662 research outputs found
Genome characterization and population genetic structure of the zoonotic pathogen, streptococcus canis
Background - Streptococcus canis is an important opportunistic pathogen of dogs and cats that can also infect a wide range of additional mammals including cows where it can cause mastitis. It is also an emerging human pathogen.
Results - Here we provide characterization of the first genome sequence for this species, strain FSL S3-227 (milk isolate from a cow with an intra-mammary infection). A diverse array of putative virulence factors was encoded by the S. canis FSL S3-227 genome. Approximately 75% of these gene sequences were homologous to known Streptococcal virulence factors involved in invasion, evasion, and colonization. Present in the genome are multiple potentially mobile genetic elements (MGEs) [plasmid, phage, integrative conjugative element (ICE)] and comparison to other species provided convincing evidence for lateral gene transfer (LGT) between S. canis and two additional bovine mastitis causing pathogens (Streptococcus agalactiae, and Streptococcus dysgalactiae subsp. dysgalactiae), with this transfer possibly contributing to host adaptation. Population structure among isolates obtained from Europe and USA [bovineâ=â56, canineâ=â26, and felineâ=â1] was explored. Ribotyping of all isolates and multi locus sequence typing (MLST) of a subset of the isolates (nâ=â45) detected significant differentiation between bovine and canine isolates (Fisher exact test: Pâ=â0.0000 [ribotypes], Pâ=â0.0030 [sequence types]), suggesting possible host adaptation of some genotypes. Concurrently, the ancestral clonal complex (54% of isolates) occurred in many tissue types, all hosts, and all geographic locations suggesting the possibility of a wide and diverse niche.
Conclusion - This study provides evidence highlighting the importance of LGT in the evolution of the bacteria S. canis, specifically, its possible role in host adaptation and acquisition of virulence factors. Furthermore, recent LGT detected between S. canis and human bacteria (Streptococcus urinalis) is cause for concern, as it highlights the possibility for continued acquisition of human virulence factors for this emerging zoonotic pathogen
Noise-free scattering of the quantized electromagnetic field from a dispersive linear dielectric
We study the scattering of the quantized electromagnetic field from a linear,
dispersive dielectric using the scattering formalism for quantum fields. The
medium is modeled as a collection of harmonic oscillators with a number of
distinct resonance frequencies. This model corresponds to the Sellmeir
expansion, which is widely used to describe experimental data for real
dispersive media. The integral equation for the interpolating field in terms of
the in field is solved and the solution used to find the out field. The
relation between the in and out creation and annihilation operators is found
which allows one to calculate the S-matrix for this system. In this model, we
find that there are absorption bands, but the input-output relations are
completely unitary. No additional quantum noise terms are required.Comment: Revtex, submitted to Physical Review
Dynamic Changes in High-Sensitivity Cardiac Troponin I in Response to Anthracycline-Based Chemotherapy
Aims:
Treatment advances have improved cancer-related outcomes and shifted interest towards minimising long-term iatrogenic complications, particularly chemotherapy-related cardiotoxicity. High-sensitivity cardiac troponin I (hs-cTnI) assays accurately quantify very low concentrations of plasma troponin and enable early detection of cardiomyocyte injury prior to the development of myocardial dysfunction. The profile of hs-cTnI in response to anthracycline-based treatment has not previously been described.
Materials and methods:
This was a multicentre prospective observational cohort study. Female patients with newly diagnosed invasive breast cancer scheduled to receive anthracycline-based (epirubicin) chemotherapy were recruited. Blood sampling was carried out before and 24 h after each cycle. Hs-cTnI concentrations were measured using the Abbott ARCHITECTSTAT assay.
Results:
We recruited 78 women with a median (interquartile range) age of 52 (49â61) years. The median baseline troponin concentration was 1 (1â4) ng/l and the median cumulative epirubicin dose was 394 (300â405) mg/m2. Following an initial 33% fall 24 h after anthracycline dosing (P < 0.001), hs-cTnI concentrations increased by a median of 50% (P < 0.001) with each successive treatment cycle. In total, 45 patients had troponin measured immediately before the sixth treatment cycle, 21 (46.6%) of whom had hs-cTnI concentrations âĽ16 ng/l, indicating myocardial injury. Plasma hs-cTnI concentrations before the second treatment cycle were a strong predictor of subsequent myocardial injury.
