A global database for metacommunity ecology, integrating species, traits, environment and space

The use of functional information in the form of species traits plays an important role in explaining biodiversity patterns and responses to environmental changes. Although relationships between species composition, their traits, and the environment have been extensively studied on a case-by-case basis, results are variable, and it remains unclear how generalizable these relationships are across ecosystems, taxa and spatial scales. To address this gap, we collated 80 datasets from trait-based studies into a global database for metaCommunity Ecology: Species, Traits, Environment and Space; “CESTES”. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available. By its harmonized structure, and the diversity of ecosystem types, taxonomic groups, and spatial scales it covers, the CESTES database provides an important opportunity for synthetic trait-based research in community ecology

Review of Kaon Physics at CERN and in Europe

The Kaon physics program at CERN and in Europe will be presented. I will first give a short review of recent results form the NA48/2 and NA62 experiments, with special emphasis to the measurement of RK , the ratio of Kaon leptonic decays rates, K → eν and K → μν, using the full minimum bias data sample collected in 2007-2008. The main subject of the talk will be the study of the highly suppressed decay K → πνν. While its rate can be predicted with minimal theoretical uncertainty in the Standard Model (BR ∼ 8 × 10−11), the smallness of BR and the challenging experimental signature make it very difficult to measure. The branching ratio for this decay is thus a sensitive probe of the flavour sector of the SM. The aim of NA62 is the measurement of the K → πνν BR with ∼ 10% precision in two years of data taking. This will require the observation of 10K decays in the experiment's fiducial volume, as well as the use of high-performance systems for precision tracking, particle identification, and photon vetoing. These aspects of the experiment will also allow NA62 to carry out a rich program of searches for lepton flavour and/or number violating K decays. Data taking will start in October 2014. The physics prospects and the status of the construction and commissioning of the NA62 experiment will be presented. In the last part of the talk I will report on Kaon physics results and prospects from other experiments at CERN (e.g. LHCb) and in Europe (e.g. KLOE and KLOE-2) and briefly mention the status in US

Application of full-genome analysis to diagnose rare monogenic disorders.

Current genetic testenhancer and narrows the diagnostic intervals for rare diseases provide a diagnosis in only a modest proportion of cases. The Full-Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to detect small variants, structural variants with breakpoint resolution, and phasing. We built a variant prioritization pipeline and tested FGA's utility for diagnosis of rare diseases in a clinical setting. FGA identified structural variants and small variants with an overall diagnostic yield of 40% (20 of 50 cases) and 35% in exome-negative cases (8 of 23 cases), 4 of these were structural variants. FGA detected and mapped structural variants that are missed by short reads, including non-coding duplication, and phased variants across long distances of more than 180 kb. With the prioritization algorithm, longer DNA technologies could replace multiple tests for monogenic disorders and expand the range of variants detected. Our study suggests that genomes produced from technologies like FGA can improve variant detection and provide higher resolution genome maps for future application

Application of full-genome analysis to diagnose rare monogenic disorders.

Current genetic testenhancer and narrows the diagnostic intervals for rare diseases provide a diagnosis in only a modest proportion of cases. The Full-Genome Analysis method, FGA, combines long-range assembly and whole-genome sequencing to detect small variants, structural variants with breakpoint resolution, and phasing. We built a variant prioritization pipeline and tested FGA's utility for diagnosis of rare diseases in a clinical setting. FGA identified structural variants and small variants with an overall diagnostic yield of 40% (20 of 50 cases) and 35% in exome-negative cases (8 of 23 cases), 4 of these were structural variants. FGA detected and mapped structural variants that are missed by short reads, including non-coding duplication, and phased variants across long distances of more than 180 kb. With the prioritization algorithm, longer DNA technologies could replace multiple tests for monogenic disorders and expand the range of variants detected. Our study suggests that genomes produced from technologies like FGA can improve variant detection and provide higher resolution genome maps for future application

