Neuroconductor: an R platform for medical imaging analysis

Neuroconductor (https://neuroconductor.org) is an open-source platform for rapid testing and dissemination of reproducible computational imaging software. The goals of the project are to: (i) provide a centralized repository of R software dedicated to image analysis, (ii) disseminate software updates quickly, (iii) train a large, diverse community of scientists using detailed tutorials and short courses, (iv) increase software quality via automatic and manual quality controls, and (v) promote reproducibility of image data analysis. Based on the programming language R (https://www.r-project.org/), Neuroconductor starts with 51 inter-operable packages that cover multiple areas of imaging including visualization, data processing and storage, and statistical inference. Neuroconductor accepts new R package submissions, which are subject to a formal review and continuous automated testing. We provide a description of the purpose of Neuroconductor and the user and developer experience

Arsenic exposure, diabetes-related genes and diabetes prevalence in a general population from Spain

Inorganic arsenic exposure may be associated with diabetes, but the evidence at low-moderate levels is not sufficient. Polymorphisms in diabetes-related genes have been involved in diabetes risk. We evaluated the association of inorganic arsenic exposure on diabetes in the Hortega Study, a representative sample of a general population from Valladolid, Spain. Total urine arsenic was measured in 1451 adults. Urine arsenic speciation was available in 295 randomly selected participants. To account for the confounding introduced by non-toxic seafood arsenicals, we designed a multiple imputation model to predict the missing arsenobetaine levels. The prevalence of diabetes was 8.3%. The geometric mean of total arsenic was 66.0 µg/g. The adjusted odds ratios (95% confidence interval) for diabetes comparing the highest with the lowest tertile of total arsenic were 1.76 (1.01, 3.09) and 2.14 (1.47, 3.11) before and after arsenobetaine adjustment, respectively. Polymorphisms in several genes including IL8RA, TXN, NR3C2, COX5A and GCLC showed suggestive differential associations of urine total arsenic with diabetes. The findings support the role of arsenic on diabetes and the importance of controlling for seafood arsenicals in populations with high seafood intake. Suggestive arsenic-gene interactions require confirmation in larger studies

Restricted likelihood ratio testing for zero variance components in linear mixed models.

The goal of our article is to provide a transparent, robust, and computationally feasible statistical platform for restricted likelihood ratio testing (RLRT) for zero variance components in linear mixed models. This problem is nonstandard because under the null hypothesis the parameter is on the boundary of the parameter space. Our proposed approach is different from the asymptotic results of Stram and Lee who assumed that the outcome vector can be partitioned into many independent subvectors. Thus, our methodology applies to a wider class of mixed models, which includes models with a moderate number Of Clusters or nonparametric smoothing components. We propose two approximations to the finite sample null distribution of the RLRT statistic. Both approximations converge weakly to the asymptotic distribution obtained by Strain and Lee when their assumptions hold. When their assumptions do not hold, we show in extensive simulation studies that both approximations outpertform the Strain and Lee approximation and the parametric bootstrap. We also identify and address numerical problems associated with standard mixed model software. Our methods are motivated by and applied to a large longitudinal study on air Pollution health effects in a highly Susceptible cohort. Relevant software is posted as an online supplement

A tensor-based population value decomposition to explain rectal toxicity after prostate cancer radiotherapy.

International audienceIn prostate cancer radiotherapy the association between the dose distribution and the occurrence of undesirable side-effects is yet to be revealed. In this work a method to perform population analysis by comparing the dose distributions is proposed. The method is a tensor-based approach that generalises an existing method for 2D images and allows for the highlighting of over irradiated zones correlated with rectal bleeding after prostate cancer radiotherapy. Thus, the aim is to contribute to the elucidation of the dose patterns correlated with rectal toxicity. The method was applied to a cohort of 63 patients and it was able to build up a dose pattern characterizing the difference between patients presenting rectal bleeding after prostate cancer radiotherapy and those who did not