ALBERT

Description: Looking beyond stratification: a model-based analysis of the biological drivers of oxygen depletion in the North Sea Biogeosciences Discussions, 12, 12543-12610, 2015 Author(s): F. Große, N. Greenwood, M. Kreus, H. J. Lenhart, D. Machoczek, J. Pätsch, L. A. Salt, and H. Thomas The problem of low oxygen conditions, often referred to as hypoxia, occurs regularly in the North Sea, a temperate European shelf sea. Stratification represents a major process regulating the seasonal dynamics of bottom oxygen. However, lowest oxygen conditions in the North Sea do not occur in the regions of strongest stratification. This suggests that stratification is an important prerequisite for hypoxia, but that the complex interaction between hydrodynamics and the biological processes drives its development. In this study we use the ecosystem model HAMSOM-ECOHAM5 to provide a general characteristic of the different North Sea oxygen regimes, and to quantify the impact of the different physical and biological factors driving the oxygen dynamics below the thermocline and in the bottom layer. We show that the North Sea can be subdivided into three different regimes in terms of oxygen dynamics: (1) a highly productive, non-stratified coastal regime, (2) a productive, seasonally stratified regime with a small sub-thermocline volume, and (3) a productive, seasonally stratified regime with a large sub-thermocline volume, with regime 2 being highly susceptible to hypoxic conditions. Our analysis of the different processes driving the oxygen development reveals that inter-annual variations in the oxygen conditions are caused by variations in primary production, while spatial differences can be attributed to differences in stratification and water depth. In addition, we show that benthic bacteria represent the main oxygen consumers in the bottom layer, consistently accounting for more than 50 % of the overall consumption. By providing these valuable insights, we show that ecosystem models can be a useful tool for the interpretation of observations and the estimation of the impact of anthropogenic drivers on the North Sea oxygen conditions.

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: Stimulated Brillouin scattering during electron gyro-harmonic heating at EISCAT Annales Geophysicae, 33, 983-990, 2015 Author(s): H. Y. Fu, W. A. Scales, P. A. Bernhardt, S. J. Briczinski, M. J. Kosch, A. Senior, M. T. Rietveld, T. K. Yeoman, and J. M. Ruohoniemi Observations of secondary radiation, stimulated electromagnetic emission (SEE), produced during ionospheric modification experiments using ground-based, high-power, high-frequency (HF) radio waves are considered. The High Frequency Active Auroral Research Program (HAARP) facility is capable of generating narrowband SEE in the form of stimulated Brillouin scatter (SBS) and stimulated ion Bernstein scatter (SIBS) in the SEE spectrum. Such narrowband SEE spectral lines have not been reported using the European Incoherent Scatter (EISCAT) heater facility before. This work reports the first EISCAT results of narrowband SEE spectra and compares them to SEE previously observed at HAARP during electron gyro-harmonic heating. An analysis of experimental SEE data shows observations of emission lines within 100 Hz of the pump frequency, interpreted as SBS, during the 2012 July EISCAT campaign. Experimental results indicate that SBS strengthens as the pump frequency approaches the third electron gyro-harmonic. Also, for different heater antenna beam angles, the CUTLASS radar backscatter induced by HF radio pumping is suppressed near electron gyro-harmonics, whereas electron temperature enhancement weakens as measured by EISCAT/UHF radar. The main features of these new narrowband EISCAT observations are generally consistent with previous SBS measurements at HAARP.

Description: Optimizing the impact of temperature on bio-hydrogen production from food waste and its derivatives under no pH control using statistical modelling Biogeosciences Discussions, 12, 12823-12850, 2015 Author(s): A. Sattar, C. Arslan, C. Ji, S. Sattar, K. Yousaf, and S. Hashim The effect of temperature on bio-hydrogen production by co-digestion of sewerage sludge with food waste and its two derivatives, i.e. noodle waste and rice waste, was investigated by statistical modelling. Experimental results showed that increasing temperature from mesophilic (37 °C) to thermophilic (55 °C) was an effective mean for increasing bio-hydrogen production from food waste and noodle waste, but it caused a negative impact on bio-hydrogen production from rice waste. The maximum cumulative bio-hydrogen production of 650 mL was obtained from noodle waste under mesophilic temperature condition. Most of the production was observed during 48 h of incubation that continued till 72 h of incubation, and a decline in pH during this interval was 4.3 and 4.4 from a starting value of 7 under mesophilic and thermophilic conditions, respectively. Most of glucose consumption was also observed during 72 h of incubation and the maximum consumption was observed during the first 24 h, which was the same duration where the maximum pH drop occurred. The maximum hydrogen yields of 82.47 mL VS −1 , 131.38 mL COD −1 , and 44.90 mL glucose −1 were obtained from mesophilic food waste, thermophilic noodle waste and mesophilic rice waste respectively. The production of volatile fatty acids increased with an increase in time and temperature from food waste and noodle waste reactors whereas it decreased with temperature in rice waste reactors. The statistical modelling returned good results with high values of coefficient of determination ( R 2 ) for each waste type when it was opted for the study of cumulative hydrogen production, glucose consumption and volatile fatty acid production. The 3-D response surface plots developed by the statistical models helped a lot in developing better understanding of the impact of temperature and incubation time.

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: Some of the most dangerous pathogens such as Mycobacterium tuberculosis and Yersinia pestis evolve clonally . This means that little or no recombination occurs between strains belonging to these species. Paradoxically, although different members of these species show extreme sequence similarity of orthologous genes, some show considerable intraspecies phenotypic variation, the source of which remains elusive. To examine the possible sources of phenotypic variation within clonal pathogenic bacterial species, we carried out an extensive genomic and pan-genomic analysis of the sources of genetic variation available to a large collection of clonal and nonclonal pathogenic bacterial species. We show that while nonclonal species diversify through a combination of changes to gene sequences, gene loss and gene gain, gene loss completely dominates as a source of genetic variation within clonal species. Indeed, gene loss is so prevalent within clonal species as to lead to levels of gene content variation comparable to those found in some nonclonal species that are much more diverged in their gene sequences and that acquire a substantial number of genes horizontally. Gene loss therefore needs to be taken into account as a potential dominant source of phenotypic variation within clonal bacterial species.

