ALBERT

Description: We present a catalogue of 2D, point spread function-corrected de Vacouleurs, Sérsic, de Vacouleurs+Exponential, and Sérsic+Exponential fits of ~7 x 10 5 spectroscopically selected galaxies drawn from the Sloan Digital Sky Survey (SDSS) Data Release 7. Fits are performed for the SDSS r band utilizing the fitting routine galfit and analysis pipeline pymorph . We compare these fits to prior catalogues. Fits are analysed using a physically motivated flagging system. The flags suggest that more than 90 per cent of two-component fits can be used for analysis. We show that the fits follow the expected behaviour for early and late galaxy types. The catalogues provide a robust set of structural and photometric parameters for future galaxy studies. We show that some biases remain in the measurements, e.g. the presence of bars significantly affect the bulge measurements although the bulge ellipticity may be used to separate barred and non-barred galaxies, and about 15 per cent of bulges of two-component fits are also affected by resolution. The catalogues are available in electronic format. We also provide an interface for generating postage stamp images of the 2D model and residual as well as the 1D profile. These images can be generated for a user-uploaded list of galaxies on demand.

Description: We present new narrow-band (Hα and [O  iii ]) images and optical spectrophotometry of H  ii regions for a gas-rich low-surface-brightness irregular galaxy, KKR 17. The central surface brightness of the galaxy is μ 0 ( B ) = 24.15 ± 0.03 mag s –2 . The galaxy was detected by the Arecibo Legacy Fast ALFA survey (ALFALFA). Its mass is dominated by neutral hydrogen (H  i ) gas. In contrast, both the stellar masses of the bright H  ii and diffuse stellar regions are small. In addition, the fit to the spectral energy distribution to each region shows the stellar populations of H  ii and diffuse regions are different. The bright H  ii region contains a large fraction of O-type stars, revealing recent strong star formation, whereas the diffuse region is dominated by median age stars with a typical age of ~600 Myr. Using McGaugh's abundance model, we found that the average metallicity of KKR 17 is 12 + (O/H) = 8.0 ± 0.1. The star-formation rate of KKR 17 is 0.21 ± 0.04 M  yr –1 , which is ~1/5 of our Milky Way's. Based on the analysis results for young stellar clusters in the H  ii region, the bright H  ii region has two sub-components with different velocities and metallicities. This may be caused by the outflow of massive stars or merging events. However, the mechanism triggering star formation in the H  ii region is still uncertain.

Description: We review the results of the 1988 multiwavelength campaign on the late-type eclipsing binary YY Geminorum. Observations include: broad-band optical and near-infrared photometry, simultaneous optical and ultraviolet ( IUE ) spectroscopy, X-ray ( Ginga ) and radio (VLA) data. From models fitted to the optical light curves, fundamental physical parameters have been determined together with evidence for transient maculations (spots) located near quadrature longitudes and intermediate latitudes. Eclipses were observed at optical, ultraviolet and radio wavelengths. Significant drops in 6 cm radio emission near the phases of both primary and secondary eclipse indicate relatively compact radio emitting volumes that may lie between the binary components. IUE observations during secondary eclipse are indicative of a uniform chromosphere saturated with Mg  ii emission and an extended volume of Lyα emission. Profile fitting of high-dispersion Hα spectra confirms the chromospheric saturation and indicates significant Hα opacity to heights of a few per cent of the photospheric radius. There is evidence for an enhanced Hα emission region visible near phase 0.25–0.35 which may be associated with a large spot on the primary and with two small optical flares which were also observed at other wavelengths: one in microwave radiation and the other in X-rays. For both flares, L X / L opt is consistent with energy release in closed magnetic structures.

Description: To make relevant predictions about observable emission, hydrodynamical simulation codes must employ schemes that account for radiative losses, but the large dimensionality of accurate radiative transfer schemes is often prohibitive. Stamatellos and collaborators introduced a scheme for smoothed particle hydrodynamics (SPH) simulations based on the notion of polytropic pseudo-clouds that uses only local quantities to estimate cooling rates. The computational approach is extremely efficient and works well in cases close to spherical symmetry, such as in star formation problems. Unfortunately, the method, which takes the local gravitational potential as an input, can be inaccurate when applied to non-spherical configurations, limiting its usefulness when studying discs or stellar collisions, among other situations of interest. Here, we introduce the ‘pressure scale height method,’ which incorporates the fluid pressure scaleheight into the determination of column densities and cooling rates, and show that it produces more accurate results across a wide range of physical scenarios while retaining the computational efficiency of the original method. The tested models include spherical polytropes as well as discs with specified density and temperature profiles. We focus on applying our techniques within an SPH code, although our method can be implemented within any particle-based Lagrangian or grid-based Eulerian hydrodynamic scheme. Our new method may be applied in a broad range of situations, including within the realm of stellar interactions, collisions, and mergers.

Description: We measure and quantify properties of galactic outflows and diffuse gas at z ≥ 1 in cosmological hydrodynamical simulations. Our novel subresolution model, Multi-Phase Particle Integrator (MUPPI), implements supernova feedback using fully local gas properties, where the wind velocity and mass loading are not given as input. We find the following trends at z  = 2 by analysing central galaxies having a stellar mass higher than 10 9 M . The outflow velocity and mass outflow rate ( $\dot{M}_{\rm out}$ ) exhibit positive correlations with galaxy mass and with the star formation rate (SFR). However, most of the relations present a large scatter. The outflow mass loading factor () is between 0.2 and 10. The comparison effective model generates a constant outflow velocity, and a negative correlation of with halo mass. The number fraction of galaxies where outflow is detected decreases at lower redshifts, but remains more than 80 per cent over z  = 1–5. The outflow velocity correlation with SFR becomes flatter at z  = 1, and displays a negative correlation with halo mass in massive galaxies. Our study demonstrates that both the MUPPI and effective models produce significant outflows at ~1/10 of the virial radius; at the same time shows that the properties of outflows generated can be different from the input speed and mass loading in the effective model. Our MUPPI model, using local properties of gas in the subresolution recipe, is able to develop galactic outflows whose properties correlate with global galaxy properties , and consistent with observations.

Description: Long-duration gamma-ray bursts (GRBs) are thought to come from the core collapse of Wolf–Rayet stars. Whereas their stellar masses M * have a rather narrow distribution, the population of GRBs is very diverse, with gamma-ray luminosities L spanning several orders of magnitude. This suggests the existence of a ‘hidden’ stellar variable whose burst-to-burst variation leads to a spread in L . Whatever this hidden variable is, its variation should not noticeably affect the shape of GRB light curves, which display a constant luminosity (in a time-average sense) followed by a sharp drop at the end of the burst seen with Swift /XRT. We argue that such a hidden variable is progenitor star's large-scale magnetic flux. Shortly after the core collapse, most of stellar magnetic flux accumulates near the black hole (BH) and remains there. The flux extracts BH rotational energy and powers jets of roughly a constant luminosity, L j . However, once BH mass accretion rate $\dot{M}$ falls below ~ L j / c 2 , the flux becomes dynamically important and diffuses outwards, with the jet luminosity set by the rapidly declining mass accretion rate, $L_{\rm j}\sim \dot{M}c^2$ . This provides a potential explanation for the sharp end of GRBs and the universal shape of their light curves. During the GRB, gas infall translates spatial variation of stellar magnetic flux into temporal variation of L j . We make use of the deviations from constancy in L j to perform stellar magnetic flux ‘tomography’. Using this method, we infer the presence of magnetized tori in the outer layers of progenitor stars for GRB 920513 and GRB 940210.

Description: We make use of a large set of fast simulations of an intensity mapping experiment with characteristics similar to those expected of the Square Kilometre Array in order to study the viability and limits of blind foreground subtraction techniques. In particular, we consider three different approaches: polynomial fitting, principal component analysis (PCA) and independent component analysis (ICA). We review the motivations and algorithms for the three methods, and show that they can all be described, using the same mathematical framework, as different approaches to the blind source separation problem. We study the efficiency of foreground subtraction both in the angular and radial (frequency) directions, as well as the dependence of this efficiency on different instrumental and modelling parameters. For well-behaved foregrounds and instrumental effects, we find that foreground subtraction can be successful to a reasonable level on most scales of interest. We also quantify the effect that the cleaning has on the recovered signal and power spectra. Interestingly, we find that the three methods yield quantitatively similar results, with PCA and ICA being almost equivalent.

Description: Observed galaxies with high stellar masses or in dense environments have low specific star formation rates, i.e. they are quenched. Based on cosmological hydrodynamic simulations that include a prescription where quenching occurs in regions dominated by hot (〉10 5.4  K) gas, we argue that this hot gas quenching in haloes 〉10 12 M drives both mass quenching (i.e. central quenching) and environment quenching (i.e. satellite quenching). These simulations reproduce a broad range of locally observed trends among quenching, halo mass, stellar mass, environment, and distance to halo centre. Mass quenching is independent of environment because ~10 12 –10 13 M ‘mass quenching haloes’ inhabit a large range of environments. On the other hand, environment quenching is independent of stellar mass because galaxies of all stellar masses may live in dense environments as satellites of groups and clusters. As in observations, the quenched fraction of satellites increases with halo mass and decreases with distance to the centre of the group or cluster. We investigate pre-processing in group haloes, ejected former satellites, and hot gas that extends beyond the virial radius. The agreement of our model with key observational trends suggests that hot gas in massive haloes plays a leading role in quenching low-redshift galaxies.

