Complete off-shell effects in top quark pair hadroproduction with leptonic decay at next-to-leading order

Results for next-to-leading order QCD corrections to the pp(p\bar{p}) -> t \bar{t} -> W^+W^- b\bar{b} -> e^{+} \nu_{e} \mu^{-} \bar{\nu}_{\mu} b \bar{b} +X processes with complete off-shell effects are presented for the first time. Double-, single- and non-resonant top contributions of the order {\cal{O}}(\alpha_{s}^3 \alpha^4) are consistently taken into account, which requires the introduction of a complex-mass scheme for unstable top quarks. Moreover, the intermediate W bosons are treated off-shell. Comparison to the narrow width approximation for top quarks, where non-factorizable corrections are not accounted for is performed. Besides the total cross section and its scale dependence, several differential distributions at the TeVatron run II and the LHC are given. In case of the TeVatron the forward-backward asymmetry of the top is recalculated afresh. With inclusive selection cuts, the forward-backward asymmetry amounts to A^{t}_{FB} = 0.051 +/- 0.0013. Furthermore, the corrections with respect to leading order are positive and of the order 2.3% for the TeVatron and 47% for the LHC. A study of the scale dependence of our NLO predictions indicates that the residual theoretical uncertainty due to higher order corrections is 8% for the TeVatron and 9% for the LHC.Comment: 35 pages, 39 figures, 3 tables. References and note added, version to appear in JHE

Hadronic final states in deep-inelastic scattering with Sherpa

We extend the multi-purpose Monte-Carlo event generator Sherpa to include processes in deeply inelastic lepton-nucleon scattering. Hadronic final states in this kinematical setting are characterised by the presence of multiple kinematical scales, which were up to now accounted for only by specific resummations in individual kinematical regions. Using an extension of the recently introduced method for merging truncated parton showers with higher-order tree-level matrix elements, it is possible to obtain predictions which are reliable in all kinematical limits. Different hadronic final states, defined by jets or individual hadrons, in deep-inelastic scattering are analysed and the corresponding results are compared to HERA data. The various sources of theoretical uncertainties of the approach are discussed and quantified. The extension to deeply inelastic processes provides the opportunity to validate the merging of matrix elements and parton showers in multi-scale kinematics inaccessible in other collider environments. It also allows to use HERA data on hadronic final states in the tuning of hadronisation models.Comment: 32 pages, 22 figure

Barriers to integration of bioinformatics into undergraduate life sciences education: A national study of US life sciences faculty uncover significant barriers to integrating bioinformatics into undergraduate instruction

Bioinformatics, a discipline that combines aspects of biology, statistics, mathematics, and computer science, is becoming increasingly important for biological research. However, bioinformatics instruction is not yet generally integrated into undergraduate life sciences curricula. To understand why we studied how bioinformatics is being included in biology education in the US by conducting a nationwide survey of faculty at two- and four-year institutions. The survey asked several open-ended questions that probed barriers to integration, the answers to which were analyzed using a mixed-methods approach. The barrier most frequently reported by the 1,260 respondents was lack of faculty expertise/training, but other deterrents-lack of student interest, overly-full curricula, and lack of student preparation-were also common. Interestingly, the barriers faculty face depended strongly on whether they are members of an underrepresented group and on the Carnegie Classification of their home institution. We were surprised to discover that the cohort of faculty who were awarded their terminal degree most recently reported the most preparation in bioinformatics but teach it at the lowest rate

WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads

Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics. 2009;10(1):430.Background Metagenomics is a new field of research on natural microbial communities. High-throughput sequencing techniques like 454 or Solexa-Illumina promise new possibilities as they are able to produce huge amounts of data in much shorter time and with less efforts and costs than the traditional Sanger technique. But the data produced comes in even shorter reads (35-100 basepairs with Illumina, 100-500 basepairs with 454-sequencing). CARMA is a new software pipeline for the characterisation of species composition and the genetic potential of microbial samples using short, unassembled reads. Results In this paper, we introduce WebCARMA, a refined version of CARMA available as a web application for the taxonomic and functional classification of unassembled (ultra-)short reads from metagenomic communities. In addition, we have analysed the applicability of ultra-short reads in metagenomics. Conclusions We show that unassembled reads as short as 35 bp can be used for the taxonomic classification of a metagenome. The web application is freely available at http://webcarma.cebitec.uni-bielefeld.d

Achievements and new knowledge unraveled by metagenomic approaches

Metagenomics has paved the way for cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. In recent years, significant progress has been made in this research area. A major breakthrough was the improvement and development of high-throughput next-generation sequencing technologies. The application of these technologies resulted in the generation of large datasets derived from various environments such as soil and ocean water. The analyses of these datasets opened a window into the enormous phylogenetic and metabolic diversity of microbial communities living in a variety of ecosystems. In this way, structure, functions, and interactions of microbial communities were elucidated. Metagenomics has proven to be a powerful tool for the recovery of novel biomolecules. In most cases, functional metagenomics comprising construction and screening of complex metagenomic DNA libraries has been applied to isolate new enzymes and drugs of industrial importance. For this purpose, several novel and improved screening strategies that allow efficient screening of large collections of clones harboring metagenomes have been introduced

