G2019S Mutation of Leucine-Rich Repeat Kinase 2 Is a Cause of Lewy Body Dementia in Patients With North African Ancestors.

Background: Mutations in the LRRK2 gene are the most common genetic cause of Parkinson disease but are believed to play no significant role in Lewy body disease (LBD).

Objectives: As the frequency of G2019S LRRK2 mutation is extremely high in North African patients with Parkinson disease, we postulate that the high prevalence of LBD in North Africa might be due to the same mutation because LBD and Parkinson disease share many clinical, pathological, and genetic features.

Methods: We screened patients with LBD or prodromal LBD for the G2019S mutation of LRRK2.

Bayesian Network structure learning algorithm for highly missing and non imputable data: Application to breast cancer radiotherapy data.

It is not uncommon for real-life data produced in healthcare to have a higher proportion of missing data than in other scopes. To take into account these missing data, imputation is not always desired by healthcare experts, and complete case analysis can lead to a significant loss of data. The algorithm proposed here, allows the learning of Bayesian Network graphs when both imputation and complete case analysis are not possible.

Towards a More Accurate Differential Analysis of Multiple Imputed Proteomics Data with mi4limma.

Imputing missing values is a common practice in label-free quantitative proteomics. Imputation replaces a missing value by a user-defined one. However, the imputation itself is not optimally considered downstream of the imputation process.

How visual attention span and phonological skills contribute to N170 print tuning: An EEG study in French dyslexic students.

Developmental dyslexia is a disorder characterized by a sustainable learning deficit in reading. Based on ERP-driven approaches focusing on the visual word form area, electrophysiological studies have pointed a lack of visual expertise for written word recognition in dyslexic readers by contrasting the left-lateralized N170 amplitudes elicited by alphabetic versus non-alphabetic stimuli. Here, we investigated in 22 dyslexic participants and 22 age-matched control subjects how two behavioural abilities potentially affected in dyslexic readers (phonological and visual attention skills) contributed to the N170 expertise during a word detection task.

Accounting for multiple imputation-induced variability for differential analysis in mass spectrometry-based label-free quantitative proteomics.

Imputing missing values is common practice in label-free quantitative proteomics. Imputation aims at replacing a missing value with a user-defined one. However, the imputation itself may not be optimally considered downstream of the imputation process, as imputed datasets are often considered as if they had always been complete.

The MHC class I MICA gene is a histocompatibility antigen in kidney transplantation.

The identity of histocompatibility loci, besides human leukocyte antigen (HLA), remains elusive. The major histocompatibility complex (MHC) class I MICA gene is a candidate histocompatibility locus. Here, we investigate its role in a French multicenter cohort of 1,356 kidney transplants.

Fitting and Cross-Validating Cox Models to Censored Big Data With Missing Values Using Extensions of Partial Least Squares Regression Models.

Fitting Cox models in a big data context -on a massive scale in terms of volume, intensity, and complexity exceeding the capacity of usual analytic tools-is often challenging. If some data are missing, it is even more difficult. We proposed algorithms that were able to fit Cox models in high dimensional settings using extensions of partial least squares regression to the Cox models.

Temporal multiomic modeling reveals a B-cell receptor proliferative program in chronic lymphocytic leukemia.

B-cell receptor (BCR) signaling is crucial for the pathophysiology of most mature B-cell lymphomas/leukemias and has emerged as a therapeutic target whose effectiveness remains limited by the occurrence of mutations. Therefore, deciphering the cellular program activated downstream this pathway has become of paramount importance for the development of innovative therapies. Using an original ex vivo model of BCR-induced proliferation of chronic lymphocytic leukemia cells, we generated 108 temporal transcriptional and proteomic profiles from 1 h up to 4 days after BCR activation.

Combining label-free and label-based accurate quantifications with SWATH-MS: Comparison with SRM and PRM for the evaluation of bovine muscle type effects.

