Numerical convergence of the block-maxima approach to the Generalized Extreme Value distribution

In this paper we perform an analytical and numerical study of Extreme Value distributions in discrete dynamical systems. In this setting, recent works have shown how to get a statistics of extremes in agreement with the classical Extreme Value Theory. We pursue these investigations by giving analytical expressions of Extreme Value distribution parameters for maps that have an absolutely continuous invariant measure. We compare these analytical results with numerical experiments in which we study the convergence to limiting distributions using the so called block-maxima approach, pointing out in which cases we obtain robust estimation of parameters. In regular maps for which mixing properties do not hold, we show that the fitting procedure to the classical Extreme Value Distribution fails, as expected. However, we obtain an empirical distribution that can be explained starting from a different observable function for which Nicolis et al. [2006] have found analytical results.Comment: 34 pages, 7 figures; Journal of Statistical Physics 201

Recognition of homo- and heterosubtypic variants of influenza A viruses by human CD8+ T lymphocytes

In the present study, the recognition of epitope variants of influenza A viruses by human CTL was investigated. To this end, human CD8(+) CTL clones, specific for natural variants of the HLA-B*3501-restricted epitope in the nucleoprotein (NP(418-426)), were generated. As determined in (51)Cr release assays and by flow cytometry with HLA-B*3501-peptide tetrameric complexes, CTL clones were found to be specific for epitopes within one subtype or cross-reactive with heterosubtypic variants of the epitope. Using eight natural variants of the epitope, positions in the 9-mer important for T cell recognition and involved in escape from CTL immunity were identified and visualized using multidimensional scaling. It was shown that positions 4 and 5 in the 9-mer epitope were important determinants of T cell specificity. The in vivo existence of CD8(+) cells cross-reactive with homo- and heterosubtypic variants of the epitope was further confirmed using polyclonal T cell populations obtained after stimulation of PBMC with different influenza A viruses. Based on the observed recognition patterns of the clonal and polyclonal T cell populations and serology, it is hypothesized that consecutive infections with influenza viruses containing different variants of the epitope select for cross-reactive T cells in vivo

The common PKD1 p.(Ile3167Phe) variant is hypomorphic and associated with very early onset, biallelic polycystic kidney disease

Biallelic PKD1 variants, including hypomorphic variants, can cause very early onset polycystic kidney disease (VEO-PKD). A family with unexplained recurrent VEO-PKD and neonatal demise in one dizygotic twin was referred for clinical testing. Further individuals with the putative hypomorphic PKD1 variant, p.(Ile3167Phe), were identified from the UK 100,000 genomes project (100 K), UK Biobank (UKBB), and a review of the literature. We identified a likely pathogenic PKD1 missense paternal variant and the putative hypomorphic PKD1 variant from the unaffected mother in the deceased twin but only the paternal PKD1 variant in the surviving dizygotic twin. Analysis of 100 K cases identified a second family with two siblings with similar biallelic inheritance who presented at birth with VEO-PKD and reached kidney failure in their teens unlike other affected relatives. Finally, a survey of 618 UKBB cases confirmed that adult patients monoallelic for PKD1 p.(Ile3167Phe) had normal kidney function. Our data reveals that p.(Ile3167Phe) is the second most common PKD1 hypomorphic variant identified and is neutral in heterozygosity but is associated with VEO-PKD when inherited in trans with a pathogenic PKD1 variant. Care should be taken to ensure that it is not automatically filtered from sequence data for VEO cases

Bodily tides near spin-orbit resonances

Spin-orbit coupling can be described in two approaches. The method known as "the MacDonald torque" is often combined with an assumption that the quality factor Q is frequency-independent. This makes the method inconsistent, because the MacDonald theory tacitly fixes the rheology by making Q scale as the inverse tidal frequency. Spin-orbit coupling can be treated also in an approach called "the Darwin torque". While this theory is general enough to accommodate an arbitrary frequency-dependence of Q, this advantage has not yet been exploited in the literature, where Q is assumed constant or is set to scale as inverse tidal frequency, the latter assertion making the Darwin torque equivalent to a corrected version of the MacDonald torque. However neither a constant nor an inverse-frequency Q reflect the properties of realistic mantles and crusts, because the actual frequency-dependence is more complex. Hence the necessity to enrich the theory of spin-orbit interaction with the right frequency-dependence. We accomplish this programme for the Darwin-torque-based model near resonances. We derive the frequency-dependence of the tidal torque from the first principles, i.e., from the expression for the mantle's compliance in the time domain. We also explain that the tidal torque includes not only the secular part, but also an oscillating part. We demonstrate that the lmpq term of the Darwin-Kaula expansion for the tidal torque smoothly goes through zero, when the secondary traverses the lmpq resonance (e.g., the principal tidal torque smoothly goes through nil as the secondary crosses the synchronous orbit). We also offer a possible explanation for the unexpected frequency-dependence of the tidal dissipation rate in the Moon, discovered by LLR

Atmospheric ammonia, acid gas and aerosol monitoring in Northern Ireland. Year 1: March 2019 - February 2020

