Rewiring of the phosphoproteome executes two meiotic divisions in budding yeast

The cell cycle is ordered by a controlled network of kinases and phosphatases. To generate gametes via meiosis, two distinct and sequential chromosome segregation events occur without an intervening S phase. How canonical cell cycle controls are modified for meiosis is not well understood. Here, using highly synchronous budding yeast populations, we reveal how the global proteome and phosphoproteome change during the meiotic divisions. While protein abundance changes are limited to key cell cycle regulators, dynamic phosphorylation changes are pervasive. Our data indicate that two waves of cyclin-dependent kinase (Cdc28Cdk1) and Polo (Cdc5Polo) kinase activity drive successive meiotic divisions. These two distinct phases of phosphorylation are ensured by the meiosis-specific Spo13 protein, which rewires the phosphoproteome. Spo13 binds to Cdc5Polo to promote phosphorylation in meiosis I, particularly of substrates containing a variant of the canonical Cdc5Polo motif. Overall, our findings reveal that a master regulator of meiosis directs the activity of a kinase to change the phosphorylation landscape and elicit a developmental cascade.</p

Interfacial charge transfer in nanoscale polymer transistors

Interfacial charge transfer plays an essential role in establishing the relative alignment of the metal Fermi level and the energy bands of organic semiconductors. While the details remain elusive in many systems, this charge transfer has been inferred in a number of photoemission experiments. We present electronic transport measurements in very short channel ($L < 100$ nm) transistors made from poly(3-hexylthiophene) (P3HT). As channel length is reduced, the evolution of the contact resistance and the zero-gate-voltage conductance are consistent with such charge transfer. Short channel conduction in devices with Pt contacts is greatly enhanced compared to analogous devices with Au contacts, consistent with charge transfer expectations. Alternating current scanning tunneling microscopy (ACSTM) provides further evidence that holes are transferred from Pt into P3HT, while much less charge transfer takes place at the Au/P3HT interface.Comment: 19 preprint pages, 6 figure

Entropy Production in Relativistic Hydrodynamics

The entropy production occurring in relativistic hydrodynamical systems such as the quark-gluon plasma (QGP) formed in high-energy nuclear collisions is explored. We study mechanisms which change the composition of the fluid, i.e. particle production and/or chemical reactions, along with chemo- and thermo-diffusion. These effects complement the conventional dissipative effects of shear viscosity, bulk viscosity, and heat conductivity.Comment: 15 pages; LaTex. Accepted for publication in Physics Letters B. - Two typos corrected and one reference adde

Non-functional properties in the model-driven development of service-oriented systems

Systems based on the service-oriented architecture (SOA) principles have become an important cornerstone of the development of enterprise-scale software applications. They are characterized by separating functions into distinct software units, called services, which can be published, requested and dynamically combined in the production of business applications. Service-oriented systems (SOSs) promise high flexibility, improved maintainability, and simple re-use of functionality. Achieving these properties requires an understanding not only of the individual artifacts of the system but also their integration. In this context, non-functional aspects play an important role and should be analyzed and modeled as early as possible in the development cycle. In this paper, we discuss modeling of non-functional aspects of service-oriented systems, and the use of these models for analysis and deployment. Our contribution in this paper is threefold. First, we show how services and service compositions may be modeled in UML by using a profile for SOA (UML4SOA) and how non-functional properties of service-oriented systems can be represented using the non-functional extension of UML4SOA (UML4SOA-NFP) and the MARTE profile. This enables modeling of performance, security and reliable messaging. Second, we discuss formal analysis of models which respect this design, in particular we consider performance estimates and reliability analysis using the stochastically timed process algebra PEPA as the underlying analytical engine. Last but not least, our models are the source for the application of deployment mechanisms which comprise model-to-model and model-to-text transformations implemented in the framework VIATRA. All techniques presented in this work are illustrated by a running example from an eUniversity case study

Distributional theory for the DIA method

The DIA method for the detection, identification and adaptation of model misspecifications combines estimation with testing. The aim of the present contribution is to introduce a unifying framework for the rigorous capture of this combination. By using a canonical model formulation and a partitioning of misclosure space, we show that the whole estimation–testing scheme can be captured in one single DIA estimator. We study the characteristics of this estimator and discuss some of its distributional properties. With the distribution of the DIA estimator provided, one can then study all the characteristics of the combined estimation and testing scheme, as well as analyse how they propagate into final outcomes. Examples are given, as well as a discussion on how the distributional properties compare with their usage in practice

Weighing the Giants - I. Weak-lensing masses for 51 massive galaxy clusters: project overview, data analysis methods and cluster images

