Bauschinger effect in thin metallic films by fem simulations

Unpassivated free-standing gold and aluminum thin films (thickness ~ 200-400 nm, mean grain size dm,Au≈ 70-80nm, dm,Al≈ 120-200nm), subjected to tensile tests show Bauschinger effect (BE) during unloading [1, 2]. The focus of this work is to investigate the effect of microstructural heterogeneity such as grain sizes on the BE and the macroscopic deformation behavior in thin metallic films. The finite element code LAGAMINE is used to model the response of films involving sets of grains with different strengths. The numerical results are compared with experimental results from tensile tests on aluminum thin films from the work of Rajagopalan, et al. [2]

Quality of life after the initial treatments of non-small cell lung cancer: a persistent predictor for patients' survival.

International audienceBACKGROUND: Health-related quality of life (HRQoL) before treatment may predict survival of patients with non-small-cell lung cancer (NSCLC). We investigated the predictive role of HRQoL after the initial treatments, on the survival of these patients. METHODS: A prospective multi-center study conducted in northeastern France. The SF-36 and European Organization for Research and Treatment of Cancer, Quality of Life Questionnaire Core-30 (QLQ C-30) were mailed to patients 3 months after the end of the diagnostic process. High scores for functioning dimensions on both questionnaires indicated better QoL, and low scores for symptom dimensions on the QLQ C-30 indicated few symptoms. Cox regression modeling was used to identify predictive factors of survival. RESULTS: In total, 230 (63.5%) patients responded to the SF-36 and QLQ C-30. Before completing the questionnaires, almost 60% of patients had undergone some chemotherapy, about 10% underwent radio/chemotherapy or both and more than 30% underwent surgery or surgery plus chemo/radiotherapy.On SF-36, the highest mean score was for social functioning dimension (55.5 ± 28), and the lowest was for the physical role dimension (17.9 ± 32.2).On QLQ C-30, for the functioning dimensions, the highest mean score was for cognitive functioning (74.6 ± 25.9) and the lowest was for role functioning (47.2 ± 34.1). For symptom dimensions, the lowest score was for diarrhoea (11.5 ± 24.2) and the highest was for fatigue (59.7 ± 27.7).On multivariate analysis, high bodily pain, social functioning and general health scores (SF-36) were associated with a lower risk of death (hazard ratio 0.580; 95% confidence interval [0.400-0.840], p = 0.004; HR 0.652 [0.455-0.935], p < 0.02; HR 0.625 [0.437-0.895] respectively). Better general QoL on QLQ C-30 was related to lower risk of death (HR 0.689 [0.501-0.946], p = 0.02). CONCLUSION: Adding to previous knowledge about factors that may influence patients QoL, this study shows a persisting relationship between better perceived health in HRQoL after the initial treatment of NSCLC and better survival

PlantRNA, a database for tRNAs of photosynthetic eukaryotes.

International audiencePlantRNA database (http://plantrna.ibmp.cnrs.fr/) compiles transfer RNA (tRNA) gene sequences retrieved from fully annotated plant nuclear, plastidial and mitochondrial genomes. The set of annotated tRNA gene sequences has been manually curated for maximum quality and confidence. The novelty of this database resides in the inclusion of biological information relevant to the function of all the tRNAs entered in the library. This includes 5'- and 3'-flanking sequences, A and B box sequences, region of transcription initiation and poly(T) transcription termination stretches, tRNA intron sequences, aminoacyl-tRNA synthetases and enzymes responsible for tRNA maturation and modification. Finally, data on mitochondrial import of nuclear-encoded tRNAs as well as the bibliome for the respective tRNAs and tRNA-binding proteins are also included. The current annotation concerns complete genomes from 11 organisms: five flowering plants (Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Medicago truncatula and Brachypodium distachyon), a moss (Physcomitrella patens), two green algae (Chlamydomonas reinhardtii and Ostreococcus tauri), one glaucophyte (Cyanophora paradoxa), one brown alga (Ectocarpus siliculosus) and a pennate diatom (Phaeodactylum tricornutum). The database will be regularly updated and implemented with new plant genome annotations so as to provide extensive information on tRNA biology to the research community

Distinct and Specific Role of NlpC/P60 Endopeptidases LytA and LytB in Cell Elongation and Division of Lactobacillus plantarum

