ALBERT

Description: We examine a sample of 1495 galaxies in the CANDELS fields to determine the evolution of two-component galaxies, including bulges and discs, within massive galaxies at the epoch 1 〈  z  〈 3 when the Hubble sequence forms. We fit all of our galaxies’ light profiles with a single Sérsic fit, as well as with a combination of exponential and Sérsic profiles. The latter is done in order to describe a galaxy with an inner and an outer component, or bulge and disc component. We develop and use three classification methods (visual, F -test and the residual flux fraction) to separate our sample into one-component galaxies (disc/spheroids-like galaxies) and two-component galaxies (galaxies formed by an ‘inner part’ or bulge and an ‘outer part’ or disc). We then compare the results from using these three different ways to classify our galaxies. We find that the fraction of galaxies selected as two-component galaxies increases on average 50 per cent from the lowest mass bin to the most massive galaxies, and decreases with redshift by a factor of 4 from z  = 1 to 3. We find that single Sérsic ‘disc-like’ galaxies have the highest relative number densities at all redshifts, and that two-component galaxies have the greatest increase and become at par with Sérsic discs by z  = 1. We also find that the systems we classify as two-component galaxies have an increase in the sizes of their outer components, or ‘discs’, by about a factor of 3 from z  = 3 to 1.5, while the inner components or ‘bulges’ stay roughly the same size. This suggests that these systems are growing from the inside out, whilst the bulges or protobulges are in place early in the history of these galaxies. This is also seen to a lesser degree in the growth of single ‘disc-like’ galaxies versus ‘spheroid-like’ galaxies over the same epoch.

Description: Using the idea of regularization of singularities due to the variability of the fundamental constants in cosmology we study the cyclic universe models. We find two models of oscillating and non-singular mass density and pressure (‘non-singular’ bounce) regularized by varying gravitational constant G despite the scale factor evolution is oscillating and having sharp turning points (‘singular’ bounce). Both violating (big-bang) and non-violating (phantom) null energy condition models appear. Then, we extend this idea on to the multiverse containing cyclic individual universes with either growing or decreasing entropy though leaving the net entropy constant. In order to get an insight into the key idea, we consider the doubleverse with the same geometrical evolution of the two ‘parallel’ universes with their physical evolution [physical coupling constants c ( t ) and G ( t )] being different. An interesting point is that there is a possibility to exchange the universes at the point of maximum expansion – the fact which was already noticed in quantum cosmology. Similar scenario is also possible within the framework of Brans–Dicke theory where varying G ( t ) is replaced by the dynamical Brans–Dicke field ( t ) though these theories are slightly different.

Description: In the thermal dark matter (DM) paradigm, primordial interactions between DM and Standard Model particles are responsible for the observed DM relic density. In Bœhm et al., we showed that weak-strength interactions between DM and radiation (photons or neutrinos) can erase small-scale density fluctuations, leading to a suppression of the matter power spectrum compared to the collisionless cold DM (CDM) model. This results in fewer DM subhaloes within Milky Way-like DM haloes, implying a reduction in the abundance of satellite galaxies. Here we use very high-resolution N -body simulations to measure the dynamics of these subhaloes. We find that when interactions are included, the largest subhaloes are less concentrated than their counterparts in the collisionless CDM model and have rotation curves that match observational data, providing a new solution to the ‘too big to fail’ problem.

Description: The recent discovery of the gravitational wave source GW150914 has revealed a coalescing binary black hole (BBH) with masses of ~30 M . Previous proposals for the origin of such a massive binary include Population III (PopIII) stars. PopIII stars are efficient producers of BBHs and of a gravitational wave background (GWB) in the 10–100 Hz band, and also of ionizing radiation in the early Universe. We quantify the relation between the amplitude of the GWB ( gw ) and the electron scattering optical depth ( e ), produced by PopIII stars, assuming that f esc 10 per cent of their ionizing radiation escapes into the intergalactic medium. We find that PopIII stars would produce a GWB that is detectable by the future O5 LIGO/Virgo if e 0.07, consistent with the recent Planck measurement of e = 0.055 ± 0.09. Moreover, the spectral index of the background from PopIII BBHs becomes as small as dln gw /dln f 0.3 at f 30 Hz, which is significantly flatter than the value ~2/3 generically produced by lower redshift and less-massive BBHs. A detection of the unique flattening at such low frequencies by the O5 LIGO/Virgo will indicate the existence of a high-chirp mass, high-redshift BBH population, which is consistent with the PopIII origin. A precise characterization of the spectral shape near 30–50 Hz by the Einstein Telescope could also constrain the PopIII initial mass function and star formation rate.

Description: We employ very high resolution simulations of isolated Milky Way-like galaxies to study the effect of triaxial dark matter haloes on exponential stellar discs. Non-adiabatic halo shape changes can trigger two-armed grand-design spiral structures which extend all the way to the edge of the disc. Their pattern speed coincides with the inner Lindblad resonance indicating that they are kinematic density waves which can persist up to several Gyr. In dynamically cold discs, grand-design spirals are swing amplified and after a few Gyr can lead to the formation of (multi-armed) transient recurrent spirals. Stellar discs misaligned to the principal planes of the host triaxial halo develop characteristic integral shaped warps, but otherwise exhibit very similar spiral structures as aligned discs. For the grand-design spirals in our simulations, their strength dependence with radius is determined by the torque on the disc, suggesting that by studying grand-design spirals without bars it may be possible to set constraints on the tidal field and host dark matter halo shape.

Description: Intrinsic galaxy shape and angular momentum alignments can arise in cosmological large-scale structure due to tidal interactions or galaxy formation processes. Cosmological hydrodynamical simulations have recently come of age as a tool to study these alignments and their contamination to weak gravitational lensing. We probe the redshift and luminosity evolution of intrinsic alignments in Horizon-AGN between z = 0 and 3 for galaxies with an r -band absolute magnitude of M r ≤ –20. Alignments transition from being radial at low redshifts and high luminosities, dominated by the contribution of ellipticals, to being tangential at high redshift and low luminosities, where discs dominate the signal. This cannot be explained by the evolution of the fraction of ellipticals and discs alone: intrinsic evolution in the amplitude of alignments is necessary. The alignment amplitude of elliptical galaxies alone is smaller in amplitude by a factor of ~=2, but has similar luminosity and redshift evolution as in current observations and in the non-linear tidal alignment model at projected separations of 1 Mpc. Alignments of discs are null in projection and consistent with current low-redshift observations. The combination of the two populations yields an overall amplitude a factor of ~=4 lower than observed alignments of luminous red galaxies with a steeper luminosity dependence. The restriction on accurate galaxy shapes implies that the galaxy population in the simulation is complete only to M r ≤ –20. Higher resolution simulations will be necessary to avoid extrapolation of the intrinsic alignment predictions to the range of luminosities probed by future surveys.

Description: The spins of stellar-mass black holes (BHs) and the power outputs of their jets are measurable quantities. Unfortunately, the currently employed methods do not agree and the results are controversial. Two major issues concern the measurements of BH spin and beam (jet) power. The former issue can be resolved by future observations. But the latter issue can be resolved now, if we pay attention to what is expected from theoretical considerations. The question of whether a correlation has been found between the power outputs of few objects and the spins of their BHs is moot because BH beam power does not scale with the square of the spin of the BH. We show that the theoretical BH beam power is a strongly non-linear function of spin that cannot be approximated by a quadratic relation, as is generally stated when the influence of the magnetic field is not accounted for in the Blandford & Znajek model. The BH beam power of ballistic jets should scale a lot more steeply with BH spin irrespective of the magnetic field assumed to thread the horizon and the spin range considered. This behaviour may already be visible in the analyses of radio observations by Narayan & McClintock and Russell et al. In agreement with previous studies, we also find that the power output that originates in the inner regions of the surrounding accretion discs is higher than that from the BHs and it cannot be ignored in investigations of continuous compact jets from these systems.

Description: We present deep spectroscopy of three Galactic planetary nebulae (PNe) with large abundance discrepancy factors: NGC 6153, M 1-42 and Hf 2-2. The spectra were obtained with Very Large Telescope/Ultraviolet and Visual Echelle Spectrograph and cover the whole optical range (3040–11 000 Å) with a spectral resolution of ~20 000. For all three PNe, several hundred emission lines were detected and identified, with more than 70 per cent of them as permitted lines. Most of these permitted lines are excited by recombination. Numerous weak optical recombination lines (ORLs) of O ii , C ii , N ii and Ne ii were detected in the spectra and accurate fluxes measured. Line flux tables were compiled and ready for use by the community of nebular astrophysics. These ORLs were critically analysed using the effective recombination coefficients recently calculated for the optical recombination spectrum of N ii and O ii under the physical conditions of photoionized gaseous nebulae. Plasma diagnostics based on the heavy element ORLs were carried out using the new atomic data. Elemental abundances derived from the ORLs were systematically higher than those derived from the collisionally excited lines (CELs) by a factor of ~11, 22 and 80 for NGC 6153, M 1-42 and Hf 2-2, respectively. The electron temperatures derived from the heavy element ORLs are systematically lower than those derived from the CELs. These ORL versus CEL abundance and temperature discrepancies, previously observed in the three PNe through deep spectroscopy with medium to low spectral resolution, are thus confirmed by our analysis of the deep echelle spectra using the new atomic data.

Description: The birth of the first luminous sources and the ensuing epoch of reionization are best studied via the redshifted 21-cm emission line, the signature of the first two imprinting the last. In this work, we present a fully Bayesian method, hibayes , for extracting the faint, global (sky-averaged) 21-cm signal from the much brighter foreground emission. We show that a simplified (but plausible) Gaussian model of the 21-cm emission from the Cosmic Dawn epoch (15 z 30), parametrized by an amplitude $A_{\rm H\,\small {I}}$ , a frequency peak $\nu _{\rm H\,\small {I}}$ and a width $\sigma _{\rm H\,\small {I}}$ , can be extracted even in the presence of a structured foreground frequency spectrum (parametrized as a seventh-order polynomial), provided sufficient signal-to-noise (400 h of observation with a single dipole). We apply our method to an early, 19-min-long observation from the Large aperture Experiment to detect the Dark Ages, constraining the 21-cm signal amplitude and width to be $-890 \lt A_{\rm H\,\small {I}} \lt 0$ mK and $\sigma _{\rm H\,\small {I}} \gt 6.5$ MHz (corresponding to z 〉 1.9 at redshift z ~= 20) respectively at the 95-per cent confidence level in the range 13.2 〈 z 〈 27.4 (100 〉 〉 50 MHz).

