ALBERT

Description: The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.

Description: O -GlcNAcylation is an inducible, highly dynamic and reversible post-translational modification, mediated by a unique enzyme named O -linked N -acetyl- d -glucosamine ( O -GlcNAc) transferase (OGT). In response to nutrients, O -GlcNAc levels are differentially regulated on many cellular proteins involved in gene expression, translation, immune reactions, protein degradation, protein–protein interaction, apoptosis and signal transduction. In contrast to eukaryotic cells, little is known about the role of O -GlcNAcylation in the viral life cycle. Here, we show that the overexpression of the OGT reduces the replication efficiency of Kaposi's sarcoma-associated herpesvirus (KSHV) in a dose-dependent manner. In order to investigate the global impact of O -GlcNAcylation in the KSHV life cycle, we systematically analyzed the 85 annotated KSHV-encoded open reading frames for O -GlcNAc modification. For this purpose, an immunoprecipitation (IP) strategy with three different approaches was carried out and the O -GlcNAc signal of the identified proteins was properly controlled for specificity. Out of the 85 KSHV-encoded proteins, 18 proteins were found to be direct targets for O -GlcNAcylation. Selected proteins were further confirmed by mass spectrometry for O -GlcNAc modification. Correlation of the functional annotation and the O -GlcNAc status of KSHV proteins showed that the predominant targets were proteins involved in viral DNA synthesis and replication. These results indicate that O -GlcNAcylation plays a major role in the regulation of KSHV propagation.

Description: Galectins are potent adhesion/growth-regulatory effectors with characteristic expression profiles. Understanding the molecular basis of gene regulation in each case requires detailed information on copy number of genes and sequence(s) of their promoter(s). Our report reveals plasticity in this respect between galectins and species. We here describe occurrence of a two-gene constellation for human galectin (Gal)-7 and define current extent of promoter-sequence divergence. Interestingly, cross-species genome analyses also detected single-copy display. Because the regulatory potential will then be different, extrapolations of expression profiles are precluded between respective species pairs. Gal-4 coding in chromosomal vicinity was found to be confined to one gene, whereas copy-number variation also applied to Gal-9. The example of rat Gal-9 teaches the lesson that the presence of multiple bands in Southern blotting despite a single-copy gene constellation is attributable to two pseudogenes. The documented copy-number variability should thus be taken into consideration when studying regulation of galectin genes, in a species and in comparison between species.

Description: In studying the molecular basis for the potent immune activity of previously described gamma and delta inulin particles and to assist in production of inulin adjuvants under Good Manufacturing Practice, we identified five new inulin isoforms, bringing the total to seven plus the amorphous form. These isoforms comprise the step-wise inulin developmental series amorphous -〉 alpha-1 (AI-1) -〉 alpha-2 (AI-2) -〉 gamma (GI) -〉 delta (DI) -〉 zeta (ZI) -〉 epsilon (EI) -〉 omega (OI) in which each higher isoform can be made either by precipitating dissolved inulin or by direct conversion from its precursor, both cases using regularly increasing temperatures. At higher temperatures, the shorter inulin polymer chains are released from the particle and so the key difference between isoforms is that each higher isoform comprises longer polymer chains than its precursor. An increasing trend of degree of polymerization is confirmed by end-group analysis using 1 H nuclear magnetic resonance spectroscopy. Inulin isoforms were characterized by the critical temperatures of abrupt phase-shifts (solubilizations or precipitations) in water suspensions. Such (aqueous) "melting" or "freezing" points are diagnostic and occur in strikingly periodic steps reflecting quantal increases in noncovalent bonding strength and increments in average polymer lengths. The (dry) melting points as measured by modulated differential scanning calorimetry similarly increase in regular steps. We conclude that the isoforms differ in repeated increments of a precisely repeating structural element. Each isoform has a different spectrum of biological activities and we show the higher inulin isoforms to be more potent alternative complement pathway activators.

Description: The methylotrophic yeast, Pichia pastoris , is an important organism used for the production of therapeutic proteins. Previously, we have reported the glycoengineering of this organism to produce human-like N -linked glycans but up to now no one has addressed engineering the O -linked glycosylation pathway. Typically, O -linked glycans produced by wild-type P. pastoris are linear chains of four to five α-linked mannose residues, which may be capped with β- or phospho-mannose. Previous genetic engineering of the N-linked glycosylation pathway of P. pastoris has eliminated both of these two latter modifications, resulting in O -linked glycans which are linear α-linked mannose structures. Here, we describe a method for the co-expression of an α-1,2-mannosidase, which reduces these glycans to primarily a single O -linked mannose residue. In doing so, we have reduced the potential of these glycans to interact with carbohydrate-binding proteins, such as dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin. Furthermore, the introduction of the enzyme protein- O -linked-mannose β-1,2- N -acetylglucosaminyltransferase 1, resulted in the capping of the single O -linked mannose residues with N -acetylglucosamine. Subsequently, this glycoform was extended into human-like sialylated glycans, similar in structure to α-dystroglycan-type glycoforms. As such, this represents the first example of sialylated O -linked glycans being produced in yeast and extends the utility of the P. pastoris production platform beyond N -linked glycosylated biotherapeutics to include molecules possessing O -linked glycans.

Description: Neurons and other cells require intracellular transport of essential components for viability and function. Previous work has shown that while net amyloid precursor protein (APP) transport is generally anterograde, individual vesicles containing APP move bi-directionally. This discrepancy highlights our poor understanding of the in vivo regulation of APP-vesicle transport. Here, we show that reduction of presenilin (PS) or suppression of gamma-secretase activity substantially increases anterograde and retrograde velocities for APP vesicles. Strikingly, PS deficiency has no effect on an unrelated cargo vesicle class containing synaptotagmin, which is powered by a different kinesin motor. Increased velocities caused by PS or gamma-secretase reduction require functional kinesin-1 and dynein motors. Together, our findings suggest that a normal function of PS is to repress kinesin-1 and dynein motor activity during axonal transport of APP vesicles. Furthermore, our data suggest that axonal transport defects induced by loss of PS-mediated regulatory effects on APP-vesicle motility could be a major cause of neuronal and synaptic defects observed in Alzheimer's Disease (AD) pathogenesis. Thus, perturbations of APP/PS transport could contribute to early neuropathology observed in AD, and highlight a potential novel therapeutic pathway for early intervention, prior to neuronal loss and clinical manifestation of disease.

Description: With age, muscle mass and integrity are progressively lost leaving the elderly frail, weak and unable to independently care for themselves. Defined as sarcopenia, this age-related muscle atrophy appears to be multifactorial but its definite cause is still unknown. Mitochondrial dysfunction has been implicated in this process. Using a novel transgenic mouse model of mitochondrial DNA (mtDNA) double-strand breaks (DSBs) that presents a premature aging-like phenotype, we studied the role of mtDNA damage in muscle wasting. We caused DSBs in mtDNA of adult mice using a ubiquitously expressed mitochondrial-targeted endonuclease, mito- Pst I. We found that a short, transient systemic mtDNA damage led to muscle wasting and a decline in locomotor activity later in life. We found a significant decline in muscle satellite cells, which decreases the muscle's capacity to regenerate and repair during aging. This phenotype was associated with impairment in acetylcholinesterase (AChE) activity and assembly at the neuromuscular junction (NMJ), also associated with muscle aging. Our data suggests that systemic mitochondrial dysfunction plays important roles in age-related muscle wasting by preferentially affecting the myosatellite cell pool.

Description: Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation.

Description: We present a methodology for infrasonic remote sensing of winds in the stratosphere that does not require discrete ground-truth events. Our method uses measured time delays between arrays of sensors to provide group velocities (referred to here as celerities) and then minimizes the difference between observed and predicted celerities by perturbing an initial atmospheric specification. Because we focus on interarray propagation effects, it is not necessary to simulate the full propagation path from source to receiver. This feature allows us to use a relatively simple forward model that is applicable over short-regional distances. By focusing on stratospheric returns, we show that our non-linear inversion scheme converges much better if the starting model contains a strong stratospheric duct. Using the Horizontal Wind Model (HWM)/Mass Spectrometer Incoherent Scatter (MSISE) empirical climatology as a starting model, we demonstrate that the inversion scheme is robust to large uncertainties in backazimuth, but that uncertainties in the measured trace velocity and celerity require the use of prior constraints to ensure suitable convergence. The inversion of synthetic data, using realistic estimates of measurement error, shows that our scheme will nevertheless improve upon a starting model under most scenarios. The inversion scheme is applied to infrasound data recorded from a large event on 2010 December 25, which is presumed to be a bolide, using data from a nine-element infrasound network in Utah. We show that our recorded data require a stronger zonal wind speed in the stratosphere than is present in the HWM profile, and are more consistent with the Ground-to-Space (G2S) profile.

Description: Coda- Q is a stochastic parameter reflecting the heterogeneities of medium that seismic waves travel through. We confirmed that coda- Q would vary with the stress loaded to an elastic medium using numerical simulations of seismic wave propagation. When the stress is loaded, cracks in the crust could either close or newly open. The closure and opening of the cracks are not random but depending on the magnitude and the direction of the stress and the crack aspect ratio. The cracks in the medium after loading stress could be aligned in a specific orientation, and elastic wave velocity field would become anisotropic due to the alignment of specific crack orientations. Elastic wave velocity is in general faster along the direction corresponding with the crack orientation while slower along the perpendicular direction. In the numerical simulation, the effect of anisotropy in elastic wave velocity field due to the selective closure and opening of the cracks is calculated using a 2-D finite difference method assuming elastic wave velocity to be a function of the magnitude of loaded stress. The coda- Q calculated from seismic waves simulated for a model varies when the averaged normal stress changes. Our simulation indicated that the sensitivity of coda- Q –1 , that is the reciprocal of the coda- Q , would be 1.0 10 –2 (1.0 MPa –1 ) against the magnitude of the confining pressure and 1.0 10 –3 (1.0 deg –1 ) against the direction of principal stress. We would like to conclude that coda- Q , a stochastic parameter reflecting heterogeneities of subsurface medium, could become a quantitative state indicator of the stress field of the medium where seismic waves propagate through. Spatiotemporal variation of coda- Q reflects change in the stress field in the crust.

Description: How do body-wave traveltimes constrain the Earth's radial (1-D) seismic structure? Existing 1-D seismological models underpin 3-D seismic tomography and earthquake location algorithms. It is therefore crucial to assess the quality of such 1-D models, yet quantifying uncertainties in seismological models is challenging and thus often ignored. Ideally, quality assessment should be an integral part of the inverse method. Our aim in this study is twofold: (i) we show how to solve a general Bayesian non-linear inverse problem and quantify model uncertainties, and (ii) we investigate the constraint on spherically symmetric P -wave velocity ( V P ) structure provided by body-wave traveltimes from the EHB bulletin (phases Pn , P , PP and PKP ). Our approach is based on artificial neural networks, which are very common in pattern recognition problems and can be used to approximate an arbitrary function. We use a Mixture Density Network to obtain 1-D marginal posterior probability density functions (pdfs), which provide a quantitative description of our knowledge on the individual Earth parameters. No linearization or model damping is required, which allows us to infer a model which is constrained purely by the data. We present 1-D marginal posterior pdfs for the 22 V P parameters and seven discontinuity depths in our model. P -wave velocities in the inner core, outer core and lower mantle are resolved well, with standard deviations of ~0.2 to 1 per cent with respect to the mean of the posterior pdfs. The maximum likelihoods of V P are in general similar to the corresponding ak135 values, which lie within one or two standard deviations from the posterior means, thus providing an independent validation of ak135 in this part of the radial model. Conversely, the data contain little or no information on P -wave velocity in the D '' layer, the upper mantle and the homogeneous crustal layers. Further, the data do not constrain the depth of the discontinuities in our model. Using additional phases available in the ISC bulletin, such as PcP , PKKP and the converted phases SP and ScP , may enhance the resolvability of these parameters. Finally, we show how the method can be extended to obtain a posterior pdf for a multidimensional model space. This enables us to investigate correlations between model parameters.

