ALBERT

Description: Motivated by the recent report of the detailed spectra of IC 443 and W44 based on four years of observations with the Fermi Large Area Telescope, -rays produced via proton–proton interaction in the two supernova remnants (SNRs) have been investigated in the diffusive shock acceleration scenario. In the model, a part of the SNR shell transporting into ambient dense molecular clouds (MCs), and a shock with a relatively low Alfvén Mach number can be produced. Relativistic protons are accelerated in the shock via the diffusive acceleration process; moreover, a break in the particle distribution is induced since the damping of Alfvén waves when the shock transporting into partly ionized plasma. A spectrum of the accelerated protons in the shock can be obtained in the test-particle case, taking into account the effect of the ambient partly ionized plasma on the acceleration process. Furthermore, hadronic -rays with a peak around several GeVs are reproduced as the protons inelastically colliding with the ambient matter of the crushed gas. The observed -ray spectral distributions of the SNR IC 443 and W44 can be successfully reproduced using the static model in the test-particle scenario. It can be concluded that the observed -rays can be explained in the diffusive shock case as the shock waves transporting into the dense MCs for the two remnants.

Description: We present a clustering analysis of X-ray selected active galactic nuclei (AGN) by compiling X-ray samples from the literature and re-estimating the dark-matter (DM) halo masses of AGN in a uniform manner. We find that moderate-luminosity AGN ( L 2–10 keV  ~= 10 42 –10 44 erg s –1 ) in the z  ~= 0–1.3 Universe are typically found in DM haloes with masses of ~10 13 M . We then compare our findings to the theoretical predictions of the coupled galaxy and black hole formation model galform . We find good agreement when our calculation includes the hot-halo mode of accretion on to the central black hole. This type of accretion, which is additional to the common cold accretion during disc instabilities and galaxy mergers, is tightly coupled to the AGN feedback in the model. The hot-halo mode becomes prominent in DM haloes with masses greater than ~10 12.5 M , where AGN feedback typically operates, giving rise to a distinct class of moderate-luminosity AGN that inhabit rich clusters and superclusters. Cold gas fuelling of the black hole cannot produce the observationally inferred DM halo masses of X-ray AGN. Switching off AGN feedback in the model results in a large population of luminous quasars ( L 2–10 keV  〉 10 44 erg s –1 ) in DM haloes with masses up to ~10 14 M , which is inconsistent with the observed clustering of quasars. The abundance of hot-halo AGN decreases significantly in the z ~= 3–4 universe. At such high redshifts, the cold accretion mode is solely responsible for shaping the environment of moderate-luminosity AGN. Our analysis supports two accretion modes (cold and hot) for the fuelling of supermassive black holes and strongly underlines the importance of AGN feedback in cosmological models both of galaxy formation and black hole growth.

Description: A major stage of radio interferometric data processing is calibration or the estimation of systematic errors in the data and the correction for such errors. A stochastic error (noise) model is assumed, and in most cases, this underlying model is assumed to be Gaussian. However, outliers in the data due to interference or due to errors in the sky model would have adverse effects on processing based on a Gaussian noise model. Most of the shortcomings of calibration such as the loss in flux or coherence, and the appearance of spurious sources, could be attributed to the deviations of the underlying noise model. In this paper, we propose to improve the robustness of calibration by using a noise model based on Student's t -distribution. Student's t -noise is a special case of Gaussian noise when the variance is unknown. Unlike Gaussian-noise-model-based calibration, traditional least-squares minimization would not directly extend to a case when we have a Student's t -noise model. Therefore, we use a variant of the expectation–maximization algorithm, called the expectation–conditional maximization either algorithm, when we have a Student's t -noise model and use the Levenberg–Marquardt algorithm in the maximization step. We give simulation results to show the robustness of the proposed calibration method as opposed to traditional Gaussian-noise-model-based calibration, especially in preserving the flux of weaker sources that are not included in the calibration model.

Description: A single open magnetic flux tube spanning the solar photosphere (solar radius ~= R ) and the lower corona (R  + 10 Mm) is modelled in magnetohydrostatic equilibrium within a realistic stratified atmosphere subject to solar gravity. Such flux tubes are observed to remain relatively stable for up to a day or more, and it is our aim to apply the model as the background condition for numerical studies of energy transport mechanisms from the surface to the corona. We solve analytically an axially symmetric 3D structure for the model, with magnetic field strength, plasma density, pressure and temperature all consistent with observational and theoretical estimates. The self-similar construction ensures the magnetic field is divergence free. The equation of pressure balance for this particular set of flux tubes can be integrated analytically to find the pressure and density corrections required to preserve the magnetohydrostatic equilibrium. The model includes a number of free parameters, which makes the solution applicable to a variety of other physical problems and it may therefore be of more general interest.

Description: We report photometric detections of orbital and superorbital signals, and negative orbital sidebands, in the light curves of the nova-like cataclysmic variables AQ Mensae and IM Eridani. The frequencies of the orbital, superorbital and sideband signals are 7.0686 (3), 0.263 (3) and 7.332 (3) cycles d –1 (c d –1 ) in AQ Mensae, and 6.870 (1), 0.354 (7) and 7.226 (1) c d –1 in IM Eridani. We also find a spectroscopic orbital frequency in IM Eridani of 6.86649 (2) c d –1 . These observations can be reproduced by invoking an accretion disc that is tilted with respect to the orbital plane. This model works well for X-ray binaries, in which irradiation by a primary neutron star can account for the disc's tilt. A likely tilt mechanism has yet to be identified in CVs, yet the growing collection of observational evidence indicates that the phenomenon of tilt is indeed at work in this class of object. The results presented in this paper bring the number of CVs known to display signals associated with retrograde disc precession to 12. We also find AQ Men to be an eclipsing system. The eclipse depths are highly variable, which suggests that the eclipses are grazing. This finding raises the possibility of probing variations in disc tilt by studying systematic variations in the eclipse profile.

Description: We investigate the onset of pressure-driven toroidal-mode instabilities in accretion mounds on neutron stars by 3D magnetohydrodynamic (MHD) simulations using the pluto MHD code. Our results confirm that for mounds beyond a threshold mass, instabilities form finger-like channels at the periphery, resulting in mass-loss from the magnetically confined mound. Ring-like mounds with hollow interior show the instabilities at the inner edge as well. We perform the simulations for mounds of different sizes to investigate the effect of the mound mass on the growth rate of the instabilities. We also investigate the effect of such instabilities on observables such as cyclotron resonant scattering features and timing properties of such systems.

Description: External fields in Milgromian dynamics (MD or MOND) break the Strong Equivalence Principle (SEP) and change the dynamics of self-bound stellar systems moving in space-varying background gravitational fields. We study two kinds of re-virialization of the stellar systems: the violent phase transition and the adiabatic phase transition for systems moving on radial orbits, where the external field evolves from strong to weak and whose corresponding dynamics change from Newtonian to Milgromian. We find that the time-scale for the phase transformation from Newtonian to Milgromian gravity lies only within one to a few crossing times for low-density globular clusters with masses ranging from 10 4 M to 10 6 M . Thus, a globular cluster can appear frozen in the Newtonian regime despite being in the Milgromian regime for not longer than a few crossing times. We also study the kinematics and anisotropy profiles of the systems. The velocity dispersions of the systems are larger after the phase transitions, especially for the outer regions of the stellar systems. Moreover, the isotropic systems become radially anisotropic, especially for the outer parts, after the process caused by the dynamical phase transition. Deeper Milgromian systems have more radially anisotropic velocity dispersion functions. We also find that the final profiles of density, velocity dispersion and anisotropy do not depend on the details of the phase transition. That is, the mass distribution and kinematics of the end-states of the globular clusters do not depend on the rapidity of the transition from Newtonian to Milgromian gravity. Thus, the transition from the Newtonian to the Milgromian regime naturally induces a significant radially anisotropic velocity distribution in a globular cluster.

Description: Using a fast semi-analytic raytracing code, we study the variability of relativistically broadened Fe–Kα lines due to discoseismic oscillations concentrated in the innermost regions of accretion discs around black holes. The corrugation mode, or c-mode, is of particular interest as its natural frequency corresponds well to the ~0.1–15 Hz range observed for low-frequency quasi-periodic oscillations (LFQPOs) for lower spins. Comparison of the oscillation phase dependent variability and quasi-periodic oscillation-phase stacked Fe–Kα line observations will allow such discoseismic models to be confirmed or ruled out as a source of particular LFQPOs. The spectral range and frequency of the variability of the Fe–Kα line due to c-modes can also potentially be used to constrain the black hole spin if observed with sufficient temporal and spectral resolution.

Description: We present and discuss accurate and densely mapped BVR C I C light curves of the neon Nova Mon 2012, supplemented by the evolution in Stromgren b and y bands and in the integrated flux of relevant emission lines. Our monitoring started with the optical discovery of the nova (50 days past the first detection in gamma-rays by Fermi -LAT) and extend to day +270, well past the end of the super-soft phase in X-rays. The nova was discovered during the nebular decline, well past t 3 and the transition to optically thin ejecta. It displayed very smoothly evolving light curves. A bifurcation between y and V light curves took place at the start of the super-soft X-ray source (SSS) phase, and a knee developed towards the end of the SSS phase. The apparent magnitude of the nova at the unobserved optical maximum is constrained to +3 ≤  V  ≤ 4.5. The appearance, grow in amplitude and then demise of a 0.29585 (±0.00002) days orbital modulation of the optical brightness was followed along the nova evolution. The observed modulation, identical in phase and period with the analogue seen in the X-ray and satellite ultraviolet, has a near-sinusoidal shape and a weak secondary minimum at phase 0.5. We favour an interpretation in terms of super-imposed ellipsoidal distortion of the Roche lobe filling companion and irradiation of its side facing the WD. Similar light curves are typical of symbiotic stars where a Roche lobe filling giant is irradiated by a very hot WD. Given the high orbital inclination, mutual occultation between the donor star and the accretion disc could contribute to the observed modulation. The optical+infrared spectral energy distribution of Nova Mon 2012 during the quiescence preceding outburst is nicely fitted by an early K-type main-sequence star (~K3V) at 1.5 kpc distance, reddened by E ( B  –  V ) = 0.38, with a WD companion and an accretion disc contributing to the observed blue excess and moderate Hα emission. A typical early K-type main-sequence star with a mass of ~0.75 M and a radius of ~0.8 R would fill its Roche lobe for a P  = 0.29585 d orbital period and a more massive WD companion (as implied by the large Ne overabundance of the ejecta).

Description: The redshift dependence of the abundance of galaxy clusters is very sensitive to the statistical properties of primordial density perturbations. It can thus be used to probe small deviations from Gaussian initial conditions. Such deviations constitute a very important signature of many inflationary scenarios, and are thus expected to provide crucial information on physical processes which took place in the very early Universe. We have determined the biases which may be introduced in the estimation of cosmological parameters by wrongly assuming the absence of primordial non-Gaussianities. Although we find that the estimation of the present-day dark energy density using cluster counts is not very sensitive to the non-Gaussian properties of the density field, we show that the biases can be considerably larger in the estimation of the dark energy equation of state parameter w and of the amplitude of the primordial density perturbations. Our results suggest that a significant level of non-Gaussianity at cluster scales may be able to reconcile the constraint on the amplitude of the primordial perturbations obtained using galaxy cluster number counts from the Planck Sunyaev–Zeldovich Catalog with that obtained from the primary cosmic microwave background anisotropies measured by the Planck satellite.

Description: We report results from our 1D radiative transfer modelling of dust in the hydrogen-deficient planetary nebula IRAS 18333–2357 located in the globular cluster M22. A spectral energy distribution was constructed from archival UV, optical and IR data including Akari photometry at its 18, 65, 90, 140 and 160 μm bands. An archival Spitzer spectrum shows several aromatic infrared bands indicating a carbon-rich dust shell. The spectral energy distribution is well fitted by a model which considers a modified Mathis–Rumpl–Nordsieck grain size distribution and a radial density function which includes compression of the nebula by its interaction with the Galactic halo gas. The model indicates that a significant amount of cold dust, down to a temperature of 50 K, is present at the outer edge of the nebula. At the inner edge, the dust temperature is 97 K. The dust shell has a size of 26 ± 6.3 arcsec. We find a large amount of excess emission, over the emission from thermal equilibrium dust, in the mid-IR region. This excess emission may have originated from the thermally fluctuating dust grains with size ~12 Å in the UV field of the hot central star. These grains, however, come from the same population and conditions as the thermal equilibrium grains. The dust mass of this grain population is (1.2 ± 0.73) 10 –3 M and for the thermal equilibrium grains it is (1.4 ± 0.60) 10 –4 M , leading to a total dust mass of (1.3 ± 0.91) 10 –3 M . The derived dust-to-gas mass ratio is 0.3 ± 0.21. For a derived bolometric luminosity of (1700 ± 1230) L and an assumed central star mass of (0.55 ± 0.02) M , the surface gravity is derived to be log g  = 4.6 ± 0.24. We propose that the progenitor of IRAS 18333–2357 had possibly evolved from an early stellar merger case and the hydrogen-deficient nebula results from a late thermal pulse. The hydrogen-rich nebula, which was ejected by the progenitor during its normal asymptotic giant branch evolution, might have been stripped off by its strong interaction with the Galactic halo gas.

