ALBERT

Description: : As sequencing becomes cheaper and more widely available, there is a greater need to quickly and effectively analyze large-scale genomic data. While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable with other annotation web servers, AVIA v2.0 represents an enhanced web-based server that extends genomic annotations to cell-specific transcripts and protein-level functional annotations. With AVIA’s improved interface, users can better visualize their data, perform comprehensive searches and categorize both coding and non-coding variants. Availability and implementation : AVIA is freely available through the web at http://avia.abcc.ncifcrf.gov . Contact : Hue.Vuong@fnlcr.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n -dimensional setting. Availability and implementation: The R package MultiMeta can be downloaded from CRAN. Contact: dragana.vuckovic@burlo.trieste.it ; vi1@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Fluorescence microscopy allows us to observe fluorescently labeled molecules in diverse biological processes and organelle structures within living cells. However, the diffraction limit restricts its spatial resolution to about half of its wavelength, limiting the capability of biological observation at the molecular level. Structured-illumination microscopy (SIM), a type of super-resolution microscopy, doubles the spatial resolution in all three dimensions by illuminating the sample with a patterned excitation light, followed by computer reconstruction. SIM uses a relatively low illumination power compared with other methods of super-resolution microscopy and is easily available for multicolor imaging. SIM has great potential for meeting the requirements of live-cell imaging. Recent developments in diverse types of SIM have achieved higher spatial (~50 nm lateral) and temporal (~100 Hz) resolutions. Here, we review recent advancements in SIM and discuss its application in noninvasive live-cell imaging.

Description: One of the most popular super-resolution microscopies that breaks the diffraction barrier is stimulated emission depletion (STED) microscopy. As the optical set-up of STED microscopy is based on a laser scanning microscopy (LSM) system, it potentially has several merits of LSM like confocal or two-photon excitation LSM. In this article, we first describe the principles of STED microscopy and then describe the features of our newly developed two-photon excitation STED microscopy. On the basis of our recent results and those of other researchers, we conclude by discussing future research and new technologies in this field.

Description: The electrically automated ultrathin sectioning apparatus, which has been developed in recent years, can produce consecutive ultrathin sections with a diamond knife and a gallium ion beam. These newly developed apparatuses, however, have several shortcomings, such as the limited block cutting area, thermal damage to the sample by the focused ion beam and a sample electronic charge. To overcome these faults and for easier scanning electron microscopy three-dimensional fine structural reconstruction, we have developed a new cutting method using a deep ultraviolet laser, which we have named the ‘LANTome (Light Ablation Nanotome)’. Using this method, we confirmed the widening of sectioning areas, shortening of the sectioning time, automatic smoothing of rough surfaces, no sample electronic charge and minimal heat effects on the sample tissue, such as thermal denaturation.

Description: Recent advances in nanoscopy, which breaks the diffraction barrier and can visualize structures smaller than the diffraction limit in cells, have encouraged biologists to investigate cellular processes at molecular resolution. Since nanoscopy depends not only on special optics but also on ‘smart’ photophysical properties of photocontrollable fluorescent probes, including photoactivatability, photoswitchability and repeated blinking, it is important for biologists to understand the advantages and disadvantages of fluorescent probes and to choose appropriate ones for their specific requirements. Here, we summarize the characteristics of currently available fluorescent probes based on both proteins and synthetic compounds applicable to nanoscopy and provide a guideline for selecting optimal probes for specific applications.

Description: As one of the most powerful tools in the biological investigation of cellular structures and dynamic processes, fluorescence microscopy has undergone extraordinary developments in the past decades. The advent of super-resolution techniques has enabled fluorescence microscopy – or rather nanoscopy – to achieve nanoscale resolution in living specimens and unravelled the interior of cells with unprecedented detail. The methods employed in this expanding field of microscopy, however, are especially prone to the detrimental effects of optical aberrations. In this review, we discuss how super-resolution microscopy techniques based upon single-molecule switching, stimulated emission depletion and structured illumination each suffer from aberrations in different ways that are dependent upon intrinsic technical aspects. We discuss the use of adaptive optics as an effective means to overcome this problem.

Description: We performed a detailed analysis of elemental abundances, dust features, and polycyclic aromatic hydrocarbons (PAHs) in the C-rich planetary nebula (PN) Wray16-423 in the Sagittarius dwarf spheroidal galaxy, based on a unique data set taken from the Subaru/HDS, MPG/ESO FEROS, HST /WFPC2, and Spitzer /IRS. We performed the first measurements of Kr, Fe, and recombination O abundance in this PN. The extremely small [Fe/H] implies that most Fe atoms are in the solid phase, considering into account the abundance of [Ar/H]. The Spitzer /IRS spectrum displays broad 16–24 μm and 30 μm features, as well as PAH bands at 6–9 and 10–14 μm. The unidentified broad 16–24 μm feature may not be related to iron sulphide (FeS), amorphous silicate, or PAHs. Using the spectral energy distribution model, we derived the luminosity and effective temperature of the central star, and the gas and dust masses. The observed elemental abundances and derived gas mass are in good agreement with asymptotic giant branch nucleosynthesis models for an initial mass of 1.90 M and a metallicity of Z  = 0.004. We infer that respectively about 80, 50, and 90 per cent of the Mg, S, and Fe atoms are in the solid phase. We also assessed the maximum possible magnesium sulphide (MgS) and iron-rich sulphide (Fe50S) masses and tested whether these species can produce the band flux of the observed 30 μm feature. Depending on what fraction of the sulphur is in sulphide molecules such as CS, we conclude that MgS and Fe50S could be possible carriers of the 30 μm feature in this PN.

Description: We investigate the evolution of the H β + [O iii ] and [O ii ] luminosity functions from z  ~ 0.8 to ~5 in four redshift slices per emission line using data from the High- z Emission Line Survey (HiZELS). This is the first time that the H β + [O iii ] and [O ii ] luminosity functions have been studied at these redshifts in a self-consistent analysis. This is also the largest sample of [O ii ] and H β + [O iii ] emitters (3475 and 3298 emitters, respectively) in this redshift range, with large comoving volumes ~1  x  10 6  Mpc –3 in two independent volumes (COSMOS and UDS), greatly reducing the effects of cosmic variance. The emitters were selected by a combination of photometric redshift and colour–colour selections, as well as spectroscopic follow-up, including recent spectroscopic observations using DEIMOS and MOSFIRE on the Keck Telescopes and FMOS on Subaru. We find a strong increase in L * and a decrease in * for both H β + [O iii ] and [O ii ] emitters. We derive the [O ii ] star formation history of the Universe since z  ~ 5 and find that the cosmic star formation rate density (SFRD) rises from z  ~ 5 to ~3 and then drops towards z  ~ 0. We also find that our star formation history is able to reproduce the evolution of the stellar mass density up to z  ~ 5 based only on a single tracer of star formation. When comparing the H β + [O iii ] SFRDs to the [O ii ] and H α SFRD measurements in the literature, we find that there is a remarkable agreement, suggesting that the H β + [O iii ] sample is dominated by star-forming galaxies at high- z rather than AGNs.

Description: We present a ‘two-fluid’ implementation of dust in smoothed particle hydrodynamics (SPH) in the test particle limit. The scheme is able to handle both short and long stopping times and reproduces the short friction time limit, which is not properly handled in other implementations. We apply novel tests to verify its accuracy and limitations, including multidimensional tests that have not been previously applied to the drag-coupled dust problem and which are particularly relevant to self-gravitating protoplanetary discs. Our tests demonstrate several key requirements for accurate simulations of gas–dust mixtures. First, in standard SPH particle jitter can degrade the dust solution, even when the gas density is well reproduced. The use of integral gradients, a Wendland kernel and a large number of neighbours can control this, albeit at a greater computational cost. Secondly, when it is necessary to limit the artificial viscosity we recommend using the Cullen & Dehnen switch, since the alternative, using α ~ 0.1, can generate a large velocity noise up to v   0.3 c s in the dust particles. Thirdly, we find that an accurate dust density estimate requires 〉400 neighbours, since, unlike the gas, the dust particles do not feel regularization forces. This density noise applies to all particle-based two-fluid implementations of dust, irrespective of the hydro solver and could lead to numerically induced fragmentation. Although our tests show accurate dusty gas simulations are possible, care must be taken to minimize the contribution from numerical noise.

Description: Halo abundance matching has been used to construct a one-parameter mapping between galaxies and dark matter haloes by assuming that halo mass and galaxy luminosity (or stellar mass) are monotonically related. While this approach has been reasonably successful, it is known that galaxies must be described by at least two parameters, as can be seen from the two-parameter Fundamental Plane on which massive early-type galaxies lie. In this paper, we derive a connection between initial dark matter density perturbations in the early Universe and present-day virialized dark matter haloes by assuming simple spherical collapse combined with conservation of mass and energy. We find that z  = 0 halo concentration, or alternatively the inner slope of the halo density profile α, is monotonically and positively correlated with the collapse redshift of the halo. This is qualitatively similar to the findings of some previous works based on numerical simulations, with which we compare our results. We then describe how the halo mass and concentration (or inner slope α) can be used as two halo parameters in combination with two parameters of early-type galaxies to create an improved abundance matching scheme. In a forthcoming paper, we will show an application of this scheme to galaxies on the Fundamental Plane.

Description: Large surveys have shown that red galaxies are preferentially aligned with their haloes, while blue galaxies have a more isotropic distribution. Since haloes generally align with their filaments, this introduces a bias in the measurement of the cosmic shear from weak lensing. It is therefore vitally important to understand why this difference arises. We explore the stability of different disc orientations within triaxial haloes. We show that, in the absence of gas, the disc orientation is most stable when its spin is along the minor axis of the halo. Instead when gas cools on to a disc, it is able to form in almost arbitrary orientation, including off the main planes of the halo (but avoiding an orientation perpendicular to the halo's intermediate axis). Substructure helps gasless galaxies reach alignment with the halo faster, but has less effect on galaxies when gas is cooling on to the disc. Our results provide a novel and natural interpretation for why red, gas poor galaxies are preferentially aligned with their halo, while blue, star-forming, galaxies have nearly random orientations, without requiring a connection between galaxies’ current star formation rate and their merger history.

Description: In this work, we investigate the bifurcations of relative equilibria in the gravitational potential of asteroids. A theorem concerning a conserved quantity, which is about the eigenvalues and number of relative equilibria, is presented and proved. The conserved quantity can restrict the number of non-degenerate equilibria in the gravitational potential of an asteroid. It is concluded that the number of non-degenerate equilibria in the gravitational field of an asteroid varies in pairs and is an odd number. In addition, the conserved quantity can also restrict the kinds of bifurcations of relative equilibria in the gravitational potential of an asteroid when the parameter varies. Furthermore, studies have shown that there exist transcritical bifurcations, quasi-transcritical bifurcations, saddle–node bifurcations, saddle–saddle bifurcations, binary saddle–node bifurcations, supercritical pitchfork bifurcations, and subcritical pitchfork bifurcations for the relative equilibria in the gravitational potential of asteroids. It is found that for the asteroid 216 Kleopatra, when the rotation period varies as a parameter, the number of relative equilibria changes from 7 to 5 to 3 to 1, and the bifurcations for the relative equilibria are saddle–node bifurcations and saddle–saddle bifurcations.

Description: We examine the relationship between star formation and active galactic nuclei (AGN) activity by constructing matched samples of local (0 〈  z  〈 0.6) radio-loud and radio-quiet AGN in the Herschel -Astrophysical Terahertz Large Area Survey fields. Radio-loud AGN are classified as high-excitation and low-excitation radio galaxies using their emission lines and WISE 22-μm luminosity. AGN accretion and jet powers in these active galaxies are traced by [O iii ] emission-line and radio luminosity, respectively. Star formation rates (SFRs) and specific star formation rates (SSFRs) were derived using Herschel 250-μm luminosity and stellar mass measurements from the Sloan Digital Sky Survey–Max Planck Institute for Astrophysics-John Hopkins University catalogue. In the past, star formation studies of AGN have mostly focused on high-redshift sources to observe the thermal dust emission that peaks in the far-infrared, which limited the samples to powerful objects. However, with Herschel we can expand this to low redshifts. Our stacking analyses show that SFRs and SSFRs of both radio-loud and radio-quiet AGN increase with increasing AGN power but that radio-loud AGN tend to have lower SFR. Additionally, radio-quiet AGN are found to have approximately an order of magnitude higher SSFRs than radio-loud AGN for a given level of AGN power. The difference between the star formation properties of radio-loud and -quiet AGN is also seen in samples matched in stellar mass.