Conclusions:
Cardiotoxicity arising from anthracycline therapy is detectable in the earliest stages of breast cancer treatment and is cumulative with each treatment cycle. This injury is most reliably determined from blood sampling carried out before rather than after each treatment cycle
A straw drift chamber spectrometer for studies of rare kaon decays
We describe the design, construction, readout, tests, and performance of
planar drift chambers, based on 5 mm diameter copperized Mylar and Kapton
straws, used in an experimental search for rare kaon decays. The experiment
took place in the high-intensity neutral beam at the Alternating Gradient
Synchrotron of Brookhaven National Laboratory, using a neutral beam stop, two
analyzing dipoles, and redundant particle identification to remove backgrounds
Predicted modulated differential rates for direct WIMP searches at low energy transfers
The differential event rate for direct detection of dark matter, both the
time averaged and the modulated one due to the motion of the Earth, are
discussed. The calculations focus on relatively light cold dark matter
candidates (WIMP) and low energy transfers. It is shown that for sufficiently
light WIMPs the extraction of relatively large nucleon cross sections is
possible. Furthermore for some WIMP masses the modulation amplitude may change
sign, meaning that, in such a case, the maximum rate may occur six months later
than naively expected. This effect can be exploited to yield information about
the mass of the dark matter candidate, if and when the observation of the
modulation of the event rate is established.Comment: 16 pages, 22 figures; references adde
Parity-Violating Interaction Effects I: the Longitudinal Asymmetry in pp Elastic Scattering
The proton-proton parity-violating longitudinal asymmetry is calculated in
the lab-energy range 0--350 MeV, using a number of different, latest-generation
strong-interaction potentials--Argonne V18, Bonn-2000, and Nijmegen-I--in
combination with a weak-interaction potential consisting of rho- and
omega-meson exchanges--the model known as DDH. The complete scattering problem
in the presence of parity-conserving, including Coulomb, and parity-violating
potentials is solved in both configuration- and momentum-space. The predicted
parity-violating asymmetries are found to be only weakly dependent upon the
input strong-interaction potential adopted in the calculation. Values for the
rho- and omega-meson weak coupling constants and
are determined by reproducing the measured asymmetries at 13.6 MeV, 45 MeV, and
221 MeV.Comment: 24 pages, 8 figures, submitted to Physical Review
Multilevel Methods: Emergent Issues and Future Directions in Measurement, Longitudinal Analyses and Non-Normal Outcomes
The Dependence of the Superconducting Transition Temperature of Organic Molecular Crystals on Intrinsically Non-Magnetic Disorder: a Signature of either Unconventional Superconductivity or Novel Local Magnetic Moment Formation
We give a theoretical analysis of published experimental studies of the
effects of impurities and disorder on the superconducting transition
temperature, T_c, of the organic molecular crystals kappa-ET_2X and beta-ET_2X
(where ET is bis(ethylenedithio)tetrathiafulvalene and X is an anion eg I_3).
The Abrikosov-Gorkov (AG) formula describes the suppression of T_c both by
magnetic impurities in singlet superconductors, including s-wave
superconductors and by non-magnetic impurities in a non-s-wave superconductor.
We show that various sources of disorder lead to the suppression of T_c as
described by the AG formula. This is confirmed by the excellent fit to the
data, the fact that these materials are in the clean limit and the excellent
agreement between the value of the interlayer hopping integral, t_perp,
calculated from this fit and the value of t_perp found from angular-dependant
magnetoresistance and quantum oscillation experiments. If the disorder is, as
seems most likely, non-magnetic then the pairing state cannot be s-wave. We
show that the cooling rate dependence of the magnetisation is inconsistent with
paramagnetic impurities. Triplet pairing is ruled out by several experiments.
If the disorder is non-magnetic then this implies that l>=2, in which case
Occam's razor suggests that d-wave pairing is realised. Given the proximity of
these materials to an antiferromagnetic Mott transition, it is possible that
the disorder leads to the formation of local magnetic moments via some novel
mechanism. Thus we conclude that either kappa-ET_2X and beta-ET_2X are d-wave
superconductors or else they display a novel mechanism for the formation of
localised moments. We suggest systematic experiments to differentiate between
these scenarios.Comment: 18 pages, 5 figure
An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics
For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types
Search for direct production of charginos and neutralinos in events with three leptons and missing transverse momentum in âs = 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 fbâ1 of protonâproton 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
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