LibCPIXE: a PIXE simulation open-source library for multilayered samples

Most particle induced X-ray emission (PIXE) data analysis codes are not focused on handling multilayered samples. We have developed an open-source library called "LibCPIXE", for PIXE data analysis. It is written in standard C and implements functions for simulating X-ray yields of PIXE spectra taken from arbitrary samples, including multilayered targets. The library is designed to be fast, portable, modular and scalable, as well as to facilitate its incorporation into any existing program. In order to demonstrate the capabilities of the library, a program called CPIXE was developed and used to analyze various real samples involving both bulk and layered samples. Just as the library, the CPIXE source code is freely available under the General Public License. We demonstrate that it runs both under GNU/Linux systems as well as under MS Windows. There is in principle no limitation to port it to other platforms

The Emergence of Altruistic Punishment: Via Freedom to Enforcement

In human societies, cooperative behaviour in public goods interactions is usually enforced through institutions that impose sanctions on free-riders. Many experiments on public goods games have shown that in the absence of such institutions, individuals are often willing to punish defectors, even at a cost to themselves, effectively taking the law into their own hands. Theoretical models confirm that social norms prescribing the punishment of deviant behaviour are stable: once established, they prevent invasion by dissident minorities. But how can such costly punishing behaviour gain a foothold in the population? A surprisingly simple model shows that if individuals have the option to stand aside and abstain from the public goods interaction, this paves the way for the emergence and establishment of cooperative behaviour based on the punishment of defectors. Thus the freedom to withdraw from the public enterprise leads to a self-enforcing prosocial norm. Paradoxically, the option of individual autarky may be an important step for the emergence of institutions punishing the non-cooperation of their members. Conversely, public goods interactions which are obligatory rather than voluntary are unlikely to gain a foothold in the population

COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome

Item does not contain fulltextMOTIVATION: Complexome profiling combines native gel electrophoresis with mass spectrometry to obtain the inventory, composition and abundance of multiprotein assemblies in an organelle. Applying complexome profiling to determine the effect of a mutation on protein complexes requires separating technical and biological variations from the variations caused by that mutation. RESULTS: We have developed the COmplexome Profiling ALignment (COPAL) tool that aligns multiple complexome profiles with each other. It includes the abundance profiles of all proteins on two gels, using a multi-dimensional implementation of the dynamic time warping algorithm to align the gels. Subsequent progressive alignment allows us to align multiple profiles with each other. We tested COPAL on complexome profiles from control mitochondria and from Barth syndrome (BTHS) mitochondria, which have a mutation in tafazzin gene that is involved in remodeling the inner mitochondrial membrane phospholipid cardiolipin. By comparing the variation between BTHS mitochondria and controls with the variation among either, we assessed the effects of BTHS on the abundance profiles of individual proteins. Combining those profiles with gene set enrichment analysis allows detecting significantly affected protein complexes. Most of the significantly affected protein complexes are located in the inner mitochondrial membrane (mitochondrial contact site and cristae organizing system, prohibitins), or are attached to it (the large ribosomal subunit). AVAILABILITY AND IMPLEMENTATION: COPAL is written in python and is available from http://github.com/cmbi/copal. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Supersymmetric Model of a 2D Long-Range Bose Liquid

The model Hamiltonian of a two-dimensional Bose liquid (proposed earlier by Kane, Kivelson, Lee and Zhang as the Hamiltonian which has Jastrow-type wavefunctions as the ground-state solution), is shown to possess nonrelativistic supersymmetry. For the special value of the coupling constant $\alpha=1/2$ the quantum mechanics described by this Hamiltonian is shown to be equivalent to the dynamics of (complex) eigenvalues of random Gaussian ensemble of normal complex matrices. For general $\alpha$, an exact relation between the equal-time current-current and density-density correlation functions is obtained, and used to derive an asymptotically exact (at low wavevectors q) spectrum of single-particle excitations beyond the superfluid ground-state (realized at low $\alpha$'s). The ground-state at very large $\alpha$ is shown to be of ``Quantum Hexatic" type, possessing long-range orientational order and quasi-long-range translational order but with zero shear modulus. Possible scenaria of the ground-state phase transitions as function of $\alpha$ are discussed.Comment: Revtex; 12 pages, 1 Postscript figur

Thermal Conductivity near H_c2 for spin-triplet superconducting States with line nodes in Sr_2RuO_4

