A systematic account of the genus Plagiostoma (Gnomoniaceae, Diaporthales) based on morphology, host-associations, and a four-gene phylogeny

Members of the genus Plagiostoma inhabit leaves, stems, twigs, and branches of woody and herbaceous plants predominantly in the temperate Northern Hemisphere. An account of all known species of Plagiostoma including Cryptodiaporthe is presented based on analyses of morphological, cultural, and DNA sequence data. Multigene phylogenetic analyses of DNA sequences from four genes (β-tubulin, ITS, rpb2, and tef1-α) revealed eight previously undescribed phylogenetic species and an association between a clade composed of 11 species of Plagiostoma and the host family Salicaceae. In this paper these eight new species of Plagiostoma are described, four species are redescribed, and four new combinations are proposed. A key to the 25 accepted species of Plagiostoma based on host, shape, and size of perithecia, perithecial arrangement in the host, and microscopic characteristics of the asci and ascospores is provided. Disposition of additional names in Cryptodiaporthe and Plagiostoma is also discussed

Constraint Reasoning and Kernel Clustering for Pattern Decomposition with Scaling

Abstract. Motivated by an important and challenging task encountered in material discovery, we consider the problem of finding K basis patterns of numbers that jointly compose N observed patterns while enforcing additional spatial and scaling constraints. We propose a Constraint Pro-gramming (CP) model which captures the exact problem structure yet fails to scale in the presence of noisy data about the patterns. We allevi-ate this issue by employing Machine Learning (ML) techniques, namely kernel methods and clustering, to decompose the problem into smaller ones based on a global data-driven view, and then stitch the partial solu-tions together using a global CP model. Combining the complementary strengths of CP and ML techniques yields a more accurate and scalable method than the few found in the literature for this complex problem.

On the possibility of light string resonances at the LHC and Tevatron from Randall-Sundrum throats

In string realizations of the Randall-Sundrum scenario, the higher-spin Regge excitations of Standard Model states localized near the IR brane are warped down to close to the TeV scale. We argue that, as a consequence of the localization properties of Randall-Sundrum models of flavour, the lightest such resonance is the spin-3/2 excitation of the right-handed top quark over a significant region of parameter space. A mild accidental cancellation allows this resonance to be as light or lighter than the Kaluza-Klein excitations of the Standard Model states. We consider from a bottom-up effective theory point of view the production and possible observability of such a spin-3/2 excitation at the LHC and Tevatron. Current limits are weaker than might be expected because of the excess of WWjj events at the Tevatron reported by CDF for an invariant mass of 400-500 GeV.Comment: 17 pages, 6 figures Version published in JHEP with minor correction

Leaf-inhabiting genera of the Gnomoniaceae, Diaporthales

The Gnomoniaceae are characterised by ascomata that are generally immersed, solitary, without a stroma, or aggregated with a rudimentary stroma, in herbaceous plant material especially in leaves, twigs or stems, but also in bark or wood. The ascomata are black, soft-textured, thin-walled, and pseudoparenchymatous with one or more central or eccentric necks. The asci usually have a distinct apical ring. The Gnomoniaceae includes species having ascospores that are small, mostly less than 25 μm long, although some are longer, and range in septation from non-septate to one-septate, rarely multi-septate. Molecular studies of the Gnomoniaceae suggest that the traditional classification of genera based on characteristics of the ascomata such as position of the neck and ascospores such as septation have resulted in genera that are not monophyletic. In this paper the concepts of the leaf-inhabiting genera in the Gnomoniaceae are reevaluated using multiple genes, specifically nrLSU, translation elongation factor 1-alpha (tef1-α), and RNA polymerase II second largest subunit (rpb2) for 64 isolates. ITS sequences were generated for 322 isolates. Six genera of leaf-inhabiting Gnomoniaceae are defined based on placement of their type species within the multigene phylogeny. The new monotypic genus Ambarignomonia is established for an unusual species, A. petiolorum. A key to 59 species of leaf-inhabiting Gnomoniaceae is presented and 22 species of Gnomoniaceae are described and illustrated

