352 research outputs found
Hydroxymethylated Cytosines Are Associated with Elevated C to G Transversion Rates
It has long been known that methylated cytosines deaminate at higher rates than unmodified cytosines and constitute mutational hotspots in mammalian genomes. The repertoire of naturally occurring cytosine modifications, however, extends beyond 5-methylcytosine to include its oxidation derivatives, notably 5-hydroxymethylcytosine. The effects of these modifications on sequence evolution are unknown. Here, we combine base-resolution maps of methyl- and hydroxymethylcytosine in human and mouse with population genomic, divergence and somatic mutation data to show that hydroxymethylated and methylated cytosines show distinct patterns of variation and evolution. Surprisingly, hydroxymethylated sites are consistently associated with elevated C to G transversion rates at the level of segregating polymorphisms, fixed substitutions, and somatic mutations in tumors. Controlling for multiple potential confounders, we find derived C to G SNPs to be 1.43-fold (1.22-fold) more common at hydroxymethylated sites compared to methylated sites in human (mouse). Increased C to G rates are evident across diverse functional and sequence contexts and, in cancer genomes, correlate with the expression of Tet enzymes and specific components of the mismatch repair pathway (MSH2, MSH6, and MBD4). Based on these and other observations we suggest that hydroxymethylation is associated with a distinct mutational burden and that the mismatch repair pathway is implicated in causing elevated transversion rates at hydroxymethylated cytosines
Numerical benchmark campaign of cost action tu1404 – microstructural modelling
This paper presents the results of the numerical benchmark campaign on modelling of hydration and microstructure development of cementitious materials. This numerical benchmark was performed in the scope of COST Action TU1404 “Towards the next generation of standards for service life of cement-based materials and structures”. Seven modelling groups took part in the campaign applying different models for prediction of mechanical properties (elastic moduli or compressive strength) in cement pastes and mortars. The simulations were based on published experimental data. The experimental data (both input and results used for validation) were open to the participants. The purpose of the benchmark campaign was to identify the needs of different models in terms of input experimental data, verify predictive potential of the models and finally to provide reference cases for new models in the future. The results of the benchmark show that a relatively high scatter in the predictions can arise between different models, in particular at early ages (e.g. elastic Young’s modulus predicted at 1 d in the range 6-20 GPa), while it reduces at later age, providing relatively good agreement with experimental data. Even though the input data was based on a single experimental dataset, the large differences between the results of the different models were found to be caused by distinct assumed properties for the individual phases at the microstructural level, mainly because of the scatter in the nanoindentation-derived properties of the C-S-H phase.</jats:p
Measurements of and Production in + Collisions at = 200 GeV
We report measurements of charmed-hadron (, ) production cross
sections at mid-rapidity in + collisions at a center-of-mass energy of
200 GeV by the STAR experiment. Charmed hadrons were reconstructed via the
hadronic decays , and their charge conjugates,
covering the range of 0.62.0 GeV/ and 2.06.0 GeV/ for
and , respectively. From this analysis, the charm-pair production cross
section at mid-rapidity is = 170 45
(stat.) (sys.) b. The extracted charm-pair cross section is
compared to perturbative QCD calculations. The transverse momentum differential
cross section is found to be consistent with the upper bound of a Fixed-Order
Next-to-Leading Logarithm calculation.Comment: 15 pages, 16 figures. Revised version submitted to Phys. Rev.
System size and energy dependence of near-side di-hadron correlations
Two-particle azimuthal () and pseudorapidity ()
correlations using a trigger particle with large transverse momentum () in
+Au, Cu+Cu and Au+Au collisions at =\xspace 62.4 GeV and
200~GeV from the STAR experiment at RHIC are presented. The \ns correlation is
separated into a jet-like component, narrow in both and
, and the ridge, narrow in but broad in .
Both components are studied as a function of collision centrality, and the
jet-like correlation is studied as a function of the trigger and associated
. The behavior of the jet-like component is remarkably consistent for
different collision systems, suggesting it is produced by fragmentation. The
width of the jet-like correlation is found to increase with the system size.