Description: We have developed a network optimization method for regional-scale microseismic monitoring networks and applied it to optimize the densification of the existing seismic network in northeastern Switzerland. The new network will build the backbone of a 10-yr study on the neotectonic activity of this area that will help to better constrain the seismic hazard imposed on nuclear power plants and waste repository sites. This task defined the requirements regarding location precision (0.5 km in epicentre and 2 km in source depth) and detection capability [magnitude of completeness M c  = 1.0 ( M L )]. The goal of the optimization was to find the geometry and size of the network that met these requirements. Existing stations in Switzerland, Germany and Austria were considered in the optimization procedure. We based the optimization on the simulated annealing approach proposed by Hardt & Scherbaum, which aims to minimize the volume of the error ellipsoid of the linearized earthquake location problem ( D -criterion). We have extended their algorithm to: calculate traveltimes of seismic body waves using a finite difference ray tracer and the 3-D velocity model of Switzerland, calculate seismic body-wave amplitudes at arbitrary stations assuming the Brune source model and using scaling and attenuation relations recently derived for Switzerland, and estimate the noise level at arbitrary locations within Switzerland using a first-order ambient seismic noise model based on 14 land-use classes defined by the EU-project CORINE and open GIS data. We calculated optimized geometries for networks with 10–35 added stations and tested the stability of the optimization result by repeated runs with changing initial conditions. Further, we estimated the attainable magnitude of completeness ( M c ) for the different sized optimal networks using the Bayesian Magnitude of Completeness (BMC) method introduced by Mignan et al. The algorithm developed in this study is also applicable to smaller optimization problems, for example, small local monitoring networks. Possible applications are volcano monitoring, the surveillance of induced seismicity associated with geotechnical operations and many more. Our algorithm is especially useful to optimize networks in populated areas with heterogeneous noise conditions and if complex velocity structures or existing stations have to be considered.

Description: Fluid injection in and withdrawal from wells are basic procedures in mining activities and deep resources exploitation, such as oil and gas extraction, permeability enhancement for geothermal exploitation and waste fluid disposal. All of these activities have the potential to induce seismicity, as exemplified by the 2006 Basel earthquake ( M L 3.4). Despite several decades of experience, the mechanisms of induced seismicity are not known in detail, which prevents effective risk assessment and/or mitigation. In this study, we provide an interpretation of induced seismicity based on computation of Coulomb stress changes that result from fluid injection/withdrawal at depth, mainly focused on the interpretation of induced seismicity due to stimulation of a geothermal reservoir. Seismicity is, theoretically, more likely where Coulomb stress changes are larger. For modeling purposes, we simulate the thermodynamic evolution of a system after fluid injection/withdrawal. The associated changes in pressure and temperature are subsequently considered as sources of incremental stress changes, which are then converted to Coulomb stress changes on favourably oriented faults, taking into account the background regional stress. Numerical results are applied to the water injection that was performed to create the fractured reservoir at the enhanced-geothermal-system site, Soultz-sous-Forets (France). Our approach describes well the observed seismicity, and provides an explanation for the different behaviors of a system when fluids are injected or withdrawn.

Description: We report on a broad-band high-resolution attenuation model for the North China Craton and surrounding regions based on regional Lg -wave data. Vertical broad-band waveforms recorded at 39 stations from 176 crustal earthquakes are collected to extract the Lg -wave amplitude spectra between 0.05 and 10.0 Hz. We use the dual-station method to generate a preliminary Q Lg model and use it as the initial model. Then, we combine the dual- and single-station data together to jointly invert the Q Lg distribution and Lg source excitation functions. These inversions are conducted independently at individual frequencies without using any a priori assumption about the frequency dependences in Q Lg and source terms. The maximum spatial resolution is approximately 1° x 1° in well-covered areas for frequencies between 0.05 and 2.0 Hz. The Q Lg image is then used to determine the relationship between the attenuation and different geological structures. Results show an average Q 0 (1 Hz Q Lg ) of 374 for the entire North China Craton with an increasing trend from east to west. Average Q 0 values are 337, 361 and 421 for the east, central and west blocks, respectively. For the surrounding regions, the Eastern Tibetan plateau has a very low Q 0 of 188, while the Northeast China Plate and the Tianshan–Xingmeng fold belts are characterized by high Q 0 values of 506 and 424, respectively. We also investigate regional variations of the Lg attenuation in low-frequency band between 0.2 and 1.0 Hz.

Description: We present a systematic study on the influence of pressure (0.1–600 MPa), temperature (750–1200 °C), carbon dioxide fugacity (log f CO 2  = –4.41 to 3.60) and time (2–12 hr) on the chemical and physical properties of carbonate rock. Our experiments aim to reproduce the conditions at the periphery of magma chamber where carbonate host rock is influenced by, but not readily assimilated by, magma. This permits the investigation of the natural conditions at which circulating fluids/gases promote infiltration reactions typical of metasomatic skarns that can involve large volumes of subvolcanic carbonate basements. Results show that, providing that carbon dioxide is retained in the pore space, decarbonation does not proceed at any magmatic pressure and temperature. However, when the carbon dioxide is free to escape, decarbonation can occur rapidly and is not hindered by a low initial porosity or permeability. Together with carbon dioxide and lime, portlandite, a mineral commonly found in voluminous metasomatic skarns, readily forms during carbonate decomposition. Post-experimental analyses highlight that thermal microcracking, a result of the highly anisotropic thermal expansion of calcite, exerts a greater influence on rock physical properties (porosity, ultrasonic wave velocities and elastic moduli) than decarbonation. Our data suggest that this will be especially true at the margins of dykes or magma bodies, where temperatures can reach up to 1200 °C. However, rock compressive strength is significantly reduced by both thermal cracking and decarbonation, explained by the relative weakness of lime + portlandite compared to calcite, and an increase in grain size with increasing temperature. Metasomatic skarns, whose petrogenetic reactions may involve a few tens of cubic kilometres, could therefore represent an important source of volcanic instability.

Description: The scattering of plane SH waves incident on a circular sectorial canyon is considered. An accurate region-matching technique is applied to derive a rigorous series solution. Appropriate wavefunctions are employed to describe antiplane motions. Judicious basis functions, involving Gegenbauer polynomials, are well utilized to correctly capture the singular behaviour in stress fields near the canyon bottom. The enforcement of matching conditions on the auxiliary boundary leads to the determination of unknown coefficients. Plotted results demonstrate the influence of pertinent parameters on surface and subsurface motions. Both steady-state and transient results are included. The solution technique proposed achieves a considerable reduction in the computational effort, facilitating benchmark computations. The derived series solution enriches the limited list of series solutions presently known for canyon problems related to SH -wave scattering.

Description: We present 3-D models of the P- and S -wave velocity distributions in the crust and uppermost mantle beneath Sicily, Calabria (Southern Italy), and surrounding submerged areas, obtained by tomographic inversion of traveltimes of regional body waves phases. Our method combines double-difference tomographic inversion with a post-processing procedure [Weighted Average Model method (WAM)]. This procedure was applied to a set of models consistent with the experimental data. We tested the ability of the WAM procedure to mitigate the uncertainty associated with the arbitrary nature of the many input parameters required for each inversion. The local reliability and resolution of the obtained models have been assessed through: synthetic tests, experimental tests carried out with independent data sets and unconventional tests based on the analysis of the internal consistency of the P - and S -velocity models. The tomographic images provide a detailed sketch of P- and S- wave velocity anomalies. These clearly show the shape of the Sicilian-Maghrebian belt beneath Sicily and Calabrian Arc at different depths. Low V P and Vs bodies are imaged beneath Stromboli and Marsili volcanoes in the southern Tyrrhenian, whereas high and low seismic velocities alternate beneath the Etna giving inferences on the possible depth of the mantle melting feeding the volcano. In the upper crust, the main sedimentary basins and tectonic features are also well imaged. Finally, tomographic cross sections show the trend of the Moho in the study area, where its depth ranges between 35 and 40 km beneath the Sicilian belt and between 15 and 22 km in the southern Tyrrhenian basin and Ionian Sea.

Description: We used two tracks of ALOS PALSAR images to investigate the focal mechanism and slip distribution of the 2011 March 24, M W 6.8 Burma strike-slip earthquake. Three different SAR techniques, namely conventional interferometry, SAR pixel offsets (SPO) and multiple-aperture InSAR (MAI), were employed to obtain the coseismic surface deformation fields along the ~30 km length of the fault rupture. Along-track measurements from SPO and MAI techniques show a high correlation, and were subsequently used to precisely determine the location and extent of the surface fault trace. The best-fitting fault model geometry derived from an iterative inversion technique suggests that the rupture occurred on a near-vertical sinistral strike-slip fault west of the Nam Ma fault with a strike of 70°. A maximum slip of 4.2 m occurs at a depth of 2.5 km, with significant slip constrained only to the upper 10 km of the crust.

Description: Knowledge of the mantle reflectivity structure is highly dependent on our ability to efficiently extract, and properly interpret, small seismic arrivals. Among the various data types and techniques, long-period SS/PP precursors and high-frequency receiver functions are routinely utilized to increase the confidence of the recovered mantle stratifications at distinct spatial scales. However, low resolution and a complex Fresnel zone are glaring weaknesses of SS precursors, while over-reliance on receiver distribution is a formidable challenge for the analysis of converted waves from oceanic regions. A promising high frequency alternative to receiver functions is P ' P ' precursors, which are capable of resolving mantle structures at vertical and lateral resolution of ~5 and ~200 km, respectively, owing to their spectral content, shallow angle of incidence and near-symmetric Fresnel zones. This study presents a novel processing method for both SS (or PP) and P ' P ' precursors based on deconvolution, stacking, Radon transform and depth migration. A suite of synthetic tests is performed to quantify the fidelity and stability of this method under different data conditions. Our multiresolution survey of the mantle at targeted areas near Nazca-South America subduction zone reveal both olivine and garnet related transitions at depths below 400 km. We attribute a depressed 660 to thermal variations, whereas compositional variations atop the upper-mantle transition zone are needed to explain the diminished or highly complex reflected/scattered signals from the 410 km discontinuity. We also observe prominent P ' P ' reflections within the transition zone, and the anomalous amplitudes near the plate boundary zone indicate a sharp (~10 km thick) transition that likely resonates with the frequency content of P ' P ' precursors. The migration of SS precursors in this study shows no evidence of split 660 reflections, but potential majorite–ilmenite (590–640 km) and ilmenite–perovskite transitions (740–750 km) are identified based on similarly processed high-frequency P ' P ' precursors. Additional findings of severely scattered energy in the lithosphere and distinct lower mantle reflections at ~800 km could be potentially important but require further verifications. Overall, our improved imaging methods and the strong sensitivity of P ' P ' precursors to the existence, depth, sharpness and strength of reflective structures offer significant future promise for the understanding of mantle mineralogy and dynamics.

Description: Time-dependent probabilistic seismic hazard assessment requires a stochastic description of earthquake occurrences. While short-term seismicity models are well-constrained by observations, the recurrences of characteristic on-fault earthquakes are only derived from theoretical considerations, uncertain palaeo-events or proxy data. Despite the involved uncertainties and complexity, simple statistical models for a quasi-period recurrence of on-fault events are implemented in seismic hazard assessments. To test the applicability of statistical models, such as the Brownian relaxation oscillator or the stress release model, we perform a systematic comparison with deterministic simulations based on rate- and state-dependent friction, high-resolution representations of fault systems and quasi-dynamic rupture propagation. For the specific fault network of the Lower Rhine Embayment, Germany, we run both stochastic and deterministic model simulations based on the same fault geometries and stress interactions. Our results indicate that the stochastic simulators are able to reproduce the first-order characteristics of the major earthquakes on isolated faults as well as for coupled faults with moderate stress interactions. However, we find that all tested statistical models fail to reproduce the characteristics of strongly coupled faults, because multisegment rupturing resulting from a spatiotemporally correlated stress field is underestimated in the stochastic simulators. Our results suggest that stochastic models have to be extended by multirupture probability distributions to provide more reliable results.

Description: Stress waves, known as acoustic emissions (AEs), are released by localized inelastic deformation events during the progressive failure of brittle rocks. Although several numerical models have been developed to simulate the deformation and damage processes of rocks, such as non-linear stress–strain behaviour and localization of failure, only a limited number have been capable of providing quantitative information regarding the associated seismicity. Moreover, the majority of these studies have adopted a pseudo-static approach based on elastic strain energy dissipation that completely disregards elastodynamic effects. This paper describes a new AE modelling technique based on the combined finite-discrete element method (FEM/DEM), a numerical tool that simulates material failure by explicitly considering fracture nucleation and propagation in the modelling domain. Given the explicit time integration scheme of the solver, stress wave propagation and the effect of radiated seismic energy can be directly captured. Quasi-dynamic seismic information is extracted from a FEM/DEM model with a newly developed algorithm based on the monitoring of internal variables (e.g. relative displacements and kinetic energy) in proximity to propagating cracks. The AE of a wing crack propagation model based on this algorithm are cross-analysed by traveltime inversion and energy estimation from seismic recordings. Results indicate a good correlation of AE initiation times and locations, and scaling of energies, independently calculated with the two methods. Finally, the modelling technique is validated by simulating a laboratory compression test on a granite sample. The micromechanical parameters of the heterogeneous model are first calibrated to reproduce the macroscopic stress–strain response measured during standard laboratory tests. Subsequently, AE frequency–magnitude statistics, spatial clustering of source locations and the evolution of AE rate are investigated. The distribution of event magnitude tends to decay as power law while the spatial distribution of sources exhibits a fractal character, in agreement with experimental observations. Moreover, the model can capture the decrease of seismic b value associated with the macrorupture of the rock sample and the transition of AE spatial distribution from diffuse, in the pre-peak stage, to strongly localized at the peak and post-peak stages, as reported in a number of published laboratory studies. In future studies, the validated FEM/DEM-AE modelling technique will be used to obtain further insights into the micromechanics of rock failure with potential applications ranging from laboratory-scale microcracking to engineering-scale processes (e.g. excavations within mines, tunnels and caverns, petroleum and geothermal reservoirs) to tectonic earthquakes triggering.

