1,298 research outputs found
The Cauchy problem for a class of two-dimensional nonlocal nonlinear wave equations governing anti-plane shear motions in elastic materials
This paper is concerned with the analysis of the Cauchy problem of a general
class of two-dimensional nonlinear nonlocal wave equations governing anti-plane
shear motions in nonlocal elasticity. The nonlocal nature of the problem is
reflected by a convolution integral in the space variables. The Fourier
transform of the convolution kernel is nonnegative and satisfies a certain
growth condition at infinity. For initial data in Sobolev spaces,
conditions for global existence or finite time blow-up of the solutions of the
Cauchy problem are established.Comment: 15 pages. "Section 6 The Anisotropic Case" added and minor changes.
Accepted for publication in Nonlinearit
Close Packing of Atoms, Geometric Frustration and the Formation of Heterogeneous States in Crystals
To describe structural peculiarities in inhomogeneous media caused by the
tendency to the close packing of atoms a formalism based on the using of the
Riemann geometry methods (which were successfully applied lately to the
description of structures of quasicrystals and glasses) is developed. Basing on
this formalism we find in particular the criterion of stability of precipitates
of the Frank-Kasper phases in metallic systems. The nature of the ''rhenium
effect'' in W-Re alloys is discussed.Comment: 14 pages, RevTex, 2 PostScript figure
A probabilistic model for gene content evolution with duplication, loss, and horizontal transfer
We introduce a Markov model for the evolution of a gene family along a
phylogeny. The model includes parameters for the rates of horizontal gene
transfer, gene duplication, and gene loss, in addition to branch lengths in the
phylogeny. The likelihood for the changes in the size of a gene family across
different organisms can be calculated in O(N+hM^2) time and O(N+M^2) space,
where N is the number of organisms, is the height of the phylogeny, and M
is the sum of family sizes. We apply the model to the evolution of gene content
in Preoteobacteria using the gene families in the COG (Clusters of Orthologous
Groups) database
Prospecting environmental mycobacteria: combined molecular approaches reveal unprecedented diversity
Background: Environmental mycobacteria (EM) include species commonly found in various terrestrial and aquatic environments, encompassing animal and human pathogens in addition to saprophytes. Approximately 150 EM species can be separated into fast and slow growers based on sequence and copy number differences of their 16S rRNA genes. Cultivation methods are not appropriate for diversity studies; few studies have investigated EM diversity in soil despite their importance as potential reservoirs of pathogens and their hypothesized role in masking or blocking M. bovis BCG vaccine.
Methods: We report here the development, optimization and validation of molecular assays targeting the 16S rRNA gene to assess diversity and prevalence of fast and slow growing EM in representative soils from semi tropical and temperate areas. New primer sets were designed also to target uniquely slow growing mycobacteria and used with PCR-DGGE, tag-encoded Titanium amplicon pyrosequencing and quantitative PCR.
Results: PCR-DGGE and pyrosequencing provided a consensus of EM diversity; for example, a high abundance of pyrosequencing reads and DGGE bands corresponded to M. moriokaense, M. colombiense and M. riyadhense. As expected pyrosequencing provided more comprehensive information; additional prevalent species included M. chlorophenolicum, M. neglectum, M. gordonae, M. aemonae. Prevalence of the total Mycobacterium genus in the soil samples ranged from 2.3×107 to 2.7×108 gene targets g−1; slow growers prevalence from 2.9×105 to 1.2×107 cells g−1.
