Lagrangian and Eulerian dataset of the wake downstream of a smooth cylinder at a Reynolds number equal to 3900.

The dataset contains Eulerian velocity and pressure fields, and Lagrangian particle trajectories of the wake flow downstream of a smooth cylinder at a Reynolds number equal to 3900. An open source Direct Numerical Simulation (DNS) flow solver named Incompact3d was used to calculate the Eulerian field around the cylinder. The synthetic Lagrangian tracer particles were transported using a fourth-order Runge-Kutta scheme in time and trilinear interpolations in space. Trajectories of roughly 200,000 particles for two 3D sub-domains are available to the public. This dataset can be used as a test case for tracking algorithm assessment, exploring the Lagrangian physics, statistic analyses, machine learning, and data assimilation interests

Dealing with paralogy in RADseq data: in silico detection and single nucleotide polymorphism validation in Robinia pseudoacacia L.

peer reviewedThe RADseq technology allows researchers to efficiently develop thousands of polymorphic loci across multiple individuals with little or no prior information on the genome. However, many questions remain about the biases inherent to this technology. Notably, sequence misalignments arising from paralogy may affect the development of single nucleotide polymorphism (SNP) markers and the estimation of genetic diversity. We evaluated the impact of putative paralog loci on genetic diversity estimation during the development of SNPs from a RADseq dataset for the nonmodel tree species Robinia pseudoacacia L. We sequenced nine genotypes and analyzed the frequency of putative paralogous RAD loci as a function of both the depth of coverage and the mismatch threshold allowed between loci. Putative paralogy was detected in a very variable number of loci, from 1% to more than 20%, with the depth of coverage having a major influence on the result. Putative paralogy artificially increased the observed degree of polymorphism and resulting estimates of diversity. The choice of the depth of coverage also affected diversity estimation and SNP validation: A low threshold decreased the chances of detecting minor alleles while a high threshold increased allelic dropout. SNP validation was better for the low threshold (4×) than for the high threshold (18×) we tested. Using the strategy developed here, we were able to validate more than 80% of the SNPs tested by means of individual genotyping, resulting in a readily usable set of 330 SNPs, suitable for use in population genetics applications

Lagrangian coherent track initialisation

Advances in time-resolved three-dimensional Particle Tracking Velocimetry (4D-PTV) techniques have been consistently revealed more accurate Lagrangian particle motions. A novel track initialisation technique as a complementary part of 4D-PTV, based on local temporal and spatial coherency of neighbour trajectories, is proposed. The proposed Lagrangian Coherent Track Initialisation (LCTI) applies physics-based Finite Time Lyapunov Exponent (FTLE) to build four frame coherent tracks. We locally determine Lagrangian Coherent Structures (LCS) among neighbour trajectories by using the FTLE boundaries (i.e., ridges) to distinguish clusters of coherent motions. To evaluate the proposed technique, we created an open-access synthetic Lagrangian and Eulerian dataset of the wake downstream of a smooth cylinder at a Reynolds number equal to 3900 obtained from three-dimensional (3D) Direct Numerical Simulation (DNS). Performance of the proposed method based on three characteristic parameters, temporal scale, particle concentration (i.e., density), and noise ratio, showed robust behaviour in finding true tracks compared to the recent initialisation algorithms. Sensitivity of LCTI to the number of untracked and wrong tracks are also discussed. We address the capability of using the proposed method as a function of a 4D-PTV scheme in the Lagrangian Particle Tracking (LPT) challenge. We showed that LCTI prevents 4D-PTV divergence in flows with high particle concentrations. Finally, the LCTI behaviour was demonstrated in a jet impingement experiment. LCTI was found to be a reliable tracking tool in complex flow motions, with a strength revealed for flows with high velocity and acceleration gradients

ESMO Open

Background Whole exome sequencing and RNA sequencing (WES/RNASeq) should now be implemented in the clinical practice in order to increase access to optimal care for cancer patients. Providing results to Tumour Boards in a relevant time frame—that is, compatible with the clinical pathway—is crucial. Assessing the feasibility of this implementation in the French care system is the primary objective of the Multipli study, as one of the four pilot projects of the national France Genomic Medicine 2025 (FGM 2025) plan. The Multipli study encompasses two innovative trials which will be driven in around 2400 patients suffering from a soft-tissue sarcoma (Multisarc) or a metastatic colorectal carcinoma (Acompli). Methods Prior to launching the FGM 2025 cancer pilot study itself, the performance of the Multipli genomic workflow has been evaluated through each step, from the samples collection to the Molecular Tumour Board (MTB) report. Two Multipli-assigned INCa-labelled molecular genetics centres, the CEA-CNRGH sequencing platform and the Institut Bergonié’s Bioinformatics Platform were involved in a multicentric study. The duration of each step of the genomic workflow was monitored and bottlenecks were identified. Results Thirty barriers which could affect the quality of the samples, sequencing results and the duration of each step of the genomic pathway were identified and mastered. The global turnaround time from the sample reception to the MTB report was of 44 calendar days. Conclusion Our results demonstrate the feasibility of tumour genomic analysis by WES/RNASeq within a time frame compatible with the current cancer patient care. Lessons learnt from the Multipli WES/RNASeq Platforms Workflow Study will constitute guidelines for the forthcoming Multipli study and more broadly for the future clinical routine practice in the first two France Genomic Medicine 2025 platforms