Description: We assemble a sample of 24 hydrogen-poor superluminous supernovae (SLSNe). Parameterizing the light-curve shape through rise and decline time-scales shows that the two are highly correlated. Magnetar-powered models can reproduce the correlation, with the diversity in rise and decline rates driven by the diffusion time-scale. Circumstellar interaction models can exhibit a similar rise–decline relation, but only for a narrow range of densities, which may be problematic for these models. We find that SLSNe are approximately 3.5 mag brighter and have light curves three times broader than SNe Ibc, but that the intrinsic shapes are similar. There are a number of SLSNe with particularly broad light curves, possibly indicating two progenitor channels, but statistical tests do not cleanly separate two populations. The general spectral evolution is also presented. Velocities measured from Fe  ii are similar for SLSNe and SNe Ibc, suggesting that diffusion time differences are dominated by mass or opacity. Flat velocity evolution in most SLSNe suggests a dense shell of ejecta. If opacities in SLSNe are similar to other SNe Ibc, the average ejected mass is higher by a factor 2–3. Assuming  = 0.1 cm 2 g –1 , we estimate a mean (median) SLSN ejecta mass of 10 M (6 M ), with a range of 3–30 M . Doubling the assumed opacity brings the masses closer to normal SNe Ibc, but with a high-mass tail. The most probable mechanism for generating SLSNe seems to be the core collapse of a very massive hydrogen-poor star, forming a millisecond magnetar.

Description: We develop and test an algorithm to rescale a simulated dark-matter particle distribution or halo catalogue from a standard gravity model to that of a modified gravity model. This method is based on that of Angulo & White but with some additional ingredients to account for (i) scale-dependent growth of linear density perturbations and (ii) screening mechanisms that are generic features of viable modified gravity models. We attempt to keep the method as general as possible, so that it may plausibly be applied to a wide range of modified theories, although tests against simulations are restricted to a subclass of f ( R ) models at this stage. We show that rescaling allows the power spectrum of matter to be reproduced at the ~3 per cent level in both real and redshift space up to k  = 0.1 h Mpc –1 if we change the box size and alter the particle displacement field; this limit can be extended to k  = 1 h Mpc –1 if we additionally alter halo internal structure. We simultaneously develop an algorithm that can be applied directly to a halo catalogue, in which case the halo mass function and clustering can be reproduced at the ~5 per cent level. Finally, we investigate the clustering of halo particle distributions, generated from rescaled halo catalogues, and find that a similar accuracy can be reached.

Description: In order to study the galaxy population of galaxy clusters with photometric data, one must be able to accurately discriminate between cluster members and non-members. The redMaPPer cluster finding algorithm treats this problem probabilistically, focusing exclusively on the red galaxy population. Here, we utilize Sloan Digital Sky Survey (SDSS) and Galaxy And Mass Assembly spectroscopic membership rates to validate the redMaPPer membership probability estimates for clusters with z [0.1, 0.3]. We find small – but correctable – biases, sourced by three different systematics. The first two were expected a priori, namely blue cluster galaxies and correlated structure along the line of sight. The third systematic is new: the redMaPPer template fitting exhibits a non-trivial dependence on photometric noise, which biases the original redMaPPer probabilities when utilizing noisy data. After correcting for these effects, we find exquisite agreement (1 per cent) between the photometric probability estimates and the spectroscopic membership rates, demonstrating that we can robustly recover cluster membership estimates from photometric data alone. As a byproduct of our analysis we find that on average unavoidable projection effects from correlated structure contribute 6 per cent of the richness of a redMaPPer galaxy cluster. This work also marks the second public release of the SDSS redMaPPer cluster catalogue.

Description: The underlying mechanisms driving the quenching of dwarf-mass satellite galaxies remain poorly constrained, but recent studies suggest they are particularly inefficient for those satellites with stellar mass 10 9 M . We investigate the characteristic evolution of these systems with chemodynamical simulations and idealized models of their tidal/hydrodynamic interactions within the 10 $^{\rm 13{\rm -}13.5}$ -M group-mass hosts in which they are preferentially quenched. Our fiducial simulations highlight the role played by secular star formation and stellar bars, and demonstrate a transition from a gas-rich to passive, H i -deficient state (i.e. SFR ≤ –1, def $_{\rm H\, {\small {I}}}$  ≥ 0.5) within 6 Gyr of first infall. Furthermore, in the 8–10 Gyr in which these systems have typically been resident within group hosts, the bulge-to-total ratio of an initially bulgeless disc can increase to 0.3 〈 B/T 〈 0.4, its specific angular momentum R reduce to ~0.5, and strong bisymmetries formed. Ultimately, this scenario yields satellites resembling dwarf S0s, a result that holds for a variety of infall inclinations/harassments albeit with broad scatter. The key assumptions here lie in the rapid removal of the satellite's gaseous halo upon virial infall, and the satellite's local intragroup medium density being defined by the host's spherically averaged profile. We demonstrate how quenching can be greatly enhanced if the satellite lies in an overdensity, consistent with recent cosmological-scale simulations but contrasting with observationally inferred quenching mechanisms/time-scales; an appraisal of these results with respect to the apparent preferential formation of dS0s/S0s in groups is also given.

Description: The observation of galaxy and gas distributions, as well as cosmological simulations in a CDM cold dark matter universe, suggests that clusters of galaxies are still accreting mass and are not expected to be in equilibrium. In this work, we investigate the possibility to evaluate the departure from virial equilibrium in order to detect, in that balance, effects from a dark matter–dark energy interaction. We continue, from previous works, using a simple model of interacting dark sector, the Layzer–Irvine equation for dynamical virial evolution, and employ optical observations in order to obtain the mass profiles through weak-lensing and X-ray observations giving the intracluster gas temperatures. Through a Monte Carlo method, we generate, for a set of clusters, measurements of observed virial ratios, interaction strength, rest virial ratio and departure from equilibrium factors. We found a compounded interaction strength of $-1.99^{+2.56}_{-16.00}$ , compatible with no interaction, but also a compounded rest virial ratio of –0.79 ± 0.13, which would entail a 2 detection. We confirm quantitatively that clusters of galaxies are out of equilibrium but further investigation is needed to constrain a possible interaction in the dark sector.

Description: With the advent of modern multidetector heterodyne instruments that can result in observations generating thousands of spectra per minute it is no longer feasible to reduce these data as individual spectra. We describe the automated data reduction procedure used to generate baselined data cubes from heterodyne data obtained at the James Clerk Maxwell Telescope (JCMT). The system can automatically detect baseline regions in spectra and automatically determine regridding parameters, all without input from a user. Additionally, it can detect and remove spectra suffering from transient interference effects or anomalous baselines. The pipeline is written as a set of recipes using the ORAC-DR pipeline environment with the algorithmic code using Starlink software packages and infrastructure. The algorithms presented here can be applied to other heterodyne array instruments and have been applied to data from historical JCMT heterodyne instrumentation.

Description: We present a sub-100 pc-scale analysis of the CO molecular gas emission and kinematics of the gravitational lens system SDP.81 at redshift 3.042 using Atacama Large Millimetre/submillimetre Array (ALMA) science verification data and a visibility-plane lens reconstruction technique. We find clear evidence for an excitation-dependent structure in the unlensed molecular gas distribution, with emission in CO (5–4) being significantly more diffuse and structured than in CO (8–7). The intrinsic line luminosity ratio is r 8–7/5–4  = 0.30 ± 0.04, which is consistent with other low-excitation starbursts at z  ~ 3. An analysis of the velocity fields shows evidence for a star-forming disc with multiple velocity components that is consistent with a merger/post-coalescence merger scenario, and a dynamical mass of M (〈1.56 kpc) = 1.6 ± 0.6  x  10 10 M . Source reconstructions from ALMA and the Hubble Space Telescope show that the stellar component is offset from the molecular gas and dust components. Together with Karl G. Jansky Very Large Array CO (1–0) data, they provide corroborative evidence for a complex ~2 kpc-scale starburst that is embedded within a larger ~15 kpc structure.

Description: We present a detailed study based on infrared (IR) photometry of all Galactic RV Tauri stars from the General Catalogue of Variable Stars (GCVS). RV Tauri stars are the brightest among the Population II Cepheids. They are thought to evolve away from the asymptotic giant branch (AGB) towards the white dwarf domain. IRAS detected several RV Tauri stars because of their large IR excesses and it was found that they occupy a specific region in the [12] – [25], [25] – [60] IRAS two-colour diagram. We used the all sky survey of Wide-field Infrared Survey Explorer to extend these studies and compare the IR properties of all RV Tauri stars in the GCVS with a selected sample of post-AGB objects with the goal to place the RV Tauri pulsators in the context of post-AGB evolution. Moreover, we correlated the IR properties of both the RV Tauri stars and the comparison sample with other observables like binarity and the presence of a photospheric chemical anomaly called depletion. We find that Galactic RV Tauri stars display a range of IR properties and we differentiate between disc sources, objects with no IR excess and objects for which the spectral energy distribution (SED) is uncertain. We obtain a clear correlation between disc sources and binarity. RV Tauri stars with a variable mean magnitude are exclusively found among the disc sources. We also find evidence for disc evolution among the binaries. Furthermore our studies show that the presence of a disc seems to be a necessary but not sufficient condition for the depletion process to become efficient.

Description: Accretion flows around black holes generally result in mass-outflows that exhibit irregular behaviour quite often. Using 2D time-dependent hydrodynamical calculations, we show that the mass-outflow is unstable in the cases of thick accretion flows such as the low angular momentum accretion flow and the advection-dominated accretion flow. For the low angular momentum flow, the inward accreting matter on the equatorial plane interacts with the outflowing gas along the rotational axis and the centrifugally supported oblique shock is formed at the interface of both the flows, when the viscosity parameter α is as small as α ≤ 10 –3 . The hot and rarefied blobs, which result in the eruptive mass-outflow, are generated in the inner shocked region and grow up towards the outer boundary. The advection-dominated accretion flow attains finally in the form of a torus disc with the inner edge of the disc at 3 R g  ≤  r  ≤ 6 R g and the centre at 6 R g  ≤  r  ≤ 10 R g , and a series of hot blobs is intermittently formed near the inner edge of the torus and grows up along the outer surface of the torus. As a result, the luminosity and the mass-outflow rate are modulated irregularly where the luminosity is enhanced by 10–40 per cent and the mass-outflow rate is increased by a factor of few up to 10. We interpret the unstable nature of the outflow to be due to the Kelvin–Helmholtz instability, examining the Richardson number for the Kelvin–Helmholtz criterion in the inner region of the flow. We propose that the flare phenomena of Sgr A* may be induced by the unstable mass-outflow as is found in this work.

Description: We consider the issue of selecting parameters and their associated ranges for carrying out searches for continuous gravitational waves from steadily rotating neutron stars. We consider three different cases: (i) the ‘classic’ case of a star spinning about a principal axis; (ii) a biaxial star, not spinning about a principal axis; (iii) a triaxial star spinning steady, but not about a principal axis [as described by Jones]. The first of these emits only at one frequency; the other two at a pair of harmonically related frequencies. We show that in all three cases, when written in terms of the original ‘source parameters’, there exist a number of discrete degeneracies, with different parameter values giving rise to the same gravitational wave signal. We show how these can be removed by suitably restricting the source parameter ranges. In the case of the model as written down by Jones, there is also a continuous degeneracy. We show how to remove this through a suitable rewriting in terms of ‘waveform parameters’, chosen so as to make the specializations to the other stellar models particularly simple. We briefly consider the (non-trivial) relation between the assignments of prior probabilities on one set of parameters verses the other. The results of this paper will be of use when designing strategies for carrying out searches for such multiharmonic gravitational wave signals, and when performing parameter estimation in the event of a detection.

Description: Using 2D numerical hydrodynamical simulations of Type Ia supernova remnants (SNR Ia) we show that iron clumps few times denser than the rest of the SN ejecta might form protrusions in an otherwise spherical SNR. Such protrusions exist in some SNR Ia, e.g. SNR 1885 and Tycho. Iron clumps are expected to form in the deflagration to detonation explosion model. In SNR Ia where there are two opposite protrusions, termed ‘ears’, such as Kepler's SNR and SNR G1.9+0.3, our scenario implies that the dense clumps, or iron bullets, were formed along an axis. Such a preferred axis can result from a rotating white dwarf progenitor. If our claim holds, this offers an important clue to the SN Ia explosion scenario.

Description: Using photometry and high-resolution spectroscopy we investigate for the first time the physical connection between the open clusters NGC 5617 and Trumpler 22. Based on new CCD photometry we report their spatial proximity and common age of ~70 Myr. Based on high-resolution spectra collected using the HERMES and UCLES spectrographs on the Anglo-Australian telescope, we present radial velocities and abundances for Fe, Na, Mg, Al, Si, Ca, and Ni. The measured radial velocities are –38.63 ± 2.25 km s –1 for NGC 5617 and –38.46 ± 2.08 km s –1 for Trumpler 22. The mean metallicity of NGC 5617 was found to be [Fe/H] = –0.18 ± 0.02 and for Trumpler 22 was found to be [Fe/H] = –0.17 ± 0.04. The two clusters share similar abundances across the other elements, indicative of a common chemical enrichment history of these clusters. Together with common motions and ages we confirm that NGC 5617 and Trumpler 22 are a primordial binary cluster pair in the Milky Way.