ALPHA® and DELTA® network A new network of 25 ammonia (NH3) monitoring sites implementing the UKCEH ALPHA® method (ALPHA® network) and 4 reactive gases and aerosols monitoring sites implementing the UKCEH DELTA® method (DELTA® network) was established in spring 2019 across Northern Ireland. The ALPHA® sites were selected to provide representative coverage of i) the range of modelled concentrations from FRAME (using the most recent 5 km NH3 emissions data for 2016), (ii) each of seven major dominant emission source classifications: cattle (beef and dairy), pigs & poultry, sheep, mixed, non-agricultural, fertiliser and background (very low emission density, < 1 kg N ha-1 yr-1), and (iii) spatial coverage across Northern Ireland. The aims of the measurements are to (i) explore spatial and temporal patterns in NH3 concentrations, (ii) compare results with the FRAME atmospheric transport model and for verification of UK NAEI emissions inventory and FRAME model, (iii) monitor and assess relationship between NH3 and interacting gases (HNO3, SO2) and inorganic particulate phase composition. Measurement data over the same period from existing UK long-term national network sites (Coleraine, Hillsborough, Lough Navar), and from the Ballynahone Bog project in Northern Ireland are also included in the report, to complement the network data. All measurements are made through monthly time-integrated sampling, which is cost-efficient for providing annual means while permitting detection of seasonal trends in the data. The first measurements in the ALPHA® and DELTA® networks started in early March 2019. The first full year of ratified monthly ALPHA® and DELTA® data for the period March 2019 – February 2020 are presented in this report. Calibration of ALPHA® NH3 data An annual field calibrated ALPHA® uptake rate is derived for each calendar year from the regression of passive ALPHA® versus active DELTA® measurements at nine inter-comparison sites in the UK National Ammonia Monitoring Network. The calibration is usually carried out in April each year, based on a full year of data from the preceding year. The updated uptake rate is then applied retrospectively to ALPHA® data for the year of calibration. Calibrated uptake rates derived from the UK national network are applied to the Northern Ireland ALPHA® network data. These were 0.0031665 m3 h-1 and 0.0031277 m3 h-1, for 2019 and 2020, respectively. At AFBI25 Hillsborough, ALPHA® and DELTA® measurement are co-located with parallel measurements

Sugarcane root length density and distribution from root intersection counting on a trench-profile

Root length density (RLD) is a critical feature in determining crops potential to uptake water and nutrients, but it is difficult to be measured. No standard method is currently available for assessing RLD in the soil. In this study, an in situ method used for other crops for studying root length density and distribution was tested for sugarcane (Saccharum spp.). This method involved root intersection counting (RIC) on a Rhodic Eutrudox profile using grids with 0.05 x 0.05 m and modeling RLD from RIC. The results were compared to a conventional soil core-sampled method (COR) (volume 0.00043 m³). At four dates of the cropping season in three tillage treatments (plowing soil, minimum tillage and direct planting), with eight soil depths divided in 0.1 m soil layer (between 0-0.6 and 1.6-1.8 m) and three horizontal distances from the row (0-0.23, 0.23-0.46 and 0.46-0.69 m), COR and RIC methods presented similar RLD results. A positive relationship between COR and RIC was found (R² = 0.76). The RLD profiles considering the average of the three row distances per depth obtained using COR and RIC (mean of four dates and 12 replications) were close and did not differ at each depth of 0.1 m within a total depth of 0.6 m. Total RLD between 0 and 0.6 m was 7.300 and 7.100 m m-2 for COR and RIC respectively. For time consumption, the RIC method was tenfold less time-consuming than COR and RIC can be carried out in the field with no need to remove soil samples. The RLD distribution in depth and row distance (2-D variability) by RIC can be assessed in relation to the soil properties in the same soil profiles. The RIC method was suitable for studying these 2-D (depth and row distance in the soil profile) relationships between soil, tillage and root distribution in the field.A densidade de comprimento de raízes (DCR) é uma característica importante para determinar o potencial de absorção de água e nutrientes das plantas, mas é difícil de ser medida. Nenhum método padrão está atualmente disponível para avaliar a DCR no solo. Neste estudo, um método in situ usado em outras culturas para estudo da densidade de comprimento e distribuições das raízes foi testado para a cana-de-açúcar (Saccharum spp.). O método envolveu contagem de intersecções de raízes (CIR) no perfil de um Latossolo Vermelho eutroférrico, usando grade com quadrículas de 0.05 x 0.05 m, modelizando a DCR a partir da CIR. Os resultados foram comparados com o método do trado cilíndrico (TRA) (volume de 0.00043 m-3). Em quatro épocas durante o ciclo em três manejos do solo (plantio convencional, cultivo mínimo e plantio direto), em oito profundidades divididas a cada 0.1 m (entre 0 - 0.6 e 1.6 - 1.8 m) e três distâncias horizontais em relação à linha de plantio (0 - 0.23, 0.23 - 0.46 e 0.46 - 0.69 m), os métodos TRA e CIR apresentaram resultados de DCR similares. Encontrou-se positiva entre TRA e CIR (R² = 0,76). As DCRs nos perfis, considerando as médias das três distâncias da linha por profundidade, obtida utilizando-se de TRA e CIR (média de quatro datas e 12 repetições), foram próximas e não diferiram a cada 0.1 m de profundidade até 0.6 m de profundidade. A DCR total entre 0 e 0.6 m foi de 7.300 e 7.100 m m-2 para TRA e CIR, respectivamente. Para o tempo de realização, o método CIR foi 10 vezes mais rápido do que TRA e o método CIR pode ser realizado no campo, sem necessidade de remover amostras de solo. A distribuição da DCR em profundidade e distância da linha (variabilidade 2D) pelo método CIR pode ser avaliada em relação às propriedades do solo nos mesmos perfis do solo. O método CIR foi apropriado para estudos dessas relações 2D (profundidade e distância da linha no perfil do solo) entre solo, manejo e distribuição de raízes no campo

TRY plant trait database – enhanced coverage and open access

Plant traits—the morphological, anatomical, physiological, biochemical and phenological characteristics of plants—determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits—almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives