EPSAT-SG: a satellite method for precipitation estimation; its concepts and implementation for the AMMA experiment

International audienceThis paper presents a new rainfall estimation method, EPSAT-SG which is a frame for method design. The first implementation has been carried out to meet the requirement of the AMMA database on a West African domain. The rainfall estimation relies on two intermediate products: a rainfall probability and a rainfall potential intensity. The first one is computed from MSG/SEVIRI by a feed forward neural network. First evaluation results show better properties than direct precipitation intensity assessment by geostationary satellite infra-red sensors. The second product can be interpreted as a conditional rainfall intensity and, in the described implementation, it is extracted from GPCP-1dd. Various implementation options are discussed and comparison of this embedded product with 3B42 estimates demonstrates the importance of properly managing the temporal discontinuity. The resulting accumulated rainfall field can be presented as a GPCP downscaling. A validation based on ground data supplied by AGRHYMET (Niamey) indicates that the estimation error has been reduced in this process. The described method could be easily adapted to other geographical area and operational environment

Combined microsatellite and FGFR3 mutation analysis enables a highly sensitive detection of urothelial cell carcinoma in voided urine

PURPOSE: Fibroblast growth factor receptor 3 (FGFR3) mutations were reported recently at a high frequency in low-grade urothelial cell carcinoma (UCC). We investigated the feasibility of combining microsatellite analysis (MA) and the FGFR3 status for the detection of UCC in voided urine. EXPERIMENTAL DESIGN: In a prospective setting, 59 UCC tissues and matched urine samples were obtained, and subjected to MA (23 markers) and FGFR3 mutation analysis (exons 7, 10, and 15). In each case, a clinical record with tumor and urine features was provided. Fifteen patients with a negative cystoscopy during follow-up served as controls. RESULTS: A mutation in the FGFR3 gene was found in 26 (44%) UCCs of which 22 concerned solitary pTaG1/2 lesions. These mutations were absent in the 15 G3 tumors. For the 6 cases with leukocyturia, 46 microsatellite alterations were found in the tumor. Only 1 of these was also detected in the urine. This was 125 of 357 for the 53 cases without leukocyte contamination. The sensitivity of MA on voided urine was lower for FGFR3-positive UCC (15 of 21; 71%) as compared with FGFR3 wild-type UCC (29 of 32; 91%). By including the FGFR3 mutation, the sensitivity of molecular cytology increased to 89% and was superior to the sensitivity of morphological cytology (25%) for every clinical subdivision. The specificity was 14 of 15 (93%) for the two (molecular and morphological) cytological approaches. CONCLUSIONS: Molecular urine cytology by MA and FGFR3 mutation analysis enables a highly sensitive and specific detection of UCC. The similarity of molecular profiles in tumor and urine corroborate their clonal relation

Some discussions of D. Fearnhead and D. Prangle's Read Paper "Constructing summary statistics for approximate Bayesian computation: semi-automatic approximate Bayesian computation"

This report is a collection of comments on the Read Paper of Fearnhead and Prangle (2011), to appear in the Journal of the Royal Statistical Society Series B, along with a reply from the authors

Sampling constrained probability distributions using Spherical Augmentation

Statistical models with constrained probability distributions are abundant in machine learning. Some examples include regression models with norm constraints (e.g., Lasso), probit, many copula models, and latent Dirichlet allocation (LDA). Bayesian inference involving probability distributions confined to constrained domains could be quite challenging for commonly used sampling algorithms. In this paper, we propose a novel augmentation technique that handles a wide range of constraints by mapping the constrained domain to a sphere in the augmented space. By moving freely on the surface of this sphere, sampling algorithms handle constraints implicitly and generate proposals that remain within boundaries when mapped back to the original space. Our proposed method, called {Spherical Augmentation}, provides a mathematically natural and computationally efficient framework for sampling from constrained probability distributions. We show the advantages of our method over state-of-the-art sampling algorithms, such as exact Hamiltonian Monte Carlo, using several examples including truncated Gaussian distributions, Bayesian Lasso, Bayesian bridge regression, reconstruction of quantized stationary Gaussian process, and LDA for topic modeling.Comment: 41 pages, 13 figure

The Standard Model with gravity couplings

In this paper, we examine the coupling of matter fields to gravity within the framework of the Standard Model of particle physics. The coupling is described in terms of Weyl fermions of a definite chirality, and employs only (anti)self-dual or left-handed spin connection fields. It is known from the work of Ashtekar and others that such fields can furnish a complete description of gravity without matter. We show that conditions ensuring the cancellation of perturbative chiral gauge anomalies are not disturbed. We also explore a global anomaly associated with the theory, and argue that its removal requires that the number of fundamental fermions in the theory must be multiples of 16. In addition, we investigate the behavior of the theory under discrete transformations P, C and T; and discuss possible violations of these discrete symmetries, including CPT, in the presence of instantons and the Adler-Bell-Jackiw anomaly.Comment: Extended, and replaced with LaTex file. 25 Page

ICMSF Methods Studies. XV. Comparison of Four Media and Methods for Enumerating Staphylococcus aureus in Powdered Milk.