Description: We used Arecibo Observatory and the Green Bank Telescope to observe OH in 12 early-type galaxies with known reservoirs of dense gas. We present three new detections of OH in absorption in the 1667 MHz line. One objective of our survey was to find evidence of molecular outflows, but our sensitivity and the strength of the OH absorption were insufficient to detect outflows. The detected sources have infrared luminosities and dust temperatures among the lowest of any galaxy detected in OH absorption. The ratio L HCN / L CO , a measure of the dense gas fraction in galaxies, is a powerful selector of OH megamasers for galaxies with high infrared luminosity. In early-type galaxies, which have much lower infrared luminosities, L HCN / L CO is also a promising tool for discovering OH, but in absorption rather than in maser emission. In addition to dense molecular gas, a radio continuum source and a favourable line of sight to the observer are likely key factors in detecting OH absorbers.

Description: The initial mass function (IMF) of the Arches cluster, which was formed a few million years ago in the harsh environment of the Galactic Centre (GC), has long been a target of interest to those who study the GC and the theory of star formation. The distinct star-forming conditions in the GC might have caused the cluster to have a shallower slope or an elevated lower mass cutoff in its IMF. But its mass function (MF) has been revealed only down to 1–2 M (the lower limit of resolved stars), and the low-end MF of the Arches is still unknown. To estimate the unresolved part of the Arches MF, we have devised a novel photometric method that involves the histogram of pixel intensities in the observed image, which contains information on the unresolved, faint stars. By comparing the pixel intensity histograms (PIHs) of numerous artificial images constructed from model IMFs with the observed PIH, we find that the best-fitting model IMF for the Arches cluster has a cutoff mass less than or similar to 0.1 M and a shape very close to that of the Kroupa MF. Our findings imply that the IMF of the Arches cluster is similar to those found in the Galactic disc.

Description: Motivation: Mapping of high-throughput sequencing data and other bulk sequence comparison applications have motivated a search for high-efficiency sequence alignment algorithms. The bit-parallel approach represents individual cells in an alignment scoring matrix as bits in computer words and emulates the calculation of scores by a series of logic operations composed of AND, OR, XOR, complement, shift and addition. Bit-parallelism has been successfully applied to the longest common subsequence (LCS) and edit-distance problems, producing fast algorithms in practice. Results: We have developed BitPAl, a bit-parallel algorithm for general, integer-scoring global alignment. Integer-scoring schemes assign integer weights for match, mismatch and insertion/deletion. The BitPAl method uses structural properties in the relationship between adjacent scores in the scoring matrix to construct classes of efficient algorithms, each designed for a particular set of weights. In timed tests, we show that BitPAl runs 7–25 times faster than a standard iterative algorithm. Availability and implementation: Source code is freely available for download at http://lobstah.bu.edu/BitPAl/BitPAl.html . BitPAl is implemented in C and runs on all major operating systems. Contact : jloving@bu.edu or yhernand@bu.edu or gbenson@bu.edu Supplementary information : Supplementary data are available at Bioinformatics online.

Description: : Next-generation sequencing (NGS) has a large potential in HIV diagnostics, and genotypic prediction models have been developed and successfully tested in the recent years. However, albeit being highly accurate, these computational models lack computational efficiency to reach their full potential. In this study, we demonstrate the use of graphics processing units (GPUs) in combination with a computational prediction model for HIV tropism. Our new model named gCUP, parallelized and optimized for GPU, is highly accurate and can classify 〉175 000 sequences per second on an NVIDIA GeForce GTX 460. The computational efficiency of our new model is the next step to enable NGS technologies to reach clinical significance in HIV diagnostics. Moreover, our approach is not limited to HIV tropism prediction, but can also be easily adapted to other settings, e.g. drug resistance prediction. Availability and implementation: The source code can be downloaded at http://www.heiderlab.de Contact: d.heider@wz-straubing.de

Description: : We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the reverse (complement) lexicographical order without a separate sorting step. The implementation is among the fastest for indexing short reads and the only one that practically works for reads of averaged kilobases in length. Availability and implementation: https://github.com/lh3/ropebwt2 Contact: hengli@broadinstitute.org

Description: : AliView is an alignment viewer and editor designed to meet the requirements of next-generation sequencing era phylogenetic datasets. AliView handles alignments of unlimited size in the formats most commonly used, i.e. FASTA, Phylip, Nexus, Clustal and MSF. The intuitive graphical interface makes it easy to inspect, sort, delete, merge and realign sequences as part of the manual filtering process of large datasets. AliView also works as an easy-to-use alignment editor for small as well as large datasets. Availability and implementation: AliView is released as open-source software under the GNU General Public License, version 3.0 (GPLv3), and is available at GitHub ( www.github.com/AliView ). The program is cross-platform and extensively tested on Linux, Mac OS X and Windows systems. Downloads and help are available at http://ormbunkar.se/aliview Contact: anders.larsson@ebc.uu.se Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections. Result: We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k -mer spectrum. With high-quality k -mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size. Availability and implementation: Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at http://trowel-ec.sourceforge.net . Contact: euncheon.lim@tue.mpg.de or weigel@tue.mpg.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : The application of protein–protein docking in large-scale interactome analysis is a major challenge in structural bioinformatics and requires huge computing resources. In this work, we present MEGADOCK 4.0, an FFT-based docking software that makes extensive use of recent heterogeneous supercomputers and shows powerful, scalable performance of 〉97% strong scaling. Availability and Implementation: MEGADOCK 4.0 is written in C++ with OpenMPI and NVIDIA CUDA 5.0 (or later) and is freely available to all academic and non-profit users at: http://www.bi.cs.titech.ac.jp/megadock . Contact: akiyama@cs.titech.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online

Description: Motivation: The identification of active transcriptional regulatory elements is crucial to understand regulatory networks driving cellular processes such as cell development and the onset of diseases. It has recently been shown that chromatin structure information, such as DNase I hypersensitivity (DHS) or histone modifications, significantly improves cell-specific predictions of transcription factor binding sites. However, no method has so far successfully combined both DHS and histone modification data to perform active binding site prediction. Results: We propose here a method based on hidden Markov models to integrate DHS and histone modifications occupancy for the detection of open chromatin regions and active binding sites. We have created a framework that includes treatment of genomic signals, model training and genome-wide application. In a comparative analysis, our method obtained a good trade-off between sensitivity versus specificity and superior area under the curve statistics than competing methods. Moreover, our technique does not require further training or sequence information to generate binding location predictions. Therefore, the method can be easily applied on new cell types and allow flexible downstream analysis such as de novo motif finding. Availability and implementation: Our framework is available as part of the Regulatory Genomics Toolbox. The software information and all benchmarking data are available at http://costalab.org/wp/dh-hmm . Contact: ivan.costa@rwth-aachen.de or eduardo.gusmao@rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: A proper target or marker is essential in any diagnosis (e.g. an infection or cancer). An ideal diagnostic target should be both conserved in and unique to the pathogen. Currently, these targets can only be identified manually, which is time-consuming and usually error-prone. Because of the increasingly frequent occurrences of emerging epidemics and multidrug-resistant ‘superbugs’, a rapid diagnostic target identification process is needed. Results: A new method that can identify uniquely conserved regions (UCRs) as candidate diagnostic targets for a selected group of organisms solely from their genomic sequences has been developed and successfully tested. Using a sequence-indexing algorithm to identify UCRs and a k -mer integer-mapping model for computational efficiency, this method has successfully identified UCRs within the bacteria domain for 15 test groups, including pathogenic, probiotic, commensal and extremophilic bacterial species or strains. Based on the identified UCRs, new diagnostic primer sets were designed, and their specificity and efficiency were tested by polymerase chain reaction amplifications from both pure isolates and samples containing mixed cultures. Availability and implementation: The UCRs identified for the 15 bacterial species are now freely available at http://ucr.synblex.com . The source code of the programs used in this study is accessible at http://ucr.synblex.com/bacterialIdSourceCode.d.zip Contact: yazhousun@synblex.com Supplementary Information: Supplementary data are available at Bioinformatics online.

Description: Motivation: A popular method for classification of protein domain movements apportions them into two main types: those with a ‘hinge’ mechanism and those with a ‘shear’ mechanism. The intuitive assignment of domain movements to these classes has limited the number of domain movements that can be classified in this way. Furthermore, whether intended or not, the term ‘shear’ is often interpreted to mean a relative translation of the domains. Results: Numbers of occurrences of four different types of residue contact changes between domains were optimally combined by logistic regression using the training set of domain movements intuitively classified as hinge and shear to produce a predictor for hinge and shear. This predictor was applied to give a 10-fold increase in the number of examples over the number previously available with a high degree of precision. It is shown that overall a relative translation of domains is rare, and that there is no difference between hinge and shear mechanisms in this respect. However, the shear set contains significantly more examples of domains having a relative twisting movement than the hinge set. The angle of rotation is also shown to be a good discriminator between the two mechanisms. Availability and implementation: Results are free to browse at http://www.cmp.uea.ac.uk/dyndom/interface/ . Contact: sjh@cmp.uea.ac.uk . Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Recent studies on human disease have revealed that aberrant interaction between proteins probably underlies a substantial number of human genetic diseases. This suggests a need to investigate disease inheritance mode using interaction, and based on which to refresh our conceptual understanding of a series of properties regarding inheritance mode of human disease. Results: We observed a strong correlation between the number of protein interactions and the likelihood of a gene causing any dominant diseases or multiple dominant diseases, whereas no correlation was observed between protein interaction and the likelihood of a gene causing recessive diseases. We found that dominant diseases are more likely to be associated with disruption of important interactions. These suggest inheritance mode should be understood using protein interaction. We therefore reviewed the previous studies and refined an interaction model of inheritance mode, and then confirmed that this model is largely reasonable using new evidences. With these findings, we found that the inheritance mode of human genetic diseases can be predicted using protein interaction. By integrating the systems biology perspectives with the classical disease genetics paradigm, our study provides some new insights into genotype–phenotype correlations. Contact: haodapeng@ems.hrbmu.edu.cn or biofomeng@hotmail.com Supplementary information: Supplementary data are available at Bioinformatics online.