Description: We investigate the feasibility of detecting 21 cm absorption features in the afterglow spectra of high redshift long Gamma Ray Bursts (GRBs). This is done employing simulations of cosmic reionization, together with estimates of the GRB radio afterglow flux and the instrumental characteristics of the LOw Frequency ARray (LOFAR). We find that absorption features could be marginally (with a S/N larger than a few) detected by LOFAR at z 7 if the GRB is a highly energetic event originating from Pop III stars, while the detection would be easier if the noise were reduced by one order of magnitude, i.e. similar to what is expected for the first phase of the Square Kilometre Array (SKA1-low). On the other hand, more standard GRBs are too dim to be detected even with ten times the sensitivity of SKA1-low, and only in the most optimistic case can a S/N larger than a few be reached at z 9.

Description: We present observations of Swift J1112.2–8238, and identify it as a candidate relativistic tidal disruption flare. The outburst was first detected by Swift /Burst Alert Telescope (BAT) in 2011 June as an unknown, long-lived (order of days) gamma-ray transient source. We show that its position is consistent with the nucleus of a faint galaxy for which we establish a likely redshift of z  = 0.89 based on a single emission line that we interpret as the blended [O  ii ] 3727 doublet. At this redshift, the peak X-ray/gamma-ray luminosity exceeded 10 47 erg s –1 , while a spatially coincident optical transient source had i '  ~ 22 ( M g  ~ –21.4 at z  = 0.89) during early observations, ~20 d after the Swift trigger. These properties place Swift J1112.2–8238 in a very similar region of parameter space to the two previously identified members of this class, Swift J1644+57 and Swift J2058+0516. As with those events the high-energy emission shows evidence for variability over the first few days, while late-time observations, almost 3 yr post-outburst, demonstrate that it has now switched off. Swift J1112.2–8238 brings the total number of such events observed by Swift to three, interestingly all detected by Swift over a ~3 month period (〈3 per cent of its total lifetime as of 2015 March). While this suggests the possibility that further examples may be uncovered by detailed searches of the BAT archives, the lack of any prime candidates in the years since 2011 means these events are undoubtedly rare.

Description: We present updated analytical solutions of continuity equations for power-law beam electrons precipitating in (a) purely collisional losses and (b) purely ohmic losses. The solutions of continuity equation (CE) normalized on electron density presented in Dobranskis & Zharkova are found by method of characteristics eliminating a mistake in the density characteristic pointed out by Emslie et al. The corrected electron beam differential densities (DD) for collisions are shown to have energy spectra with the index of –( + 1)/2, coinciding with the one derived from the inverse problem solution by Brown, while being lower by 1/2 than the index of –/2 obtained from CE for electron flux. This leads to a decrease of the index of mean electron spectra from –( – 2.5) (CE for flux) to –( – 2.0) (CE for electron density). The similar method is applied to CE for electrons precipitating in electric field induced by the beam itself. For the first time, the electron energy spectra are calculated for both constant and variable electric fields by using CE for electron density. We derive electron DD for precipitating electrons (moving towards the photosphere, μ = +1) and ‘returning’ electrons (moving towards the corona, μ = –1). The indices of DD energy spectra are reduced from – – 1 (CE for flux) to – (CE for electron density). While the index of mean electron spectra is increased by 0.5, from – + 0.5 (CE for flux) to – + 1(CE for electron density). Hard X-ray intensities are also calculated for relativistic cross-section for the updated differential spectra revealing closer resemblance to numerical Fokker–Planck (FP) solutions.

Description: The cores of Arp 220, the closest ultraluminous infrared starburst galaxy, provide an opportunity to study interactions of cosmic rays under extreme conditions. In this paper, we model the populations of cosmic rays produced by supernovae in the central molecular zones of both starburst nuclei. We find that ~65–100 per cent of cosmic rays are absorbed in these regions due to their huge molecular gas contents, and thus, the nuclei of Arp 220 nearly complete proton calorimeters. As the cosmic ray protons collide with the interstellar medium, they produce secondary electrons that are also contained within the system and radiate synchrotron emission. Using results from 2 tests between the model and the observed radio spectral energy distribution, we predict the emergent -ray and high-energy neutrino spectra and find the magnetic field to be at milligauss levels. Because of the extremely intense far-infrared radiation fields, the -ray spectrum steepens significantly at TeV energies due to – absorption.

Description: We present a detailed analysis of an astrophysical mechanism that generates cosmological magnetic fields during the Epoch of Reionization. It is based on the photoionization of the intergalactic medium by the first sources formed in the Universe. First the induction equation is derived, then the characteristic length and time-scales of the mechanism are identified, and finally numerical applications are carried out for first stars, primordial galaxies and distant powerful quasars. In these simple examples, the strength of the generated magnetic fields varies between the order of 10 –23  G on hundreds of kiloparsecs and 10 –19  G on hundreds of parsecs in the neutral intergalactic medium between the Strömgren spheres of the sources. Thus, this mechanism contributes to the premagnetization of the whole Universe before large-scale structures are in place. It operates with any ionizing source, at any time during the Epoch of Reionization. Finally, the generated fields possess a characteristic spatial configuration which may help discriminate these seeds from those produced by different mechanisms.

Description: We report the identification of elongated (triaxial or prolate) galaxies in cosmological simulations at z ~= 2. These are preferentially low-mass galaxies ( M * ≤ 10 9.5 M ), residing in dark matter (DM) haloes with strongly elongated inner parts, a common feature of high-redshift DM haloes in the cold dark matter cosmology. Feedback slows formation of stars at the centres of these haloes, so that a dominant and prolate DM distribution gives rise to galaxies elongated along the DM major axis. As galaxies grow in stellar mass, stars dominate the total mass within the galaxy half-mass radius, making stars and DM rounder and more oblate. A large population of elongated galaxies produces a very asymmetric distribution of projected axis ratios, as observed in high- z galaxy surveys. This indicates that the majority of the galaxies at high redshifts are not discs or spheroids but rather galaxies with elongated morphologies.

Description: There is much evidence that planet formation is occurring in the disc around the Herbig Be star HD100546. To learn more about the processes occurring in this disc, we conducted high-resolution imaging at 43/45 GHz with the Australia Telescope Compact Array. Multiple array configurations were used, providing a best spatial resolution of ~0.15 arcsec, or 15 au at HD100546's distance of ~100 pc. Significant structure is revealed, but its precise form is dependent on the u – v plane sampling used for the image reconstruction. At a resolution of ≤30 au, we detected an inner gap in the disc with a radius of ~25 au and a position angle approximately along the known disc major axis. With different weighting, and an achieved resolution of ~15 au, emission appears at the centre and the disc takes on the shape of an incomplete ring, much like a horseshoe, again with a gap radius of ~25 au. The position angle of the disc major axis and its inclination from face-on are determined to be 140° ± 5° and 40° ± 5°, respectively. The ~25 au gap radius is confirmed by a null in the real part of the binned visibilities at 320 ± 10 k, whilst the non-axisymmetric nature is also confirmed through significant structure in the imaginary component. The emission mechanism at the central peak is most likely to be free–free emission from a stellar or disc wind. Overall our data support the picture of at least one, but probably several, giant planets orbiting HD100546 within 25 au.

Description: We present a fast iterative fast Fourier transform (FFT) based reconstruction algorithm that allows for non-parallel redshift-space distortions (RSDs). We test our algorithm on both N -body dark matter simulations and mock distributions of galaxies designed to replicate galaxy survey conditions. We compare solenoidal and irrotational components of the redshift distortion and show that an approximation of this distortion leads to a better estimate of the real-space potential (and therefore faster convergence) than ignoring the RSD when estimating the displacement field. Our iterative reconstruction scheme converges in two iterations for the mock samples corresponding to Baryon Oscillation Spectroscopic Survey CMASS Data Release 11 when we start with an approximation of the RSD. The scheme takes six iterations when the initial estimate, measured from the redshift-space overdensity, has no RSD correction. Slower convergence would be expected for surveys covering a larger angle on the sky. We show that this FFT based method provides a better estimate of the real-space displacement field than a configuration space method that uses finite difference routines to compute the potential for the same grid resolution. Finally, we show that a lognormal transform of the overdensity, used as a proxy for the linear overdensity, is beneficial in estimating the full displacement field from a dense sample of tracers. However, the lognormal transform of the overdensity does not perform well when estimating the displacements from sparser simulations with a more realistic galaxy density.

Description: We investigate the properties of dark matter haloes and subhaloes in an f ( R ) gravity model with | f R 0 | = 10 –6 , using a very-high-resolution N -body simulation. The model is a borderline between being cosmologically interesting and yet still consistent with current data. We find that the halo mass function in this model has a maximum 20 per cent enhancement compared with the -cold-dark-matter (CDM) predictions between z  = 1 and 0. Because of the chameleon mechanism which screens the deviation from standard gravity in dense environments, haloes more massive than 10 13 h –1 M in this f ( R ) model have very similar properties to haloes of similar mass in CDM, while less massive haloes, such as that of the Milky Way, can have steeper inner density profiles and higher velocity dispersions due to their weaker screening. The halo concentration is remarkably enhanced for low-mass haloes in this model due to a deepening of the total gravitational potential. Contrary to the naive expectation, the halo formation time z f is later for low-mass haloes in this model, a consequence of these haloes growing faster than their counterparts in CDM at late times and the definition of z f . Subhaloes, especially those less massive than 10 11 h –1 M , are substantially more abundant in this f ( R ) model for host haloes less massive than 10 13 h –1 M . We discuss the implications of these results for the Milky Way satellite abundance problem. Although the overall halo and subhalo properties in this borderline f ( R ) model are close to their CDM predictions, our results suggest that studies of the Local Group and astrophysical systems, aided by high-resolution simulations, can be valuable for further tests of it.

Description: Mass-to-light versus colour relations (MLCRs), derived from stellar population synthesis models, are widely used to estimate galaxy stellar masses ( M * ), yet a detailed investigation of their inherent biases and limitations is still lacking. We quantify several potential sources of uncertainty, using optical and near-infrared (NIR) photometry for a representative sample of nearby galaxies from the Virgo cluster. Our method for combining multiband photometry with MLCRs yields robust stellar masses, while errors in M * decrease as more bands are simultaneously considered. The prior assumptions in one's stellar population modelling dominate the error budget, creating a colour-dependent bias of up to 0.6 dex if NIR fluxes are used (0.3 dex otherwise). This matches the systematic errors associated with the method of spectral energy distribution (SED) fitting, indicating that MLCRs do not suffer from much additional bias. Moreover, MLCRs and SED fitting yield similar degrees of random error (~0.1–0.14 dex) when applied to mock galaxies and, on average, equivalent masses for real galaxies with M *  ~ 10 8–11 M . The use of integrated photometry introduces additional uncertainty in M * measurements, at the level of 0.05–0.07 dex. We argue that using MLCRs, instead of time-consuming SED fits, is justified in cases with complex model parameter spaces (involving, for instance, multiparameter star formation histories) and/or for large data sets. Spatially resolved methods for measuring M * should be applied for small sample sizes and/or when accuracies less than 0.1 dex are required. An appendix provides our MLCR transformations for 10 colour permutations of the grizH filter set.

Description: The inverse Compton catastrophe is defined as a dramatic rise in the luminosity of inverse Compton scattered photons. It is described by a non-linear loop of radiative processes that sets in for high values of the electron compactness and is responsible for the efficient transfer of energy from electrons to photons, predominantly through inverse Compton scatterings. We search for the conditions that drive a magnetized non-thermal source to the inverse Compton catastrophe regime and study its multiwavelength (MW) photon spectrum. We develop a generic analytical framework and use numerical calculations as a backup to the analytical predictions. We find that the escaping radiation from a source in the Compton catastrophe regime bears some unique features. The MW photon spectrum is a broken power law with a break at ~ m e c 2 due to the onset of the Klein–Nishina suppression. The spectral index below the break energy depends on the electron and magnetic compactnesses logarithmically, while it is independent of the electron power-law index ( s ). The maximum radiating power emerges typically in the -ray regime, at energies ~ m e c 2 (~ max m e c 2 ) for s  〉 2 ( s   2), where max is the maximum Lorentz factor of the injected electron distribution. We apply the principles of the inverse Compton catastrophe to blazars and -ray bursts using the analytical framework we developed, and show how these can be used to impose robust constraints on the source parameters.

Description: We construct equilibrium configurations of magnetized, two-fluid neutron stars using an iterative numerical method. Working in Newtonian framework we assume that the neutron star has two regions: the core, which is modelled as a two-component fluid consisting of type-II superconducting protons and superfluid neutrons, and the crust, a region composed of normal matter. Taking a new step towards more complete equilibrium models, we include the effect of entrainment, which implies that a magnetic force acts on neutrons, too. We consider purely poloidal field cases and present improvements to an earlier numerical scheme for solving equilibrium equations, by introducing new convergence criteria. We find that entrainment results in qualitative differences in the structure of field lines along the magnetic axis.