Description: We used strong-motion records from the 2012 May 20 and 29 Emilia-Romagna earthquakes ( M w 6.1 and 5.9, respectively) and four aftershocks with magnitudes ranging between 4.9 and 5.5 to analyse the S -wave spectral amplitude decay with distance and estimate acceleration source functions and site effects. The data set consists of six earthquakes, 44 stations and 248 records with hypocentral distances in the range 10 〈 r  〈 100 km. We rotated the accelerograms to calculate transverse and radial components of the acceleration spectrum. We found non-parametric attenuation functions that describe the spectral amplitude decay of SH and SV waves with distance at 60 different frequencies between 0.1 and 40 Hz. These attenuation functions provide an estimate of the quality factor Q at each frequency analysed. Assuming that geometrical spreading is 1/ r for r  ≤ r x and 1/( r x r ) 0.5 for r  〉 r x with r x  = 60 km and normalizing at 15 km (the recording distance where the attenuation functions start to decay), we find that the average Q for SH waves can be approximated by Q SH  = 82 ± 1 f  1.2±0.02 and by Q SV  = 79 ± 1 f  1.24±0.03 for SV waves in the frequency range 0.10 ≤ f  ≤ 10.7 Hz. At higher frequencies, 11.8 ≤ f  ≤ 40 Hz, the frequency dependence of Q weakens and is approximated by Q SH  = 301 ± 1 f   0.36±0.04 and Q SV  = 384 ± 1 f  0.28±0.04 . These results indicate that the S -wave attenuation is radially isotropic at local distances in the epicentral area. Nevertheless, we used these attenuation parameters separately to correct the radial (with Q SV ) and transverse (with Q SH ) components of the acceleration spectra and to separate source and site effects using a non-parametric spectral inversion scheme. We found that the source function of the main event and the bigger aftershocks show enhanced low frequency radiation between 0.4 and 3.0 Hz. We converted the source functions into far-field source acceleration spectra and interpreted the resulting source spectra in terms of Brune's model. The stress drops obtained range between approximately 0.9 and 2.9 MPa. Although all the recording stations used are located in the Po Plain, the site functions obtained from the spectral inversion show important amplification variability between the sites. We compared these site functions with the average horizontal to vertical spectral ratios calculated for each station, and we found consistent results for most stations.

Description: The tension between the meaning of causality in science and law or public policy is well-known; however, defendants in product liability cases or industries that might be affected by a government regulation may try to convince the factfinder to require evidence of a causal relationship that meets the standards of science. From the perspective of public health, however, people may be exposed unnecessarily to a health risk during the time period between the establishment of reasonably strong evidence of a causal relationship and the overwhelming evidence required for scientific causality. The Bayesian paradigm enables one to update information from epidemiologic studies as they accumulate, providing estimates of the probability that the relative risk of a particular harm from exposure exceeds a threshold value, e.g. 2.0 or 4.0 that is sufficient to meet the preponderance of the evidence standard or to support a health initiative. In order to diminish the role of the initial prior distribution, which may be quite subjective, the first case-control study or an analysis of adverse event and case reports is used to determine two prior distributions. One is the most favourable to the defendant, or industry that might be regulated, which is consistent with the previous data. The other is centred on or near the estimated relative risk from the first study. The method is applied to the studies that linked aspirin use to Reye syndrome and demonstrates that the evidence of a causal association was sufficiently strong in 1982, when the Food and Drug Administration first proposed that the public be warned of the risk, to support the regulation. Thus, lives would have been saved had the warning been given at the end of 1982 rather than in early 1985.

Description: In law, inferences of causation are sometimes made through a structured process in which multiple participants play various roles, and make decisions concerning various logical components of the overall inference (such as legal rules, policy objectives, presumptions, evidence, burdens of proof and findings of fact). This article illustrates such a process using empirical research into compensation decisions in the USA for injuries allegedly caused by vaccinations. Empirical research into actual legal processes is essential, in order to discover how various players approach their sub-tasks of decision-making. It also provides insights for areas outside of law, such as non-monotonic logic, cognitive science, sociology and artificial intelligence.

Description: Situations of causal factual uncertainty are relatively common in law. The problems and difficulties regarding ‘factual causation’ in law point to the need of ‘evidence’ and ‘proof’ models that are adequate and capable to accommodate the tests and methodologies used to explain and demonstrate it in a legal context. Given the configuration of the situations of causal factual uncertainty and the available ‘evidence’ and ‘proof’ models, I argue that it is justified to use an ‘argumentative-narrative’ model for ‘proving causation’ in law. However, considering that each model of ‘evidence’ and ‘proof’ reveals a different kind of ‘rationality’ that can still be viewed in different ways, I also argue that we must try to match the perspective we have on the ‘rationality’ behind the chosen model of ‘evidence’ and ‘proof’ with the ‘rationality’ underlying ‘causation’ in law.

Description: At least in some cases, the values confronted in legal decision-making appear to be incommensurable. Some legal theorists resist incommensurability because they fear that this presents an overwhelming obstacle to rational decision-making. By offering a close analysis of proportionality and, more particularly, measures of proportional value satisfaction, I show that this fear is unfounded. Comparative measures of proportional value satisfaction do not require the values to be commensurable. However, assuming incommensurability presents us with the problem of public significance in the proportional satisfaction of values. When two values are commensurable, this public significance is provided by the mediating effects of the overarching third value that provides the common measure of the values. However, when this common measure is removed, then the public significance of value satisfaction must be otherwise achieved. This is why I propose an equal proportional value satisfaction as the most appropriate proportionality maximand. Under equal proportional value satisfaction, the proportional satisfaction of any one value has significance for each and every other value. This kind of public significance is interpersonal rather than impersonal (or second-personal rather than third-personal). The article then shows that the legal process that is most appropriate to equal proportionality is a process that implements defeasible legal rules.

Description: In order to allocate the risk between parties in legal adjudication, we use evidentiary techniques with the main device among them being the standard of proof (SoP). The traditional view holds the grade of probability to be the parameter that shifts when moving to different standards. However, as soon as we dig slightly deeper, an incoherent picture is being revealed. In this article, I challenge the accepted view and try to show that it faces insurmountable problems concerning the rationality, the grammatical consistency and the impact of the SoP for the acceptability of verdicts. At the end of the article, I shortly discuss the theory of epistemological contextualism and propose a framework that allows rational distinctions to be drawn between different standards of proof. In the second part of this project (forthcoming), I will defend a contextualist view according to which shifting parameter is not the grade of (aleatory) probability, but instead the Set of Epistemic Defeaters in play.

Description: There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.

Description: We believe that undergraduate biology students must acquire a foundational background in computing including how to formulate a computational problem; develop an algorithmic solution; implement their solution in software and then test, document and use their code to explore biological phenomena. Moreover, by learning these skills in the first year, students acquire a powerful tool set that they can use and build on throughout their studies. To address this need, we have developed a first-year undergraduate course that teaches students the foundations of computational thinking and programming in the context of problems in biology. This article describes the structure and content of the course and summarizes assessment data on both affective and learning outcomes.

Description: Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes.

Description: The aim of this paper is to study the relations between the Hausdorff dimensions of k -quasilines and the theory of extremal quasiconformal mappings. We show that there is an open and dense subset (Strebel points) of the universal Teichmüller space T (H) such that, for every [ f ] in the set, the Hausdorff dimension of the k -quasiline determined by [ f ] is strictly less than 1 + k 2 . We also show that there are some points [ f ] != [id] outside the open and dense set in the universal Teichmüller space such that the Hausdorff dimension of the quasiline determined by [ f ] is 1. Moreover, some results on the Hausdorff dimensions of the quasilines varying in the asymptotic Teichmüller space are also obtained.

Description: Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.

Description: A new uniqueness result for a general n th order differential equation is obtained. We show that some previous results follow immediately from our theorem.

Description: Consider a discrete uniformly elliptic divergence form equation on the d ≥3 dimensional lattice Z d with random coefficients. In Conlon and Spencer [ Trans. Amer. Math. Soc. , http://www.math.lsa.umich.edu/~conlon/paper/hom10.pdf ], rate of convergence results in homogenization and estimates on the difference between the averaged Green's function and the homogenized Green's function for random environments which satisfy a Poincaré inequality were obtained. Here, these results are extended to certain environments in which correlations can have arbitrarily small power law decay. These environments are simply related via a convolution to environments which do satisfy a Poincaré inequality.

Description: In this paper, we prove that, for any a , M N with ( a , M ) = 1, there are infinitely many Carmichael numbers m such that m a mod M .

Description: We give a topological analogue for openness of a criterion for flatness that originates with Auslander. Over a normal base of dimension n , failure of openness is detected by a vertical component in the n th fibred power of the morphism.

Description: Investigated are regular maps from real algebraic varieties into real Fermat varieties. It is proved that under some natural assumptions, all such maps are null homotopic.

Description: Let ( M , g ) be a complete non-compact Riemannian manifold. We consider operators of the form g + V , where g is the non-negative Laplacian associated with the metric g , and V a locally integrable function. Let be a Riemannian covering, with Laplacian g and potential . If the operator + V is non-negative on ( M , g ), then the operator is non-negative on . In this note, we show that the converse statement is true provided that is a co-amenable subgroup of 1 ( M ).

Description: Peak interpolation is concerned with a foundational kind of mathematical task: building functions in a fixed algebra A , which have prescribed values or behaviour on a fixed closed subset (or on several disjoint subsets). In this paper, we do the same but now A is an algebra of operators on a Hilbert space. We briefly survey this noncommutative peak interpolation , which we have studied with coauthors in a long series of papers, and whose basic theory now appears to be approaching its culmination. This programme developed from, and is based partly on, theorems of Hay and Read whose proofs were spectacular, but therefore inaccessible to an uncommitted reader. We give short proofs of these results, using recent progress in noncommutative peak interpolation, and conversely give examples of the use of these theorems in peak interpolation. For example, we prove a useful new noncommutative peak interpolation theorem.

Description: We show how a parameterized family of maps of the spine of a manifold can be used to construct a family of homeomorphisms of the ambient manifold which have the inverse limits of the spine maps as global attractors. We describe applications to unimodal families of interval maps, to rotation sets, and to the standard family of circle maps.

Description: For every prime p , we give infinitely many examples of torsors under abelian varieties over Q that are locally trivial but not divisible by p in the Weil–Châtelet group. We also give an example of a locally trivial torsor under an elliptic curve over Q that is not divisible by 4 in the Weil–Châtelet group. This gives a negative answer to a question of Cassels.

Description: We show that at least of the zeros of the Riemann zeta-function are simple, assuming the Riemann hypothesis. This was previously established by Conrey, Ghosh and Gonek [ Proc. London Math. Soc. 76 (1998) 497–522] under the additional assumption of the generalized Lindelöf hypothesis. We are able to remove this hypothesis by careful use of the generalized Vaughan identity.

Description: We construct an infinite family of hyperbolic, homologically thin knots that are not quasi-alternating. To establish the latter, we argue that the branched double-cover of each knot in the family does not bound a negative-definite 4-manifold with trivial first homology and bounded second Betti number. This fact depends in turn on information from the correction terms in Heegaard Floer homology, which we establish by way of a relationship to, and calculation of, the Turaev torsion.

Description: We observe that E -resultant of a very ample rank 2 vector bundle E on a real projective curve (with no real points) is nonnegative when restricted to the space of real sections. Moreover, we show that if E has a section vanishing at exactly two points and the degree d of E satisfies d ( d – 6) ≥ 4( g – 1), then this polynomial cannot be written as a sum of squares.