Description: : Recently, several high profile studies collected cell viability data from panels of cancer cell lines treated with many drugs applied at different concentrations. Such drug sensitivity data for cancer cell lines provide suggestive treatments for different types and subtypes of cancer. Visualization of these datasets can reveal patterns that may not be obvious by examining the data without such efforts. Here we introduce Drug/Cell-line Browser (DCB), an online interactive HTML5 data visualization tool for interacting with three of the recently published datasets of cancer cell lines/drug-viability studies. DCB uses clustering and canvas visualization of the drugs and the cell lines, as well as a bar graph that summarizes drug effectiveness for the tissue of origin or the cancer subtypes for single or multiple drugs. DCB can help in understanding drug response patterns and prioritizing drug/cancer cell line interactions by tissue of origin or cancer subtype. Availability and implementation: DCB is an open source Web-based tool that is freely available at: http://www.maayanlab.net/LINCS/DCB Contact: avi.maayan@mssm.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Clinical and neuropathological similarities between dementia with Lewy bodies (DLB), Parkinson's and Alzheimer's diseases (PD and AD, respectively) suggest that these disorders may share etiology. To test this hypothesis, we have performed an association study of 54 genomic regions, previously implicated in PD or AD, in a large cohort of DLB cases and controls. The cohort comprised 788 DLB cases and 2624 controls. To minimize the issue of potential misdiagnosis, we have also performed the analysis including only neuropathologically proven DLB cases (667 cases). The results show that the APOE is a strong genetic risk factor for DLB, confirming previous findings, and that the SNCA and SCARB2 loci are also associated after a study-wise Bonferroni correction, although these have a different association profile than the associations reported for the same loci in PD. We have previously shown that the p.N370S variant in GBA is associated with DLB, which, together with the findings at the SCARB2 locus, suggests a role for lysosomal dysfunction in this disease. These results indicate that DLB has a unique genetic risk profile when compared with the two most common neurodegenerative diseases and that the lysosome may play an important role in the etiology of this disorder. We make all these data available.

Description: Mitochondrial DNA mutations at MT-ATP6 gene are relatively common in individuals suffering from striatal necrosis syndromes. These patients usually do not show apparent histochemical and/or biochemical signs of oxidative phosphorylation dysfunction. Because of this, MT-ATP6 is not typically analyzed in many other mitochondrial disorders that have not been previously associated to mutations in this gene. To correct this bias, we have performed a screening of the MT-ATP6 gene in a large collection of patients suspected of suffering different mitochondrial DNA (mtDNA) disorders. In three cases, biochemical, molecular-genetics and other analyses in patient tissues and cybrids were also carried out. We found three new pathologic mutations. Two of them in patients showing phenotypes that have not been commonly associated to mutations in the MT-ATP6 gene. These results remark the importance of sequencing the MT-ATP6 gene in patients with striatal necrosis syndromes, but also within other mitochondrial pathologies. This gene should be sequenced at least in all those patients suspected of suffering an mtDNA disorder disclosing normal results for histochemical and biochemical analyses of respiratory chain.

Description: Immunoglobulin-like domain containing receptor 1 ( ILDR1 ) is a poorly characterized gene that was first identified in lymphoma cells. Recently, ILDR1 has been found to be responsible for autosomal recessive hearing impairment DFNB42. Patients with ILDR1 mutations cause bilateral non-progressive moderate-to-profound sensorineural hearing impairment. However, the etiology and mechanism of ILDR1 -related hearing loss remains to be elucidated. In order to uncover the pathology of DFNB42 deafness, we used the morpholino injection technique to establish an ildr1b -morphant zebrafish model. Ildr1b -morphant zebrafish displayed defective hearing and imbalanced swimming, and developmental delays were seen in the semicircular canals of the inner ear. The gene expression profile and real-time PCR revealed down-regulation of atp1b2b (encoding Na + /K + transporting, beta 2b polypeptide) in ildr1b -morphant zebrafish. We found that injection of atp1b2b mRNA into ildr1b -knockdown zebrafish could rescue the phenotype of developmental delay of the semicircular canals. Moreover, ildr1b -morphant zebrafish had reduced numbers of lateral line neuromasts due to the disruption of lateral line primordium migration. In situ hybridization showed the involvement of attenuated FGF signaling and the chemokine receptor 4b ( cxcr4b ) and chemokine receptor 7b ( cxcr7b ) in posterior lateral line primordium of ildr1b -morphant zebrafish. We concluded that Ildr1b is crucial for the development of the inner ear and the lateral line system. This study provides the first evidence for the mechanism of Ildr1b on hearing in vivo and sheds light on the pathology of DFNB42.

Description: Huntington's disease (HD) is an inherited neurodegenerative disorder caused by abnormal expansion of CAG repeats in the gene encoding huntingtin. Mutant huntingtin undergoes proteolytic processing and its N-terminal fragment containing polyglutamine repeat accumulates as inclusion not only in nucleus but also in cytoplasm and neuronal processes. Here, we demonstrate that removal of ubiquitin ligase Ube3a selectively from HD mice brain resulted in accelerated disease phenotype and shorter lifespan in comparison with HD mice. The deficiency of Ube3a in HD mice brain also caused significant increase in global aggregates load, and these aggregates were less ubiquitinated when compared with age-matched HD mice. These Ube3a -maternal deficient HD mice also showed drastic reduction of DARPP-32, a dopamine-regulated phoshphoprotein in their striatum. These results emphasize the crucial role of Ube3a in the progression of HD and its immense potential as therapeutic target.

Description: Parent-of-origin-specific expression at imprinted genes is regulated by allele-specific DNA methylation at imprinting control regions (ICRs). This mechanism of gene regulation, where one element controls allelic expression of multiple genes, is not fully understood. Furthermore, the mechanism of gene dysregulation through ICR epimutations, such as loss or gain of DNA methylation, remains a mystery. We have used genetic mouse models to dissect ICR-mediated genetic and epigenetic regulation of imprinted gene expression. The H19/insulin-like growth factor 2 (Igf2) ICR has a multifunctional role including insulation, activation and repression. Microdeletions at the human H19/IGF2 ICR (IC1) are proposed to be responsible for IC1 epimutations associated with imprinting disorders such as Beckwith–Wiedemann syndrome (BWS). Here, we have generated and characterized a mouse model that mimics BWS microdeletions to define the role of the deleted sequence in establishing and maintaining epigenetic marks and imprinted expression at the H19/IGF2 locus. These mice carry a 1.3 kb deletion at the H19/Igf2 ICR [2,3] removing two of four CCCTC-binding factor (CTCF) sites and the intervening sequence, ~75% of the ICR. Surprisingly, the 2,3 deletion does not perturb DNA methylation at the ICR; however, it does disrupt imprinted expression. While repressive functions of the ICR are compromised by the deletion regardless of tissue type, insulator function is only disrupted in tissues of mesodermal origin where a significant amount of CTCF is poly(ADP-ribosyl)ated. These findings suggest that insulator activity of the H19/Igf2 ICR varies by cell type and may depend on cell-specific enhancers as well as posttranslational modifications of the insulator protein CTCF.

Description: Cerebral cavernous malformation (CCM) is a disease of vascular malformations known to be caused by mutations in one of three genes: CCM1 , CCM2 or CCM3 . Despite several studies, the mechanism of CCM lesion onset remains unclear. Using a Ccm1 knockout mouse model, we studied the morphogenesis of early lesion formation in the retina in order to provide insight into potential mechanisms. We demonstrate that lesions develop in a stereotypic location and pattern, preceded by endothelial hypersprouting as confirmed in a zebrafish model of disease. The vascular defects seen with loss of Ccm1 suggest a defect in endothelial flow response. Taken together, these results suggest new mechanisms of early CCM disease pathogenesis and provide a framework for further study.

Description: Genomic imprinting is the epigenetic process that results in monoallelic expression of genes depending on parental origin. These genes are known to be critical for placental development and fetal growth in mammals. Aberrant epigenetic profiles at imprinted loci, such as DNA methylation defects, are surprisingly rare in pregnancies with compromised fetal growth, while variations in transcriptional output from the expressed alleles of imprinted genes are more commonly reported in pregnancies complicated with intrauterine growth restriction (IUGR). To determine if PLAGL1 and HYMAI , two imprinted transcripts deregulated in Transient Neonatal Diabetes Mellitus, are involved in non-syndromic IUGR we compared the expression and DNA methylation levels in a large cohort of placental biopsies from IUGR and uneventful pregnancies. This revealed that despite appropriate maternal methylation at the shared PLAGL1 / HYMAI promoter, there was a loss of correlation between PLAGL1 and HYMAI expression in IUGR. This incongruity was due to higher HYMAI expression in IUGR gestations, coupled with PLAGL1 down-regulation in placentas from IUGR girls, but not boys. The PLAGL1 protein is a zinc-finger transcription factor that has been shown to be a master coordinator of a genetic growth network in mice. We observe PLAGL1 binding to the H19 / IGF2 shared enhancers in placentae, with significant correlations between PLAGL1 levels with H19 and IGF2 expression levels. In addition, PLAGL1 binding and expression also correlate with expression levels of metabolic regulator genes SLC2A4 , TCF4 and PPAR1 . Our results strongly suggest that fetal growth can be influenced by altered expression of the PLAGL1 gene network in human placenta.