Description: Several dedicated surveys focusing on early-type galaxies (ETGs) reveal that significant fractions of them are detectable in all interstellar medium phases studied to date. We select ETGs from the Herschel Reference Survey that have both far-infrared Herschel and either H  i or CO detection (or both). We derive their star formation rates (SFRs), stellar masses and dust masses via modelling their spectral energy distributions. We combine these with literature information on their atomic and molecular gas properties, in order to relate their star formation, total gas mass and dust mass on global scales. The ETGs deviate from the dust mass–SFR relation and the Schmidt–Kennicutt relation that SDSS star-forming galaxies define: compared to SDSS galaxies, ETGs have more dust at the same SFR, or less SFR at the same dust mass. When placing them in the M * –SFR plane, ETGs show a much lower specific SFR as compared to normal star-forming galaxies. ETGs show a large scatter compared to the Schmidt–Kennicutt relation found locally within our Galaxy, extending to lower SFRs and gas mass surface densities. Using an ETG's SFR and the Schmidt–Kennicutt law to predict its gas mass leads to an underestimate. ETGs have similar observed-gas-to-modelled-dust mass ratios to star-forming galaxies of the same stellar mass, as well as they exhibit a similar scatter.

Description: We report on the identification of the new Galactic Centre (GC) transient Swift J174540.7–290015 as a likely low-mass X-ray binary located at only 16 arcsec from Sgr A * . This transient was detected on 2016 February 6, during the Swift GC monitoring, and it showed long-term spectral variations compatible with a hard- to soft-state transition. We observed the field with XMM–Newton on February 26 for 35 ks, detecting the source in the soft state, characterized by a low level of variability and a soft X-ray thermal spectrum with a high energy tail (detected by INTEGRAL up to ~50 keV), typical of either accreting neutron stars or black holes. We observed: (i) a high column density of neutral absorbing material, suggesting that Swift J174540.7–290015 is located near or beyond the GC and; (ii) a sub-Solar iron abundance, therefore we argue that iron is depleted into dust grains. The lack of detection of Fe K absorption lines, eclipses or dipping suggests that the accretion disc is observed at a low inclination angle. Radio (Very Large Array) observations did not detect any radio counterpart to Swift J174540.7–290015. No evidence for X-ray or radio periodicity is found. The location of the transient was observed also in the near-infrared (near-IR) with gamma-ray burst optical near-IR detector at MPG/European Southern Observatory La Silla 2.2 m telescope and VLT/ NaCo pre- and post-outburst. Within the Chandra error region, we find multiple objects that display no significant variations.

Description: This is the first of two papers describing the observations and cataloguing of deep 3-GHz observations of the Lockman Hole North using the Karl G. Jansky Very Large Array. The aim of this paper is to investigate, through the use of simulated images, the uncertainties and accuracy of source-finding routines, as well as to quantify systematic effects due to resolution, such as source confusion and source size. While these effects are not new, this work is intended as a particular case study that can be scaled and translated to other surveys. We use the simulations to derive uncertainties in the fitted parameters, as well as bias corrections for the actual catalogue (presented in Paper II). We compare two different source-finding routines, OBIT and AEGEAN, and two different effective resolutions, 8 and 2.75  arcsec. We find that the two routines perform comparably well, with OBIT being slightly better at de-blending sources, but slightly worse at fitting resolved sources. We show that 30–70 per cent of sources are missed or fit inaccurately once the source size becomes larger than the beam, possibly explaining source count errors in high-resolution surveys. We also investigate the effect of blending, finding that any sources with separations smaller than the beam size are fit as single sources. We show that the use of machine-learning techniques can correctly identify blended sources up to 90 per cent of the time, and prior-driven fitting can lead to a 70 per cent improvement in the number of de-blended sources.

Description: We present evidence for a small glitch in the spin evolution of the millisecond pulsar J0613–0200, using the EPTA Data Release 1.0, combined with Jodrell Bank analogue filterbank times of arrival (TOAs) recorded with the Lovell telescope and Effelsberg Pulsar Observing System TOAs. A spin frequency step of 0.82(3) nHz and frequency derivative step of –1.6(39)  x  10 –19 Hz s –1 are measured at the epoch of MJD 50888(30). After PSR B1821–24A, this is only the second glitch ever observed in a millisecond pulsar, with a fractional size in frequency of / = 2.5(1)  x  10 –12 , which is several times smaller than the previous smallest glitch. PSR J0613–0200 is used in gravitational wave searches with pulsar timing arrays, and is to date only the second such pulsar to have experienced a glitch in a combined 886 pulsar-years of observations. We find that accurately modelling the glitch does not impact the timing precision for pulsar timing array applications. We estimate that for the current set of millisecond pulsars included in the International Pulsar Timing Array, there is a probability of ~50 per cent that another glitch will be observed in a timing array pulsar within 10 years.

Description: We exploit Atacama Large Interferometer Array (ALMA) 870 μm observations to measure the star formation rates (SFRs) of eight X-ray detected active galactic nuclei (AGNs) in a z 3.1 protocluster, four of which reside in extended Lyα haloes (often termed Lyman-alpha blobs: LABs). Three of the AGNs are detected by ALMA and have implied SFRs of 220–410 M  yr –1 ; the non-detection of the other five AGNs places SFR upper limits of 210 M  yr –1 . The mean SFR of the protocluster AGNs (110–210 M  yr –1 ) is consistent (within a factor of 0.7–2.3) with that found for co-eval AGNs in the field, implying that the galaxy growth is not significantly accelerated in these systems. However, when also considering ALMA data from the literature, we find evidence for elevated mean SFRs (up-to a factor of 5.9 over the field) for AGNs at the protocluster core, indicating that galaxy growth is significantly accelerated in the central regions of the protocluster. We also show that all of the four protocluster LABs are associated with an ALMA counterpart within the extent of their Lyα emission. The SFRs of the ALMA sources within the LABs (150–410 M  yr –1 ) are consistent with those expected for co-eval massive star-forming galaxies in the field. Furthermore, the two giant LABs (with physical extents of 100 kpc) do not host more luminous star formation than the smaller LABs, despite being an order of magnitude brighter in Lyα emission. We use these results to discuss star formation as the power source of LABs.

Description: We present the discovery of a new, peculiar form of double-periodic pulsation in RR Lyrae stars. In four, long-period ( P 〉 0.6 d) stars observed by the Optical Gravitational Lensing Experiment, and classified as fundamental mode pulsators (RRab), we detect additional, low-amplitude variability, with period shorter than fundamental mode period. The period ratios fall in a range similar to double-mode fundamental and first overtone RR Lyrae stars (RRd), with the exception of one star, in which the period ratio is significantly lower and nearly exactly equals 0.7. Although period ratios are fairly different for the four stars, the light-curve shapes corresponding to the dominant, fundamental mode are very similar. The peak-to-peak amplitudes and amplitude ratios (Fourier parameters R 21 and R 31 ) are among the highest observed in RRab stars of similar period, while Fourier phases ( 21 and 31 ) are among the lowest observed in RRab stars. If the additional variability is interpreted as due to radial first overtone, then, the four stars are the most extreme RRd variables of the longest pulsation periods known. Indeed, the observed period ratios can be well modelled with high-metallicity pulsation models. However, at such long pulsation periods, first overtone is typically damped. Five other candidates, with weak signature of additional variability, sharing the same characteristics, were also detected and are briefly discussed.

Description: The Laser Interferometer Gravitational-Wave Observatory (LIGO) detection of gravitational waves that take away 5 per cent of the total mass of two merging black holes points out on the importance of considering varying gravitational mass of a system in the framework of the Einstein general theory of relativity. We calculate the acceleration of a particle in the non-stationary field of a quasi-spherical system composed of a large number of objects emitting gravitational waves. It is shown that reduction of the gravitational mass of the system due to emitting gravitational waves leads to a repulsive gravitational force that diminishes with time but never disappears. This repulsive force may be related to the observed expansion of the Universe.

Description: Radiative feedback is an important consequence of cluster formation in giant molecular clouds (GMCs) in which newly formed clusters heat and ionize their surrounding gas. The process of cluster formation, and the role of radiative feedback, has not been fully explored in different GMC environments. We present a suite of simulations which explore how the initial gravitational boundedness, and radiative feedback, affect cluster formation. We model the early evolution (〈5 Myr) of turbulent, 10 6 M clouds with virial parameters ranging from 0.5 to 5. To model cluster formation, we use cluster sink particles, coupled to a raytracing scheme, and a custom subgrid model which populates a cluster via sampling an initial mass function (IMF) with an efficiency of 20 per cent per free-fall time. We find that radiative feedback only decreases the cluster particle formation efficiency by a few per cent. The initial virial parameter plays a much stronger role in limiting cluster formation, with a spread of cluster formation efficiencies of 37–71 per cent for the most unbound to the most bound model. The total number of clusters increases while the maximum mass cluster decreases with an increasing initial virial parameter, resulting in steeper mass distributions. The star formation rates in our cluster particles are initially consistent with observations but rise to higher values at late times. This suggests that radiative feedback alone is not responsible for dispersing a GMC over the first 5 Myr of cluster formation.

Description: Large redshift surveys capable of measuring the baryon acoustic oscillation (BAO) signal have proven to be an effective way of measuring the distance–redshift relation in cosmology. Building off the work in Zhu et al., we develop a technique to directly constrain the distance–redshift relation from BAO measurements without splitting the sample into redshift bins. We apply the redshift weighting technique in Zhu et al. to the clustering of galaxies from 1000 Quick particle mesh (QPM) mock simulations after reconstruction and achieve a 0.75 per cent measurement of the angular diameter distance D A at z = 0.64 and the same precision for Hubble parameter H at z = 0.29. These QPM mock catalogues mimic the clustering and noise level of the Baryon Oscillation Spectroscopic Survey Data Release 12 (DR12). We compress the correlation functions in the redshift direction on to a set of weighted correlation functions. These estimators give unbiased D A and H measurements across the entire redshift range of the combined sample. We demonstrate the effectiveness of redshift weighting in improving the distance and Hubble parameter estimates. Instead of measuring at a single ‘effective’ redshift as in traditional analyses, we report our D A and H measurements at all redshifts. The measured fractional error of D A ranges from 1.53 per cent at z = 0.2 to 0.75 per cent at z = 0.64. The fractional error of H ranges from 0.75 per cent at z = 0.29 to 2.45 per cent at z = 0.7. Our measurements are consistent with a Fisher forecast to within 10–20 per cent depending on the pivot redshift. We further show the results are robust against the choice of fiducial cosmologies, galaxy bias models, and redshift–space distortions streaming parameters.

