1,011 research outputs found
Pairwise statistical significance of local sequence alignment using multiple parameter sets and empirical justification of parameter set change penalty
Background: Accurate estimation of statistical significance of a pairwise alignment is an important problem in sequence comparison. Recently, a comparative study of pairwise statistical significance with database statistical significance was conducted. In this paper, we extend the earlier work on pairwise statistical significance by incorporating with it the use of multiple parameter sets.
Results: Results for a knowledge discovery application of homology detection reveal that using multiple parameter sets for pairwise statistical significance estimates gives better coverage than using a single parameter set, at least at some error levels. Further, the results of pairwise statistical significance using multiple parameter sets are shown to be significantly better than database statistical significance estimates reported by BLAST and PSI-BLAST, and comparable and at times significantly better than SSEARCH. Using non-zero parameter set change penalty values give better performance than zero penalty.
Conclusion: The fact that the homology detection performance does not degrade when using multiple parameter sets is a strong evidence for the validity of the assumption that the alignment score distribution follows an extreme value distribution even when using multiple parameter sets. Parameter set change penalty is a useful parameter for alignment using multiple parameter sets. Pairwise statistical significance using multiple parameter sets can be effectively used to determine the relatedness of a (or a few) pair(s) of sequences without performing a time-consuming database search
Borrelia recurrentis employs a novel multifunctional surface protein with anti-complement, anti-opsonic and invasive potential to escape innate immunity
Borrelia recurrentis, the etiologic agent of louse-borne relapsing fever in humans, has evolved strategies, including antigenic variation, to evade immune defence, thereby causing severe diseases with high mortality rates. Here we identify for the first time a multifunctional surface lipoprotein of B. recurrentis, termed HcpA, and demonstrate that it binds human complement regulators, Factor H, CFHR-1, and simultaneously, the host protease plasminogen. Cell surface bound factor H was found to retain its activity and to confer resistance to complement attack. Moreover, ectopic expression of HcpA in a B. burgdorferi B313 strain, deficient in Factor H binding proteins, protected the transformed spirochetes from complement-mediated killing. Furthermore, HcpA-bound plasminogen/plasmin endows B. recurrentis with the potential to resist opsonization and to degrade extracellular matrix components. Together, the present study underscores the high virulence potential of B. recurrentis. The elucidation of the molecular basis underlying the versatile strategies of B. recurrentis to escape innate immunity and to persist in human tissues, including the brain, may help to understand the pathological processes underlying louse-borne relapsing fever
Atmospheric Evolution
Earth's atmosphere has evolved as volatile species cycle between the
atmosphere, ocean, biomass and the solid Earth. The geochemical, biological and
astrophysical processes that control atmospheric evolution are reviewed from an
"Earth Systems" perspective, with a view not only to understanding the history
of Earth, but also to generalizing to other solar system planets and
exoplanets.Comment: 34 pages, 3 figures, 2 tables. Accepted as a chapter in
"Encyclopaedia of Geochemistry", Editor Bill White, Springer-Nature, 201
Thermal Properties of Graphene, Carbon Nanotubes and Nanostructured Carbon Materials
Recent years witnessed a rapid growth of interest of scientific and
engineering communities to thermal properties of materials. Carbon allotropes
and derivatives occupy a unique place in terms of their ability to conduct
heat. The room-temperature thermal conductivity of carbon materials span an
extraordinary large range - of over five orders of magnitude - from the lowest
in amorphous carbons to the highest in graphene and carbon nanotubes. I review
thermal and thermoelectric properties of carbon materials focusing on recent
results for graphene, carbon nanotubes and nanostructured carbon materials with
different degrees of disorder. A special attention is given to the unusual size
dependence of heat conduction in two-dimensional crystals and, specifically, in
graphene. I also describe prospects of applications of graphene and carbon
materials for thermal management of electronics.Comment: Review Paper; 37 manuscript pages; 4 figures and 2 boxe
Heterogeneity and the dynamics of technology adoption
We estimate the demand for a videocalling technology in the presence of both network effects and heterogeneity. Using a unique dataset from a large multinational firm, we pose and estimate a fully dynamic model of technology adoption. We propose a novel identification strategy based on
post-adoption technology usage to disentangle equilibrium beliefs concerning the evolution of the network from observed and unobserved heterogeneity in technology adoption costs and use benefits. We find that employees have significant heterogeneity in both adoption costs and network benefits, and have preferences for diverse networks. Using our estimates, we evaluate a number of counterfactual adoption policies, and find that a policy of strategically targeting the right subtype for initial adoption can lead to a faster-growing and larger network than a policy of uncoordinated or diffuse adoption
Capecitabine plus oxaliplatin as first-line treatment in patients with advanced biliary system adenocarcinoma: a prospective multicentre phase II trial