Description: MicroRNAs (miRNAs) have emerged as a class of small, endogenous, regulatory RNAs that exhibit the ability to epigenetically modulate the translation of mRNAs into proteins. This feature enables them to control cell phenotypes and, consequently, modify cell function in a disease context. The role of inflammatory miRNAs in Alzheimer's disease (AD) and their ability to modulate glia responses are now beginning to be explored. In this study, we propose to disclose the functional role of miR-155, one of the most well studied immune-related miRNAs in AD-associated neuroinflammatory events, employing the 3xTg AD animal model. A strong upregulation of miR-155 levels was observed in the brain of 12-month-old 3xTg AD animals. This event occurred simultaneously with an increase of microglia and astrocyte activation, and before the appearance of extracellular Aβ aggregates, suggesting that less complex Aβ species, such as Aβ oligomers may contribute to early neuroinflammation. In addition, we investigated the contribution of miR-155 and the c-Jun transcription factor to the molecular mechanisms that underlie Aβ-mediated activation of glial cells. Our results suggest early miR-155 and c-Jun upregulation in the 3xTg AD mice, as well as in Aβ-activated microglia and astrocytes, thus contributing to the production of inflammatory mediators such as IL-6 and IFN-β. This effect is associated with a miR-155-dependent decrease of suppressor of cytokine signaling 1. Furthermore, since c-Jun silencing decreases the levels of miR-155 in Aβ-activated microglia and astrocytes, we propose that miR-155 targeting can constitute an interesting and promising approach to control neuroinflammation in AD.

Description: Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the huntingtin ( HTT ) gene. Disease pathogenesis derives, at least in part, from the long polyglutamine tract encoded by mutant HTT . Therefore, considerable effort has been dedicated to the development of therapeutic strategies that significantly reduce the expression of the mutant HTT protein. Antisense oligonucleotides (ASOs) targeted to the CAG repeat region of HTT transcripts have been of particular interest due to their potential capacity to discriminate between normal and mutant HTT transcripts. Here, we focus on phosphorodiamidate morpholino oligomers (PMOs), ASOs that are especially stable, highly soluble and non-toxic. We designed three PMOs to selectively target expanded CAG repeat tracts (CTG22, CTG25 and CTG28), and two PMOs to selectively target sequences flanking the HTT CAG repeat (HTTex1a and HTTex1b). In HD patient–derived fibroblasts with expanded alleles containing 44, 77 or 109 CAG repeats, HTTex1a and HTTex1b were effective in suppressing the expression of mutant and non-mutant transcripts. CTGn PMOs also suppressed HTT expression, with the extent of suppression and the specificity for mutant transcripts dependent on the length of the targeted CAG repeat and on the CTG repeat length and concentration of the PMO. PMO CTG25 reduced HTT-induced cytotoxicity in vitro and suppressed mutant HTT expression in vivo in the N171-82Q transgenic mouse model. Finally, CTG28 reduced mutant HTT expression and improved the phenotype of Hdh Q7/Q150 knock-in HD mice. These data demonstrate the potential of PMOs as an approach to suppressing the expression of mutant HTT.

Description: Reduced expression of SMN protein causes spinal muscular atrophy (SMA), a neurodegenerative disorder leading to motor neuron dysfunction and loss. However, the molecular mechanisms by which SMN regulates neuronal dysfunction are not fully understood. Here, we report that reduced SMN protein level alters miRNA expression and distribution in neurons. In particular, miR-183 levels are increased in neurites of SMN-deficient neurons. We demonstrate that miR-183 regulates translation of mTor via direct binding to its 3' UTR. Interestingly, local axonal translation of mTor is reduced in SMN-deficient neurons, and this can be recovered by miR-183 inhibition. Finally, inhibition of miR-183 expression in the spinal cord of an SMA mouse model prolongs survival and improves motor function of Smn -mutant mice. Together, these observations suggest that axonal miRNAs and the mTOR pathway are previously unidentified molecular mechanisms contributing to SMA pathology.

Description: Microphthalmia-associated transcription factor ( MITF ) is a master regulator of pigmented cell survival and differentiation with direct transcriptional links to cell cycle, apoptosis and pigmentation. In mouse, Mitf is expressed early and uniformly in optic vesicle (OV) cells as they evaginate from the developing neural tube, and null Mitf mutations result in microphthalmia and pigmentation defects. However, homozygous mutations in MITF have not been identified in humans; therefore, little is known about its role in human retinogenesis. We used a human embryonic stem cell (hESC) model that recapitulates numerous aspects of retinal development, including OV specification and formation of retinal pigment epithelium (RPE) and neural retina progenitor cells (NRPCs), to investigate the earliest roles of MITF. During hESC differentiation toward a retinal lineage, a subset of MITF isoforms was expressed in a sequence and tissue distribution similar to that observed in mice. In addition, we found that promoters for the MITF-A , -D and -H isoforms were directly targeted by Visual Systems Homeobox 2 (VSX2), a transcription factor involved in patterning the OV toward a NRPC fate. We then manipulated MITF RNA and protein levels at early developmental stages and observed decreased expression of eye field transcription factors, reduced early OV cell proliferation and disrupted RPE maturation. This work provides a foundation for investigating MITF and other highly complex, multi-purposed transcription factors in a dynamic human developmental model system.

Description: The p.N478D missense mutation in human mitochondrial poly(A) polymerase (mtPAP) has previously been implicated in a form of spastic ataxia with optic atrophy. In this study, we have investigated fibroblast cell lines established from family members. The homozygous mutation resulted in the loss of polyadenylation of all mitochondrial transcripts assessed; however, oligoadenylation was retained. Interestingly, this had differential effects on transcript stability that were dependent on the particular species of transcript. These changes were accompanied by a severe loss of oxidative phosphorylation complexes I and IV, and perturbation of de novo mitochondrial protein synthesis. Decreases in transcript polyadenylation and in respiratory chain complexes were effectively rescued by overexpression of wild-type mtPAP. Both mutated and wild-type mtPAP localized to the mitochondrial RNA-processing granules thereby eliminating mislocalization as a cause of defective polyadenylation. In vitro polyadenylation assays revealed severely compromised activity by the mutated protein, which generated only short oligo(A) extensions on RNA substrates, irrespective of RNA secondary structure. The addition of LRPPRC/SLIRP, a mitochondrial RNA-binding complex, enhanced activity of the wild-type mtPAP resulting in increased overall tail length. The LRPPRC/SLIRP effect although present was less marked with mutated mtPAP, independent of RNA secondary structure. We conclude that (i) the polymerase activity of mtPAP can be modulated by the presence of LRPPRC/SLIRP, (ii) N478D mtPAP mutation decreases polymerase activity and (iii) the alteration in poly(A) length is sufficient to cause dysregulation of post-transcriptional expression and the pathogenic lack of respiratory chain complexes.

Description: During postnatal development, neuronal activity controls the remodeling of initially imprecise neuronal connections through the regulation of gene expression. MeCP2 binds to methylated DNA and modulates gene expression during neuronal development and MECP2 mutation causes the autistic disorder Rett syndrome. To investigate a role for MeCP2 in neuronal circuit refinement and to identify activity-dependent MeCP2 transcription regulations, we leveraged the precise organization and accessibility of olfactory sensory axons to manipulation of neuronal activity through odorant exposure in vivo . We demonstrate that olfactory sensory axons failed to develop complete convergence when Mecp2 is deficient in olfactory sensory neurons (OSNs) in an otherwise wild-type animal. Furthermore, we demonstrate that expression of selected adhesion genes was elevated in Mecp2 -deficient glomeruli, while acute odor stimulation in control mice resulted in significantly reduced MeCP2 binding to these gene loci, correlating with increased expression. Thus, MeCP2 is required for both circuitry refinement and activity-dependent transcriptional responses in OSNs.

Description: Simultaneous generation of neural cells and that of the nutrient-supplying vasculature during brain development is called neurovascular coupling. We report on a transgenic mouse with impaired transforming growth factor β (TGFβ)-signalling in forebrain-derived neural cells using a Foxg1-cre knock-in to drive the conditional knock-out of the Tgfbr2 . Although the expression of FOXG1 is assigned to neural progenitors and neurons of the telencephalon, Foxg1 cre/+ ; Tgfbr2 flox/flox (Tgfbr2-cKO) mutants displayed intracerebral haemorrhage. Blood vessels exhibited an atypical, clustered appearance were less in number and displayed reduced branching. Vascular endothelial growth factor (VEGF) A, insulin-like growth factor (IGF) 1, IGF2, TGFβ, inhibitor of DNA binding (ID) 1, thrombospondin (THBS) 2, and a disintegrin and metalloproteinase with thrombospondin motifs (ADAMTS) 1 were altered in either expression levels or tissue distribution. Accordingly, human umbilical vein endothelial cells (HUVEC) displayed branching defects after stimulation with conditioned medium (CM) that was derived from primary neural cultures of the ventral and dorsal telencephalon of Tgfbr2-cKO. Supplementing CM of Tgfbr2-cKO with VEGFA rescued these defects, but application of TGFβ aggravated them. HUVEC showed reduced migration towards CM of mutants compared with controls. Supplementing the CM with growth factors VEGFA, fibroblast growth factor (FGF) 2 and IGF1 partially restored HUVEC migration. In contrast, TGFβ supplementation further impaired migration of HUVEC. We observed differences along the dorso-ventral axis of the telencephalon with regard to the impact of these factors on the phenotype. Together these data establish a TGFBR2-dependent molecular crosstalk between neural and endothelial cells during brain vessel development. These findings will be useful to further elucidate neurovascular interaction in general and to understand pathologies of the blood vessel system such as intracerebral haemorrhages, hereditary haemorrhagic telangiectasia, Alzheimeŕs disease, cerebral amyloid angiopathy or tumour biology.