Description: We analyse the evolution of colour gradients predicted by the hydrodynamical models of early-type galaxies (ETGs) in Pipino et al., which reproduce fairly well the chemical abundance pattern and the metallicity gradients of local ETGs. We convert the star formation (SF) and metal content into colours by means of stellar population synthetic model and investigate the role of different physical ingredients, as the initial gas distribution and content, and SF , i.e. the normalization of SF rate. From the comparison with high-redshift data, a full agreement with optical rest-frame observations at z   1 is found, for models with low SF , whereas some discrepancies emerge at 1 〈  z  〈 2, despite our models reproduce quite well the data scatter at these redshifts. To reconcile the prediction of these high SF systems with the shallower colour gradients observed at lower z we suggest intervention of one to two dry mergers. We suggest that future studies should explore the impact of wet galaxy merging, interactions with environment, dust content and a variation of the initial mass function from the galactic centres to the peripheries.

Description: The interaction between a planet located in the inner region of a disc and the warped outer region is studied. We consider the stage of evolution after the planet has cleared-out a gap, so that the planetary orbit evolves only under the gravitational potential from the disc. We develop a secular analysis and compute the evolution of the orbital elements by solving Lagrange's equations valid to second order in the eccentricity. We also perform numerical simulations with the full disc potential. In general, the interaction between the disc and the planet leads to the precession of the orbit. The orbital plane therefore becomes tilted relative to the disc's inner parts, with no change in the eccentricity. When the inclination approaches 90°, there is an instability and the eccentricity increases. In this case, both the inclination and the eccentricity develop large variations, with the orbit becoming retrograde. As the eccentricity reaches high values, we would expect tidal capture on a short orbit of the planet by the star to occur. This instability happens when the disc is severely warped, or if there is a significant amount of mass in a ring inclined by at least 45° relative to the initial orbital plane. The inclination of the orbit does not depend on the semimajor axis nor on the planet's mass. However, for a significant inclination to be generated on a time-scale of at most a few Myr, the planet should be beyond the snow line. The process described here would therefore produce two distinct populations of inclined planets: one with objects beyond the snow line with at most moderate eccentricities, and another with objects on short circularized orbits.

Description: Hubble Space Telescope observations of globular clusters (GCs) in the Antennae galaxy show clusters of clusters, or regions in the galaxy that span hundreds of parsec, where many of the GCs are doomed to collide, and eventually merge. Several such objects appear likely to present a significant range in ages, hence possibly metallicities, and their merger could plausibly lead to multimetallic GCs. Here we explore this process with direct-summation N -body simulations with graphics processing unit hardware. Our results reveal that colliding GCs with different metallicities and ages can produce a GC with multiplicity and occupation fractions not unlike those observed in multimetallic clusters. In our simulations, the merged clusters have a phase with a larger amount of flattening than average, as a consequence of rapid rotation – thus suggesting that relatively recent mergers may play a role in producing highly flattened, multimetallic clusters. We additionally explore the role of the King parameter of the cluster in the occupation fractions with a set of 160 direct-summation simulations and find that for equal size clusters the King parameter of the progenitor clusters determines the occupation fractions in the merger product, while in unequal size mergers the size of the clusters dominates the distribution of stars in the new GC. In particular, we find that the observed distribution of populations in  Cen can be described to some extent with our dynamical models.

Description: We present a simulation analysis of weak gravitational lensing flexion and shear measurement using shapelet decomposition, and identify differences between flexion and shear measurement noise in deep survey data. Taking models of galaxies from the Hubble Space Telescope Ultra Deep Field (HUDF) and applying a correction for the HUDF point spread function, we generate lensed simulations of deep, optical imaging data from Hubble's Advanced Camera for Surveys, with realistic galaxy morphologies. We find that flexion and shear estimates differ in our measurement pipeline: whereas intrinsic galaxy shape is typically the dominant contribution to noise in shear estimates, pixel noise due to finite photon counts and detector read noise is a major contributor to uncertainty in flexion estimates, across a broad range of galaxy signal-to-noise. This pixel noise also increases more rapidly as galaxy signal-to-noise decreases than is found for shear estimates. We provide simple power-law fitting functions for this behaviour, for both flexion and shear, allowing the effect to be properly accounted for in future forecasts for flexion measurement. Using the simulations, we also quantify the systematic biases of our shapelet flexion and shear measurement pipeline for deep Hubble data sets such as Galaxy Evolution from Morphology and SEDs, Space Telescope A901/902 Galaxy Evolution Survey or Cosmic Evolution Survey. Flexion measurement biases are found to be significant but consistent with previous studies.

Description: We use an adaptation of the BzK s technique to select ~40 000 z  ~ 2 galaxies (to K AB = 24), including ~5000 passively evolving (PE) objects (to K AB = 23), from 2.5 deg 2 of deep Canada–France–Hawaii Telescope (CFHT) imaging. The passive galaxy luminosity function (LF) exhibits a clear peak at R  = 22 and a declining faint-end slope ( $\alpha = -0.12 ^{+0.16}_{-0.14}$ ), while that of star-forming galaxies is characterized by a steep faint-end slope [ $\alpha = -1.43\pm 0.02({\rm systematic})^{+0.05}_{-0.04}({\rm random})$ ]. The details of the LFs are somewhat sensitive (at the 〈25 per cent level) to cosmic variance even in these large (~0.5 deg 2 ) fields, with the D2 field (located in the Cosmological Evolution Survey, COSMOS field) most discrepant from the mean. The shape of the z  ~ 2 stellar mass function of passive galaxies is remarkably similar to that at z  ~ 0.9, save for a factor of ~4 lower number density. This similarity suggests that the same mechanism may be responsible for the formation of passive galaxies seen at both these epochs. This same formation mechanism may also operate down to z  ~ 0 if the local PE galaxy mass function, known to be two-component, contains two distinct galaxy populations. This scenario is qualitatively in agreement with recent phenomenological mass-quenching models and extends them to span more than three quarters of the history of the Universe.

Description: Among all known young nearby neutron stars, we search for the neutron star that was born in the same supernova event that formed the Antlia supernova remnant (SNR). We also look for a runaway star that could have been the former companion to the neutron star (if it exists) and then got ejected due to the same supernova. We find the pulsar PSR J0630–2834 to be the best candidate for a common origin with the Antlia SNR. In that scenario, the SNR is 1.2 Myr old and is presently located at a distance of 138 pc. We consider the runaway star HIP 47155 a former companion candidate to PSR J0630–2834. The encounter time and place is consistent with both stars being ejected from the Antlia SNR. We measured the radial velocity of HIP 47155 as 32.42 ± 0.70 km s –1 .

Description: Broad-band coronagraphy with deep nulling and small inner working angle has the potential of delivering images and spectra of exoplanets and other faint objects. In recent years, many coronagraphic schemes have been proposed, the most promising being the optical vortex phase mask coronagraphs. In this paper, a new scheme of broad-band optical scalar vortex coronagraph is proposed and characterized experimentally in the laboratory. Our setup employs a pair of computer-generated phase gratings (one of them containing a singularity) to control the chromatic dispersion of phase plates and achieves a constant peak-to-peak attenuation below 1 10 –3 over a bandwidth of 120 nm centred at 700 nm. An inner working angle of ~/ D is demonstrated along with a raw contrast of 11.5 mag at 2/ D .

Description: A deformation of a neutron star due to its own magnetic field is an important issue in gravitational wave astronomy, since a misaligned rotator with small ellipticity may emit continuous gravitational wave that may be observed by ground-based detectors. Recently, Mastrano et al. evaluated deformations induced by both poloidal and toroidal magnetic field in non-barotropic model stars by neglecting the gravitational field perturbation (Cowling approximation). Following their treatment in non-barotropic fluid and magnetic configurations, we here assess the effect of gravitational perturbation that they neglected. We show that the ellipticity computed with gravitational perturbation is roughly twice as large as that obtained by Cowling approximation. We should allow this amount of error in using the neat analytic treatment proposed by them.

Description: Following the discovery of short-period oscillations in the low-mass pre-white-dwarf component of an eclipsing binary, we have explored the radial (p-mode) stability of extremely low mass stars across a range of composition, effective temperature and luminosity. We have identified the instability boundaries associated with low- to high-order radial oscillations (0 ≤  n  ≤ 13) and show that these are a strong function of both composition and radial order ( n ). The blue edge shifts to higher effective temperature and luminosity with decreasing hydrogen abundance. In addition, high-order modes are more easily excited, and small islands of high-radial-order instability develop, some of which may correspond to real stars. The excitation mechanism is discussed with reference to these instability islands. If the envelope of the low-mass pre-white dwarf 1SWASP J024743.37–251549.2 (J0247–25B) is depleted in hydrogen, it is unstable to high-order p modes. Driving is by the classical mechanism operating in the second helium-ionization zone, with some support from the first helium-ionization zone. The instability is very sensitive to composition, temperature and luminosity. The reported periods, temperature and luminosity of J0247–25B require the envelope hydrogen abundance to lie in the range 0.2 X 0.3, in agreement with current evolution models.

Description: We present an accurate analysis of the H 2 absorption lines from the z abs  ~ 2.4018 damped Lyα system towards HE 0027–1836 observed with the Very Large Telescope Ultraviolet and Visual Echelle Spectrograph (VLT/UVES) as a part of the European Southern Observatory Large Programme ‘The UVES large programme for testing fundamental physics’ to constrain the variation of proton-to-electron mass ratio, μ   m p / m e . We perform cross-correlation analysis between 19 individual exposures taken over three years and the combined spectrum to check the wavelength calibration stability. We notice the presence of a possible wavelength-dependent velocity drift especially in the data taken in 2012. We use available asteroids spectra taken with UVES close to our observations to confirm and quantify this effect. We consider single- and two-component Voigt profiles to model the observed H 2 absorption profiles. We use both linear regression analysis and Voigt profile fitting where μ/μ is explicitly considered as an additional fitting parameter. The two-component model is marginally favoured by the statistical indicators and we get μ/μ = –2.5 ± 8.1 stat  ± 6.2 sys ppm. When we apply the correction to the wavelength-dependent velocity drift, we find μ/μ = –7.6 ± 8.1 stat  ± 6.3 sys ppm. It will be important to check the extent to which the velocity drift we notice in this study is present in UVES data used for previous μ/μ measurements.

Description: Young stellar objects in the inner Galactic region 10° 〈  l  〈 15° and –1° 〈  b  〈 1° were studied using GLIMPSE images and the GLIMPSE data catalogue. A total of 1107 Class I and 1566 Class II sources were identified in this Galactic region. With the help of GLIMPSE 5.8- and 8-μm images, we identified the presence of 10 major star forming sites in the Galactic mid-plane, 8 of which are filamentary while 2 are possible clusters of Class I and II sources. The length of the identified filaments are estimated as 8–33 arcmin (~9–56 pc). The occurrence of a hub–filamentary system is observed in many filamentary star forming sites. Most of the Class I sources are found to be aligned along the length of these filamentary structures, while Class II sources have a random distribution. The mass and age distribution of 425 Class I and 241 Class II sources associated with filaments and clusters were studied through analysis of their spectral energy distribution. Most of the Class I sources detected have mass 〉8 M , while Class II sources have relatively low masses. Class I sources have ages ≤0.5 Myr, while Class II sources have ages in the range ~0.1–3 Myr. By combining our results with information from high mass star forming tracers, we demonstrate that large numbers of high-mass stars are being formed in the 10 regions studied here.

Description: Forthcoming weak lensing shear measurements in surveys such as Large Synoptic Survey Telescope will be sensitive to short-time-scale atmospheric deflections. Orthogonal transfer (OT) imagers reduce the point spread function (PSF) ellipticity and size induced by atmospheric deflections using on-chip electronic tip-tilt corrections, but they also provide a large volume of data on the short-time-scale behaviour of the PSF. We use the OT imager Orthogonal Parallel Transfer Imaging Camera to show that short-time-scale-induced ellipticities obey the t –1/2 time dependence described in Heymans et al. and de Vries et al. even at time-scales shorter than 1 s. We also demonstrate the utility of OT imagers for measuring this relationship on an exposure-by-exposure basis and show evidence for a weak correlation between local windspeed conditions and the rate of decline of atmospheric-induced ellipticity. In addition, we determine that the ellipticity induced by centroid deflections declines more gradually with time than the atmospheric-induced instantaneous ellipticity.