Description: Let G be one of the Ricci-flat holonomy groups SU( n ), Sp( n ), Spin(7) or G 2 , and M a compact manifold of dimension 2 n , 4 n , 8 or 7, respectively. We prove that the natural map from the moduli space of torsion-free G -structures on M to the moduli space of Ricci-flat metrics is open, and that the image is a smooth manifold. For the exceptional cases G = Spin(7) and G 2 , we extend the result to asymptotically cylindrical manifolds.

Description: We improve the results of Booker and Krishnamurthy ( Compos. Math. 147 (2011) 669–715) by allowing restricted sets of poles among the unramified twists. This allows for a clean statement of the GL(2) converse theorem which includes all cases of Eisenstein series.

Description: Let G be a solvable subgroup of the automorphism group Aut( X ) of a compact Kähler manifold X of complex dimension n , and let N ( G ) be the normal subgroup of G consisting of elements with null entropy. Let us denote by G * the image of G under the natural map from Aut( X ) to GL( V , R ), where V is the Dolbeault cohomology group H 1, 1 ( X , R ). Assume that the Zariski closure of G * in GL( V C ) is connected. The main aim of this paper is to show that, when the rank r ( G ) of the quotient group G / N ( G ) is equal to n – 1 and the identity component of Aut( X ) is trivial, then the normal subgroup N ( G ) of G is finite. This affirmatively answers a question in Invent. Math. posed by D.-Q. Zhang.

Description: The dihedral angle formed at junctions between two plagioclase grains and a grain of augite is only very rarely in textural equilibrium in gabbros from kilometre-scale crustal layered intrusions. The median of a population of these disequilibrium angles, cpp , varies systematically within a single layered intrusion, remaining constant over large stretches of stratigraphy with significant increases and decreases associated with the addition or reduction respectively of the number of phases on the liquidus of the bulk magma. The stepwise changes in cpp are present in the Upper Zone of the Bushveld Complex, the Megacyclic Unit I of the Sept Iles Intrusion, and the Layered Series of the Skaergaard intrusion. The plagioclase-bearing cumulates of Rum have a bimodal distribution of cpp , dependent on whether the cumulus assemblage includes clinopyroxene. The presence of the stepwise changes is independent of the order of arrival of cumulus phases and of the composition of either the cumulus phases or the inferred composition of the interstitial liquid. The only parameter that behaves in an exactly analogous manner to cpp is the rate of change in enthalpy with temperature ( H / T ) during crystallization. Both H / T and cpp increase with the addition of a liquidus phase, and decrease with the removal of a liquidus phase. The replacement of one phase by another has little effect on H / T and no discernible effect on cpp . An increase of H / T results in an increase in the fraction of the total enthalpy budget that is the latent heat of crystallization (the fractional latent heat). It also increases the mass crystallized in each incremental temperature drop (the crystal productivity). These increases of both fractional latent heat and crystal productivity are likely to cause an increase in the time taken to form three-grain junctions in the mush via thermal buffering of a thickened mushy layer. We suggest these are the underlying causes of stepwise increases in cpp . Stepwise changes in the geometry of three-grain junctions in fully solidified gabbros thus provide a clear microstructural marker for the progress of fractionation down the liquid line of descent in layered intrusions.

Description: High-resolution sampling in monogenetic fields has the potential to reveal fine-scale heterogeneity of the mantle, a feature that may be overwhelmed by larger fluxes of magma, or missed by under-sampling. The Quaternary Auckland Volcanic Field (AVF) in northern New Zealand is a basaltic field of 51 small-volume volcanic centres, and is one of the best-sampled examples of a monogenetic volcanic field. We present data for 12 centres in the volcanic field. These show the large compositional variations between volcanoes as well as through single eruptive sequences. Whole-rock compositions range from subalkaline basalt in the larger centres, through alkali basalt to nephelinite in the smallest centres. Fractional crystallization has had a limited effect in many of the centres, but high-pressure clinopyroxene crystallization may have occurred in others. Three end-members are observed in Pb isotope space, indicating that distinct mantle source components are involved in the petrogenesis of the magmas. Whole-rock multi-element patterns show that the larger centres have prominent positive Sr anomalies and lack K anomalies, whereas the smaller centres have prominent negative K anomalies and lack Sr anomalies. The melting parameters and compositions of the sources involved are modelled using trace element ratios and multi-element patterns, and three components are characterized: (1) fertile peridotite with a Pb-isotope composition similar to Pacific mid-ocean ridge basalt; (2) eclogite domains with a HIMU-like isotope composition dispersed within the fertile peridotite; (3) slightly depleted subduction-metasomatized peridotitic lithospheric mantle (containing c . 3% subduction fluids). Modelling shows that melting in the AVF begins in garnet-bearing fertile asthenosphere (with preferential melting of eclogite domains) and that melts are variably diluted by melts of the lithospheric source. The U–Th isotope compositions of the end-members in the AVF show 230 Th excess [( 230 Th/ 232 Th) ratios of 1·11–1·38], with the samples of lower ( 230 Th/ 232 Th) exhibiting higher ( 238 U/ 232 Th), which we attribute to the dilution effect of the melts from the lithospheric mantle source. Modelling reveals a correlation between melting in the asthenosphere, the degree of melting and incorporation of the metasomatized lithospheric mantle source, and the resultant size of the volcanic centre. This suggests that the scale of the eruption may essentially be controlled by asthenospheric mantle dynamics.

Description: The origin of mafic and ultramafic sills exhibiting different whole-rock compositional profiles (e.g. I-, C-, D-, M- and S-shaped profiles) remains controversial. We have addressed this issue by revisiting three ~100 m thick Siberian dolerite sills (Vavukansky, Kuz’movsky and Vilyuysky) that display remarkable internal differentiation. The Vavukansky sill has an M-shaped profile with prominent basal and top reversals showing inward increases in whole-rock MgO, Mg-number [100Mg/(Mg + Fe)] and normative An content [100An/(An + Ab)], followed by the Layered and Upper Border Series with inward decreases in these indices. The Kuz’movsky and Vilyuysky sills both show S-shaped profiles similar to the Vavukansky sill, but lack a top reversal. These whole-rock M- and S-shaped profiles are accompanied by similar profiles in mineral compositions. Plagioclase and, to a lesser extent, olivine show systematic inward increases in An content and Mg-number, respectively, across basal and top reversals. These compositional trends are followed by inward decreases in these ratios in the interiors of the Vavukansky and Kuz’movsky sills. Currently accepted models attribute whole-rock M- and S-shaped compositional profiles to crystal settling, compositional convection or compaction operating in closed systems. Our observations challenge these traditional interpretations because variations in mineral compositions observed in marginal reversals cannot result from closed-system fractionation. We suggest instead that initially the sills evolved as open systems that were slowly inflated by magmas that became gradually more primitive with time. The inflation was accompanied by in situ crystallization that preserved the preceding fractionation history of the injected magmas by forming basal and top reversals with minerals becoming more primitive inwards. This process culminated with rapid inflation of the sills to their current size owing to a major influx of primitive magma. Subsequently, magma flow through the sills ceased and they evolved as closed systems by fractional crystallization. This resulted in the Layered and Upper Border Series with minerals becoming more evolved inwards. This model can be extended to explain other compositional profiles and petrological features in mafic and ultramafic sills.

Description: The genomes of related species contain valuable information on the history of the considered taxa. Great apes in particular exhibit variation of evolutionary patterns along their genomes. However, the great ape data also bring new challenges, such as the presence of incomplete lineage sorting and ancestral shared polymorphisms. Previous methods for genome-scale analysis are restricted to very few individuals or cannot disentangle the contribution of mutation rates and fixation biases. This represents a limitation both for the understanding of these forces as well as for the detection of regions affected by selection. Here, we present a new model designed to estimate mutation rates and fixation biases from genetic variation within and between species. We relax the assumption of instantaneous substitutions, modeling substitutions as mutational events followed by a gradual fixation. Hence, we straightforwardly account for shared ancestral polymorphisms and incomplete lineage sorting. We analyze genome-wide synonymous site alignments of human, chimpanzee, and two orangutan species. From each taxon, we include data from several individuals. We estimate mutation rates and GC-biased gene conversion intensity. We find that both mutation rates and biased gene conversion vary with GC content. We also find lineage-specific differences, with weaker fixation biases in orangutan species, suggesting a reduced historical effective population size. Finally, our results are consistent with directional selection acting on coding sequences in relation to exonic splicing enhancers.

Description: Genetic control of male or female gonad development displays between different groups of organisms a remarkable diversity of "master sex-determining genes" at the top of the genetic hierarchies, whereas downstream components surprisingly appear to be evolutionarily more conserved. Without much further studies, conservation of sequence has been equalized to conservation of function. We have used the medaka fish to investigate the generality of this paradigm. In medaka, the master male sex-determining gene is dmrt1bY , a highly conserved downstream regulator of sex determination in vertebrates. To understand its function in orchestrating the complex gene regulatory network, we have identified targets genes and regulated pathways of Dmrt1bY. Monitoring gene expression and interactions by transgenic fluorescent reporter fish lines, in vivo tissue-chromatin immunoprecipitation and in vitro gene regulation assays revealed concordance but also major discrepancies between mammals and medaka, notably amongst spatial, temporal expression patterns and regulations of the canonical Hedgehog and R-spondin/Wnt/Follistatin signaling pathways. Examination of Foxl2 protein distribution in the medaka ovary defined a new subpopulation of theca cells, where ovarian-type aromatase transcriptional regulation appears to be independent of Foxl2. In summary, these data show that the regulation of the downstream regulatory network of sex determination is less conserved than previously thought.

Description: We present measurements of higher order clustering of galaxies in the latest release of the Canada–France–Hawaii Telescope Legacy Survey (CFHTLS)-Wide. We construct a series of volume-limited sample of galaxies containing more than one million galaxies over the redshift range 0.2 〈  z  〈 1 in the four independent fields of the CFHTLS-Wide. Using a counts-in-cells technique we measure the variance ${\bar{\xi }}_2$ and the hierarchical moments $S_{n}= {{\bar{\xi }}_n / {\bar{\xi }}_2^{n-1}}$ (3 ≤  n  ≤ 5) as a function of redshift and angular scale. We find that the measured field-to-field scatter in our estimators is in excellent agreement with analytical predictions. At small scales, corresponding to the highly non-linear regime, we find tentative evidence at the 1 level that the hierarchical moments increase with redshift. At large scales, corresponding to the weakly non-linear regime, our measurements are marginally consistent with perturbation theory predictions for standard cold dark matter cosmology using a simple linear bias. The predictions of perturbation theory tend to slightly overestimate our measurements, which may be a signature of non-linear bias.

Description: We estimate cosmic microwave background (CMB) polarization power spectra and temperature–polarization cross-spectra, from the 9-year data of the Wilkinson Microwave Anisotropy Probe ( WMAP ). Foreground cleaning is implemented using minimum variance linear combinations of the coefficients of needlet decompositions of sky maps for all WMAP channels, to produce maps for CMB temperature anisotropies ( T -mode) and polarization ( E and B -modes), for nine different years of observation. The final power spectra are computed from averages of all possible cross-year power spectra obtained using foreground-cleaned maps for the different years. Our analysis technique yields a measurement of the EE spectrum that is in excellent agreement with theoretical expectations from the current cosmological model. By comparison, the publicly available WMAP EE power spectrum is higher on average (and significantly higher than the predicted EE spectrum from the current best fit) at scales larger than about a degree, an excess that is not confirmed by our analysis. Our TE and TB measurements are in good agreement overall with the WMAP ones and are compatible with the theoretical expectations, although a few data points are off by a few standard deviations, and yield a reduced 2 somewhat above expectation. As predicted for a standard cosmological model with low tensor-to-scalar ratio, the EB and BB power spectra obtained in our analysis are compatible with zero.

Description: We present optical integral field unit observations of two gas pillars surrounding the Galactic young massive star cluster NGC 3603. The high S/N and spectral resolution of these data have allowed us to accurately quantify the Hα, [N ii ] and [S ii ] emission line shapes, and we find a mixture of broad (FWHM ~ 70–100 km s –1 ) and narrow (〈50 km s –1 ) components. The broad components are found close to the edges of both pillars, suggesting that they originate in turbulent mixing layers (TMLs) driven by the effect of the star cluster wind. Both pillars exhibit surprisingly high ionized gas densities of 〉10 000 cm –3 . In one pillar we found that these high densities are only found in the narrow component, implying that they must originate from deeper within the pillar than the broad component. From this, together with our kinematical data, we conclude that the narrow component traces a photoevaporation flow, and that the TML forms at the interface with the hot wind. On the pillar surfaces, we find a consistent offset in radial velocity between the narrow (brighter) components of Hα and [N ii ] of ~5–8 km s –1 , for which we were unable to find a satisfactory explanation. We urge the theoretical community to simulate mechanical and radiative cloud interactions in more detail to address the many unanswered questions raised by this study.