Description: The dwarf spheroidal galaxies (dSphs) in the Milky Way are the primary targets in the indirect searches for particle dark matter. To set robust constraints on candidate dark matter particles, understanding the dark halo structure of these systems is of substantial importance. In this paper, we first evaluate the astrophysical factors for dark matter annihilation and decay for 24 dSphs, taking into account a non-spherical dark halo, using generalized axisymmetric mass models based on axisymmetric Jeans equations. First, from a fitting analysis of the most recent kinematic data available, our axisymmetric mass models are a much better fit than previous spherical ones, thus, our work should be the most realistic and reliable estimator for astrophysical factors. Secondly, we find that among analysed dSphs, the ultra-faint dwarf galaxies Triangulum II and Ursa Major II are the most promising but large uncertain targets for dark matter annihilation while the classical dSph Draco is the most robust and detectable target for dark matter decay. It is also found that the non-sphericity of luminous and dark components influences the estimate of astrophysical factors, even though these factors largely depend on the sample size, the prior range of parameters and the spatial extent of the dark halo. Moreover, owing to these effects, the constraints on the dark matter annihilation cross-section are more conservative than those of previous spherical works. These results are important for optimizing and designing dark matter searches in current and future multi-messenger observations by space and ground-based telescopes.

Description: Invertebrate animal species that can withstand temperatures as high as 37°C, the human body temperature, are limited. In the present study, we utilized the two-spotted cricket, Gryllus bimaculatus , which lives in tropical and subtropical regions, as an animal model of human pathogenic bacterial infection. Injection of Pseudomonas aeruginosa or Staphylococcus aureus into the hemolymph killed crickets. Injected P. aeruginosa or S. aureus proliferated in the hemolymph until the cricket died. The ability of these pathogenic bacteria to kill the crickets was blocked by the administration of antibiotics. S. aureus gene-knockout mutants of virulence factors, including cvfA, agr and srtA , exhibited decreased killing ability compared with the parent strain. The dose at which 50% of crickets were killed by P. aeruginosa or S. aureus was not decreased at 37°C compared with that at 27°C. Injection of Listeria monocytogenes , which upregulates toxin expression at 37°C, killed crickets, and the dose at which 50% of crickets were killed was decreased at 37°C compared with that at 27°C. These findings suggest that the two-spotted cricket is a useful model animal for evaluating the virulence properties of various human pathogenic bacteria at variable temperature including 37°C.

Description: We investigate how nightside cooling and surface friction affect surface temperatures and large-scale circulation for tidally locked Earth-like planets. For each scenario, we vary the orbital period between P rot = 1 and 100 d and capture changes in climate states. We find drastic changes in climate states for different surface friction scenarios. For very efficient surface friction ( t s,fric = 0.1 d), the simulations for short rotation periods ( P rot ≤ 10 d) show predominantly standing extratropical Rossby waves. These waves lead to climate states with two high-latitude westerly jets and unperturbed meridional direct circulation. In most other scenarios, simulations with short rotation periods exhibit instead dominance by standing tropical Rossby waves. Such climate states have a single equatorial westerly jet, which disrupts direct circulation. Experiments with weak surface friction ( t s,fric = 10–100 d) show decoupling between surface temperatures and circulation, which leads to strong cooling of the nightside. The experiment with t s,fric = 100 d assumes climate states with easterly flow (retrograde rotation) for medium and slow planetary rotations P rot = 12–100 d. We show that an increase of nightside cooling efficiency by one order of magnitude compared to the nominal model leads to a cooling of the nightside surface temperatures by 80–100 K. The dayside surface temperatures only drop by 25 K at the same time. The increase in thermal forcing suppresses the formation of extratropical Rossby waves on small planets ( R P = 1 R Earth ) in the short rotation period regime ( P rot ≤ 10 d).

Description: There are various ways of achieving an enlarged understanding of a concept of interest. One way is by giving its proper definition. Another is by giving something else a proper definition and then using it to model or formally represent the original concept. Between the two we find varying shades of grey. We might open up a concept by a direct lexical definition of the predicate that expresses it, or by a theory whose theorems define it implicitly. At the other end of the spectrum, the modelling-this-as-that option also admits of like variation, ranging from models rooted in formal representability theorems to models conceived of as having only heuristic value. There exist on both sides of this divide further differences still. In one of them, both the definiendum and definiens of a definition are words or phrases of some common natural language. In others, the item of interest is a natural language expression and its representation is furnished by the artificial linguistic system that models it. The modern history of these approaches is both very large and growing. Much of this evolution has given too short a shrift to the history of the demotion of ‘intuitive’ concepts in favour of the artificially contrived ones intended to model them. A working assumption of this article is that in the absence of a good understanding of what motivated the modelling-turn in the foundations of mathematics and the intuitive theory of truth, the whole notion of formal representability will have been inadequately understood. In the interests of space, I will concentrate on seminal issues in set theory as dealt with by Russell and Frege, and in the theory of truth in natural languages as dealt with by Tarski. The nub of the present focus is the representational role of model theory in the logics of formalized languages.

Description: An important distinction is that between selective abductions , which select an optimal candidate from given multitude of possible explanations, and creative abductions , which introduce new theoretical concepts and models. The article focuses on creative abductions, which are essential for scientific progress, although they are rarely discussed in the literature. Scientifically, fruitful creative abductions are demarcated from purely speculative abductions by means of three virtues which are possessed by the former but not by the latter: (i) providing unification , (ii) detecting common causes and (iii) generating novel predictions by means of which they can be independently tested . Based on historical examples it is demonstrated that common cause abduction from correlated dispositions is the fundamental abductive operation by which new theoretical concepts and models are scientifically generated. Statistical factor analysis can be regarded as a statistical generalization of common cause abduction.

Description: This article investigates the appropriateness of LP-based reasoning to machine ethics, an interdisciplinary field of inquiry that emerges from the need of imbuing autonomous agents with the capacity for moral decision making. The first contribution of the article is that of identifying morality viewpoints, as studied in moral philosophy and psychology, which are amenable to computational modelling, and then mapping them to appropriate LP-based reasoning features. The identified viewpoints are covered by two morality themes: moral permissibility and the dual-process model. In the second contribution, various LP-based reasoning features are applied to model these identified morality viewpoints, via classic moral examples taken offthe-shelf from the literature. For this purpose, our Q UALM system, which features a combination of LP abduction, updating and counterfactuals, supported by LP tabling mechanisms, are mainly employed. The applications are also supported by other existing LP-based systems, featuring preference handling and probabilistic reasoning, which complement Q UALM in addressing the morality viewpoints in question.

Description: Using detailed modelling, we analyse the spectra observed from the sample galaxies at z  ~ 0.8 presented by Ly et al., constraining the models by the [O iii ]5007+4959/[O iii ]4363 line ratios. Composite models (shock + photoionization) are adopted. Shock velocities ≥100 km s –1 and pre-shock densities n 0  ~ 200 cm –3 characterize the gas surrounding the starburst (SB), while n 0 are higher by a factor of 1.5–10 in the AGN emitting gas. SB effective temperatures are similar to those of quiescent galaxies ( T * ~ 4–7  x  10 4  K). Cloud geometrical thicknesses in the SB are ≤10 16  cm, indicating major fragmentation, while in AGN they reach 〉10 pc. O/H are about solar for all the objects, except for a few AGN clouds with O/H = 0.3–0.5 solar. SB models reproduce most of the data within the observational errors. About half of the objects’ spectra are well fitted by an accreting AGN. Some galaxies show multiple radiation sources, such as SB + AGN, or a double AGN.

Description: We present a method of comparing the Galactic systems realized by two astrometric catalogues. The systematic differences between positions and proper motions are represented by vector spherical harmonics. To extract the signal from the noise, we use a statistical criterion adapted to using healpix data pixelization to determine the significance of all the accessible harmonics. We also use a new analytical method that includes the magnitude equation in the vector spherical harmonics technique. The influence of the magnitude equation on the determination of the mutual orientation and rotation of the PPMXL and UCAC4 Galactic reference frames has been found in the range of J magnitudes from 10.25 to 15.75 mag. The angles of mutual orientation and the rates of mutual rotation of the Galactic frames under consideration depend on magnitude and can reach the level of 10 mas in orientation and 0.7 mas yr –1 for spin. We make a kinematic study of the low degree harmonics in the representation of the systematic differences between the Galactic proper motions. We have found that, averaged over the magnitude range, the biases of the Oort constants due to systematic differences of proper motions between the two catalogues, which are as large as 〈 A 〉 = 1.60 ± 0.41 and 〈 B 〉 = –1.91 ± 0.32 km s –1 kpc –1 , are greater than the standard errors of their evaluation in the systems of these catalogues. The theoretical equations used in this paper are based on real vector harmonics. We present a set of formulae to convert them into the complex function formalism.

Description: We present a way of searching for non-transiting exoplanets with dusty tails. In the transiting case, the extinction by dust during the transit removes more light from the beam than is scattered into it. Thus, the forward scattering component of the light is best seen either just prior to ingress, or just after egress, but with reduced amplitude over the larger peak that is obscured by the transit. This picture suggests that it should be equally productive to search for positive-going peaks in the flux from non-transiting exoplanets with dusty tails. We discuss what amplitudes are expected for different orbital inclination angles. The signature of such objects should be distinct from normal transits, starspots, and most – but not all – types of stellar pulsations.

Description: We present results from three-dimensional, numerical relativity simulations of a tilted black hole-thick accretion disc system. The simulations are analysed using tracer particles in the disc which are advected with the flow. Such tracers, which we employ in these new simulations for the first time, provide a powerful means to analyse in detail the complex dynamics of tilted black hole–torus systems. We show how its use helps to gain insight into the overall dynamics of the system, discussing the origin of the observed black hole precession and the development of a global non-axisymmetric m = 1 mode in the disc. Our three-dimensional simulations show the presence of quasi-periodic oscillations (QPOs) in the instantaneous accretion rate, with frequencies in a range compatible with those observed in low-mass X-ray binaries with either a black hole or a neutron star component. The frequency ratio of the dominant low-frequency peak and the first overtone is o 1 / f ~ 1.9, a frequency ratio not attainable when modelling the QPOs as p -mode oscillations in axisymmetric tori.

Description: We present a multiwavelength investigation of the young stellar population and star formation activities around the H ii region Sharpless 311. Using our deep near-infrared observations and archival Spitzer -IRAC observations, we have detected a total of 125 young stellar objects (YSOs) in an area of ~86 arcmin 2 . The YSO sample includes eight Class I and 117 Class II candidate YSOs. The mass completeness of the identified YSO sample is estimated to be 1.0 M . The ages and masses of the majority of the candidate YSOs are estimated to be in the range ~0.1–5 Myr and ~0.3–6 M , respectively. The 8-μm image of S311 displays an approximately spherical cavity around the ionizing source, which was possibly created by the expansion of the H ii region. The spatial distribution of the candidate YSOs reveals that a significant number of them are distributed systematically along the 8-μm emission with a majority clustered around the eastern border of the H ii region. Four clumps/compact H ii regions are detected in the radio continuum observations at 1280 MHz, which may have been formed during the expansion of the H ii region. The estimated dynamical age of the region, main-sequence lifetime of the ionizing source, the spatial distribution and ages of the candidate YSOs indicate triggered star formation in the complex.