Description: We present a method for populating dark matter simulations with haloes of mass below the resolution limit. It is based on stochastically sampling a field derived from the density field of the halo catalogue, using constraints from the conditional halo mass function n ( m |). We test the accuracy of the method and show its application in the context of building mock galaxy samples. We find that this technique allows precise reproduction of the two-point statistics of galaxies in mock samples constructed with this method. Our results demonstrate that the main information content of a simulation can be communicated efficiently using only a catalogue of the more massive haloes.

Description: This paper deals with the boundary control problems for the system described by first-order hyperbolic partial integro-differential equations with nonlocal boundary conditions by means of the deformation formulas. It is shown that the associated operator with nonlocal terms generates a C 0 -semigroup and the system defines an abstract boundary control system in L 2 -space. On the basis of the construction of integral kernel function, the ordinal and evolutional deformation formulas are established for a general class of Volterra integro-differential equations with nonlocal terms. By applying a special form of the formulas, a design of feedback boundary control law is given, which makes the scalar boundary control system null controllable in finite time. Furthermore, the null controllability result is extended to coupled nonsymmetric first-order hyperbolic systems by using appropriate linear transformations. Applications to physically important coupled systems are also given.

Description: Motivation: Pyrosequencing technology provides an important new approach to more extensively characterize diverse sequence populations and detect low frequency variants. However, the promise of this technology has been difficult to realize, as careful correction of sequencing errors is crucial to distinguish rare variants (~1%) in an infected host with high sensitivity and specificity. Results: We developed a new approach, referred to as Indel and Carryforward Correction (ICC), to cluster sequences without substitutions and locally correct only indel and carryforward sequencing errors within clusters to ensure that no rare variants are lost. ICC performs sequence clustering in the order of (i) homopolymer indel patterns only, (ii) indel patterns only and (iii) carryforward errors only, without the requirement of a distance cutoff value. Overall, ICC removed 93–95% of sequencing errors found in control datasets. On pyrosequencing data from a PCR fragment derived from 15 HIV-1 plasmid clones mixed at various frequencies as low as 0.1%, ICC achieved the highest sensitivity and similar specificity compared with other commonly used error correction and variant calling algorithms. Availability and implementation: Source code is freely available for download at http://indra.mullins.microbiol.washington.edu/ICC . It is implemented in Perl and supported on Linux, Mac OS X and MS Windows. Contact: jmullins@uw.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Tiki proteins appear to antagonize Wnt signalling pathway by acting as Wnt proteases, thereby affecting Wnt solubility by its amino-terminal cleavage. Tiki1 protease activity was shown to be metal ion-dependent and was inhibited by chelating agents and thus was tentatively proposed to be a metalloprotease. Nevertheless, Tiki proteins exhibit no detectable sequence similarity to previously described metalloproteases, but instead have been reported as being homologues of TraB proteins (Pfam ID: PF01963), a widely distributed family of unknown function and structure. Here, we show that Tiki proteins are members of a new superfamily of domains contained not just in TraB proteins, but also in erythromycin esterase (Pfam ID: PF05139), DUF399 (domain of unknown function 399; Pfam ID: PF04187) and MARTX toxins that contribute to host invasion and pathogenesis by bacteria. We establish the core fold of this enzymatic domain and its catalytic residues. Contact: luis.sanchezpulido@dpag.ox.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The research area metabolomics achieved tremendous popularity and development in the last couple of years. Owing to its unique interdisciplinarity, it requires to combine knowledge from various scientific disciplines. Advances in the high-throughput technology and the consequently growing quality and quantity of data put new demands on applied analytical and computational methods. Exploration of finally generated and analyzed datasets furthermore relies on powerful tools for data mining and visualization. Results: To cover and keep up with these requirements, we have created MeltDB 2.0, a next-generation web application addressing storage, sharing, standardization, integration and analysis of metabolomics experiments. New features improve both efficiency and effectivity of the entire processing pipeline of chromatographic raw data from pre-processing to the derivation of new biological knowledge. First, the generation of high-quality metabolic datasets has been vastly simplified. Second, the new statistics tool box allows to investigate these datasets according to a wide spectrum of scientific and explorative questions. Availability: The system is publicly available at https://meltdb.cebitec.uni-bielefeld.de . A login is required but freely available. Contact: nkessler@cebitec.uni-bielefeld.de

Description: Motivation: High - throughput next - generation sequencing technologies enable increasingly fast and affordable sequencing of genomes and transcriptomes, with a broad range of applications. The quality of the sequencing data is crucial for all applications. A significant portion of the data produced contains errors, and ever more efficient error correction programs are needed. Results: We propose RACER (Rapid and Accurate Correction of Errors in Reads), a new software program for correcting errors in sequencing data. RACER has better error-correcting performance than existing programs, is faster and requires less memory. To support our claims, we performed extensive comparison with the existing leading programs on a variety of real datasets. Availability: RACER is freely available for non-commercial use at www.csd.uwo.ca/~ilie/RACER/ . Contact: ilie@csd.uwo.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Interactions between various types of molecules that regulate crucial cellular processes are extensively investigated by high-throughput experiments and require dedicated computational methods for the analysis of the resulting data. In many cases, these data can be represented as a bipartite graph because it describes interactions between elements of two different types such as the influence of different experimental conditions on cellular variables or the direct interaction between receptors and their activators/inhibitors. One of the major challenges in the analysis of such noisy datasets is the statistical evaluation of the relationship between any two elements of the same type. Here, we present SICOP (significant co-interaction patterns), an implementation of a method that provides such an evaluation based on the number of their common interaction partners, their so-called co-interaction. This general network analytic method, proved successful in diverse fields, provides a framework for assessing the significance of this relationship by comparison with the expected co-interaction in a suitable null model of the same bipartite graph. SICOP takes into consideration up to two distinct types of interactions such as up- or downregulation. The tool is written in Java and accepts several common input formats and supports different output formats, facilitating further analysis and visualization. Its key features include a user-friendly interface, easy installation and platform independence. Availability: The software is open source and available at cna.cs.uni-kl.de/SICOP under the terms of the GNU General Public Licence (version 3 or later). Contact: agnes.horvat@iwr.uni-heidelberg.de or zweig@cs.uni-kl.de

Description: : Molecular recognition features (MoRFs) are small, intrinsically disordered regions in proteins that undergo a disorder-to-order transition on binding to their partners. MoRFs are involved in protein–protein interactions and may function as the initial step in molecular recognition. The aim of this work was to collect, organize and store all membrane proteins that contain MoRFs. Membrane proteins constitute ~30% of fully sequenced proteomes and are responsible for a wide variety of cellular functions. MoRFs were classified according to their secondary structure, after interacting with their partners. We identified MoRFs in transmembrane and peripheral membrane proteins. The position of transmembrane protein MoRFs was determined in relation to a protein’s topology. All information was stored in a publicly available mySQL database with a user-friendly web interface. A Jmol applet is integrated for visualization of the structures. mpMoRFsDB provides valuable information related to disorder-based protein–protein interactions in membrane proteins. Availability: http://bioinformatics.biol.uoa.gr/mpMoRFsDB Contact: shamodr@biol.uoa.gr

Description: : The signaling Petri net (SPN) simulator, designed to provide insights into the trends of molecules’ activity levels in response to an external stimulus, contributes to the systems biology necessity of analyzing the dynamics of large-scale cellular networks. Implemented into the freely available software, BioLayout Express 3D , the simulator is publicly available and easy to use, provided the input files are prepared in the GraphML format, typically using the network editing software, yEd, and standards specific to the software. However, analysis of complex networks represented using other systems biology formatting languages (on which popular software, such as CellDesigner and Cytoscape, are based) requires manual manipulation, a step that is prone to error and limits the use of the SPN simulator in BioLayout Express 3D . To overcome this, we present a Cytoscape plug-in that enables users to automatically convert networks for analysis with the SPN simulator from the standard systems biology markup language. The automation of this step opens the SPN simulator to a far larger user group than has previously been possible. Availability and implementation: Distributed under the GNU General Public License Version 3 at http://apps.cytoscape.org/apps/spnconverter . Contact: christine@picb.ac.cn

Description: Motivation: Conformational diversity is a key concept in the understanding of different issues related with protein function such as the study of catalytic processes in enzymes, protein-protein recognition, protein evolution and the origins of new biological functions. Here, we present a database of proteins with different degrees of conformational diversity. Conformational Diversity of Native State (CoDNaS) is a redundant collection of three-dimensional structures for the same protein derived from protein data bank. Structures for the same protein obtained under different crystallographic conditions have been associated with snapshots of protein dynamism and consequently could characterize protein conformers. CoDNaS allows the user to explore global and local structural differences among conformers as a function of different parameters such as presence of ligand, post-translational modifications, changes in oligomeric states and differences in pH and temperature. Additionally, CoDNaS contains information about protein taxonomy and function, disorder level and structural classification offering useful information to explore the underlying mechanism of conformational diversity and its close relationship with protein function. Currently, CoDNaS has 122 122 structures integrating 12 684 entries, with an average of 9.63 conformers per protein. Availability: The database is freely available at http://www.codnas.com.ar/ . Contact: gusparisi@gmail.com

Description: Motivation: Recent experimental advancements allow determining positions of nucleosomes for complete genomes. However, the resulting nucleosome occupancy maps are averages of heterogeneous cell populations. Accordingly, they represent a snapshot of a dynamic ensemble at a single time point with an overlay of many configurations from different cells. To study the organization of nucleosomes along the genome and to understand the mechanisms of nucleosome translocation, it is necessary to retrieve features of specific conformations from the population average. Results: Here, we present a method for identifying non-overlapping nucleosome configurations that combines binary-variable analysis and a Monte Carlo approach with a simulated annealing scheme. In this manner, we obtain specific nucleosome configurations and optimized solutions for the complex positioning patterns from experimental data. We apply the method to compare nucleosome positioning at transcription factor binding sites in different mouse cell types. Our method can model nucleosome translocations at regulatory genomic elements and generate configurations for simulations of the spatial folding of the nucleosome chain. Availability: Source code, precompiled binaries, test data and a web-based test installation are freely available at http://bioinformatics.fh-stralsund.de/nucpos/ Contact: gero.wedemann@fh-stralsund.de Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Wolbachia , endosymbiotic bacteria of the order Rickettsiales, are widespread in arthropods but also present in nematodes. In arthropods, A and B supergroup Wolbachia are generally associated with distortion of host reproduction. In filarial nematodes, including some human parasites, multiple lines of experimental evidence indicate that C and D supergroup Wolbachia are essential for the survival of the host, and here the symbiotic relationship is considered mutualistic. The origin of this mutualistic endosymbiosis is of interest for both basic and applied reasons: How does a parasite become a mutualist? Could intervention in the mutualism aid in treatment of human disease? Correct rooting and high-quality resolution of Wolbachia relationships are required to resolve this question. However, because of the large genetic distance between Wolbachia and the nearest outgroups, and the limited number of genomes so far available for large-scale analyses, current phylogenies do not provide robust answers. We therefore sequenced the genome of the D supergroup Wolbachia endosymbiont of Litomosoides sigmodontis , revisited the selection of loci for phylogenomic analyses, and performed a phylogenomic analysis including available complete genomes (from isolates in supergroups A, B, C, and D). Using 90 orthologous genes with reliable phylogenetic signals, we obtained a robust phylogenetic reconstruction, including a highly supported root to the Wolbachia phylogeny between a (A + B) clade and a (C + D) clade. Although we currently lack data from several Wolbachia supergroups, notably F, our analysis supports a model wherein the putatively mutualist endosymbiotic relationship between Wolbachia and nematodes originated from a single transition event.

Description: Many insects rely on bacterial symbionts with tiny genomes specialized for provisioning nutrients lacking in host diets. Xylem sap and phloem sap are both deficient as insect diets, but differ dramatically in nutrient content, potentially affecting symbiont genome evolution. For sap-feeding insects, sequenced symbiont genomes are available only for phloem-feeding examples from the suborder Sternorrhyncha and xylem-feeding examples from the suborder Auchenorrhyncha, confounding comparisons. We sequenced genomes of the obligate symbionts, Sulcia muelleri and Nasuia deltocephalinicola , of the phloem-feeding pest insect, Macrosteles quadrilineatus (Auchenorrhyncha: Cicadellidae). Our results reveal that Nasuia- ALF has the smallest bacterial genome yet sequenced (112 kb), and that the Sulcia- ALF genome (190 kb) is smaller than that of Sulcia in other insect lineages. Together, these symbionts retain the capability to synthesize the 10 essential amino acids, as observed for several symbiont pairs from xylem-feeding Auchenorrhyncha. Nasuia retains genes enabling synthesis of two amino acids, DNA replication, transcription, and translation. Both symbionts have lost genes underlying ATP synthesis through oxidative phosphorylation, possibly as a consequence of the enriched sugar content of phloem. Shared genomic features, including reassignment of the UGA codon from Stop to tryptophan, and phylogenetic results suggest that Nasuia -ALF is most closely related to Zinderia , the betaproteobacterial symbiont of spittlebugs. Thus, Nasuia / Zinderia and Sulcia likely represent ancient associates that have co-resided in hosts since the divergence of leafhoppers and spittlebugs 〉200 Ma, and possibly since the origin of the Auchenorrhyncha, 〉260 Ma.

