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Improved strain-level metagenome assembly for modern long reads
No full textNational audienceAdvances in long-read sequencing technologies from PacBio and Oxford Nanopore Technologies (ONT) have paved the way for the development of methods that significantly improve the quality of metagenome assemblies, particularly with the modern PacBio HiFi and ONT R10.4 technologies. Nevertheless, standard metagenome assemblers, while providing high-quality species-level reconstructions, are often unable to distinguish and accurately reconstruct genomes of highly similar bacterial strains (i.e., with >99% sequence identity). Moreover, several long-readbased methods have been recently proposed to address the challenge of reconstructing bacterial strain genomes (or haplotypes) from metagenomic data.In this work we show that existing metagenome assembly tools either produce highly fragmented assemblies or generate longer contigs at the expense of numerous strain-level misassemblies. We also present Strainberry2, an improved version of Strainberry, specifically designed for PacBio HiFi and ONT R10.4 sequencing data, aimed at providing a better balance between contiguity and strain-level accuracy. As is common for strain-separation methods, Strainberry2 takes as input a strain-oblivious metagenome assembly (i.e., a species-level assembly) together with a set of accurate long reads. It produces an augmented assembly that recovers strain diversity - absent in the input assembly - by generating strain-specific sequences. Strainberry2 distinguishes itself from competing methods by introducing an upstream dereplication step and a novel strain-phasing algorithm. The dereplication step is aimed at reducing ambiguous read mappings, which are critical for reliably detecting single-nucleotide and structural variants. The strain-phasing algorithm uses an iterative approach that leverages an implicit variant graph constructed from co-occurring single-nucleotide variants in the reads. At each iteration, candidate bacterial haplotypes are defined, while retaining only those supported by a sufficient number of reads.We ran Strainberry2 and state-of-the-art standard and strain-aware metagenome assemblers on 64 simulated datasets, covering different sequencing technologies, varying numbers of strains, multiple bacterial species, and either uniform or staggered strain abundances. We further ran these tools with real sequencing data on the ZymoBIOMICS Gut Microbiome Standard mock community, which includes five highly similar strains of Escherichia coli and for which both PacBio HiFi and ONT R10.4 reads are publicly available. The resulting assemblies were evaluated with MetaQUAST. To overcome the limitations of MetaQUAST in assessing assemblies against highly similar reference genomes, we complemented the evaluation with a k-mer-based approach. On the 64 simulated datasets, Strainberry2 achieved, on average, comparable or significantly better results across all qualitative metrics (e.g., 2-7X fewer misassemblies according to MetaQUAST and at least 10X fewer k-mer-based strain-switch errors). On the real-data mock community, Strainberry2 showed the same trend, particularly with ONT R10.4 data. With PacBio HiFi reads, Strainberry2 delivered results on par with the state-of-the-art hifiasm-meta, providing slightly higher accuracy across qualitative metrics. While hifiasm-meta reached greater contiguity (4X higher NGA50), this came at the cost of 20% more duplicated sequences, highlighting the more balanced trade-off achieved by Strainberry2.</p
BER Prediction of Distributed MISO Systems Using Beamsteering with Phase Compensation in mmWave Channels
No full textInternational audienceThis paper presents theoretical derivations for predicting the bit error rate (BER) of distributed antenna systems (DAS) in 3GPP clustered delay line channels with partial blockage accounting for typical millimeter wave (mmWave) propagation conditions. Assuming that the receiver equalizer is not updated during sudden blockage events, a statistical analysis is led to provide the probability density functions for received symbols under such blockage conditions. Three beamforming techniques—maximum ratio transmission (MRT), beamsteering (BS), and a proposed combination of BS with phase compensation (PC)—are considered in line-of-sight scenarios. Analytical BER predictions of the proposed PC-BS are validated through simulations, offering insights for optimizing DAS in mmWave environments. In particular, we conclude that PC-BS performs very close to MRT while being much simpler to implement and much more suited to mmWave electronics