Measurement of the form factors of charged kaon semileptonic decays

International audienceA measurement of the form factors of charged kaon semileptonic decays is presented, based on 4.4 × 10$^{6}$K$^{±}$ → π$^{0}$e$^{±}$ν$_{e}$ (K$_{e3}^{±}$ ) and 2.3 × 10$^{6}$K$^{±}$ → π$^{0}$μ±ν$_{μ}$ (K$_{μ3}^{±}$ ) decays collected in 2004 by the NA48/2 experiment. The results are obtained with improved precision as compared to earlier measurements. The combination of measurements in the K$_{e3}^{±}$ and K$_{μ3}^{±}$ modes is also presented

First observation and study of the K±→π0π0μ±νK^{\pm} \rightarrow \pi^{0} \pi^{0} \mu^{\pm} \nu decay

The NA48/2 experiment at CERN reports the first observation of the $K^{\pm} \rightarrow \pi^{0} \pi^{0} \mu^{\pm} \nu$ decay based on a sample of 2437 candidates with 15% background contamination collected in 2003-2004. The decay branching ratio in the kinematic region of the squared dilepton mass above $0.03$~GeV$^2/c^4$ is measured to be $(0.65 \pm 0.03) \times 10^{-6}$. The extrapolation to the full kinematic space, using a specific model, is found to be $(3.45 \pm 0.17) \times 10^{-6}$, in agreement with chiral perturbation theory predictions

First observation and study of the K±→π0π0μ±νK^{\pm} \rightarrow \pi^{0} \pi^{0} \mu^{\pm} \nu decay

International audienceThe NA48/2 experiment at CERN reports the first observation of the K$^{±}$ → π$^{0}$π$^{0}$μ$^{±}$ν decay based on a sample of 2437 candidates with 15% background contamination collected in 2003–2004. The decay branching ratio in the kinematic region of the squared dilepton mass above 0.03 GeV$^{2}$/c$^{4}$ is measured to be (0.65 ± 0.03) × 10$^{−6}$. The extrapolation to the full kinematic space, using a specific model, is found to be (3.45 ± 0.16) × 10$^{−6}$, in agreement with chiral perturbation theory predictions

CESTES - A global database for metaCommunity Ecology: Species, Traits, Environment and Space

CESTES is a global database for metaCommunity Ecology: Species, Traits, Environment and Space. It compiles 80 datasets from trait-based studies. Each dataset includes four matrices: species community abundances or presences/absences across multiple sites, species trait information, environmental variables and spatial coordinates of the sampling sites. CESTES presents a harmonized structure and covers a diversity of ecosystem types (marine, terrestrial, freshwater), taxonomic groups (plants, vertebrates, invertebrates...), geographical regions, and spatial scales. The CESTES database is a live database: it will be maintained and expanded in the future as new datasets become available (https://icestes.github.io/sharedata). A zipped folder called “CESTES.zip” includes two alternative formats for the CESTES database: - a “xCESTES” folder that includes 80 Excel files (one file per dataset), each named according to the following structure: “AuthorPublicationYear.xlsx” - a “rCESTES” folder that includes the CESTES core processed database (comm, traits, envir, coord matrices) as an R list object “CESTES.RData” plus two R scripts, and two metadata tables for data processing and exploration. This “CESTES.zip” folder also includes: - an extended metadata table, “CESTES_metadata.xlsx”, that provides the general metadata information of all the datasets, - a tutorial document, “HOW_TO_SHARE_MY_DATA_FOR_CESTES.pdf”, that explains how to share data for integrating future datasets in the database. A second zipped folder, called "ceste.zip", corresponds to the non-spatial ancillary to CESTES. We provide access to 10 additional datasets that were not completely suitable for the CESTES database, due to the absence of spatial information or insufficient metadata but that were potentially valuable for their three other data matrices (comm, traits, envir). They follow the same structure as CESTES, except that they do not present the “coord” sheet and sometimes include only partial metadata. The “ceste.zip” zipped folder includes the 10 data files + 1 metadata file called "ceste_metadata.xlsx"