149 research outputs found
Distinguishing regional from within-codon rate heterogeneity in DNA sequence alignments
We present an improved phylogenetic factorial hidden Markov model (FHMM) for detecting two types of mosaic structures in DNA sequence alignments, related to (1) recombination and (2) rate heterogeneity. The focus of the present work is on improving the modelling of the latter aspect. Earlier papers have modelled different degrees of rate heterogeneity with separate hidden states of the FHMM. This approach fails to appreciate the intrinsic difference between two types of rate heterogeneity: long-range regional effects, which are potentially related to differences in the selective pressure, and the short-term periodic patterns within the codons, which merely capture the signature of the genetic code. We propose an improved model that explicitly distinguishes between these two effects, and we assess its performance on a set of simulated DNA sequence alignments
PolyEDA: Combining Estimation of Distribution Algorithms and Linear Inequality Constraints
Algorithmus , Linearität , Ungleichhei
Jamming at Zero Temperature and Zero Applied Stress: the Epitome of Disorder
We have studied how 2- and 3- dimensional systems made up of particles
interacting with finite range, repulsive potentials jam (i.e., develop a yield
stress in a disordered state) at zero temperature and applied stress. For each
configuration, there is a unique jamming threshold, , at which
particles can no longer avoid each other and the bulk and shear moduli
simultaneously become non-zero. The distribution of values becomes
narrower as the system size increases, so that essentially all configurations
jam at the same in the thermodynamic limit. This packing fraction
corresponds to the previously measured value for random close-packing. In fact,
our results provide a well-defined meaning for "random close-packing" in terms
of the fraction of all phase space with inherent structures that jam. The
jamming threshold, Point J, occurring at zero temperature and applied stress
and at the random close-packing density, has properties reminiscent of an
ordinary critical point. As Point J is approached from higher packing
fractions, power-law scaling is found for many quantities. Moreover, near Point
J, certain quantities no longer self-average, suggesting the existence of a
length scale that diverges at J. However, Point J also differs from an ordinary
critical point: the scaling exponents do not depend on dimension but do depend
on the interparticle potential. Finally, as Point J is approached from high
packing fractions, the density of vibrational states develops a large excess of
low-frequency modes. All of these results suggest that Point J may control
behavior in its vicinity-perhaps even at the glass transition.Comment: 21 pages, 20 figure
Many body physics from a quantum information perspective
The quantum information approach to many body physics has been very
successful in giving new insight and novel numerical methods. In these lecture
notes we take a vertical view of the subject, starting from general concepts
and at each step delving into applications or consequences of a particular
topic. We first review some general quantum information concepts like
entanglement and entanglement measures, which leads us to entanglement area
laws. We then continue with one of the most famous examples of area-law abiding
states: matrix product states, and tensor product states in general. Of these,
we choose one example (classical superposition states) to introduce recent
developments on a novel quantum many body approach: quantum kinetic Ising
models. We conclude with a brief outlook of the field.Comment: Lectures from the Les Houches School on "Modern theories of
correlated electron systems". Improved version new references adde
Measurement of and charged current inclusive cross sections and their ratio with the T2K off-axis near detector
We report a measurement of cross section and the first measurements of the cross section
and their ratio
at (anti-)neutrino energies below 1.5
GeV. We determine the single momentum bin cross section measurements, averaged
over the T2K -flux, for the detector target material (mainly
Carbon, Oxygen, Hydrogen and Copper) with phase space restricted laboratory
frame kinematics of 500 MeV/c. The
results are and $\sigma(\nu)=\left( 2.41\
\pm0.022{\rm{(stat.)}}\pm0.231{\rm (syst.)}\ \right)\times10^{-39}^{2}R\left(\frac{\sigma(\bar{\nu})}{\sigma(\nu)}\right)=
0.373\pm0.012{\rm (stat.)}\pm0.015{\rm (syst.)}$.Comment: 18 pages, 8 figure
Genetic tools for coronary risk assessment in type 2 diabetes: A cohort study from the ACCORD clinical trial
