Nonlinear mode coupling in rotating stars and the r-mode instability in neutron stars

We develop the formalism required to study the nonlinear interaction of modes in rotating Newtonian stars in the weakly nonlinear regime. The formalism simplifies and extends previous treatments. At linear order, we elucidate and extend slightly a formalism due to Schutz, show how to decompose a general motion of a rotating star into a sum over modes, and obtain uncoupled equations of motion for the mode amplitudes under the influence of an external force. Nonlinear effects are added perturbatively via three-mode couplings. We describe a new, efficient way to compute the coupling coefficients, to zeroth order in the stellar rotation rate, using spin-weighted spherical harmonics. We apply this formalism to derive some properties of the coupling coefficients relevant to the nonlinear interactions of unstable r-modes in neutron stars, postponing numerical integrations of the coupled equations of motion to a later paper. From an astrophysical viewpoint, the most interesting result of this paper is that many couplings of r-modes to other rotational modes (modes with zero frequencies in the non-rotating limit) are small: either they vanish altogether because of various selection rules, or they vanish to lowest order in the angular velocity. In zero-buoyancy stars, the coupling of three r-modes is forbidden entirely and the coupling of two r-modes to one hybrid rotational mode vanishes to zeroth order in rotation frequency. In incompressible stars, the coupling of any three rotational modes vanishes to zeroth order in rotation frequency.Comment: 62 pages, no figures. Corrected error in computation of coupling coefficients, added new selection rule and an appendix on energy and angular momentum of mode

On the use of Process Mining and Machine Learning to support decision making in systems design

Research on process mining and machine learning techniques has recently received a significant amount of attention by product development and management communities. Indeed, these techniques allow both an automatic process and activity discovery and thus are high added value services that help reusing knowledge to support decision-making. This paper proposes a double layer framework aiming to identify the most significant process patterns to be executed depending on the design context. Simultaneously, it proposes the most significant parameters for each activity of the considered process pattern. The framework is applied on a specific design example and is partially implemented.FUI GONTRAN

Third Order Effect of Rotation on Stellar Oscillations of a β\beta-Cephei Star

Here the effect of rotation up to third order in the angular velocity of a star on the p, f and g modes is investigated. To do this, the third-order perturbation formalism presented by Soufi et al. (1998) and revised by Karami (2008), was used. I quantify by numerical calculations the effect of rotation on the oscillation frequencies of a uniformly rotating $\beta$-Cephei star with 12 $M_\odot$. For an equatorial velocity of 90 $\rm km s^{-1}$, it is found that the second- and third-order corrections for $(l,m)=(5,-4)$, for instance, are of order of 0.07% of the frequency for radial order $n=-3$ and reaches up to 0.6% for $n=-20$.Comment: 13 pages, 2 figures, 10 table

Cell-selective labeling using amino acid precursors for proteomic studies of multicellular environments.

We report a technique to selectively and continuously label the proteomes of individual cell types in coculture, named cell type-specific labeling using amino acid precursors (CTAP). Through transgenic expression of exogenous amino acid biosynthesis enzymes, vertebrate cells overcome their dependence on supplemented essential amino acids and can be selectively labeled through metabolic incorporation of amino acids produced from heavy isotope-labeled precursors. When testing CTAP in several human and mouse cell lines, we could differentially label the proteomes of distinct cell populations in coculture and determine the relative expression of proteins by quantitative mass spectrometry. In addition, using CTAP we identified the cell of origin of extracellular proteins secreted from cells in coculture. We believe that this method, which allows linking of proteins to their cell source, will be useful in studies of cell-cell communication and potentially for discovery of biomarkers

A seismological analysis of Delta Scuti stars in the Pleiades cluster

A comparison between the oscillation frequencies of six multi-periodic Delta Scuti stars of the Pleiades cluster and the eigenfrequencies of rotating stellar models that match the corresponding stellar parameters has been carried out. The assumption that all the stars considered have some common parameters, such as metallicity, distance or age, is imposed as a constraint. As a result, we have a best fit solution associated with a cluster metallicity of [Fe/H] ~ 0.067, an age between 70x10^6 and 100x10^6 yr and a distance modulus of mv-Mv=5.60-5.70 mag. All the stars were found to oscillate mainly in non-radial, low degree, low order p modes. Estimates of mass and rotation rates for each star are also obtainedComment: 10 pages, 7 figure

Asteroseismology and Interferometry

Asteroseismology provides us with a unique opportunity to improve our understanding of stellar structure and evolution. Recent developments, including the first systematic studies of solar-like pulsators, have boosted the impact of this field of research within Astrophysics and have led to a significant increase in the size of the research community. In the present paper we start by reviewing the basic observational and theoretical properties of classical and solar-like pulsators and present results from some of the most recent and outstanding studies of these stars. We centre our review on those classes of pulsators for which interferometric studies are expected to provide a significant input. We discuss current limitations to asteroseismic studies, including difficulties in mode identification and in the accurate determination of global parameters of pulsating stars, and, after a brief review of those aspects of interferometry that are most relevant in this context, anticipate how interferometric observations may contribute to overcome these limitations. Moreover, we present results of recent pilot studies of pulsating stars involving both asteroseismic and interferometric constraints and look into the future, summarizing ongoing efforts concerning the development of future instruments and satellite missions which are expected to have an impact in this field of research.Comment: Version as published in The Astronomy and Astrophysics Review, Volume 14, Issue 3-4, pp. 217-36