Four media were examined for their usefulness in enumerating Staphylococcus aureus inoculated (a) into milk that was then dried or (b) directly into dried milk powder. In all, seven strains of S. aureus were inoculated individually into each preparation and were enumerated after two periods of storage (18 to 19 d and 60 to 61 d). Fourteen laboratories from twelve countries participated in the comparison which found that direct plating on agar medium in 14-cm petri dishes may be as useful as enrichment followed by streaking. Plating on Baird-Parker medium or on Hauschild pork plasma fibrinogen medium and a MPN method using Giolitti and Cantoni's broth with Tween 80 were equally sensitive for enumerating S. aureus in dried milk powder. The use of Hauschild medium may eliminate the need for supplementary tests to confirm colonies as S. aureus , but in some cases was found to fail in some laboratories. Giolitti and Cantoni's broth without Tween 80 generally was less useful than the three other media for enumerating S. aureus . S. aureus inoculated into milk that was then dried survived longer than when inoculated into dried milk

Grain legumes and dryland cereals for enhancing carbon sequestration in semi-arid and sub-humid agro-ecologies of Africa and South Asia

Sorghum, millets (pearl and finger millet) and grain legumes (chickpea, common bean, cowpea, lentils, pigeon pea and soybean), collectively referred to as GLDC under the CGIAR research program on Grain Legumes and Dryland Cereals, are commonly grown, eaten and traded by small holder farmers in Africa and South Asia. These crops contribute to food and nutritional security, environmental sustainability, and economic growth in the region. However, their possible contribution to carbon sequestration through biomass production and accumulation of soil organic carbon (SOC) is not known. To find out more about their contribution, and how to increase SOC, this study reviewed the evidence of carbon sequestration in farming systems that integrate GLDC in Africa and South Asia. A total of 437 publications reporting SOC and its proxies across 32 countries in Africa (N=250 studies) and South Asia (N=187) were identified as sources of evidence for carbon sequestration. Among these, 179 publications provided appropriate control groups for evaluating changes in aboveground carbon when GLDC were integrated under intercrop (n=38), crop rotation (n=8) or agroforestry (n=13), or when improved varieties of GLDC were compared with local varieties (n=14). A further 81 publications compared SOC content at the start and the end of the experiment while 43 publications compared SOC between farms growing GLDC and those which did not. Aboveground carbon of GLDC was found to be 1.51±0.05 Mg/ha in Africa and 2.29±0.10 Mg/ha in South Asia. Absolute SOC concentration in the topsoil (0-30 cm) was 0.96±0.06% in Africa and 0.58±0.04 in South Asia. It was observed that GLDC produced more aboveground carbon and significantly increased SOC when grown as intercrops and in crop rotations. The increase, however, depended on the species and whether the crop was a legume or a cereal. The largest amount of aboveground carbon (>2 Mg/ha) was found in cereals (and pigeon pea) while the largest increase in SOC was found in farming systems that included legumes. Aboveground carbon of improved varieties of GLDC was lower compared to local varieties. Soils which had low initial (32%) showed the greatest potential for carbon sequestration when GLDC were grown. Among the GLDC crops, pigeon pea which is a perennial grain legume showed the highest biomass production and carbon sequestration in the soil when integrated into farming systems in Africa and South Asia. Findings from this study underscore the importance of aboveground residues in regulating the addition of carbon to the soil, and the role of legumes in the enhancement of SOC

Population Genomics and Phylogeography of an Australian Dairy Factory Derived Lytic Bacteriophage

In this study, we present the full genomic sequences and evolutionary analyses of a serially sampled population of 28 Lactococcus lactis–infecting phage belonging to the 936-like group in Australia. Genome sizes were consistent with previously available genomes ranging in length from 30.9 to 32.1 Kbp and consisted of 55–65 open reading frames. We analyzed their genetic diversity and found that regions of high diversity are correlated with high recombination rate regions (P value = 0.01). Phylogenetic inference showed two major clades that correlate well with known host range. Using the extended Bayesian Skyline model, we found that population size has remained mostly constant through time. Moreover, the dispersion pattern of these genomes is in agreement with human-driven dispersion as suggested by phylogeographic analysis. In addition, selection analysis found evidence of positive selection on codon positions of the Receptor Binding Protein (RBP). Likewise, positively selected sites in the RBP were located within the neck and head region in the crystal structure, both known determinants of host range. Our study demonstrates the utility of phylogenetic methods applied to whole genome data collected from populations of phage for providing insights into applied microbiology

Sustainable Sources of Biomass for Bioremediation of Heavy Metals in Waste Water Derived from Coal-Fired Power Generation

Biosorption of heavy metals using dried algal biomass has been extensively described but rarely implemented. We contend this is because available algal biomass is a valuable product with a ready market. Therefore, we considered an alternative and practical approach to algal bioremediation in which algae were cultured directly in the waste water stream. We cultured three species of algae with and without nutrient addition in water that was contaminated with heavy metals from an Ash Dam associated with coal-fired power generation and tested metal uptake and bioremediation potential. All species achieved high concentrations of heavy metals (to 8% dry mass). Two key elements, V and As, reached concentrations in the biomass of 1543 mg.kg−1 DW and 137 mg.kg−1 DW. Growth rates were reduced by more than half in neat Ash Dam water than when nutrients were supplied in excess. Growth rate and bioconcentration were positively correlated for most elements, but some elements (e.g. Cd, Zn) were concentrated more when growth rates were lower, indicating the potential to tailor bioremediation depending on the pollutant. The cosmopolitan nature of the macroalgae studied, and their ability to grow and concentrate a suite of heavy metals from industrial wastes, highlights a clear benefit in the practical application of waste water bioremediation