472 research outputs found
Fracture of complex metallic alloys: An atomistic study of model systems
Molecular dynamics simulations of crack propagation are performed for two
extreme cases of complex metallic alloys (CMAs): In a model quasicrystal the
structure is determined by clusters of atoms, whereas the model C15 Laves phase
is a simple periodic stacking of a unit cell. The simulations reveal that the
basic building units of the structures also govern their fracture behaviour.
Atoms in the Laves phase play a comparable role to the clusters in the
quasicrystal. Although the latter are not rigid units, they have to be regarded
as significant physical entities.Comment: 6 pages, 4 figures, for associated avi file, see
http://www.itap.physik.uni-stuttgart.de/~frohmut/MOVIES/C15.LJ.011.100.av
Plastic shrinkage cracking of concrete - Roles of osmotic suction
Plastic shrinkage cracking of concrete occurs when the stresses arising in the concrete, due to a combination of suction and restraints of deformation such as reinforcement or formwork, equal its strength. However, three different types of suctions should be distinguished, namely total, matric and osmotic suctions. Although the total suction comprises matric and osmotic suctions, it is often used interchangeably with matric suction, with the underlying unconfirmed assumption that either the osmotic suction or its effect is negligible. In this paper, after a discussion of the pore moisture suctions and strength of unsaturated early-age concrete, experimental investigations of the suctions arising in, and the tensile strength and shear strength of, fly ash mixed with solutions of different osmotic suctions are described. It was found that osmotic suction has negligible effect on the shear and tensile strength, and hence, by inference, the inter-particle stresses in the fly ash mixture and early-age concrete. This strongly suggests that the role played by osmotic suction in the plastic shrinkage cracking of concrete is minimal and, accordingly, justifies the focus of earlier researchers on matric suction only
CP violation Beyond the MSSM: Baryogenesis and Electric Dipole Moments
We study electroweak baryogenesis and electric dipole moments in the presence
of the two leading-order, non-renormalizable operators in the Higgs sector of
the MSSM. Significant qualitative and quantitative differences from MSSM
baryogenesis arise due to the presence of new CP-violating phases and to the
relaxation of constraints on the supersymmetric spectrum (in particular, both
stops can be light). We find: (1) spontaneous baryogenesis, driven by a change
in the phase of the Higgs vevs across the bubble wall, becomes possible; (2)
the top and stop CP-violating sources can become effective; (3) baryogenesis is
viable in larger parts of parameter space, alleviating the well-known
fine-tuning associated with MSSM baryogenesis. Nevertheless, electric dipole
moments should be measured if experimental sensitivities are improved by about
one order of magnitude.Comment: 33 pages, 6 figure
Single-Scale Natural SUSY
We consider the prospects for natural SUSY models consistent with current
data. Recent constraints make the standard paradigm unnatural so we consider
what could be a minimal extension consistent with what we now know. The most
promising such scenarios extend the MSSM with new tree-level Higgs interactions
that can lift its mass to at least 125 GeV and also allow for flavor-dependent
soft terms so that the third generation squarks are lighter than current bounds
on the first and second generation squarks. We argue that a common feature of
almost all such models is the need for a new scale near 10 TeV, such as a scale
of Higgsing or confinement of a new gauge group. We consider the question
whether such a model can naturally derive from a single mass scale associated
with supersymmetry breaking. Most such models simply postulate new scales,
leaving their proximity to the scale of MSSM soft terms a mystery. This
coincidence problem may be thought of as a mild tuning, analogous to the usual
mu problem. We find that a single mass scale origin is challenging, but suggest
that a more natural origin for such a new dynamical scale is the gravitino
mass, m_{3/2}, in theories where the MSSM soft terms are a loop factor below
m_{3/2}. As an example, we build a variant of the NMSSM where the singlet S is
composite, and the strong dynamics leading to compositeness is triggered by
masses of order m_{3/2} for some fields. Our focus is the Higgs sector, but our
model is compatible with a light stop (with the other generation squarks heavy,
or with R-parity violation or another mechanism to hide them from current
searches). All the interesting low-energy mass scales, including linear terms
for S playing a key role in EWSB, arise dynamically from the single scale
m_{3/2}. However, numerical coefficients from RG effects and wavefunction
factors in an extra dimension complicate the otherwise simple story.Comment: 32 pages, 3 figures; version accepted by JHE
A reexamination of information theory-based methods for DNA-binding site identification