Rebiopsy Feasibility and Clinical Impact on Metastatic Non-Small-Cell Lung Cancer With EGFR/ALK/ROS Oncogenic Driver Progression After Optimal Targeted Therapy: A Multicenter Real-World Analysis
No full textInternational audienceFeasibility and clinical impact of rebiopsy for a new mutational profile in metastatic non-small-cell lung cancer patients with oncogenic driver progressing after tyrosine kinase inhibitors (TKIs) is poorly studied. In this retrospective multicentric analysis, rebiopsy was performed in 53.4% of cases, providing a new information in 40.3% of cases and enabled identification of resistance mechanisms in 20% of cases. Overall survival did not differ between patients with and without rebiopsy. Background: For metastatic non-small-cell lung cancer (mNSCLC) patients with oncogenic driver progression after tyrosine kinase inhibitors (TKIs), obtaining a new mutational profile is recommended to assess the mechanism of resistance. The feasibility of that recommendation and its clinical impact remain poorly studied. Methods: mNSCLC patients with EGFR mutation and ALK or ROS translocation progressing on optimal TKI therapy were screened for inclusion in an immunochemotherapy trial not requiring a new molecular profile determination. This analysis evaluated the rebiopsy rate and its clinical impact. Results: Among 148 patients, 79 (53.4%) analyzable re-biopsies showed 72/132 (54.6%) with EGFR mutations, 7/13 (53.8%) had ALK translocations and no (0/5) ROS translocations. Seventynine re-biopsies were tissue (37, 46.8%), liquid (26, 32.9%) or both samples (16, 20.3%). For patients harboring EGFR mutations, the rebiopsy was not contributive for 12/72 (16.7%), the initial mutation was not found for 9/72 (12.5%) and only the unchanged initial profile was detected for 22/72 (30.6%); new information was provided for 29/72 (40.3%). Among patients with ALK-translocated mNSCLCs, re-biopsies enabled identification of resistance mechanisms for 20%. Overall survival did not differ between patients with rebiopsy and those without. Conclusions: In this population of patients with oncogenic driver progression under optimal targeted TKIs and in sufficiently good general condition to be included in an immunochemotherapy trial, only half were re-biopsied. Rebiopsy does not seem to improve the outcomes of these patients
Proof-of-Eligibility and Ephemeral participation to Solve Consensus in a Permissionless Environment
No full textAdaptation follow human attention: Gaze-assisted medical segment anything model
No full textInternational audienceegment Anything Model (SAM) has demonstrated state-of-the-art performance in most segmentation tasks. However, due to insufficient training in the medical domain, SAM’s ability to generalize to medical images is limited. Although preliminary efforts have fine-tuned SAM for the medical domain, the fine-tuned model still struggles with variability in medical tasks. Some recent studies have explored weakly supervised learning to mitigate SAM’s performance degradation in the medical domain. However, the effectiveness of weakly supervised learning is heavily dependent on the quality of weakly supervised information, with performance significantly dropping as the quality declines. Doctors’ attention is closely related to the target area during diagnosis. Integrating gaze information into SAM’s adaptation process for medical image segmentation enhances efficiency and significantly improves performance in medical tasks. In this paper, we first propose a Gaze-assisted medical segment Anything Model (GAM), which utilizes gaze information to enable the adaptation of SAM in medical images following doctor’s attention. It has two innovations: 1) Feature-level adaptation: Gaze Alignment (GA) learning makes the feature-level adaptation follow the doctor’s attention which mines the human guidance from gaze heatmaps and guides model to extract general features for downstream tasks. 2) Output-level adaptation: Gaze-Balance (GB) learning makes the output-level adaptation follow the doctor’s attention which utilizes gaze heatmaps to enhance the human-focused area and solve the problem of over/under segmentation from the output-level. Our promising results on 7 tasks with 12 targets have demonstrated the powerful adaptation ability of our GAM in the medical domain. Our GAM demonstrates significant potential for low-cost clinical assistance in medical diagnosis, enabling SAM to adapt to the medical image domain without disrupting clinical workflows. We have released the full source code..