Description: It has been argued that scale is the central problem in ecology ( Levin, 1992 ). Studies on carbon cycles and global climate change, the current major themes in modern ecology, require the interfacing of phenomena that occur on different scales of space, time, and ecological organization. For several decades, tremendous efforts have been made to reveal the general patterns of, and the mechanisms for the global carbon cycles. However, many uncertainties remain, particularly on local to regional scales. To reduce these uncertainties, regional collaborations across the board of nations are required.

Description: Aims Boreal forest is the largest and contains the most soil carbon among global terrestrial biomes. Soil respiration during the prolonged winter period may play an important role in the carbon cycles in boreal forests. This study aims to explore the characteristics of winter soil respiration in the boreal forest and to show how it is regulated by environmental factors, such as soil temperature, soil moisture and snowpack. Methods Soil respiration in an old-growth larch forest ( Larix gmelinii Ruppr.) in Northeast China was intensively measured during the winter soil-freezing process in 2011 using an automated soil CO 2 flux system. The effects of soil temperature, soil moisture and thin snowpack on soil respiration and its temperature sensitivity were investigated. Important Findings Total soil respiration and heterotrophic respiration both showed a declining trend during the observation period, and no significant difference was found between soil respiration and heterotrophic respiration until the snowpack exceeded 20cm. Soil respiration was exponentially correlated with soil temperature and its temperature sensitivity (Q 10 value) for the entire measurement duration was 10.5. Snow depth and soil moisture both showed positive effects on the temperature sensitivity of soil respiration. Based on the change in the Q 10 value, we proposed a ‘freeze–thaw critical point’ hypothesis, which states that the Q 10 value above freeze–thaw critical point is much higher than that below it (16.0 vs . 3.5), and this was probably regulated by the abrupt change in soil water availability during the soil-freezing process. Our findings suggest interactive effects of multiple environmental factors on winter soil respiration and recommend adopting the freeze–thaw critical point to model soil respiration in a changing winter climate.

Description: Aims Clear-cutting is a common forest management practice, especially in subtropical China. However, the potential ecological consequences of clear-cutting remain unclear. In particular, the effect of clear-cutting on soil processes, such as the carbon cycle, has not been quantified in subtropical forests. Here, we investigated the response of soil respiration (Rs) to clear-cutting during a 12-month period in a subtropical forest in eastern China. Methods We randomly selected four clear-cut (CC) plots and four corresponding undisturbed forest (UF) plots. Measurements of Rs were made at monthly time points and were combined with continuous climatic measurements in both CC and UF. Daily Rs was estimated by interpolating data with an exponential model dependent on soil temperature. Daily Rs was cumulated to annual Rs estimates. Important Findings In the first year after clear-cutting, annual estimates of Rs in CC (508±23g C m –2 yr –1 ) showed no significant difference to UF plots (480±12g C m –2 yr –1 ). During the summer, soil temperatures were usually higher, whereas the soil volumetric water content was lower in CC than in UF plots. The long-term effects of clear-cutting on Rs are not significant, although there might be effects during the first several months after clear-cutting. Compared with previous work, this pattern was more pronounced in our subtropical forest than in the temperate and boreal forests that have been studied by others. With aboveground residuals off-site after clear-cutting, our results indicate that the stimulation of increasing root debris, as well as environmental changes, will not lead to a significant increase in Rs. In addition, long-term Rs will not show a significant decrease from the termination of root respiration, and this observation might be because of the influence of fast-growing vegetation after clear-cutting in situ .

Description: Aims Understanding carbon (C) and nitrogen (N) dynamics and their dependence on the stand density of an even-aged, mature forest provides knowledge that is important for forest management. This study investigated the differences in ecosystem total C and N storage and flux between a low-density stand (LD) and a high-density stand (HD) and examined the effects of stand density on aboveground net primary productivity (ANPP), total belowground C allocation (TBCA) and net ecosystem production (NEP) in a naturally regenerated, 65- to 75-year-old Pinus densiflora S. et Z. forest. Methods LD (450 trees ha –1 ) and HD (842 trees ha –1 ) were established in an even-aged, mature P. densiflora forest in September 2006. The forest had been naturally regenerated following harvesting, and the stand density was naturally maintained without any artificial management such as thinning. The diameter at breast height (DBH ≥ 5.0cm) of all live stems within the stands was measured yearly from 2007 to 2011. To compare C and N storage and fluxes in LD and HD, C and N pools in aboveground and belowground biomass, the forest floor, coarse woody debris (CWD) and soil; soil CO 2 efflux ( R S ); autotrophic respiration ( R A ); litter production; and soil N availability were measured. Further, ANPP, TBCA and NEP were estimated from plot-based measurement data. Important Findings Ecosystem C (Mg C ha –1 ) and N (Mg N ha –1 ) storage was, respectively, 173.0±7.3 (mean ± SE) and 4.69±0.30 for LD and 162±11.8 and 4.08±0.18 for HD. There were no significant differences in C and N storage in the ecosystem components, except for soils, between the two stands. In contrast, there were significant differences in aboveground ANPP and TBCA between the two stands ( P 〈 0.05). Litterfall, biomass increment and R S were major C flux components with values of, respectively, 3.89, 3.74 and 9.07 Mg C ha –1 year –1 in LD and 3.15, 2.94 and 7.06 Mg C ha –1 year –1 in HD. Biometric-based NEP (Mg C ha –1 year –1 ) was 4.18 in LD and 5.50 in HD. Although the even-aged, mature P. densiflora forest had similar C and N allocation patterns, it showed different C and N dynamics depending on stand density. The results of the current study will be useful for elucidating the effects of stand density on C and N storage and fluxes, which are important issues in managing natural mature forest ecosystems.

Description: Aims Tropical forest plays a key role in global C cycle; however, there are few studies on the C budget in the tropical rainforests in Asia. This study aims to (i) reveal the seasonal patterns of total soil respiration ( R T ), litter respiration ( R L ) and soil respiration without surface organic litter ( R NL ) in the primary and secondary Asian tropical mountain rainforests and (ii) quantify the effects of soil temperature, soil moisture and substrate availability on soil respiration. Methods The seasonal dynamics of soil CO 2 efflux was measured by an automatic chamber system (Li-8100), within the primary and secondary tropical mountain rainforests located at the Jianfengling National Reserve in Hainan Island, China. The litter removal treatment was used to assess the contribution of litter to belowground CO 2 production. Important Findings The annual R T was higher in the primary forest (16.73±0.87 Mg C ha –1 ) than in the secondary forest (15.10±0.26 Mg C ha –1 ). The rates of R T , R NL and R L were all significantly higher in the hot and wet season (May–October) than those in the cool and dry season (November–April). Soil temperature at 5cm depth could explain 55–61% of the seasonal variation in R T , and the temperature sensitivity index ( Q 10 ) ranked by R L ( Q 10 = 3.39) 〉 R T (2.17) 〉 R NL (1.76) in the primary forest and by R L (4.31) 〉 R T (1.86) 〉 R NL (1.58) in the secondary forest. The contribution of R L to R T was 22–23%, while litter input and R T had 1 month time lag. In addition, the seasonal variation of R T was mainly determined by soil temperature and substrate availability. Our findings suggested that global warming and increased substrate availability are likely to cause considerable losses of soil C in the tropical forests.

Description: Aims Understanding of the ecophysiological dynamics of forest canopy photosynthesis and its spatial and temporal scaling is crucial for revealing ecological response to climate change. Combined observations and analyses of plant ecophysiology and optical remote sensing would enable us to achieve these studies. In order to examine the utility of spectral vegetation indices (VIs) for assessing ecosystem-level photosynthesis, we investigated the relationships between canopy-scale photosynthetic productivity and canopy spectral reflectance over seasons for 5 years in a cool, temperate deciduous broadleaf forest at ‘Takayama’ super site in central Japan. Methods Daily photosynthetic capacity was assessed by in situ canopy leaf area index (LAI), (LAI x V cmax [single-leaf photosynthetic capacity]), and the daily maximum rate of gross primary production (GPP max ) was estimated by an ecosystem carbon cycle model. We examined five VIs: normalized difference vegetation index (NDVI), enhanced vegetation index (EVI), green–red vegetation index (GRVI), chlorophyll index (CI) and canopy chlorophyll index (CCI), which were obtained by the in situ measurements of canopy spectral reflectance. Important Findings Our in situ observation of leaf and canopy characteristics, which were analyzed by an ecosystem carbon cycling model, revealed that their phenological changes are responsible for seasonal and interannual variations in canopy photosynthesis. Significant correlations were found between the five VIs and canopy photosynthetic capacity over the seasons and years; four of the VIs showed hysteresis-type relationships and only CCI showed rather linear relationship. Among the VIs examined, we applied EVI–GPP max relationship to EVI data obtained by Moderate Resolution Imaging Spectroradiometer to estimate the temporal and spatial variation in GPP max over central Japan. Our findings would improve the accuracy of satellite-based estimate of forest photosynthetic productivity in fine spatial and temporal resolutions, which are necessary for detecting any response of terrestrial ecosystem to meteorological fluctuations.

Description: Aims This study aimed to develop radial growth models and to predict the potential spatial distribution of Pinus densiflora (Japanese red pine) and Quercus spp. (Oaks) in South Korea, considering topographic and climatic factors. Methods We used a dataset of diameter at breast height and radial growth estimates of individual trees, topographic and climatic factors in systematic sample plots distributed over the whole of South Korea. On the basis that radial growth is attributed primarily to tree age, we developed a radial growth model employing tree age as an explanatory variable. We estimated standard growth (SG), defined as radial growth of the tree at age 30, to eliminate the influence of tree age on radial growth. In addition, SG estimates including the Topographic Wetness Index, temperature and precipitation were calculated by the Generalized Additive Model. Important Findings As a result of variogram analysis of SG, we found spatial autocorrelation between SG, topographic and climatic factors. Incremental temperature had negative impacts on radial growth of P. densiflora and positive impacts on that of Quercus spp. Precipitation was associated with positive effects on both tree species. Based on the model, we found that radial growth of P. densiflora would be more vulnerable than that of Quercus spp. to climatic factors. Through simulation with the radial growth model, it was predicted that P. densiflora stands would be gradually replaced with Quercus spp. stands in eastern coastal and southern regions of South Korea in the future. The models developed in this study will be helpful for understanding the impact of climatic factors on tree growth and for predicting changes in distribution of P. densiflora and Quercus spp. due to climate change in South Korea.

Description: Aims Vast grasslands on the Tibetan Plateau are almost all under livestock grazing. It is unclear, however, what is the role that the grazing will play in carbon cycle of the grassland under future climate warming. We found in our previous study that experimental warming can shift the optimum temperature of saturated photosynthetic rate into higher temperature in alpine plants. In this study, we proposed and tested the hypothesis that livestock grazing would alter the warming effect on photosynthetic and respiration through changing physical environments of grassland plants. Methods Experimental warming was carried by using an infrared heating system to increase the air temperature by 1.2 and 1.7°C during the day and night, respectively. The warming and ambient temperature treatments were crossed over to the two grazing treatments, grazing and un-grazed treatments, respectively. To assess the effects of grazing and warming, we examined photosynthesis, dark respiration, maximum rates of the photosynthetic electron transport ( J max ), RuBP carboxylation ( V cmax ) and temperature sensitivity of respiration Q 10 in Gentiana straminea , an alpine species widely distributed on the Tibetan grassland. Leaf morphological and chemical properties were also examined to understand the physiological responses. Important findings 1) Light-saturated photosynthetic rate ( A max ) of G. straminea showed similar temperature optimum at around 16°C in plants from all experimental conditions. Experimental warming increased A max at all measuring temperatures from 10 to 25°C, but the positive effect of the warming occurred only in plants grown under the un-grazed conditions. Under the same measuring temperature, A max was significantly higher in plants from the grazed than the un-grazed condition. 2) There was significant crossing effect of warming and grazing on the temperature sensitivity ( Q 10 ) of leaf dark respiration. Under the un-grazed condition, plants from the warming treatment showed lower respiration rate but similar Q 10 in comparison with plants from the ambient temperature treatment. However, under the grazed condition Q 10 was significantly lower in plants from the warming than the ambient treatment. 3) The results indicate that livestock grazing can alter the warming effects on leaf photosynthesis and temperature sensitivity of leaf dark respiration through changing physical environment of the grassland plants. The study suggests for the first time that grazing effects should be taken into account in predicting global warming effects on photosynthesis and respiration of plants in those grasslands with livestock grazing.

Description: Arguments need to be judged against other arguments. The decision to accept or reject an argument is generally a global decision that involves examining the same question for other arguments that oppose or can defend the argument in question. This article presents the acceptability semantics for abstract argumentation that through a recursive definition gives a global assignment of the acceptable and non-acceptable subsets of arguments. This semantics stems from the aim to formalize directly the generally accepted intuition that: ‘An argument can be accepted if and only if all its challenging arguments can be rejected.’ The acceptability semantics tightly integrates the notion of defending against a challenging argument by counter-attacking it with the notion of self-defeating (or self-rejecting) arguments that (help to) bring about their own non-acceptability. The proposal is motivated by earlier studies of the semantics of Logic Programming (LP) in terms of argumentation, where the basic well founded and stable model semantics of LP can be uniformly captured using a recursively defined argumentation semantics for Negation as Failure and where these standard semantics of LP can be further extended through argumentation.

Description: This article is concerned with the design and analysis of polynomial time algorithms for determining whether a Planar Quantified Integer Program (PQIP) is feasible. A PQIP can be described briefly as an integer program involving two variables, in which each variable can be either universally or existentially quantified. There are four types of PQIPs, depending on how the variables are quantified (existentially or universally). In this article, we present two new, simple, and efficient algorithms for the case as well as a detailed account of the complexity of the other cases. Moreover, we discuss certification with respect to the provided algorithms.

Description: In the present article, the quantifiers over propositions are first introduced into the language for reasoning about probability, then the complexity issues for validity problems dealing with the corresponding hierarchy of probabilistic sentences are investigated. We prove, among other things, the $${\Pi }_{1}^{1}$$ -completeness for the general validity and also indicate the least level in the hierarchy for which the validity problem is undecidable.

Description: We use mosaics to provide a simple, sound, complete and terminating tableau reasoning procedure for the temporal logic of until and since over general linear time.

Description: The aim of what semantic science is to have scientific ontologies, data and hypotheses represented and published in machine understandable forms that enable predictions on new cases. There is much work on developing scientific ontologies and representing scientific data in terms of these ontologies. The next step is to publish hypotheses that can make (probabilistic) predictions on the published data and can be used for prediction on new cases. The published data can be used to evaluate hypotheses. To make a prediction in a particular case, hypotheses are combined to form models. This article considers feature-based semantic science where the data and new cases are described in terms of features. A prediction for a new case is made by building a model made up of hypotheses that fit together, are consistent with the ontologies used, and are adequate for the case. We give some desiderata for such models, and show how the construction of such models is a form of abduction. We provide a definition for models that satisfies these criteria and prove that it produces a coherent probability distribution over the values of interest.

Description: In this article we present methods of transition from one perspective on logic to others, and apply this in particular to obtain a coalgebraic presentation of logic. The central ingredient in this process is to view consequence relations as morphisms in a category.

Description: We consider the expressive power of the first-order structure 〈, C 〉 where is either of two of different domains of extended regions in Euclidean space, and C(x,y) is the topological relation ‘Region x is in contact with region y .’ We prove two main theorems: Let $$\mathcal{P}$$ [Q] be the domain of bounded, non-empty, rational polyhedra in two- or three-dimensional Euclidean space. A relation over $$\mathcal{P}$$ [Q] is definable in the structure 〈 $$\mathcal{P}$$ [Q], C 〉 if and only if is arithmetic and invariant under rational PL-homeomorphisms of the space to itself. We also extend this result to a number of other domains, including the domain of all polyhedra and the domain of semi-algebraic regions. Let $$\mathcal{R}$$ be the space of bounded, non-empty, closed regular regions in n -dimensional Euclidean space. Any analytical relation over lower dimensional (i.e. empty interior) compact point sets that is invariant under homeomorphism is implicitly definable in the structure 〈 $$\mathcal{R}$$ , C 〉.

Description: We present age distribution matching , a theoretical formalism for predicting how galaxies of luminosity L and colour C occupy dark matter haloes. Our model supposes that there are just two fundamental properties of a halo that determine the colour and brightness of the galaxy it hosts: the maximum circular velocity V max and the redshift z starve that correlates with the epoch at which the star formation in the galaxy ceases. The halo property z starve is intended to encompass physical characteristics of halo mass assembly that may deprive the galaxy of its cold gas supply and, ultimately, quench its star formation. The new, defining feature of the model is that, at fixed luminosity, galaxy colour is in monotonic correspondence with z starve , with the larger values of z starve being assigned redder colours. We populate an N -body simulation with a mock galaxy catalogue based on age distribution matching and show that the resulting mock galaxy distribution accurately describes a variety of galaxy statistics. Our model suggests that halo and galaxy assembly are indeed correlated. We make publicly available our low-redshift, Sloan Digital Sky Survey M r  〈 –19 mock galaxy catalogue, and main progenitor histories of all z  = 0 haloes, at http://logrus.uchicago.edu/~aphearin

Description: The incidence of intranight optical variability (INOV) is known to differ significantly among different classes of powerful active galactic nuclei (AGN). A number of statistical methods have been employed in the literature for testing the presence of INOV in the light curves, sometimes leading to discordant results. In this paper, we compare the INOV characteristics of six prominent classes of AGN, as evaluated using three commonly used statistical tests, namely the 2 -test, the modified C -test and the F -test, which has recently begun to gain popularity. The AGN classes considered are: radio-quiet quasars, radio-intermediate quasars, lobe-dominated quasars, low optical polarization core-dominated quasars, high optical polarization core-dominated quasars and TeV blazars. Our analysis is based on a large body of AGN monitoring data, involving 262 sessions of intranight monitoring of a total 77 AGN, using 1–2 m class optical telescopes located in India. In order to compare the usefulness of the statistical tests, we have also subjected them to a ‘sanity check’ by comparing the number of false positives yielded by each test with the corresponding statistical prediction. The present analysis is intended to serve as a benchmark for future INOV studies of AGN of different classes.

Description: Using spectropolarimetry, we investigate the large-scale magnetic topologies of stars hosting close-in exoplanets. A small survey of 10 stars has been done with the twin instruments Télescope Bernard Lyot /NARVAL and Canada–France–Hawaii Telescope/ESPaDOnS between 2006 and 2011. Each target consists of circular polarization observations covering 7–22 d. For each of the seven targets in which a magnetic field was detected, we reconstructed the magnetic field topology using Zeeman–Doppler imaging. Otherwise, a detection limit has been estimated. Three new epochs of observations of Boo are presented, which confirm magnetic polarity reversal. We estimate that the cycle period is 2 yr, but recall that a shorter period of 240 d cannot still be ruled out. The result of our survey is compared to the global picture of stellar magnetic field properties in the mass–rotation diagram. The comparison shows that these giant planet-host stars tend to have similar magnetic field topologies to stars without detected hot Jupiters. This needs to be confirmed with a larger sample of stars.

Description: We present the first theoretical study of metals in damped-Lyα (DLA) systems at redshift z ~= 7. The features of cold, primordial gas are studied by means of N -body, hydro, chemistry simulations, including atomic and molecular non-equilibrium chemistry, cooling, star formation for Population III and Population II-I regimes, stellar evolution, cosmic metal spreading according to proper yields (for He, C, O, Si, Fe, Mg, S, etc.) and lifetimes and feedback effects. Theoretical expectations are then compared to recently available constraints from DLA observations. We find that DLA galaxies at z ~= 7 account for ~10 per cent of the whole galaxy population and for most of the metal-poor galaxies at these epochs. About 7 per cent of these DLA galaxies contain purely pristine material and ~34 per cent of them consist of very weakly polluted gas, being, therefore, suitable candidates as Population III sites. The remaining ~59 per cent are enriched above ~10 –4 Z . Additionally, DLA candidates appear to have: gas masses 2 x 10 8 M ; very low star formation rate, ~ 10 – 3 – 10 – 2 M yr – 1 (significantly weaker than late-time counterparts); mean molecular fractions covering a fairly wide range, x mol ~ 10 – 3 -10 – 6 ; typical metallicities Z 10 –3 Z and H i column densities $N_{\rm H\,{{\small I}}}\gtrsim 3\times 10^{20}\, {\rm cm}^{-2}$ (in agreement with recent observations). They present no or weak correlations between their gas mass and Z , $N_{\rm H\,{{\small I}}}$ , or x mol ; a moderate correlation between x mol and Z , linked to the ongoing molecular-driven star formation and metal pollution processes; a mild anticorrelation between $N_{\rm H\,{{\small I}}}$ and x mol , due to H depletion into molecules; and a chemical content that is subject to environmental dependences.

Description: We present new Gemini spectroscopical data of the extended emission-line region of the 3C 305 radio galaxy in order to achieve a final answer to the long-standing question about the ionizing mechanism. The spectra show strong kinematic disturbances within the most intense line-emitting region. The relative intensities of the emission lines agree with the hypothesis that the gas is shocked during the interaction of powerful radio jets with the ambient medium. The emission from the recombination region acts as a very effective cooling mechanism, which is supported by the presence of a neutral outflow. However, the observed intensity is almost an order of magnitude lower than expected in a pure shock model. So, autoionizing shock models, in low-density and low-abundance regimes, are required in order to account for the observed emission within the region. This scenario also supports the hypothesis that the optical emitting gas and the X-ray plasma are in pressure balance.

Description: In a recent work (Paper I), we explored the dependence of galaxy stellar population properties derived from broad-band spectral energy distribution fitting on the fitting parameters, e.g. star formation histories (SFHs), age grid, metallicity, initial mass function (IMF), dust reddening and reddening law, filter setup and wavelength coverage. In this paper, we consider the case that also redshift is a free parameter in the fit and study whether one can obtain reasonable estimates of photometric redshifts and stellar population properties at once . As in Paper I, we use mock star-forming as well as passive galaxies placed at various redshifts (0.5–3) as test particles. Mock star-forming galaxies are extracted from a semi-analytical galaxy formation model. We show that for high-redshift star-forming galaxies, photometric redshifts, stellar masses and reddening can be determined simultaneously when using a broad wavelength coverage (including the Lyman and the 4000 Å break) and a wide template setup in the fit. Masses are similarly well recovered (median ~0.2 dex) as at fixed redshift. For old galaxies with little recent star formation (which are at lower redshift in the simulation), masses are better recovered than in the fixed redshift case, such that the median recovered stellar mass improves by up to 0.3 dex (at fixed IMF) whereas the uncertainty in the redshift accuracy increases by only ~0.05. However, a failure in redshift recovery also means a failure in mass recovery. As at fixed redshift, mismatches in SFH and degeneracies between age, dust and now also redshift cause underestimated ages, overestimated reddening and underestimated masses. Stellar masses are best determined at low redshift without reddening in the fit. Masses are then underestimated by only ~0.1 dex whereas redshifts are similarly well recovered. Not surprisingly, the recovery of properties is substantially better for passive galaxies, for which e.g. the mass is recovered only slightly worse than at fixed redshift (underestimated by ~0.02 dex instead of ~0.01, at fixed IMF) using a setup including metallicity effects. In all cases, the recovery of physical parameters is crucially dependent on the wavelength coverage adopted in the fitting because the redshift recovery depends on the wavelength coverage. As is well known, redshifts are best recovered for a wavelength coverage including the Lyman and 4000 Å break. As in Paper I, all effects from changing templates, the wavelength coverage and filters are quantified and scaling relations for the transformation of stellar masses obtained using different fitting parameters, including stellar population models, are provided.

Description: Previous studies of globular cluster (GC) systems show that there appears to be a universal specific GC formation efficiency which relates the total mass of GCs to the virial mass of host dark matter haloes, M vir . In this paper, the specific frequency, S N , and specific GC formation efficiency, , are derived as functions of M vir in Milgromian dynamics, i.e. in modified Newtonian dynamics. In Milgromian dynamics, for the galaxies with GCs, the mass of the GC system, M GC , is a two-component function of M vir instead of a simple linear relation. An observer in a Milgromian universe, who interprets this universe as being Newtonian/Einsteinian, will incorrectly infer a universal constant fraction between the mass of the GC system and a (false) dark matter halo of the baryonic galaxy. In contrast to a universal constant of , in a Milgromian universe, for galaxies with M vir ≤ 10 12 M , decreases with the increase of M vir , while for massive galaxies with M vir 〉 10 12 M , increases with the increase of M vir .

Description: New collisions’ strengths for the mid-infrared (mid-IR) and optical transitions in Ne v are presented. Breit–Pauli-R-Matrix calculations for electron impact excitation are carried out with fully resolved near-threshold resonances at very low energies. In particular, the fine-structure lines at 14 and 24 μm due to transitions among the ground state levels 1s 2 2s 2 2p 3 3 P 0, 1, 2 , and the optical/near-ultraviolet lines at 2973, 3346 and 3426 Å transitions among the 3 P 0, 1, 2 , 1 D 2 , 1 S 0 levels are described. Maxwellian-averaged collision strengths are tabulated for all forbidden transitions within the ground configuration. While some significant differences are found for both the far infrared and the optical transitions compared to previous results, computed line emissivity ratios are in good agreement, but change rapidly in the low temperature range T e  〈 10 000 K. An analysis of the 14/24 μm ratio in low-energy-density (LED) plasma conditions reveals considerable variation; the effective rate coefficient may be dominated by the very low energy behaviour rather than the Maxwellian-averaged collision strengths. Computed values suggest a possible solution to the anomalous mid-IR ratios found to be lower than theoretical limits observed from planetary nebulae and Seyfert galaxies. While such LED conditions may be present in infrared sources, they might be inconsistent with photoionization equilibrium models.