Description: By exploiting the data base of early-type galaxy (ETG) members of the WINGS survey of nearby clusters, we address here the long debated question of the origin and shape of the Fundamental Plane (FP). Our data suggest that different physical mechanisms concur in shaping and ‘tilting’ the FP with respect to the virial plane (VP) expectation. In particular, a ‘hybrid solution’ in which the structure of galaxies and their stellar population are the main contributors to the FP tilt seems to be favoured. We find that the bulk of the tilt should be attributed to structural non-homology, while stellar population effects play an important but less crucial role. In addition, our data indicate that the differential FP tilt between the V and K band is due to a sort of entanglement between structural and stellar population effects, for which the inward steepening of colour profiles ( V  –  K ) tends to increase at increasing the stellar mass of ETGs. The same kind of analysis applied to the ATLAS 3 D and Sloan Digital Sky Survey (SDSS) data in common with WINGS ( WSDSS throughout the paper) confirms our results, the only remarkable difference being the less important role that our data attribute to the stellar mass-to-light-ratio (stellar populations) in determining the FP tilt . The ATLAS 3 D data also suggest that the FP tilt depends as well on the dark matter (DM) fraction and on the rotational contribution to the kinetic energy ( V rot /), thus again pointing towards the above-mentioned ‘hybrid solution’. We show that the global properties of the FP, i.e. its tilt and tightness, can be understood in terms of the underlying correlation among mass, structure and stellar population of ETGs, for which, at increasing the stellar mass, ETGs become (on average) ‘older’ and more centrally concentrated. Finally, we show that a Malmquist-like selection effect may mimic a differential evolution of the mass-to-light ratio for galaxies of different masses. This should be taken into account in the studies investigating the amount of the so-called ‘downsizing’ phenomenon.

Description: I present a new algorithm, Curved-sky grAvitational Lensing for Cosmological Light conE simulatioNS ( calclens ), for efficiently computing weak gravitational lensing shear signals from large N -body light cone simulations over a curved sky. This new algorithm properly accounts for the sky curvature and boundary conditions, is able to produce redshift-dependent shear signals including corrections to the Born approximation by using multiple-plane ray tracing and properly computes the lensed images of source galaxies in the light cone. The key feature of this algorithm is a new, computationally efficient Poisson solver for the sphere that combines spherical harmonic transform and multigrid methods. As a result, large areas of sky (~10 000 square degrees) can be ray traced efficiently at high resolution using only a few hundred cores. Using this new algorithm and curved-sky calculations that only use a slower but more accurate spherical harmonic transform Poisson solver, I study the convergence, shear E-mode, shear B-mode and rotation mode power spectra. Employing full-sky E/B-mode decompositions, I confirm that the numerically computed shear B-mode and rotation mode power spectra are equal at high accuracy (1 per cent) as expected from perturbation theory up to second order. Coupled with realistic galaxy populations placed in large N -body light cone simulations, this new algorithm is ideally suited for the construction of synthetic weak lensing shear catalogues to be used to test for systematic effects in data analysis procedures for upcoming large-area sky surveys. The implementation presented in this work, written in c and employing widely available software libraries to maintain portability, is publicly available at http://code.google.com/p/calclens .

Description: Quasar accretion disc winds observed via broad absorption lines (BALs) in the UV produce strong continuous absorption in X-rays. The X-ray absorber is believed to serve critically as a radiative shield to keep the outflow ionizations low enough for radiative driving. However, previous studies have shown that ‘mini-BAL’ and narrow absorption line (NAL) outflows have dramatically less X-ray absorption than BALs. Here, we examine X-ray and rest-frame UV spectra of eight mini-BAL quasars with outflow speeds in the range 0.1–0.2c to test the hypothesis that these extreme speeds require a strong shield. We find that the X-ray absorption is weak or moderate, with neutral-equivalent column densities N H  〈 few 10 22 cm –2 , consistent with mini-BALs at lower speeds. We use photoionization models to show that the amount of shielding consistent with our data is too weak to control the outflow ionizations and, therefore, it is not important for the acceleration. Shielding in complex geometries also seems unlikely because the alleged shield would need to extinguish the ionizing far-UV flux while avoiding detection in X-rays and the near-UV. We argue that the outflow ionizations are kept moderate, instead, by high gas densities in small clouds. If the mini-BALs form at radial distances of the order of R ~ 2 pc from the central quasar (broadly consistent with theoretical models and with the mini-BAL variabilities observed here and in previous work), and the total column densities in the mini-BAL gas are N H 10 21 cm –2 , then the total radial extent of outflow clouds is only R clouds 3 x 10 13 cm in cases of no/weak shielding or R clouds 3 x 10 14 cm behind the maximum shield allowed by our data. This implies radial filling factors R clouds / R 5 x 10 – 6 or 5 x 10 – 5 for the unshielded or maximally shielded cases, respectively. Compared to the transverse sizes 8 x 10 15 cm (based on measured line depths), the outflows have shapes like thin ‘pancakes’ viewed face-on, or they occupy larger volumes like a spray of many dense clouds with a small volume filling factor. These results favour models with magnetic confinement in magnetic disc winds. To the extent that BALs, mini-BALs and NALs probe the same general outflow phenomenon, our result for dense substructures should apply to all three outflow types.

Description: The estimated stellar masses of galaxies are widely used to characterize how the galaxy population evolves over cosmic time. If stellar masses can be estimated in a robust manner, free from any bias, global diagnostics such as the stellar mass function can be used to constrain the physics of galaxy formation. We explore how galaxy stellar masses, estimated by fitting broad-band spectral energy distributions (SEDs) with stellar population models, can be biased as a result of commonly adopted assumptions for the star formation and chemical enrichment histories, recycled fractions and dust attenuation curves of galaxies. We apply the observational technique of broad-band SED fitting to model galaxy SEDs calculated by the theoretical galaxy formation model GALFORM, isolating the effect of each of these assumptions. We find that, averaged over the entire galaxy population, the common assumption of exponentially declining star formation histories does not, by itself, adversely affect stellar mass estimation. However, we also show that this result does not hold when considering galaxies that have undergone a recent burst of star formation. We show that fixing the metallicity in SED fitting or using sparsely sampled metallicity grids can introduce mass-dependent systematics into stellar mass estimates. We find that the common assumption of a star–dust geometry corresponding to a uniform foreground dust screen can cause the stellar masses of dusty model galaxies to be significantly underestimated. Finally, we show that stellar mass functions recovered by applying SED fitting to model galaxies at high redshift can differ significantly in both shape and normalization from the intrinsic mass functions predicted by a given model. In particular, the effects of dust can reduce the normalization at the high-mass end by up to 0.6 dex in some cases. Given these differences, our methodology of using stellar masses estimated from model galaxy SEDs offers a new, self-consistent way to compare model predictions with observations. We conclude that great care should be taken when comparing theoretical galaxy formation models to observational results based on the estimated stellar masses of high-redshift galaxies.

Description: We analyse the 2D correlation function of the Sloan Digital Sky Survey-III Baryon Oscillation Spectroscopic Survey (BOSS) CMASS sample of massive galaxies of the ninth data release to measure cosmic expansion H and the angular diameter distance D A at a mean redshift of 〈 z 〉 = 0.57. We apply, for the first time, a new correlation function technique called clustering wedges μ ( s ). Using a physically motivated model, the anisotropic baryonic acoustic feature in the galaxy sample is detected at a significance level of 4.7 compared to a featureless model. The baryonic acoustic feature is used to obtain model-independent constraints cz / H / r s = 12.28 ± 0.82 (6.7 percent accuracy) and D A / r s =  9.05 ± 0.27 (3.0 per cent) with a correlation coefficient of –0.5, where r s is the sound horizon scale at the end of the baryonic drag era. We conduct thorough tests on the data and 600 simulated realizations, finding robustness of the results regardless of the details of the analysis method. Combining this with r s constraints from the cosmic microwave background, we obtain H (0.57) = 90.8 ± 6.2 km s –1 Mpc –1 and D A (0.57) = 1386 ± 45 Mpc. We use simulations to forecast results of the final BOSS CMASS data set. We apply the reconstruction technique on the simulations demonstrating that the sharpening of the anisotropic baryonic acoustic feature should improve the detection as well as tighten constraints of H and D A by ~30 per cent on average.

Description: We present an analysis of Chandra archival, pre-explosion data of the positions of three nearby (〈25 Mpc) Type Ia supernovae, SN2011iv, SN2012cu and SN2012fr. No sources corresponding to the progenitors were found in any of the observations. Combining all sources with well-defined backgrounds does not reveal any evidence for X-ray emission from the progenitors either. We calculated upper limits on the bolometric luminosities of the progenitors, under the assumption that they were black bodies with effective temperatures between 30 and 150 eV, corresponding to ‘canonical’ supersoft X-ray sources. The upper limits of SN2012fr straddle the Eddington luminosity of canonical supersoft sources, but fainter canonical supersoft sources cannot be ruled out by this study. We also compare our upper limits with known compact binary supersoft X-ray sources. This study is a continuation of the campaign to directly detect or constrain the X-ray characteristics of pre-explosion observations of nearby Type Ia supernova progenitors; with the results reported in Nielsen, Voss & Nelemans (see reference in Introduction), the number of nearby Type Ia supernovae for which pre-explosion images are available in the Chandra archive is now 13 and counting.

Description: In this work, we report the Photodetector Array Camera and Spectrometer (PACS) 100 μm/160 μm detections of a sample of 42 GALEX -selected and far-infrared (FIR)-detected Lyman break galaxies (LBGs) at z  ~ 1 located in the Cosmic Evolution Survey (COSMOS) field and analyse their ultraviolet (UV) to FIR properties. The detection of these LBGs in the FIR indicates that they have a dust content high enough so that its emission can be directly detected. According to a spectral energy distribution (SED) fitting with stellar population templates to their UV-to-near-IR observed photometry, PACS-detected LBGs tend to be bigger ( R eff  ~ 4.1 kpc), more massive [log ( M * /M ) ~ 10.7], dustier [ E s ( B  –  V ) ~ 0.40], redder in the UV continuum (β ~ –0.60) and UV-brighter [log ( L UV /L ) ~ 10.1] than PACS-undetected LBGs. PACS-detected LBGs at z  ~ 1 are mostly disc-like galaxies and are located over the green valley and red sequence of the colour–magnitude diagram of galaxies at their redshift. By using their UV and IR emission, we find that PACS-detected LBGs tend to be less dusty and have slightly higher total star formation rates (SFRs) than other PACS-detected UV-selected galaxies within the same redshift range. As a consequence of the selection effect due to the depth of the FIR observations employed, all our PACS-detected LBGs have total IR luminosities, L IR , higher than 10 11 L and thus are luminous IR galaxies. However, none of the PACS-detected LBGs are in the ultra-luminous IR galaxy (ULIRG) regime, L IR  ≥ 10 12 L , where the FIR observations are complete. The finding of ULIRGs-LBGs at higher redshifts ( z  ~ 3) suggests an evolution of the FIR emission of LBGs with cosmic time. In an IRX–β diagram, PACS-detected LBGs at z  ~ 1 tend to be located around the relation for local starburst similarly to other UV-selected PACS-detected galaxies at the same redshift. Consequently, the dust-correction factors obtained with their UV continuum slope allow us to determine their total SFR, unlike at higher redshifts. However, the dust attenuation derived from UV to NIR SED fitting overestimates the total SFR for most of our PACS-detected LBGs in an age-dependent way: the overestimation factor is higher in younger galaxies. This is likely due to the typical degeneracy between dust attenuation and age in the SED fitting with synthetic templates and highlights the importance of the FIR measurements in the analysis of star-forming galaxies at intermediate redshifts.

Description: We study 23 previously published Kepler targets to perform a consistent grid-based Bayesian asteroseismic analysis and compare our results to those obtained via the Asteroseismic Modelling Portal. We find differences in the derived stellar parameters of many targets and their uncertainties. While some of these differences can be attributed to systematic effects between stellar evolutionary models, we show that the different methodologies deliver incompatible uncertainties for some parameters. Using non-adiabatic models and our capability to measure surface effects, we also investigate the dependency of these surface effects on the stellar parameters. Our results suggest a dependence of the magnitude of the surface effect on the mixing length parameter which also, but only minimally, affects the determination of stellar parameters. While some stars in our sample show no surface effect at all, the most significant surface effects are found for stars that are close to the Sun's position in the Hertzsprung–Russell diagram.