Description: Obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. Increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. Here we take a comparative genomics approach to investigate two prominent bacterial symbionts (BFo1 and BFo2) isolated from geographically separated populations of western flower thrips, Frankliniella occidentalis. Our multifaceted approach to classifying these symbionts includes concatenated multilocus sequence analysis (MLSA) phylogenies, ribosomal multilocus sequence typing (rMLST), construction of whole-genome phylogenies, and in-depth genomic comparisons. We showed that the BFo1 genome clusters more closely to species in the genus Erwinia, and is a putative close relative to Erwinia aphidicola . BFo1 is also likely to have shared a common ancestor with Erwinia pyrifoliae/Erwinia amylovora and the nonpathogenic Erwinia tasmaniensis and genetic traits similar to Erwinia billingiae . The BFo1 genome contained virulence factors found in the genus Erwinia but represented a divergent lineage. In contrast, we showed that BFo2 belongs within the Enterobacteriales but does not group closely with any currently known bacterial species. Concatenated MLSA phylogenies indicate that it may have shared a common ancestor to the Erwinia and Pantoea genera, and based on the clustering of rMLST genes, it was most closely related to Pantoea ananatis but represented a divergent lineage. We reconstructed a core genome of a putative common ancestor of Erwinia and Pantoea and compared this with the genomes of BFo bacteria. BFo2 possessed none of the virulence determinants that were omnipresent in the Erwinia and Pantoea genera. Taken together, these data are consistent with BFo2 representing a highly novel species that maybe related to known Pantoea .

Description: Strange VLF bursts in northern Scandinavia: case study of the afternoon "mushroom-like" hiss on 8 December 2013 Annales Geophysicae, 33, 991-995, 2015 Author(s): J. Manninen, N. G. Kleimenova, A. Kozlovsky, I. A. Kornilov, L. I. Gromova, Y. V. Fedorenko, and T. Turunen We investigate a non-typical very low frequency (VLF) 1–4 kHz hiss representing a sequence of separated noise bursts with a strange "mushroom-like" shape in the frequency–time domain, each one lasting several minutes. These strange afternoon VLF emissions were recorded at Kannuslehto (KAN, ϕ = 67.74° N, λ = 26.27° E; L ∼ 5.5) in northern Finland during the late recovery phase of the small magnetic storm on 8 December 2013. The left-hand (LH) polarized 2–3 kHz "mushroom caps" were clearly separated from the right-hand (RH) polarized "mushroom stems" at the frequency of about 1.8–1.9 kHz, which could match the lower ionosphere waveguide cutoff (the first transverse resonance of the Earth–ionosphere cavity). We hypothesize that this VLF burst sequence could be a result of the modulation of the VLF hiss electron–cyclotron instability from the strong Pc5 geomagnetic pulsations observed simultaneously at ground-based stations as well as in the inner magnetosphere by the Time History of Events and Macroscale Interactions during Substorms mission probe (THEMIS-E; ThE). This assumption is confirmed by a similar modulation of the intensity of the energetic (1–10 keV) electrons simultaneously observed by the same ThE spacecraft. In addition, the data of the European Incoherent Scatter Scientific Association (EISCAT) radar at Tromsø show a similar quasi-periodicity in the ratio of the Hall-to-Pedersen conductance, which may be used as a proxy for the energetic particle precipitation enhancement. Our findings suggest that this strange mushroom-like shape of the considered VLF hiss could be a combined mutual effect of the magnetospheric ULF–VLF (ultra low frequency–very low frequency) wave interaction and the ionosphere waveguide propagation.

Description: Stable isotope study of a new chondrichthyan fauna (Kimmeridgian, Porrentruy, Swiss Jura): an unusual freshwater-influenced isotopic composition for the hybodont shark Asteracanthus Biogeosciences Discussions, 12, 12899-12921, 2015 Author(s): L. Leuzinger, L. Kocsis, J.-P. Billon-Bruyat, S. Spezzaferri, and T. Vennemann Chondrichthyan teeth (sharks, rays and chimaeras) are mineralised in isotopic equilibrium with the surrounding water, and parameters such as water temperature and salinity can be inferred from the oxygen isotopic composition (δ 18 O p ) of their bioapatite. We analysed a new chondrichthyan assemblage, as well as teeth from bony fish (Pycnodontiformes). All specimens are from Kimmeridgian coastal marine deposits of the Swiss Jura (vicinity of Porrentruy, Ajoie district, NW Switzerland). While the overall faunal composition and the isotopic composition of bony fish are consistent with marine conditions, unusually low δ 18 O p values were measured for the hybodont shark Asteracanthus . These values are also lower compared to previously published data from older European Jurassic localities. Additional analyses on material from Solothurn (Kimmeridgian, NW Switzerland) also have comparable, low- 18 O isotopic compositions for Asteracanthus . The data are hence interpreted to represent a so far unique, freshwater-influenced isotopic composition for this shark that is classically considered as a marine genus. While reproduction in freshwater or brackish realms is established for other hybodonts, a similar behaviour for Asteracanthus is proposed here. Regular excursions into lower salinity waters can be linked to the age of the deposits and correspond to an ecological adaptation, most likely driven by the Kimmeridgian transgression and by the competition of the primitive shark Asteracanthus with the rapidly diversifying neoselachians (modern sharks).

Description: Climate change impacts on net primary production (NPP) and export production (EP) regulated by increasing stratification and phytoplankton community structure in CMIP5 models Biogeosciences Discussions, 12, 12851-12897, 2015 Author(s): W. Fu, J. Randerson, and J. K. Moore We examine climate change impacts on net primary production (NPP) and export production (sinking particulate flux; EP) with simulations from nine Earth System Models (ESMs) performed in the framework of the fifth Coupled Model Inter-comparison Project (CMIP5). Global NPP and EP are reduced considerably by the end of the century for the intense warming scenario of Representative Concentration Pathway (RCP) 8.5. Relative to the 1990s, global NPP in the 2090s is reduced by 2.3–16 % and EP by 7–18 %. The models with the largest increases in stratification (and largest relative reductions in NPP and EP) also show the largest positive biases in stratification for the contemporary period, suggesting some potential overestimation of climate impacts on NPP and EP. All of the CMIP5 models show an increase in stratification in response to surface ocean warming and freshening that is accompanied by decreases in NPP, EP, and surface macronutrient concentrations. There is considerable variability across models in the absolute magnitude of these fluxes, surface nutrient concentrations, and their perturbations by climate change, indicating large model uncertainties. The negative response of NPP and EP to stratification increases reflects a bottom-up control, as nutrient flux to the euphotic zone declines. Models with dynamic phytoplankton community structure show larger declines in EP than in NPP. This is driven by phytoplankton community composition shifts, with a reduced percentage of NPP by large phytoplankton under RCP 8.5, as smaller phytoplankton are favored under the increasing nutrient stress. Thus, projections of the NPP response to climate change in the CMIP5 models are critically dependent on the simulated phytoplankton community structure, the efficiency of the biological pump, and the resulting (highly variable) levels of regenerated production. Community composition is represented relatively simply in the CMIP5 models, and should be expanded to better capture the spatial patterns and the changes in export efficiency that are necessary for predicting climate impacts on NPP.