Assessing contextual descriptive features for plot-based classification of urban areas

A methodology for mapping urban land-use types integrating information from multiple data sources (high spatial resolution imagery, LiDAR data, and cadastral plots) is presented. A large set of complementary descriptive features that allow distinguishing different urban structures (historical, urban, residential, and industrial) is extracted and, after a selection process, a plot-based image classification approach applied, facilitating to directly relate the classification results and the urban descriptive parameters computed to the existent land-use/land-cover units in geospatial databases. The descriptive features are extracted by considering different hierarchical scale levels with semantic meaning in urban environments: buildings, plots, and urban blocks. Plots are characterised by means of image-based (spectral and textural), three-dimensional, and geometrical features. In addition, two groups of contextual features are defined: internal and external. Internal contextual features describe the main land cover types inside the plot (buildings and vegetation). External contextual features describe each object in terms of the properties of the urban block to which it belongs. After the evaluation in an heterogeneous Mediterranean urban area, the land-use classification accuracy values obtained show that the complementary descriptive features proposed improve the characterisation of urban typologies. A progressive introduction of the different groups of descriptive features in the classification tests show how the subsequent addition of internal and external contextual features have a positive effect by increasing the final accuracy of the urban classes considered in this study. © 2012 Elsevier B.V.The authors appreciate the financial support provided by the Spanish Ministry of Science and Innovation and FEDER in the framework of the projects CGL2009-14220 and CGL2010-19591/BTE, and the support of the Spanish Instituto Geografico Nacional (IGN).Hermosilla, T.; Ruiz Fernández, LÁ.; Recio Recio, JA.; Cambra López, M. (2012). Assessing contextual descriptive features for plot-based classification of urban areas. Landscape and Urban Planning. 106(1):124-137. doi:10.1016/j.landurbplan.2012.02.008S124137106

Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in √s = 7 TeV pp collisions with the ATLAS detector

A search for the direct production of charginos and neutralinos in final states with three electrons or muons and missing transverse momentum is presented. The analysis is based on 4.7 fb−1 of proton–proton collision data delivered by the Large Hadron Collider and recorded with the ATLAS detector. Observations are consistent with Standard Model expectations in three signal regions that are either depleted or enriched in Z-boson decays. Upper limits at 95% confidence level are set in R-parity conserving phenomenological minimal supersymmetric models and in simplified models, significantly extending previous results

Jet size dependence of single jet suppression in lead-lead collisions at sqrt(s(NN)) = 2.76 TeV with the ATLAS detector at the LHC

Measurements of inclusive jet suppression in heavy ion collisions at the LHC provide direct sensitivity to the physics of jet quenching. In a sample of lead-lead collisions at sqrt(s) = 2.76 TeV corresponding to an integrated luminosity of approximately 7 inverse microbarns, ATLAS has measured jets with a calorimeter over the pseudorapidity interval |eta| < 2.1 and over the transverse momentum range 38 < pT < 210 GeV. Jets were reconstructed using the anti-kt algorithm with values for the distance parameter that determines the nominal jet radius of R = 0.2, 0.3, 0.4 and 0.5. The centrality dependence of the jet yield is characterized by the jet "central-to-peripheral ratio," Rcp. Jet production is found to be suppressed by approximately a factor of two in the 10% most central collisions relative to peripheral collisions. Rcp varies smoothly with centrality as characterized by the number of participating nucleons. The observed suppression is only weakly dependent on jet radius and transverse momentum. These results provide the first direct measurement of inclusive jet suppression in heavy ion collisions and complement previous measurements of dijet transverse energy imbalance at the LHC.Comment: 15 pages plus author list (30 pages total), 8 figures, 2 tables, submitted to Physics Letters B. All figures including auxiliary figures are available at http://atlas.web.cern.ch/Atlas/GROUPS/PHYSICS/PAPERS/HION-2011-02

