Targeted enrichment of genomic DNA regions for next-generation sequencing

In this review, we discuss the latest targeted enrichment methods and aspects of their utilization along with second-generation sequencing for complex genome analysis. In doing so, we provide an overview of issues involved in detecting genetic variation, for which targeted enrichment has become a powerful tool. We explain how targeted enrichment for next-generation sequencing has made great progress in terms of methodology, ease of use and applicability, but emphasize the remaining challenges such as the lack of even coverage across targeted regions. Costs are also considered versus the alternative of whole-genome sequencing which is becoming ever more affordable. We conclude that targeted enrichment is likely to be the most economical option for many years to come in a range of settings

Description of superdeformed nuclei in the interacting boson model

The interacting boson model is extended to describe the spectroscopy of superdeformed bands. Microscopic structure of the model in the second minimum is discussed and superdeformed bosons are introduced as the new building blocks. Solutions of a quadrupole Hamiltonian are implemented through the $1/N$ expansion method. Effects of the quadrupole parameters on dynamic moment of inertia and electric quadrupole transition rates are discussed and the results are used in a description of superdeformed bands in the Hg-Pb and Gd-Dy regions.Comment: 18 pages revtex, 9 figures available upon reques

Life path analysis: scaling indicates priming effects of social and habitat factors on dispersal distances

1. Movements of many animals along a life-path can be separated into repetitive ones within home ranges and transitions between home ranges. We sought relationships of social and environmental factors with initiation and distance of transition movements in 114 buzzards Buteo buteo that were marked as nestlings with long-life radio tags. 2. Ex-natal dispersal movements of 51 buzzards in autumn were longer than for 30 later in their first year and than 35 extra-natal movements between home ranges after leaving nest areas. In the second and third springs, distances moved from winter focal points by birds that paired were the same or less than for unpaired birds. No post-nuptial movement exceeded 2 km. 3. Initiation of early ex-natal dispersal was enhanced by presence of many sibs, but also by lack of worm-rich loam soils. Distances travelled were greatest for birds from small broods and with relatively little short grass-feeding habitat near the nest. Later movements were generally enhanced by the absence of loam soils and short grassland, especially with abundance of other buzzards and probable poor feeding habitats (heathland, long grass). 4. Buzzards tended to persist in their first autumn where arable land was abundant, but subsequently showed a strong tendency to move from this habitat. 5. Factors that acted most strongly in ½-km buffers round nests, or round subsequent focal points, usually promoted movement compared with factors acting at a larger scale. Strong relationships between movement distances and environmental characteristics in ½-km buffers, especially during early ex-natal dispersal, suggested that buzzards became primed by these factors to travel far. 6. Movements were also farthest for buzzards that had already moved far from their natal nests, perhaps reflecting genetic predisposition, long-term priming or poor habitat beyond the study area

Theoretical description of deformed proton emitters: nonadiabatic coupled-channel method

The newly developed nonadiabatic method based on the coupled-channel Schroedinger equation with Gamow states is used to study the phenomenon of proton radioactivity. The new method, adopting the weak coupling regime of the particle-plus-rotor model, allows for the inclusion of excitations in the daughter nucleus. This can lead to rather different predictions for lifetimes and branching ratios as compared to the standard adiabatic approximation corresponding to the strong coupling scheme. Calculations are performed for several experimentally seen, non-spherical nuclei beyond the proton dripline. By comparing theory and experiment, we are able to characterize the angular momentum content of the observed narrow resonance.Comment: 12 pages including 10 figure

Measuring Black Hole Spin in OJ287

We model the binary black hole system OJ287 as a spinning primary and a non-spinning secondary. It is assumed that the primary has an accretion disk which is impacted by the secondary at specific times. These times are identified as major outbursts in the light curve of OJ287. This identification allows an exact solution of the orbit, with very tight error limits. Nine outbursts from both the historical photographic records as well as from recent photometric measurements have been used as fixed points of the solution: 1913, 1947, 1957, 1973, 1983, 1984, 1995, 2005 and 2007 outbursts. This allows the determination of eight parameters of the orbit. Most interesting of these are the primary mass of $1.84\cdot 10^{10} M_\odot$, the secondary mass $1.46\cdot 10^{8} M_\odot$, major axis precession rate $39^\circ.1$ per period, and the eccentricity of the orbit 0.70. The dimensionless spin parameter is $0.28\:\pm\:0.01$ (1 sigma). The last parameter will be more tightly constrained in 2015 when the next outburst is due. The outburst should begin on 15 December 2015 if the spin value is in the middle of this range, on 3 January 2016 if the spin is 0.25, and on 26 November 2015 if the spin is 0.31. We have also tested the possibility that the quadrupole term in the Post Newtonian equations of motion does not exactly follow Einstein's theory: a parameter $q$ is introduced as one of the 8 parameters. Its value is within 30% (1 sigma) of the Einstein's value $q = 1$. This supports the $no-hair theorem$ of black holes within the achievable precision. We have also measured the loss of orbital energy due to gravitational waves. The loss rate is found to agree with Einstein's value with the accuracy of 2% (1 sigma).Comment: 12 pages, 4 figures, IAU26