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: Technical Note: A simple calculation algorithm to separate high-resolution CH 4 flux measurements into ebullition and diffusion-derived components Biogeosciences Discussions, 12, 12923-12945, 2015 Author(s): M. Hoffmann, M. Schulz-Hanke, J. Garcia Alba, N. Jurisch, U. Hagemann, T. Sachs, M. Sommer, and J. Augustin Processes driving the production, transformation and transport of methane (CH 4 ) in wetland ecosystems are highly complex. Thus, serious challenges are constitutes in terms of the mechanistic process understanding, the identification of potential environmental drivers and the calculation of reliable CH 4 emission estimates. We present a simple calculation algorithm to separate open-water CH 4 fluxes measured with automatic chambers into diffusion- and ebullition-derived components, which helps facilitating the identification of underlying dynamics and potential environmental drivers. Flux separation is based on ebullition related sudden concentration changes during single measurements. A variable ebullition filter is applied, using the lower and upper quartile and the interquartile range (IQR). Automation of data processing is achieved by using an established R-script, adjusted for the purpose of CH 4 flux calculation. The algorithm was tested using flux measurement data (July to September 2013) from a former fen grassland site, converted into a shallow lake as a result of rewetting ebullition and diffusion contributed 46 and 55 %, respectively, to total CH 4 emissions, which is comparable to those previously reported by literature. Moreover, the separation algorithm revealed a concealed shift in the diurnal trend of diffusive fluxes throughout the measurement period.

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: Gene expression evolution occurs through changes in cis - or trans -regulatory elements or both. Interactions between transcription factors (TFs) and their binding sites (TFBSs) constitute one of the most important points where these two regulatory components intersect. In this study, we investigated the evolution of TFBSs in the promoter regions of different Saccharomyces strains and species. We divided the promoter of a gene into the proximal region and the distal region, which are defined, respectively, as the 200-bp region upstream of the transcription starting site and as the 200-bp region upstream of the proximal region. We found that the predicted TFBSs in the proximal promoter regions tend to be evolutionarily more conserved than those in the distal promoter regions. Additionally, Saccharomyces cerevisiae strains used in the fermentation of alcoholic drinks have experienced more TFBS losses than gains compared with strains from other environments (wild strains, laboratory strains, and clinical strains). We also showed that differences in TFBSs correlate with the cis component of gene expression evolution between species (comparing S. cerevisiae and its sister species Saccharomyces paradoxus ) and within species (comparing two closely related S. cerevisiae strains).

Description: Gene duplication is a key factor contributing to phenotype diversity across and within species. Although the availability of complete genomes has led to the extensive study of genomic duplications, the dynamics and variability of gene duplications mediated by retrotransposition are not well understood. Here, we predict mRNA retrotransposition and use comparative genomics to investigate their origin and variability across primates. Analyzing seven anthropoid primate genomes, we found a similar number of mRNA retrotranspositions (~7,500 retrocopies) in Catarrhini (Old Word Monkeys, including humans), but a surprising large number of retrocopies (~10,000) in Platyrrhini (New World Monkeys), which may be a by-product of higher long interspersed nuclear element 1 activity in these genomes. By inferring retrocopy orthology, we dated most of the primate retrocopy origins, and estimated a decrease in the fixation rate in recent primate history, implying a smaller number of species-specific retrocopies. Moreover, using RNA-Seq data, we identified approximately 3,600 expressed retrocopies. As expected, most of these retrocopies are located near or within known genes, present tissue-specific and even species-specific expression patterns, and no expression correlation to their parental genes. Taken together, our results provide further evidence that mRNA retrotransposition is an active mechanism in primate evolution and suggest that retrocopies may not only introduce great genetic variability between lineages but also create a large reservoir of potentially functional new genomic loci in primate genomes.

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: Nitrogen export from a boreal stream network following forest harvesting: seasonal nitrate removal and conservative export of organic forms Biogeosciences Discussions, 12, 12061-12089, 2015 Author(s): J. Schelker, R. Sponseller, E. Ring, L. Högbom, S. Löfgren, and H. Laudon Boreal streams are under pressure from large scale disturbance by forestry. Recent scenarios predict an increase in forest production in Scandinavia to meet market demands and to mitigate higher anthropogenic CO 2 emissions. Increased fertilization and shorter forest rotations are anticipated which will likely enhance the pressure on boreal streams in the near future. Among the major environmental impacts of forest harvesting is the increased mobilization of inorganic nitrogen (N), primarily as nitrate (NO 3 - ) into surface waters. But whereas NO 3 - inputs to first-order streams have been previously described, their downstream fate and impact is not well understood. We evaluated the downstream fate of N inputs in a boreal landscape that has been altered by forest harvests over a 10 year period to estimate the effects of multiple clear-cuts on aquatic N export in a boreal stream network. Small streams showed substantial leaching of NO 3 - in response to harvests with concentrations increasing by ~ 15 fold. NO 3 - concentrations at two sampling stations further downstream in the network were strongly seasonal and increased significantly in response to harvesting at the medium size, but not at the larger stream. Nitrate removal efficiency, E r , calculated as the percentage of "forestry derived" NO 3 - that was retained within the landscape using a mass balance model was highest during the snow melt season followed by the growing season, but declined continuously throughout the dormant season. In contrast, export of organic N from the landscape indicated little removal and was essentially conservative. Overall, net removal of NO 3 - between 2008 and 2011 accounted for ~ 70 % of the total NO 3 - mass exported from harvested patches distributed across the landscape. These results highlight the capacity and limitation of N-limited terrestrial and aquatic ecosystems to buffer inorganic N mobilization that arises from multiple clear-cuts within meso-scale boreal watersheds.