Unlocking an efficient synergistic plasma-photocatalyst-light-emitting diode for the elimination of simulated contaminated air from the agri-food industries
No full textInternational audienceThis study presents the development of an innovative plasma light-emitting-diode (LED)-based planar continuous reactor designed for the removal of indoor air pollutants. A simultaneous elimination of volatile organic compounds and bacteria was investigated with one pass. The reactor demonstrated significant photocatalytic degradation of pollutant mixtures. The photocatalyst, composed of titanium dioxide (TiO2) nanoparticles deposited on glass fibers, exhibited high efficiency, as confirmed by scanning electron microscope analysis, which showed spherical TiO2 nanoparticles with an average diameter of 100 nm. The LED reactor enhanced the quantum yield of the catalyst, resulting in a high removal rate for the pollutant mixture (ethyl acetate and Escherichia coli). The association of dielectric barrier discharge (DBD) plasma for pollutant removal revealed superior bacterial inactivation compared to photocatalysis. The efficiency of plasma DBD improved significantly with increasing applied voltage, showing an impressive removal of ethyl acetate of 62 % at 18 kV. The antibacterial activity was markedly enhanced at this voltage, achieving a Log inactivation of 1.89 log CFU (similar to 99 % of removal). This hybrid approach demonstrated an eco-friendly treatment by decomposing ozone produced during the plasma process while further enhancing pollutant degradation. Overall, this work highlights the potential of combining AOPs, plasma DBD and photocatalysis, to achieve efficient and sustainable indoor air purification
A methodology for the characterization of the climate action on internally insulated buildings equipped with thermal breaker systems identifying seasonal and daily contributions
No full textInternational audienceThis paper presents a new statistical method, based on transient thermal analysis, for characterising the thermal loads on buildings with internal insulation and thermal breaker systems (TBSs). The fa and ccedil;ade of an internally insulated reinforced concrete building is modelled as a wall with a one-dimensional heat transfer regime and realistic climate boundary conditions. Particular emphasis is placed on the uncertainties associated with the thermal properties of the constituent materials and the parameters governing thermal transfer. Firstly, the thermal response of the system is examined for a reference set of thermal parameters. The seasonal and daily variations in thermal load are identified and analysed statistically. The results are consistent with current recommendations. Subsequently, a sensitivity analysis was performed to determine the parameter combinations that maximise the characteristic thermal load values. The results show that the model response is primarily influenced by the solar adsorption coefficient and the thermal properties of concrete. Finally, the simulation outcomes for these parameter sets across a range of urban locations in France are compared with the relevant guidelines. Overall, it was observed that the design of TBS should account for seasonal temperature variations of up to 43 degrees C and daily variations of up to 12 degrees C
Random Walk in the Complete Graph : Hitting and Cover Times
No full textInternational audienceWe consider the moments and the distribution of the hitting and cover times of a random walk in the complete graph. We study both the time needed to reach any subset of states and the time needed to visit all the states of a subset at least once. We obtain recurrence relations for the moments of all orders and we use these relations to analyze the asymptotic behavior of the hitting and cover times distributions when the number of states tends to infinity
Exposure to biomechanical risk factors for occupational wear and tear in women and men in the CONSTANCES cohort
No full textInternational audienceIntroduction: As part of the 2023 pension reform in France, a fund for the prevention of occupational wear and tear (called FIPU) has been created to prevent premature aging and musculoskeletal disorders. According to French law, the FIPU only considers exposure to three biomechanical criteria: manual handling of loads, strenuous postures and mechanical vibrations. The aim of our study was to identify the occupational categories most exposed to the three FIPU criteria, as well as an additional biomechanical risk factor of musculoskeletal disorders (MSD): repetitive work.Methods: Cross-sectional analyses involved 23,092 adults aged 45 or over and working at inclusion in the French CONSTANCES cohort (Consultants des centres d'examens de santé), in 2013–2017. Exposures to the three FIPU criteria and to repetitive work were described according to gender and occupational categories (based on a French group of occupations nomenclature (FAPs)). The analysis considered the sampling design and the correction for non-participation. A participant was considered exposed if, for manual handling of loads, high perceived physical exertion reached ≥ 15 on the Borg scale and >2 h/day for carry heavy load [1]; for strenuous postures the cut-off was set at >2h/day [2] and for mechanical vibrations >2h/day for the use of vibrating tools and >4h/day for operating a construction vehicle [3]. A participant was considered to be exposed to repetitive work with >4 h/day of exposure [3].Results: Some groups of occupations (FAPs) were found to be more exposed than others to the criteria identified by FIPU. For men, the FAPs most exposed to at least one of the three FIPU criteria were skilled construction workers (structural and finishing work: 95.8% and 88.1%) and metal forming (86.0%). For women, the FAPs most affected were home care aides (80.3%), care assistants (79.2%) and childcare assistants (77.1%). The addition of the repetitive work factor increased the proportion of exposed workers, particularly women, and brings out new occupations compared to those obtained with the FIPU criteria. These include workers in process industries and cashiers.Discussion: This study provides precise quantitative data on exposure to biomechanical risk factors in France, differentiated by gender. Our study is based exclusively on the three FIPU criteria and includes repetitive work. However, based on these criteria, defined by law, it does not consider other known MSD risk factors, such as psychosocial and organizational factors.Conclusion: Results of this study could be useful in helping the FIPU to better target the populations of workers concerned and to guide actions to prevent occupational wear and tear and premature ageing in France