Description: We present evidence for a strong relationship between galaxy size and environment for the quiescent population in the redshift range 1 〈  z  〈 2. Environments were measured using projected galaxy overdensities on a scale of 400 kpc, as determined from ~96 000 K -band-selected galaxies from the UKIDSS Ultra Deep Survey (UDS). Sizes were determined from ground-based K -band imaging, calibrated using space-based CANDELS HST observations in the centre of the UDS field, with photometric redshifts and stellar masses derived from 11-band photometric fitting. From the resulting size–mass relation, we confirm that quiescent galaxies at a given stellar mass were typically ~50 per cent smaller at z  ~ 1.4 compared to the present day. At a given epoch, however, we find that passive galaxies in denser environments are on average significantly larger at a given stellar mass. The most massive quiescent galaxies ( M *  〉 2 10 11  M ) at z  〉 1 are typically 50 per cent larger in the highest density environments compared to those in the lowest density environments. Using Monte Carlo simulations, we reject the null hypothesis that the size–mass relation is independent of environment at a significance 〉4.8 for the redshift range 1 〈  z  〈 2. In contrast, the evidence for a relationship between size and environment is much weaker for star-forming galaxies.

Description: We present the results from the Very Large Array radio continuum total power and polarized intensity observations of Stephan's Quintet at 1.43 and 4.86 GHz, along with complementary 4.85- and 8.35-GHz Effelsberg observations. Our study shows a large envelope of radio emission encompassing all the member galaxies and hence a large volume of intergalactic matter. Infall of the galaxy NGC 7318B produces a ridge of intergalactic, polarized emission, for which the magnetic field strength has been estimated as 11.0 ± 2.2 μG, with an ordered component of 2.6 ± 0.8 μG. The energy density of the field within the ridge area is of the same order as estimates of the thermal component, implying that the magnetic field has a significant role in the dynamics of the intergalactic matter. We also report that the tidal dwarf galaxy candidate SQ-B possesses a strong and highly anisotropic magnetic field, with a total strength equal to 6.5 ± 1.9 μG and an ordered component reaching 3.5 ± 1.2 μG, which is comparable to that found in normal-sized galaxies.

Description: We present a simple and efficient phenomenological model for the two-dimensional two-point galaxy correlation function that works well over a wide range of scales, from large scales down to scales as small as 25 h –1 Mpc. Our model incorporates non-linear effects and a scale-dependent galaxy bias on small scales, and it allows the redshift-space distortions to be scale and direction dependent. We validate our model using LasDamas mock catalogues and apply it to the Sloan Digital Sky Survey (SDSS) Data Release Seven (DR7) luminous red galaxies (LRGs). Using only the monopole and quadrupole of the correlation function measured from the SDSS DR7 LRGs, we obtain improved measurements H ( z ) r s ( z d )/ c  = 0.0433 ± 0.0042, D A ( z )/ r s ( z d ) = 6.59 ± 0.46 and f ( z ) 8 ( z ) = 0.429 ± 0.089 at z  = 0.35, using the scale range 25 〈  s  〈 120 h –1 Mpc. We expect our results and model to be useful in tightening dark energy and gravity constraints from the full analysis of current and future galaxy clustering data.

Description: We study the formation and evolution of filamentary configurations of dark matter haloes in voids. Our investigation uses the high-resolution cold dark matter simulation CosmoGrid to look for void systems resembling the VGS_31 elongated system of three interacting galaxies that was recently discovered by the Void Galaxy Survey inside a large void in the Sloan Digital Sky Survey galaxy redshift survey. H  i data revealed these galaxies to be embedded in a common elongated envelope, possibly embedded in intravoid filament. In the CosmoGrid simulation we look for systems similar to VGS_31 in mass, size and environment. We find a total of eight such systems. For these systems, we study the distribution of neighbour haloes, the assembly and evolution of the main haloes and the dynamical evolution of the haloes, as well as the evolution of the large-scale structure in which the systems are embedded. The spatial distribution of the haloes follows that of the dark matter environment. We find that VGS_31-like systems have a large variation in formation time, having formed between 10 Gyr ago and the present epoch. However, the environments in which the systems are embedded evolved to resemble each other substantially. Each of the VGS_31-like systems is embedded in an intravoid wall, that no later than z  = 0.5 became the only prominent feature in its environment. While part of the void walls retain a rather featureless character, we find that around half of them are marked by a pronounced and rapidly evolving substructure. Five haloes find themselves in a tenuous filament of a few h –1 Mpc long inside the intravoid wall. Finally, we compare the results to observed data from VGS_31. Our study implies that the VGS_31 galaxies formed in the same (proto)filament, and did not meet just recently. The diversity amongst the simulated halo systems indicates that VGS_31 may not be typical for groups of galaxies in voids.

Description: Using 3D numerical hydrodynamical simulations, we show that jets launched prior to Type Ia supernova (SN Ia) explosion in the core-degenerate (CD) scenario can account for the appearance of two opposite lobes (‘Ears’) along the symmetry axis of the SN remnant (SNR). In the double-degenerate (DD) and CD scenarios the merger of the two degenerate compact objects is very likely to lead to the formation of an accretion disc, that might launch two opposite jets. In the CD scenario, these jets interact with the envelope ejected during the preceding common envelope phase. If explosion occurs shortly after the merger process, the exploding gas and the jets will collide with the ejected nebula, leading to SNR with axisymmetric components including ‘Ears’. We also explore the possibility that the jets are launched by the companion white dwarf prior to its merger with the core. This last process is similar to the one where jets are launched in some pre-planetary nebulae. The SNR ‘Ears’ in this case are formed by a spherical SN Ia explosion inside an elliptical planetary nebula-like object. We compare our numerical results with two SNRs – Kepler and G299.2–2.9.

Description: Low-mass star-forming regions are more complex than the simple spherically symmetric approximation that is often assumed. We apply a more realistic infall/outflow physical model to molecular/continuum observations of three late Class 0 protostellar sources with the aims of (a) proving the applicability of a single physical model for all three sources and (b) deriving physical parameters for the molecular gas component in each of the sources. We have observed several molecular species in multiple rotational transitions. The observed line profiles were modelled in the context of a dynamical model which incorporates infall and bipolar outflows, using a three-dimensional radiative transfer code. This results in constraints on the physical parameters and chemical abundances in each source. Self-consistent fits to each source are obtained. We constrain the characteristics of the molecular gas in the envelopes as well as in the molecular outflows. We find that the molecular gas abundances in the infalling envelope are reduced, presumably due to freeze-out, whilst the abundances in the molecular outflows are enhanced, presumably due to dynamical activity. Despite the fact that the line profiles show significant source-to-source variation, which primarily derives from variations in the outflow viewing angle, the physical parameters of the gas are found to be similar in each core.

Description: We present predictions for hydrogen and helium emission line luminosities from circumstellar matter around Type Ia supernovae (SNe Ia) using time dependent photoionization modelling. Early high-resolution ESO/Very Large Telescope (VLT) optical echelle spectra of the SN Ia 2000cx were taken before and up to ~70 d after maximum to probe the existence of such narrow emission lines from the supernova. We detect no such lines, and from our modelling place an upper limit on the mass-loss rate for the putative wind from the progenitor system, $\skew4\dot{M}\lesssim 1.3\times 10^{-5} \,{\rm M}_{\odot }\,{\rm yr}^{-1}$ , assuming a speed of 10 km s –1 and solar abundances for the wind. If the wind would be helium-enriched and/or faster, the upper limit on $\skew4\dot{M}$ could be significantly higher. In the helium-enriched case, we show that the best line to constrain the mass-loss would be He i 10 830. In addition to confirming the details of interstellar Na i and Ca ii absorption towards SN 2000cx as discussed by Patat et al., we also find evidence for 6613.56 Å diffuse interstellar band absorption in the Milky Way. We also discuss measurements of the X-ray emission from the interaction between the supernova ejecta and the wind and we re-evaluate observations of SN 1992A obtained ~16 d after maximum by Schlegel & Petre. We find an upper limit of $\skew4\dot{M}\sim 1.3\times 10^{-5} \,{\rm M}_{\odot }\,{\rm yr}^{-1}$ which is significantly higher than that estimated by Schlegel & Petre. These results, together with the previous observational work on the normal SNe Ia 1994D and 2001el, disfavour a symbiotic star in the upper mass-loss rate regime (so-called Mira-type systems) from being the likely progenitor scenario for these SNe. Our model calculations are general, and can also be used for the subclass of SNe Ia that do show circumstellar interaction, e.g. the recent PTF 11kx. To constrain hydrogen in late-time spectra, we present ESO/VLT and ESO/New Technology Telescope optical and infrared observations of SNe Ia 1998bu and 2000cx in the nebular phase, 251-388 d after maximum. We see no signs of hydrogen line emission in SNe 1998bu and 2000cx at these epochs, and from the absence of Hα with a width of the order of ~10 3 km s –1 , we argue from modelling that the mass of such hydrogen-rich gas must be 0.03 M for both supernovae. Comparing similar upper limits with recent models of Pan et al., it seems that hydrogen-rich donors with a separation of 5 times the radius of the donor may be ruled out for the five SNe Ia 1998bu, 2000cx, 2001el, 2005am and 2005cf. Larger separation, helium-rich donors, or a double-degenerate origin for these supernovae seems more likely. Our models have also been used to put the limit on hydrogen-rich gas in the recent SN 2011fe, and for this supernova, a double-degenerate origin seems likely.

Description: We build differential-reddening maps for 66 Galactic globular clusters (GCs) with archival Hubble Space Telescope WFC/ACS F 606 W and F 814 W photometry. Because of the different GC sizes (characterized by the half-light radius R h ) and distances to the Sun, the WFC/ACS field of view (200 arcsec x 200 arcsec) coverage ( R obs ) lies in the range 1 R obs / R h 15 for about 85 per cent of the sample, with about 10 per cent covering only the inner ( R obs R h ) parts. We divide the WFC/ACS field of view across each cluster in a regular cell grid and extract the stellar-density Hess diagram from each cell, shifting it in colour and magnitude along the reddening vector until matching the mean diagram. Thus, the maps correspond to the internal dispersion of the reddening around the mean. Depending on the number of available stars (i.e. probable members with adequate photometric errors), the angular resolution of the maps range from 7 arcsec x 7 arcsec to 20 arcsec x 20 arcsec. We detect spatially variable extinction in the 66 GCs studied, with mean values ranging from 〈E(B-V)〉0.018 (NGC 6981) up to 〈E(B-V)〉0.016 (Palomar 2). Differential-reddening correction decreases the observed foreground reddening and the apparent distance modulus but, since they are related to the same value of E ( B  –  V ), the distance to the Sun is conserved. Fits to the mean-ridge lines of the highly extincted and photometrically scattered GC Palomar 2 show that age and metallicity also remain unchanged after the differential-reddening correction, but measurement uncertainties decrease because of the reduced scatter. The lack of systematic variations of 〈E(B-V)〉 with both the foreground reddening and the sampled cluster area indicates that the main source of differential reddening is interstellar.

Description: We present a physically motivated semi-analytic model to understand the clustering of high-redshift Lyman α emitters (LAEs). We show that the model parameters constrained by the observed luminosity functions can be used to predict large-scale bias and angular correlation function of LAEs. These predictions are shown to reproduce the observations remarkably well. We find that average masses of dark matter haloes hosting LAEs brighter than the threshold narrow-band magnitude ~25 are ~10 11 M . These are smaller than that of typical Lyman break galaxies (LBGs) brighter than a similar threshold continuum magnitude by a factor of ~10. This results in a smaller clustering strength of LAEs compared to LBGs. However, using the observed relationship between the UV continuum and Lyman α luminosity of LAEs, we show that both LAEs and LBGs belong to the same parent galaxy population with narrow-band techniques having greater efficiency in picking up galaxies with low UV luminosity. We also show that the lack of evidence for the presence of the one-halo term in the observed LAE angular correlation functions can be attributed to a sub-Poisson distribution of LAEs in dark matter haloes as a result of their low halo occupations.