Description: The detailed, atomistic-level understanding of molecular signaling along the tumor-suppressive Hippo signaling pathway that controls tissue homeostasis by balancing cell proliferation and death through apoptosis is a promising avenue for the discovery of novel anticancer drug targets. The activation of kinases such as Mammalian STE20-Like Protein Kinases 1 and 2 (MST1 and MST2)—modulated through both homo- and heterodimerization (e.g. interactions with Ras association domain family, RASSF, enzymes)—is a key upstream event in this pathway and remains poorly understood. On the other hand, RASSFs (such as RASSF1A or RASSF5) act as important apoptosis activators and tumor suppressors, although their exact regulatory roles are also unclear. We present recent molecular studies of signaling along the Ras-RASSF-MST pathway, which controls growth and apoptosis in eukaryotic cells, including a variety of modern molecular modeling and simulation techniques. Using recently available structural information, we discuss the complex regulatory scenario according to which RASSFs perform dual signaling functions, either preventing or promoting MST2 activation, and thus control cell apoptosis. Here, we focus on recent studies highlighting the special role being played by the specific interactions between the helical Salvador/RASSF/Hippo (SARAH) domains of MST2 and RASSF1a or RASSF5 enzymes. These studies are crucial for integrating atomistic-level mechanistic information about the structures and conformational dynamics of interacting proteins, with information available on their system-level functions in cellular signaling.

Description: Big-data-based edge biomarker is a new concept to characterize disease features based on biomedical big data in a dynamical and network manner, which also provides alternative strategies to indicate disease status in single samples. This article gives a comprehensive review on big-data-based edge biomarkers for complex diseases in an individual patient, which are defined as biomarkers based on network information and high-dimensional data. Specifically, we firstly introduce the sources and structures of biomedical big data accessible in public for edge biomarker and disease study. We show that biomedical big data are typically ‘small-sample size in high-dimension space', i.e. small samples but with high dimensions on features (e.g. omics data) for each individual, in contrast to traditional big data in many other fields characterized as ‘large-sample size in low-dimension space', i.e. big samples but with low dimensions on features. Then, we demonstrate the concept, model and algorithm for edge biomarkers and further big-data-based edge biomarkers. Dissimilar to conventional biomarkers, edge biomarkers, e.g. module biomarkers in module network rewiring-analysis, are able to predict the disease state by learning differential associations between molecules rather than differential expressions of molecules during disease progression or treatment in individual patients. In particular, in contrast to using the information of the common molecules or edges (i.e.molecule-pairs) across a population in traditional biomarkers including network and edge biomarkers, big-data-based edge biomarkers are specific for each individual and thus can accurately evaluate the disease state by considering the individual heterogeneity. Therefore, the measurement of big data in a high-dimensional space is required not only in the learning process but also in the diagnosing or predicting process of the tested individual. Finally, we provide a case study on analyzing the temporal expression data from a malaria vaccine trial by big-data-based edge biomarkers from module network rewiring-analysis. The illustrative results show that the identified module biomarkers can accurately distinguish vaccines with or without protection and outperformed previous reported gene signatures in terms of effectiveness and efficiency.

Description: Molecular interrogation of a biological sample through DNA sequencing, RNA and microRNA profiling, proteomics and other assays, has the potential to provide a systems level approach to predicting treatment response and disease progression, and to developing precision therapies. Large publicly funded projects have generated extensive and freely available multi-assay data resources; however, bioinformatic and statistical methods for the analysis of such experiments are still nascent. We review multi-assay genomic data resources in the areas of clinical oncology, pharmacogenomics and other perturbation experiments, population genomics and regulatory genomics and other areas, and tools for data acquisition. Finally, we review bioinformatic tools that are explicitly geared toward integrative genomic data visualization and analysis. This review provides starting points for accessing publicly available data and tools to support development of needed integrative methods.

Description: One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks—and how can they change as a result of mutations? Morphogenesis provides an excellent model system to study how simple molecular networks robustly control complex processes on the macroscopic scale despite molecular noise, and how important functional variants can emerge from small genetic changes. Recent advancements in three-dimensional imaging technologies, computer algorithms and computer power now allow us to develop and analyse increasingly realistic models of biological control. Here, we present our pipeline for image-based modelling that includes the segmentation of images, the determination of displacement fields and the solution of systems of partial differential equations on the growing, embryonic domains. The development of suitable mathematical models, the data-based inference of parameter sets and the evaluation of competing models are still challenging, and current approaches are discussed.

Description: Owing greatly to the advancement of next-generation sequencing (NGS), the amount of NGS data is increasing rapidly. Although there are many NGS applications, one of the most commonly used techniques ‘RNA sequencing (RNA-seq)’ is rapidly replacing microarray-based techniques in laboratories around the world. As more and more of such techniques are standardized, allowing technicians to perform these experiments with minimal hands-on time and reduced experimental/operator-dependent biases, the bottleneck of such techniques is clearly visible; that is, data analysis. Further complicating the matter, increasing evidence suggests most of the genome is transcribed into RNA; however, the majority of these RNAs are not translated into proteins. These RNAs that do not become proteins are called ‘noncoding RNAs (ncRNAs)’. Although some time has passed since the discovery of ncRNAs, their annotations remain poor, making analysis of RNA-seq data challenging. Here, we examine the current limitations of RNA-seq analysis using case studies focused on the detection of novel transcripts and examination of their characteristics. Finally, we validate the presence of novel transcripts using biological experiments, showing novel transcripts can be accurately identified when a series of filters is applied. In conclusion, novel transcripts that are identified from RNA-seq must be examined carefully before proceeding to biological experiments.

Description: Functional genomics has enormous potential to facilitate our understanding of normal and disease-specific physiology. In the past decade, intensive research efforts have been focused on modeling functional relationship networks, which summarize the probability of gene co-functionality relationships. Such modeling can be based on either expression data only or heterogeneous data integration. Numerous methods have been deployed to infer the functional relationship networks, while most of them target the global (non-context-specific) functional relationship networks. However, it is expected that functional relationships consistently reprogram under different tissues or biological processes. Thus, advanced methods have been developed targeting tissue-specific or developmental stage-specific networks. This article brings together the state-of-the-art functional relationship network modeling methods, emphasizes the need for heterogeneous genomic data integration and context-specific network modeling and outlines future directions for functional relationship networks.

Description: Identification of drug–target interactions is an important process in drug discovery. Although high-throughput screening and other biological assays are becoming available, experimental methods for drug–target interaction identification remain to be extremely costly, time-consuming and challenging even nowadays. Therefore, various computational models have been developed to predict potential drug–target associations on a large scale. In this review, databases and web servers involved in drug–target identification and drug discovery are summarized. In addition, we mainly introduced some state-of-the-art computational models for drug–target interactions prediction, including network-based method, machine learning-based method and so on. Specially, for the machine learning-based method, much attention was paid to supervised and semi-supervised models, which have essential difference in the adoption of negative samples. Although significant improvements for drug–target interaction prediction have been obtained by many effective computational models, both network-based and machine learning-based methods have their disadvantages, respectively. Furthermore, we discuss the future directions of the network-based drug discovery and network approach for personalized drug discovery based on personalized medicine, genome sequencing, tumor clone-based network and cancer hallmark-based network. Finally, we discussed the new evaluation validation framework and the formulation of drug–target interactions prediction problem by more realistic regression formulation based on quantitative bioactivity data.

Description: Atherosclerosis is one of the principle pathologies of cardiovascular disease with blood cholesterol a significant risk factor. The World Health Organization estimates that approximately 2.5 million deaths occur annually because of the risk from elevated cholesterol, with 39% of adults worldwide at future risk. Atherosclerosis emerges from the combination of many dynamical factors, including haemodynamics, endothelial damage, innate immunity and sterol biochemistry. Despite its significance to public health, the dynamics that drive atherosclerosis remain poorly understood. As a disease that depends on multiple factors operating on different length scales, the natural framework to apply to atherosclerosis is mathematical and computational modelling. A computational model provides an integrated description of the disease and serves as an in silico experimental system from which we can learn about the disease and develop therapeutic hypotheses. Although the work completed in this area to date has been limited, there are clear signs that interest is growing and that a nascent field is establishing itself. This article discusses the current state of modelling in this area, bringing together many recent results for the first time. We review the work that has been done, discuss its scope and highlight the gaps in our understanding that could yield future opportunities.

Description: We present Bioinformatics Autodiscovery of Training Materials (BATMat), an open-source, Google-based, targeted, automatic search tool for training materials related to bioinformatics. BATMat helps gain access with one click to filtered and portable information containing links to existing materials (when present). It also offers functionality to sort results according to source site or title. Availability: http://imbatmat.com Contact: piar301@gmail.com

Description: Occurrence of entomopathogenic fungi on phylloplanes in Tilia x europaea crowns between 1 and 13 m was assessed in urban parks. Prevalence of fungal infections in ladybirds (Coleoptera: Coccinellidae) collected from Tilia x europaea was assessed to determine whether fungi found on phylloplanes also occurred as infections in ladybirds. Isaria spp. was most abundant on phylloplanes (mean colony forming units (CFU) per leaf ± SE, 0.33 ± 0.03) followed by Beauveria spp. (0.22 ± 0.02 CFU per leaf) and Lecanicillium spp. (0.19 ± 0.02 CFU per leaf). Densities of inoculum were higher in inner crowns and decreased with height, although Lecanicillium spp. peaked at 5–7 m. Upper phylloplane surfaces harboured higher densities of Isaria spp. and Beauveria spp. than lower surfaces, whereas Lecanicillium spp. was equally distributed. Most prevalent on ladybirds were Isaria spp. (20.6% Harmonia axyridis ; 4.8% natives), Lecanicillium spp. (13.6% H. axyridis ; 4.8% natives), with fewer Beauveria spp. infections (2.6% H. axyridis ). Molecular identification revealed Beauveria bassiana , B. pseudobassiana , Isaria farinosa and Lecanicillium muscarium among isolates of both tree and ladybird origin. Tilia x europaea phylloplanes support a diverse assemblage of entomopathogenic fungal species with a different prevalence in coccinellids compared to their relative abundance in this habitat.

Description: Sulfate-reducing prokaryotes (SRPs) and antibiotic resistance genes (ARGs) in sediments could be biomarkers for evaluating the environmental impacts of human activities, although factors governing their distribution are not clear yet. By using metagenomic approach, this study investigated the distributions of SRPs and ARGs in marine sediments collected from 12 different coastal locations of Hong Kong, which exhibited different pollution levels and were classified into two groups based on sediment parameters. Our results showed that relative abundances of major SRP genera to total prokaryotes were consistently lower in the more seriously polluted sediments ( P -value 〈 0.05 in 13 of 20 genera), indicating that the relative abundance of SRPs is a negatively correlated biomarker for evaluating human impacts. Moreover, a unimodel distribution pattern for SRPs along with the pollution gradient was observed. Although total ARGs were enriched in sediments from the polluted sites, distribution of single major ARG types could be explained neither by individual sediment parameters nor by corresponding concentration of antibiotics. It supports the hypothesis that the persistence of ARGs in sediments may not need the selection of antibiotics. In summary, our study provided important hints of the niche differentiation of SRPs and behavior of ARGs in marine coastal sediment.