Description: We present an analysis of the 3–79 keV NuSTAR spectrum of the low-luminosity active galactic nucleus NGC 7213. In agreement with past observations, we find a lower limit to the high-energy cut-off of E c  〉 140 keV, no evidence for a Compton-reflected continuum and the presence of an iron K α complex, possibly produced in the broad-line region. From the application of the mytorus model, we find that the line-emitting material is consistent with the absence of a significant Compton reflection if arising from a Compton-thin torus of gas with a column density of $5.0^{+2.0}_{-1.6}\times 10^{23}$ cm –2 . We report variability of the equivalent width of the iron lines on the time-scale of years using archival observations from XMM–Newton , Chandra and Suzaku . This analysis suggests a possible contribution from dusty gas. A fit with a Comptonization model indicates the presence of a hot corona with a temperature kT e  〉 40 keV and an optical depth   1, assuming a spherical geometry.

Description: PSR J1357–6429 is a young and energetic radio pulsar detected in X-rays and -rays. It powers a compact pulsar wind nebula with a jet visible in X-rays and a large-scale plerion detected in X-ray and TeV ranges. Previous multiwavelength studies suggested that the pulsar has a significant proper motion of about 180 mas yr –1 , implying an extremely high transverse velocity of about 2000 km s –1 . In order to verify this, we performed radio-interferometric observations of PSR J1357–6429 with the Australia Telescope Compact Array (ATCA) in the 2.1-GHz band. We detected the pulsar with a mean flux density of 212 ± 5 μJy and obtained the most accurate pulsar position: RA =  $13^{\rm h}57^{\rm m}02{^{\rm s}_{.}}525(14)$ , Dec. = –64°29 ' 29 ${^{\prime\prime}_{.}}$ 89(15). Using both new and archival ATCA data, we did not find any proper motion and estimated its 90 per cent upper limit as μ 〈 106 mas yr –1 . The pulsar shows a highly polarized single pulse, as was observed earlier at 1.4 GHz. Spectral analysis revealed a shallow spectral index α  = 0.5 ± 0.1. Based on our new radio position of the pulsar, we discount the claim of an optical counterpart candidate reported previously.

Description: We address the problem of line confusion in intensity-mapping surveys and explore the possibility to mitigate line foreground contamination by progressively masking the brightest pixels in the observed map. We consider experiments targeting CO(1–0) at z  = 3, Ly α at z  = 7, and C  ii at z  = 7, and use simulated intensity maps, which include both clustering and shot-noise components of the signal and possible foregrounds, in order to test the efficiency of our method. We find that for CO and Ly α, it is quite possible to remove most of the foreground contribution from the maps via only 1–3 per cent pixel masking. The C  ii maps will be more difficult to clean, however, due to instrumental constraints and the high-intensity foreground contamination involved. While the masking procedure sacrifices much of the astrophysical information present in our maps, we demonstrate that useful cosmological information in the targeted lines can be successfully retrieved.

Description: We analyse the Suzaku X-ray Imaging Spectrometer data of the central region of supernova remnant G332.5-5.6. The X-ray data are well described by a single non-equilibrium ionization thermal model, vnei , with an absorbing hydrogen column density of 1.4 $^{+0.4}_{-0.1}$   x  10 21  cm –2 . The plasma is characterized by an electron temperature of 0.49 $^{+0.08}_{-0.06}$ keV with subsolar abundances for O (0.58 $^{+0.06}_{-0.05}$ solar value) and Fe (0.72 $^{+0.06}_{-0.05}$ solar value) and slightly overabundance for Mg (1.23 $^{+0.14}_{-0.14}$ solar value). It seems that the central X-ray emission originates from a projection effect or evaporation of residual clouds inside G332.5-5.6. We estimate a distance of 3.0 ± 0.8 kpc for G332.5-5.6 based on the extinction–distance relation. G332.5-5.6 has an age of 7–9 kyr.

Description: In interstellar media, stable hydrogen-containing molecules, like CH 3 OH, may be easily dissociated following irradiation by energetic cosmic rays, to form either stable or unstable chemical species. Laboratory experiments have already proved that when ices containing CH 3 OH are irradiated with high-energy photons or energetic particles, many chemical primary fragments are formed, due to the dissociation of C-H or O-H bonds. Are these hydrogen-containing molecules chemically stable in dark dust clouds? What is the behaviour of molecules like CH 3 OH in non-energy-induced processes? An understanding of the thermal reactions between methanol and radical species in their ground states at cryogenic temperatures is of primary importance in the astrochemical context. We experimentally show that the reaction between ground-state nitrogen atoms and CH 3 OH leads to dehydrogenation processes of methanol to form CH 3 O, H 2 CO and HCO chemical fragments via thermal chemistry initiated at temperatures below 10 K. These results underline the problem of the low chemical stability of some species formed and destroyed in interstellar media without any contribution of cosmic ray particles or high-energy photons.

Description: We present a detailed clustering analysis of the young stellar population across the star-forming ring galaxy NGC 6503, based on the deep Hubble Space Telescope photometry obtained with the Legacy ExtraGalactic UV Survey. We apply a contour-based map analysis technique and identify in the stellar surface density map 244 distinct star-forming structures at various levels of significance. These stellar complexes are found to be organized in a hierarchical fashion with 95 per cent being members of three dominant super-structures located along the star-forming ring. The size distribution of the identified structures and the correlation between their radii and numbers of stellar members show power-law behaviours, as expected from scale-free processes. The self-similar distribution of young stars is further quantified from their autocorrelation function, with a fractal dimension of ~1.7 for length-scales between ~20 pc and 2.5 kpc. The young stellar radial distribution sets the extent of the star-forming ring at radial distances between 1 and 2.5 kpc. About 60 per cent of the young stars belong to the detected stellar structures, while the remaining stars are distributed among the complexes, still inside the ring of the galaxy. The analysis of the time-dependent clustering of young populations shows a significant change from a more clustered to a more distributed behaviour in a time-scale of ~60 Myr. The observed hierarchy in stellar clustering is consistent with star formation being regulated by turbulence across the ring. The rotational velocity difference between the edges of the ring suggests shear as the driving mechanism for this process. Our findings reveal the interesting case of an inner ring forming stars in a hierarchical fashion.

Description: We used a new generation of asymptotic giant branch (AGB) stellar models that include dust formation in the stellar winds to find the links between evolutionary models and the observed properties of a homogeneous sample of Large Magellanic Cloud (LMC) planetary nebulae (PNe). Comparison between the evolutionary yields of elements such as CNO and the corresponding observed chemical abundances is a powerful tool to shed light on evolutionary processes such as hot bottom burning (HBB) and third dredge-up (TDU). We found that the occurrence of HBB is needed to interpret the nitrogen-enriched (log (N/H) + 12 〉 8) PNe. In particular, N-rich PNe with the lowest carbon content are nicely reproduced by AGB models of mass M  ≥ 6 M , whose surface chemistry reflects the pure effects of HBB. PNe with log (N/H) + 12 〈 7.5 correspond to ejecta of stars that have not experienced HBB, with initial mass below ~3 M . Some of these stars show very large carbon abundances, owing to the many TDU episodes experienced. We found from our LMC PN sample that there is a threshold to the amount of carbon accumulated at AGB surfaces, log (C/H) + 12 〈 9. Confirmation of this constraint would indicate that, after the C-star stage is reached, AGBs experience only a few thermal pulses, which suggests a rapid loss of the external mantle, probably owing to the effects of radiation pressure on carbonaceous dust particles present in the circumstellar envelope. The implications of these findings for AGB evolution theories and the need to extend the PN sample currently available are discussed.

Description: Young tidal dwarf galaxies (TDGs) are observed in the tidal debris of gas-rich interacting galaxies. In contrast to what is generally assumed to be the case for isolated dwarf galaxies, TDGs are not embedded in their own dark matter (DM) sub-halo. Hence, they are more sensitive to stellar feedback and could be disrupted on a short time-scale. Detailed numerical and observational studies demonstrate that isolated DM-dominated dwarf galaxies can have lifetimes of more than 10 Gyr. For TDGs that evolve in a tidal field with compressing accelerations equal to the gravitational acceleration within a DM sub-halo typical of an isolated dwarf galaxy, a similar survival time is expected. The tidal acceleration profile depends on the virial mass of the host galaxy and the distance between the TDG and its host. We analytically compare the tidal compression to the gravitational acceleration due to either cuspy or cored DM sub-haloes of various virial masses. For example, the tidal field at a distance of 100 kpc to a host halo of 10 13 M can be as stabilizing as a 10 9 M DM sub-halo. By linking the tidal field to the equivalent gravitational field of a DM sub-halo, we can use existing models of isolated dwarfs to estimate the survivability of TDGs. We show that part of the unexpectedly high dynamical masses inferred from observations of some TDGs can be explained by tidal compression and hence TDGs require to contain less unobservable matter to understand their rotation curves.

Description: Near-IR (NIR) spectroscopy is presented for Nova Scorpii 2014. It is shown that the outburst occurred in a symbiotic binary system – an extremely rare configuration for a classical nova outburst to occur in but appropriate for the eruption of a recurrent nova of the T CrB class. We estimate the spectral class of secondary as M5III ± (two sub-classes). The maximum magnitude versus rate of decline relations give an unacceptably large value of 37.5 kpc for the distance. The spectra are typical of the He/N class of novae with strong He  i and H lines. The profiles are broad and flat topped with full width at zero intensities approaching 9000–10 000 km s –1 and also have a sharp narrow component superposed which is attributable to emission from the giant's wind. Hot shocked gas, accompanied by X-rays and -rays, is expected to form when the high-velocity ejecta from the nova ploughs into the surrounding giant wind. Although X-ray emission was observed no -ray emission was reported. It is also puzzling that no signature of a decelerating shock is seen in the NIR, seen in similar systems like RS Oph, V745 Sco and V407 Cyg, as rapid narrowing of the line profiles. The small outburst amplitude and the giant secondary strongly suggest that Nova Sco 2014 could be a recurrent nova.

Description: We investigate the abundance of galactic molecular hydrogen (H 2 ) in the ‘Evolution and Assembly of GaLaxies and their Environments’ (EAGLE) cosmological hydrodynamic simulations. We assign H 2 masses to gas particles in the simulations in post-processing using two different prescriptions that depend on the local dust-to-gas ratio and the interstellar radiation field. Both result in H 2 galaxy mass functions that agree well with observations in the local and high-redshift Universe. The simulations reproduce the observed scaling relations between the mass of H 2 and the stellar mass, star formation rate and stellar surface density. Towards high redshifts, galaxies in the simulations display larger H 2 mass fractions and lower H 2 depletion time-scales, also in good agreement with observations. The comoving mass density of H 2 in units of the critical density, $\Omega _{\rm H_2}$ , peaks at z   1.2–1.5, later than the predicted peak of the cosmic star formation rate activity, at z   2. This difference stems from the decrease in gas metallicity and increase in interstellar radiation field with redshift, both of which hamper H 2 formation. We find that the cosmic H 2 budget is dominated by galaxies with $M_{\rm H_2} 〉 10^9\,\rm M_{{\odot }}$ , star formation rates $ 〉 \,\!\!10\,\rm M_{{\odot }}\,\rm yr^{-1}$ and stellar masses M stellar 〉 10 10 M , which are readily observable in the optical and near-IR. The match between the H 2 properties of galaxies that emerge in the simulations and observations is remarkable, particularly since H 2 observations were not used to adjust parameters in EAGLE.

Description: The detection of planar structures within the satellite systems of both the Milky Way (MW) and Andromeda (M31) has been reported as being in stark contradiction to the predictions of the standard cosmological model ( cold dark matter – CDM). Given the ambiguity in defining a planar configuration, it is unclear how to interpret the low incidence of the MW and M31 planes in CDM. We investigate the prevalence of satellite planes around galactic mass haloes identified in high-resolution cosmological simulations. We find that planar structures are very common, and that ~10 per cent of CDM haloes have even more prominent planes than those present in the Local Group. While ubiquitous, the planes of satellite galaxies show a large diversity in their properties. This precludes using one or two systems as small-scale probes of cosmology, since a large sample of satellite systems is needed to obtain a good measure of the object-to-object variation. This very diversity has been misinterpreted as a discrepancy between the satellite planes observed in the Local Group and CDM predictions. In fact, ~10 per cent of CDM galactic haloes have planes of satellites that are as infrequent as the MW and M31 planes. The look-elsewhere effect plays an important role in assessing the detection significance of satellite planes and accounting for it leads to overestimating the significance level by a factor of 30 and 100 for the MW and M31 systems, respectively.

Description: We use a suite of cooling halo simulations to study a new mechanism for rapid accretion of hot halo gas on to star-forming galaxies. Correlated supernova (SN) events create converging ‘superbubbles’ in the halo gas. Where these collide, the density increases, driving cooling filaments of low-metallicity gas that feed the disc. At our current numerical resolution (~20 pc; m gas = 4 x 10 4 M ) we are only able to resolve the most dramatic events; however, as we increase the numerical resolution, we find that the filaments persist for longer, driving continued late-time star formation. This suggests that SN-driven accretion could act as an efficient mechanism for extracting cold gas from the hot halo, driving late-time star formation in disc galaxies. We show that such filament feeding leads to a peak star formation rate of ~3 M yr –1 , consistent with estimates for the Milky Way (MW). The filaments we resolve extend to ~50 kpc, reaching column densities of N ~ 10 18  cm –2 . We show that such structures can plausibly explain the broad dispersion in Mg  ii absorption seen along sightlines to quasars. Our results suggest a dual role for stellar feedback in galaxy formation, suppressing hot-mode accretion while promoting cold-mode accretion along filaments. Finally, since the filamentary gas has higher angular momentum than that coming from hot-mode accretion, we show that this leads to the formation of substantially larger gas discs.