This is the first in a series of papers in which we measure accurate weak-lensing masses for 51 of the most X-ray luminous galaxy clusters known at redshifts 0.15<z<0.7, in order to calibrate X-ray and other mass proxies for cosmological cluster experiments. The primary aim is to improve the absolute mass calibration of cluster observables, currently the dominant systematic uncertainty for cluster count experiments. Key elements of this work are the rigorous quantification of systematic uncertainties, high-quality data reduction and photometric calibration, and the "blind" nature of the analysis to avoid confirmation bias. Our target clusters are drawn from RASS X-ray catalogs, and provide a versatile calibration sample for many aspects of cluster cosmology. We have acquired wide-field, high-quality imaging using the Subaru and CFHT telescopes for all 51 clusters, in at least three bands per cluster. For a subset of 27 clusters, we have data in at least five bands, allowing accurate photo-z estimates of lensed galaxies. In this paper, we describe the cluster sample and observations, and detail the processing of the SuprimeCam data to yield high-quality images suitable for robust weak-lensing shape measurements and precision photometry. For each cluster, we present wide-field color optical images and maps of the weak-lensing mass distribution, the optical light distribution, and the X-ray emission, providing insights into the large-scale structure in which the clusters are embedded. We measure the offsets between X-ray centroids and Brightest Cluster Galaxies in the clusters, finding these to be small in general, with a median of 20kpc. For offsets <100kpc, weak-lensing mass measurements centered on the BCGs agree well with values determined relative to the X-ray centroids; miscentering is therefore not a significant source of systematic uncertainty for our mass measurements. [abridged]Comment: 26 pages, 19 figures (Appendix C not included). Accepted after minor revisio

A Quasar Catalog with Simultaneous UV, Optical and X-ray Observations by Swift

We have compiled a catalog of optically-selected quasars with simultaneous observations in UV/optical and X-ray bands by the Swift Gamma Ray Burst Explorer. Objects in this catalog are identified by matching the Swift pointings with the Sloan Digital Sky Survey Data Release 5 quasar catalog. The final catalog contains 843 objects, among which 637 have both UVOT and XRT observations and 354 of which are detected by both instruments. The overall X-ray detection rate is ~60% which rises to ~85% among sources with at least 10 ks of XRT exposure time. We construct the time-averaged spectral energy distribution for each of the 354 quasars using UVOT photometric measurements and XRT spectra. From model fits to these SEDs, we find that the big blue bump contributes about 0.3 dex to the quasar luminosity. We re-visit the alpha_ox-L_uv relation by selecting a clean sample with only type 1 radio-quiet quasars; the dispersion of this relation is reduced by at least 15% compared to studies that use non-simultaneous UV/optical and X-ray data. We only found a weak correlation between L/L_Edd and alpha_uv. We do not find significant correlations between alpha_x and alpha_ox, alpha_ox and alpha_uv, and alpha_x and Log L(0.3-10 keV). The correlations between alpha_uv and alpha_x, alpha_ox and alpha_x, alpha_ox and alpha_uv, L/L_Edd and alpha_x, and L/L_Edd and alpha_ox are stronger amongst low-redshift quasars, indicating that these correlations are likely driven by the changes of SED shape with accretion state.Comment: 63 pages, 22 figures, accepted by ApJ

Versatility in phospho-dependent molecular recognition of the XRCC1 and XRCC4 DNA-damage scaffolds by aprataxin-family FHA domains

Aprataxin, aprataxin and PNKP-like factor (APLF) and polynucleotide kinase phosphatase (PNKP) are key DNA-repair proteins with diverse functions but which all contain a homologous forkhead-associated (FHA) domain. Their primary binding targets are casein kinase 2-phosphorylated forms of the XRCC1 and XRCC4 scaffold molecules which respectively coordinate single-stranded and double-stranded DNA break repair pathways. Here, we present the high-resolution X-ray structure of a complex of phosphorylated XRCC4 with APLF, the most divergent of the three FHA domain family members. This, combined with NMR and biochemical analysis of aprataxin and APLF binding to singly and multiply-phosphorylated forms of XRCC1 and XRCC4, and comparison with PNKP reveals a pattern of distinct but overlapping binding specificities that are differentially modulated by multi-site phosphorylation. Together, our data illuminate important differences between activities of the three phospho-binding domains, in spite of a close evolutionary relationship between them

Kepler eclipsing binary stars. VII. the catalogue of eclipsing binaries found in the entire Kepler data set

The primary Kepler Mission provided nearly continuous monitoring of ~200,000 objects with unprecedented photometric precision. We present the final catalog of eclipsing binary systems within the 105 deg2 Kepler field of view. This release incorporates the full extent of the data from the primary mission (Q0-Q17 Data Release). As a result, new systems have been added, additional false positives have been removed, ephemerides and principal parameters have been recomputed, classifications have been revised to rely on analytical models, and eclipse timing variations have been computed for each system. We identify several classes of systems including those that exhibit tertiary eclipse events, systems that show clear evidence of additional bodies, heartbeat systems, systems with changing eclipse depths, and systems exhibiting only one eclipse event over the duration of the mission. We have updated the period and galactic latitude distribution diagrams and included a catalog completeness evaluation. The total number of identified eclipsing and ellipsoidal binary systems in the Kepler field of view has increased to 2878, 1.3% of all observed Kepler targets