Use of extensive habitat inventories in biodiversity studies

International audienceLarge monitoring programs exist in many countries and are necessary to assess present and past biodiversity status and to evaluate the consequences of habitat degradation or destruction. Using such an extensive data set of the floristic richness in the Paris Ile-de-France region (France), we compared different sampling efforts and protocols in different habitat units to highlight the best methods for assessing the actual plant biodiversity. Our results indicate that existing data can be used for a general understanding of site differences, but analysts should be aware of the limitations of the data due to non-random selection of sites, inconsistent observer knowledge, and inconsistent sampling period. The average species diversity recorded in a specific habitat does not necessarily reflect its actual diversity, unless the monitoring effort was very strong. Overall, increasing the sampling effort in a given region allows improvement of the (1) number of habitats visited, (2) the total sampled area for a given habitat type, (3) the number of seasons investigated. Our results indicate that the sampling effort should be planned with respect to these functional, spatial and temporal heterogeneities, and to the question examined. While the effort should be applied to as many habitats as possible for the purpose of capturing a large proportion of regional diversity, or comparing different regions, inventories should be conducted in different seasons for the purpose of comparing species richness in different habitats

CLARCS, a C++ Library for Automated Registration and Comparison of Surfaces: Medical Applications

International audienceIn this paper we present the methods implemented in the CLARCS (C++ Library for Automated Registration and Comparison of Surfaces) library. This library allows some basic and high level processing on free-form surfaces, represented as point sets or meshes. Three methods are the "building bricks" of CLARCS; they allow (i) the rigid/affine/non-linear registration of two point sets, (ii) the computation of the mid-sagittal plane of one point set, (iii) the computation of a mean point set from several point sets, and the variability around this mean. These methods are all based on a common methodological framework, in which the point sets/meshes are represented either as a Gaussian mixture model or as a draw of such a model. We propose some applications of the methods implemented in CLARCS on different sets of medical data

Patterns of genomic change in residual disease after neoadjuvant chemotherapy for estrogen receptor-positive and HER2-negative breast cancer

Background: Treatment of patients with residual disease after neoadjuvant chemotherapy for breast cancer is an unmet clinical need. We hypothesised that tumour subclones showing expansion in residual disease after chemotherapy would contain mutations conferring drug resistance. Methods: We studied oestrogen receptor and/or progesterone receptor-positive, HER2-negative tumours from 42 patients in the EORTC 10994/BIG 00-01 trial who failed to achieve a pathological complete response. Genes commonly mutated in breast cancer were sequenced in pre and post-treatment samples. Results: Oncogenic driver mutations were commonest in PIK3CA (38% of tumours), GATA3 (29%), CDH1 (17%), TP53 (17%) and CBFB (12%); and amplification was commonest for CCND1 (26% of tumours) and FGFR1 (26%). The variant allele fraction frequently changed after treatment, indicating that subclones had expanded and contracted, but there were changes in both directions for all of the commonly mutated genes. Conclusions: We found no evidence that expansion of clones containing recurrent oncogenic driver mutations is responsible for resistance to neoadjuvant chemotherapy. The persistence of classic oncogenic mutations in pathways for which targeted therapies are now available highlights their importance as drug targets in patients who have failed chemotherapy but provides no support for a direct role of driver oncogenes in resistance to chemotherapy. ClinicalTrials.gov: EORTC 10994/BIG 1-00 Trial registration number NCT00017095.SCOPUS: ar.jDecretOANoAutActifinfo:eu-repo/semantics/publishe

Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

Association analysis was applied to a panel of accessions of Embrapa Rice Core Collection (ERiCC) with 86 SSR and field data from two experiments. A clear subdivision between lowland and upland accessions was apparent, thereby indicating the presence of population structure. Thirty-two accessions with admixed ancestry were identified through structure analysis, these being discarded from association analysis, thus leaving 210 accessions subdivided into two panels. The association of yield and grain-quality traits with SSR was undertaken with a mixed linear model, with markers and subpopulation as fixed factors, and kinship matrix as a random factor. Eight markers from the two appraised panels showed significant association with four different traits, although only one (RM190) maintained the marker-trait association across years and cultivation. The significant association detected between amylose content and RM190 was in agreement with previous QTL analyses in the literature. Herein, the feasibility of undertaking association analysis in conjunction with germplasm characterization was demonstrated, even when considering low marker density. The high linkage disequilibrium expected in rice lines and cultivars facilitates the detection of marker-trait associations for implementing marker assisted selection, and the mining of alleles related to important traits in germplasm

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure fl ux through the autophagy pathway (i.e., the complete process including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defi ned as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium ) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the fi eld understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation it is imperative to delete or knock down more than one autophagy-related gene. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways so not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

Landslide tsunamis: Comparison between depth-averaged and Navier–Stokes models

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The December 22, 2018 Anak Krakatau, Indonesia, Landslide and Tsunami: Preliminary Modeling Results

International audienceOn the evening of December 22, 2018, the coasts of the Sunda Strait, Indonesia, were hit by a tsunami generated by the collapse of a part of the Anak Krakatau volcano. Hundreds of people were killed, thousands were injured and displaced. This paper presents a preliminary modeling of the volcano flank collapse and the tsunami generated based on the results of a 2D depth-averaged coupled model involving a granular rheology and a Coulomb friction for the slide description and dispersive effects for the water flow part. With a reconstructed total volume (subaerial and submarine) of the landslide of 150 million m 3 inferred from pre and post-collapse satellite and aerial images , the comparison of the simulated water waves with the observations (tide gauges located all around the strait, photographs and field surveys) is satisfactory. Due to the lack of information for the submarine part of the landslide, 2 Alexandre Paris et al. the reconstructed submarine slope is assumed to be approximately constant. A significant time delay on the results and particularly in the Bandar Lampung Bay could be attributed to imprecisions of bathymetric data. The sensitivity to the basal friction and to dispersive effects is analyzed through numerical tests. Results show that the influence of the basal friction angle on the simulated wave heights decreases with distance and that a value of 2°gives consistent results with the observations. The dispersive effects are assessed by comparing water waves simulated by a shallow water model and a Boussinesq model. Simulations with frequency dispersion produce longer wave periods and smaller wave amplitudes in the Sunda Strait and particularly in deep waters

Post-operative assessment in Deep Brain Stimulation based on multimodal images: registration workflow and validation.

International audienceMovement disorders in Parkinson disease patients may require functional surgery, when medical therapy isn't effective. In Deep Brain Stimulation (DBS) electrodes are implanted within the brain to stimulate deep structures such as SubThalamic Nucleus (STN). This paper describes successive steps for constructing a digital Atlas gathering patient's location of electrodes and contacts for post operative assessment. 12 patients who had undergone bilateral STN DBS have participated to the study. Contacts on post-operative CT scans were automatically localized, based on black artefacts. For each patient, post operative CT images were rigidly registered to pre operative MR images. Then, pre operative MR images were registered to a MR template (super-resolution Collin27 average MRI template). This last registration was the combination of global affine, local affine and local non linear registrations, respectively. Four different studies were performed in order to validate the MR patient to template registration process, based on anatomical landmarks and clinical scores (i.e., Unified Parkinson's disease rating Scale). Visualisation software was developed for displaying into the template images the stimulated contacts represented as cylinders with a colour code related to the improvement of the UPDRS. The automatic contact localization algorithm was successful for all the patients. Validation studies for the registration process gave a placement error of 1.4 +/- 0.2 mm and coherence with UPDRS scores. The developed visualization tool allows post-operative assessment for previous interventions. Correlation with additional clinical scores will certainly permit to learn more about DBS and to better understand clinical side-effects