Road blocks on paleogenomes - polymerase extension profiling reveals the frequency of blocking lesions in ancient DNA

Although the last few years have seen great progress in DNA sequence retrieval from fossil specimens, some of the characteristics of ancient DNA remain poorly understood. This is particularly true for blocking lesions, i.e. chemical alterations that cannot be bypassed by DNA polymerases and thus prevent amplification and subsequent sequencing of affected molecules. Some studies have concluded that the vast majority of ancient DNA molecules carry blocking lesions, suggesting that the removal, repair or bypass of blocking lesions might dramatically increase both the time depth and geographical range of specimens available for ancient DNA analysis. However, previous studies used very indirect detection methods that did not provide conclusive estimates on the frequency of blocking lesions in endogenous ancient DNA. We developed a new method, polymerase extension profiling (PEP), that directly reveals occurrences of polymerase stalling on DNA templates. By sequencing thousands of single primer extension products using PEP methodology, we have for the first time directly identified blocking lesions in ancient DNA on a single molecule level. Although we found clear evidence for blocking lesions in three out of four ancient samples, no more than 40% of the molecules were affected in any of the samples, indicating that such modifications are far less frequent in ancient DNA than previously thought

Glassy dynamics in thin films of polystyrene

Glassy dynamics was investigated for thin films of atactic polystyrene by complex electric capacitance measurements using dielectric relaxation spectroscopy. During the isothermal aging process the real part of the electric capacitance increased with time, whereas the imaginary part decreased with time. It follows that the aging time dependences of real and imaginary parts of the electric capacitance were primarily associated with change in volume (film thickness) and dielectric permittivity, respectively. Further, dielectric permittivity showed memory and rejuvenation effects in a similar manner to those observed for poly(methyl methacrylate) thin films. On the other hand, volume did not show a strong rejuvenation effect.Comment: 7 pages, 7 figures. Phys. Rev. E (in press

3D Magnetic Analysis of the CMS Magnet

The CMS magnetic system consists of a super-conducting solenoid coil, 12.5 m long and 6 m free bore diameter, and of an iron flux-return yoke, which includes the central barrel, two end-caps and the ferromagnetic parts of the hadronic forward calorimeter. The magnetic flux density in the center of the solenoid is 4 T. To carry out the magnetic analysis of the CMS magnetic system, several 3D models were developed to perform magnetic field and force calculations using the Vector Fields code TOSCA. The analysis includes a study of the general field behavior, the calculation of the forces on the coil generated by small axial, radial displacements and angular tilts, the calculation of the forces on the ferromagnetic parts, the calculation of the fringe field outside the magnetic system, and a study of the field level in the chimneys for the current leads and the cryogenic lines. A procedure to reconstruct the field inside a cylindrical volume starting from the values of the magnetic flux density on the cylinder surface is considered. Special TOSCA-GEANT interface tools have being developed to input the calculated magnetic field into the detector simulation package.Comment: 4 pages, 6 figures, 1 equation, 14 reference

Status report of the CMS superconducting coil project

The CMS superconducting coil is designed for one of the two large experiments of LHC at CERN. This coil 12.5 m long, 6 m diameter and 2.7 GJ stored energy is a common project of the CMS Collaboration. It is a four-layer coil, equipped with a self-supporting conductor capable of carrying 20 kA to reach the maximum potential field of 4 T. It has been designed with a considerable contribution from CEA- Saclay for the engineering, ETH-Zurich for the conductor, INFN-Genova for the winding and CERN for the general coordination and construction of the ancillaries. The project entered the construction phase one year ago. The civil engineering is well advanced and ready to accept part of the yoke components already built. The coil itself has finished the pre-industrialization phase and the construction is beginning in industry. Most of the important contracts have been awarded and the foreseen schedule is now based on contractual engagements. A quick overview of the features of the project as well as a status report of the main activities are given. (6 refs)

The Incredible Shrinking Dewlap: Signal Size, Skin Elasticity, and Mechanical Design in the Green Anole Lizard (Anolis Carolinensis)