Description: Despite the shallow convective envelopes of Scuti pulsators, solar-like oscillations are theoretically predicted to be excited in those stars as well. To search for such stochastic oscillations, we organized a spectroscopic multisite campaign for the bright, metal-rich Sct star Puppis. We obtained a total of 2763 high-resolution spectra using four telescopes. We discuss the reduction and analysis with the iodine cell technique, developed for searching low-amplitude radial velocity variations, in the presence of high-amplitude variability. Furthermore, we have determined the angular diameter of Puppis to be 1.68 ± 0.03 mas, translating into a radius of 3.52 ± 0.07 R . Using this value, the frequency of maximum power of possible solar-like oscillations is expected at ~43 ± 2 c d –1 (498 ± 23 μHz). The dominant Scuti-type pulsation mode of Puppis is known to be the radial fundamental mode which allows us to determine the mean density of the star, and therefore an expected large frequency separation of 2.73 c d –1 (31.6 μHz). We conclude that (1) the radial velocity amplitudes of the Scuti pulsations are different for different spectral lines; (2) we can exclude solar-like oscillations to be present in Puppis with an amplitude per radial mode larger than 0.5 m s –1 .

Description: We present an analytic model for bolometric light curves which are powered by the interaction between supernova ejecta and a dense circumstellar medium. This model is aimed at modelling Type IIn supernovae to determine the properties of their supernova ejecta and circumstellar medium. Our model is not restricted to the case of steady mass loss and can be applied broadly. We only consider the case in which the optical depth of the unshocked circumstellar medium is not high enough to affect the light curves. We derive the luminosity evolution based on an analytic solution for the evolution of a dense shell created by the interaction. We compare our model bolometric light curves to observed bolometric light curves of three Type IIn supernovae (2005ip, 2006jd, 2010jl) and show that our model can constrain their supernova ejecta and circumstellar medium properties. Our analytic model is supported by numerical light curves from the same initial conditions.

Description: The ever increasing size and complexity of data coming from simulations of cosmic structure formation demand equally sophisticated tools for their analysis. During the past decade, the art of object finding in these simulations has hence developed into an important discipline itself. A multitude of codes based upon a huge variety of methods and techniques have been spawned yet the question remained as to whether or not they will provide the same (physical) information about the structures of interest. Here we summarize and extent previous work of the ‘halo finder comparison project’: we investigate in detail the (possible) origin of any deviations across finders. To this extent, we decipher and discuss differences in halo-finding methods, clearly separating them from the disparity in definitions of halo properties. We observe that different codes not only find different numbers of objects leading to a scatter of up to 20 per cent in the halo mass and V max function, but also that the particulars of those objects that are identified by all finders differ. The strength of the variation, however, depends on the property studied, e.g. the scatter in position, bulk velocity, mass and the peak value of the rotation curve is practically below a few per cent, whereas derived quantities such as spin and shape show larger deviations. Our study indicates that the prime contribution to differences in halo properties across codes stems from the distinct particle collection methods and – to a minor extent – the particular aspects of how the procedure for removing unbound particles is implemented. We close with a discussion of the relevance and implications of the scatter across different codes for other fields such as semi-analytical galaxy formation models, gravitational lensing and observables in general.

Description: The well-established Type Ia remnant of Tycho's supernova (SN 1572) reveals discrepant ambient medium-density estimates based on either the measured dynamics or the X-ray emission properties. This discrepancy can potentially be solved by assuming that the supernova remnant (SNR) shock initially moved through a stellar wind bubble, but is currently evolving in the uniform interstellar medium with a relatively low density. We investigate this scenario by combining hydrodynamical simulations of the wind-loss phase and the SNR evolution with a coupled X-ray emission model, which includes non-equilibrium ionization. For the explosion models we use the well-known W7 deflagration model and the delayed detonation model that was previously shown to provide good fits to the X-ray emission of Tycho's SNR. Our simulations confirm that a uniform ambient density cannot simultaneously reproduce the dynamical and X-ray emission properties of Tycho. In contrast, models that considered that the remnant was evolving in a dense, but small, wind bubble reproduce reasonably well both the measured X-ray emission spectrum and the expansion parameter of Tycho's SNR. Finally, we discuss possible mass-loss scenarios in the context of single- and double-degenerate models which possibly could form such a small dense wind bubble.

Description: We present a numerical study of the evolution of molecular clouds, from their formation by converging flows in the warm interstellar medium, to their destruction by the ionizing feedback of the massive stars they form. We improve with respect to our previous simulations by including a different stellar-particle formation algorithm, which allows them to have masses corresponding to single stars rather than to small clusters, and with a mass distribution following a near-Salpeter stellar initial mass function. We also employ a simplified radiative-transfer algorithm that allows the stellar particles to feedback on the medium at a rate that depends on their mass and the local density. Our results are as follows: (a) contrary to the results from our previous study, where all stellar particles injected energy at a rate corresponding to a star of ~10 M , the dense gas is now completely evacuated from 10 pc regions around the stars within 10–20 Myr, suggesting that this feat is accomplished essentially by the most massive stars. (b) At the scale of the whole numerical simulations, the dense gas mass is reduced by up to an order of magnitude, although star formation (SF) never shuts off completely, indicating that the feedback terminates SF locally, but new SF events continue to occur elsewhere in the clouds. (c) The SF efficiency (SFE) is maintained globally at the ~10 per cent level, although locally, the cloud with largest degree of focusing of its accretion flow reaches SFE ~30 per cent. (d) The virial parameter of the clouds approaches unity before the stellar feedback begins to dominate the dynamics, becoming much larger once feedback dominates, suggesting that clouds become unbound as a consequence of the stellar feedback, rather than unboundness being the cause of a low SFE. (e) The erosion of the filaments that feed the star-forming clumps produces chains of isolated dense blobs reminiscent of those observed in the vicinity of the dark globule B68.

Description: We present a detailed analysis of absorption systems along the line of sight towards QSO PKS 0237–233 using a high-resolution spectrum of signal-to-noise ratio ~60–80 obtained with the Ultraviolet and Visual Echelle Spectrograph mounted on the Very Large Telescope (VLT/UVES). This line of sight is known to show a remarkable overdensity of C iv systems that has been interpreted as revealing the presence of a supercluster of galaxies. A detailed analysis of each of these absorption systems is presented. In particular, for the z abs  = 1.6359 (with two components of log N H I [cm –2 ] = 18.45, 19.05) and z abs  = 1.6720 (log N H I  = 19.78) sub-damped Lyα systems (sub-DLAs), we measure accurate abundances (resp. [O/H] = –1.63 ± 0.07 and [Zn/H] = –0.57 ± 0.05 relative to solar). While the depletion of refractory elements on to dust grains in both sub-DLAs is not noteworthy, photoionization models show that ionization effects are important in a part of the absorbing gas of the sub-DLA at z abs  = 1.6359 (H i is 95 per cent ionized) and in a part of the gas of the sub-DLA at z abs  = 1.6720. The C iv clustering properties along the line of sight is studied in order to investigate the nature of the observed overdensity. We conclude that despite the unusually high number of C iv systems detected along the line of sight, there is no compelling evidence for the presence of a single unusual overdensity and that the situation is consistent with chance coincidence.

Description: We present a statistically optimal and model-independent method to extract the pressure profile of hot gas in the intracluster medium (ICM). Using the thermal Sunyaev–Zeldovich effect, we constrain the mean pressure profile of the ICM by appropriately considering all primary cosmic microwave background (CMB) and instrumental noise correlations, while using the maximum resolution and sensitivity of all frequency channels. As a first application, we analyse CMB maps of Wilkinson Microwave Anisotropy Probe 9-year data through a study of the Meta-Catalogue of X-ray Detected Clusters of Galaxies. We constrain the universal pressure profile out to 4 R 500 with 15 confidence, though our measurements are only significant out to R 200 . Using a temperature profile constrained from X-ray observations, we measure the mean gas mass fraction out to R 200 . Within statistical and systematic uncertainties, our constraints are compatible with the cosmic baryon fraction and the expected gas fraction in haloes. While Planck multifrequency CMB data are expected to reduce statistical uncertainties by a factor of ~20, we argue that systematic errors in determining mass of clusters dominate the uncertainty in gas mass fraction measurements at the level of ~20 per cent.

Description: In the present work we report theoretical Stark widths and shifts calculated using the Griem semi-empirical approach, corresponding to 237 spectral lines of Mg iii . Data are presented for an electron density of 10 17 cm –3 and temperatures T  = 0.5–10.0 (10 4 K). The matrix elements used in these calculations have been determined from 23 configurations of Mg iii : 2s 2 2p 6 , 2s 2 2p 5 3p, 2s 2 2p 5 4p, 2s 2 2p 5 4f and 2s 2 2p 5 5f for even parity and 2s 2 2p 5 n s ( n  = 3–6), 2s 2 2p 5 n d ( n  = 3–9), 2s 2 2p 5 5g and 2s2p 6 n p ( n  = 3–8) for odd parity. For the intermediate coupling (IC) calculations, we use the standard method of least-squares fitting from experimental energy levels by means of the Cowan computer code. Also, in order to test the matrix elements used in our calculations, we present calculated values of 70 transition probabilities of Mg iii spectral lines and 14 calculated values of radiative lifetimes of Mg iii levels. There is good agreement between our calculations and experimental radiative lifetimes. Spectral lines of Mg iii are relevant in astrophysics and also play an important role in the spectral analysis of laboratory plasma. Theoretical trends of the Stark broadening parameter versus the temperature for relevant lines are presented. No values of Stark parameters can be found in the bibliography.

Description: We present chemical abundance measurements from high-resolution observations of five sub-damped Lyman α absorbers (sub-DLAs) at 1.7 〈  z  〈 2.4 observed with the Magellan Inamori Kyocera Echelle (MIKE) spectrograph on the 6.5-m Magellan II (Clay) telescope. Lines of Zn ii , Mg i , Mg ii , Al ii , Al iii , S ii , Si ii , Si iv , C ii , C ii *, C iv , Ni ii , Mn ii and Fe ii were detected and column densities were determined. The metallicity of the absorbing gas, inferred from the nearly undepleted element Zn, is in the range of 〈–0.95 to +0.25 dex for the five absorbers in our sample, with three of the systems being near-solar or supersolar. We also investigate the effect of ionization on the observed abundances using photoionization modelling. Combining our data with other sub-DLA and DLA data from the literature, we report the most complete existing determination of the metallicity versus redshift relation for sub-DLAs and DLAs. We confirm the suggestion from previous investigations that sub-DLAs are, on average, more metal rich than DLAs and may evolve faster. We also discuss relative abundances and abundance ratios in these absorbers. The more metal-rich systems show significant dust depletion levels, as suggested by the ratios [Zn/Cr] and [Zn/Fe]. For the majority of the systems in our sample, the [Mn/Fe] versus [Zn/H] trend is consistent with that seen previously for lower redshift sub-DLAs. We also measure the velocity width values for the sub-DLAs in our sample from unsaturated absorption lines of Fe ii 2344, 2374, 2600 Å, and examine where these systems lie in a plot of metallicity versus velocity dispersion. Finally, we examine cooling rate versus H i column density in these sub-DLAs, and compare this with the data from DLAs and the Milky Way interstellar medium. We find that most of the systems in our sample show higher cooling rate values compared to those seen in the DLAs.

Description: Rate coefficients for spontaneous and stimulated radiative association of the He $_{2}^{+}$ molecular ion on the spin-quartet manifold are presented as functions of temperature considering the association with rotational-vibrational states of the lowest quartet electronic states $b^{4}\Sigma ^{+}_{u}$ and $c^{4}\Sigma ^{+}_{g}$ from the continuum states of the low-lying excited quartet states. The rate coefficients are obtained from the cross sections for radiative association, which are calculated by solving the Schrödinger equations for bound and continuum states supported by the corresponding Born–Oppenheimer potential energy curves. The rate coefficients for radiative association to the b state are several orders of magnitude larger than for radiative association to the c state. For all considered temperatures the spontaneous $1^{4}\Pi _{g} \rightarrow b^{4}\Sigma ^{+}_{u}$ process is dominant. Stimulation of the radiative association by blackbody radiation has a significant influence only on the $c^{4}\Sigma ^{+}_{g} \rightarrow b^{4}\Sigma ^{+}_{u}$ process at temperatures below 1000 K.

