Phage display selection of HIV specific conserved mimotopes with IgG from long-term non-progressors

Poster presentation Background The aim of this study is to identify conserved epitopes of HIV-1 neutralizing antibodies in polyclonal plasma from LTNP to finally derive vaccine candidates. Materials and methods The presence of neutralizing antibodies in 9 LTNP sera was proved by in vitro neutralization assays. Phage displayed peptide libraries were screened with LTNP IgG. HIV-specific mimotopes were analyzed for homology to the gp120 structure by a software (3DEX) especially developed for this purpose. Mice were immunized with interesting phages and their sera were analyzed for neutralizing activities against HIV-1. Results After biopannings, between 19% and 75% HIV-specific phage clones were identified by ELISA. Mimotope sequences were identified and could be aligned by 3DEX to linear or conformational epitopes on gp120. A peptide specific immune response was detected in sera of immunized mice. The first mice sera analyzed showed neutralizing activities against HIV-1. Conclusion Mimotopes could be selected from LTNP sera that represent conformational epitopes on gp120. Those ones inducing neutralizing antibodies upon immunization potentially are suited to derive vaccine candidates

TOWARDS OBJECT-BASED EVALUATION OF INDIVIDUAL FIRES AT GLOBAL SCALES

Fire is a complex biophysical variable that has shaped the land surface for over 400 million years and continues to play important roles in landscape management, atmospheric emissions, and ecology. Our understanding of global fire patterns has improved dramatically in recent decades, coincident with the rise of systematic acquisition and development of global thematic products based on satellite remote sensing. Currently, there are several operational algorithms which map burned area, relying on coarse spatial resolution sensors with high temporal frequencies to identify fire-affected surfaces. While wildfires have been analyzed over large areas at the pixel level, object-based methods can provide more detailed attributes about individual fires such as fire size, severity, and spread rate. This dissertation evaluates burned area products using object-based methods to quantify errors in burn shapes and to extract individual fires from existing datasets. First, a wall-to-wall intercomparison of four publicly available burned area products highlights differences in the spatial and temporal patterns of burning identified by each product. The results of the intercomparison show that the MODIS Collection 6 MCD64A1 Burned Area product mapped the most burned area out of the four products, and all products except the Copernicus Burnt Area product showed agreement with regard to temporal burning patterns. In order to determine the fitness of the MCD64A1 product for mapping fire shapes, a framework for evaluating the shape accuracy of individual fires was developed using existing object-based metrics and a novel metric, the “edge error”. The object-based accuracy assessment demonstrated that MCD64A1 preserves the fire shape well compared to medium resolution data. Based on this result, an algorithm for extracting individual fires from MCD64A1 data was developed which improves upon existing algorithms through its use of an uncertainty-based approach rather than empirically driven approaches. The individual fires extracted by this algorithm were validated against medium resolution data in Canada and Alaska using object-based metrics, and the results indicate the algorithm provides an improvement over similar datasets. Overall, this dissertation demonstrates the capability of coarse resolution burned area products to accurately identify individual fire shapes and sizes. Recommendations for future work include improving the quality assessment of burned area products and continuing research into identifying spatiotemporal patterns in fire size distributions over large areas

Effect of body length, trophic position and habitat use on mercury concentrations of sharks from contrasted ecosystems in the southwestern Indian Ocean