Description: The aftershock distribution of the 1933 Sanriku-oki outer trench earthquake is estimated by using modern relocation methods and a newly developed velocity structure to examine the spatial extent of the source-fault and the possibility of a triggered interplate seismicity. In this study, we first examined the regional data quality of the 1933 earthquake based on smoked-paper records and then relocated the earthquakes by using the 3-D velocity structure and double-difference method. The improvements of hypocentre locations using these methods were confirmed by the examination of recent earthquakes that are accurately located based on ocean bottom seismometer data. The results show that the 1933 aftershocks occurred under both the outer- and inner-trench-slope regions. In the outer-trench-slope region, aftershocks are distributed in a ~280-km-long area and their depths are shallower than 50 km. Although we could not constrain the fault geometry from the hypocentre distribution, the depth distribution suggests the whole lithosphere is probably not under deviatoric tension at the time of the 1933 earthquake. The occurrence of aftershocks under the inner trench slope was also confirmed by an investigation of waveform frequency difference between outer and inner trench earthquakes as recorded at Mizusawa. The earthquakes under the inner trench slope were shallow (depth less double equals30 km) and the waveforms show a low-frequency character similar to the waveforms of recent, precisely located earthquakes in the same area. They are also located where recent activity of interplate thrust earthquakes is high. These suggest that the 1933 outer-trench-slope main shock triggered interplate earthquakes, which is an unusual case in the order of occurrence in contrast with the more common pairing of a large initial interplate shock with subsequent outer-slope earthquakes. The off-trench earthquakes are distributed about 80 km width in the trench perpendicular direction. This wide width cannot be explained from a single high-angle fault confined at a shallow depth (depth less double equals50 km). The upward motion of the 1933 tsunami waveform records observed at Sanriku coast also cannot be explained from a single high-angle west-dipping normal fault. If we consider additional fault, involvement of high-angle, east-dipping normal faults can better explain the tsunami first motion and triggering of the aftershock in a wide area under the outer trench slope. Therefore multiple off-trench normal faults may have activated during the 1933 earthquake. We also relocated recent (2001–2012) seismicity by the same method. The results show that the present seismicity in the outer-trench-slope region can be divided into several groups along the trench. Comparison of the 1933 rupture dimensions based on our aftershock relocations with the morphologies of fault scarps in the outer trench slope suggest that the rupture was limited to the region where fault scarps are largely trench parallel and cross cut the seafloor spreading fabric. These findings imply that bending geometry and structural segmentation of the incoming plate largely controls the spatial extent of the 1933 seismogenic faulting. In this shallow rupture model for this largest outer trench earthquake, triggered seismicity in the forearc and structural control of faulting represent an important deformation styles for off-trench and shallow megathrust zones.

Description: NGC 6946, known as the Fireworks galaxy because of its high supernova rate and high star formation, is embedded in a very extended H i halo. Its northern spiral arm is well detached from the galactic main body. We found that this arm contains a large (~300 pc in size) Red Ellipse, named according to a strong contamination of the Hα emission line on its optical images. The ellipse is accompanied by a short parallel arc and a few others still smaller and less regular; a bright star cluster is seen inside these features. The complicated combination of arcs seems to be unique; it is only a bit similar to some SNRs. However, the long-slit spectral data obtained with the Russian 6-m telescope did not confirm the origin of the nebula as a result of a single SN outburst. The emission-line spectrum corresponds to the photoionization by young hot stars with a small contribution of shock ionization. The most likely explanation of the Red Ellipse is a superbubble created by a collective feedback of massive stars in the star cluster located in the NE side of the Red Ellipse. However, the very regular elliptical shape of the nebulae seems strange.

Description: Gravity is believed to be important on multiple physical scales in molecular clouds. However, quantitative constraints on gravity are still lacking. We derive an analytical formula which provides estimates on multiscale gravitational energy distribution using the observed surface density probability distribution function (PDF). Our analytical formalism also enables one to convert the observed column density PDF into an estimated volume density PDF, and to obtain average radial density profile ( r ). For a region with $N_{\rm col} \sim N^{-\gamma _{\rm N}}$ , the gravitational energy spectra is $E_{\rm p}(k)\sim k^{-4(1 - 1/\gamma _{\rm N})}$ . We apply the formula to observations of molecular clouds, and find that a scaling index of –2 of the surface density PDF implies that ~ r –2 and E p ( k ) ~ k –2 . The results are valid from the cloud scale (a few parsec) to around ~ 0.1 pc. Because of the resemblance the scaling index of the gravitational energy spectrum and the that of the kinetic energy power spectrum of the Burgers turbulence (where E ~ k –2 ), our result indicates that gravity can act effectively against turbulence over a multitude of physical scales. This is the critical scaling index which divides molecular clouds into two categories: clouds like Orion and Ophiuchus have shallower power laws, and the amount of gravitational energy is too large for turbulence to be effective inside the cloud. Because gravity dominates, we call this type of cloud g-type clouds. On the other hand, clouds like the California molecular cloud and the Pipe nebula have steeper power laws, and turbulence can overcome gravity if it can cascade effectively from the large scale. We call this type of cloud t-type clouds. The analytical formula can be used to determine if gravity is dominating cloud evolution when the column density PDF can be reliably determined.

Description: Birds can be classified into altricial and precocial. The hatchlings of altricial birds are almost naked, whereas those of precocial birds are covered with natal down. This regulatory divergence is thought to reflect environmental adaptation, but the molecular basis of the divergence is unclear. To address this issue, we chose the altricial zebra finch and the precocial chicken as the model animals. We noted that zebra finch hatchlings show natal down growth suppressed anterior dorsal (AD) skin but partially down-covered posterior dorsal (PD) skin. Comparing the transcriptomes of AD and PD skins, we found that the feather growth promoter SHH (sonic hedgehog) was expressed higher in PD skin than in AD skin. Moreover, the data suggested that the FGF (fibroblast growth factor)/Mitogen-activated protein kinase (MAPK) signaling pathway is involved in natal down growth suppression and that FGF16 is a candidate upstream signaling suppressor. Ectopic expression of FGF16 on chicken leg skin showed downregulation of SHH , upregulation of the feather growth suppressor FGF10 , and suppression of feather bud elongation, similar to the phenotype found in zebra finch embryonic AD skin. Therefore, we propose that FGF16 -related signals suppress natal down elongation and cause the naked AD skin in zebra finch. Our study provides insights into the regulatory divergence in natal down formation between precocial and altricial birds.

Description: The cadherin–catenin complex (CCC) mediates cell–cell adhesion in bilaterian animals by linking extracellular cadherin-based adhesions to the actin cytoskeleton. However, it is unknown whether the basic organization of the complex is conserved across all metazoans. We tested whether protein interactions and actin-binding properties of the CCC are conserved in a nonbilaterian animal, the sea anemone Nematostella vectensis . We demonstrated that N. vectensis has a complete repertoire of cadherin–catenin proteins, including two classical cadherins, one α-catenin, and one β-catenin. Using size-exclusion chromatography and multi-angle light scattering, we showed that α-catenin and β-catenin formed a heterodimer that bound N. vectensis Cadherin-1 and -2. Nematostella vectensis α-catenin bound F-actin with equivalent affinity as either a monomer or an α/β-catenin heterodimer, and its affinity for F-actin was, in part, regulated by a novel insert between the N- and C-terminal domains. Nematostella vectensis α-catenin inhibited Arp2/3 complex-mediated nucleation of actin filaments, a regulatory property previously thought to be unique to mammalian αE-catenin. Thus, despite significant differences in sequence, the key interactions of the CCC are conserved between bilaterians and cnidarians, indicating that the core function of the CCC as a link between cell adhesions and the actin cytoskeleton is ancestral in the eumetazoans.

Description: Nucleotide insertions/deletions are ubiquitous in eukaryotic genomes, and the resulting hemizygous (unpaired) DNA has significant, heritable effects on adjacent DNA. However, little is known about the genetic behavior of insertion DNA. Here, we describe a binary transgenic system to study the behavior of insertion DNA during meiosis. Transgenic Arabidopsis lines were generated to carry two different defective reporter genes on nonhomologous chromosomes, designated as "recipient" and "donor" lines. Double hemizygous plants (harboring unpaired DNA) were produced by crossing between the recipient and the donor, and double homozygous lines (harboring paired DNA) via self-pollination. The transfer of the donor’s unmutated sequence to the recipient generated a functional β-glucuronidase gene, which could be visualized by histochemical staining and corroborated by polymerase chain reaction amplification and sequencing. More than 673 million seedlings were screened, and the results showed that meiotic ectopic recombination in the hemizygous lines occurred at a frequency 〉6.49-fold higher than that in the homozygous lines. Gene conversion might have been exclusively or predominantly responsible for the gene correction events. The direct measurement of ectopic recombination events provided evidence that an insertion, in the absence of an allelic counterpart, could scan the entire genome for homologous counterparts with which to pair. Furthermore, the unpaired (hemizygous) architectures could accelerate ectopic recombination between itself and interchromosomal counterparts. We suggest that the ectopic recombination accelerated by hemizygous architectures may be a general mechanism for interchromosomal recombination through ubiquitously dispersed repeat sequences in plants, ultimately contributing to genetic renovation and eukaryotic evolution.

Description: Adaptation of a complex trait often requires the accumulation of many modifications to finely tune its underpinning molecular components to novel environmental requirements. The investigation of cis -acting regulatory modifications can be used to pinpoint molecular systems partaking in such complex adaptations. Here, we identify cis -acting modifications with the help of an interspecific crossing scheme designed to distinguish modifications derived in each of the two sister species, Arabidopsis halleri and A. lyrata . Allele-specific expression levels were assessed in three environmental conditions chosen to reflect interspecific ecological differences: cold exposure, dehydration, and standard conditions. The functions described by Gene Ontology categories enriched in cis -acting mutations are markedly different in A. halleri and A. lyrata , suggesting that polygenic adaptation reshaped distinct polygenic molecular functions in the two species. In the A. halleri lineage, an excess of cis -acting changes affecting metal transport and homeostasis was observed, confirming that the well-known heavy metal tolerance of this species is the result of polygenic selection. In A. lyrata , we find a marked excess of cis -acting changes among genes showing a transcriptional response to cold stress in the outgroup species A. thaliana . The adaptive relevance of these changes will have to be validated. We finally observed that polygenic molecular functions enriched in derived cis -acting changes are more constrained at the amino acid level. Using the distribution of cis -acting variation to tackle the polygenic basis of adaptation thus reveals the contribution of mutations of small effect to Darwinian adaptation.

