sgsR: a structurally guided sampling toolbox for LiDAR-based forest inventories

Establishing field inventories can be labor intensive, logistically challenging and expensive. Optimizing a sample to derive accurate forest attribute predictions is a key management-level inventory objective. Traditional sampling designs involving pre-defined, interpreted strata could result in poor selection of within-strata sampling intensities, leading to inaccurate estimates of forest structural variables. The use of airborne laser scanning (ALS) data as an applied forest inventory tool continues to improve understanding of the composition and spatial distribution of vegetation structure across forested landscapes. The increased availability of wall-to-wall ALS data is promoting the concept of structurally guided sampling (SGS), where ALS metrics are used as an auxiliary data source driving stratification and sampling within management-level forest inventories. In this manuscript, we present an open-source R package named sgsR that provides a robust toolbox for implementing various SGS approaches. The goal of this package is to provide a toolkit to facilitate better optimized allocation of sample units and sample size, as well as to assess and augment existing plot networks by accounting for current forest structural conditions. Here, we first provide justification for SGS approaches and the creation of the sgsR toolbox. We then briefly describe key functions and workflows the package offers and provide two reproducible examples. Avenues to implement SGS protocols according to auxiliary data needs are presented

Identification of a BRCA2-Specific modifier locus at 6p24 related to breast cancer risk

Common genetic variants contribute to the observed variation in breast cancer risk for BRCA2 mutation carriers; those known to date have all been found through population-based genome-wide association studies (GWAS). To comprehensively identify breast cancer risk modifying loci for BRCA2 mutation carriers, we conducted a deep replication of an ongoing GWAS discovery study. Using the ranked P-values of the breast cancer associations with the imputed genotype of 1.4 M SNPs, 19,029 SNPs were selected and designed for inclusion on a custom Illumina array that included a total of 211,155 SNPs as part of a multi-consortial project. DNA samples from 3,881 breast cancer affected and 4,330 unaffected BRCA2 mutation carriers from 47 studies belonging to the Consortium of Investigators of Modifiers of BRCA1/2 were genotyped and available for analysis. We replicated previously reported breast cancer susceptibility alleles in these BRCA2 mutation carriers and for several regions (including FGFR2, MAP3K1, CDKN2A/B, and PTHLH) identified SNPs that have stronger evidence of association than those previously published. We also identified a novel susceptibility allele at 6p24 that was inversely associated with risk in BRCA2 mutation carriers (rs9348512; per allele HR = 0.85, 95% CI 0.80-0.90, P = 3.9×10−8). This SNP was not associated with breast cancer risk either in the general population or in BRCA1 mutation carriers. The locus lies within a region containing TFAP2A, which encodes a transcriptional activation protein that interacts with several tumor suppressor genes. This report identifies the first breast cancer risk locus specific to a BRCA2 mutation background. This comprehensive update of novel and previously reported breast cancer susceptibility loci contributes to the establishment of a panel of SNPs that modify breast cancer risk in BRCA2 mutation carriers. This panel may have clinical utility for women with BRCA2 mutations weighing options for medical prevention of breast cancer

Genome-Wide Association Study in BRCA1 Mutation Carriers Identifies Novel Loci Associated with Breast and Ovarian Cancer Risk

BRCA1-associated breast and ovarian cancer risks can be modified by common genetic variants. To identify further cancer risk-modifying loci, we performed a multi-stage GWAS of 11,705 BRCA1 carriers (of whom 5,920 were diagnosed with breast and 1,839 were diagnosed with ovarian cancer), with a further replication in an additional sample of 2,646 BRCA1 carriers. We identified a novel breast cancer risk modifier locus at 1q32 for BRCA1 carriers (rs2290854, P = 2.7×10-8, HR = 1.14, 95% CI: 1.09-1.20). In addition, we identified two novel ovarian cancer risk modifier loci: 17q21.31 (rs17631303, P = 1.4×10-8, HR = 1.27, 95% CI: 1.17-1.38) and 4q32.3 (rs4691139, P = 3.4×10-8, HR = 1.20, 95% CI: 1.17-1.38). The 4q32.3 locus was not associated with ovarian cancer risk in the general population or BRCA2 carriers, suggesting a BRCA1-specific associat

Comparison of XRD, XANES and TGA methods to assess the O/M ratio of Th0.60Am0.40O2-x

The mixed oxide Th0.60Am0.40O2-x has been synthesized and characterized after reductive and oxidative thermal treatments. Both materials are monophasic solid solutions. The determination of O/M ratio was achieved combining XRD, XANES and TGA, showing the consistence between the three methods. This study represents a further step in our investigation of the Th-Am-O system and improves it comprehension.JRC.E.4-Nuclear fuel