Description: We present a detailed analysis of spectral line profiles in Type Ia supernova (SN Ia) spectra. We focus on the feature at ~3500–4000 Å, which is commonly thought to be caused by blueshifted absorption of Ca H&K. Unlike some other spectral features in SN Ia spectra, this feature often has two overlapping (blue and red) components. It is accepted that the red component comes from photospheric calcium. However, it has been proposed that the blue component is caused by either high-velocity calcium (from either abundance or density enhancements above the photosphere of the supernova, SN) or Si ii 3858. By looking at multiple data sets and model spectra, focusing on spectra near maximum brightness, we conclude that the blue component of the Ca H&K feature is caused by Si ii 3858 for most SNe Ia, although high-velocity calcium is likely important for some SNe. The strength of the Si ii 3858 feature varies strongly with the light-curve shape of an SN. As a result, the velocity measured from a single-Gaussian fit to the full line profile correlates with light-curve shape. The velocity of the Ca H&K component of the profile does not correlate with light-curve shape, contrary to previous claims. We detail the pitfalls of assuming that the blue component of the Ca H&K feature is caused by calcium, with implications for our understanding of SN Ia progenitors, explosions and cosmology.

Description: Subject of this paper is the statistical properties of ellipticity alignments between galaxies evoked by their coupled angular momenta. Starting from physical angular momentum models, we bridge the gap towards ellipticity correlations, ellipticity spectra and derived quantities such as aperture moments, comparing the intrinsic signals with those generated by gravitational lensing, with the projected galaxy sample of Euclid in mind. We investigate the dependence of intrinsic ellipticity correlations on cosmological parameters and show that intrinsic ellipticity correlations give rise to non-Gaussian likelihoods as a result of non-linear functional dependences. Comparing intrinsic ellipticity spectra to weak lensing spectra we quantify the magnitude of their contaminating effect on the estimation of cosmological parameters and find that biases on dark energy parameters are very small in an angular momentum-based model in contrast to the linear alignment model commonly used. Finally, we quantify whether intrinsic ellipticities can be measured in the presence of the much stronger weak lensing induced ellipticity correlations, if prior knowledge on a cosmological model is assumed.

Description: In this paper, I present a new method that has been developed for determining the brightness of a cloudless night sky, on the basis of widely available amateur observations of comets. The tests show the correctness of the method, which makes it possible to determine the level of light pollution, defined as the brightness of the artificial sky glow, through the use of the archival observations of comets. The use of data bases of comet observations in Poland in the period 1994–2009 has led to a positive verification of the known model map of the brightness of the night sky. Also, it has been possible to find changes in the level of light pollution in this period, at the selected observation sites.

Description: We present a complete sample of molecular clumps containing compact and ultracompact H ii (UC H ii ) regions between  = 10° and 60° and | b | 〈 1°, identified by combining the APEX Telescope Large Area Survey of the Galaxy submm and CORNISH radio continuum surveys with visual examination of archival infrared data. Our sample is complete to optically thin, compact and UC H ii regions driven by a zero-age main-sequence star of spectral type B0 or earlier embedded within a 1000 M clump. In total we identify 213 compact and UC H ii regions, associated with 170 clumps. Unambiguous kinematic distances are derived for these clumps and used to estimate their masses and physical sizes, as well as the Lyman continuum fluxes and sizes of their embedded H ii regions. We find a clear lower envelope for the surface density of molecular clumps hosting massive star formation of 0.05 g cm –2 , which is consistent with a similar sample of clumps associated with 6.7 GHz masers. The mass of the most massive embedded stars is closely correlated with the mass of their natal clump. Young B stars appear to be significantly more luminous in the ultraviolet than predicted by current stellar atmosphere models. The properties of clumps associated with compact and UC H ii regions are very similar to those associated with 6.7 GHz methanol masers and we speculate that there is little evolution in the structure of the molecular clumps between these two phases. Finally, we identify a significant peak in the surface density of compact and UC H ii -regions associated with the W49A star-forming complex, noting that this complex is truly one of the most massive and intense regions of star formation in the Galaxy.

Description: We present full Stokes radio polarization observations of the quasar PKS B2126–158 ( z  = 3.268) from 1 to 10 GHz using the Australia Telescope Compact Array. The source has large fractional circular polarization (CP), m c | V |/ I , detected at high significance across the entire band (from 15 to 90 per 128 MHz subband). This allows us to construct the most robust CP spectrum of an active galactic nucleus (AGN) jet to date. We find m c    +0.60 ± 0.03 from 1.5 to 6.5 GHz, with a peak of m c ~ 1 per cent before the spectrum turns over somewhere between 6.5 and 8 GHz, above which m c    –3.0 ± 0.4 . The fractional linear polarization (LP; p ) varies from 0.2 to ~1 per cent across our frequency range and is strongly anticorrelated with the fractional CP, with a best-fitting power law giving m c    p –0.24 ± 0.03 . This is the first clear relation between the observed LP and CP of an AGN jet, revealing the action of Faraday conversion of LP to CP within the jet. More detailed modelling in conjunction with high spatial resolution observations are required to determine the true driving force behind the conversion (i.e. magnetic twist or internal Faraday rotation). In particular determining whether the observed Faraday rotation is internal or entirely external to the jet is key to this goal. The simplest interpretation of our observations favours some internal Faraday rotation, implying that Faraday rotation-driven conversion of LP to CP is the dominant CP generation mechanism. In this case, a small amount of vector-ordered magnetic field along the jet axis is required, along with internal Faraday rotation from the low-energy end of the relativistic electron energy spectrum in an electron–proton-dominated jet.

Description: We present new H i observations of Hoag's Object (HO) obtained with the Westerbork Synthesis Radio Telescope. The data show that the luminous optical ring around the elliptical body has a bright H i counterpart that shares the kinematical properties of the optical ring. The entire H i structure is twice as large as the optical ring and shows a mild warp in its outer regions relative to the inner ring. We detect two additional H i sources close in redshift to that of HO, and report on a newly identified SDSS optical companion galaxy. The H i sources are ~0.3 and ~1 Mpc away in projected distance, and the companion galaxy is also ~1 Mpc away. Our main conclusion is that the H i detected in HO shows no indication that this galaxy has experienced a recent (less than ~1 Gyr ago) accretion event. At least one of the two additional H i detected objects does not have an optical counterpart. One possibility is that this object is an H i filament left over from an interaction shaping HO, in which case this interaction must also have occurred at least 1–2 Gyr ago.

Description: We report the first comparative study of strong Mg ii absorbers ( W r  ≥ 1.0 Å) seen towards radio-loud quasars of core-dominated (CDQ) and lobe-dominated (LDQ) types and normal quasars (QSOs). The CDQ and LDQ samples were derived from the Sloan Digital Sky Survey Data Release 7 after excluding known ‘broad-absorption-line’ quasars and blazars. The Mg ii associated absorption systems having a velocity offset v  〈 5000 km s –1 from the systemic velocity of the background quasar were also excluded. Existing spectroscopic data for redshift-matched sightlines of 3975 CDQs and 1583 LDQs, covering an emission redshift range 0.39–4.87, were analysed and 864 strong Mg ii absorbers were found, covering the redshift range 0.45–2.17. The conclusions reached using this well-defined large data set of strong Mg ii absorbers are (i) the number density, d N /d z , towards CDQs shows a small, marginally significant excess (~9 per cent at 1.5 significance) over the estimate available for QSOs; (ii) in the redshift space, this difference is reflected in terms of a 1.6 excess of d N /d z over the QSOs, within the narrow redshift interval 1.2–1.8; (iii) the d N /dβ distribution (with β =  v / c ) for CDQs shows a significant excess (at 3.75 level) over the distribution found for a redshift- and luminosity-matched sample of QSOs, at β in the range 0.05–0.1. This leads us to infer that a significant fraction of strong Mg ii absorption systems seen in this offset velocity range are probably associated with the CDQs and might be accelerated into the line of sight by their powerful jets and/or due to the accretion-disc outflows close to our direction. Support to this scenario comes from a consistency check in which we consider only the spectral range corresponding to β 〉 0.2. The computed redshift distribution for strong Mg ii absorbers towards CDQs now shows excellent agreement with that known for QSOs, as indeed is expected for purely intervening absorption systems. Thus, it appears that for CDQs (and blazars) the associated strong Mg ii absorbers can be seen at much larger velocities relative to the nucleus than the commonly adopted upper limit of 5000 km s –1 .

Description: Dynamics of a complete sample of small perihelion distance near-parabolic comets discovered in the years 2006–2010 are studied (i.e. of 22 comets of q osc  〈 3.1 au). First, osculating orbits are obtained after a very careful positional data inspection and processing, including where appropriate, the method of data partitioning for determination of pre- and post-perihelion orbit for tracking then its dynamical evolution. The non-gravitational acceleration in the motion is detected for 50 per cent of investigated comets, in a few cases for the first time. Different sets of non-gravitational parameters are determined from pre- and post-perihelion data for some of them. The influence of the positional data structure on the possibility of the detection of non-gravitational effects and the overall precision of orbit determination is widely discussed. Secondly, both original and future orbits were derived by means of numerical integration of swarms of virtual comets obtained using a Monte Carlo cloning method. This method allows us to follow the uncertainties of orbital elements at each step of dynamical evolution. The complete statistics of original and future orbits that includes significantly different uncertainties of 1/ a -values is presented, also in the light of our results obtained earlier. Basing on 108 comets examined by us so far, we conclude that only one of them, C/2007 W1 Boattini, seems to be a serious candidate for an interstellar comet. We also found that 53 per cent of 108 near-parabolic comets escaping in the future from the Solar system, and the number of comets leaving the Solar system as so called Oort spike comets (i.e. comets suffering very small planetary perturbations) is 14 per cent. A new method for cometary orbit quality assessment is also proposed by means of modifying the original method, introduced by Marsden, Sekanina & Everhart. This new method leads to a better diversification of orbit quality classes for contemporary comets.

Description: We present the chemical abundance measurements of the first large, medium-resolution, uniformly selected damped Lyman α system (DLA) survey. The sample contains 99 DLAs towards 89 quasars selected from the SDSS DR5 DLA sample in a uniform way. We analyse the metallicities and kinematic diagnostics, including the velocity width of 90 per cent of the optical depth, v 90 , and the equivalent widths of the Si ii 1526 ( W 1526 ), C iv 1548 and Mg ii 2796 transitions. To avoid strong line-saturation effects on the metallicities measured in medium-resolution spectra (FWHM ~ 71 km s –1 ), we derived metallicities from metal transitions which absorbed at most 35 per cent of the quasar continuum flux. We find the evolution in cosmic mean metallicity of the sample, 〈 Z 〉 = (–0.04 ± 0.13) z  – (1.06 ± 0.36), consistent with no evolution over the redshift range z ~ [2.2, 4.4], but note that the majority of our sample falls at z ~ [2.2, 3.5]. The apparent lack of metallicity evolution with redshift is also seen in a lack of evolution in the median v 90 and W 1526 values. While this result may seem to conflict with other large surveys that have detected significant metallicity evolution, such as Rafelski et al. who found 〈 Z 〉 = (–0.22 ± 0.03) z  – (0.65 ± 0.09) over z ~ [0, 5], several tests show that these surveys are not inconsistent with our new result. However, over the smaller redshift range covered by our uniformly selected sample, the true evolution of the cosmic mean metallicity in DLAs may be somewhat flatter than the Rafelski et al. estimate.

Description: Expulsion of neutron-rich matter following the merger of neutron star binaries is crucial to the radioactively powered electromagnetic counterparts of these events and to their relevance as sources of r -process nucleosynthesis. Here we explore the long-term (viscous) evolution of remnant black hole accretion discs formed in such mergers by means of two-dimensional, time-dependent hydrodynamical simulations. The evolution of the electron fraction due to charged-current weak interactions is included, and neutrino self-irradiation is modelled as a lightbulb that accounts for the disc geometry and moderate optical depth effects. Over several viscous times (~1 s), a fraction of ~10 per cent of the initial disc mass is ejected as a moderately neutron-rich wind ( Y e  ~ 0.2) powered by viscous heating and nuclear recombination, with neutrino self-irradiation playing a sub-dominant role. Although the properties of the outflow vary in time and direction, their mean values in the heavy-element production region are relatively robust to variations in the initial conditions of the disc and the magnitude of its viscosity. The outflow is sufficiently neutron-rich that most of the ejecta forms heavy r -process elements with mass number A   130, thus representing a new astrophysical source of r -process nucleosynthesis, distinct from that produced in the dynamical ejecta. Due to its moderately high entropy, disc outflows contain a small residual fraction ~1 per cent of helium, which could produce a unique spectroscopic signature.