Description: The Uranian satellite Miranda presents a high inclination (4 $_{.}^{\circ}$ 338) and evidence of resurfacing. For the past 20 years it has been accepted that this inclination is due to the past trapping into the 3:1 resonance with Umbriel. These last years there is a renewal of interest for the Uranian system since the Hubble Space Telescope permitted the detection of an inner system of rings and small embedded satellites, their dynamics being of course ruled by the main satellites. For this reason, we here propose to revisit the long-term dynamics of Miranda, using modern tools like intensive computing facilities and new chaos indicators [Mean Exponential Growth factor of Nearby Orbits (MEGNO) and frequency map analysis]. As in the previous studies, we find the resonance responsible for the inclination of Miranda and the secondary resonances associated, likely to have stopped the rise of Miranda's inclination at 4 $_{.}^{\circ}$ 5, identify with the frequency analysis tool the libration arguments of the secondary resonances involved, and show in particular that capture into a 3:1 secondary resonance and subsequent capture into a 2:1 secondary resonance may have disrupted the primary resonance with an inclination of Miranda of 4 $_{.}^{\circ}$ 395.

Description: We have developed a new screening methodology for identifying all genes that control the expression of a target gene through genetic or metabolic interactions. The screen combines mutant libraries with luciferase reporter constructs, whose expression can be monitored in vivo and over time in different environmental conditions. We apply the method to identify the genes that control the expression of the gene acs , encoding the acetyl coenzyme A synthetase, in Escherichia coli . We confirm most of the known genetic regulators, including CRP–cAMP, IHF and components of the phosphotransferase system. In addition, we identify new regulatory interactions, many of which involve metabolic intermediates or metabolic sensing, such as the genes pgi, pfkA , sucB and lpdA , encoding enzymes in glycolysis and the TCA cycle. Some of these novel interactions were validated by quantitative reverse transcriptase-polymerase chain reaction. More generally, we observe that a large number of mutants directly or indirectly influence acs expression, an effect confirmed for a second promoter, sdhC . The method is applicable to any promoter fused to a luminescent reporter gene in combination with a deletion mutant library.

Description: Tandem repeats (TRs) are often present in proteins with crucial functions, responsible for resistance, pathogenicity and associated with infectious or neurodegenerative diseases. This motivates numerous studies of TRs and their evolution, requiring accurate multiple sequence alignment. TRs may be lost or inserted at any position of a TR region by replication slippage or recombination, but current methods assume fixed unit boundaries, and yet are of high complexity. We present a new global graph-based alignment method that does not restrict TR unit indels by unit boundaries. TR indels are modeled separately and penalized using the phylogeny-aware alignment algorithm. This ensures enhanced accuracy of reconstructed alignments, disentangling TRs and measuring indel events and rates in a biologically meaningful way. Our method detects not only duplication events but also all changes in TR regions owing to recombination, strand slippage and other events inserting or deleting TR units. We evaluate our method by simulation incorporating TR evolution, by either sampling TRs from a profile hidden Markov model or by mimicking strand slippage with duplications. The new method is illustrated on a family of type III effectors, a pathogenicity determinant in agriculturally important bacteria Ralstonia solanacearum. We show that TR indel rate variation contributes to the diversification of this protein family.

Description: A renewed interest in non-coding RNA (ncRNA) has led to the discovery of novel RNA species and post-transcriptional ribonucleoside modifications, and an emerging appreciation for the role of ncRNA in RNA epigenetics. Although much can be learned by amplification-based analysis of ncRNA sequence and quantity, there is a significant need for direct analysis of RNA, which has led to numerous methods for purification of specific ncRNA molecules. However, no single method allows purification of the full range of cellular ncRNA species. To this end, we developed a multidimensional chromatographic platform to resolve, isolate and quantify all canonical ncRNAs in a single sample of cells or tissue, as well as novel ncRNA species. The applicability of the platform is demonstrated in analyses of ncRNA from bacteria, human cells and plasmodium-infected reticulocytes, as well as a viral RNA genome. Among the many potential applications of this platform are a system-level analysis of the dozens of modified ribonucleosides in ncRNA, characterization of novel long ncRNA species, enhanced detection of rare transcript variants and analysis of viral genomes.

Description: The synthesis of protein from messenger RNA during translation is a highly dynamic process that plays a key role in controlling the efficiency and fidelity of genome-wide protein expression. The availability of aminoacylated transfer RNA (tRNA) is a major factor influencing the speed of ribosomal movement, which depending on codon choices, varies considerably along a transcript. Furthermore, it has been shown experimentally that tRNA availability can vary significantly under different growth and stress conditions, offering the cell a way to adapt translational dynamics across the genome. Existing models of translation have neglected fluctuations of tRNA pools, instead assuming fixed tRNA availabilities over time. This has lead to an incomplete understanding of this process. Here, we show for the entire Escherichia coli genome how and to what extent translational speed profiles, which capture local aspects of translational elongation, respond to measured shifts in tRNA availability. We find that translational profiles across the genome are affected to differing degrees, with genes that are essential or related to fundamental processes such as translation, being more robust than those linked to regulation. Furthermore, we reveal how fluctuating tRNA availability influences profiles of specific sequences known to play a significant role in translational control of gene expression.

Description: Central to Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-Cas systems are repeated RNA sequences that serve as Cas-protein–binding templates. Classification is based on the architectural composition of associated Cas proteins, considering repeat evolution is essential to complete the picture. We compiled the largest data set of CRISPRs to date, performed comprehensive, independent clustering analyses and identified a novel set of 40 conserved sequence families and 33 potential structure motifs for Cas-endoribonucleases with some distinct conservation patterns. Evolutionary relationships are presented as a hierarchical map of sequence and structure similarities for both a quick and detailed insight into the diversity of CRISPR-Cas systems. In a comparison with Cas-subtypes, I-C, I-E, I-F and type II were strongly coupled and the remaining type I and type III subtypes were loosely coupled to repeat and Cas1 evolution, respectively. Subtypes with a strong link to CRISPR evolution were almost exclusive to bacteria; nevertheless, we identified rare examples of potential horizontal transfer of I-C and I-E systems into archaeal organisms. Our easy-to-use web server provides an automated assignment of newly sequenced CRISPRs to our classification system and enables more informed choices on future hypotheses in CRISPR-Cas research: http://rna.informatik.uni-freiburg.de/CRISPRmap .

Description: Escherichia coli Exonuclease IX (ExoIX), encoded by the xni gene, was the first identified member of a novel subfamily of ubiquitous flap endonucleases (FENs), which possess only one of the two catalytic metal-binding sites characteristic of other FENs. We have solved the first structure of one of these enzymes, that of ExoIX itself, at high resolution in DNA-bound and DNA-free forms. In the enzyme–DNA cocrystal, the single catalytic site binds two magnesium ions. The structures also reveal a binding site in the C-terminal domain where a potassium ion is directly coordinated by five main chain carbonyl groups, and we show this site is essential for DNA binding. This site resembles structurally and functionally the potassium sites in the human FEN1 and exonuclease 1 enzymes. Fluorescence anisotropy measurements and the crystal structures of the ExoIX:DNA complexes show that this potassium ion interacts directly with a phosphate diester in the substrate DNA.

Description: One of the obstacles hindering a better understanding of cancer is its heterogeneity. However, computational approaches to model cancer heterogeneity have lagged behind. To bridge this gap, we have developed a new probabilistic approach that models individual cancer cases as mixtures of subtypes. Our approach can be seen as a meta-model that summarizes the results of a large number of alternative models. It does not assume predefined subtypes nor does it assume that such subtypes have to be sharply defined. Instead given a measure of phenotypic similarity between patients and a list of potential explanatory features, such as mutations, copy number variation, microRNA levels, etc., it explains phenotypic similarities with the help of these features. We applied our approach to Glioblastoma Multiforme (GBM). The resulting model Prob_GBM, not only correctly inferred known relationships but also identified new properties underlining phenotypic similarities. The proposed probabilistic framework can be applied to model relations between similarity of gene expression and a broad spectrum of potential genetic causes.

Description: Estrogen regulates over a thousand genes, with an equal number of them being induced or repressed. The distinct mechanisms underlying these dual transcriptional effects remain largely unknown. We derived comprehensive views of the transcription machineries assembled at estrogen-responsive genes through integrating multiple types of genomic data. In the absence of estrogen, the majority of genes formed higher-order chromatin structures, including DNA loops tethered to protein complexes involving RNA polymerase II (Pol II), estrogen receptor alpha (ERα) and ERα-pioneer factors. Genes to be ‘repressed’ by estrogen showed active transcription at promoters and throughout the gene bodies; genes to be ‘induced’ exhibited active transcription initiation at promoters, but with transcription paused in gene bodies. In the presence of estrogen, the majority of estrogen-induced genes retained the original higher-order chromatin structures, whereas most estrogen-repressed genes underwent a chromatin reconfiguration. For estrogen-induced genes, estrogen enhances transcription elongation, potentially through recruitment of co-activators or release of co-repressors with unique roles in elongation. For estrogen-repressed genes, estrogen treatment leads to chromatin structure reconfiguration, thereby disrupting the originally transcription-efficient chromatin structures. Our in silico studies have shown that estrogen regulates gene expression, at least in part, through modifying previously assembled higher-order complexes, rather than by facilitating de novo assembly of machineries.

Description: The mineralocorticoid receptor (MR) is a ligand-induced transcription factor belonging to the steroid receptor family and involved in water-electrolyte homeostasis, blood pressure regulation, inflammation and fibrosis in the renocardiovascular system. The MR shares a common hormone-response-element with the glucocorticoid receptor but nevertheless elicits MR-specific effects including enhanced epidermal growth factor receptor (EGFR) expression via unknown mechanisms. The EGFR is a receptor tyrosine kinase that leads to activation of MAP kinases, but that can also function as a signal transducer for other signaling pathways. In the present study, we mechanistically investigate the interaction between a newly discovered MR- but not glucocorticoid receptor- responsive-element (=MRE1) of the EGFR promoter, specificity protein 1 (SP1) and MR to gain general insights into MR-specificity. Biological relevance of the interaction for EGFR expression and consequently for different signaling pathways in general is demonstrated in human, rat and murine vascular smooth muscle cells and cells of EGFR knockout mice. A genome-wide promoter search for identical binding regions followed by quantitative PCR validation suggests that the identified MR-SP1–MRE1 interaction might be applicable to other genes. Overall, a novel principle of MR-specific gene expression is explored that applies to the pathophysiologically relevant expression of the EGFR and potentially also to other genes.

Description: Selective inhibitory crosstalk has been known to occur within the signaling pathways of the dioxin (AhR) and estrogen (ERα) receptors. More specifically, ERα represses a cytochrome P450-encoding gene ( CYP1A1 ) that converts cellular estradiol into a metabolite that inhibits the cell cycle, while it has no effect on a P450-encoding gene ( CYP1B1 ) that converts estrodiol into a genotoxic product. Here we show that ERα represses CYP1A1 by targeting the Dnmt3B DNA methyltransferase and concomitant DNA methylation of the promoter. We also find that histone H2A.Z can positively contribute to CYP1A1 gene expression, and its presence at that gene is inversely correlated with DNA methylation. Taken together, our results provide a framework for how ERα can repress transcription, and how that impinges on the production of an enzyme that generates genotoxic estradiol metabolites, and potential breast cancer progression. Finally, our results reveal a new mechanism for how H2A.Z can positively influence gene expression, which is by potentially competing with DNA methylation events in breast cancer cells.

Description: TFIIIB and TFIIIC are multi-subunit factors required for transcription by RNA polymerase III. We present a genome-wide high-resolution footprint map of TFIIIB–TFIIIC complexes in Saccharomyces cerevisiae , obtained by paired-end sequencing of micrococcal nuclease-resistant DNA. On tRNA genes, TFIIIB and TFIIIC form stable complexes with the same distinctive occupancy pattern but in mirror image, termed ‘bootprints’. Global analysis reveals that the TFIIIB–TFIIIC transcription complex exhibits remarkable structural elasticity: tRNA genes vary significantly in length but remain protected by TFIIIC. Introns, when present, are markedly less protected. The RNA polymerase III transcription terminator is flexibly accommodated within the transcription complex and, unexpectedly, plays a major structural role by delimiting its 3'-boundary. The ETC sites, where TFIIIC binds without TFIIIB, exhibit different bootprints, suggesting that TFIIIC forms complexes involving other factors. We confirm six ETC sites and report a new site ( ETC10 ). Surprisingly, TFIIIC, but not TFIIIB, interacts with some centromeric nucleosomes, suggesting that interactions between TFIIIC and the centromere may be important in the 3D organization of the nucleus.