Depleted dissolved organic carbon and distinct bacterial communities in the water column of a rapid-flushing coral reef ecosystem

Author Posting. © The Author(s), 2011. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in The ISME Journal 5 (2011): 1374–1387, doi:10.1038/ismej.2011.12.Coral reefs are highly productive ecosystems bathed in unproductive, low-nutrient oceanic waters, where microbially-dominated food webs are supported largely by bacterioplankton recycling of dissolved compounds. Despite evidence that benthic reef organisms efficiently scavenge particulate organic matter and inorganic nutrients from advected oceanic waters, our understanding of the role of bacterioplankton and dissolved organic matter in the interaction between reefs and the surrounding ocean remains limited. Here we present the results of a four-year study conducted in a well-characterized coral reef ecosystem (Paopao Bay, Moorea, French Polynesia) where changes in bacterioplankton abundance and dissolved organic carbon (DOC) concentrations were quantified and bacterial community structure variation was examined along spatial gradients of the reef:ocean interface. Our results illustrate that the reef is consistently depleted in concentrations of both DOC and bacterioplankton relative to offshore waters (averaging 79 µmol L-1 DOC and 5.5 X 108 cells L-1 offshore and 68 µmol L-1 DOC and 3.1 X 108 cells L-1 over the reef, respectively) across a four year time period. In addition, using a suite of culture-independent measures of bacterial community structure, we found consistent differentiation of reef bacterioplankton communities from those offshore or in a nearby embayment across all taxonomic levels. Reef habitats were enriched in Gamma-, Delta-, and Beta-proteobacteria, Bacteriodetes, Actinobacteria and Firmicutes. Specific bacterial phylotypes, including members of the SAR11, SAR116, Flavobacteria, and Synechococcus clades, exhibited clear gradients in relative abundance among nearshore habitats. Our observations indicate that this reef system removes oceanic DOC and exerts selective pressures on bacterioplankton community structure on timescales approximating reef water residence times, observations which are notable both because fringing reefs do not exhibit long residence times (unlike those characteristic of atoll lagoons) and because oceanic DOC is generally recalcitrant to degradation by ambient microbial assemblages. Our findings thus have interesting implications for the role of oceanic DOM and bacterioplankton in the ecology and metabolism of reef ecosystems.This project was supported by the US National Science Foundation Moorea Coral Reef Long Term Ecological Research project (NSF OCE-0417412) through minigrants to CAC and NSF OCE-0927411 to CAC as well as the MIRADA-LTERs program (NSF DEB-0717390 to LAZ)

African ancestry of New World, Bemisia tabaci-whitefly species

Bemisia tabaci whitefly species are some of the world’s most devastating agricultural pests and plant-virus disease vectors. Elucidation of the phylogenetic relationships in the group is the basis for understanding their evolution, biogeography, gene-functions and development of novel control technologies. We report here the discovery of five new Sub-Saharan Africa (SSA) B. tabaci putative species, using the partial mitochondrial cytochrome oxidase 1 gene: SSA9, SSA10, SSA11, SSA12 and SSA13. Two of them, SSA10 and SSA11 clustered with the New World species and shared 84.8‒86.5% sequence identities. SSA10 and SSA11 provide new evidence for a close evolutionary link between the Old and New World species. Re-analysis of the evolutionary history of B. tabaci species group indicates that the new African species (SSA10 and SSA11) diverged from the New World clade c. 25 million years ago. The new putative species enable us to: (i) re-evaluate current models of B. tabaci evolution, (ii) recognise increased diversity within this cryptic species group and (iii) re-estimate divergence dates in evolutionary time

Efficient Matrix-Element Matching with Sector Showers

A Markovian shower algorithm based on "sector antennae" is presented and its main properties illustrated. Tree-level full-color matrix elements can be automatically incorporated in the algorithm and are re-interpreted as process-dependent 2 -> n antenna functions. In hard parts of phase-space, these functions generate tree-level matrix-element corrections to the shower. In soft parts, they should improve the logarithmic accuracy of it. The number of matrix-element evaluations required per order of matching is 1, with an unweighting efficiency that remains very high for arbitrary numbers of legs. Total rates can be augmented to NLO precision in a straightforward way. As a proof of concept, we present an implementation in the publicly available VINCIA plug-in to the PYTHIA 8 event generator, for hadronic $Z^0$ decays including tree-level matrix elements through ${\cal O}(\alpha_s^4)$.Comment: 35 pages, 24 figure