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: A case study on generation mechanisms of a sporadic sodium layer above Tromsø (69.6° N) during a night of high auroral activity Annales Geophysicae, 33, 941-953, 2015 Author(s): T. Takahashi, S. Nozawa, T. T. Tsuda, Y. Ogawa, N. Saito, T. Hidemori, T. D. Kawahara, C. Hall, H. Fujiwara, N. Matuura, A. Brekke, M. Tsutsumi, S. Wada, T. Kawabata, S. Oyama, and R. Fujii We have quantitatively evaluated generation mechanisms of a sporadic sodium layer (SSL) based on observational data obtained by multiple instruments at a high-latitude station: Ramfjordmoen, Tromsø, Norway (69.6° N, 19.2° E). The sodium lidar observed an SSL at 21:18 UT on 22 January 2012. The SSL was observed for 18 min, with a maximum sodium density of about 1.9 × 10 10 m −3 at 93 km with a 1.1 km thickness. The European Incoherent Scatter (EISCAT) UHF radar observed a sporadic E layer (Es layer) above 90 km from 20:00 to 23:00 UT. After 20:00 UT, the Es layer gradually descended and reached 94 km at 21:18 UT when the SSL appeared at the same altitude. In this event, considering the abundance of sodium ions (10 % or less), the Es layer could provide only about 37 % or less of the sodium atoms to the SSL. We have investigated a temporal development of the normal sodium ion layer with a consideration of chemical reactions and the effect of the (southwestward) electric field using observational values of the neutral temperature, electron density, horizontal neutral wind, and electric field. This calculation has shown that those processes, including contributions of the Es layer, would provide about 88 % of sodium atoms of the SSL. The effects of meteor absorption and auroral particle sputtering appear to be less important. Therefore, we have concluded that the major source of the SSL was sodium ions in a normal sodium ion layer. Two processes – namely the downward transportation of sodium ions from a normal sodium ion layer due to the electric field and the additional supply of sodium ions from the Es layer under relatively high electron density conditions (i.e., in the Es layer) – played a major role in generating the SSL in this event. Furthermore, we have found that the SSL was located in a lower-temperature region and that the temperature inside the SSL did not show any remarkable temperature enhancements.

Description: Viruses rely completely on the hosts’ machinery for translation of viral transcripts. However, for most viruses infecting humans, codon usage preferences (CUPrefs) do not match those of the host. Human papillomaviruses (HPVs) are a showcase to tackle this paradox: they present a large genotypic diversity and a broad range of phenotypic presentations, from asymptomatic infections to productive lesions and cancer. By applying phylogenetic inference and dimensionality reduction methods, we demonstrate first that genes in HPVs are poorly adapted to the average human CUPrefs, the only exception being capsid genes in viruses causing productive lesions. Phylogenetic relationships between HPVs explained only a small proportion of CUPrefs variation. Instead, the most important explanatory factor for viral CUPrefs was infection phenotype, as orthologous genes in viruses with similar clinical presentation displayed similar CUPrefs. Moreover, viral genes with similar spatiotemporal expression patterns also showed similar CUPrefs. Our results suggest that CUPrefs in HPVs reflect either variations in the mutation bias or differential selection pressures depending on the clinical presentation and expression timing. We propose that poor viral CUPrefs may be central to a trade-off between strong viral gene expression and the potential for eliciting protective immune response.

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: Huntington's disease (HD) is a hereditary neurodegenerative disorder characterized by brain atrophy particularly in striatum leading to personality changes, chorea and dementia. Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase in the crossroad of many signaling pathways that is highly pleiotropic as it phosphorylates more than hundred substrates including structural, metabolic, and signaling proteins. Increased GSK-3 activity is believed to contribute to the pathogenesis of neurodegenerative diseases like Alzheimer's disease and GSK-3 inhibitors have been postulated as therapeutic agents for neurodegeneration. Regarding HD, GSK-3 inhibitors have shown beneficial effects in cell and invertebrate animal models but no evident efficacy in mouse models. Intriguingly, those studies were performed without interrogating GSK-3 level and activity in HD brain. Here we aim to explore the level and also the enzymatic activity of GSK-3 in the striatum and other less affected brain regions of HD patients and of the R6/1 mouse model to then elucidate the possible contribution of its alteration to HD pathogenesis by genetic manipulation in mice. We report a dramatic decrease in GSK-3 levels and activity in striatum and cortex of HD patients with similar results in the mouse model. Correction of the GSK-3 deficit in HD mice, by combining with transgenic mice with conditional GSK-3 expression, resulted in amelioration of their brain atrophy and behavioral motor and learning deficits. Thus, our results demonstrate that decreased brain GSK-3 contributes to HD neurological phenotype and open new therapeutic opportunities based on increasing GSK-3 activity or attenuating the harmful consequences of its decrease.

Description: Spinocerebellar ataxia type 6 (SCA6) is dominantly inherited neurodegenerative disease, caused by an expansion of CAG repeat encoding a polyglutamine (PolyQ) tract in the Ca v 2.1 voltage-gated calcium channel. Its key pathological features include selective degeneration of the cerebellar Purkinje cells (PCs), a common target for PolyQ-induced toxicity in various SCAs. Mutant Ca v 2.1 confers toxicity primarily through a toxic gain-of-function mechanism; however, its molecular basis remains elusive. Here, we studied the cerebellar gene expression patterns of young Sca6 -MPI 118Q/118Q knockin (KI) mice, which expressed mutant Ca v 2.1 from an endogenous locus and recapitulated many phenotypic features of human SCA6. Transcriptional signatures in the MPI 118Q/118Q mice were distinct from those in the Sca1 154Q/2Q mice, a faithful SCA1 KI mouse model. Temporal expression profiles of the candidate genes revealed that the up-regulation of genes associated with microglial activation was initiated before PC degeneration and was augmented as the disease progressed. Histological analysis of the MPI 118Q/118Q cerebellum showed the predominance of M1-like pro-inflammatory microglia and it was concomitant with elevated expression levels of tumor necrosis factor, interleukin-6, Toll-like receptor (TLR) 2 and 7. Genetic ablation of MyD88, a major adaptor protein conveying TLR signaling, altered expression patterns of M1/M2 microglial phenotypic markers in the MPI 118Q/118Q cerebellum. More importantly, it ameliorated PC loss and partially rescued motor impairments in the early disease phase. These results suggest that early neuroinflammatory response may play an important role in the pathogenesis of SCA6 and its modulation could pave the way for slowing the disease progression during the early stage of the disease.

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: Numerical study of upper hybrid to Z -mode leakage during electromagnetic pumping of groups of striations in the ionosphere Annales Geophysicae, 33, 1019-1030, 2015 Author(s): B. Eliasson and T. B. Leyser We investigate numerically the interaction between ionospheric magnetic field-aligned density striations and a left-hand circularly polarized ( L )-mode wave. The L -mode wave is scattered into upper hybrid (UH) waves which are partially trapped in the striations, but leak energy to electromagnetic waves in the Z -mode branch. For small-amplitude (1 %) striations, this loss mechanism leads to a significant reduction in amplitude of the UH waves. For several striations organized in a lattice, the leaking of Z -mode waves is compensated by influx of Z -mode radiation from neighboring striations, leading to an increased amplitude of the weakly trapped UH waves. For large-amplitude (10 %) striations the trapped UH waves rapidly increase in amplitude far beyond the threshold for parametric instabilities, and the Z -mode leakage is less important. The results have relevance for the growth of striations and the onset of UH and lower hybrid turbulence during electromagnetic high-frequency pumping of ionospheric plasma, which require large-amplitude UH waves.