International audienceThe non-essential metal mercury (Hg) can have deleterious effects on health of organisms, and tends to bioaccumulate with age in long-lived organisms and to biomagnify along food chains. Because sharks are fished for human consumption and their Hg levels are frequently above the maximum Hg concentration recommended for fish consumption, understanding the drivers of Hg concentration is of considerable interest. Total Hg concentrations were analysed in muscle tissues of 14 shark and 2 batoid species (n = 339 individuals) sampled across multiple habitats (coastal, oceanic and bathyal) in the southwestern Indian Ocean. Stable isotope ratios of carbon (δ13C) and nitrogen (δ15N) were analysed to assess whether relative trophic position and foraging habitats affected Hg concentrations. Hg concentrations increased with δ15N and body length, highlighting the mechanisms of bioaccumulation and biomagnification in relation with the trophic position and size of the individuals. Habitats where elasmobranchs were collected also affected their Hg concentrations. Bathyal sharks had high Hg concentrations that were almost similar to those of oceanic species, despite their lower relative trophic position. Higher bioavailability of Hg due to its enhanced methylation in deeper waters was considered as the most likely explanation for this result. These results highlight that multiple factors contribute to mercury accumulation in elasmobranchs

strengthening agricultural decisions in countries at risk of food insecurity the geoglam crop monitor for early warning

n/

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Quality Assessment of Pre-Classification Maps Generated from Spaceborne/Airborne Multi-Spectral Images by the Satellite Image Automatic Mapper™ and Atmospheric/Topographic Correction™-Spectral Classification Software Products: Part 2 — Experimental Results

This paper complies with the Quality Assurance Framework for Earth Observation (QA4EO) international guidelines to provide a metrological/statistically-based quality assessment of the Spectral Classification of surface reflectance signatures (SPECL) secondary product, implemented within the popular Atmospheric/Topographic Correction (ATCOR™) commercial software suite, and of the Satellite Image Automatic Mapper™ (SIAM™) software product, proposed to the remote sensing (RS) community in recent years. The ATCOR™-SPECL and SIAM™ physical model-based expert systems are considered of potential interest to a wide RS audience: in operating mode, they require neither user-defined parameters nor training data samples to map, in near real-time, a spaceborne/airborne multi-spectral (MS) image into a discrete and finite set of (pre-attentional first-stage) spectral-based semi-concepts (e.g., “vegetation”), whose informative content is always equal or inferior to that of target (attentional second-stage) land cover (LC) concepts (e.g., “deciduous forest”). For the sake of simplicity, this paper is split into two: Part 1—Theory and Part 2—Experimental results. The Part 1 provides the present Part 2 with an interdisciplinary terminology and a theoretical background. To comply with the principle of statistics and the QA4EO guidelines discussed in the Part 1, the present Part 2 applies an original adaptation of a novel probability sampling protocol for thematic map quality assessment to the ATCOR™-SPECL and SIAM™ pre-classification maps, generated from three spaceborne/airborne MS test images. Collected metrological/ statistically-based quality indicators (QIs) comprise: (i) an original Categorical Variable Pair Similarity Index (CVPSI), capable of estimating the degree of match between a test pre-classification map’s legend and a reference LC map’s legend that do not coincide and must be harmonized (reconciled); (ii) pixel-based Thematic (symbolic, semantic) QIs (TQIs) and (iii) polygon-based sub-symbolic (non-semantic) Spatial QIs (SQIs), where all TQIs and SQIs are provided with a degree of uncertainty in measurement. Main experimental conclusions of the present Part 2 are the following. (I) Across the three test images, the CVPSI values of the SIAM™ pre-classification maps at the intermediate and fine semantic granularities are superior to those of the ATCOR™-SPECL single-granule maps. (II) TQIs of both the ATCOR™-SPECL and the SIAM™ tend to exceed community-agreed reference standards of accuracy. (III) Across the three test images and the SIAM™’s three semantic granularities, TQIs of the SIAM™ tend to be significantly higher (in statistical terms) than the ATCOR™-SPECL’s. Stemming from the proposed experimental evidence in support to theoretical considerations, the final conclusion of this paper is that, in compliance with the QA4EO objectives, the SIAM™ software product can be considered eligible for injecting prior spectral knowledge into the pre-attentive vision first stage of a novel generation of hybrid (combined deductive and inductive) RS image understanding systems, capable of transforming large-scale multi-source multi-resolution EO image databases into operational, comprehensive and timely knowledge/information products