<p>Abstract</p> <p>Background</p> <p>Searching for transcription factor binding sites in genome sequences is still an open problem in bioinformatics. Despite substantial progress, search methods based on information theory remain a standard in the field, even though the full validity of their underlying assumptions has only been tested in artificial settings. Here we use newly available data on transcription factors from different bacterial genomes to make a more thorough assessment of information theory-based search methods.</p> <p>Results</p> <p>Our results reveal that conventional benchmarking against artificial sequence data leads frequently to overestimation of search efficiency. In addition, we find that sequence information by itself is often inadequate and therefore must be complemented by other cues, such as curvature, in real genomes. Furthermore, results on skewed genomes show that methods integrating skew information, such as <it>Relative Entropy</it>, are not effective because their assumptions may not hold in real genomes. The evidence suggests that binding sites tend to evolve towards genomic skew, rather than against it, and to maintain their information content through increased conservation. Based on these results, we identify several misconceptions on information theory as applied to binding sites, such as negative entropy, and we propose a revised paradigm to explain the observed results.</p> <p>Conclusion</p> <p>We conclude that, among information theory-based methods, the most unassuming search methods perform, on average, better than any other alternatives, since heuristic corrections to these methods are prone to fail when working on real data. A reexamination of information content in binding sites reveals that information content is a compound measure of search and binding affinity requirements, a fact that has important repercussions for our understanding of binding site evolution.</p
[3H]Adenine is a suitable radioligand for the labeling of G protein-coupled adenine receptors but shows high affinity to bacterial contaminations in buffer solutions
[3H]Adenine has previously been used to label the newly discovered G protein-coupled murine adenine receptors. Recent reports have questioned the suitability of [3H]adenine for adenine receptor binding studies because of curious results, e.g. high specific binding even in the absence of mammalian protein. In this study, we showed that specific [3H]adenine binding to various mammalian membrane preparations increased linearly with protein concentration. Furthermore, we found that Tris-buffer solutions typically used for radioligand binding studies (50 mM, pH 7.4) that have not been freshly prepared but stored at 4°C for some time may contain bacterial contaminations that exhibit high affinity binding for [3H]adenine. Specific binding is abolished by heating the contaminated buffer or filtering it through 0.2-μm filters. Three different, aerobic, gram-negative bacteria were isolated from a contaminated buffer solution and identified as Achromobacter xylosoxidans, A. denitrificans, and Acinetobacter lwoffii. A. xylosoxidans, a common bacterium that can cause nosocomial infections, showed a particularly high affinity for [3H]adenine in the low nanomolar range. Structure–activity relationships revealed that hypoxanthine also bound with high affinity to A. xylosoxidans, whereas other nucleobases (uracil, xanthine) and nucleosides (adenosine, uridine) did not. The nature of the labeled site in bacteria is not known, but preliminary results indicate that it may be a high-affinity purine transporter. We conclude that [3H]adenine is a well-suitable radioligand for adenine receptor binding studies but that bacterial contamination of the employed buffer solutions must be avoided
Use of Data-Biased Random Walks on Graphs for the Retrieval of Context-Specific Networks from Genomic Data
Extracting network-based functional relationships within genomic datasets is an important challenge in the computational analysis of large-scale data. Although many methods, both public and commercial, have been developed, the problem of identifying networks of interactions that are most relevant to the given input data still remains an open issue. Here, we have leveraged the method of random walks on graphs as a powerful platform for scoring network components based on simultaneous assessment of the experimental data as well as local network connectivity. Using this method, NetWalk, we can calculate distribution of Edge Flux values associated with each interaction in the network, which reflects the relevance of interactions based on the experimental data. We show that network-based analyses of genomic data are simpler and more accurate using NetWalk than with some of the currently employed methods. We also present NetWalk analysis of microarray gene expression data from MCF7 cells exposed to different doses of doxorubicin, which reveals a switch-like pattern in the p53 regulated network in cell cycle arrest and apoptosis. Our analyses demonstrate the use of NetWalk as a valuable tool in generating high-confidence hypotheses from high-content genomic data
Human Gene Coexpression Landscape: Confident Network Derived from Tissue Transcriptomic Profiles