Description: Observation of a new type of low-frequency waves at comet 67P/Churyumov-Gerasimenko Annales Geophysicae, 33, 1031-1036, 2015 Author(s): I. Richter, C. Koenders, H.-U. Auster, D. Frühauff, C. Götz, P. Heinisch, C. Perschke, U. Motschmann, B. Stoll, K. Altwegg, J. Burch, C. Carr, E. Cupido, A. Eriksson, P. Henri, R. Goldstein, J.-P. Lebreton, P. Mokashi, Z. Nemeth, H. Nilsson, M. Rubin, K. Szegö, B. T. Tsurutani, C. Vallat, M. Volwerk, and K.-H. Glassmeier We report on magnetic field measurements made in the innermost coma of 67P/Churyumov-Gerasimenko in its low-activity state. Quasi-coherent, large-amplitude (δ B / B ~ 1), compressional magnetic field oscillations at ~ 40 mHz dominate the immediate plasma environment of the nucleus. This differs from previously studied cometary interaction regions where waves at the cometary ion gyro-frequencies are the main feature. Thus classical pickup-ion-driven instabilities are unable to explain the observations. We propose a cross-field current instability associated with newborn cometary ion currents as a possible source mechanism.

Description: Hydroxy fatty acids in fresh snow samples from northern Japan: long-range atmospheric transport of Gram-negative bacteria by Asian winter monsoon Biogeosciences Discussions, 12, 13375-13397, 2015 Author(s): P. Tyagi, S. Yamamoto, and K. Kawamura Hydroxy fatty acids (FAs) in fresh snow from Sapporo, one of the heaviest snowfall regions in the world, have been studied to ascertain the airborne bacterial endotoxin concentrations and their biomass. The presence of β-hydroxy FAs (C 9 –C 28 ), constituents of Gram-negative bacteria (GNB), suggests long-range transport of soil microbes. Likewise, the occurrence of α- and ω-hydroxy FAs (C 9 –C 30 and C 9 –C 28 , respectively) in snow reveals their contribution from epicuticular waxes and soil microorganisms. Estimated endotoxin and GNB mass can aid in assessing their possible impacts on the diversity and functioning of aquatic and terrestrial ecosystems, as well as lethal effects on pedestrians through dispersal of microbes. Air mass back trajectories together with hydroxy FAs unveil their sources from Siberia, Russian Far East and North China by the Asian monsoon. This study highlights the role of fresh snow that reduces the human health risk of GNB and endotoxin by scavenging from the air.

Description: Spliceosomal introns are a hallmark of eukaryotic genes that are hypothesized to play important roles in genome evolution but have poorly understood origins. Although most introns lack sequence homology to each other, new families of spliceosomal introns that are repeated hundreds of times in individual genomes have recently been discovered in a few organisms. The prevalence and conservation of these introner elements (IEs) or introner-like elements in other taxa, as well as their evolutionary relationships to regular spliceosomal introns, are still unknown. Here, we systematically investigate introns in the widespread marine green alga Micromonas and report new families of IEs, numerous intron presence–absence polymorphisms, and potential intron insertion hot-spots. The new families enabled identification of conserved IE secondary structure features and establishment of a novel general model for repetitive intron proliferation across genomes. Despite shared secondary structure, the IE families from each Micromonas lineage bear no obvious sequence similarity to those in the other lineages, suggesting that their appearance is intimately linked with the process of speciation. Two of the new IE families come from an Arctic culture ( Micromonas Clade E2) isolated from a polar region where abundance of this alga is increasing due to climate induced changes. The same two families were detected in metagenomic data from Antarctica—a system where Micromonas has never before been reported. Strikingly high identity between the Arctic isolate and Antarctic coding sequences that flank the IEs suggests connectivity between populations in the two polar systems that we postulate occurs through deep-sea currents. Recovery of Clade E2 sequences in North Atlantic Deep Waters beneath the Gulf Stream supports this hypothesis. Our research illuminates the dynamic relationships between an unusual class of repetitive introns, genome evolution, speciation, and global distribution of this sentinel marine alga.

Description: Cellular Ca 2+ homeostasis is tightly regulated and is pivotal to life. Inositol 1,4,5-trisphosphate receptors (IP 3 Rs) and ryanodine receptors (RyRs) are the major ion channels that regulate Ca 2+ release from intracellular stores. Although these channels have been extensively investigated in multicellular organisms, an appreciation of their evolution and the biology of orthologs in unicellular organisms is largely lacking. Extensive phylogenetic analyses reveal that the IP 3 R gene superfamily is ancient and diverged into two subfamilies, IP 3 R-A and IP 3 R-B/RyR, at the dawn of Opisthokonta. IP 3 R-B/RyR further diversified into IP 3 R-B and RyR at the stem of Filozoa. Subsequent evolution and speciation of Holozoa is associated with duplication of IP 3 R-A and RyR genes, and loss of IP 3 R-B in the vertebrate lineages. To gain insight into the properties of IP 3 R important for the challenges of multicellularity, the IP 3 R-A and IP 3 R-B family orthologs were cloned from Capsaspora owczarzaki, a close unicellular relative to Metazoa (designated as CO.IP 3 R-A and CO.IP 3 R-B). Both proteins were targeted to the endoplasmic reticulum. However, CO.IP 3 R-A, but strikingly not CO.IP 3 R-B, bound IP 3 , exhibited robust Ca 2+ release activity and associated with mammalian IP 3 Rs. These data indicate strongly that CO.IP 3 R-A as an exemplar of ancestral IP 3 R-A orthologs forms bona fide IP 3 -gated channels. Notably, however, CO.IP 3 R-A appears not to be regulated by Ca 2+ , ATP or Protein kinase A-phosphorylation. Collectively, our findings explore the origin, conservation, and diversification of IP 3 R gene families and provide insight into the functionality of ancestral IP 3 Rs and the added specialization of these proteins in Metazoa.

