4,374 research outputs found
Making sense of EST sequences by CLOBBing them
No full textAbstract Background Expressed sequence tags (ESTs) are single pass reads from randomly selected cDNA clones. They provide a highly cost-effective method to access and identify expressed genes. However, they are often prone to sequencing errors and typically define incomplete transcripts. To increase the amount of information obtainable from ESTs and reduce sequencing errors, it is necessary to cluster ESTs into groups sharing significant sequence similarity. Results As part of our ongoing EST programs investigating 'orphan' genomes, we have developed a clustering algorithm, CLOBB (Cluster on the basis of BLAST similarity) to identify and cluster ESTs. CLOBB may be used incrementally, preserving original cluster designations. It tracks cluster-specific events such as merging, identifies 'superclusters' of related clusters and avoids the expansion of chimeric clusters. Based on the Perl scripting language, CLOBB is highly portable relying only on a local installation of NCBI's freely available BLAST executable and can be usefully applied to > 95 % of the current EST datasets. Analysis of the Danio rerio EST dataset demonstrates that CLOBB compares favourably with two less portable systems, UniGene and TIGR Gene Indices. Conclusions CLOBB provides a highly portable EST clustering solution and is freely downloaded from: http://www.nematodes.org/CLOBB</p
Search for the decay Bs0→D*∓π±
No full textA search for the decay Bs0→D*∓π± is presented using a data sample corresponding to an integrated luminosity of 1.0 fb-1 of pp collisions collected by LHCb. This decay is expected to be mediated by a W-exchange diagram, with little contribution from rescattering processes, and therefore a measurement of the branching fraction will help us to understand the mechanism behind related decays such as Bs0→π+π- and Bs0→DD̅ . Systematic uncertainties are minimized by using B0→D*∓π± as a normalization channel. We find no evidence for a signal, and set an upper limit on the branching fraction of B(Bs0→D*∓π±)<6.1(7.8)×10-6 at 90% (95%) confidence level
Measurement of the B0–B0 oscillation frequency Δmd with the decays B0→D−π+ and B0→ J/ψK∗0
No full textThe B
0
–B
0
oscillation frequency Δmd is measured by the LHCb experiment using a dataset corresponding
to an integrated luminosity of 1.0 fb−1
of proton–proton collisions at √
s = 7 TeV, and is found to be
Δmd
=0.5156±0.0051 (stat.)±0.0033 (syst.) ps−1
. The measurement is based on results from analyses
of the decays B
0
→ D
−π
+ (D
−
→ K
+π
−π
−) and B
0
→ J/ψK
∗0
(J/ψ →μ
+μ
−,K
∗0
→ K
+π
−) and
their charge conjugated modes
Evidence for the decay B0→J/ψω and measurement of the relative branching fractions of meson decays to J/ψη and J/ψη′
No full textFirst evidence of the B 0 → J / ψ ω decay is found and the B s 0 → J / ψ η and B s 0 → J / ψ η ′ decays are studied using a dataset corresponding to an integrated luminosity of 1.0 fb -1 collected by the LHCb experiment in proton-proton collisions at a centre-of-mass energy of sqrt(s) = 7 TeV. The branching fractions of these decays are measured relative to that of the B 0 → J / ψ ρ 0 decay:frac(B (B 0 → J / ψ ω), B (B 0 → J / ψ ρ 0)) = 0.89 ± 0.19 (stat) - 0.13 + 0.07 (syst),frac(B (B s 0 → J / ψ η), B (B 0 → J / ψ ρ 0)) = 14.0 ± 1.2 (stat) - 1.5 + 1.1 (syst) - 1.0 + 1.1 (frac(f d, f s)),frac(B (B s 0 → J / ψ η ′), B (B 0 → J / ψ ρ 0)) = 12.7 ± 1.1 (stat) - 1.3 + 0.5 (syst) - 0.9 + 1.0 (frac(f d, f s)), where the last uncertainty is due to the knowledge of f d / f s, the ratio of b-quark hadronization factors that accounts for the different production rate of B 0 and B s 0 mesons. The ratio of the branching fractions of B s 0 → J / ψ η ′ and B s 0 → J / ψ η decays is measured to befrac(B (B s 0 → J / ψ η ′), B (B s 0 → J / ψ η)) = 0.90 ± 0.09 (stat) - 0.02 + 0.06 (syst)
Modelagem e simulação da emissão de material particulado a partir da queima de bagaço em uma usina de açúcar e álcool