This is an open-access article distributed under the terms of the Creative Commons Attribution License.[Background]: Analysis of gene expression data using genome-wide microarrays is a technique often used in genomic studies to find coexpression patterns and locate groups of co-transcribed genes. However, most studies done at global >omic> scale are not focused on human samples and when they correspond to human very often include heterogeneous datasets, mixing normal with disease-altered samples. Moreover, the technical noise present in genome-wide expression microarrays is another well reported problem that many times is not addressed with robust statistical methods, and the estimation of errors in the data is not provided. [Methodology/Principal Findings]: Human genome-wide expression data from a controlled set of normal-healthy tissues is used to build a confident human gene coexpression network avoiding both pathological and technical noise. To achieve this we describe a new method that combines several statistical and computational strategies: robust normalization and expression signal calculation; correlation coefficients obtained by parametric and non-parametric methods; random cross-validations; and estimation of the statistical accuracy and coverage of the data. All these methods provide a series of coexpression datasets where the level of error is measured and can be tuned. To define the errors, the rates of true positives are calculated by assignment to biological pathways. The results provide a confident human gene coexpression network that includes 3327 gene-nodes and 15841 coexpression-links and a comparative analysis shows good improvement over previously published datasets. Further functional analysis of a subset core network, validated by two independent methods, shows coherent biological modules that share common transcription factors. The network reveals a map of coexpression clusters organized in well defined functional constellations. Two major regions in this network correspond to genes involved in nuclear and mitochondrial metabolism and investigations on their functional assignment indicate that more than 60% are house-keeping and essential genes. The network displays new non-described gene associations and it allows the placement in a functional context of some unknown non-assigned genes based on their interactions with known gene families. [Conclusions/Significance]: The identification of stable and reliable human gene to gene coexpression networks is essential to unravel the interactions and functional correlations between human genes at an omic scale. This work contributes to this aim, and we are making available for the scientific community the validated human gene coexpression networks obtained, to allow further analyses on the network or on some specific gene associations. The data are available free online at http://bioinfow.dep.usal.es/coexpression/. © 2008 Prieto et al.Funding and grant support was provided by the Ministery of Health, Spanish Government (ISCiii-FIS, MSyC; Project reference PI061153) and by the Ministery of Education, Castilla-Leon Local Government (JCyL; Project reference CSI03A06).Peer Reviewe
Study of decays to the final state and evidence for the decay
A study of decays is performed for the first time
using data corresponding to an integrated luminosity of 3.0
collected by the LHCb experiment in collisions at centre-of-mass energies
of and TeV. Evidence for the decay
is reported with a significance of 4.0 standard deviations, resulting in the
measurement of
to
be .
Here denotes a branching fraction while and
are the production cross-sections for and mesons.
An indication of weak annihilation is found for the region
, with a significance of
2.4 standard deviations.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://lhcbproject.web.cern.ch/lhcbproject/Publications/LHCbProjectPublic/LHCb-PAPER-2016-022.html,
link to supplemental material inserted in the reference
Age before beauty? Relationships between fertilization success and age-dependent ornaments in barn swallows
When males become more ornamented and reproduce more successfully as they grow older, phenotypic correlations between ornament exaggeration and reproductive success can be confounded with age effects in cross-sectional studies, and thus say relatively little about sexual selection on these traits. This is exemplified here in a correlative study of male fertilization success in a large colony of American barn swallows (Hirundo rustica erythrogaster). Previous studies of this species have indicated that two sexually dimorphic traits, tail length and ventral plumage coloration, are positively correlated with male fertilization success, and a mechanism of sexual selection by female choice has been invoked. However, these studies did not control for potential age-related variation in trait expression. Here, we show that male fertilization success was positively correlated with male tail length but not with plumage coloration. We also show that 1-year-old males had shorter tails and lower fertilization success than older males. This age effect accounted for much of the covariance between tail length and fertilization success. Still, there was a positive relationship between tail length and fertilization success among older males. But as this group consisted of males from different age classes, an age effect may be hidden in this relationship as well. Our data also revealed a longitudinal increase in both tail length and fertilization success for individual males. We argue that age-dependent ornament expression and reproductive performance in males complicate inferences about female preferences and sexual selection
- …