Description: Marriage rules, the community prescriptions that dictate who an individual can or cannot marry, are extremely diverse and universally present in traditional societies. A major focus of research in the early decades of modern anthropology, marriage rules impose social and economic forces that help structure societies and forge connections between them. However, in those early anthropological studies, the biological benefits or disadvantages of marriage rules could not be determined. We revisit this question by applying a novel simulation framework and genome-wide data to explore the effects of Asymmetric Prescriptive Alliance, an elaborate set of marriage rules that has been a focus of research for many anthropologists. Simulations show that strict adherence to these marriage rules reduces genetic diversity on the autosomes, X chromosome and mitochondrial DNA, but relaxed compliance produces genetic diversity similar to random mating. Genome-wide data from the Indonesian community of Rindi, one of the early study populations for Asymmetric Prescriptive Alliance, are more consistent with relaxed compliance than strict adherence. We therefore suggest that, in practice, marriage rules are treated with sufficient flexibility to allow social connectivity without significant degradation of biological diversity.

Description: The environment has profound effects on the expression of many traits and reaction norms describe the expression dynamics of a trait across a broad range of environmental conditions. Here, we analyze gene expression in Drosophila melanogaster across four different developmental temperatures (13–29 °C). Gene expression is highly plastic with 83.3% of the genes being differentially expressed. We distinguished three components of plasticity: 1) Dynamics of gene expression intensity (sum of change), 2) direction of change, and 3) curvature of the reaction norm (linear vs. quadratic). Studying their regulatory architecture we found that all three plasticity components were most strongly affected by the number of different transcription factors (TFs) binding to the target gene. More TFs were found in genes with less expression changes across temperatures. Although the effect of microRNAs was weaker, we consistently noted a trend in the opposite direction. The most plastic genes were regulated by fewer TFs and more microRNAs than less plastic genes. Different patterns of plasticity were also reflected by their functional characterization based on gene ontology. Our results suggest that reaction norms provide an important key to understand the functional requirements of natural populations exposed to variable environmental conditions.

Description: Recent advances in paleogenomic technologies have enabled an increasingly detailed understanding of the evolutionary relationships of now-extinct mammalian taxa. However, a number of enigmatic Quaternary species have never been characterized with molecular data, often because available fossils are rare or are found in environments that are not optimal for DNA preservation. Here, we analyze paleogenomic data extracted from bones attributed to the late Pleistocene western camel, Camelops cf. hesternus, a species that was distributed across central and western North America until its extinction approximately 13,000 years ago. Despite a modal sequence length of only around 35 base pairs, we reconstructed high-coverage complete mitochondrial genomes and low-coverage partial nuclear genomes for each specimen. We find that Camelops is sister to African and Asian bactrian and dromedary camels, to the exclusion of South American camelids (llamas, guanacos, alpacas, and vicuñas). These results contradict previous morphology-based phylogenetic models for Camelops , which suggest instead a closer relationship between Camelops and the South American camelids. The molecular data imply a Late Miocene divergence of the Camelops clade from lineages that separately gave rise to the extant camels of Eurasia. Our results demonstrate the increasing capacity of modern paleogenomic methods to resolve evolutionary relationships among distantly related lineages.

Description: Recent developments in the analysis of amino acid covariation are leading to breakthroughs in protein structure prediction, protein design, and prediction of the interactome. It is assumed that observed patterns of covariation are caused by molecular coevolution, where substitutions at one site affect the evolutionary forces acting at neighboring sites. Our theoretical and empirical results cast doubt on this assumption. We demonstrate that the strongest coevolutionary signal is a decrease in evolutionary rate and that unfeasibly long times are required to produce coordinated substitutions. We find that covarying substitutions are mostly found on different branches of the phylogenetic tree, indicating that they are independent events that may or may not be attributable to coevolution. These observations undermine the hypothesis that molecular coevolution is the primary cause of the covariation signal. In contrast, we find that the pairs of residues with the strongest covariation signal tend to have low evolutionary rates, and that it is this low rate that gives rise to the covariation signal. Slowly evolving residue pairs are disproportionately located in the protein’s core, which explains covariation methods’ ability to detect pairs of residues that are close in three dimensions. These observations lead us to propose the "coevolution paradox": The strength of coevolution required to cause coordinated changes means the evolutionary rate is so low that such changes are highly unlikely to occur. As modern covariation methods may lead to breakthroughs in structural genomics, it is critical to recognize their biases and limitations.

Description: We present a modified GPU (graphics processing unit) version of MrBayes, called ta(MC) 3 (GPU MrBayes V3.1), for Bayesian phylogenetic inference on protein data sets. Our main contributions are 1) utilizing 64-bit variables, thereby enabling ta(MC) 3 to process larger data sets than MrBayes; and 2) to use Kahan summation to improve accuracy, convergence rates, and consequently runtime. Versus the current fastest software, we achieve a speedup of up to around 2.5 (and up to around 90 vs. serial MrBayes), and more on multi-GPU hardware. GPU MrBayes V3.1 is available from http://sourceforge.net/projects/mrbayes-gpu/ .

Description: Understanding the genetic and molecular bases of the ability to distinguish self from nonself (allorecognition) and mechanisms underlying evolution of allorecognition systems is an important endeavor for understanding cases where it becomes dysfunctional, such as in autoimmune disorders. In filamentous fungi, allorecognition can result in vegetative or heterokaryon incompatibility, which is a type of programmed cell death that occurs following fusion of genetically different cells. Allorecognition is genetically controlled by het loci, with coexpression of any combination of incompatible alleles triggering vegetative incompatibility. Herein, we identified, characterized, and inferred the evolutionary history of candidate het loci in the filamentous fungus Neurospora crassa . As characterized het loci encode proteins carrying an HET domain, we annotated HET domain genes in 25 isolates from a natural population along with the N. crassa reference genome using resequencing data. Because allorecognition systems can be affected by frequency-dependent selection favoring rare alleles (i.e., balancing selection), we mined resequencing data for HET domain loci whose alleles displayed elevated levels of variability, excess of intermediate frequency alleles, and deep gene genealogies. From these analyses, 34 HET domain loci were identified as likely to be under balancing selection. Using transformation, incompatibility assays and genetic analyses, we determined that one of these candidates functioned as a het locus ( het-e ). The het-e locus has three divergent allelic groups that showed signatures of positive selection, intra- and intergroup recombination, and trans-species polymorphism. Our findings represent a compelling case of balancing selection functioning on multiple alleles across multiple loci potentially involved in allorecognition.

Description: Scoring the impact of noncoding variation on the function of cis -regulatory regions, on their chromatin state, and on the qualitative and quantitative expression levels of target genes is a fundamental problem in evolutionary genomics. A particular challenge is how to model the divergence of quantitative traits and to identify relationships between the changes across the different levels of the genome, the chromatin activity landscape, and the transcriptome. Here, we examine the use of the Ornstein–Uhlenbeck (OU) model to infer selection at the level of predicted cis -regulatory modules (CRMs), and link these with changes in transcription factor binding and chromatin activity. Using publicly available cross-species ChIP-Seq and STARR-Seq data we show how OU can be applied genome-wide to identify candidate transcription factors for which binding site and CRM turnover is correlated with changes in regulatory activity. Next, we profile open chromatin in the developing eye across three Drosophila species. We identify the recognition motifs of the chromatin remodelers, Trithorax-like and Grainyhead as mostly correlating with species-specific changes in open chromatin. In conclusion, we show in this study that CRM scores can be used as quantitative traits and that motif discovery approaches can be extended towards more complex models of divergence.