Description: Phylogenetic networks are a generalization of evolutionary trees that can be used to represent reticulate processes such as hybridization and recombination. Here, we introduce a new approach called TriLoNet (Trinet Level- one Network algorithm) to construct such networks directly from sequence alignments which works by piecing together smaller phylogenetic networks. More specifically, using a bottom up approach similar to Neighbor-Joining, TriLoNet constructs level-1 networks (networks that are somewhat more general than trees) from smaller level-1 networks on three taxa. In simulations, we show that TriLoNet compares well with Lev1athan, a method for reconstructing level-1 networks from three-leaved trees. In particular, in simulations we find that Lev1athan tends to generate networks that overestimate the number of reticulate events as compared with those generated by TriLoNet. We also illustrate TriLoNet’s applicability using simulated and real sequence data involving recombination, demonstrating that it has the potential to reconstruct informative reticulate evolutionary histories. TriLoNet has been implemented in JAVA and is freely available at https://www.uea.ac.uk/computing/TriLoNet .

Description: The growing number of sequenced genomes allows us now to address a key question in genetics and evolutionary biology: which genomic changes underlie particular phenotypic changes between species? Previously, we developed a computational framework called Forward Genomics that associates phenotypic to genomic differences by focusing on phenotypes that are independently lost in different lineages. However, our previous implementation had three main limitations. Here, we present two new Forward Genomics methods that overcome these limitations by (1) directly controlling for phylogenetic relatedness, (2) controlling for differences in evolutionary rates, and (3) computing a statistical significance. We demonstrate on large-scale simulated data and on real data that both new methods substantially improve the sensitivity to detect associations between phenotypic and genomic differences. We applied these new methods to detect genomic differences involved in the loss of vision in the blind mole rat and the cape golden mole, two independent subterranean mammals. Forward Genomics identified several genes that are enriched in functions related to eye development and the perception of light, as well as genes involved in the circadian rhythm. These new Forward Genomics methods represent a significant advance in our ability to discover the genomic basis underlying phenotypic differences between species. Source code: https://github.com/hillerlab/ForwardGenomics/

Description: Phylogenetic trees are pervasively used to depict evolutionary relationships. Increasingly, researchers need to visualize large trees and compare multiple large trees inferred for the same set of taxa (reflecting uncertainty in the tree inference or genuine discordance among the loci analyzed). Existing tree visualization tools are however not well suited to these tasks. In particular, side-by-side comparison of trees can prove challenging beyond a few dozen taxa. Here, we introduce Phylo.io , a web application to visualize and compare phylogenetic trees side-by-side. Its distinctive features are: highlighting of similarities and differences between two trees, automatic identification of the best matching rooting and leaf order, scalability to large trees, high usability, multiplatform support via standard HTML5 implementation, and possibility to store and share visualizations. The tool can be freely accessed at http://phylo.io and can easily be embedded in other web servers. The code for the associated JavaScript library is available at https://github.com/DessimozLab/phylo-io under an MIT open source license.

Description: When viruses spread, outbreaks can be spawned in previously unaffected regions. Depending on the time and mode of introduction, each regional outbreak can have its own epidemic dynamics. The migration and phylodynamic processes are often intertwined and need to be taken into account when analyzing temporally and spatially structured virus data. In this article, we present a fully probabilistic approach for the joint reconstruction of phylodynamic history in structured populations (such as geographic structure) based on a multitype birth–death process. This approach can be used to quantify the spread of a pathogen in a structured population. Changes in epidemic dynamics through time within subpopulations are incorporated through piecewise constant changes in transmission parameters. We analyze a global human influenza H3N2 virus data set from a geographically structured host population to demonstrate how seasonal dynamics can be inferred simultaneously with the phylogeny and migration process. Our results suggest that the main migration path among the northern, tropical, and southern region represented in the sample analyzed here is the one leading from the tropics to the northern region. Furthermore, the time-dependent transmission dynamics between and within two HIV risk groups, heterosexuals and injecting drug users, in the Latvian HIV epidemic are investigated. Our analyses confirm that the Latvian HIV epidemic peaking around 2001 was mainly driven by the injecting drug user risk group.

Description: Ribosomal proteins (r-proteins) are increasingly used as an alternative to ribosomal rRNA for prokaryotic systematics. However, their routine use is difficult because r-proteins are often not or wrongly annotated in complete genome sequences, and there is currently no dedicated exhaustive database of r-proteins. RiboDB aims at fulfilling this gap. This weekly updated comprehensive database allows the fast and easy retrieval of r-protein sequences from publicly available complete prokaryotic genome sequences. The current version of RiboDB contains 90 r-proteins from 3,750 prokaryotic complete genomes encompassing 38 phyla/major classes and 1,759 different species. RiboDB is accessible at http://ribodb.univ-lyon1.fr and through ACNUC interfaces.

Description: We applied high-throughput sequencing to eye tissue from several species of basal vertebrates (a hagfish, two species of lamprey, and five species of gnathostome fish), and we analyzed the mRNA sequences for the proteins underlying activation of the phototransduction cascade. The molecular phylogenies that we constructed from these sequences are consistent with the 2R WGD model of two rounds of whole genome duplication. Our analysis suggests that agnathans retain an additional representative (that has been lost in gnathostomes) in each of the gene families we studied; the evidence is strong for the G-protein α subunit (GNAT) and the cGMP phosphodiesterase (PDE6), and indicative for the cyclic nucleotide-gated channels (CNGA and CNGB). Two of the species (the hagfish Eptatretus cirrhatus and the lamprey Mordacia mordax ) possess only a single class of photoreceptor, simplifying deductions about the composition of cascade protein isoforms utilized in their photoreceptors. For the other lamprey, Geotria australis , analysis of the ratios of transcript levels in downstream and upstream migrant animals permits tentative conclusions to be drawn about the isoforms used in four of the five spectral classes of photoreceptor. Overall, our results suggest that agnathan rod-like photoreceptors utilize the same GNAT1 as gnathostomes, together with a homodimeric PDE6 that may be agnathan-specific, whereas agnathan cone-like photoreceptors utilize a GNAT that may be agnathan-specific, together with the same PDE6C as gnathostomes. These findings help elucidate the evolution of the vertebrate phototransduction cascade from an ancestral chordate phototransduction cascade that existed prior to the vertebrate radiation.

Description: Model-based phylogenetic reconstructions increasingly consider spatial or phenotypic traits in conjunction with sequence data to study evolutionary processes. Alongside parameter estimation, visualization of ancestral reconstructions represents an integral part of these analyses. Here, we present a complete overhaul of the spatial phylogenetic reconstruction of evolutionary dynamics software, now called SpreaD3 to emphasize the use of data-driven documents, as an analysis and visualization package that primarily complements Bayesian inference in BEAST ( http://beast.bio.ed.ac.uk , last accessed 9 May 2016). The integration of JavaScript D3 libraries ( www.d3.org , last accessed 9 May 2016) offers novel interactive web-based visualization capacities that are not restricted to spatial traits and extend to any discrete or continuously valued trait for any organism of interest.

Description: Ian Crawford , Martin Elvis and James Carpenter summarize an RAS Specialist Discussion Meeting which examined how science will benefit from the use of extraterrestrial resources.

Description: Before they could join the RAS, many women were influential members of amateur astronomical societies across the country, as Allan Chapman explains.

Description: Don Kurtz , Simon Jeffrey and Conny Aerts describe discoveries in the new era of precision asteroseismology.

Description: A&G is branching out with an online platform where RAS Fellows can write about their activities, news and events, reports Sue Bowler .

Description: COPERNICUS/ESA/PPO.LABS/NORUT/COMET-SEOM INSARAP STUDY In this issue's cover feature, Tim J Wright discusses the earthquake deformation cycle and seismic hazard in the continents – the 2015 Bullerwell Lecture.

Description: The National Astronomy Meeting is in its 25th year. Ken Pounds looks back at how it started and how it has evolved.

Description: Four antibiotics (pamamycin, oligomycin A, oligomycin B and echinosporin) were isolated and characterized from the fermentation broth of the marine Streptomyces strains B8496 and B8739. Bioassays revealed that each of these compounds impaired motility and caused subsequent lysis of P. viticola zoospores in a dose- and time-dependent manner. Pamamycin displayed the strongest motility inhibitory and lytic activities (IC 50 0.1 μg mL –1 ) followed by oligomycin B (IC 50 0.15 and 0.2 μg mL –1 ) and oligomycin F (IC 50 0.3 and 0.5 μg mL –1 ). Oligomycin A and echinosporin also showed motility inhibitory activities against the zoospores with IC 50 values of 3.0 and 10.0 μg mL –1 , respectively. This is the first report of motility inhibitory and lytic activities of these antibiotics against zoospores of a phytopathogenic peronosporomycete. Structures of all the isolated compounds were determined based on detailed spectroscopic analysis.

Description: The Cadzow rank-reduction method can be effectively utilized in simultaneously denoising and reconstructing 5-D seismic data that depend on four spatial dimensions. The classic version of Cadzow rank-reduction method arranges the 4-D spatial data into a level-four block Hankel/Toeplitz matrix and then applies truncated singular value decomposition (TSVD) for rank reduction. When the observed data are extremely noisy, which is often the feature of real seismic data, traditional TSVD cannot be adequate for attenuating the noise and reconstructing the signals. The reconstructed data tend to contain a significant amount of residual noise using the traditional TSVD method, which can be explained by the fact that the reconstructed data space is a mixture of both signal subspace and noise subspace. In order to better decompose the block Hankel matrix into signal and noise components, we introduced a damping operator into the traditional TSVD formula, which we call the damped rank-reduction method. The damped rank-reduction method can obtain a perfect reconstruction performance even when the observed data have extremely low signal-to-noise ratio. The feasibility of the improved 5-D seismic data reconstruction method was validated via both 5-D synthetic and field data examples. We presented comprehensive analysis of the data examples and obtained valuable experience and guidelines in better utilizing the proposed method in practice. Since the proposed method is convenient to implement and can achieve immediate improvement, we suggest its wide application in the industry.