OBJECTIVE We evaluated whether the increasing number of genetic loci for coronary artery disease (CAD) identified in the general population could be used to predict the risk of major CAD events (MCE) among participants with type 2 diabetes at high cardiovascular risk. RESEARCH DESIGN AND METHODS A weighted genetic risk score (GRS) derived from 204 variants representative of all the 160 CAD loci identified in the general population as of December 2017 was calculated in 5,360 and 1,931 white participants in the Action to Control Cardiovascular Risk in Diabetes (ACCORD) and Outcome Reduction With Initial Glargine Intervention (ORIGIN) studies, respectively. The association between GRS and MCE (combining fatal CAD events, nonfatal myocardial infarction, and unstable angina) was assessed by Cox proportional hazards regression. RESULTS The GRS was associated with MCE risk in both ACCORD and ORIGIN (hazard ratio [HR] per SD 1.27, 95% CI 1.18–1.37, P = 4 3 10210, and HR per SD 1.35, 95% CI 1.16–1.58, P = 2 3 1024, respectively). This association was independent from interventions tested in the trials and persisted, though attenuated, after adjustment for classic cardiovascular risk predictors. Adding the GRS to clinical predictors improved incident MCE risk classification (relative integrated discrimination improvement +8%, P = 7 3 1024). The performance of this GRS was superior to that of GRS based on the smaller number of CAD loci available in previous years. CONCLUSIONS When combined into a GRS, CAD loci identified in the general population are associated with CAD also in type 2 diabetes. This GRS provides a significant improvement in the ability to correctly predict future MCE, which may increase further with the discovery of new CAD loci
Effects of dietary vegetable oil on atlantic salmon hepatocyte fatty acid desaturation and liver fatty acid compositions
Fatty acyl desaturase activities, involved in the conversion of the C18 EFA, 18:2n-6 and 18:3n-3, to the highly unsaturated fatty acids (HUFA) 20:4n-6, 20:5n-3 and 22:6n-3, are known to be under nutritional regulation. Specifically, the activity of the desaturation/elongation pathway is depressed when animals, including fish, are fed fish oils rich in n-3HUFA compared to animals fed vegetable oils rich in C18 EFA. The primary aims of the present study were a) to establish the relative importance of product inhibition (n-3HUFA) versus increased substrate concentration (C18 EFA) and, b) to determine whether 18:2n-6 and 18:3n-3 differ in their effects, on the hepatic fatty acyl desaturation/elongation pathway in Atlantic salmon (Salmo salar). Smolts were fed ten experimental diets containing blends of two vegetable oils, linseed (LO) and rapeseed oil (RO), and fish oil (FO) in a triangular mixture design for 50 weeks. Fish were sampled after 32 and 50 weeks, lipid and fatty acid composition of liver determined, fatty acyl desaturation/elongation activity estimated in hepatocytes using [1-14C]18:3n-3 as substrate, and the data subjected to regression analyses. Dietary 18:2n-6 was positively correlated, and n-3HUFA negatively correlated, with lipid content of liver. Dietary 20:5n-3 and 22:6n-3 were positively correlated with liver fatty acids with a slope greater than unity suggesting relative retention and deposition of these HUFA. In contrast, dietary 18:2n-6 and 18:3n-3 were positively correlated with liver fatty acids with a slope of less than unity suggesting metabolism via β-oxidation and/or desaturation/elongation. Consistent with this, fatty acyl desaturation/elongation in hepatocytes was significantly increased by feeding diets containing vegetable oils. Dietary 20:5n-3 and 22:6n-3 levels were negatively correlated with hepatocyte fatty acyl desaturation. At 32 weeks, 18:2n-6 but not 18:3n-3, was positively correlated with hepatocyte fatty acyl desaturation activity whereas the reverse was true at 50 weeks. The data indicate that both feedback inhibition through increased n-3HUFA and decreased C18 fatty acyl substrate concentration are probably important in determining hepatocyte fatty acyl desaturation activities, and that 18:2n-6 and 18:3n-3 may differ in their effects on this pathway
Search for Lorentz and CPT violation using sidereal time dependence of neutrino flavor transitions over a short baseline
A class of extensions of the Standard Model allows Lorentz and CPT violations, which can be identified
by the observation of sidereal modulations in the neutrino interaction rate. A search for such modulations
was performed using the T2K on-axis near detector. Two complementary methods were used in this study,
both of which resulted in no evidence of a signal. Limits on associated Lorentz and CPT-violating terms
from the Standard Model extension have been derived by taking into account their correlations in this
model for the first time. These results imply such symmetry violations are suppressed by a factor of more
than 10 20 at the GeV scale
The Physics of the B Factories
This work is on the Physics of the B Factories. Part A of this book contains a brief description of the SLAC and KEK B Factories as well as their detectors, BaBar and Belle, and data taking related issues. Part B discusses tools and methods used by the experiments in order to obtain results. The results themselves can be found in Part C
- …