No full textDissertação (mestrado) - Universidade Federal de Santa Catarina, Centro Tecnológico, Programa de Pós-Graduação em Engenharia Química, Florianópolis, 2013.A proposta deste trabalho é a modelagem fenomenológica de uma chaminé expelindo material particulado com diâmetro médio de 10 µm (MP10),15 µm e 20 µm utilizando dados adquiridos ao longo de um ano de funcionamento de uma usina de açúcar e álcool. Com este mode-lo, pretende-se estudar o comportamento do material particulado em meio ao escoamento do ar ambiente, determinando-se o grau de disper-são e as distâncias percorridas pelo mesmo, a fim de se verificar se ha-veria risco de doenças respiratórias para a população próxima à indús-tria. O modelo elaborado passou por testes de validação. O trabalho de Hall et al. (1998), que trata sobre dispersão de partículas em túnel de vento foi utilizado para esse fim. O modelo testado apresentou resulta-dos adequados para a dispersão de partículas de vidro de 105µm, con-forme os dados fornecidos no trabalho supracitado. No modelo de emis-são de particulado, três simulações foram conduzidas para melhor avali-ar os efeitos e as diferenças entre um modelo de escoamento turbulento não isotérmico e um modelo misto não isotérmico (laminar fora da cha-miné e turbulento em seu interior). O modelo de emissão de material particulado produziu um comportamento físico consistente com dados encontrados na literatura para particulados da classe MP10. A altura da chaminé (25 m) que pode lançar as partículas até cerca de 80 m do nível do chão permite deslocá-las com eficiente dispersão por longas distân-cias, reduzindo assim grandemente qualquer risco para a saúde humana. O material particulado de 10 µm chega ao chão em aproximadamente 3 h e 30 min e pode permanecer no ar por tempo indeterminado, depen-dendo de seu tamanho (Abstract : The purpose of this study is the phenomenological modeling of a chimney spewing particulate matter with a diameter of 10 µm (PM10), 15 µm and 20 µm using data acquired over an operation year in a sugar plant. With this model, we intend to study the behavior of particulate matter in the air flow through the environment, determining the degree of dispersion and the distances traveled by the same in order to verify if there is risk of respiratory diseases for the population near industry. The model developed has undergone validation testing. The work of Hall et al. (1998), which deals with dispersion of particles in the wind tunnel was used for this purpose. The model tested showed adequate results for the dispersion glass particulates of 105µm according to the data provid-ed in the above mentioned study. In the model of particle emission, three simulations were conducted to further evaluate the effects and differences between a not isothermal turbulent flow model and a non- isothermal mixed model (laminar outside the chimney and turbulent inside). The model emission of particulate matter produced a physical behavior consistent with literature data for PM10 particulates class. The stack height (25 m) which can shed particles up to about 80 m from ground level allows them to move efficiently dispersing over long dis-tances, thus greatly reducing any risk to human health. Particulate mat-ter comes to the ground in about 3 h 30 min and can stay in the air indef-initely depending on their size (<10 micrometers) and wind conditions
Prompt charm production in pp collisions at √<span style="text-decoration:overline">s</span>=7 TeV
No full textCharm production at the LHC in pp collisions at s√=7 TeV is studied with the LHCb detector. The decays D0→K−π+, D+→K−π+π+, D⁎+→D0(K−π+)π+, D+s→ϕ(K−K+)π+, Λ+c→pK−π+, and their charge conjugates are analysed in a data set corresponding to an integrated luminosity of 15 nb−1. Differential cross-sections dσ/dpT are measured for prompt production of the five charmed hadron species in bins of transverse momentum and rapidity in the region 0<pT<8 GeV/c and 2.0<y<4.5. Theoretical predictions are compared to the measured differential cross-sections. The integrated cross-sections of the charm hadrons are computed in the above pT-y range, and their ratios are reported. A combination of the five integrated cross-section measurements gives
σ(cc¯)pT<8 GeV/c,2.0<y<4.5=1419±12(stat)±116(syst)±65(frag) μb,
where the uncertainties are statistical, systematic, and due to the fragmentation functions
40Ar/39Ar dating of Quaternary lavas in northwest Iran: constraints on the landscape evolution and incision rates of the Turkish-Iranian plateau