Description: Motivation: Stem cell differentiation is largely guided by master transcriptional regulators, but it also depends on the expression of other types of genes, such as cell cycle genes, signaling genes, metabolic genes, trafficking genes, etc. Traditional approaches to understanding gene expression patterns across multiple conditions, such as principal components analysis or K-means clustering, can group cell types based on gene expression, but they do so without knowledge of the differentiation hierarchy. Hierarchical clustering can organize cell types into a tree, but in general this tree is different from the differentiation hierarchy itself. Methods: Given the differentiation hierarchy and gene expression data at each node, we construct a weighted Euclidean distance metric such that the minimum spanning tree with respect to that metric is precisely the given differentiation hierarchy. We provide a set of linear constraints that are provably sufficient for the desired construction and a linear programming approach to identify sparse sets of weights, effectively identifying genes that are most relevant for discriminating different parts of the tree. Results: We apply our method to microarray gene expression data describing 38 cell types in the hematopoiesis hierarchy, constructing a weighted Euclidean metric that uses just 175 genes. However, we find that there are many alternative sets of weights that satisfy the linear constraints. Thus, in the style of random-forest training, we also construct metrics based on random subsets of the genes and compare them to the metric of 175 genes. We then report on the selected genes and their biological functions. Our approach offers a new way to identify genes that may have important roles in stem cell differentiation. Contact: tperkins@ohri.ca Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Principal component analysis (PCA) is a basic tool often used in bioinformatics for visualization and dimension reduction. However, it is known that PCA may not consistently estimate the true direction of maximal variability in high-dimensional, low sample size settings, which are typical for molecular data. Assuming that the underlying signal is sparse, i.e. that only a fraction of features contribute to a principal component (PC), this estimation consistency can be retained. Most existing sparse PCA methods use L1-penalization, i.e. the lasso , to perform feature selection. But, the lasso is known to lack variable selection consistency in high dimensions and therefore a subsequent interpretation of selected features can give misleading results. Results: We present S4VDPCA, a sparse PCA method that incorporates a subsampling approach, namely stability selection. S4VDPCA can consistently select the truly relevant variables contributing to a sparse PC while also consistently estimate the direction of maximal variability. The performance of the S4VDPCA is assessed in a simulation study and compared to other PCA approaches, as well as to a hypothetical oracle PCA that ‘knows’ the truly relevant features in advance and thus finds optimal, unbiased sparse PCs. S4VDPCA is computationally efficient and performs best in simulations regarding parameter estimation consistency and feature selection consistency. Furthermore, S4VDPCA is applied to a publicly available gene expression data set of medulloblastoma brain tumors. Features contributing to the first two estimated sparse PCs represent genes significantly over-represented in pathways typically deregulated between molecular subgroups of medulloblastoma. Availability and implementation: Software is available at https://github.com/mwsill/s4vdpca . Contact: m.sill@dkfz.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Glycans play critical roles in many biological processes, and their structural diversity is key for specific protein-glycan recognition. Comparative structural studies of biological molecules provide useful insight into their biological relationships. However, most computational tools are designed for protein structure, and despite their importance, there is no currently available tool for comparing glycan structures in a sequence order- and size-independent manner. Results: A novel method, GS-align, is developed for glycan structure alignment and similarity measurement. GS-align generates possible alignments between two glycan structures through iterative maximum clique search and fragment superposition. The optimal alignment is then determined by the maximum structural similarity score, GS-score, which is size-independent. Benchmark tests against the Protein Data Bank (PDB) N -linked glycan library and PDB homologous/non-homologous N -glycoprotein sets indicate that GS-align is a robust computational tool to align glycan structures and quantify their structural similarity. GS-align is also applied to template-based glycan structure prediction and monosaccharide substitution matrix generation to illustrate its utility. Availability and implementation: http://www.glycanstructure.org/gsalign . Contact: wonpil@ku.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Impedance-based technologies are advancing methods for measuring proliferation of adherent cell cultures non-invasively and in real time. The analysis of the resulting data has so far been hampered by inappropriate computational methods and the lack of systematic data to evaluate the characteristics of the assay. Results: We used a commercially available system for impedance-based growth measurement (xCELLigence) and compared the reported cell index with data from microscopy. We found that the measured signal correlates linearly with the cell number throughout the time of an experiment with sufficient accuracy in subconfluent cell cultures. The resulting growth curves for various colon cancer cells could be well described with the empirical Richards growth model, which allows for extracting quantitative parameters (such as characteristic cycle times). We found that frequently used readouts like the cell index at a specific time or the area under the growth curve cannot be used to faithfully characterize growth inhibition. We propose to calculate the average growth rate of selected time intervals to accurately estimate time-dependent IC50 values of drugs from growth curves. Contact: nils.bluethgen@charite.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: We have coupled a fast, parametrized star cluster evolution code to a Markov Chain Monte Carlo code to determine the distribution of probable initial conditions of observed star clusters, that may serve as a starting point for future N -body calculations. In this paper, we validate our method by applying it to a set of star clusters which have been studied in detail numerically with N -body simulations and Monte Carlo methods: the Galactic globular clusters M4, 47 Tucanae, NGC 6397, M22, Centauri, Palomar 14 and Palomar 4, the Galactic open cluster M67, and the M31 globular cluster G1. For each cluster, we derive a distribution of initial conditions that, after evolution up to the cluster's current age, evolves to the currently observed conditions. We find that there is a connection between the morphology of the distribution of initial conditions and the dynamical age of a cluster and that a degeneracy in the initial half-mass radius towards small radii is present for clusters that have undergone a core collapse during their evolution. We find that the results of our method are in agreement with N -body and Monte Carlo studies for the majority of clusters. We conclude that our method is able to find reliable posteriors for the determined initial mass and half-mass radius for observed star clusters, and thus forms an suitable starting point for modelling an observed cluster's evolution.

Description: We present a panoramic study of the Fornax dwarf spheroidal galaxy, using data obtained as part of the VLT Survey Telescope (VST) ATLAS Survey. The data presented here – a subset of the full survey – uniformly cover a region of 25 deg 2 centred on the galaxy, in g , r and i bands. This large area coverage reveals two key differences to previous studies of Fornax. First, data extending beyond the nominal tidal radius of the dwarf highlight the presence of a second distinct red giant branch population. This bluer red giant branch appears to be co-eval with the horizontal branch population. Secondly, a shell structure located approximately 1 $_{.}^{\circ}$ 4 from the centre of Fornax is shown to be a mis-identified background overdensity of galaxies. This last result casts further doubt on the hypothesis that Fornax underwent a gas-rich merger in its relatively recent past.

Description: Far-infrared (FIR)–radio correlation is a well-established empirical connection between continuum radio and dust emission of star-forming galaxies, often used as a tool in determining star formation rates. Here we expand the point made by Murphy that in the case of some interacting star-forming galaxies there is a non-thermal emission from the gas bridge in between them, which might cause a dispersion in this correlation. Galactic interactions and mergers have been known to give rise to tidal shocks and disrupt morphologies especially in the smaller of the interacting components. Here we point out that these shocks can also heat the gas and dust and will inevitably accelerate particles and result in a tidal cosmic ray population in addition to standard galactic cosmic rays in the galaxy itself. This would result in a non-thermal emission not only from the gas bridges of interacting systems, but from interacting galaxies as a whole in general. Thus both tidal heating and additional non-thermal radiation will obviously affect the FIR–radio correlation of these systems, the only question is how much. In this scenario the FIR–radio correlation is not stable in interacting galaxies, but rather evolves as the interaction/merger progresses. To test this hypothesis and probe the possible impact of tidal cosmic ray population, we have analysed a sample of 43 infrared-bright star-forming interacting galaxies at different merger stages. We have found that their FIR–radio correlation parameter and radio emission spectral index vary noticeably over different merger stages and behave as it would be expected from our tidal-shock scenario. Important implications of departure of interacting galaxies from the FIR–radio correlation are discussed.

Description: We report the alignment and shape of dark matter, stellar, and hot gas distributions in the EAGLE (Evolution and Assembly of GaLaxies and their Environments) and cosmo-OWLS (OverWhelmingly Large Simulations) simulations. The combination of these state-of-the-art hydrodynamical cosmological simulations enables us to span four orders of magnitude in halo mass (11 ≤ log 10 ( M 200 /[ h –1 M ]) ≤ 15), a wide radial range (–2.3 ≤ log 10 ( r /[ h –1 Mpc]) ≤ 1.3) and redshifts 0 ≤  z  ≤ 1. The shape parameters of the dark matter, stellar and hot gas distributions follow qualitatively similar trends: they become more aspherical (and triaxial) with increasing halo mass, radius, and redshift. We measure the misalignment of the baryonic components (hot gas and stars) of galaxies with their host halo as a function of halo mass, radius, redshift, and galaxy type (centrals versus satellites and early- versus late-type). Overall, galaxies align well with the local distribution of the total (mostly dark) matter. However, the stellar distributions on galactic scales exhibit a median misalignment of about 45–50 deg with respect to their host haloes. This misalignment is reduced to 25–30 deg in the most massive haloes (13 ≤ log 10 ( M 200 /[ h –1 M ]) ≤ 15). Half of the disc galaxies in the EAGLE simulations have a misalignment angle with respect to their host haloes larger than 40 deg. We present fitting functions and tabulated values for the probability distribution of galaxy–halo misalignment to enable a straightforward inclusion of our results into models of galaxy formations based on purely collisionless N -body simulations.

Description: We develop a simple dynamical model for the evolution of gas in the centres of barred spiral galaxies, using the Milky Way's Central Molecular Zone (CMZ, i.e. the central few hundred pc) as a case study. We show that, in the presence of a galactic bar, gas in a disc in the central regions of a galaxy will be driven inwards by angular momentum transport induced by acoustic instabilities within the bar's inner Lindblad resonance. This transport process drives turbulence within the gas that temporarily keeps it strongly gravitationally stable and prevents the onset of rapid star formation. However, at some point the rotation curve must transition from approximately flat to approximately solid body, and the resulting reduction in shear reduces the transport rates and causes gas to build up, eventually producing a gravitationally unstable region that is subject to rapid and violent star formation. For the observed rotation curve of the Milky Way, the accumulation happens ~100 pc from the centre of the Galaxy, in good agreement with the observed location of gas clouds and young star clusters in the CMZ. The characteristic time-scale for gas accumulation and star formation is of the order of 10–20 Myr. We argue that similar phenomena should be ubiquitous in other barred spiral galaxies.

Description: One of the major sources of the X-ray emitting hot gas around galaxies is the feedback from supernovae (SNe), but most of this metal-enriched feedback material is often not directly detected in X-ray observations. This missing galactic feedback problem is extremely prominent in early-type galaxy bulges, where there is little cool gas to make the Type Ia SNe ejecta radiate at lower temperature beyond the X-ray domain. We herein present a deep Suzaku observation of an S0 galaxy NGC 5866, which is relatively rich in molecular gas as an S0 galaxy and shows significant evidence of cool–hot gas interaction. By jointly analysing the Suzaku and an archival Chandra data, we measure the Fe/O abundance ratio to be $\rm 7.63_{-5.52}^{+7.28}$ relative to solar values. This abundance ratio is much higher than those of spiral galaxies, and even among the highest ones of S0 and elliptical galaxies. NGC 5866 also simultaneously has the highest Fe/O abundance ratio and molecular gas mass among a small sample of gas-poor early-type galaxies. An estimation of the Fe budget indicates that NGC 5866 could preserve a larger than usual fraction, but far from the total amount of Fe injected by Type Ia SNe. We also find that the hot gas temperature increases from inner to outer haloes, with the inner region has a temperature of ~ 0.25 keV, clearly lower than that expected from Type Ia SNe heating. This low temperature could be most naturally explained by additional cooling processes related to the cool–hot gas interaction as being indicated by the existence of many extraplanar dusty filaments. Our results indicate that the large cool gas content and the presence of cool–hot gas interaction in the inner region of NGC 5866 have significantly reduced the specific energy of the SN ejecta and so the velocity of the galactic outflow. The galaxy could thus preserve a considerable fraction of the metal-enriched feedback material from being blown out.