Breakup Reactions of 11Li within a Three-Body Model

We use a three-body model to investigate breakup reactions of 11Li (n+n+9Li) on a light target. The interaction parameters are constrained by known properties of the two-body subsystems, the 11Li binding energy and fragmentation data. The remaining degrees of freedom are discussed. The projectile-target interactions are described by phenomenological optical potentials. The model predicts dependence on beam energy and target, differences between longitudinal and transverse momentum distributions and provides absolute values for all computed differential cross sections. We give an almost complete series of observables and compare with corresponding measurements. Remarkably good agreement is obtained. The relative neutron-9Li p-wave content is about 40%. A p-resonance, consistent with measurements at about 0.5 MeV of width about 0.4 MeV, seems to be necessary. The widths of the momentum distributions are insensitive to target and beam energy with a tendency to increase towards lower energies. The transverse momentum distributions are broader than the longitudinal due to the diffraction process. The absolute values of the cross sections follow the neutron-target cross sections and increase strongly for beam energies decreasing below 100 MeV/u.Comment: 19 pages, 14 figures, RevTeX, psfig.st

The <i>Castalia</i> mission to Main Belt Comet 133P/Elst-Pizarro

We describe Castalia, a proposed mission to rendezvous with a Main Belt Comet (MBC), 133P/Elst-Pizarro. MBCs are a recently discovered population of apparently icy bodies within the main asteroid belt between Mars and Jupiter, which may represent the remnants of the population which supplied the early Earth with water. Castalia will perform the first exploration of this population by characterising 133P in detail, solving the puzzle of the MBC’s activity, and making the first in situ measurements of water in the asteroid belt. In many ways a successor to ESA’s highly successful Rosetta mission, Castalia will allow direct comparison between very different classes of comet, including measuring critical isotope ratios, plasma and dust properties. It will also feature the first radar system to visit a minor body, mapping the ice in the interior. Castalia was proposed, in slightly different versions, to the ESA M4 and M5 calls within the Cosmic Vision programme. We describe the science motivation for the mission, the measurements required to achieve the scientific goals, and the proposed instrument payload and spacecraft to achieve these

Effective interaction between helical bio-molecules

The effective interaction between two parallel strands of helical bio-molecules, such as deoxyribose nucleic acids (DNA), is calculated using computer simulations of the "primitive" model of electrolytes. In particular we study a simple model for B-DNA incorporating explicitly its charge pattern as a double-helix structure. The effective force and the effective torque exerted onto the molecules depend on the central distance and on the relative orientation. The contributions of nonlinear screening by monovalent counterions to these forces and torques are analyzed and calculated for different salt concentrations. As a result, we find that the sign of the force depends sensitively on the relative orientation. For intermolecular distances smaller than $6\AA$ it can be both attractive and repulsive. Furthermore we report a nonmonotonic behaviour of the effective force for increasing salt concentration. Both features cannot be described within linear screening theories. For large distances, on the other hand, the results agree with linear screening theories provided the charge of the bio-molecules is suitably renormalized.Comment: 18 pages, 18 figures included in text, 100 bibliog

Search for the glueball candidates f0(1500) and fJ(1710) in gamma gamma collisions

Data taken with the ALEPH detector at LEP1 have been used to search for gamma gamma production of the glueball candidates f0(1500) and fJ(1710) via their decay to pi+pi-. No signal is observed and upper limits to the product of gamma gamma width and pi+pi- branching ratio of the f0(1500) and the fJ(1710) have been measured to be Gamma_(gamma gamma -> f0(1500)). BR(f0(1500)->pi+pi-) < 0.31 keV and Gamma_(gamma gamma -> fJ(1710)). BR(fJ(1710)->pi+pi-) < 0.55 keV at 95% confidence level.Comment: 10 pages, 3 figure

Heavy Quarks and Heavy Quarkonia as Tests of Thermalization

We present here a brief summary of new results on heavy quarks and heavy quarkonia from the PHENIX experiment as presented at the "Quark Gluon Plasma Thermalization" Workshop in Vienna, Austria in August 2005, directly following the International Quark Matter Conference in Hungary.Comment: 8 pages, 5 figures, Quark Gluon Plasma Thermalization Workshop (Vienna August 2005) Proceeding