Conclusions: This combined molecular approach enabled an unprecedented qualitative and quantitative assessment of EM across soil samples. Good concordance was found between methods and the bioinformatics analysis was validated by random resampling. Sequences from most pathogenic groups associated with slow growth were identified in extenso in all soils tested with a specific assay, allowing to unmask them from the Mycobacterium whole genus, in which, as minority members, they would have remained undetected
The ansamycin antibiotic, rifamycin SV, inhibits BCL6 transcriptional repression and forms a complex with the BCL6-BTB/POZ domain
BCL6 is a transcriptional repressor that is over-expressed due to chromosomal translocations, or other abnormalities, in ~40% of diffuse large B-cell lymphoma. BCL6 interacts with co-repressor, SMRT, and this is essential for its role in lymphomas. Peptide or small molecule inhibitors, which prevent the association of SMRT with BCL6, inhibit transcriptional repression and cause apoptosis of lymphoma cells in vitro and in vivo. In order to discover compounds, which have the potential to be developed into BCL6 inhibitors, we screened a natural product library. The ansamycin antibiotic, rifamycin SV, inhibited BCL6 transcriptional repression and NMR spectroscopy confirmed a direct interaction between rifamycin SV and BCL6. To further determine the characteristics of compounds binding to BCL6-POZ we analyzed four other members of this family and showed that rifabutin, bound most strongly. An X-ray crystal structure of the rifabutin-BCL6 complex revealed that rifabutin occupies a partly non-polar pocket making interactions with tyrosine58, asparagine21 and arginine24 of the BCL6-POZ domain. Importantly these residues are also important for the interaction of BLC6 with SMRT. This work demonstrates a unique approach to developing a structure activity relationship for a compound that will form the basis of a therapeutically useful BCL6 inhibitor
Exploring the oral microbiota of children at various developmental stages of their dentition in the relation to their oral health
<p>Abstract</p> <p>Background</p> <p>An understanding of the relation of commensal microbiota to health is essential in preventing disease. Here we studied the oral microbial composition of children (N = 74, aged 3 - 18 years) in natural transition from their deciduous to a permanent dentition and related the microbial profiles to their oral health status. The microbial composition of saliva was assessed by barcoded pyrosequencing of the V5-V6 hypervariable regions of the 16 S rRNA, as well as by using phylogenetic microarrays.</p> <p>Results</p> <p>Pyrosequencing reads (126174 reads, 1045 unique sequences) represented 8 phyla and 113 higher taxa in saliva samples. Four phyla - Firmicutes, Bacteriodetes, Proteobacteria and Actinobacteria - predominated in all groups. The deciduous dentition harboured a higher proportion of Proteobacteria (Gammaproteobacteria, Moraxellaceae) than Bacteroidetes, while in all other groups Bacteroidetes were at least as abundant as Proteobacteria. Bacteroidetes (mainly genus <it>Prevotella</it>), Veillonellaceae family, Spirochaetes and candidate division TM7 increased with increasing age, reflecting maturation of the microbiome driven by biological changes with age.</p> <p>Microarray analysis enabled further analysis of the individual salivary microbiota. Of 350 microarray probes, 156 gave a positive signal with, on average, 77 (range 48-93) probes per individual sample.</p> <p>A caries-free oral status significantly associated with the higher signal of the probes targeting <it>Porphyromonas catoniae </it>and <it>Neisseria flavescens</it>.</p> <p>Conclusions</p> <p>The potential role of <it>P. catoniae </it>and <it>N. flavescens </it>as oral health markers should be assessed in large-scale clinical studies. The combination of both, open-ended and targeted molecular approaches provides us with information that will increase our understanding of the interplay between the human host and its microbiome.</p
Search for Branons at LEP
We search, in the context of extra-dimension scenarios, for the possible
existence of brane fluctuations, called branons. Events with a single photon or
a single Z-boson and missing energy and momentum collected with the L3 detector
in e^+ e^- collisions at centre-of-mass energies sqrt{s}=189-209$ GeV are
analysed. No excess over the Standard Model expectations is found and a lower
limit at 95% confidence level of 103 GeV is derived for the mass of branons,
for a scenario with small brane tensions. Alternatively, under the assumption
of a light branon, brane tensions below 180 GeV are excluded
Study of Spin and Decay-Plane Correlations of W Bosons in the e+e- -> W+W- Process at LEP
Data collected at LEP at centre-of-mass energies \sqrt(s) = 189 - 209 GeV are
used to study correlations of the spin of W bosons using e+e- -> W+W- -> lnqq~
events. Spin correlations are favoured by data, and found to agree with the
Standard Model predictions. In addition, correlations between the W-boson decay
planes are studied in e+e- -> W+W- -> lnqq~ and e+e- -> W+W- -> qq~qq~ events.
Decay-plane correlations, consistent with zero and with the Standard Model
predictions, are measured
Ultrarelativistic sources in nonlinear electrodynamics
The fields of rapidly moving sources are studied within nonlinear
electrodynamics by boosting the fields of sources at rest. As a consequence of
the ultrarelativistic limit the delta-like electromagnetic shock waves are
found. The character of the field within the shock depends on the theory of
nonlinear electrodynamics considered. In particular, we obtain the field of an
ultrarelativistic charge in the Born-Infeld theory.Comment: 10 pages, 3 figure
Measurement of the Cross Section for Open-Beauty Production in Photon-Photon Collisions at LEP
The cross section for open-beauty production in photon-photon collisions is
measured using the whole high-energy and high-luminosity data sample collected
by the L3 detector at LEP. This corresponds to 627/pb of integrated luminosity
for electron-positron centre-of-mass energies from 189GeV to 209GeV. Events
containing b quarks are identified through their semi-leptonic decay into
electrons or muons. The e+e- -> e+e-b b~X cross section is measured within our
fiducial volume and then extrapolated to the full phase space. These results
are found to be in significant excess with respect to Monte Carlo predictions
and next-to-leading order QCD calculations
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