Description: According to the standard cosmological scenario, superclusters are objects that have just passed the turn-around point and are collapsing. The dynamics of very few superclusters have been analysed up to now. In this paper, we study the supercluster SC0028-0005, at redshift 0.22, identify the most prominent groups and/or clusters that make up the supercluster, and investigate the dynamic state of this structure. For the membership identification, we have used photometric and spectroscopic data from Sloan Digital Sky Survey Data Release 10, finding six main structures in a flat spatial distribution. We have also used a deep multiband observation with MegaCam/Canada–France–Hawaii Telescope to estimate de mass distribution through the weak-lensing effect. For the dynamical analysis, we have determined the relative distances along the line of sight within the supercluster using the Fundamental Plane of early-type galaxies. Finally, we have computed the peculiar velocities of each of the main structures. The 3D distribution suggests that SC0028-005 is indeed a collapsing supercluster, supporting the formation scenario of these structures. Using the spherical collapse model, we estimate that the mass within r  = 10 Mpc should lie between 4 and 16  x  10 15 M . The farthest detected members of the supercluster suggest that within ~60 Mpc the density contrast is  ~ 3 with respect to the critical density at z  = 0.22, implying a total mass of ~4.6–16  x  10 17 M , most of which in the form of low-mass galaxy groups or smaller substructures.

Description: We present CCD UBVRI photometry of the field of the open cluster NGC 6866. Structural parameters of the cluster are determined utilizing the stellar density profile of the stars in the field. We calculate the probabilities of the stars being physical members of the cluster, using their astrometric data, and perform further analyses using only the most probable members. The reddening and metallicity of the cluster were determined by independent methods. The LAMOST spectra and the ultraviolet excess of the F- and G-type main-sequence stars in the cluster indicate that the metallicity of the cluster is about the solar value. We estimated the reddening E ( B – V ) = 0.074 ± 0.050 mag using the U – B versus B – V two-colour diagram. The distance modula, the distance and the age of NGC 6866 were derived as μ = 10.60 ± 0.10 mag, d  = 1189 ± 75 pc and t  = 813 ± 50 Myr, respectively, by fitting colour–magnitude diagrams of the cluster with the PARSEC isochrones. The Galactic orbit of NGC 6866 indicates that the cluster is orbiting in a slightly eccentric orbit with e  = 0.12. The mass function slope x  = 1.35 ± 0.08 was derived by using the most probable members of the cluster.

Description: The mean absolute extinction towards the central parsec of the Milky Way is A K ~= 3 mag, including both foreground and Galactic Centre dust. Here we present a measurement of dust extinction within the Galactic old nuclear star cluster (NSC), based on combining differential extinctions of NSC stars with their l proper motions along Galactic longitude. Extinction within the NSC preferentially affects stars at its far side, and because the NSC rotates, this causes higher extinctions for NSC stars with negative l , as well as an asymmetry in the l -histograms. We model these effects using an axisymmetric dynamical model of the NSC in combination with simple models for the dust distribution. Comparing the predicted asymmetry to data for ~7100 stars in several NSC fields, we find that dust associated with the Galactic Centre mini-spiral with extinction A K ~= 0.15–0.8 mag explains most of the data. The largest extinction A K ~= 0.8 mag is found in the region of the Western arm of the mini-spiral. Comparing with total A K determined from stellar colours, we determine the extinction in front of the NSC. Finally, we estimate that for a typical extinction of A K ~= 0.4 the statistical parallax of the NSC changes by ~0.4 per cent.

Description: Regardless of the physical origin of stellar magnetic fields – fossil or dynamo induced - an inclination angle between the magnetic and rotation axes is very often observed. Absence of observational evidence in this direction in the solar case has led to generally assume that its global magnetic field and rotation axes are well aligned. We present the detection of a monthly periodic signal of the photospheric solar magnetic field at all latitudes, and especially near the poles, revealing that the main axis of the Sun's magnetic field is not aligned with the surface rotation axis. This result reinforces the view of our Sun as a common intermediate-mass star. Furthermore, this detection challenges and imposes a strong observational constraint to modern solar dynamo theories.

Description: Motivation: The storage and transmission of high-throughput sequencing data consumes significant resources. As our capacity to produce such data continues to increase, this burden will only grow. One approach to reduce storage and transmission requirements is to compress this sequencing data. Results: We present a novel technique to boost the compression of sequencing that is based on the concept of bucketing similar reads so that they appear nearby in the file. We demonstrate that, by adopting a data-dependent bucketing scheme and employing a number of encoding ideas, we can achieve substantially better compression ratios than existing de novo sequence compression tools, including other bucketing and reordering schemes. Our method, Mince, achieves up to a 45% reduction in file sizes (28% on average) compared with existing state-of-the-art de novo compression schemes. Availability and implementation : Mince is written in C++11, is open source and has been made available under the GPLv3 license. It is available at http://www.cs.cmu.edu/~ckingsf/software/mince . Contact: carlk@cs.cmu.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Current methods for motif discovery from chromatin immunoprecipitation followed by sequencing (ChIP-seq) data often identify non-targeted transcription factor (TF) motifs, and are even further limited when peak sequences are similar due to common ancestry rather than common binding factors. The latter aspect particularly affects a large number of proteins from the Cys 2 His 2 zinc finger (C2H2-ZF) class of TFs, as their binding sites are often dominated by endogenous retroelements that have highly similar sequences. Here, we present recognition code-assisted discovery of regulatory elements (RCADE) for motif discovery from C2H2-ZF ChIP-seq data. RCADE combines predictions from a DNA recognition code of C2H2-ZFs with ChIP-seq data to identify models that represent the genuine DNA binding preferences of C2H2-ZF proteins. We show that RCADE is able to identify generalizable binding models even from peaks that are exclusively located within the repeat regions of the genome, where state-of-the-art motif finding approaches largely fail. Availability and implementation: RCADE is available as a webserver and also for download at http://rcade.ccbr.utoronto.ca/ . Supplementary information: Supplementary data are available at Bioinformatics online. Contact: t.hughes@utoronto.ca

Description: Motivation: Phylogenetic estimates from published studies can be archived using general platforms like Dryad (Vision, 2010) or TreeBASE (Sanderson et al. , 1994). Such services fulfill a crucial role in ensuring transparency and reproducibility in phylogenetic research. However, digital tree data files often require some editing (e.g. rerooting) to improve the accuracy and reusability of the phylogenetic statements. Furthermore, establishing the mapping between tip labels used in a tree and taxa in a single common taxonomy dramatically improves the ability of other researchers to reuse phylogenetic estimates. As the process of curating a published phylogenetic estimate is not error-free, retaining a full record of the provenance of edits to a tree is crucial for openness, allowing editors to receive credit for their work and making errors introduced during curation easier to correct. Results : Here, we report the development of software infrastructure to support the open curation of phylogenetic data by the community of biologists. The backend of the system provides an interface for the standard database operations of creating, reading, updating and deleting records by making commits to a git repository. The record of the history of edits to a tree is preserved by git’s version control features. Hosting this data store on GitHub ( http://github.com/ ) provides open access to the data store using tools familiar to many developers. We have deployed a server running the ‘phylesystem-api’, which wraps the interactions with git and GitHub. The Open Tree of Life project has also developed and deployed a JavaScript application that uses the phylesystem-api and other web services to enable input and curation of published phylogenetic statements. Availability and implementation : Source code for the web service layer is available at https://github.com/OpenTreeOfLife/phylesystem-api . The data store can be cloned from: https://github.com/OpenTreeOfLife/phylesystem . A web application that uses the phylesystem web services is deployed at http://tree.opentreeoflife.org/curator . Code for that tool is available from https://github.com/OpenTreeOfLife/opentree . Contact : mtholder@gmail.com

Description: Motivation: Chromatin Immunoprecipitation followed by sequencing (ChIP-seq) detects genome-wide DNA–protein interactions and chromatin modifications, returning enriched regions (ERs), usually associated with a significance score. Moderately significant interactions can correspond to true, weak interactions, or to false positives; replicates of a ChIP-seq experiment can provide co-localised evidence to decide between the two cases. We designed a general methodological framework to rigorously combine the evidence of ERs in ChIP-seq replicates, with the option to set a significance threshold on the repeated evidence and a minimum number of samples bearing this evidence. Results : We applied our method to Myc transcription factor ChIP-seq datasets in K562 cells available in the ENCODE project. Using replicates, we could extend up to 3 times the ER number with respect to single-sample analysis with equivalent significance threshold. We validated the ‘rescued’ ERs by checking for the overlap with open chromatin regions and for the enrichment of the motif that Myc binds with strongest affinity; we compared our results with alternative methods (IDR and jMOSAiCS), obtaining more validated peaks than the former and less peaks than latter, but with a better validation. Availability and implementation : An implementation of the proposed method and its source code under GPLv3 license are freely available at http://www.bioinformatics.deib.polimi.it/MSPC/ and http://mspc.codeplex.com/ , respectively. Contact : marco.morelli@iit.it Supplementary information: Supplementary Material are available at Bioinformatics online.

Description: : We announce the release of kSNP3.0, a program for SNP identification and phylogenetic analysis without genome alignment or the requirement for reference genomes. kSNP3.0 is a significantly improved version of kSNP v2. Availability and implementation : kSNP3.0 is implemented as a package of stand-alone executables for Linux and Mac OS X under the open-source BSD license. The executable packages, source code and a full User Guide are freely available at https://sourceforge.net/projects/ksnp/files/ Contact: barryghall@gmail.com

Description: Motivation: We have created an R package named phylogeo that provides a set of geographic utilities for sequencing-based microbial ecology studies. Although the geographic location of samples is an important aspect of environmental microbiology, none of the major software packages used in processing microbiome data include utilities that allow users to map and explore the spatial dimension of their data. phylogeo solves this problem by providing a set of plotting and mapping functions that can be used to visualize the geographic distribution of samples, to look at the relatedness of microbiomes using ecological distance, and to map the geographic distribution of particular sequences. By extending the popular phyloseq package and using the same data structures and command formats, phylogeo allows users to easily map and explore the geographic dimensions of their data from the R programming language. Availability and Implementation: phylogeo is documented and freely available http://zachcp.github.io/phylogeo Contact : zcharlop@rockefeller.edu

Description: : Gener is a development module for programming chemical controllers based on DNA strand displacement. Gener is developed with the aim of providing a simple interface that minimizes the opportunities for programming errors: Gener allows the user to test the computations of the DNA programs based on a simple two-domain strand displacement algebra, the minimal available so far. The tool allows the user to perform stepwise computations with respect to the rules of the algebra as well as exhaustive search of the computation space with different options for exploration and visualization. Gener can be used in combination with existing tools, and in particular, its programs can be exported to Microsoft Research’s DSD tool as well as to LaTeX. Availability and implementation : Gener is available for download at the Cosbi website at http://www.cosbi.eu/research/prototypes/gener as a windows executable that can be run on Mac OS X and Linux by using Mono. Contact : ozan@cosbi.eu

Description: Motivation: Molecular dynamics simulations provide atomic insight into the physicochemical characteristics of lipid membranes and hence, a wide range of force field families capable of modelling various lipid types have been developed in recent years. To model membranes in a biologically realistic lipid composition, simulation systems containing multiple different lipids must be assembled. Results: We present a new web service called MemGen that is capable of setting up simulation systems of heterogenous lipid membranes. MemGen is not restricted to certain lipid force fields or lipid types, but instead builds membranes from uploaded structure files which may contain any kind of amphiphilic molecule. MemGen works with any all-atom or united-atom lipid representation. Availability and implementation: MemGen is freely available without registration at http://memgen.uni-goettingen.de . Contact: jhub@gwdg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: We compare the shapes and intrinsic alignments of galaxies in the MassiveBlack-II (MBII) cosmological hydrodynamic simulation to those in an identical dark matter-only (DMO) simulation. Understanding the impact of baryonic physics on galaxy shapes should prove useful for creating mock galaxy catalogues based on DMO simulations that mimic intrinsic alignments in hydrodynamic simulations. The dark matter subhaloes are typically rounder in MBII, and the shapes of stellar matter in low-mass galaxies are more misaligned with the shapes of dark matter of the corresponding subhaloes in the DMO simulation. At z  = 0.06, the fractional difference in the mean misalignment angle between MBII and DMO simulations varies from ~28to12 per cent in the mass range 10 10.8 –6.0  x  10 14 h –1 M . We study the dark matter halo shapes and alignments as a function of radius, and find that while galaxies in MBII are more aligned with the inner parts of their dark matter subhaloes, there is no radial trend in their alignments with the corresponding subhalo in the DMO simulation. This result highlights the importance of baryonic physics in determining galaxy alignments with inner parts of their halo. Finally, we find that the stellar-dark matter misalignment suppresses the ellipticity–direction (ED) correlation of galaxies in comparison to that of dark matter haloes. In the projected shape–density correlation ( w + ), higher mean ellipticities of the stellar component reduce this effect, but differences of the order of 30–40 per cent remain on scales 〉1 Mpc.

Description: We present a new method to find voids in cosmological simulations based on the tidal and the velocity shear tensors definitions of the cosmic web. We use the fractional anisotropy (FA) computed from the eigenvalues of each web scheme as a void tracer. We identify voids using a watershed transform based on the local minima of the FA field without making any assumption on the shape or structure of the voids. We test the method on the Bolshoi simulation and report on the abundance and radial averaged profiles for the density, velocity and FA. We find that voids in the velocity shear web are smaller than voids in the tidal web, with a particular overabundance of very small voids in the inner region of filaments/sheets. We classify voids as subcompensated/overcompensated depending on the absence/presence of an overdense matter ridge in their density profile, finding that close to 65 and 35 per cent of the total population are classified into each category, respectively. Finally, we find evidence for the existence of universal profiles from the radially averaged profiles for density, velocity and FA. This requires that the radial coordinate is normalized to the effective radius of each void. Put together, all these results show that the FA is a reliable tracer for voids, which can be used in complementarity to other existing methods and tracers.