The expression of male secondary sexual traits can be dynamic, changing size, shape, color, or structure over the course of different seasons. However, the factors underlying such changes are poorly understood. In male Anolis carolinensis lizards, a morphological secondary sexual signal called the dewlap changes size seasonally within individuals. Here, we test the hypothesis that seasonal changes in male dewlap size are driven by increased use and extension of the dewlap in spring and summer, when males are breeding, relative to the winter and fall. We captured male green anole lizards prior to the onset of breeding and constrained the dewlap in half of them such that it could not be extended. We then measured dewlap area in the spring, summer, and winter, and dewlap skin and belly skin elasticity in summer and winter. Dewlaps in unconstrained males increase in area from spring to summer and then shrink in the winter, whereas the dewlaps of constrained males consistently shrink from spring to winter. Dewlap skin is significantly more elastic than belly skin, and skin overall is more elastic in the summer relative to winter. These results show that seasonal changes in dewlap size are a function of skin elasticity and display frequency, and suggest that the mechanical properties of signaling structures can have important implications for signal evolution and design

Assortative matching with large firms

Two cornerstones of empirical and policy analysis of firms, in macro, labor and industrial organization, are the determinants of the firm size distribution and the determinants of sorting between workers and firms. We propose a unifying theory of production where management resolves a tradeoff between hiring more versus better workers. The span of control or size is therefore intimately intertwined with the sorting pattern. We provide a condition for sorting that captures this tradeoff between the quantity and quality of workers and that generalizes Becker's sorting condition. A system of differential equations determines the equilibrium allocation, the firm size, and wages, and allows us to characterize the allocation of the quality and quantity of labor to firms of different productivity. We show that our model nests a large number of widely used existing models. We also augment the model to incorporate labor market frictions in the presence of sorting with large firms

Hole-burning experiments within solvable glassy models

We reproduce the results of non-resonant spectral hole-burning experiments with fully-connected (equivalently infinite-dimensional) glassy models that are generalizations of the mode-coupling approach to nonequilibrium situations. We show that an ac-field modifies the integrated linear response and the correlation function in a way that depends on the amplitude and frequency of the pumping field. We study the effect of the waiting and recovery-times and the number of oscillations applied. This calculation will help descriminating which results can and which cannot be attributed to dynamic heterogeneities in real systems.Comment: 4 pages, 8 figures, RevTe

Kinematically complete experimental study of Compton scattering at helium atoms near the ionization threshold

Compton scattering is one of the fundamental interaction processes of light with matter. Already upon its discovery [1] it was described as a billiard-type collision of a photon kicking a quasi-free electron. With decreasing photon energy, the maximum possible momentum transfer becomes so small that the corresponding energy falls below the binding energy of the electron. Then ionization by Compton scattering becomes an intriguing quantum phenomenon. Here we report a kinematically complete experiment on Compton scattering at helium atoms below that threshold. We determine the momentum correlations of the electron, the recoiling ion, and the scattered photon in a coincidence experiment finding that electrons are not only emitted in the direction of the momentum transfer, but that there is a second peak of ejection to the backward direction. This finding links Compton scattering to processes as ionization by ultrashort optical pulses [2], electron impact ionization [3,4], ion impact ionization [5,6], and neutron scattering [7] where similar momentum patterns occur.Comment: 7 pages, 4 figure

The U-shapes of occupational mobility

Using administrative panel data on 100 % of Danish population we document a new set of facts characterizing the patterns of occupational mobility. We find that a worker’s probability of switching occupation is U-shaped in his position in the wage distribution in his occupation. It is the workers with the highest or lowest wages in their occupations who have the highest probability of leaving the occupation. Workers with higher (lower) relative wage within their occupation tend to switch to occupations with higher (lower) average wages. Higher (lower) paid workers within their occupation tend to leave it when relative productivity of that occupation declines (rises). These facts are not implied by existing theories of occupational mobility that mostly treat occupations as horizontally differentiated sets of tasks. We suggest that it might be productive to think of occupations as forming vertical hierarchies. Workers who are unsure of their abilities learn about them by observing their output realizations. Employment opportunities in each occupation are scarce inducing competition among workers for them. Complementarities in the production function between worker’s ability and productivity of an occupation induce sorting of workers into occupations according to their expected ability. We present an equilibrium model of occupational choice with these features and show analytically that it is consistent with patterns of mobility described above