The ridge, previously observed in Au+Au collisions at = 200
GeV, is also found in Cu+Cu collisions and in collisions at
=\xspace 62.4 GeV, but is found to be substantially smaller at
=\xspace 62.4 GeV than at = 200 GeV for the
same average number of participants ().
Measurements of the ridge are compared to models.Comment: 17 pages, 14 figures, submitted to Phys. Rev.
Damage accumulation in thin ruthenium films induced by repetitive exposure to femtosecond XUV pulses below the single shot ablation threshold
The process of damage accumulation in thin ruthenium films exposed to multiple femtosecond XUV free electron laser FEL pulses below the critical angle of reflectance at the Free electron LASer facility in Hamburg FLASH was experimentally analyzed. The multi shot damage threshold is found to be lower than single shot damage threshold. Detailed analysis of the damage morphology and its dependence on irradiation conditions justifies the assumption that cavitation induced by the FEL pulse is the prime mechanism responsible for multi shot damage in optical coating
Measurements of Dihadron Correlations Relative to the Event Plane in Au+Au Collisions at GeV
Dihadron azimuthal correlations containing a high transverse momentum (\pt)
trigger particle are sensitive to the properties of the nuclear medium created
at RHIC through the strong interactions occurring between the traversing parton
and the medium, i.e. jet-quenching. Previous measurements revealed a strong
modification to dihadron azimuthal correlations in Au+Au collisions with
respect to \pp\ and \dAu\ collisions. The modification increases with the
collision centrality, suggesting a path-length dependence to the jet-quenching
effect. This paper reports STAR measurements of dihadron azimuthal correlations
in mid-central (20-60\%) Au+Au collisions at \snn=200~GeV as a function of
the trigger particle's azimuthal angle relative to the event plane,
\phis=|\phit-\psiEP|. The azimuthal correlation is studied as a function of
both the trigger and associated particle \pt. The subtractions of the
combinatorial background and anisotropic flow, assuming Zero Yield At Minimum
(\zyam), are described. The away-side correlation is strongly modified, and the
modification varies with \phis, which is expected to be related to the
path-length that the away-side parton traverses. The pseudo-rapidity (\deta)
dependence of the near-side correlation, sensitive to long range \deta
correlations (the ridge), is also investigated. The ridge and jet-like
components of the near-side correlation are studied as a function of \phis.
The ridge appears to drop with increasing \phis while the jet-like component
remains approximately constant. ...Comment: 50 pages, 39 figures, 6 table
Inclusive charged hadron elliptic flow in Au + Au collisions at = 7.7 - 39 GeV
A systematic study is presented for centrality, transverse momentum ()
and pseudorapidity () dependence of the inclusive charged hadron elliptic
flow () at midrapidity() in Au+Au collisions at
= 7.7, 11.5, 19.6, 27 and 39 GeV. The results obtained with
different methods, including correlations with the event plane reconstructed in
a region separated by a large pseudorapidity gap and 4-particle cumulants
(), are presented in order to investigate non-flow correlations and
fluctuations. We observe that the difference between and
is smaller at the lower collision energies. Values of , scaled by
the initial coordinate space eccentricity, , as a function
of are larger in more central collisions, suggesting stronger collective
flow develops in more central collisions, similar to the results at higher
collision energies. These results are compared to measurements at higher
energies at the Relativistic Heavy Ion Collider ( = 62.4 and 200
GeV) and at the Large Hadron Collider (Pb + Pb collisions at =
2.76 TeV). The values for fixed rise with increasing collision
energy within the range studied (). A comparison to
viscous hydrodynamic simulations is made to potentially help understand the
energy dependence of . We also compare the results to UrQMD
and AMPT transport model calculations, and physics implications on the
dominance of partonic versus hadronic phases in the system created at Beam
Energy Scan (BES) energies are discussed.Comment: 20 pages, 12 figures. Version accepted by PR
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