Variability of humidity conditions in the Arctic during the first International Polar Year, 1882-83

Of all the early instrumental data for the Arctic, the meteorological data gathered during the first International Polar Year, in 1882–83 (IPY-1), are the best in terms of coverage, quality and resolution. Research carried out during IPY-1 scientific expeditions brought a significant contribution to the development of hygrometry in polar regions at the end of the 19th century. The present paper gives a detailed analysis of a unique series of humidity measurements that were carried out during IPY-1 at hourly resolutions at nine meteorological stations, relatively evenly distributed in the High Arctic. It gives an overall view of the humidity conditions prevalent in the Arctic at that time. The results show that the spatial distribution of atmospheric water vapour pressure (e) and relative humidity (RH) in the Arctic during IPY-1 was similar to the present. In the annual course the highest values of e were noted in July and August, while the lowest occurred in the cold half of the year. In comparison to present-day conditions (1961–1990), the mean values of RH in the IPY-1 period (September 1882 to July 1883) were higher by 2.4–5.6%. Most of the changes observed between historical and modern RH values are not significant. The majority of historical daily RH values lie between a distance of less than two standard deviations from current long-term monthly means

Multiethnic meta-analysis identifies ancestry-specific and cross-ancestry loci for pulmonary function

Nearly 100 loci have been identified for pulmonary function, almost exclusively in studies of European ancestry populations. We extend previous research by meta-analyzing genome-wide association studies of 1000 Genomes imputed variants in relation to pulmonary function in a multiethnic population of 90,715 individuals of European (N = 60,552), African (N = 8429), Asian (N = 9959), and Hispanic/Latino (N = 11,775) ethnicities. We identify over 50 additional loci at genome-wide significance in ancestry-specific or multiethnic meta-analyses. Using recent fine-mapping methods incorporating functional annotation, gene expression, and differences in linkage disequilibrium between ethnicities, we further shed light on potential causal variants and genes at known and newly identified loci. Several of the novel genes encode proteins with predicted or established drug targets, including KCNK2 and CDK12. Our study highlights the utility of multiethnic and integrative genomics approaches to extend existing knowledge of the genetics of l

Polygenic transcriptome risk scores for COPD and lung function improve cross-ethnic portability of prediction in the NHLBI TOPMed program

While polygenic risk scores (PRSs) enable early identification of genetic risk for chronic obstructive pulmonary disease (COPD), predictive performance is limited when the discovery and target populations are not well matched. Hypothesizing that the biological mechanisms of disease are shared across ancestry groups, we introduce a PrediXcan-derived polygenic transcriptome risk score (PTRS) to improve cross-ethnic portability of risk prediction. We constructed the PTRS using summary statistics from application of PrediXcan on large-scale GWASs of lung function (forced expiratory volume in 1 s [FEV1] and its ratio to forced vital capacity [FEV1/FVC]) in the UK Biobank. We examined prediction performance and cross-ethnic portability of PTRS through smoking-stratified analyses both on 29,381 multi-ethnic participants from TOPMed population/family-based cohorts and on 11,771 multi-ethnic participants from TOPMed COPD-enriched studies. Analyses were carried out for two dichotomous COPD traits (moderate-to-severe and severe COPD) and two quantitative lung function traits (FEV1 and FEV1/FVC). While the proposed PTRS showed weaker associations with disease than PRS for European ancestry, the PTRS showed stronger association with COPD than PRS for African Americans (e.g., odds ratio [OR] = 1.24 [95% confidence interval [CI]: 1.08–1.43] for PTRS versus 1.10 [0.96–1.26] for PRS among heavy smokers with ≥ 40 pack-years of smoking) for moderate-to-severe COPD. Cross-ethnic portability of the PTRS was significantly higher than the PRS (paired t test p < 2.2 × 10−16 with portability gains ranging from 5% to 28%) for both dichotomous COPD traits and across all smoking strata. Our study demonstrates the value of PTRS for improved cross-ethnic portability compared to PRS in predicting COPD risk