Description: The next Galactic supernova is expected to bring great opportunities for the direct detection of gravitational waves (GW), full flavour neutrinos, and multiwavelength photons. To maximize the science return from such a rare event, it is essential to have established classes of possible situations and preparations for appropriate observations. To this end, we use a long-term numerical simulation of the core-collapse supernova (CCSN) of a 17 M red supergiant progenitor to self-consistently model the multimessenger signals expected in GW, neutrino, and electromagnetic messengers. This supernova model takes into account the formation and evolution of a protoneutron star, neutrino-matter interaction, and neutrino transport, all within a two-dimensional shock hydrodynamics simulation. With this, we separately discuss three situations: (i) a CCSN at the Galactic Center, (ii) an extremely nearby CCSN within hundreds of parsecs, and (iii) a CCSN in nearby galaxies within several Mpc. These distance regimes necessitate different strategies for synergistic observations. In a Galactic CCSN, neutrinos provide strategic timing and pointing information. We explore how these in turn deliver an improvement in the sensitivity of GW analyses and help to guarantee observations of early electromagnetic signals. To facilitate the detection of multimessenger signals of CCSNe in extremely nearby and extragalactic distances, we compile a list of nearby red supergiant candidates and a list of nearby galaxies with their expected CCSN rates. By exploring the sequential multimessenger signals of a nearby CCSN, we discuss preparations for maximizing successful studies of such an unprecedented stirring event.

Description: Recent observations of active galactic nucleus (AGN) activity in massive galaxies (log M * / M  〉 10.4) show the following: (1) at z 〈 1, AGN-hosting galaxies do not show enhanced merger signatures compared with normal galaxies, (2) also at z 〈 1, most AGNs are hosted by quiescent galaxies and (3) at z 〉 1, the percentage of AGNs in star-forming galaxies increases and becomes comparable to the AGN percentage in quiescent galaxies at z ~ 2. How can major mergers explain AGN activity in massive quiescent galaxies that have no merger features and no star formation to indicate a recent galaxy merger? By matching merger events in a cosmological N -body simulation to the observed AGN incidence probability in the COSMOS survey, we show that major merger-triggered AGN activity is consistent with the observations. By distinguishing between ‘peak’ AGNs (recently merger-triggered and hosted by star-forming galaxies) and ‘faded’ AGNs (merger-triggered a long time ago and now residing in quiescent galaxies), we show that the AGN occupation fraction in star-forming and quiescent galaxies simply follows the evolution of the galaxy merger rate. Since the galaxy merger rate drops dramatically at z 〈 1, the only AGNs left to be observed are the ones triggered by old mergers that are now in the declining phase of their nuclear activity, hosted by quiescent galaxies. As we go towards higher redshifts, the galaxy merger rate increases and the percentages of ‘peak’ AGNs and ‘faded’ AGNs become comparable.

Description: Relativistic jets can form from at least some tidal disruption events (TDEs) of (sub-)stellar objects around supermassive black holes. We detect the millimetre (MM) emission of IGR J12580+0134 – the nearest TDE known in the galaxy NGC 4845 at the distance of only 17 Mpc, based on Planck all-sky survey data. The data show significant flux jumps after the event, followed by substantial declines, in all six high-frequency Planck bands from 100 to 857 GHz. We further show that the evolution of the MM flux densities is well consistent with our model prediction from an off-axis jet, as was initially suggested from radio and X-ray observations. This detection represents the second TDE with MM detections; the other is Sw J1644+57, an on-axis jetted TDE at redshift of 0.35. Using the on- and off-axis jet models developed for these two TDEs as templates, we estimate the detection potential of similar events with the Large Millimeter Telescope (LMT) and the Atacama Large Millimeter/submillimeter Array (ALMA). Assuming an exposure of 1 h, we find that the LMT (ALMA) can detect jetted TDEs up to redshifts z ~ 1 (2), for a typical disrupted star mass of ~1 M . The detection rates of on- and off-axis TDEs can be as high as ~0.6 (13) and 10 (220) yr –1 , respectively, for the LMT (ALMA). We briefly discuss how such observations, together with follow-up radio monitoring, may lead to major advances in understanding the jetted TDEs themselves and the ambient environment of the circumnuclear medium.

Description: A debate has arisen concerning the fundamental nature of luminous blue variables (LBVs) and their role in stellar evolution. While Smith & Tombleson proposed that their isolated environments indicate that LBVs must be largely the product of binary evolution, Humphreys et al. have recently expressed the view that the traditional single-star view still holds if one appropriately selects a subsample of LBVs. This paper finds the claim of Humphreys et al. to be quantitatively unjustified. A statistical test of ‘candidate’ as opposed to ‘confirmed’ LBVs shows no significant difference (〈1) between their environments. Even if the sample is further subdivided as proposed, the three most luminous LBVs are spatially dispersed similar to late O-type dwarfs, which have much longer median lifetimes than expected for classical LBVs. The lower luminosity LBVs have a distribution associated with red supergiants (RSGs), but these RSGs are dominated by stars of 10–15 M initial mass, with much longer lifetimes than expected for those lower luminosity LBVs. If one's view is restricted to the highest luminosity LBVs, then the appropriate comparison is with early O-type stars that are their presumed progenitors; when this is done, it is clear that even the high-luminosity LBVs are more dispersed than expected. Humphreys et al. also suggest that velocities of LBVs support the single-star view, being inconsistent with runaways. A quantitative analysis of the radial velocity distribution of LBVS in M31 and M33 contradicts this; modest runway speeds expected from mass gainers in binary evolution are consistent with the observed velocities, although the data lack the precision to discriminate.

Description: Primordial dark matter (DM) haloes are the smallest gravitationally bound DM structures from which the first stars, black holes and galaxies form and grow in the early universe. However, their structures are sensitive to the free streaming scale of DM, which in turn depends on the nature of DM particles. In this work, we test the hypothesis that the slope of the central cusps in primordial DM haloes near the free streaming scale depends on the nature of merging process. By combining and analysing data from a cosmological simulation with the cutoff in the small-scale matter power spectrum as well as a suite of controlled, high-resolution simulations of binary mergers, we find that (1) the primordial DM haloes form preferentially through major mergers in radial orbits; (2) their central DM density profile is more susceptible to a merging process compared to that of galaxy- and cluster-sized DM haloes; (3) consecutive major mergers drive the central density slope to approach the universal form characterized by the Navarro–Frenk–White profile, which is shown to be robust to the impacts of mergers and serves an attractor solution for the density structure of DM haloes. Our work highlights the importance of dynamical processes on the structure formation during the Dark Ages.

Description: The discovery of lithium-rich giants contradicts expectations from canonical stellar evolution. Here we report on the serendipitous discovery of 20 Li-rich giants observed during the Gaia -ESO Survey, which includes the first nine Li-rich giant stars known towards the CoRoT fields. Most of our Li-rich giants have near-solar metallicities and stellar parameters consistent with being before the luminosity bump. This is difficult to reconcile with deep mixing models proposed to explain lithium enrichment, because these models can only operate at later evolutionary stages: at or past the luminosity bump. In an effort to shed light on the Li-rich phenomenon, we highlight recent evidence of the tidal destruction of close-in hot Jupiters at the sub-giant phase. We note that when coupled with models of planet accretion, the observed destruction of hot Jupiters actually predicts the existence of Li-rich giant stars, and suggests that Li-rich stars should be found early on the giant branch and occur more frequently with increasing metallicity. A comprehensive review of all known Li-rich giant stars reveals that this scenario is consistent with the data. However, more evolved or metal-poor stars are less likely to host close-in giant planets, implying that their Li-rich origin requires an alternative explanation, likely related to mixing scenarios rather than external phenomena.

Description: A key physical quantity during reionization is the size of H  ii regions. Previous studies found a characteristic bubble size which increases rapidly during reionization, with apparent agreement between simulations and analytic excursion set theory. Using four different methods, we critically examine this claim. In particular, we introduce the use of the watershed algorithm – widely used for void finding in galaxy surveys – which we show to be an unbiased method with the lowest dispersion and best performance on Monte Carlo realizations of a known bubble size probability density function (PDF). We find that a friends-of-friends algorithm declares most of the ionized volume to be occupied by a network of volume-filling regions connected by narrow tunnels. For methods tuned to detect the volume-filling regions, previous apparent agreement between simulations and theory is spurious, and due to a failure to correctly account for the window function of measurement schemes. The discrepancy is already obvious from visual inspection. Instead, H  ii regions in simulations are significantly larger (by factors of 10–1000 in volume) than analytic predictions. The size PDF is narrower, and evolves more slowly with time, than predicted. It becomes more sharply peaked as reionization progresses. These effects are likely caused by bubble mergers, which are inadequately modelled by analytic theory. Our results have important consequences for high-redshift 21 cm observations, the mean free path of ionizing photons, and the visibility of Lyα emitters, and point to a fundamental failure in our understanding of the characteristic scales of the reionization process.

Description: We determine the automorphism group of the split Cartan modular curves $X_{{\rm split}}(p)$ for all primes $p$ .

Description: We give a necessary and sufficient condition for a hyperbolic Coxeter group with planar nerve to have Sierpiłski curve as its Gromov boundary.

Description: An exact analytical solution is presented for the effective dynamic transverse shear modulus in a heterogeneous fluid-filled porous solid containing cylindrical inclusions. The complex and frequency-dependent properties of the dynamic shear modulus are caused by the physical mechanism of mesoscopic-scale wave-induced fluid flow whose scale is smaller than wavelength but larger than the size of pores. Our model consists of three phases: a long cylindrical inclusion, a cylindrical shell of poroelastic matrix material with different mechanical and/or hydraulic properties than the inclusion and an outer region of effective homogeneous medium of laterally infinite extent. The behavior of both the inclusion and the matrix is described by Biot's consolidation equations, whereas the surrounding effective medium which is used to describe the effective transverse shear properties of the inner poroelastic composite is assumed to be a viscoelastic solid whose complex transverse shear modulus needs to be determined. The determined effective transverse shear modulus is used to quantify the S -wave attenuation and velocity dispersion in heterogeneous fluid-filled poroelastic rocks. The calculation shows the relaxation frequency and relative position of various fluid saturation dispersion curves predicted by this study exhibit very good agreement with those of a previous 2-D finite-element simulation. For the double-porosity model (inclusions having a different solid frame than the matrix but the same pore fluid as the matrix) the effective shear modulus also exhibits a size-dependent characteristic that the relaxation frequency moves to lower frequencies by two orders of magnitude if the radius of the cylindrical poroelastic composite increases by one order of magnitude. For the patchy-saturation model (inclusions having the same solid frame as the matrix but with a different pore fluid from the matrix), the heterogeneity in pore fluid cannot cause any attenuation in the transverse shear modulus at all. A comparison with the case of spherical inclusions illustrates that the transverse shear modulus for the cylindrical inclusion exhibits more S -wave attenuation than spherical inclusions.