No full textWe report five new <sup>40</sup>Ar/<sup>39</sup>Ar ages for basaltic lavas in the Maku region of northwest Iran, between ca. 1.87 and 0.40 Ma, which help constrain the tectonic and landscape evolution of this part of the Turkish–Iranian plateau. Flows originated from the composite volcanoes Ararat (Agri Dagi), Tendürek and Yigit Dagi, in eastern Turkey (Anatolia). These volcanoes are within the Turkish–Iranian plateau, which is a consequence of the Arabia–Eurasia collision, but has a poorly constrained evolution and surface uplift history. Current plateau elevations are typically 1.5–2 km, and relief between non-volcanic summits and basins is typically on the scale of ∼1 km. Samples are from flows that passed along pre-existing river valleys. Gorges were cut by re-established rivers after the eruptions, but the great majority of the local relief (∼95 per cent) lies above the sampled flows and so most likely pre-dates the volcanism. Gorge depths and lava ages allow local Quaternary fluvial incision rates to be calculated, which are ∼0.01 to 0.05 mm yr−1. These rates imply slow surface uplift of this part of the Turkish–Iranian plateau during the Quaternary. We therefore constrain the generation of the great majority of relief in the study area to be pre-Quaternary, and caused by the tectonic construction of the plateau, rather than a subcrustal origin related to the Quaternary magmatism
Co-localization of AR, GnRH, and CRH in MPO neurons, determined by dual-fluorescence immunohistochemistry and confocal laser-scanning microscopy.
No full text<p>A) Main distribution of AR, GnRH, and CRH in control female rat brain (3v = third ventricle). Adapted from reference <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0006638#pone.0006638-Paxinos1" target="_blank">[47]</a>. B–D) Co-localization of AR, GnRH, CRH, and NeuN immunoreactivity in MPO neurons. E) Co-localization of rabbit polyclonal AR antibody and mouse monoclonal AR antibody in hypothalamic MPO. F and G) Co-localization of mouse monoclonal AR antibody with GnRH or CRH immunoreactivity in hypothalamic MPO neurons. In panels B–G, arrows indicate co-localization. Scale bars, 100 µm.</p
Precision measurement of D meson mass differences
No full textUsing three- and four-body decays of D mesons produced in semileptonic b-hadron decays, precision measurements of D meson mass differences are made together with a measurement of the D 0 mass. The measurements are based on a dataset corresponding to an integrated luminosity of 1.0 fb−1 collected in pp collisions at 7 TeV. Using the decay D 0 → K + K − K − π +, the D 0 mass is measured to be M(D0)=1864.75±0.15(stat)±0.11(syst)MeV/c2.
The mass differences
M(D+)−M(D0)=4.76±0.12(stat)±0.07(syst)MeV/c2,M(Ds)−M(D+)=98.68±0.03(stat)±0.04(syst)MeV/c2
are measured using the D 0 → K + K − π + π − and D+(s)→K+K−π+ mode
Molecular detection of bioluminescent dinoflagellates in surface waters of the Patagonian Shelf during early austral summer 2008
No full textWe investigated the distribution of bioluminescent dinoflagellates in the Patagonian Shelf region using “universal” PCR primers for the dinoflagellate luciferase gene. Luciferase gene sequences and single cell PCR tests, in conjunction with taxonomic identification by microscopy, allowed us to identify and quantify bioluminescent dinoflagellates. We compared these data to coincidental discrete optical measurements of stimulable bioluminescence intensity. Molecular detection of the luciferase gene showed that bioluminescent dinoflagellates were widespread across the majority of the Patagonian Shelf region. Their presence was comparatively underestimated by optical bioluminescence measurements, whose magnitude was affected by interspecific differences in bioluminescence intensity and by the presence of other bioluminescent organisms. Molecular and microscopy data showed that the complex hydrography of the area played an important role in determining the distribution and composition of dinoflagellate populations. Dinoflagellates were absent south of the Falkland Islands where the cold, nutrient-rich, and well-mixed waters of the Falklands Current favoured diatoms instead. Diverse populations of dinoflagellates were present in the warmer, more stratified waters of the Patagonian Shelf and Falklands Current as it warmed northwards. Here, the dinoflagellate population composition could be related to distinct water masses. Our results provide new insight into the prevalence of bioluminescent dinoflagellates in Patagonian Shelf waters and demonstrate that a molecular approach to the detection of bioluminescent dinoflagellates in natural waters is a promising tool for ecological studies of these organisms
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