telephone questionnaires administered to the mothers. The odds ratios (OR) and their 95 % confidence intervals were estimated using unconditional logistic regression models adjusted for potential confounders. Results AML, but not ALL, was non-significantly associated with alcohol drinking during pregnancy [OR = 1.3 (0.8–2.0)] with a significant positive dose–response trend (p-trend = 0.02). Pre-conception paternal smoking was significantly associated with ALL [OR = 1.2 (1.1–1.5)] and AML [OR = 1.5 (1.0–2.3)]. CL was not associated with maternal smoking [OR = 1.0 (0.8–1.2)], or maternal coffee [OR = 0.9 (0.8–1.1)] or tea drinking [OR = 0.9 (0.8–1.1)] during pregnancy. However, a high consumption of coffee (\textgreater2 cups/day) was significantly associated with ALL [OR = 1.3 (1.0–1.8)]. Conclusions The findings constitute additional evidence that maternal alcohol drinking during pregnancy may be involved in AML, and that paternal smoking before pregnancy may be a risk factor for CL. The role of maternal coffee drinking in CL remains unclear and should be investigated further in consortium analyses and in large birth cohort studies with exposure assessment more contemporaneous with the exposure, before the occurrence of the diseas