Description: How populations that inhabit the same geographical area become genetically differentiated is not clear. To investigate this, we characterized phenotypic and genetic differences between two populations of Saccharomyces cerevisiae that in some cases inhabit the same environment but show relatively little gene flow. We profiled stress sensitivity in a group of vineyard isolates and a group of oak-soil strains and found several niche-related phenotypes that distinguish the populations. We performed bulk-segregant mapping on two of the distinguishing traits: The vineyard-specific ability to grow in grape juice and oak-specific tolerance to the cell wall damaging drug Congo red. To implicate causal genes, we also performed a chemical genomic screen in the lab-strain deletion collection and identified many important genes that fell under quantitative trait loci peaks. One gene important for growth in grape juice and identified by both the mapping and the screen was SSU1 , a sulfite-nitrite pump implicated in wine fermentations. The beneficial allele is generated by a known translocation that we reasoned may also serve as a genetic barrier. We found that the translocation is prevalent in vineyard strains, but absent in oak strains, and presents a postzygotic barrier to spore viability. Furthermore, the translocation was associated with a fitness cost to the rapid growth rate seen in oak-soil strains. Our results reveal the translocation as a dual-function locus that enforces ecological differentiation while producing a genetic barrier to gene flow in these sympatric populations.

Description: Species tree reconstruction has been a subject of substantial research due to its central role across biology and medicine. A species tree is often reconstructed using a set of gene trees or by directly using sequence data. In either of these cases, one of the main confounding phenomena is the discordance between a species tree and a gene tree due to evolutionary events such as duplications and losses. Probabilistic methods can resolve the discordance by coestimating gene trees and the species tree but this approach poses a scalability problem for larger data sets. We present MixTreEM-DLRS: A two-phase approach for reconstructing a species tree in the presence of gene duplications and losses. In the first phase, MixTreEM, a novel structural expectation maximization algorithm based on a mixture model is used to reconstruct a set of candidate species trees, given sequence data for monocopy gene families from the genomes under study. In the second phase, PrIME-DLRS, a method based on the DLRS model (Åkerborg O, Sennblad B, Arvestad L, Lagergren J. 2009. Simultaneous Bayesian gene tree reconstruction and reconciliation analysis. Proc Natl Acad Sci U S A. 106(14):5714–5719), is used for selecting the best species tree. PrIME-DLRS can handle multicopy gene families since DLRS, apart from modeling sequence evolution, models gene duplication and loss using a gene evolution model (Arvestad L, Lagergren J, Sennblad B. 2009. The gene evolution model and computing its associated probabilities. J ACM. 56(2):1–44). We evaluate MixTreEM-DLRS using synthetic and biological data, and compare its performance with a recent genome-scale species tree reconstruction method PHYLDOG ( Boussau B, Szöllősi GJ, Duret L, Gouy M, Tannier E, Daubin V. 2013 . Genome-scale coestimation of species and gene trees. Genome Res. 23(2):323–330) as well as with a fast parsimony-based algorithm Duptree (Wehe A, Bansal MS, Burleigh JG, Eulenstein O. 2008. Duptree: a program for large-scale phylogenetic analyses using gene tree parsimony. Bioinformatics 24(13):1540–1541). Our method is competitive with PHYLDOG in terms of accuracy and runs significantly faster and our method outperforms Duptree in accuracy. The analysis constituted by MixTreEM without DLRS may also be used for selecting the target species tree, yielding a fast and yet accurate algorithm for larger data sets. MixTreEM is freely available at http://prime.scilifelab.se/mixtreem/ .

Description: Contrasting with birds and mammals, poikilothermic vertebrates often have homomorphic sex chromosomes, possibly resulting from high rates of sex-chromosome turnovers and/or occasional X–Y recombination. Strong support for the latter mechanism was provided by four species of European tree frogs, which inherited from a common ancestor (~5 Ma) the same pair of homomorphic sex chromosomes (linkage group 1, LG1), harboring the candidate sex-determining gene Dmrt1. Here, we test sex linkage of LG1 across six additional species of the Eurasian Hyla radiation with divergence times ranging from 6 to 40 Ma. LG1 turns out to be sex linked in six of nine resolved cases. Mapping the patterns of sex linkage to the Hyla phylogeny reveals several transitions in sex-determination systems within the last 10 My, including one switch in heterogamety. Phylogenetic trees of DNA sequences along LG1 are consistent with occasional X–Y recombination in all species where LG1 is sex linked. These patterns argue against one of the main potential causes for turnovers, namely the accumulation of deleterious mutations on nonrecombining chromosomes. Sibship analyses show that LG1 recombination is strongly reduced in males from most species investigated, including some in which it is autosomal. Intrinsically low male recombination might facilitate the evolution of male heterogamety, and the presence of important genes from the sex-determination cascade might predispose LG1 to become a sex chromosome.

Description: It has been hypothesised that positive associations between age and levels of oxidative stress-generated damage to DNA may be related to an age-dependent decline in DNA repair activity. The objective of this study was to investigate the association between age and repair activity of oxidatively damaged DNA in peripheral blood mononuclear cells (PBMCs). We isolated PBMCs from subjects aged 18–83 years, as part of a health survey of the Danish population that focussed on lifestyle factors. The level of DNA repair activity was measured as incisions on potassium bromate-damaged DNA by the comet assay. There was an inverse association between age and DNA repair activity with a 0.65% decline in activity per year from age 18 to 83 (95% confidence interval: 0.16–1.14% per year). Univariate regression analysis also indicated inverse associations between DNA repair activity and waist-hip ratio ( P 〈 0.05) and plasma concentrations of glycosylated hemoglobin ( P = 0.07). However, multivariate regression analysis only showed an inverse association between age and DNA repair activity ( P 〈 0.05), indicating that the decline in repair activity was not mediated by metabolic risk factors. In summary, the results show an inverse association between age and DNA repair activity of oxidatively damaged DNA.