Description: Pneumoconiosis is the most serious occupational disease in China and its leading cause is occupational silica exposure. Pneumoconiosis takes several years to develop depending on the exposure level of silica. However, individual variation in the susceptibility to pneumoconiosis has been observed among the subjects with similar exposure. We conducted a genome-wide screening with 710 999 single nucleotide polymorphisms (SNPs) in a cohort of 400 coal workers (202 cases and 198 exposed controls) for pneumoconiosis susceptible loci. Seven promising variants were evaluated in an independent cohort of 568 coal workers (323 cases and 245 exposed controls), followed by a second replication on 463 iron ore workers (167 cases and 296 exposed controls). By pooling all of the genome-wide association studies and replication stages together, we found a genome-wide significant ( P 〈 5.0 x 10 –8 ) association for rs73329476 ( P = 1.74 x 10 –8 , OR = 2.17, 95% CI = 1.66–2.85) and two additional replicated associations for rs4320486 ( P 〈 0.05) and rs117626015 ( P 〈 0.05) with combined P -values of 4.29 x 10 –6 and 5.05 x 10 –6 , respectively. In addition, the risk allele T of rs73329476 was significantly associated with lower mRNA expression levels of carboxypeptidase M ( CPM ) in total cellular RNA from whole blood of 156 healthy individuals ( P = 0.0252). The identified pneumoconiosis susceptibility loci may provide new insights into the pathogenesis of pneumoconiosis, and may also have some clinical utility for risk prediction for pneumoconiosis and high-risk population screening for workers with occupational silica exposure.

Description: Hearing function is known to be heritable, but few significant and reproducible associations of genetic variants have been identified to date in the adult population. In this study, genome-wide association results of hearing function from the G-EAR consortium and TwinsUK were used for meta-analysis. Hearing ability in eight population samples of Northern and Southern European ancestry ( n = 4591) and the Silk Road ( n = 348) was measured using pure-tone audiometry and summarized using principal component (PC) analysis. Genome-wide association analyses for PC1–3 were conducted separately in each sample assuming an additive model adjusted for age, sex and relatedness of subjects. Meta-analysis was performed using 2.3 million single-nucleotide polymorphisms (SNPs) tested against each of the three PCs of hearing ability in 4939 individuals. A single SNP lying in intron 6 of the salt-inducible kinase 3 ( SIK3 ) gene was found to be associated with hearing PC2 ( P = 3.7 x 10 –8 ) and further supported by whole-genome sequence in a subset. To determine the relevance of this gene in the ear, expression of the Sik3 protein was studied in mouse cochlea of different ages. Sik3 was expressed in murine hair cells during early development and in cells of the spiral ganglion during early development and adulthood. Our results suggest a developmental role of Sik3 in hearing and may be required for the maintenance of adult auditory function.

Description: Genome instability, epigenetic remodelling and structural chromosomal rearrangements are hallmarks of cancer. However, the coordinated epigenetic effects of constitutional chromosomal rearrangements that disrupt genes associated with congenital neurodevelopmental diseases are poorly understood. To understand the genetic–epigenetic interplay at breakpoints of chromosomal translocations disrupting CG-rich loci, we quantified epigenetic modifications at DLGAP4 ( SAPAP4), a key post-synaptic density 95 (PSD95) associated gene, truncated by the chromosome translocation t(8;20)(p12;q11.23), co-segregating with cerebellar ataxia in a five-generation family. We report significant epigenetic remodelling of the DLGAP4 locus triggered by the t(8;20)(p12;q11.23) translocation and leading to dysregulation of DLGAP4 expression in affected carriers. Disruption of DLGAP4 results in monoallelic hypermethylation of the truncated DLGAP4 promoter CpG island. This induced hypermethylation is maintained in somatic cells of carriers across several generations in a t(8;20) dependent-manner however, is erased in the germ cells of the translocation carriers. Subsequently, chromatin remodelling of the locus-perturbed monoallelic expression of DLGAP4 mRNAs and non-coding RNAs in haploid cells having the translocation. Our results provide new mechanistic insight into the way a balanced chromosomal rearrangement associated with a neurodevelopmental disorder perturbs allele-specific epigenetic mechanisms at breakpoints leading to the deregulation of the truncated locus.

Description: We conducted blinded psychiatric assessments of 26 Amish subjects (52 ± 11 years) from four families with prevalent bipolar spectrum disorder, identified 10 potentially pathogenic alleles by exome sequencing, tested association of these alleles with clinical diagnoses in the larger Amish Study of Major Affective Disorder (ASMAD) cohort, and studied mutant potassium channels in neurons. Fourteen of 26 Amish had bipolar spectrum disorder. The only candidate allele shared among them was rs78247304, a non-synonymous variant of KCNH7 (c.1181G〉A, p.Arg394His). KCNH7 c.1181G〉A and nine other potentially pathogenic variants were subsequently tested within the ASMAD cohort, which consisted of 340 subjects grouped into controls subjects and affected subjects from overlapping clinical categories (bipolar 1 disorder, bipolar spectrum disorder and any major affective disorder). KCNH7 c.1181G〉A had the highest enrichment among individuals with bipolar spectrum disorder ( 2 = 7.3) and the strongest family-based association with bipolar 1 ( P = 0.021), bipolar spectrum ( P = 0.031) and any major affective disorder ( P = 0.016). In vitro, the p.Arg394His substitution allowed normal expression, trafficking, assembly and localization of HERG3/Kv11.3 channels, but altered the steady-state voltage dependence and kinetics of activation in neuronal cells. Although our genome-wide statistical results do not alone prove association, cumulative evidence from multiple independent sources (parallel genome-wide study cohorts, pharmacological studies of HERG-type potassium channels, electrophysiological data) implicates neuronal HERG3/Kv11.3 potassium channels in the pathophysiology of bipolar spectrum disorder. Such a finding, if corroborated by future studies, has implications for mental health services among the Amish, as well as development of drugs that specifically target HERG3/Kv11.3.

Description: Complex III (cytochrome bc 1 ) is a protein complex of the mitochondrial inner membrane that transfers electrons from ubiquinol to cytochrome c . Its assembly requires the coordinated expression of mitochondrial-encoded cytochrome b and nuclear-encoded subunits and assembly factors. Complex III deficiency is a severe multisystem disorder caused by mutations in subunit genes or assembly factors. Sequence-profile-based orthology predicts C11orf83 , hereafter named UQCC3 , to be the ortholog of the fungal complex III assembly factor CBP4 . We describe a homozygous c.59T〉A missense mutation in UQCC3 from a consanguineous patient diagnosed with isolated complex III deficiency, displaying lactic acidosis, hypoglycemia, hypotonia and delayed development without dysmorphic features. Patient fibroblasts have reduced complex III activity and lower levels of the holocomplex and its subunits than controls. They have no detectable UQCC3 protein and have lower levels of cytochrome b protein. Furthermore, in patient cells, cytochrome b is absent from a high-molecular-weight complex III. UQCC3 is reduced in cells depleted for the complex III assembly factors UQCC1 and UQCC2. Conversely, absence of UQCC3 in patient cells does not affect UQCC1 and UQCC2. This suggests that UQCC3 functions in the complex III assembly pathway downstream of UQCC1 and UQCC2 and is consistent with what is known about the function of Cbp4 and of the fungal orthologs of UQCC1 and UQCC2, Cbp3 and Cbp6. We conclude that UQCC3 functions in complex III assembly and that the c.59T〉A mutation has a causal role in complex III deficiency.

Description: Mutations in the photoreceptor-specific gene peripherin-2 ( PRPH-2 , also known as retinal degeneration slow/RDS) cause incurable retinal degeneration with a high degree of phenotypic variability. Patient phenotypes range from retinitis pigmentosa to various forms of macular and pattern dystrophy. Macular and pattern dystrophy in particular are associated with complex, poorly understood disease mechanisms, as severe vision loss is often associated both with defects in the photoreceptors, as well as the choroid and retinal pigment epithelium (RPE). Since there is currently no satisfactory model to study pattern dystrophy disease mechanisms, we generated a knockin mouse model expressing an RDS pattern dystrophy mutation, Y141C. Y141C mice exhibited clinical signs similar to those in patients including late-onset fundus abnormalities characteristic of RPE and choroidal defects and electroretinogram defects. Ultrastructural examination indicated that disc formation was initiated by the Y141C protein, but proper sizing and alignment of discs required wild-type RDS. The biochemical mechanism underlying these abnormalities was tied to defects in the normal process of RDS oligomerization which is required for proper RDS function. Y141C-RDS formed strikingly abnormal disulfide-linked complexes which were localized to the outer segment (OS) where they impaired the formation of proper OS structure. These data support a model of pattern dystrophy wherein a primary molecular defect occurring in all photoreceptors leads to secondary sequellae in adjacent tissues, an outcome which leads to macular vision loss. An understanding of the role of RDS in the interplay between these tissues significantly enhances our understanding of RDS-associated pathobiology and our ability to design rational treatment strategies.

Description: Polarization in classical Be stars results from Thomson scattering of the unpolarized light from the Be star in the circumstellar disc. Theory and observations agree that the maximum degree of polarization from isolated Be stars is 4 per cent. We report on the first optical polarimetric observations of the Be/X-ray binary EXO 2030+375. We find that the optical ( R -band) light is strongly linearly polarized with a degree of polarization of 19 per cent, the highest ever measured either in a classical or Be/X-ray binary. We argue that the interstellar medium cannot account for this high-polarization degree and that a substantial amount must be intrinsic to the source. We propose that it may result from the alignment of non-spherical ferromagnetic grains in the Be star disc due to the strong neutron star magnetic field.

Description: We present two estimators to quantify the angular power spectrum of the sky signal directly from the visibilities measured in radio interferometric observations. This is relevant for both the foregrounds and the cosmological 21-cm signal buried therein. The discussion here is restricted to the Galactic synchrotron radiation, the most dominant foreground component after point source removal. Our theoretical analysis is validated using simulations at 150 MHz, mainly for GMRT and also briefly for Low-Frequency Array. The Bare Estimator uses pairwise correlations of the measured visibilities, while the Tapered Gridded Estimator uses the visibilities after gridding in the uv plane. The former is very precise, but computationally expensive for large data. The latter has a lower precision, but takes less computation time which is proportional to the data volume. The latter also allows tapering of the sky response leading to sidelobe suppression, an useful ingredient for foreground removal. Both estimators avoid the positive bias that arises due to the system noise. We consider amplitude and phase errors of the gain, and the w -term as possible sources of errors. We find that the estimated angular power spectrum is exponentially sensitive to the variance of the phase errors but insensitive to amplitude errors. The statistical uncertainties of the estimators are affected by both amplitude and phase errors. The w -term does not have a significant effect at the angular scales of our interest. We propose the Tapered Gridded Estimator as an effective tool to observationally quantify both foregrounds and the cosmological 21-cm signal.