Peptidoglycan (PG) is an essential lattice of the bacterial cell wall that needs to be continuously remodeled to allow growth. This task is ensured by the concerted action of PG synthases that insert new material in the pre-existing structure and PG hydrolases (PGHs) that cleave the PG meshwork at critical sites for its processing. Contrasting with Bacillus subtilis that contains more than 35 PGHs, Lactobacillus plantarum is a non-sporulating rod-shaped bacterium that is predicted to possess a minimal set of 12 PGHs. Their role in morphogenesis and cell cycle remains mostly unexplored, except for the involvement of the glucosaminidase Acm2 in cell separation and the NlpC/P60 D, L-endopeptidase LytA in cell shape maintenance. Besides LytA, L. plantarum encodes three additional NlpC/P60 endopeptidases (i.e., LytB, LytC and LytD). The in silico analysis of these four endopeptidases suggests that they could have redundant functions based on their modular organization, forming two pairs of paralogous enzymes. In this work, we investigate the role of each Lyt endopeptidase in cell morphogenesis in order to evaluate their distinct or redundant functions, and eventually their synthetic lethality. We show that the paralogous LytC and LytD enzymes are not required for cell shape maintenance, which may indicate an accessory role such as in PG recycling. In contrast, LytA and LytB appear to be key players of the cell cycle. We show here that LytA is required for cell elongation while LytB is involved in the spatio-temporal regulation of cell division. In addition, both PGHs are involved in the proper positioning of the division site. The absence of LytA activity is responsible for the asymmetrical positioning of septa in round cells while the lack of LytB results in a lateral misplacement of division planes in rod-shaped cells. Finally, we show that the co-inactivation of LytA and LytB is synthetically affecting cell growth, which confirms the key roles played by both enzymes in PG remodeling during the cell cycle of L. plantarum. Based on the large distribution of NlpC/P60 endopeptidases in low-GC Gram-positive bacteria, these enzymes are attractive targets for the discovery of novel antimicrobial compounds

The urban climate of Ghent, Belgium : a case study combining a high-accuracy monitoring network with numerical simulations

As urban environments have a specific climate that poses extra challenges (e.g. increased heat stress during heat waves), gaining detailed insight into the urban climate is important. This paper presents the high-accuracy MOCCA (MOnitoring the City's Climate and Atmosphere) network, which is monitoring the urban climate of the city of Ghent since July 2016. The study illustrates the complementarity between modelling and observing the urban climate. Two different modelling approaches are used: 1 km resolution runs of the SURFEX land surface model and 100 m resolution runs of the computationally cheaper UrbClim boundary layer model. On the one hand, urban models are able to simulate the spatial variability of the urban climate. As such, these models serve as a tool to help deciding on the locations of the measurement stations. On the other hand, the MOCCA observations are used to validate the high-resolution urban model experiments for the summer (July-August-September) of 2016. Our results demonstrate that the models capture the nighttime intra-urban temperature differences, but they are not able to reproduce the observed daytime temperature differences which are determined by the micro-scale environment

Nanomechanical Characterization of the Deformation Response of Orthotropic Ti–6Al–4V

The nanoindentation‐induced mechanical deformation response is applied to identify the orthotropic elastic moduli using the Delafargue and Ulm method as well as to validate the asymmetric orthotropic CPB06 nonlinear plasticity model required in simulations of nonuniform macroscopic mechanical response of the Ti–6Al–4V alloy. Scanning electron microscope (SEM) technique allows to select the maximum penetration depth for the indentation in the deformed alpha phase and alpha–beta interphase, α and α/β, respectively. The apparent macromechanical response can be successfully derived from several residual imprints conducted at micro‐ and/or submicrometric length scale and distributed throughout samples of the investigated bulk alloy, as demonstrated by correlation with finite element simulations based on the orthotropic elastoplastic model. The accurate numerical response obtained validates the material model and the Delafargue and Ulm approach, opening a window for next generation identification methods of macromechanical plasticity models with hybrid experimental–numerical method based on instrumented indentation and the use of SEM technique

Applying FAIR Principles to plant phenotypic data management in GnpIS

GnpIS is a data repository for plant phenomics that stores whole field and greenhouse experimental data including environment measures. It allows long-term access to datasets following the FAIR principles: Findable, Accessible, Interoperable, and Reusable, by using a flexible and original approach. It is based on a generic and ontology driven data model and an innovative software architecture that uncouples data integration, storage, and querying. It takes advantage of international standards including the Crop Ontology, MIAPPE, and the Breeding API. GnpIS allows handling data for a wide range of species and experiment types, including multiannual perennial plants experimental network or annual plant trials with either raw data, i.e., direct measures, or computed traits. It also ensures the integration and the interoperability among phenotyping datasets and with genotyping data. This is achieved through a careful curation and annotation of the key resources conducted in close collaboration with the communities providing data. Our repository follows the Open Science data publication principles by ensuring citability of each dataset. Finally, GnpIS compliance with international standards enables its interoperability with other data repositories hence allowing data links between phenotype and other data types. GnpIS can therefore contribute to emerging international federations of information systems

Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies

UMR-AGAP Equipe DAVV (Diversité, adaptation et amélioration de la vigne) ; équipe ID (Intégration de Données)International audienceAbstractBackgroundAs for many crops, new high-quality grapevine varieties requiring less pesticide and adapted to climate change are needed. In perennial species, breeding is a long process which can be speeded up by gaining knowledge about quantitative trait loci linked to agronomic traits variation. However, due to the long juvenile period of these species, establishing numerous highly recombinant populations for high resolution mapping is both costly and time-consuming. Genome wide association studies in germplasm panels is an alternative method of choice, since it allows identifying the main quantitative trait loci with high resolution by exploiting past recombination events between cultivars. Such studies require adequate panel design to represent most of the available genetic and phenotypic diversity. Assessing linkage disequilibrium extent and panel power is also needed to determine the marker density required for association studies.ResultsStarting from the largest grapevine collection worldwide maintained in Vassal (France), we designed a diversity panel of 279 cultivars with limited relatedness, reflecting the low structuration in three genetic pools resulting from different uses (table vs wine) and geographical origin (East vs West), and including the major founders of modern cultivars. With 20 simple sequence repeat markers and five quantitative traits, we showed that our panel adequately captured most of the genetic and phenotypic diversity existing within the entire Vassal collection. To assess linkage disequilibrium extent and panel power, we genotyped single nucleotide polymorphisms: 372 over four genomic regions and 129 distributed over the whole genome. Linkage disequilibrium, measured by correlation corrected for kinship, reached 0.2 for a physical distance between 9 and 458 Kb depending on genetic pool and genomic region, with varying size of linkage disequilibrium blocks. This panel achieved reasonable power to detect associations between traits with high broad-sense heritability (> 0.7) and causal loci with intermediate allelic frequency and strong effect (explaining > 10 % of total variance).ConclusionsOur association panel constitutes a new, highly valuable resource for genetic association studies in grapevine, and deserves dissemination to diverse field and greenhouse trials to gain more insight into the genetic control of many agronomic traits and their interaction with the environment

Leveraging Natural History Data in One- and Two-Arm Hierarchical Bayesian Studies of Rare Disease Progression

peer reviewedThe small sample sizes inherent in rare and pediatric disease settings offer significant challenges for clinical trial design. In such settings, Bayesian adaptive trial methods can often pay dividends, allowing the sensible incorporation of auxiliary data and other relevant information to bolster that collected by the trial itself. Previous work has also included the use of one-arm trials augmented by the participants’ own natural history data, from which the future course of the disease in the absence of intervention can be predicted. Patient response can then be defined by the degree to which post-intervention observations are inconsistent with the predicted “natural” trajectory. While such trials offer obvious advantages in efficiency and ethical hazard (since they expose no new patients to a placebo, anathema to patients or their parents and caregivers), they can offer no protection against bias arising from the presence of any “placebo effect,” the tendency of patients to improve merely by being in the trial. In this paper, we investigate the impact of both static and transient placebo effects on one-arm responder studies of this type, as well as two-arm versions that incorporate a small concurrent placebo group but still borrow strength from the natural history data. We also propose more traditional Bayesian changepoint models that specify a parametric functional form for the patient’s post-intervention trajectory, which in turn allow quantification of the treatment benefit in terms of the model parameters, rather than semi-parametrically in terms of a response relative to some “null” model. We compare the operating characteristics of our designs in the context of an ongoing investigation of centronuclear myopathies (CNMs), a group of congenital neuromuscular diseases whose most common and severe form is X-linked, affecting approximately 1 in 50,000 newborn boys. Our results indicate our two-arm responder and changepoint methods can offer protection against placebo effects, improving power while protecting the trial’s Type I error rate. However, further research into innovative trial designs as well as ongoing dialog with regulatory authorities remain critically important in rare disease research

Développement d'une nouvelle technologie pour la réalisation de filtres interférentiels de type "allumette"

Stripe filters are considered as an efficient solution to perform the spectral selection within pushbroom spaceborn imagers. However their manufacturing process still remains a delicate matter. This thesis thus focuses on studying new technological ways to manufacture these microstructured optical components. A theoretical study of assembly processes, and their impact on the structure and manufacture of stripe filters, points out the numerous assets of a solution based on assembly. This approach was experimentally validated from both optical and mechanical aspects, by manufacturing prototypes. Because of their specific geometry, the spectral characterization of these components has required the development of a dedicated metrology tool. A second approach based on the principle of multilayer stacks transfer has been studied as well. The steps of this innovative process have been experimentally validated, and show interesting prospects.Pour assurer la fonction de sélection spectrale au sein d'imageurs embarqués sur satellites défilants, les filtres allumettes apparaissent comme une solution particulièrement efficace, mais dont la fabrication reste délicate. L'objectif de cette thèse a alors été d'explorer de nouvelles voies technologiques pour la réalisation de ces composants optiques microstructurés. Une étude théorique de procédés d'assemblage, ainsi que de leur impact sur la structure et la fabrication de filtres allumettes, a mis en avant les nombreux intérêts qu'offre une solution basée sur l'assemblage. Cette approche a été validée expérimentalement, à la fois sur les plans optique et mécanique, par la réalisation de composants prototypes dont la caractérisation spectrale, du fait de la géométrie particulière de ces filtres, a nécessité le développement d'un outil de métrologie dédié. Une seconde approche, plus novatrice, a également été étudiée, reposant sur le principe du transfert d'empilements multicouches. Les tests réalisés pour la validation des étapes élémentaires de ce procédé, montrent des perspectives intéressantes