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: Exposure to traffic-related particulate matter (PM) has been associated with increased risk of lung disease, cancer and cardiovascular disease especially in elderly and overweight subjects. The proposed mechanisms involve intracellular production of reactive oxygen species (ROS), inflammation and oxidation-induced DNA damage studied mainly in young normal-weight subjects. We performed a controlled cross-over, randomised, single-blinded, repeated-measure study where 60 healthy subjects (25 males and 35 females) with age 55–83 years and body mass index above 25kg/m 2 were exposed for 5h to either particle-filtered or sham-filtered air from a busy street with number of concentrations and PM 2.5 levels of 1800/cm 3 versus 23 000/cm 3 and 3 µg/m 3 versus 24 µg/m 3 , respectively. Peripheral blood mononuclear cells (PBMCs) were collected and assayed for production of ROS with and without ex vivo exposure to nanosized carbon black as well as expression of genes related to inflammation ( chemokine (C-C motif) ligand 2 , interleukin-8 and tumour necrosis factor ), oxidative stress response ( heme oxygenase (decycling)-1 ) and DNA repair ( oxoguanine DNA glycosylase ). DNA strand breaks and oxidised purines were assayed by the alkaline comet assay. No statistically significant differences were found for any biomarker immediately after exposure to PM from urban street air although strand breaks and oxidised purines combined were significantly associated with the particle number concentration during exposure. In conclusion, 5h of controlled exposure to PM from urban traffic did not change the gene expression related to inflammation, oxidative stress or DNA repair, ROS production or oxidatively damaged DNA in PBMCs from elderly overweight human subjects.

Description: Ionising radiation causes free radical–mediated damage in cellular DNA. This damage is manifested as chromosomal aberrations and micronuclei (MN) in proliferating cells. Sesamol, present in sesame seeds, has the potential to scavenge free radicals; therefore, it can reduce radiation-induced cytogenetic damage in cells. The aim of this study was to investigate the radioprotective potential of sesamol in bone marrow cells of mice and related haematopoietic system against radiation-induced genotoxicity. A comparative study with melatonin was designed for assessing the radioprotective potential of sesamol. C57BL/6 mice were administered intraperitoneally with either sesamol or melatonin (10 and 20mg/kg body weight) 30min prior to 2-Gy whole-body irradiation (WBI) and sacrificed after 24h. Total chromosomal aberrations (TCA), MN and cell cycle analyses were performed using bone marrow cells. The comet assay was performed on bone marrow cells, splenocytes and lymphocytes. Blood was drawn to study haematological parameters. Prophylactic doses of sesamol (10 and 20mg/kg) in irradiated mice reduced TCA and micronucleated polychromatic erythrocyte frequency in bone marrow cells by 57% and 50%, respectively, in comparison with radiation-only groups. Sesamol-reduced radiation-induced apoptosis and facilitated cell proliferation. In the comet assay, sesamol (20mg/kg) treatment reduced radiation-induced comets (% DNA in tail) compared with radiation only ( P 〈 0.05). Sesamol also increased granulocyte populations in peripheral blood similar to melatonin. Overall, the radioprotective efficacy of sesamol was found to be similar to that of melatonin. Sesamol treatment also showed recovery of relative spleen weight at 24h of WBI. The results strongly suggest the radioprotective efficacy of sesamol in the haematopoietic system of mice.

Description: Individualized treatment rules recommend treatments on the basis of individual patient characteristics. A high-quality treatment rule can produce better patient outcomes, lower costs and less treatment burden. If a treatment rule learned from data is to be used to inform clinical practice or provide scientific insight, it is crucial that it be interpretable; clinicians may be unwilling to implement models they do not understand, and black-box models may not be useful for guiding future research. The canonical example of an interpretable prediction model is a decision tree. We propose a method for estimating an optimal individualized treatment rule within the class of rules that are representable as decision trees. The class of rules we consider is interpretable but expressive. A novel feature of this problem is that the learning task is unsupervised, as the optimal treatment for each patient is unknown and must be estimated. The proposed method applies to both categorical and continuous treatments and produces favourable marginal mean outcomes in simulation experiments. We illustrate it using data from a study of major depressive disorder.

Description: Sufficient dimension reduction in regression aims to reduce the predictor dimension by replacing the original predictors with some set of linear combinations of them without loss of information. Numerous dimension reduction methods have been developed based on this paradigm. However, little effort has been devoted to diagnostic studies within the context of dimension reduction. In this paper we introduce methods to check goodness-of-fit for a given dimension reduction subspace. The key idea is to extend the so-called distance correlation to measure the conditional dependence relationship between the covariates and the response given a reduction subspace. Our methods require minimal assumptions, which are usually much less restrictive than the conditions needed to justify the original methods. Asymptotic properties of the test statistic are studied. Numerical examples demonstrate the effectiveness of the proposed approach.

Description: We propose a geometric framework to assess sensitivity of Bayesian procedures to modelling assumptions based on the nonparametric Fisher–Rao metric. While the framework is general, the focus of this article is on assessing local and global robustness in Bayesian procedures with respect to perturbations of the likelihood and prior, and on the identification of influential observations. The approach is based on a square-root representation of densities, which enables analytical computation of geodesic paths and distances, facilitating the definition of naturally calibrated local and global discrepancy measures. An important feature of our approach is the definition of a geometric $\epsilon$ -contamination class of sampling distributions and priors via intrinsic analysis on the space of probability density functions. We demonstrate the applicability of our framework to generalized mixed-effects models and to directional and shape data.

Description: With the discovery of an increasing number of causal genes for complex human disorders, it is crucial to assess the genetic risk of disease onset for individuals who are carriers of these causal mutations and to compare the distribution of the age-at-onset for such individuals with the distribution for noncarriers. In many genetic epidemiological studies that aim to estimate causal gene effect on disease, the age-at-onset of disease is subject to censoring. In addition, the mutation carrier or noncarrier status of some individuals may be unknown, due to the high cost of in-person ascertainment by collecting DNA samples or because of the death of older individuals. Instead, the probability of such individuals’ mutation status can be obtained from various other sources. When mutation status is missing, the available data take the form of censored mixture data. Recently, various methods have been proposed for risk estimation using such data, but none is efficient for estimating a nonparametric distribution. We propose a fully efficient sieve maximum likelihood estimation method, in which we estimate the logarithm of the hazard ratio between genetic mutation groups using B-splines, while applying nonparametric maximum likelihood estimation to the reference baseline hazard function. Our estimator can be calculated via an expectation-maximization algorithm which is much faster than existing methods. We show that our estimator is consistent and semiparametrically efficient and establish its asymptotic distribution. Simulation studies demonstrate the superior performance of the proposed method, which is used to estimate the distribution of the age-at-onset of Parkinson's disease for carriers of mutations in the leucine-rich repeat kinase 2, LRRK2, gene.