Description: We extend the theory of astrophysical maser propagation through a medium with a Zeeman-split molecular response to the case of a non-uniform magnetic field, and allow a component of the electric field of the radiation in the direction of propagation: a characteristic of radiation with orbital angular momentum. A classical reduction of the governing equations leads to a set of nine differential equations for the evolution of intensity-like parameters for each Fourier component of the radiation. Four of these parameters correspond to the standard Stokes parameters, whilst the other five represent the z -component of the electric field, and its coupling to the conventional components in the x – y -plane. A restricted analytical solution of the governing equations demonstrates a non-trivial coupling of the Stokes parameters to those representing orbital angular momentum: the z -component of the electric field can grow from a background in which only Stokes- I is non-zero. A numerical solution of the governing equations reveals radiation patterns with a radial and angular structure for the case of an ideal quadrupole magnetic field perpendicular to the propagation direction. In this ideal case, generation of radiation orbital angular momentum, like polarization, can approach 100 per cent.

Description: A halo merger tree forms the essential backbone of a semi-analytic model for galaxy formation and evolution. Recent studies have pointed out that extracting merger trees from numerical simulations of structure formation is non-trivial; different tree building algorithms can give differing merger histories. These differences should be carefully understood before merger trees are used as input for models of galaxy formation. We investigate the impact of different halo merger trees on a semi-analytic model. We find that the z  = 0 galaxy properties in our model show differences between trees when using a common parameter set. The star formation history of the universe and the properties of satellite galaxies can show marked differences between trees with different construction methods. Independently calibrating the semi-analytic model for each tree can reduce the discrepancies between the z  = 0 global galaxy properties, at the cost of increasing the differences in the evolutionary histories of galaxies. Furthermore, the underlying physics implied can vary, resulting in key quantities such as the supernova feedback efficiency differing by factors of 2. Such a change alters the regimes where star formation is primarily suppressed by supernovae. Therefore, halo merger trees extracted from a common halo catalogue using different, but reliable, algorithms can result in a difference in the semi-analytic model. Given the uncertainties in galaxy formation physics, however, these differences may not necessarily be viewed as significant.

Description: We simulate the evolution of dense-cool clumps embedded in the intracluster medium (ICM) of cooling flow clusters of galaxies in response to multiple jet-activity cycles, and find that the main heating process of the clumps is mixing with the hot shocked jets’ gas, the bubbles, while shocks have a limited role. We use the pluto hydrodynamical code in two dimensions with imposed axisymmetry, to follow the thermal evolution of the clumps. We find that the inflation process of hot bubbles, which appear as X-ray deficient cavities in observations, is accompanied by complicated induced vortices inside and around the bubbles. The vorticity induces efficient mixing of the hot bubbles’ gas with the ICM and cool clumps, resulting in a substantial increase of the temperature and entropy of the clumps. For the parameters used by us, heating by shocks barely competes with radiative cooling, even after 25 consecutive shocks excited during 0.5 Gyr of simulation. Some clumps are shaped to filamentary structure that can turn to observed optical filaments. We find that not all clumps are heated. Those that cool to very low temperatures will fall in and feed the central supermassive black hole, hence closing the feedback cycle in what is termed the cold feedback mechanism.

Description: The pulsar IGR J16393–4643 belongs to a class of highly absorbed supergiant high-mass X-ray binaries (HMXBs), characterized by a very high column density of absorbing matter. We present the results of simultaneous broad-band pulsation and spectrum analysis from a 44-ks Suzaku observation of the source. The orbital intensity profile created with the Swift Burst Alert Telescope ( Swift –BAT) light curve shows an indication of IGR J16393–4643 being an eclipsing system with a short eclipse semi-angle E  ~ 17°. For a supergiant companion star with a 20-R radius, this implies an inclination of the orbital plane in the range 39°–57°, whereas for a main-sequence B star as the companion with a 10-R radius, the inclination of the orbital plane is in the range 60°–77°. Pulse profiles created for different energy bands have complex morphology, which shows some energy dependence and increases in pulse fraction with energy. We have also investigated broad-band spectral characteristics, phase-averaged spectra and resolving the pulse phase into peak and trough phases. The phase-averaged spectrum has a very high N H (~ 3 10 23  cm –2 ) and is described by a power law ( ~ 0.9) with a high-energy cut-off above 20 keV. We find a change in the spectral index in the peak and trough phases, implying an underlying change in the source spectrum.

Description: A large class of flat axially symmetric solutions to the Vlasov–Poisson system is constructed with the property that the corresponding rotation curves are approximately flat, slightly decreasing or slightly increasing. The rotation curves are compared with measurements from real galaxies and satisfactory agreement is obtained. These facts raise the question whether the observed rotation curves for disc galaxies may be explained without introducing dark matter. Furthermore, it is shown that for the ansatz we consider stars on circular orbits do not exist in the neighbourhood of the boundary of the steady state.

Description: This paper presents a detailed analysis of two-armed spiral structure in a sample of galaxies from the Spitzer Infrared Nearby Galaxies Survey, with particular focus on the relationships between the properties of the spiral pattern in the stellar disc and the global structure and environment of the parent galaxies. Following Paper I , we have used a combination of Spitzer Space Telescope mid-infrared imaging and visible multicolour imaging to isolate the spiral pattern in the underlying stellar discs, and we examine the systematic behaviours of the observed amplitudes and shapes (pitch angles) of these spirals. In general, spiral morphology is found to correlate only weakly at best with morphological parameters such as stellar mass, gas fraction, disc/bulge ratio, and v flat . In contrast to weak correlations with galaxy structure, a strong link is found between the strength of the spiral arms and tidal forcing from nearby companion galaxies. This appears to support the longstanding suggestion that either a tidal interaction or strong bar is a necessary condition for driving grand-design spiral structure. The pitch angles of the stellar arms are only loosely correlated with the pitch angles of the corresponding arms traced in gas and young stars. We find that the strength of the shock in the gas and the contrast in the star formation rate are strongly correlated with the stellar spiral amplitude.

Description: We combine photometry from the Ultra Deep Survey (UDS), Cosmic Assembly Near-infrared Deep Extragalactic Legacy Survey (CANDELS) UDS and CANDELS the Great Observatories Origins Deep Survey-South (GOODS-S) surveys to construct the galaxy stellar mass function probing both the low- and high-mass end accurately in the redshift range 0.3 〈  z  〈 3. The advantages of using a homogeneous concatenation of these data sets include meaningful measures of environment in the UDS, due to its large area (0.88 deg 2 ), and the high-resolution deep imaging in CANDELS ( H 160  〉 26.0), affording us robust measures of structural parameters. We construct stellar mass functions for the entire sample as parametrized by the Schechter function, and find that there is a decline in the values of and of α with higher redshifts, and a nearly constant M * up to z  ~ 3. We divide the galaxy stellar mass function by colour, structure, and environment and explore the links between environmental overdensity, morphology, and the quenching of star formation. We find that a double Schechter function describes galaxies with high Sérsic index ( n  〉 2.5), similar to galaxies which are red or passive. The low-mass end of the n  〉 2.5 stellar mass function is dominated by blue galaxies, whereas the high-mass end is dominated by red galaxies. This shows that there is a possible link between morphological evolution and star formation quenching in high mass galaxies, which is not seen in lower mass systems. This in turn suggests that there are strong mass-dependent quenching mechanisms. In addition, we find that the number density of high-mass systems is elevated in dense environments, suggesting that an environmental process is building up massive galaxies quicker in over densities than in lower densities.

Description: We analyse a sample of 26 active galactic nuclei (AGN) with deep XMM–Newton observations, using principal component analysis (PCA) to find model-independent spectra of the different variable components. In total, we identify at least 12 qualitatively different patterns of spectral variability, involving several different mechanisms, including five sources which show evidence of variable relativistic reflection (MCG–6-30-15, NGC 4051, 1H 0707–495, NGC 3516 and Mrk 766) and three which show evidence of varying partial covering neutral absorption (NGC 4395, NGC 1365 and NGC 4151). In over half of the sources studied, the variability is dominated by changes in a power-law continuum, both in terms of changes in flux and power-law index, which could be produced by propagating fluctuations within the corona. Simulations are used to find unique predictions for different physical models, and we then attempt to qualitatively match the results from the simulations to the behaviour observed in the real data. We are able to explain a large proportion of the variability in these sources using simple models of spectral variability, but more complex models may be needed for the remainder. We have begun the process of building up a library of different principal components, so that spectral variability in AGN can quickly be matched to physical processes. We show that PCA can be an extremely powerful tool for distinguishing different patterns of variability in AGN, and that it can be used effectively on the large amounts of high-quality archival data available from the current generation of X-ray telescopes. We will make our PCA code available upon request to the lead author.

Description: Using N -body simulations we study the phenomenon of radial orbit instability occurring in dark matter haloes of the size of a dwarf galaxy. We carried out simulations of seven spherical models, with the same standard NFW (Navarro, Frenk & White) density profile but different anisotropy profiles of particle orbits. Four of them underwent instability: two with a constant positive anisotropy, one with an anisotropic core and an isotropic envelope and one with a very small isotropic core and an anisotropic envelope. Haloes affected by the instability become approximately axisymmetric and prolate, with the profile of the shortest-to-longest axis ratio increasing with radius. The lower limit for the central value of this axis ratio is 0.3 for an NFW halo. The density profiles of the haloes did not change significantly, whereas the velocity distributions became axisymmetric. The angular momentum modulus rose due to large-amplitude oscillations of its components perpendicular to the symmetry axis of the halo. We also studied orbits of individual particles assigning them to classical orbit families in triaxial potentials. We find that the membership of a given particle in a family depends on its initial angular momentum modulus and its components along the principal axes of matter distribution.