Description: The process of DNA mismatch repair is initiated when MutS recognizes mismatched DNA bases and starts the repair cascade. The Escherichia coli MutS protein exists in an equilibrium between dimers and tetramers, which has compromised biophysical analysis. To uncouple these states, we have generated stable dimers and tetramers, respectively. These proteins allowed kinetic analysis of DNA recognition and structural analysis of the full-length protein by X-ray crystallography and small angle X-ray scattering. Our structural data reveal that the tetramerization domains are flexible with respect to the body of the protein, resulting in mostly extended structures. Tetrameric MutS has a slow dissociation from DNA, which can be due to occasional bending over and binding DNA in its two binding sites. In contrast, the dimer dissociation is faster, primarily dependent on a combination of the type of mismatch and the flanking sequence. In the presence of ATP, we could distinguish two kinetic groups: DNA sequences where MutS forms sliding clamps and those where sliding clamps are not formed efficiently. Interestingly, this inability to undergo a conformational change rather than mismatch affinity is correlated with mismatch repair.

Description: Phosphorylation of histone H4 serine 47 (H4S47ph) is catalyzed by Pak2, a member of the p21-activated serine/threonine protein kinase (Pak) family and regulates the deposition of histone variant H3.3. However, the phosphatase(s) involved in the regulation of H4S47ph levels was unknown. Here, we show that three phosphatases (PP1α, PP1β and Wip1) regulate H4S47ph levels and H3.3 deposition. Depletion of each of the three phosphatases results in increased H4S47ph levels. Moreover, PP1α, PP1β and Wip1 bind H3-H4 in vitro and in vivo , whereas only PP1α and PP1β, but not Wip1, interact with Pak2 in vivo . These results suggest that PP1α, PP1β and Wip1 regulate the levels of H4S47ph through directly acting on H4S47ph, with PP1α and PP1β also likely regulating the activity of Pak2. Finally, depletion of PP1α, PP1β and Wip1 leads to increased H3.3 occupancy at candidate genes tested, elevated H3.3 deposition and enhanced association of H3.3 with its chaperones HIRA and Daxx. These results reveal a novel role of three phosphatases in chromatin dynamics in mammalian cells.

Description: Previously we identified Rrp1 and Rrp2 as two proteins required for the Sfr1/Swi5-dependent branch of homologous recombination (HR) in Schizosaccharomyces pombe . Here we use a yeast two-hybrid approach to demonstrate that Rrp1 and Rrp2 can interact with each other and with Swi5, an HR mediator protein. Rrp1 and Rrp2 form co-localizing methyl methanesulphonate–induced foci in nuclei, further suggesting they function as a complex. To place the Rrp1/2 proteins more accurately within HR sub-pathways, we carried out extensive epistasis analysis between mutants defining Rrp1/2, Rad51 (recombinase), Swi5 and Rad57 (HR-mediators) plus the anti-recombinogenic helicases Srs2 and Rqh1. We confirm that Rrp1 and Rrp2 act together with Srs2 and Swi5 and independently of Rad57 and show that Rqh1 also acts independently of Rrp1/2. Mutants devoid of Srs2 are characterized by elevated recombination frequency with a concomitant increase in the percentage of conversion-type recombinants. Strains devoid of Rrp1 or Rrp2 did not show a change in HR frequency, but the number of conversion-type recombinants was increased, suggesting a possible function for Rrp1/2 with Srs2 in counteracting Rad51 activity. Our data allow us to propose a model placing Rrp1 and Rrp2 functioning together with Swi5 and Srs2 in a synthesis-dependent strand annealing HR repair pathway.

Description: In eukaryotic cells, gene expression is mediated by enhancer activation of RNA polymerase at distant promoters. Recently, distinctions between enhancers and promoters have been blurred by the discovery that enhancers are associated with RNA polymerase and are sites of RNA synthesis. Here, we present an analysis of the insulin-like growth factor 2/H19 muscle enhancer. This enhancer includes a short conserved core element that is organized into chromatin typical of mammalian enhancers, binds tissue-specific transcription factors and functions on its own in vitro to activate promoter transcription. However, in a chromosomal context, this element is not sufficient to activate distant promoters. Instead, enhancer function also requires transcription in cis of a long non-coding RNA, Nctc1 . Thus, the insulin-like growth factor 2/H19 enhancer is an active transcriptional complex whose own transcription is essential to its function.

Description: Evolutionarily conserved RNA secondary structures are a robust indicator of purifying selection and, consequently, molecular function. Evaluating their genome-wide occurrence through comparative genomics has consistently been plagued by high false-positive rates and divergent predictions. We present a novel benchmarking pipeline aimed at calibrating the precision of genome-wide scans for consensus RNA structure prediction. The benchmarking data obtained from two refined structure prediction algorithms, RNAz and SISSIz, were then analyzed to fine-tune the parameters of an optimized workflow for genomic sliding window screens. When applied to consistency-based multiple genome alignments of 35 mammals, our approach confidently identifies 〉4 million evolutionarily constrained RNA structures using a conservative sensitivity threshold that entails historically low false discovery rates for such analyses (5–22%). These predictions comprise 13.6% of the human genome, 88% of which fall outside any known sequence-constrained element, suggesting that a large proportion of the mammalian genome is functional. As an example, our findings identify both known and novel conserved RNA structure motifs in the long noncoding RNA MALAT1 . This study provides an extensive set of functional transcriptomic annotations that will assist researchers in uncovering the precise mechanisms underlying the developmental ontologies of higher eukaryotes.

Description: The p53 core domain binds to response elements (REs) that contain two continuous half-sites as a cooperative tetramer, but how p53 recognizes discontinuous REs is not well understood. Here we describe the crystal structure of the p53 core domain bound to a naturally occurring RE located at the promoter of the Bcl-2-associated X protein (BAX) gene, which contains a one base-pair insertion between the two half-sites. Surprisingly, p53 forms a tetramer on the BAX-RE that is nearly identical to what has been reported on other REs with a 0-bp spacer. Each p53 dimer of the tetramer binds in register to a half-site and maintains the same protein–DNA interactions as previously observed, and the two dimers retain all the protein–protein contacts without undergoing rotation or translation. To accommodate the additional base pair, the DNA is deformed and partially disordered around the spacer region, resulting in an apparent unwinding and compression, such that the interactions between the dimers are maintained. Furthermore, DNA deformation within the p53-bound BAX-RE is confirmed in solution by site-directed spin labeling measurements. Our results provide a structural insight into the mechanism by which p53 binds to discontinuous sites with one base-pair spacer.

Description: RNA-based therapeutic approaches using splice-switching oligonucleotides have been successfully applied to rescue dystrophin in Duchenne muscular dystrophy (DMD) preclinical models and are currently being evaluated in DMD patients. Although the modular structure of dystrophin protein tolerates internal deletions, many mutations that affect nondispensable domains of the protein require further strategies. Among these, trans -splicing technology is particularly attractive, as it allows the replacement of any mutated exon by its normal version as well as introducing missing exons or correcting duplication mutations. We have applied such a strategy in vitro by using cotransfection of pre– trans -splicing molecule (PTM) constructs along with a reporter minigene containing part of the dystrophin gene harboring the stop-codon mutation found in the mdx mouse model of DMD. Optimization of the different functional domains of the PTMs allowed achieving accurate and efficient trans -splicing of up to 30% of the transcript encoded by the cotransfected minigene. Optimized parameters included mRNA stabilization, choice of splice site sequence, inclusion of exon splice enhancers and artificial intronic sequence. Intramuscular delivery of adeno-associated virus vectors expressing PTMs allowed detectable levels of dystrophin in mdx and mdx4Cv , illustrating that a given PTM can be suitable for a variety of mutations.

Description: We give explicit atomic bases of arbitrary coefficient-free cluster algebras of types A and à . This entails showing that the minimal elements of the positive semiring of these cluster algebras form a linear basis over the integers for the cluster algebra.

Description: We prove that strongly F -regular and F -pure singularities satisfy Bertini-type theorems (including in the context of pairs) by building upon a framework of Cumino, Greco and Manaresi (compare with the work of Jouanolou and Spreafico). We also prove that F -injective singularities fail to satisfy even the most basic Bertini-type results.

Description: This is the second of a pair of papers on the Delta-group structure on the braid and mapping class groups of a surface. We obtain a description of the homotopy groups of these Delta-groups and generalize to an arbitrary surface the Berrick–Cohen–Wong–Wu exact sequence relating the Brunnian braid groups of the 2-sphere to its homotopy groups. We prove a similar result for Brunnian mapping class groups.

Description: We construct a geometric realization of the Khovanov–Lauda–Rouquier algebra R associated with a symmetric Borcherds–Cartan matrix A = ( a ij ) i , j I via quiver varieties. As an application, if a ii != 0 for any i I , we prove that there exists a one-to-one correspondence between Kashiwara's lower global basis (or Lusztig's canonical basis) of U A – (g) (respectively, V A ( )) and the set of isomorphism classes of indecomposable projective graded modules over R (respectively, R ).

Description: The purpose of this paper is to study the nature of quasi-invariant measures for finitely generated non-discrete subgroups of Diff ( S 1 ). For this, we apply ideas involving the closure of these groups to find out that the regularity of the measure depends on a ‘measurable version’ of well-known problems concerning stable self-intersection of Cantor sets. As applications, we prove that every d -quasiconformal probability measure for a non-solvable and non-discrete group must be absolutely continuous. Concerning singular quasi-invariant measures, it is also proved that their associated Hausdorff measures must either be zero or of infinite mass, a result contrasting with the case of dynamically defined Cantor sets and also applicable to the examples of singular stationary measures constructed by Kaimanovich and Le Prince. As a further application of our methods, a theorem of rigidity for measurable conjugations between groups as above is obtained.

Description: We study the space of period polynomials associated with modular forms of integral weight for finite-index subgroups of the modular group. For the modular group, this space is endowed with a pairing, corresponding to the Petersson inner product on modular forms via a formula of Haberland, and with an action of Hecke operators, defined algebraically by Zagier. We generalize Haberland's formula to (not necessarily cuspidal) modular forms for finite-index subgroups, and we show that it conceals two stronger formulas. We extend the action of Hecke operators to period polynomials of modular forms, we show that the pairing on period polynomials appearing in Haberland's formula is nondegenerate, and we determine the adjoints of Hecke operators with respect to it. We give a few applications for 1 ( N ): an extension of the Eichler–Shimura isomorphism to the entire space of modular forms; the determination of the relations satisfied by the even and odd parts of period polynomials associated with cusp forms, which are independent of the period relations; and an explicit formula for Fourier coefficients of Hecke eigenforms in terms of their period polynomials, generalizing the Coefficient theorem of Manin.

Description: This study develops a spectral theory of the interior transmission problem (ITP) for heterogeneous and anisotropic elastic solids. The subject is central to the so-called qualitative methods for inverse scattering involving penetrable obstacles. Although simply stated as a coupled pair of elastodynamic wave equations, the ITP for elastic bodies is neither self-adjoint nor elliptic. To help deal with such impediments, earlier studies have established the well-posedness of an elastodynamic ITP under notably restrictive assumptions on the contrast in elastic and mass density parameters between the scatterer and the background solid. Due to lack of self-adjointness of the problem, these analyses were further successful in substantiating the discreteness of the relevant eigenvalue spectrum but not its existence. The aim of this work is to provide a systematic treatment of the ITP for elastic bodies that transcends the limitations of earlier analyses. Considering a broad range of material-contrast configurations, this paper investigates the questions of the solvability of the ITP, the discreteness of its eigenvalues and, for the first time, of the existence of such eigenvalue spectrum. Necessitated by the breadth of material configurations studied, the relevant claims are established via a suite of variational formulations, each customized to meet the needs of a particular subclass of eigenvalue problems.

Description: Rayleigh–Stokes problems have in recent years received much attention due to their importance in physics. In this article, we focus on the variable-order Rayleigh–Stokes problem for a heated generalized second grade fluid with fractional derivative. Implicit and explicit numerical methods are developed to solve the problem. The convergence, stability of the numerical methods and solvability of the implicit numerical method are discussed via Fourier analysis. Moreover, a numerical example is given and the results support the effectiveness of the theoretical analysis.

Description: In this paper, the rigorous linking of exact stochastic models to mean-field approximations is studied. Using a continuous-time Markov chain, we start from the exact formulation of a simple epidemic model on a certain class of networks, including completely connected and regular random graphs, and rigorously derive the well-known mean-field approximation that is usually justified based on biological hypotheses. We propose a unifying framework that incorporates and discusses the details of two existing proofs and we put forward a new ordinary differential equation (ODE)-based proof. The more well-known proof is based on a first-order partial differential equation approximation, while the other, more technical one, uses Martingale and Semigroup theory. We present the main steps of both proofs to investigate their applicability in different modelling contexts and to make these ideas more accessible to a broader group of applied researchers. The main result of the paper is a new ODE-based proof that may serve as a building block to prove similar convergence results for more complex networks. The new proof is based on deriving a countable system of ODEs for the moments of a distribution of interest and proving a perturbation theorem for this infinite system.