Dysferlin Forms a Dimer Mediated by the C2 Domains and the Transmembrane Domain In Vitro and in Living Cells

Dysferlin was previously identified as a key player in muscle membrane repair and its deficiency leads to the development of muscular dystrophy and cardiomyopathy. However, little is known about the oligomerization of this protein in the plasma membrane. Here we report for the first time that dysferlin forms a dimer in vitro and in living adult skeletal muscle fibers isolated from mice. Endogenous dysferlin from rabbit skeletal muscle exists primarily as a ∼460 kDa species in detergent-solubilized muscle homogenate, as shown by sucrose gradient fractionation, gel filtration and cross-linking assays. Fluorescent protein (YFP) labeled human dysferlin forms a dimer in vitro, as demonstrated by fluorescence correlation spectroscopy (FCS) and photon counting histogram (PCH) analyses. Dysferlin also dimerizes in living cells, as probed by fluorescence resonance energy transfer (FRET). Domain mapping FRET experiments showed that dysferlin dimerization is mediated by its transmembrane domain and by multiple C2 domains. However, C2A did not significantly contribute to dimerization; notably, this is the only C2 domain in dysferlin known to engage in a Ca-dependent interaction with cell membranes. Taken together, the data suggest that Ca-insensitive C2 domains mediate high affinity self-association of dysferlin in a parallel homodimer, leaving the Ca-sensitive C2A domain free to interact with membranes

Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape

We describe protein interaction quantitation (PIQ), a computational method for modeling the magnitude and shape of genome-wide DNase I hypersensitivity profiles to identify transcription factor (TF) binding sites. Through the use of machine-learning techniques, PIQ identified binding sites for >700 TFs from one DNase I hypersensitivity analysis followed by sequencing (DNase-seq) experiment with accuracy comparable to that of chromatin immunoprecipitation followed by sequencing (ChIP-seq). We applied PIQ to analyze DNase-seq data from mouse embryonic stem cells differentiating into prepancreatic and intestinal endoderm. We identified 120 and experimentally validated eight 'pioneer' TF families that dynamically open chromatin. Four pioneer TF families only opened chromatin in one direction from their motifs. Furthermore, we identified 'settler' TFs whose genomic binding is principally governed by proximity to open chromatin. Our results support a model of hierarchical TF binding in which directional and nondirectional pioneer activity shapes the chromatin landscape for population by settler TFs.National Institutes of Health (U.S.) (Common Fund 5UL1DE019581)National Institutes of Health (U.S.) (Common Fund RL1DE019021)National Institutes of Health (U.S.) (Common Fund 5TL1EB008540)National Institutes of Health (U.S.) (Grant 1U01HG007037)National Institutes of Health (U.S.) (Grant 5P01NS055923

Atomic Resolution Cryo-EM Structure Of A Nativelike CENP-A Nucleosome Aided By An Antibody Fragment

Genomic DNA in eukaryotes is organized into chromatin through association with core histones to form nucleosomes, each distinguished by their DNA sequences and histone variants. Here, we used a single-chain antibody fragment (scFv) derived from the anti-nucleosome antibody mAb PL2-6 to stabilize human CENP-A nucleosome containing a native α-satellite DNA and solved its structure by the cryo-electron microscopy (cryo-EM) to 2.6 Å resolution. In comparison, the corresponding cryo-EM structure of the free CENP-A nucleosome could only reach 3.4 Å resolution. We find that scFv binds to a conserved acidic patch on the histone H2A-H2B dimer without perturbing the nucleosome structure. Our results provide an atomic resolution cryo-EM structure of a nucleosome and insight into the structure and function of the CENP-A nucleosome. The scFv approach is applicable to the structural determination of other native-like nucleosomes with distinct DNA sequences

Critical current density: Measurements vs. reality

Different experimental techniques are employed to evaluate the critical current density (Jc), namely transport current measurements and two different magnetisation measurements forming quasi-equilibrium and dynamic critical states. Our technique-dependent results for superconducting YBa 2Cu3O7 (YBCO) film and MgB2 bulk samples show an extremely high sensitivity of Jc and associated interpretations, such as irreversibility fields and Kramer plots, which lose meaning without a universal approach. We propose such approach for YBCO films based on their unique pinning features. This approach allows us to accurately recalculate the magnetic-field-dependent Jc obtained by any technique into the Jc behaviour, which would have been measured by any other method without performing the corresponding experiments. We also discovered low-frequency-dependent phenomena, governing flux dynamics, but contradicting the considered ones in the literature. The understanding of these phenomena, relevant to applications with moving superconductors, can clarify their dramatic impact on the electric-field criterion through flux diffusivity and corresponding measurements. © Copyright EPLA, 2013