Mass spectrometry has proven to be a valuable tool for the accurate quantification of proteins. In this study, the performances of three targeted approaches, namely selected reaction monitoring (SRM), parallel reaction monitoring (PRM) and sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH-MS), to accurately quantify ten potential biomarkers of beef meat tenderness or marbling in a cohort of 64 muscle samples were evaluated. So as to get the most benefit out of the complete MS2 maps that are acquired in SWATH-MS, an original label-free quantification method to estimate protein amounts using an I-spline regression model was developed.

selectBoost: a general algorithm to enhance the performance of variable selection methods.

Motivation: With the growth of big data, variable selection has become one of the critical challenges in statistics. Although many methods have been proposed in the literature, their performance in terms of recall (sensitivity) and precision (predictive positive value) is limited in a context where the number of variables by far exceeds the number of observations or in a highly correlated setting.

Results: In this article, we propose a general algorithm, which improves the precision of any existing variable selection method.

Compatibility at amino acid position 98 of MICB reduces the incidence of graft-versus-host disease in conjunction with the CMV status.

Graft-versus-host disease (GVHD) and cytomegalovirus (CMV)-related complications are leading causes of mortality after unrelated-donor hematopoietic cell transplantation (UD-HCT). The non-conventional MHC class I gene MICB, alike MICA, encodes a stress-induced polymorphic NKG2D ligand. However, unlike MICA, MICB interacts with the CMV-encoded UL16, which sequestrates MICB intracellularly, leading to immune evasion.

Determining the number of components in PLS regression on incomplete data set.

Partial least squares regression - or PLS regression - is a multivariate method in which the model parameters are estimated using either the SIMPLS or NIPALS algorithm. PLS regression has been extensively used in applied research because of its effectiveness in analyzing relationships between an outcome and one or several components. Note that the NIPALS algorithm can provide estimates parameters on incomplete data.

Multi-omics dataset to decipher the complexity of drug resistance in diffuse large B-cell lymphoma.

The prognosis of patients with relapsed/refractory (R/R) diffuse large B-cell lymphoma (DLBCL) remains unsatisfactory and, despite major advances in genomic studies, the biological mechanisms underlying chemoresistance are still poorly understood. We conducted for the first time a large-scale differential multi-omics investigation on DLBCL patient's samples in order to identify new biomarkers that could early identify patients at risk of R/R disease and to identify new targets that could determine chemorefractoriness. We compared a well-characterized cohort of R/R versus chemosensitive DLBCL patients by combining label-free quantitative proteomics and targeted RNA sequencing performed on the same tissues samples.

BCR-associated factors driving chronic lymphocytic leukemia cells proliferation ex vivo.

A chronic antigenic stimulation is believed to sustain the leukemogenic development of chronic lymphocytic leukemia (CLL) and most of lymphoproliferative malignancies developed from mature B cells. Reproducing a proliferative stimulation ex vivo is critical to decipher the mechanisms of leukemogenesis in these malignancies. However, functional studies of CLL cells remains limited since current ex vivo B cell receptor (BCR) stimulation protocols are not sufficient to induce the proliferation of these cells, pointing out the need of mandatory BCR co-factors in this process.

Deviance residuals-based sparse PLS and sparse kernel PLS regression for censored data.

Motivation: A vast literature from the past decade is devoted to relating gene profiles and subject survival or time to cancer recurrence. Biomarker discovery from high-dimensional data, such as transcriptomic or single nucleotide polymorphism profiles, is a major challenge in the search for more precise diagnoses. The proportional hazard regression model suggested by Cox (1972), to study the relationship between the time to event and a set of covariates in the presence of censoring is the most commonly used model for the analysis of survival data.

Cascade: a R package to study, predict and simulate the diffusion of a signal through a temporal gene network.