Description: We have performed multiband UBVR C I C JHK S photometry of two young clusters located at large Galactocentric distances in the direction of the Perseus spiral arm. The obtained distances and colour excesses amount to 3.9 ± 0.11 kpc, E ( B  –  V ) = 0.62 ± 0.05 for Berkeley 94, and 4.3 ± 0.15 kpc, E ( B  –  V ) = 0.58 ± 0.06 for Berkeley 96. The respective ages, as measured from the comparison of the upper colour–magnitude diagrams to model isochrones, amount to log 10 Age(yr) = 7.5 ± 0.07 and 7.0 ± 0.07, respectively. A sequence of optical pre-main-sequence (PMS) members is proposed in both clusters. In addition, samples of objects showing ( H  –  K S ) excess are found. Part of these are suggested to be PMS cluster members of lower mass than the optical candidates. The spatial distribution of these sources, the comparison to Galactic models and to the expected number of contaminating distant red galaxies, and the spectral energy distribution in particular cases support this suggestion. The spatial distributions shown by members in different mass ranges can be interpreted in terms of the results from numerical simulations. According to these, different initial conditions and evolutionary dynamical paths are suggested for the clusters. Berkeley 94 would have formed under supervirial conditions, and followed the so-called warm collapse model in its evolution, whereas Berkeley 96 would have formed with a subvirial structure, and would have evolved following a cold collapse path. Both processes would be able to reproduce the suggested degree of mass segregation and their spatial distribution by mass range. Finally, the mass distributions of the clusters, from the most massive stars down to PMS stars around 1.3 M , are calculated. An acceptable general agreement with the Salpeter initial mass function slope is found.

Description: The class of tidal features around galaxies known as ‘shells’ or ‘umbrellas’ comprises debris that has arisen from high-mass-ratio mergers with low-impact parameter; the nearly radial orbits of the debris give rise to a unique morphology, a universal density profile and a tight correlation between positions and velocities of the material. As such they are accessible to analytical treatment, and can provide a relatively clean system for probing the gravitational potential of the host galaxy. In this work, we present a simple analytical model that describes the density profile, phase-space distribution, and geometry of a shell and whose parameters are directly related to physical characteristics of the interacting galaxies. The model makes three assumptions: the orbit of the interacting galaxies is radial, the potential of the host galaxy at the shell radius is spherical and the satellite galaxy's initial velocity distribution is Maxwellian. We quantify the error introduced by the first two assumptions and show that selecting shells by their appearance on the sky is a sufficient basis to assume that these simplifications are valid. We further demonstrate that (1) given only an image of a shell, the radial gravitational force at the shell edge and the phase-space density of the satellite are jointly constrained, (2) combining the image with measurements of either point line-of-sight velocities or integrated-light spectra will yield an independent estimate of the gravitational force at a shell and (3) an independent measurement of this force is obtained for each shell observed around a given galaxy, potentially enabling a determination of the galactic mass distribution.

Description: In the context of upcoming large-scale structure surveys such as Euclid , it is of prime importance to quantify the effect of peculiar velocities on geometric probes. Hence, the formalism to compute in redshift space the geometrical and topological one-point statistics of mildly non-Gaussian 2D and 3D cosmic fields is developed. Leveraging the partial isotropy of the target statistics, the Gram–Charlier expansion of the joint probability distribution of the field and its derivatives is reformulated in terms of the corresponding anisotropic variables. In particular, the cosmic non-linear evolution of the Minkowski functionals, together with the statistics of extrema, is investigated in turn for 3D catalogues and 2D slabs. The amplitude of the non-Gaussian redshift distortion correction is estimated for these geometric probes. In 3D, gravitational perturbation theory is implemented in redshift space to predict the cosmic evolution of all relevant Gram–Charlier coefficients. Applications to the estimation of the cosmic parameters ( z ) and β =  f / b 1 from upcoming surveys are discussed. Such statistics are of interest for anisotropic fields beyond cosmology.

Description: One of the most promising ways to study the epoch of reionization (EoR) is through radio observations of the redshifted 21-cm line emission from neutral hydrogen. These observations are complicated by the fact that the mapping of redshifts to line-of-sight positions is distorted by the peculiar velocities of the gas. Such distortions can be a source of error if they are not properly understood, but they also encode information about cosmology and astrophysics. We study the effects of redshift space distortions on the power spectrum of 21-cm radiation from the EoR using large-scale N -body and radiative transfer simulations. We quantify the anisotropy introduced in the 21-cm power spectrum by redshift space distortions and show how it evolves as reionization progresses and how it relates to the underlying physics. We go on to study the effects of redshift space distortions on LOFAR observations, taking instrument noise and foreground subtraction into account. We find that LOFAR should be able to directly observe the power spectrum anisotropy due to redshift space distortions at spatial scales around k  ~ 0.1 Mpc –1 after 1000 h of integration time. At larger scales, sample errors become a limiting factor, while at smaller scales detector noise and foregrounds make the extraction of the signal problematic. Finally, we show how the astrophysical information contained in the evolution of the anisotropy of the 21-cm power spectrum can be extracted from LOFAR observations, and how it can be used to distinguish between different reionization scenarios.

Description: Among the three cosmological enigma solved by the theory of inflation, viz. (a) large-scale flatness, (b) absence of monopoles and strings and (c) structure formation, the first two are addressed from the viewpoint of the observed scales having originated from very small ones, on which the density fluctuations of the curvaton and relics are inevitably of the order of unity or larger. By analysing strictly classically (and in two different gauges to ensure consistency) the density evolution of the smoothest possible pre-inflationary component – thermal radiation – it is found that the O(1) statistical fluctuations on the thermal wavelength scale present formidable obstacles to the linear theory of amplitude growth by the end of inflation. Since this wavelength scale exited the horizon at an early stage of inflation, it severely limits the number of e-folds of perturbative inflation. With more e-folds than 60 there will be even larger fluctuations in the radiation density that ensures inflation keeps making ‘false starts’. The only ‘way out’ is to invoke a super-homogeneous pre-inflationary fluid, at least on small scales, adding to the fine-tuning and preventing one from claiming that inflation simply ‘redshifts away’ all the relic inhomogeneities; i.e. the theory actually provided no explanation of (a) or (b), merely a tautology.

Description: Recently, a comparison between the locations of 6.7-GHz methanol masers and dust continuum emission has renewed speculation that these masers can be associated with evolved stars. The implication of such a scenario would be profound, especially for the interpretation of large surveys for 6.7-GHz masers, individual studies where high-mass star formation has been inferred from the presence of 6.7-GHz methanol masers and for the pumping mechanisms of these masers. We have investigated the two instances where 6.7-GHz methanol masers have been explicitly suggested to be associated with evolved stars, and we find the first to be associated with a standard high-mass star formation region, and the second to be a spurious detection. We also find no evidence to suggest that the methanol maser action can be supported in the environments of evolved stars. We thereby confirm their exclusive association with high-mass star formation regions.

Description: 14 stars from a sample of Magellanic Cloud objects selected to have a mid-infrared flux excess have been found to also show TiO bands in emission. The mid-infrared dust emission and the TiO band emission indicate that these stars have large amounts of hot circumstellar dust and gas in close proximity to the central star. The luminosities of the sources are typically several thousand L , while the effective temperatures are ~4000–8000 K which puts them bluewards of the giant branch. Such stars could be post-asymptotic giant branch (post-AGB) stars of mass ~0.4–0.8 M or pre-main-sequence stars (young stellar objects) with masses in the range ~7–19 M . If the stars are pre-main-sequence stars, they are substantially cooler and younger than stars at the birth line where Galactic protostars are first supposed to become optically visible out of their molecular clouds. They should therefore be hidden in their present evolutionary state, although this problem may be overcome if asymmetries are invoked or if the reduced metallicity of the Small Magellanic Cloud and Large Magellanic Cloud compared to the Galaxy makes the circumstellar material more transparent. The second explanation for these stars is that they are post-AGB or post-red giant branch stars that have recently undergone a binary interaction when the red giant of the binary system filled its Roche lobe. Being oxygen-rich, they have gone through this process before becoming carbon stars. Most of the stars vary slowly on time-scales of 1000 d or more, suggesting a changing circumstellar environment. Apart from the slow variations, most stars also show variability with periods of tens to hundreds of days. One star shows a period that is rapidly decreasing and we speculate that this star may have accreted a large blob of gas and dust on to a disc whose orbital radius is shrinking rapidly. Another star has Cepheid-like pulsations of rapidly increasing amplitude, suggesting a rapid rate of evolution. Seven stars show quasi-periodic variability and one star has a light curve similar to that of an eclipsing binary.

Description: Faint undetected sources of radio-frequency interference (RFI) might become visible in long radio observations when they are consistently present over time. Thereby, they might obstruct the detection of the weak astronomical signals of interest. This issue is especially important for Epoch of Reionization (EoR) projects that try to detect the faint redshifted H  i signals from the time of the earliest structures in the Universe. We explore the RFI situation at 30–163 MHz by studying brightness histograms of visibility data observed with Low-Frequency Array (LOFAR), similar to radio-source-count analyses that are used in cosmology. An empirical RFI distribution model is derived that allows the simulation of RFI in radio observations. The brightness histograms show an RFI distribution that follows a power-law distribution with an estimated exponent around –1.5. With several assumptions, this can be explained with a uniform distribution of terrestrial radio sources whose radiation follows existing propagation models. Extrapolation of the power law implies that the current LOFAR EoR observations should be severely RFI limited if the strength of RFI sources remains strong after time integration. This is in contrast with actual observations, which almost reach the thermal noise and are thought not to be limited by RFI. Therefore, we conclude that it is unlikely that there are undetected RFI sources that will become visible in long observations. Consequently, there is no indication that RFI will prevent an EoR detection with LOFAR.

Description: Very Large Array deep radio images at 1.4 GHz in total intensity and polarization reveal a diffuse non-thermal source in the interacting clusters A3411–A3412. Moreover, a small-size low-power radio halo at the centre of the merging cluster A3411 is found. We present here new optical and X-ray data and discuss the nature and properties of the diffuse non-thermal source. We suggest that the giant diffuse radio source is related to the presence of a large-scale filamentary structure and to multiple mergers in the A3411–A3412 complex.

Description: We describe a 325-MHz survey, undertaken with the Giant Metrewave Radio Telescope (GMRT), which covers a large part of the three equatorial fields at 9, 12 and 14.5 h of right ascension from the Herschel -Astrophysical Terahertz Large Area Survey (H-ATLAS) in the area also covered by the Galaxy And Mass Assembly (GAMA) survey. The full data set, after some observed pointings were removed during the data reduction process, comprises 212 GMRT pointings covering ~90 deg 2 of sky. We have imaged and catalogued the data using a pipeline that automates the process of flagging, calibration, self-calibration and source detection for each of the survey pointings. The resulting images have resolutions of between 14 and 24 arcsec and minimum rms noise (away from bright sources) of ~1 mJy beam –1 , and the catalogue contains 5263 sources brighter than 5. We investigate the spectral indices of GMRT sources which are also detected at 1.4 GHz and find them to agree broadly with previously published results; there is no evidence for any flattening of the radio spectral index below S 1.4  = 10 mJy. This work adds to the large amount of available optical and infrared data in the H-ATLAS equatorial fields and will facilitate further study of the low-frequency radio properties of star formation and AGN activity in galaxies out to z  ~ 1.

Description: We demonstrate a new multiwavelength technique for two-dimensional parametric modelling of galaxy surface-brightness profiles, which we have incorporated into the widely used software galfit . Our new method, named galfitm , extends galfit3 's current single-band fitting process by simultaneously using multiple images of the same galaxy to constrain a wavelength-dependent model. Each standard profile parameter may vary as a function of wavelength, with a user-definable degree of smoothness, from constant to fully free. The performance of galfitm is evaluated by fitting elliptical Sérsic profiles to ugriz imaging data for 4026 galaxies, comprising the original Sloan Digital Sky Survey (SDSS) imaging for 163 low-redshift ( v 7000 km s –1 ) galaxies and 3863 artificially redshifted (0.01 z 0.25) images of the same galaxies. Comparing results from single-band and multiband techniques, we show that galfitm significantly improves the extraction of information, particularly from bands with low signal-to-noise ratio (e.g. u and z SDSS bands) when combined with higher signal-to-noise images. We also study systematic trends in the recovered parameters, particularly Sérsic index, that appear when one performs measurements of the same galaxies at successively higher redshifts. We argue that it is vital that studies investigating the evolution of galaxy structure are careful to avoid or correct for these biases. The resulting multiband photometric structural parameters for our sample of 163 galaxies are provided. We demonstrate the importance of considering multiband measurements by showing that the Sérsic indices of spiral galaxies increase to redder wavelengths, as expected for composite bulge–disc systems. Finally, for the ellipticals in our sample, which should be well represented by single-Sérsic models, we compare our measured parameters to those from previous studies.

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.