Description: We present a method to identify ultrafaint dwarf galaxies (UFDGs) candidates in the halo of the Milky Way using the future Gaia catalogue and we explore its detection limits and completeness. The method is based on the Wavelet Transform and searches for overdensities in the combined space of sky coordinates and proper motions, using kinematics in the search for the first time. We test the method with a Gaia mock catalogue that has the Gaia Universe Model Snapshot as a background, and use a library of around 30 000 UFDGs simulated as Plummer spheres with a single stellar population. For the UFDGs, we use a wide range of structural and orbital parameters that go beyond the range spanned by real systems, where some UFDGs may remain undetected. We characterize the detection limits as function of the number of observable stars by Gaia in the UFDGs with respect to that of the background and their apparent sizes in the sky and proper motion planes. We find that the addition of proper motions in the search improves considerably the detections compared to a photometric survey at the same magnitude limit. Our experiments suggest that Gaia will be able to detect UFDGs that are similar to some of the known UFDGs even if the limit of Gaia is around 2 mag brighter than that of SDSS, with the advantage of having a full-sky catalogue. We also see that Gaia could even find some UFDGs that have lower surface brightness than the SDSS limit.

Description: We report nearly exact quantum time-independent calculations of rate coefficients for the collisional (de-)excitation of H 2 by H, from low to high temperatures. Our calculations are based on a highly accurate global potential energy surface. The reactive hydrogen exchange channels are taken into account rigorously. New collisional data are obtained for the ro-vibrational relaxation of highly excited H 2 (with internal excitation up to ~=22 000 K) for temperatures ranging from 100 to 5000 K. We also provide a comparison with the available experimental rate coefficients at room temperature. The good agreement between theory and experiment is an illustration of the accuracy of the present calculations. The new results significantly differ from previous data presently used in astrophysical models, especially at low temperatures, the difference being essentially due to the inclusion of the reactive channels. The impact of these new data in astrophysics is discussed. In particular, the cooling mechanism will have to be reviewed for several astrophysical media.

Description: The emission function from ground-based light sources predetermines the skyglow features to a large extent, while most mathematical models that are used to predict the night sky brightness require the information on this function. The radiant intensity distribution on a clear sky is experimentally determined as a function of zenith angle using the theoretical approach published only recently in MNRAS, 439, 3405–3413. We have made the experiments in two localities in Slovakia and Mexico by means of two digital single lens reflex professional cameras operating with different lenses that limit the system's field-of-view to either 180º or 167º. The purpose of using two cameras was to identify variances between two different apertures. Images are taken at different distances from an artificial light source (a city) with intention to determine the ratio of zenith radiance relative to horizontal irradiance. Subsequently, the information on the fraction of the light radiated directly into the upward hemisphere ( F ) is extracted. The results show that inexpensive devices can properly identify the upward emissions with adequate reliability as long as the clear sky radiance distribution is dominated by a largest ground-based light source. Highly unstable turbidity conditions can also make the parameter F difficult to find or even impossible to retrieve. The measurements at low elevation angles should be avoided due to a potentially parasitic effect of direct light emissions from luminaires surrounding the measuring site.

Description: We use the ‘Evolution and Assembly of GaLaxies and their Environments’ ( eagle ) suite of hydrodynamical cosmological simulations to measure offsets between the centres of stellar and dark matter components of galaxies. We find that the vast majority (〉95 per cent) of the simulated galaxies display an offset smaller than the gravitational softening length of the simulations (Plummer-equivalent  = 700 pc), both for field galaxies and satellites in clusters and groups. We also find no systematic trailing or leading of the dark matter along a galaxy's direction of motion. The offsets are consistent with being randomly drawn from a Maxwellian distribution with  ≤ 196 pc. Since astrophysical effects produce no feasible analogues for the $1.62^{+0.47}_{-0.49}$  kpc offset recently observed in Abell 3827, the observational result is in tension with the collisionless cold dark matter model assumed in our simulations.

Description: Measurements of pulsar flux densities are of great importance for understanding the pulsar emission mechanism and for predictions of pulsar survey yields and the pulsar population at large. Typically these flux densities are determined from phase-averaged ‘pulse profiles’, but this method has limited applicability at low frequencies because the observed pulses can easily be spread out by interstellar effects like scattering or dispersion, leading to a non-pulsed continuum component that is necessarily ignored in this type of analysis. In particular for the class of the millisecond pulsars (MSPs) at frequencies below 200 MHz, such interstellar effects can seriously compromise detectability and measured flux densities. In this paper, we investigate MSP spectra based on a complementary approach, namely through investigation of archival continuum imaging data. Even though these images lose sensitivity to pulsars since the on-pulse emission is averaged with off-pulse noise, they are insensitive to effects from scattering and provide a reliable way to determine the flux density and spectral indices of MSPs based on both pulsed and unpulsed components. Using the 74 MHz VLSSr as well as the 325 MHz WENSS and 1.4 GHz NVSS catalogues, we investigate the imaging flux densities of MSPs and evaluate the likelihood of spectral turn-overs in this population. We determine three new MSP spectral indices and identify six new MSPs with likely spectral turn-overs.

Description: We propose an anisotropic generalization of the line correlation function (ALCF) to separate and quantify phase information in the large-scale structure of galaxies. The line correlation function probes the strictly non-linear regime of structure formation and since phase information drops out of the power spectrum, the line correlation function provides a complementary tool to commonly used techniques based on two-point statistics. Furthermore, it is independent of linear bias as well as the Gaussian variance on the modulus of the density field and thus may also prove to be advantageous compared to the bispectrum or similar higher order statistics for certain cases. For future applications, it is vital, though, to be able to account for observational effects that cause anisotropies in the distribution of galaxies. Based on a number of numerical studies, we find that our ALCF is well suited to accomplish this task and we demonstrate how the Alcock–Paczyłski effect and kinematical redshift-space distortions can in principle be measured via the ALCF.

Description: The deepest XMM–Newton mosaic map of the central 1 $_{.}^{\circ}$ 5 of the Galaxy is presented, including a total of about 1.5 Ms of EPIC-pn cleaned exposures in the central 15 arcsec and about 200 ks outside. This compendium presents broad-band X-ray continuum maps, soft X-ray intensity maps, a decomposition into spectral components and a comparison of the X-ray maps with emission at other wavelengths. Newly discovered extended features, such as supernova remnants (SNRs), superbubbles and X-ray filaments are reported. We provide an atlas of extended features within ±1° of Sgr A * . We discover the presence of a coherent X-ray-emitting region peaking around G0.1–0.1 and surrounded by the ring of cold, mid-IR-emitting material known from previous work as the ‘Radio Arc Bubble’ and with the addition of the X-ray data now appears to be a candidate superbubble. Sgr A's bipolar lobes show sharp edges, suggesting that they could be the remnant, collimated by the circumnuclear disc, of an SN explosion that created the recently discovered magnetar, SGR J1745–2900. Soft X-ray features, most probably from SNRs, are observed to fill holes in the dust distribution, and to indicate a direct interaction between SN explosions and Galactic centre (GC) molecular clouds. We also discover warm plasma at high Galactic latitude, showing a sharp edge to its distribution that correlates with the location of known radio/mid-IR features such as the ‘GC Lobe’. These features might be associated with an inhomogeneous hot ‘atmosphere’ over the GC, perhaps fed by continuous or episodic outflows of mass and energy from the GC region.

Description: Using results from the Herschel Astrophysical Terrahertz Large-Area Survey (H-ATLAS) and the Galaxy and Mass Assembly (GAMA) project, we show that, for galaxy masses above ~= 10 8 M , 51 per cent of the stellar mass-density in the local Universe is in early-type galaxies (ETGs; Sérsic n  〉 2.5) while 89 per cent of the rate of production of stellar mass-density is occurring in late-type galaxies (LTGs; Sérsic n  〈 2.5). From this zero-redshift benchmark, we have used a calorimetric technique to quantify the importance of the morphological transformation of galaxies over the history of the Universe. The extragalactic background radiation contains all the energy generated by nuclear fusion in stars since the big bang. By resolving this background radiation into individual galaxies using the deepest far-infrared survey with the Herschel Space Observatory and a deep near-infrared/optical survey with the Hubble Space Telescope ( HST ), and using measurements of the Sérsic index of these galaxies derived from the HST images, we estimate that ~=83 per cent of the stellar mass-density formed over the history of the Universe occurred in LTGs. The difference between this value and the fraction of the stellar mass-density that is in LTGs today implies there must have been a major transformation of LTGs into ETGs after the formation of most of the stars.

Description: We investigate the star formation properties of ~800 sources detected in one of the deepest radio surveys at 1.4 GHz. Our sample spans a wide redshift range (~0.1–4) and about four orders of magnitude in star formation rate (SFR). It includes both star-forming galaxies (SFGs) and active galactic nuclei (AGNs), further divided into radio-quiet (RQ) and radio-loud objects. We compare the SFR derived from the far-infrared luminosity, as traced by Herschel , with the SFR computed from their radio emission. We find that the radio power is a good SFR tracer not only for pure SFGs but also in the host galaxies of RQ AGNs, with no significant deviation with redshift or specific SFR. Moreover, we quantify the contribution of the starburst activity in the SFG population and the occurrence of AGNs in sources with different level of star formation. Finally, we discuss the possibility of using deep radio survey as a tool to study the cosmic star formation history.

Description: Dwarf spheroidal (dSph) galaxies are prime targets for present and future -ray telescopes hunting for indirect signals of particle dark matter. The interpretation of the data requires careful assessment of their dark matter content in order to derive robust constraints on candidate relic particles. Here, we use an optimized spherical Jeans analysis to reconstruct the ‘astrophysical factor’ for both annihilating and decaying dark matter in 21 known dSphs. Improvements with respect to previous works are: (i) the use of more flexible luminosity and anisotropy profiles to minimize biases, (ii) the use of weak priors tailored on extensive sets of contamination-free mock data to improve the confidence intervals, (iii) systematic cross-checks of binned and unbinned analyses on mock and real data, and (iv) the use of mock data including stellar contamination to test the impact on reconstructed signals. Our analysis provides updated values for the dark matter content of 8 ‘classical’ and 13 ‘ultrafaint’ dSphs, with the quoted uncertainties directly linked to the sample size; the more flexible parametrization we use results in changes compared to previous calculations. This translates into our ranking of potentially-brightest and most robust targets – namely Ursa Minor, Draco, Sculptor – and of the more promising, but uncertain targets – namely Ursa Major 2, Coma – for annihilating dark matter. Our analysis of Segue 1 is extremely sensitive to whether we include or exclude a few marginal member stars, making this target one of the most uncertain. Our analysis illustrates challenges that will need to be addressed when inferring the dark matter content of new ‘ultrafaint’ satellites that are beginning to be discovered in southern sky surveys.

Description: The adsorption of H atoms and their recombination to form an H 2 molecule on slab models of the crystalline Mg 2 SiO 4 forsterite (001) and (110) surfaces was studied by means of quantum mechanical calculations based on periodic density functional theory (DFT). Present results are compared with those previously reported for the most stable (010) surface, showing the relevance of the surface morphology and their stability on the H 2 formation. Different H chemisorption states were identified, mostly on the outermost O atoms of the surfaces. In agreement with the higher instability of the (001) and (110) surfaces, the calculated adsorption energies are larger than those for the (010) surface. Computed energy barriers for the H hopping on these surfaces are exceedingly high to occur at the very low temperatures of deep space. For the adsorption of two H atoms, the most stable complexes are those in which the H atoms form Mg-H and SiOH surface groups. From these complexes, we did not identify energetically feasible paths for H 2 formation through a Langmuir–Hinshelwood mechanism on the (001) surface because the initial states are more stable than the final products. However, on the (110) surface one path was found to be exoergic with very low energy barriers. This differs to that observed for the (010) surface, for which two feasible Langmuir–Hinshelwood-based channels were identified. H 2 formation through the Eley–Rideal mechanism was also simulated, in which an incoming H atom impinges on a pre-adsorbed H atom at the (001) and (110) surfaces in a barrierless way.

