Effect of Population Size and Mutation Rate on the Evolution of RNA Sequences on an Adaptive Landscape Determined by RNA Folding.

The dynamics of populations evolving on an adaptive landscape depends on multiple factors, including the structure of the landscape, the rate of mutations, and effective population size. Existing theoretical work often makes ad hoc and simplifying assumptions about landscape structure, whereas experimental work can vary important parameters only to a limited extent. We here overcome some of these limitations by simulating the adaptive evolution of RNA molecules, whose fitness is determined by the thermodynamics of RNA secondary structure folding. We study the influence of mutation rates and population sizes on final mean population fitness, on the substitution rates of mutations, and on population diversity. We show that evolutionary dynamics cannot be understood as a function of mutation rate µ, population size N, or population mutation rate Nµ alone. For example, at a given mutation rate, clonal interference prevents the fixation of beneficial mutations as population size increases, but larger populations still arrive at a higher mean fitness. In addition, at the highest population mutation rates we study, mean final fitness increases with population size, because small populations are driven to low fitness by the relatively higher incidence of mutations they experience. Our observations show that mutation rate and population size can interact in complex ways to influence the adaptive dynamics of a population on a biophysically motivated fitness landscape

Diffusion-controlled phase growth on dislocations

We treat the problem of diffusion of solute atoms around screw dislocations. In particular, we express and solve the diffusion equation, in radial symmetry, in an elastic field of a screw dislocation subject to the flux conservation boundary condition at the interface of a new phase. We consider an incoherent second-phase precipitate growing under the action of the stress field of a screw dislocation. The second-phase growth rate as a function of the supersaturation and a strain energy parameter is evaluated in spatial dimensions d=2 and d=3. Our calculations show that an increase in the amplitude of dislocation force, e.g. the magnitude of the Burgers vector, enhances the second-phase growth in an alloy. Moreover, a relationship linking the supersaturation to the precipitate size in the presence of the elastic field of dislocation is calculated.Comment: 10 pages, 4 figures, a revised version of the paper presented in MS&T'08, October 5-9, 2008, Pittsburg

Recent results of H-mode studies on asdex

In a comparative study of various confinement regimes the H-mode demonstrated the best performance. Confinement enhancement factors (above ITER 89-P L-mode scaling) in the range of 1.6 fH 2.8 have been achieved with values depending on the divertor configuration, the wall condition, ELM behaviour and the plasma ion spicies. Long-pulse H-phases, withELMs, of up to 3.5s with constant confinement time, recycling and impurity characteristics are archived. H* -mode operation is possible without a loss of current scaling at qa values as low as 2.2. The B-limit is the same with and without ELMs. Murakami parameters are similar in H-and L-modes

Combining clustering and classification ensembles: A novel pipeline to identify breast cancer profiles

Breast Cancer is one of the most common causes of cancer death in women, representing a very complex disease with varied molecular alterations. To assist breast cancer prognosis, the classification of patients into biological groups is of great significance for treatment strategies. Recent studies have used an ensemble of multiple clustering algorithms to elucidate the most characteristic biological groups of breast cancer. However, the combination of various clustering methods resulted in a number of patients remaining unclustered. Therefore, a framework still needs to be developed which can assign as many unclustered (i.e. biologically diverse) patients to one of the identified groups in order to improve classification. Therefore, in this paper we develop a novel classification framework which introduces a new ensemble classification stage after the ensemble clustering stage to target the unclustered patients. Thus, a step-by-step pipeline is introduced which couples ensemble clustering with ensemble classification for the identification of core groups, data distribution in them and improvement in final classification results by targeting the unclustered data. The proposed pipeline is employed on a novel real world breast cancer dataset and subsequently its robustness and stability are examined by testing it on standard datasets. The results show that by using the presented framework, an improved classification is obtained. Finally, the results have been verified using statistical tests, visualisation techniques, cluster quality assessment and interpretation from clinical experts

Temperature quenching in LAB based liquid scintillator

The effect of temperature changes on the light output of LAB based liquid scintillator is investigated in a range from $-5$ to 30\,^{\circ } C with $\alpha$ -particles and electrons in a small scale setup. Two PMTs observe the scintillator liquid inside a cylindrically shaped aluminum cuvette that is heated or cooled and the temperature dependent PMT sensitivity is monitored and corrected. The $\alpha$ -emitting isotopes in dissolved radon gas and in natural Samarium (bound to a LAB solution) excite the liquid scintillator mixtures and changes in light output with temperature variation are observed by fitting light output spectra. Furthermore, also changes in light output by compton electrons, which are generated from external calibration $\gamma$ -ray sources, is analysed with varying temperature. Assuming a linear behaviour, a combined negative temperature coefficient of ${(-0.29 \pm 0.01)}{\,\%/^{\circ }}\hbox {C}$ is found. Considering hints for a particle type dependency, electrons show ${(-0.17 \pm 0.02)}{\,\%/^{\circ }}\hbox {C}$ , whereas the temperature dependency seems stronger for $\alpha$ -particles, with ${(-0.35 \pm 0.03)}{\,\%/^{\circ }}\hbox {C}$ . Due to a high sampling rate, a pulse shape analysis can be performed and shows an enhanced slow decay component at lower temperatures, pointing to reduced non-radiative triplet state de-excitations.Peer Reviewe