Description: We present a study of the prevalence and luminosity of active galactic nuclei (AGN; traced by optical spectra) as a function of both environment and galaxy interactions. For this study, we used a sample of more than 250 000 galaxies drawn from the Sloan Digital Sky Survey and, crucially, we controlled for the effect of both stellar mass and central star formation activity. Once these two factors are taken into account, the effect of the local density of galaxies and of one-on-one interactions is minimal in both the prevalence of AGN activity and AGN luminosity. This suggests that the level of nuclear activity depends primarily on the availability of cold gas in the nuclear regions of galaxies and that secular processes can drive the AGN activity in the majority of cases. Large-scale environment and galaxy interactions only affect AGN activity in an indirect manner, by influencing the central gas supply.

Description: We report the results of the photometric and spectroscopic monitoring campaign of the transient SN 2007sv. The observables are similar to those of Type IIn supernovae, a well-known class of objects whose ejecta interact with pre-existing circumstellar material (CSM). The spectra show a blue continuum at early phases and prominent Balmer lines in emission; however, the absolute magnitude at the discovery of SN 2007sv ( M R  = –14.25 ± 0.38) indicate it to be most likely a supernova impostor. This classification is also supported by the lack of evidence in the spectra of very high velocity material as expected in supernova ejecta. In addition, we find no unequivocal evidence of broad lines of α- and/or Fe-peak elements. The comparison with the absolute light curves of other interacting objects (including Type IIn supernovae) highlights the overall similarity with the prototypical impostor SN 1997bs. This supports our claim that SN 2007sv was not a genuine supernova, and was instead a supernova impostor, most likely similar to the major eruption of a luminous blue variable.

Description: The Cosmicflows-2 catalogue is a compendium of peculiar velocity measurements. While it has many objects in common with the COMPOSITE catalogue, a previously analysed collection of peculiar velocity data found to give an unexpectedly large bulk flow on large scales, the data in Cosmicflows-2 have been reanalysed to ensure consistency between distances measured using different methods. In particular, a focus on accurate distances led the authors of the Cosmicflows-2 to not correct for homogeneous or inhomogeneous Malmquist bias, both or which are corrected for in the COMPOSITE compilation. We find remarkable agreement between the COMPOSITE and the Cosmicflows-2 if the small EFAR sample of clusters located in two dense superclusters is removed from both surveys, giving results that are inconsistent with the cold dark matter standard model with Planck central parameters at the 98 per cent level. On smaller scales we find overall agreement between data sets and consistency with the standard model.

Description: We quantify the stellar abundances of neutron-rich r-process nuclei in cosmological zoom-in simulations of a Milky Way-mass galaxy from the Feedback In Realistic Environments project. The galaxy is enriched with r-process elements by binary neutron star (NS) mergers and with iron and other metals by supernovae. These calculations include key hydrodynamic mixing processes not present in standard semi-analytic chemical evolution models, such as galactic winds and hydrodynamic flows associated with structure formation. We explore a range of models for the rate and delay time of NS mergers, intended to roughly bracket the wide range of models consistent with current observational constraints. We show that NS mergers can produce [r-process/Fe] abundance ratios and scatter that appear reasonably consistent with observational constraints. At low metallicity, [Fe/H]  –2, we predict there is a wide range of stellar r-process abundance ratios, with both supersolar and subsolar abundances. Low-metallicity stars or stars that are outliers in their r-process abundance ratios are, on average, formed at high redshift and located at large galactocentric radius. Because NS mergers are rare, our results are not fully converged with respect to resolution, particularly at low metallicity. However, the uncertain rate and delay time distribution of NS mergers introduce an uncertainty in the r-process abundances comparable to that due to finite numerical resolution. Overall, our results are consistent with NS mergers being the source of most of the r-process nuclei in the Universe.

Description: We present time series spectroscopy of two short period cataclysmic variables, CC Scl and V2051 Oph, to test the efficiency of Doppler-tomography-based methods in constraining orbital parameters of evolved cataclysmic variables. We find that the Ca ii triplet lines offer superior diagnostics, revealing emission components from the mass donors and sharp images of the accretion discs. Furthermore, we use Monte Carlo methods to estimate the uncertainties from ensembles of Doppler maps. We compare our new methods against traditional radial velocity methods and show that they offer a valid route towards system parameter determination. Our analysis of CC Scl suggests a low mass ratio of q  = 0.08 ± 0.03 with a primary velocity of K 1  = 37 ± 14 km s –1 . This mass ratio is in between the pre- and post-period minimum status, however our K 1 solution favours a post-period minimum system. Our derived parameters for V2051 Oph ( q  = 0.18 ± 0.05, K 1  = 97 ± 10 km s –1 ) are in agreement with the eclipse solution ( q  = 0.19 ± 0.03), offering a direct validation of our methods.

Description: We present NuSTAR observations of the bright Seyfert 2 galaxy NGC 2110 obtained in 2012, when the source was at the highest flux level ever observed, and in 2013, when the source was at a more typical flux level. We include archival observations from other X-ray satellites, namely XMM–Newton , Suzaku , BeppoSAX , Chandra and Swift . Simultaneous NuSTAR and Swift broad-band spectra (in the 3–80 keV range) indicate a cutoff energy E c  〉 210 keV, with no detectable contribution from Compton reflection. NGC 2110 is one of the very few sources where no evidence for distant Compton-thick scattering is found and, by using temporal information collected over more than a decade, we investigate variations of the iron Kα line on time-scales of years. The Fe Kα line is likely the sum of two components: one constant (originating from distant Compton-thick material) and the other one variable and linearly correlated with the source flux (possibly arising from Compton-thin material much closer to the black hole).

Description: Dusty, star-forming galaxies have a critical role in the formation and evolution of massive galaxies in the Universe. Using deep far-infrared imaging in the range 100–500 μm obtained with the Herschel telescope, we investigate the dust-obscured star formation (SF) in the galaxy cluster XDCP J0044.0-2033 at z  = 1.58, the most massive cluster at z  〉 1.5, with a measured mass M 200  = 4.7 $^{+1.4}_{-0.9}$  10 14  M . We perform an analysis of the spectral energy distributions (SEDs) of 12 cluster members (5 spectroscopically confirmed) detected with ≥3 significance in the PACS maps, all ultraluminous infrared galaxies. The individual star formation rates (SFRs) lie in the range 155–824 M yr –1 , with dust temperatures of 24–35 K. We measure a strikingly high amount of SF in the cluster core, SFR (〈250 kpc) ≥ 1875 ± 158 M yr –1 , four times higher than the amount of SF in the cluster outskirts. This scenario is unprecedented in a galaxy cluster, showing for the first time a reversal of the SF–density relation at z ~ 1.6 in a massive cluster.

Description: Polycyclic aromatic hydrocarbons (PAHs) are believed to be the small-size tail of the interstellar carbonaceous dust grain population. Their vibrational emission is the most widely accepted source of the aromatic near-infrared features, and their rotational radiation is a likely explanation for the dust-correlated anomalous microwave emission (AME). Yet, no individual interstellar PAH molecule has been identified to date. It was recently recognized that quasi-symmetric planar PAHs ought to have a well identifiable comb-like rotational spectrum, and suggested to search for them in spectroscopic data with matched-filtering techniques. We report the results of the first such search, carried out with the Green Bank Telescope, and targeting the star-forming region IC 348 in the Perseus molecular cloud, a known source of AME. Our observations amounted to 16.75 h and spanned a 3-GHz-wide band extending from 23.3 to 26.3 GHz. Using frequency switching, we achieved a sensitivity of 0.4 mJy per 0.4 MHz channel (1). The non-detection of comb-like spectra allowed us to set upper bounds on the abundance of specific quasi-symmetric PAH molecules (specified uniquely by their moments of inertia) of approximately 0.1 per cent of the total PAH abundance. This bound generically applies to PAHs with approximately 15–100 carbon atoms.

Description: As is well known, it is necessary to derive stellar parameters from massive amounts of spectral data automatically and efficiently. However, in traditional automatic methods such as artificial neural networks (ANNs) and kernel regression (KR), it is often difficult to optimize the algorithm structure and determine the optimal algorithm parameters. Gaussian process regression (GPR) is a recently developed method that has been proven to be capable of overcoming these difficulties. Here we apply GPR to derive stellar atmospheric parameters from spectra. Through evaluating the performance of GPR on Sloan Digital Sky Survey (SDSS) spectra, Medium resolution Isaac Newton Telescope Library of Empirical Spectra (MILES) spectra, ELODIE spectra and the spectra of member stars of galactic globular clusters, we conclude that GPR can derive stellar parameters accurately and precisely, especially when we use data preprocessed with principal component analysis (PCA). We then compare the performance of GPR with that of several widely used regression methods (ANNs, support-vector regression and KR) and find that with GPR it is easier to optimize structures and parameters and more efficient and accurate to extract atmospheric parameters.