This prospective multicentre phase II study characterises the toxicity and activity of first-line capecitabine and oxaliplatin combination therapy (CAPOX) in advanced biliary system adenocarcinomas. Patients received oxaliplatin (130 mg m−2, day 1) plus capecitabine (1000 mg m−2 b.i.d., days 1–14) every 3 weeks. Patients were stratified prospectively into two groups based on location of the primary (gallbladder carcinoma (GBC) or extrahepatic cholangiocarcinoma (ECC) versus intrahepatic mass-forming type cholangiocarcinoma (ICC)). Sixty-five patients were evaluable. The response rate in 47 patients with GBC/ECC was 27% (4% complete responses), and in 23 patients (49%) stable disease (SD) was encountered. In 18 patients with ICC, we observed no objective responses, but 6 patients (33%) had SD. Median survival was 12.8 months (95% CI, 10.0–15.6) for patients with GBC or ECC (GBC: 8.2 months; 95% CI, 4.3–11.7; ECC: 16.8 months; 95% CI, 12.7–20.5), and 5.2 months (95% CI, 0.6–9.8) for ICC patients. In both cohorts, therapy was well tolerated. The most common grade 3–4 toxicity was peripheral sensory neuropathy (11 patients). Our data suggest that the CAPOX regimen is a well-tolerated and active treatment option for advanced ECC and GBC but might produce poorer results for ICC
Angular and Current-Target Correlations in Deep Inelastic Scattering at HERA
Correlations between charged particles in deep inelastic ep scattering have
been studied in the Breit frame with the ZEUS detector at HERA using an
integrated luminosity of 6.4 pb-1. Short-range correlations are analysed in
terms of the angular separation between current-region particles within a cone
centred around the virtual photon axis. Long-range correlations between the
current and target regions have also been measured. The data support
predictions for the scaling behaviour of the angular correlations at high Q2
and for anti-correlations between the current and target regions over a large
range in Q2 and in the Bjorken scaling variable x. Analytic QCD calculations
and Monte Carlo models correctly describe the trends of the data at high Q2,
but show quantitative discrepancies. The data show differences between the
correlations in deep inelastic scattering and e+e- annihilation.Comment: 26 pages including 10 figures (submitted to Eur. J. Phys. C
A Measurement of Rb using a Double Tagging Method
The fraction of Z to bbbar events in hadronic Z decays has been measured by
the OPAL experiment using the data collected at LEP between 1992 and 1995. The
Z to bbbar decays were tagged using displaced secondary vertices, and high
momentum electrons and muons. Systematic uncertainties were reduced by
measuring the b-tagging efficiency using a double tagging technique. Efficiency
correlations between opposite hemispheres of an event are small, and are well
understood through comparisons between real and simulated data samples. A value
of Rb = 0.2178 +- 0.0011 +- 0.0013 was obtained, where the first error is
statistical and the second systematic. The uncertainty on Rc, the fraction of Z
to ccbar events in hadronic Z decays, is not included in the errors. The
dependence on Rc is Delta(Rb)/Rb = -0.056*Delta(Rc)/Rc where Delta(Rc) is the
deviation of Rc from the value 0.172 predicted by the Standard Model. The
result for Rb agrees with the value of 0.2155 +- 0.0003 predicted by the
Standard Model.Comment: 42 pages, LaTeX, 14 eps figures included, submitted to European
Physical Journal
Plastisol Foaming Process. Decomposition of the Foaming Agent, Polymer Behavior in the Corresponding Temperature Range and Resulting Foam Properties
The decomposition of azodicarbonamide, used as foaming agent in PVC - plasticizer (1/1) plastisols was studied by DSC. Nineteen different plasticizers, all belonging to the ester family, two being polymeric (polyadipates), were compared. The temperature of maximum decomposition rate (in anisothermal regime at 5 K min-1 scanning rate), ranges between 434 and 452 K. The heat of decomposition ranges between 8.7 and 12.5 J g -1. Some trends of variation of these parameters appear significant and are discussed in terms of solvent (matrix) and viscosity effects on the decomposition reactions. The shear modulus at 1 Hz frequency was determined at the temperature of maximum rate of foaming agent decomposition, and differs significantly from a sample to another. The foam density was determined at ambient temperature and the volume fraction of bubbles was used as criterion to judge the efficiency of the foaming process. The results reveal the existence of an optimal shear modulus of the order of 2 kPa that corresponds roughly to plasticizer molar masses of the order of 450 ± 50 g mol-1. Heavier plasticizers, especially polymeric ones are too difficult to deform. Lighter plasticizers such as diethyl phthalate (DEP) deform too easily and presumably facilitate bubble collapse
Measurement of the B+ and B-0 lifetimes and search for CP(T) violation using reconstructed secondary vertices
The lifetimes of the B+ and B-0 mesons, and their ratio, have been measured in the OPAL experiment using 2.4 million hadronic Z(0) decays recorded at LEP. Z(0) --> b (b) over bar decays were tagged using displaced secondary vertices and high momentum electrons and muons. The lifetimes were then measured using well-reconstructed charged and neutral secondary vertices selected in this tagged data sample. The results aretau(B+) = 1.643 +/- 0.037 +/- 0.025 pstau(Bo) = 1.523 +/- 0.057 +/- 0.053 pstau(B+)/tau(Bo) = 1.079 +/- 0.064 +/- 0.041,where in each case the first error is statistical and the second systematic.A larger data sample of 3.1 million hadronic Z(o) decays has been used to search for CP and CPT violating effects by comparison of inclusive b and (b) over bar hadron decays, No evidence fur such effects is seen. The CP violation parameter Re(epsilon(B)) is measured to be Re(epsilon(B)) = 0.001 +/- 0.014 +/- 0.003and the fractional difference between b and (b) over bar hadron lifetimes is measured to(Delta tau/tau)(b) = tau(b hadron) - tau((b) over bar hadron)/tau(average) = -0.001 +/- 0.012 +/- 0.008
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