We calculate the thermal conductivity kappa in magnetic fields near H_c2 for spin-triplet superconducting states with line nodes vertical and horizontal relative to the RuO_2-planes. The method for calculating the Green's functions takes into account the spatial variation of the order parameter and superconducting flow for the Abrikosov vortex lattice. For in-plane magnetic field we obtain variations of the in-plane kappa with two-fold symmetry as a function of rotation angle where the minima and maxima occur for field directions parallel and perpendicular to the heat flow. The amplitude of the variation decreases with increasing impurity scattering and temperature. At higher temperatures the minima and maxima of the variation are interchanged. Since the results for vertical and horizontal line nodes are almost the same we cannot say which of the two pairing models is more compatible with recent measurements of kappa in Sr_2RuO_4. The observed four-fold modulation of kappa in YBa_2Cu_3O_(7-\delta) is obtained for d-wave pairing by taking into account the particular shape of the Fermi surface and the finite temperature effect. The results for kappa for the f-wave pairing state with horizontal line nodes disagree in some respects with the measurements on UPt_3.Comment: 8 pages, 6 figures. To be published in Phys. Rev.

Energy Norms and the Stability of the Einstein Evolution Equations

The Einstein evolution equations may be written in a variety of equivalent analytical forms, but numerical solutions of these different formulations display a wide range of growth rates for constraint violations. For symmetric hyperbolic formulations of the equations, an exact expression for the growth rate is derived using an energy norm. This expression agrees with the growth rate determined by numerical solution of the equations. An approximate method for estimating the growth rate is also derived. This estimate can be evaluated algebraically from the initial data, and is shown to exhibit qualitatively the same dependence as the numerically-determined rate on the parameters that specify the formulation of the equations. This simple rate estimate therefore provides a useful tool for finding the most well-behaved forms of the evolution equations.Comment: Corrected typos; to appear in Physical Review

Insufficient treatment of severe depression in neuromyelitis optica spectrum disorder

OBJECTIVE: To investigate depression frequency, severity, current treatment, and interactions with somatic symptoms among patients with neuromyelitis optica spectrum disorder (NMOSD). METHODS: In this dual-center observational study, we included 71 patients diagnosed with NMOSD according to the International Panel for NMO Diagnosis 2015 criteria. The Beck Depression Inventory (BDI) was classified into severe, moderate, or minimal/no depressive state category. We used the Fatigue Severity Scale to evaluate fatigue. Scores from the Brief Pain Inventory and the PainDETECT Questionnaire were normalized to estimate neuropathic pain. Psychotropic, pain, and immunosuppressant medications were tabulated by established classes. RESULTS: Twenty-eight percent of patients with NMOSD (n = 20) had BDI scores indicative of moderate or severe depression; 48% of patients (n = 34) endorsed significant levels of neuropathic pain. Severity of depression was moderately associated with neuropathic pain (r = 0.341, p < 0.004) but this relationship was confounded by levels of fatigue. Furthermore, only 40% of patients with moderate or severe depressive symptoms received antidepressant medical treatment. Fifty percent of those treated reported persistent moderate to severe depressive symptoms under treatment. CONCLUSIONS: Moderate and severe depression in patients with NMOSD is associated with neuropathic pain and fatigue and is insufficiently treated. These results are consistent across 2 research centers and continents. Future research needs to address how depression can be effectively managed and treated in NMOSD

Impact of densitized lapse slicings on evolutions of a wobbling black hole

We present long-term stable and second-order convergent evolutions of an excised wobbling black hole. Our results clearly demonstrate that the use of a densitized lapse function extends the lifetime of simulations dramatically. We also show the improvement in the stability of single static black holes when an algebraic densitized lapse condition is applied. In addition, we introduce a computationally inexpensive approach for tracking the location of the singularity suitable for mildly distorted black holes. The method is based on investigating the fall-off behavior and asymmetry of appropriate grid variables. This simple tracking method allows one to adjust the location of the excision region to follow the coordinate motion of the singularity.Comment: 10 pages, 8 figure

Radiation tails and boundary conditions for black hole evolutions

In numerical computations of Einstein's equations for black hole spacetimes, it will be necessary to use approximate boundary conditions at a finite distance from the holes. We point out here that ``tails,'' the inverse power-law decrease of late-time fields, cannot be expected for such computations. We present computational demonstrations and discussions of features of late-time behavior in an evolution with a boundary condition.Comment: submitted to Phys. Rev.