Crystallographic structure and charge distribution of AUO4 and A3UO6 uranates (A = Ca, Sr, Ba or Pb)

AUO4 and A3UO6 uranates (A = Ca, Sr, Ba or Pb) have been synthesized by solid state reaction. Their crystallographic structures have been studied combining Powder X-ray Diffraction (PXRD) and Extended X-ray Absorption Fine Structure (EXAFS). Depending on the nature of the alkali earth metal, the uranates compounds crystallize in different structures, in which the uranium local environment around the atoms have been identified. The U geometry has been compared to the oxidation states determined from X-ray Absorption Near Edge Spectroscopy (XANES).JRC.G.I.3-Nuclear Fuel Safet

Improving magneto-inertial attitude and position estimation by means of magnetic heading observer

International audienceThis paper studies heading estimation jointly with the attitude and position estimation of a rigid body equipped with inertial and magnetic sensors in indoor environment. In contrast with other indoor dead-reckoning approaches, no assumption is made about the nature of the movement or environment layout. Based on a previous paper, an Extended Kalman Filter is designed, which includes inertial sensor biases and magnetic disturbances. A heuristic model of the dynamic of magnetic heading disturbances is then described and added to the observer. The latter is then evaluated in terms of position and heading error on experimental data, showing that in spite of high levels of disturbances, the magnetic field alone can be used to compute heading

Structural Investigation of (U0.7Pu0.3)O2-x Mixed Oxides

Uranium-plutonium mixed oxide containing 30% of PuO2 is a candidate fuel for several fast neutron and accelerator driven reactor systems. In this work, a detailed structural investigation on sol-gel synthesized stoichiometric U0.7Pu0.3O2.00 and substoichiometric U0.7Pu0.3O2-x, using X-ray diffraction (XRD), oxygen 17 magic angle spinning nuclear magnetic resonance (17O MAS-NMR) and extended X-ray absorption fine structure (EXAFS) spectroscopy is described. As observed by XRD, U0.7Pu0.3O2.00 is monophasic with a lattice parameter in good agreement with the Vegard’s law while the U0.7Pu0.3O2-x material is biphasic. Solid solution ideality in terms of a random distribution of metal atoms is proven for U0.7Pu0.3O2.00 with 17O MAS-NMR. X-ray absorption near-edge spectroscopy (XANES) confirmed the presence of plutonium (III) in U0.7Pu0.3O2-x. EXAFS investigations indicate a similar local structure around both cations, and comparison with XRD indicates a close similarity between uranium and plutonium local structures and the long range ordering.JRC.E.4-Nuclear Fuel Safet

Structural investigation of self-irradiation damaged AmO2

Studying self-irradiated materials is an ideal means to investigate the effect of the damages on material structure and to better understand the behaviour of irradiated nuclear fuels. In this context, X-ray diffraction, X-ray absorption spectroscopy and transmission electron microscopy have been used to investigate self-irradiation damaged AmO2. Combining these techniques allows studying the microstructure and the variation of the fluorite structure at both short-range and long-range order. Thus, the increase of both interatomic distances and lattice parameter was shown, as well as the presence of nanometer sized He bubbles. As confirmed by the observed high-level of crytallinity, the fluorite structure exhibits a high radiation tolerance, which is confirmed by the low increase of the lattice parameter. This could be explained by a self-annealing mechanism of the created defects at room temperature.JRC.E.4-Nuclear fuel

Aliovalent Cation Substitution in UO2: Electronic and Local Structures of U1–yLayO2±x Solid Solutions

For nuclear fuel related applications, the oxygen stoichiometry of mixed oxides U1–yMyO2±x is an essential property as it affects fuel properties and may endanger the safe operation of nuclear reactors. A careful review of the open literature indicates that this parameter is difficult to assess properly and that the nature of the defects, i.e., oxygen vacancies or UV, in aliovalent cation–doped UO2 is still subject to controversy. To confirm the formation of UV, we have investigated the room-temperature stable U1–yLayO2±x phase using several experimental methods (e.g., XRD, XANES, and NMR) confirmed by theoretical calculations. This paper presents the experimental proof of UV and its effect we identified in both electronic and local structure. We observe that UV is formed in quasi-equimolar proportion as LaIII in U1–yLayO2±x (y = 0.06, 0.11, and 0.22) solid solutions. The fluorite structure is maintained despite the cationic substitution, but the local structure is affected as variations of the interatomic distances are found. Therefore, we provide here the definitive proof that the substitution of UIV with LaIII is not accommodated by the creation of O vacancies as has often been assumed. The UO2 fluorite structure compensates the incorporation of an aliovalent cation by the formation of UV in quasi-equimolar proportions.JRC.G.I.5-Advanced Nuclear Knowledg