Description: Feedback from outflows driven by active galactic nuclei (AGN) can affect the distribution and properties of the gaseous haloes of galaxies. We study the hydrodynamics and non-thermal emission from the forward outflow shock produced by an AGN-driven outflow. We consider a few possible profiles for the halo gas density, self-consistently constrained by the halo mass, redshift and the disc baryonic concentration of the galaxy. We show that the outflow velocity levels off at ~ 10 3 km s – 1 within the scale of the galaxy disc. Typically, the outflow can reach the virial radius around the time when the AGN shuts off. We show that the outflows are energy-driven, consistent with observations and recent theoretical findings. The outflow shock lights up the haloes of massive galaxies across a broad wavelength range. For Milky Way mass haloes, radio observations by the Jansky Very Large Array and the Square Kilometre Array and infrared/optical observations by the James Webb Space Telescope and Hubble Space Telescope can detect the emission signal of angular size ~8 arcsec from galaxies out to redshift z  ~ 5. Millimetre observations by the Atacama Large Millimeter/submillimeter Array are sensitive to non-thermal emission of angular size ~18 arcsec from galaxies at redshift z   1, while X-ray observations by Chandra , XMM–Newton and the Advanced Telescope for High Energy Astrophysics are limited to local galaxies ( z   0.1) with an emission angular size of ~2 arcmin. Overall, the extended non-thermal emission provides a new way of probing the gaseous haloes of galaxies at high redshifts.

Description: In this paper we extend the previously published dali -approximation for likelihoods to cases in which the parameter dependence is in the covariance matrix. The approximation recovers non-Gaussian likelihoods, and reduces to the Fisher matrix approach in the case of Gaussianity. It works with the minimal assumptions of having Gaussian errors on the data, and a covariance matrix that possesses a converging Taylor approximation. The resulting approximation works in cases of severe parameter degeneracies and in cases where the Fisher matrix is singular. It is at least 1000 times faster than a typical Monte Carlo Markov Chain run over the same parameter space. Two example applications, to cases of extremely non-Gaussian likelihoods, are presented – one demonstrates how the method succeeds in reconstructing completely a ring-shaped likelihood. A public code is released here: http://lnasellentin.github.io/DALI/ .

Description: Using star-forming galaxies sample in the nearby Universe (0.02 〈  z  〈 0.10) selected from the Sloan Digital Sky Survey (DR7) and Galaxy Evolution Explorer all-sky survey (GR5), we present a new empirical calibration for predicting dust extinction of galaxies from the Hα-to-FUV flux ratio. We find that the Hα dust extinction ( A Hα ) derived with Hα/Hβ ratio (Balmer decrement) increases with increasing Hα/UV ratio as expected, but there remains a considerable scatter around the relation, which is largely dependent on stellar mass and/or Hα equivalent width (EW Hα ). At fixed Hα/UV ratio, galaxies with higher stellar mass (or galaxies with lower EW Hα ) tend to be more highly obscured by dust. We quantify this trend and establish an empirical calibration for predicting A Hα with a combination of Hα/UV ratio, stellar mass, and EW Hα , with which we can successfully reduce the systematic uncertainties accompanying the simple Hα/UV approach by ~15–30 per cent. The new recipes proposed in this study will provide a convenient tool for predicting dust extinction level of galaxies particularly when Balmer decrement is not available. By comparing A Hα (derived with Balmer decrement) and A UV (derived with IR/UV luminosity ratio) for a subsample of galaxies for which AKARI far-infrared photometry is available, we demonstrate that more massive galaxies tend to have higher extra extinction towards the nebular regions compared to the stellar continuum light. Considering recent studies reporting smaller extra extinction towards nebular regions for high-redshift galaxies, we argue that the dust geometry within high-redshift galaxies resembles low-mass galaxies in the nearby Universe.

Description: We report the redshift of an unlensed, highly obscured submillimetre galaxy (SMG), HS1700.850.1, the brightest SMG ( S 850 μm  = 19.1 mJy) detected in the James Clerk Maxwell Telescope/Submillimetre Common-user Bolometer Array-2 (JCMT/SCUBA-2) Baryonic Structure Survey, based on the detection of its 12 CO line emission. Using the Institute Radio Astronomie Millimetrique Plateau de Bure Interferometer with 3.6 GHz band width, we serendipitously detect an emission line at 150.6 GHz. From a search over 14.5 GHz in the 3- and 2-mm atmospheric windows, we confirm the identification of this line as 12 CO(5–4) at z  = 2.816, meaning that it does not reside in the z  ~ 2.30 proto-cluster in this field. Measurement of the 870 μm source size (〈0.85 arcsec) from the Sub-Millimetre Array (SMA) confirms a compact emission in a S 870 μm = 14.5 mJy, L IR  ~ 10 13  L component, suggesting an Eddington-limited starburst. We use the double-peaked 12 CO line profile measurements along with the SMA size constraints to study the gas dynamics of a HyLIRG, estimating the gas and dynamical masses of HS1700.850.1. While HS1700.850.1 is one of the most extreme galaxies known in the Universe, we find that it occupies a relative void in the Lyman-Break Galaxy distribution in this field. Comparison with other extreme objects at similar epochs (HyLIRG Quasars), and cosmological simulations, suggests such an anti-bias of bright SMGs could be relatively common, with the brightest SMGs rarely occupying the most overdense regions at z = 2–4.

Description: We compare predictions of large-scale cosmological hydrodynamical simulations for neutral hydrogen absorption signatures in the vicinity of 10 11 –10 12.5 M haloes with observational measurements. Two different hydrodynamical techniques and a variety of prescriptions for gas removal in high-density regions are examined. Star formation and wind feedback play only secondary roles in the H i absorption signatures outside the virial radius, but play important roles within. Accordingly, we identify three distinct gaseous regions around a halo: the virialized region, the mesogalactic medium outside the virial radius arising from the extended haloes of galaxies out to about two turnaround radii and the intergalactic medium beyond. Predictions for the amount of absorption from the mesogalactic and intergalactic media are robust across different methodologies, and the predictions agree with the amount of absorption observed around star-forming galaxies and quasi-stellar object host galaxies. Recovering the measured amount of absorption within the virialized region, however, requires either a higher dynamic range in the simulations, additional physics, or both.

Description: In this paper, we consider random phase fluctuations imposed during wave propagation through a turbulent plasma (e.g. ionosphere) as a source of additional noise in interferometric visibilities. We derive expressions for visibility variance for the wide field of view case (FOV ~10°) by computing the statistics of Fresnel diffraction from a stochastic plasma, and provide an intuitive understanding. For typical ionospheric conditions (diffractive scale ~5–20 km at 150 MHz), we show that the resulting ionospheric ‘scintillation noise’ can be a dominant source of uncertainty at low frequencies (  200 MHz). Consequently, low-frequency widefield radio interferometers must take this source of uncertainty into account in their sensitivity analysis. We also discuss the spatial, temporal, and spectral coherence properties of scintillation noise that determine its magnitude in deep integrations, and influence prospects for its mitigation via calibration or filtering.

Description: We estimate the accretion rates of 235 Classical T Tauri star (CTTS) candidates in the Lagoon Nebula using ugri H α photometry from the VST Photometric H α survey+. Our sample consists of stars displaying H α excess, the intensity of which is used to derive accretion rates. For a subset of 87 stars, the intensity of the u -band excess is also used to estimate accretion rates. We find the mean variation in accretion rates measured using H α and u -band intensities to be ~0.17 dex, agreeing with previous estimates (0.04–0.4 dex) but for a much larger sample. The spatial distribution of CTTS align with the location of protostars and molecular gas suggesting that they retain an imprint of the natal gas fragmentation process. Strong accretors are concentrated spatially, while weak accretors are more distributed. Our results do not support the sequential star-forming processes suggested in the literature.

Description: Photometric redshifts, which have become the cornerstone of several of the largest astronomical surveys like PanStarrs, DES, J-PAS and LSST, require precise measurements of galaxy photometry in different bands using a consistent physical aperture. This is not trivial, due to the variation in the shape and width of the point spread function (PSF) introduced by wavelength differences, instrument positions and atmospheric conditions. Current methods to correct for this effect rely on a detailed knowledge of PSF characteristics as a function of the survey coordinates, which can be difficult due to the relative paucity of stars tracking the PSF behaviour. Here we show that it is possible to measure accurate, consistent multicolour photometry without knowing the shape of the PSF. The Chebyshev–Fourier functions (CHEFs) can fit the observed profile of each object and produce high signal-to-noise integrated flux measurements unaffected by the PSF. These total fluxes, which encompass all the galaxy populations, are much more useful for galaxy evolution studies than aperture photometry. We compare the total magnitudes and colours obtained using our software to traditional photometry with SExtractor , using real data from the COSMOS survey and the Hubble Ultra-Deep Field (HUDF). We also apply the CHEF technique to the recently published eXtreme Deep Field (XDF) and compare the results to those from ColorPro on the HUDF. We produce a photometric catalogue with 35 732 sources (10 823 with signal-to-noise ratio ≥5), reaching a photometric redshift precision of 2 per cent due to the extraordinary depth and wavelength coverage of the eXtreme Deep Field images.

Description: We investigate the evolution of the galaxy two-point correlation function (CF) over a wide redshift range, 0.2 〈  z   3. For the first time, the systematic analysis covers the redshifts above 1–1.5. The catalogue of ~250 000 galaxies with i +  〈 25 and known photometric redshifts in the Subaru Deep field is used. The galaxies are divided into three luminosity classes and several distance/redshift bins. First, the 2D CF is determined for each luminosity class and distance bin. Calculations are based on the quantitative differences between the surface distributions of galaxy pairs with comparable and distinctly different photometric redshifts. The power-law approximation for the CF is used. A limited accuracy of photometric redshifts as compared to the spectroscopic ones has been examined and taken into account. Then, the 3D functions for all the selected luminosities and distance are calculated. The power-law parameters of the CF, the slope and the correlation length are determined. Both parameters do not show strong variations over the whole investigated redshift range. The slope of the luminous galaxies appears to be consistently steeper than that for the fainter ones. The linear bias factor, b ( z ), grows systematically with redshift; assuming the local normalization b (0)  1.1–1.2, the bias reaches 3–3.5 at the high-redshift limit.

Description: Herbig Ae/Be stars (HAeBes) span a key mass range that links low- and high-mass stars, and thus provide an ideal window from which to explore their formation. This paper presents Very Large Telescope/X-shooter spectra of 91 HAeBes, the largest spectroscopic study of HAeBe accretion to date. A homogeneous approach to determining stellar parameters is undertaken for the majority of the sample. Measurements of the ultraviolet are modelled within the context of magnetospheric accretion, allowing a direct determination of mass accretion rates. Multiple correlations are observed across the sample between accretion and stellar properties: the youngest and often most massive stars are the strongest accretors, and there is an almost 1:1 relationship between the accretion luminosity and stellar luminosity. Despite these overall trends of increased accretion rates in HAeBes when compared to classical T Tauri stars, we also find noticeable differences in correlations when considering the Herbig Ae and Herbig Be subsets. This, combined with the difficulty in applying a magnetospheric accretion model to some of the Herbig Be stars, could suggest that another form of accretion may be occurring within Herbig Be mass range.

Description: In this first paper we discuss the linear theory and the background evolution of a new class of models we dub SCDEW: Strongly Coupled DE, plus WDM. In these models, WDM dominates today's matter density; like baryons, WDM is uncoupled. Dark energy is a scalar field ; its coupling to ancillary cold dark matter (CDM), whose today's density is 〈〈1 per cent, is an essential model feature. Such coupling, in fact, allows the formation of cosmic structures, in spite of very low WDM particle masses (~100 eV). SCDEW models yield cosmic microwave background and linear large scale features substantially undistinguishable from CDM, but thanks to the very low WDM masses they strongly alleviate CDM issues on small scales, as confirmed via numerical simulations in the second associated paper. Moreover SCDEW cosmologies significantly ease the coincidence and fine tuning problems of CDM and, by using a field theory approach, we also outline possible links with inflationary models. We also discuss a possible fading of the coupling at low redshifts which prevents non-linearities on the CDM component to cause computational problems. The (possible) low- z coupling suppression, its mechanism, and its consequences are however still open questions – not necessarily problems – for SCDEW models. The coupling intensity and the WDM particle mass, although being extra parameters in respect to CDM, are found to be substantially constrained a priori so that, if SCDEW is the underlying cosmology, we expect most data to fit also CDM predictions.

Description: The evidence that stellar systems surrounding the Milky Way (MW) are distributed in a Vast Polar Structure (VPOS) may be observationally biased by satellites detected in surveys of the northern sky. The recent discoveries of more than a dozen new systems in the Southern hemisphere thus constitute a critical test of the VPOS phenomenon. We report that the new objects are located close to the original VPOS, with half of the sample having offsets less than 20 kpc. The positions of the new satellite galaxy candidates are so well aligned that the orientation of the revised best-fitting VPOS structure is preserved to within 9°and the VPOS flattening is almost unchanged (31 kpc height). Interestingly, the shortest distance of the VPOS plane from the MW centre is now only 2.5 kpc, indicating that the new discoveries balance out the VPOS at the Galactic centre. The vast majority of the MW satellites are thus consistent with sharing a similar orbital plane as the Magellanic Clouds, confirming a hypothesis proposed by Kunkel & Demers and Lynden-Bell almost 40 yr ago. We predict the absolute proper motions of the new objects assuming they orbit within the VPOS. Independent of the VPOS results, we also predict the velocity dispersions of the new systems under three distinct assumptions: that they (i) are dark matter free star clusters obeying Newtonian dynamics, (ii) are dwarf satellites lying on empirical scaling relations of galaxies in dark matter haloes and (iii) obey modified Newtonian dynamics.