Summary: Temporal gene interactions, in response to environmental stress, form a complex system that can be efficiently described using gene regulatory networks. They allow highlighting the more influential genes and spotting some targets for biological intervention experiments. Despite that many reverse engineering tools have been designed, the Cascade package is an integrated solution adding several new and original key features such as the ability to predict changes in gene expressions after a biological perturbation in the network and graphical outputs that allow monitoring the spread of a signal through the network.

Effect of continuous positive airway pressure treatment on short-term memory performance over 24 h of sustained wakefulness in patients with obstructive sleep apnea-hypopnea syndrome.

Background: Few studies have examined the impact of continuous positive airway pressure (CPAP) therapy on short-term memory (STM) over sustained wakefulness in patients with obstructive sleep apnea-hypopnea syndrome (OSAHS). We have investigated if impaired STM can be reversed by CPAP treatment in a 24-h sustained wakefulness paradigm.

Methods: Our follow-up study was conducted with repeated-memory tasks within 12 OSAHS patients and 10 healthy controls who underwent three 32-h sessions, one before CPAP (T0) and the second (T3) and the third (T6), after 3 and 6 months of treatment, respectively, for OSAHS patients.

Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia.

Cellular behavior is sustained by genetic programs that are progressively disrupted in pathological conditions--notably, cancer. High-throughput gene expression profiling has been used to infer statistical models describing these cellular programs, and development is now needed to guide orientated modulation of these systems. Here we develop a regression-based model to reverse-engineer a temporal genetic program, based on relevant patterns of gene expression after cell stimulation.

Behavioural adjustment in response to increased predation risk: a study in three duck species.

Predation directly triggers behavioural decisions designed to increase immediate survival. However, these behavioural modifications can have long term costs. There is therefore a trade-off between antipredator behaviours and other activities.

Short-term memory performances during sustained wakefulness in patients with obstructive sleep apnea-hypopnea syndrome.

Both working and immediate memories were assessed every 4h by specific short-term memory tasks over sustained wakefulness in 12 patients with obstructive sleep apnea and hypopnea syndrome (OSAHS) and 10 healthy controls. Results indicated that OSAHS patients exhibited lower working memory performances than controls on both backward digit span and complex Sternberg tasks. Speed and accuracy on Sternberg tasks were affected by memory load in both groups.

Assessing phytoplankton structure and spatio-temporal dynamics in a freshwater ecosystem using a powerful multiway statistical analysis.

Phytoplankton dynamics and diversity are particularly difficult to analyze, especially when (i) the scale of the analysis is situated at the species level, (ii) such a diversity is high, (iii) the study covers several seasons, and (iv) sampling has been performed at many stations of the ecosystem. Fortunately, some powerful statistical methods have been developed with which each species identified can be considered in detailed spatio-temporal analyses. The Partial Triadic Analysis, a method issued from the STATIS family, was applied on a dataset corresponding to 6 stations of the largest French reservoir (Reservoir Marne) sampled 22 times over two years (2006-2007) between March and September.

Chronic food shortage and seasonal modulations of daily torpor and locomotor activity in the grey mouse lemur (Microcebus murinus).

The extent to which seasonal plasticity in torpor displayed by one of the smallest Malagasy primates (Microcebus murinus) will help survival in the context of ongoing global change-induced chronic food shortage, is unknown. Body temperature (Tb) and locomotor activity were measured by telemetry in short- (SD, winter-acclimated) and long-days (LD, summer-acclimated) males (n = 24) during an experimental 35-day calorie restriction of 40 or 80%. Under SD exposure, regardless of calorie restriction intensity, mouse lemurs immediately increased torpor depth and duration by 4.

Socio-economic correlates of municipal-level pollution emissions on Montreal Island.

Background: Differential exposure to environmental hazards is one component of the social gradient in health. Few studies have investigated the association between socioeconomic characteristics and environmental hazards in a Canadian context. We assessed the relationships between pollution emissions and socio-economic characteristics for 27 municipalities on Montreal Island.