Description: We present a model of cometary dust capable of simulating the dynamics within the first few tens of km of the comet surface. Recent measurements by the Grain Impact Analyser and Dust Accumulator and Cometary Secondary Ion Mass Analyser instruments on Rosetta show that the nucleus emits fluffy dust particles with porosities above 50 per cent and sizes up to at least mm (Fulle et al. 2015b ; Rotundi et al. 2015 ; Schulz et al. 2015 ). Retrieval of the physical properties of these particles requires a model of the effective forces governing their dynamics. Here, we present a model capable of simulating realistic, large and porous particles using hierarchical aggregates, which shows previous extrapolations to be inadequate. The main strengths of our approach are that we can simulate very large (mm-scale) non-spherical agglomerates and can accurately determine their (1) effective cross-section and ratio of cross-section to mass, (2) gas drag coefficient, and (3) light scattering properties. In practical terms, we find that a more detailed treatment of the dust structure results in three to five times higher velocities for large dust particles in the inner coma than previously estimated using spherical particles of the same mass. We apply our model to the dynamics of dust in the vicinity of the nucleus of comet 67P and successfully reproduce the dust speeds reported early on when the comet was roughly 3.5 au from the Sun. At this stage, we employ a simple spherical comet nucleus, we model activity as constant velocity gas expansion from a uniformly active surface, and use Mie scattering. We discuss pathways to improve on these simplifications in the future.

Description: This study represents the most sensitive Chandra X-ray point source catalogue of M31. Using 133 publicly available Chandra ACIS-I/S observations totalling ~1 Ms, we detected 795 X-ray sources in the bulge, north-east, and south-west fields of M31, covering an area of 0.6 deg 2 , to a limiting unabsorbed 0.5–8.0 keV luminosity of ~10 34 erg s –1 . In the inner bulge, where exposure is approximately constant, X-ray fluxes represent average values because they were determined from many observations over a long period of time. Similarly, our catalogue is more complete in the bulge fields since monitoring allowed more transient sources to be detected. The catalogue was cross-correlated with a previous XMM–Newton catalogue of M31's D 25 isophote consisting of 1948 X-ray sources, with only 979 within the field of view of our survey. We found 387 (49 per cent) of our Chandra sources (352 or 44 per cent unique sources) matched to within 5 arcsec of 352 XMM–Newton sources. Combining this result with matching done to previous Chandra X-ray sources we detected 259. new sources in our catalogue. We created X-ray luminosity functions (XLFs) in the soft (0.5–2.0 keV) and hard (2.0–8.0 keV) bands that are the most sensitive for any large galaxy based on our detection limits. Completeness-corrected XLFs show a break around 1.3 x 10 37 erg s –1 , consistent with previous work. As in past surveys, we find that the bulge XLFs are flatter than the disc, indicating a lack of bright high-mass X-ray binaries in the disc and an aging population of low-mass X-ray binaries in the bulge.

Description: We introduce a new transit search and vetting pipeline for observations from the K2 mission, and present the candidate transiting planets identified by this pipeline out of the targets in Campaigns 5 and 6. Our pipeline uses the Gaussian process-based k2sc code to correct for the K2 pointing systematics and simultaneously model stellar variability. The systematics-corrected, variability-detrended light curves are searched for transits with the box-least-squares method, and a period-dependent detection threshold is used to generate a preliminary candidate list. Two or three individuals vet each candidate manually to produce the final candidate list, using a set of automatically generated transit fits and assorted diagnostic tests to inform the vetting. We detect 145 single-planet system candidates and 5 multi-planet systems, independently recovering the previously published hot Jupiters EPIC 212110888b, WASP-55b (EPIC 212300977b) and Qatar-2b (EPIC 212756297b). We also report the outcome of reconnaissance spectroscopy carried out for all candidates with Kepler magnitude Kp ≤ 13, identifying 12 targets as likely false positives. We compare our results to those of other K2 transit search pipelines, noting that ours performs particularly well for variable and/or active stars, but that the results are very similar overall. All the light curves and code used in the transit search and vetting process are publicly available, as are the follow-up spectra.

Description: We use particle data from the Illustris simulation, combined with individual kinematic constraints on the mass of the Milky Way (MW) at specific distances from the Galactic Centre, to infer the radial distribution of the MW's dark matter halo mass. Our method allows us to convert any constraint on the mass of the MW within a fixed distance to a full circular velocity profile to the MW's virial radius. As primary examples, we take two recent (and discrepant) measurements of the total mass within 50 kpc of the Galaxy and find that they imply very different mass profiles and stellar masses for the Galaxy. The dark-matter-only version of the Illustris simulation enables us to compute the effects of galaxy formation on such constraints on a halo-by-halo basis; on small scales, galaxy formation enhances the density relative to dark-matter-only runs, while the total mass density is approximately 20 per cent lower at large Galactocentric distances. We are also able to quantify how current and future constraints on the mass of the MW within specific radii will be reflected in uncertainties on its virial mass: even a measurement of M (〈50 kpc) with essentially perfect precision still results in a 20 per cent uncertainty on the virial mass of the Galaxy, while a future measurement of M (〈100 kpc) with 10 per cent errors would result in the same level of uncertainty. We expect that our technique will become even more useful as (1) better kinematic constraints become available at larger distances and (2) cosmological simulations provide even more faithful representations of the observable Universe.

Description: We present new observations of the galaxy cluster 3C 129 obtained with the Sardinia Radio Telescope in the frequency range 6000–7200 MHz, with the aim to image the large-angular-scale emission at high-frequency of the radio sources located in this cluster of galaxies. The data were acquired using the recently commissioned ROACH2-based backend to produce full-Stokes image cubes of an area of 1° x 1° centred on the radio source 3C 129. We modelled and deconvolved the telescope beam pattern from the data. We also measured the instrumental polarization beam patterns to correct the polarization images for off-axis instrumental polarization. Total intensity images at an angular resolution of 2.9 arcmin were obtained for the tailed radio galaxy 3C 129 and for 13 more sources in the field, including 3C 129.1 at the galaxy cluster centre. These data were used, in combination with literature data at lower frequencies, to derive the variation of the synchrotron spectrum of 3C 129 along the tail of the radio source. If the magnetic field is at the equipartition value, we showed that the lifetimes of radiating electrons result in a radiative age for 3C 129 of t syn ~= 267 ± 26 Myr. Assuming a linear projected length of 488 kpc for the tail, we deduced that 3C 129 is moving supersonically with a Mach number of M  =  v gal / c s  = 1.47. Linearly polarized emission was clearly detected for both 3C 129 and 3C 129.1. The linear polarization measured for 3C 129 reaches levels as high as 70 per cent in the faintest region of the source where the magnetic field is aligned with the direction of the tail.

Description: Supernova remnants are believed to be the main sources of galactic cosmic rays (CR). Within this framework, particles are accelerated at supernova remnant shocks and then released in the interstellar medium. The mechanism through which CRs are released and the way in which they propagate still remain open issues. The main difficulty is the high non-linearity of the problem: CRs themselves excite the magnetic turbulence that confines them close to their sources. We solve numerically the coupled differential equations describing the evolution in space and time of the escaping particles and of the waves generated through the CR streaming instability. The warm ionized and warm neutral phases of the interstellar medium are considered. These phases occupy the largest fraction of the disc volume, where most supernovae explode, and are characterized by the significant presence of neutral particles. The friction between those neutrals and ions results in a very effective wave damping mechanism. It is found that streaming instability affects the propagation of CRs even in the presence of ion-neutral friction. The diffusion coefficient can be suppressed by more than a factor of ~2 over a region of few tens of pc around the remnant. The suppression increases for smaller distances. The propagation of 10 GeV particles is affected for several tens of kiloyears after escape, while 1 TeV particles are affected for few kiloyears. This might have a great impact on the interpretation of gamma-ray observations of molecular clouds located in the vicinity of supernova remnants.

Description: We have performed very large and high-resolution cosmological hydrodynamic simulations in order to investigate detectability of nebular lines in the rest-frame ultraviolet (UV) to optical wavelength range from galaxies at z 〉 7. We find that the expected line fluxes are very well correlated with the apparent UV magnitudes. The C  iv 1549 Å and C  iii ] 1909 Å lines of galaxies brighter than 26 AB magnitudes are detectable with current facilities such as the Very Large Telescope (VLT) XShooter and the Keck Multi-Object Spectrometer for Infra-Red Exploration (MOSFIRE). Metal lines such as C  iv 1549 Å, C  iii ] 1909 Å, [O  ii ] 3727 Å and [O  iii ] 4959/5007 Å are good targets for spectroscopic observation with the Thirty-Metre Telescope ( TMT ), European Extremely Large Telescope ( E-ELT ), Giant Magellan Telescope ( GMT ) and James Webb Space Telescope ( JWST ). We also expect Hα and Hβ lines to be detectable with these telescopes. Additionally, we predict the detectability of nebular lines for z 〉 10 galaxies, which will be found with JWST , the Wide-Field Infrared Survey Telescope ( WFIRST ) and First Light And Reionization Explorer ( FLARE ) (11 ≤ z ≤ 15). We conclude that the C  iv 1549 Å, C  iii ] 1909 Å, [O  iii ] 4959/5007 Å and Hβ lines from even z ~15 galaxies could be strong targets for TMT , E-ELT and JWST . We also find that magnification by gravitational lensing is of great help in detecting such high- z galaxies. According to our model, the C  iii ] 1909 Å line in z 〉 9 galaxy candidates is detectable even using current facilities.

Description: In the context of the ASAI (Astrochemical Surveys At IRAM) project, we carried out an unbiased spectral survey in the millimetre window towards the well known low-mass Class I source SVS13-A. The high sensitivity reached (3–12 mK) allowed us to detect at least six HDO broad (full width at half-maximum ~4–5 km s –1 ) emission lines with upper level energies up to E u = 837 K. A non-local thermodynamic equilibrium Large Velocity Gradient (LVG) analysis implies the presence of very hot (150–260 K) and dense (≥3  x  10 7  cm –3 ) gas inside a small radius (~25 au) around the star, supporting, for the first time, the occurrence of a hot corino around a Class I protostar. The temperature is higher than expected for water molecules are sublimated from the icy dust mantles (~100 K). Although we cannot exclude we are observing the effects of shocks and/or winds at such small scales, this could imply that the observed HDO emission is tracing the water abundance jump expected at temperatures ~220–250 K, when the activation barrier of the gas phase reactions leading to the formation of water can be overcome. We derive X ( HDO ) ~ 3  x  10 –6 , and a H 2 O deuteration ≥1.5  x  10 –2 , suggesting that water deuteration does not decrease as the protostar evolves from the Class 0 to the Class I stage.

Description: Evidence for the presence of quasi-periodic oscillations (QPOs) in the optical polarization of the blazar PKS 2155–304, during a period of enhanced gamma-ray brightness, is presented. The periodogram of the polarized flux revealed the existence of a prominent peak at T ~ 13 min, detected at 〉99.7 per cent significance, and T ~ 30 min, which was nominally significant at 〉99 per cent. This is the first evidence of QPOs in the polarization of an active galactic nucleus, potentially opening up a new avenue of studying this phenomenon.