Solving the stellar 62Ni problem with AMS

An accurate knowledge of the neutron capture cross sections of 62,63Ni is crucial since both isotopes take key positions which affect the whole reaction flow in the weak s process up to A=90. No experimental value for the 63Ni(n,gamma) cross section exists so far, and until recently the experimental values for 62Ni(n,gamma) at stellar temperatures (kT=30 keV) ranged between 12 and 37 mb. This latter discrepancy could now be solved by two activations with following AMS using the GAMS setup at the Munich tandem accelerator which are also in perfect agreement with a recent time-of-flight measurement. The resulting (preliminary) Maxwellian cross section at kT=30 keV was determined to be 30keV = 23.4 +/- 4.6 mb. Additionally, we have measured the 64Ni(gamma,n)63Ni cross section close to threshold. Photoactivations at 13.5 MeV, 11.4 MeV and 10.3 MeV were carried out with the ELBE accelerator at Forschungszentrum Dresden-Rossendorf. A first AMS measurement of the sample activated at 13.5 MeV revealed a cross section smaller by more than a factor of 2 compared to NON-SMOKER predictions.Comment: Proceedings of the 11th International Conference on Accelerator Mass Spectrometry in Rome, Sept. 14-19, 2008; to be published in Nucl. Instr. Meth.

Surface finish control by electrochemical polishing in stainless steel 316 pipes

Electrochemical machining (ECM) is a non-conventional machining process which is based on the localised anodic dissolution of any conductive material. One of the main applications of ECM is the polishing of materials with enhanced characteristics, such as high strength, heat-resistance or corrosion-resistance, i.e. electrochemical polishing. The present work presents an evaluation of the parameters involved in the ECM of Stainless Steel 316 (SS316) with the objective of predicting the resulting surface finish on the sample. The interest of studying ECM on SS316 resides on the fact that a repeatable surface finish is not easily achieved. ECM experimental tests on SS316 pipes of 1.5" (0.0381 m) diameter were conducted by varying machining parameters such as voltage, interelectrode gap, electrolyte inlet temperature, and electrolyte flow rate. The surface finish of the samples was then evaluated in order to find the significance of each of these parameters on the surface quality of the end product. Results showed that overvoltage, which is dependent on the interelectrode gap and the electrolyte temperature, is one of the main parameters affecting the surface finish; additionally there is a strong relationship between the resulting surface finish and the electrolyte flow. The interelectrode gap and inlet electrolyte temperature also affect the resulting surface finish but their influence was not so evident in this work. Finally, the variation of the electrolyte temperature during the process was found to have a great impact on the uniformity of the surface finish along the sample. We believe that this contribution enables the tailoring of the surface finish to specific applications while reducing manufacturing costs and duration of the ECM process

Relationship between incommensurability and superconductivity in Peierls distorted charge-density-wave systems

We study the pairing potential induced by fluctuations around a charge-density wave (CDW) with scattering vector Q by means of the Froehlich transformation. For general commensurability M, defined as |k+M*Q>=|k>, we find that the intraband pair scattering within the M subbands scales with M whereas the interband pair scattering becomes suppressed with increasing CDW order parameter. As a consequence superconductivity is suppressed when the Fermi energy is located between the subbands as it is usually the case for nesting induced CDW's, but due to the vertex renormalization it can be substantially enhanced when the chemical potential is shifted sufficiently inside one of the subbands. The model can help to understand the experimentally observed dependence of the superconducting transition temperature from the stripe phase incommensurability in the lanthanum cuprates.Comment: 6 pages, 3 figure

Comparative analysis of viral shedding in pediatric and adult subjects with central nervous system-associated enterovirus infections from 2013 to 2015 in Switzerland.

Several enterovirus (EV) genotypes can result in aseptic meningitis, but their routes of access to the central nervous system remain to be elucidated and may differ between the pediatric and adult populations. To assess the pattern of viral shedding in pediatric and adult subjects with acute EV meningitis and to generate EV surveillance data for Switzerland. All pediatric and adult subjects admitted to the University Hospitals of Geneva with a diagnosis of EV meningitis between 2013 and 2015 were enrolled. A quantitative EV real-time reverse transcriptase (rRT)-PCR was performed on the cerebrospinal fluid (CSF), blood, stool, urine and respiratory specimens to assess viral shedding and provide a comparative analysis of pediatric and adult populations. EV genotyping was systematically performed. EV positivity rates differed significantly between pediatric and adult subjects; 62.5% of pediatric cases (no adult case) were EV-positive in stool and blood for subjects for whom these samples were all collected. Similarly, the EV viral load in blood was significantly higher in pediatric subjects. Blood C-reactive protein levels were lower and the number of leucocytes/mm3 in the CSF were higher in non-viremic than in viremic pediatric subjects, respectively. A greater diversity of EV genotypes was observed in pediatric cases, with a predominance of echovirus 30 in children ≥3 years old and adults. In contrast to adults, EV-disseminated infections are predominant in pediatric subjects and show different patterns of EV viral shedding. This observation may be useful for clinicians and contribute to modify current practices of patient care

Photon data shed new light upon the GDR spreading width in heavy nuclei

A global study of the electric dipole strength in and below the isovector giant dipole resonance (GDR) is presented for mass numbers A>80. It relies on the recently established remarkably good match between data for the nuclear photo effect to novel photon scattering data covering the region below the neutron emission threshold as well as by average resonance neutron capture (ARC). From the wide energy coverage of these data the correlation of the GDR spreading width with energy can be studied with remarkable accuracy. A clear sensitivity to details of the nuclear shape, i.e. the beta- and gamma-deformations, is demonstrated. Based hereon a new parameterization of the energy dependence of the nuclear electric-dipole strength is proposed which - with only two new parameters - allows to describe the dipole strength in all heavy nuclei with A>80. Although it differs significantly from previous parameterizations it holds for spherical, transitional, triaxial and well deformed nuclei. The GDR spreading width depends in a regular way on the respective resonance energy, but it is independent of the photon energy.Comment: accepted by Phys. Lett. B after minor modification