Description: Galaxy–galaxy weak lensing is a direct probe of the mean matter distribution around galaxies. The depth and sky coverage of the Canada–France–Hawaii Telescope Legacy Survey yield statistically significant galaxy halo mass measurements over a much wider range of stellar masses (10 8.75 to 10 11.3 M ) and redshifts (0.2 〈  z  〈 0.8) than previous weak lensing studies. At redshift z  ~ 0.5, the stellar-to-halo mass ratio (SHMR) reaches a maximum of 4.0 ± 0.2 per cent as a function of halo mass at ~10 12.25 M . We find, for the first time from weak lensing alone, evidence for significant evolution in the SHMR: the peak ratio falls as a function of cosmic time from 4.5 ± 0.3 per cent at z  ~ 0.7 to 3.4 ± 0.2 per cent at z  ~ 0.3, and shifts to lower stellar mass haloes. These evolutionary trends are dominated by red galaxies, and are consistent with a model in which the stellar mass above which star formation is quenched ‘downsizes’ with cosmic time. In contrast, the SHMR of blue, star-forming galaxies is well fitted by a power law that does not evolve with time. This suggests that blue galaxies form stars at a rate that is balanced with their dark matter accretion in such a way that they evolve along the SHMR locus. The redshift dependence of the SHMR can be used to constrain the evolution of the galaxy population over cosmic time.

Description: We present 1000 mock galaxy catalogues (mocks) for the analysis of the low-redshift sample (LOWZ; effective redshift z  ~ 0.32) of the Baryon Oscillation Spectroscopic Survey (BOSS) Data Releases 10 and 11. These mocks have been created following the PTHalos method revised to include new developments. The main improvement is the introduction of a redshift dependence in the halo occupation distribution in order to account for the change of the galaxy number density with redshift. These mock galaxy catalogues are used in the analyses of the LOWZ galaxy clustering by the BOSS collaboration.

Description: We present two new catalogues of superclusters of galaxies out to a redshift of z  = 0.15, based on the Abell/ACO cluster redshift compilation maintained by one of us (HA). The first of these catalogues, the all-sky Main SuperCluster Catalogue (MSCC), is based on only the rich (A-) Abell clusters, and the second one, the Southern SuperCluster Catalogue (SSCC), covers declinations  〈 –17° and includes the supplementary Abell S-clusters. A tunable Friends-of-Friends algorithm was used to account for the cluster density decreasing with redshift and for different selection functions in distinct areas of the sky. We present the full list of Abell clusters used, together with their redshifts and supercluster memberships and including the isolated clusters. The SSCC contains about twice the number of superclusters than MSCC for  〈 –17°, which we found to be due to (1) new superclusters formed by A-clusters in their cores and surrounded by S-clusters (50 per cent), (2) new superclusters formed by S-clusters only (40 per cent), (3) redistribution of member clusters by fragmentation of rich (multiplicity m 〉 15) superclusters (8 per cent), and (4) new superclusters formed by the connection of A-clusters through bridges of S-clusters (2 per cent). Power-law fits to the cumulative supercluster multiplicity function yield slopes of α = –2.0 and α = –1.9 for MSCC and SSCC, respectively. This power-law behaviour is in agreement with the findings for other observational samples of superclusters, but not with that of catalogues based on cosmological simulations.

Description: We use two cosmological simulations of structure formation in the cold dark matter (CDM) scenario to study the evolutionary histories of dark matter haloes and to characterize the Lagrangian regions from which they form. We focus on haloes identified at redshift z id  = 0 and show that the classic ellipsoidal collapse model systematically overestimates their collapse times. If one imposes that halo collapse takes place at z id , this model requires starting from a significantly lower linear density contrast than what is measured in the simulations at the locations of halo formation. We attempt to explain this discrepancy by testing two key assumptions of the model. First, we show that the tides felt by collapsing haloes due to the surrounding large-scale structure evolve non-linearly. Although this effect becomes increasingly important for low-mass haloes, accounting for it in the ellipsoidal collapse model only marginally improves the agreement with N -body simulations. Second, we track the time evolution of the physical volume occupied by forming haloes and show that, after turnaround, it generally stabilizes at a well-defined redshift, z c  〉  z id , contrary to the basic assumption of extended Press–Schechter theory based on excursion sets. We discuss the implications of this result for understanding the origin of the mass dependence and scatter in the linear threshold for halo formation. Finally, we show that, when tuned for collapse at z c , a modified version of the ellipsoidal collapse model that also accounts for the triaxial nature of protohaloes predicts their linear density contrast in an unbiased way.

Description: The polarimetric measurement on the prompt phase of GRB 100826A shows that the polarization angle changes ~90° between two adjacent time intervals. We will show that this phenomenon can be naturally interpreted in the framework of the magnetic-dominated jet (MDJ) model. The MDJ model suggests that the bulk Lorentz factor of the outflow increases as r 1/3 , until reaching a saturated value sat . Electrons move in the globally ordered magnetic field advected by the jet from the central engine and produce synchrotron photons. The polarized synchrotron photons travel alone the jet direction and then collide with the cold electrons at the front of the jet. After the Compton scattering process, these photons escape from the jet and are detected by the observer locating slightly off-axis. If photons are emitted before the bulk Lorentz factor saturates, the change of polarization angle is a natural result of the acceleration of the outflow.

Description: The origin of trace hydrogen in white dwarfs (WDs) with He-dominated atmospheres is a long-standing problem, one that cannot satisfactorily be explained by the historically favoured hypothesis of accretion from the interstellar medium. Here we explore the possibility that the gradual accretion of exo-Oort cloud comets, which are a rich source of H, contributes to the apparent increase of trace H with WD cooling age. We determine how often remnant exo-Oort clouds, freshly excited from post-main-sequence stellar mass loss, dynamically inject comets inside the WD's Roche radius. We improve upon previous studies by considering a representative range of single WD masses (0.52–1.00 M ) and incorporating different cloud architectures, giant branch stellar mass loss, stellar flybys, Galactic tides and a realistic escape ellipsoid in self-consistent numerical simulations that integrate beyond 8 Gyr ages of WD cooling. We find that ~10 –5 of the material in an exo-Oort cloud is typically amassed on to the WD, and that the H deposits accumulate even as the cloud dissipates. This accumulation may account for the relatively large amount of trace H, 10 22 –10 25  g, that is determined frequently among WDs with cooling ages ≥1 Gyr. Our results also reaffirm the notion that exo-Oort cloud comets are not the primary agents of the metal budgets observed in polluted WD atmospheres.

Description: In this work, we investigate the statistical computation of the Boltzmann entropy of statistical samples. For this purpose, we use both histogram and kernel function to estimate the probability density function of statistical samples. We find that, due to coarse-graining, the entropy is a monotonic increasing function of the bin width for histogram or bandwidth for kernel estimation, which seems to be difficult to select an optimal bin width/bandwidth for computing the entropy. Fortunately, we notice that there exists a minimum of the first derivative of entropy for both histogram and kernel estimation, and this minimum point of the first derivative asymptotically points to the optimal bin width or bandwidth. We have verified these findings by large amounts of numerical experiments. Hence, we suggest that the minimum of the first derivative of entropy be used as a selector for the optimal bin width or bandwidth of density estimation. Moreover, the optimal bandwidth selected by the minimum of the first derivative of entropy is purely data-based, independent of the unknown underlying probability density distribution, which is obviously superior to the existing estimators. Our results are not restricted to one-dimensional, but can also be extended to multivariate cases. It should be emphasized, however, that we do not provide a robust mathematical proof of these findings, and we leave these issues with those who are interested in them.

Description: HD 76431 is a slow rotating post-HB star that shows an underabundance of helium by 0.5 dex relative to the solar value. These observational facts suggest that atomic diffusion could be active in its atmosphere. We have used the MMT and Bok spectra to estimate the atmospheric parameters of the target star using the model atmospheres and synthetic spectra calculated with tlusty and synspec . The derived values of the effective temperature, surface gravity, and helium abundance are consistent with those obtained by Ramspeck et al. It appears that non-local thermodynamic equilibrium (NLTE) effects are not important for HD 76431. We have used Stokes I spectra from ESPaDOnS at CFHT to perform an abundance analysis and a search for observational evidence of vertical stratification of the abundance of certain elements. The results of our abundance analysis are in good agreement with previously published data with respect to average abundances. Our numerical simulations show that carbon and nitrogen reveal signatures of vertical abundance stratification in the atmosphere of HD 76431. It appears that the carbon abundance increases towards the deeper atmospheric layers. Nitrogen also shows a similar behaviour, but in deeper atmospheric layers we obtain a significant dispersion for the estimates of its abundance. To our knowledge, this is the first demonstration of vertical abundance stratification of metals in a post-HB star and up to now it is the hottest star to show such stratification features. We also report the detection of two Si iii and one Ti iii emission lines in the spectra of HD 76431 that were not detected in previous studies.

Description: The Exoplanet Euclid Legacy Survey (ExELS) proposes to determine the frequency of cold exoplanets down to Earth mass from host separations of ~1 au out to the free-floating regime by detecting microlensing events in Galactic bulge. We show that ExELS can also detect large numbers of hot, transiting exoplanets in the same population. The combined microlensing+transit survey would allow the first self-consistent estimate of the relative frequencies of hot and cold sub-stellar companions, reducing biases in comparing ‘near-field’ radial velocity and transiting exoplanets with ‘far-field’ microlensing exoplanets. The age of the bulge and its spread in metallicity further allows ExELS to better constrain both the variation of companion frequency with metallicity and statistically explore the strength of star–planet tides. We conservatively estimate that ExELS will detect ~4100 sub-stellar objects, with sensitivity typically reaching down to Neptune-mass planets. Of these, ~600 will be detectable in both Euclid's VIS (optical) channel and Near Infrared Spectrometer and Photometer (NISP)- H -band imager, with ~90 per cent of detections being hot Jupiters. Likely scenarios predict a range of 2900–7000 for VIS and 400–1600 for H band. Twice as many can be expected in VIS if the cadence can be increased to match the 20-min H -band cadence. The separation of planets from brown dwarfs via Doppler boosting or ellipsoidal variability will be possible in a handful of cases. Radial velocity confirmation should be possible in some cases, using 30 m-class telescopes. We expect secondary eclipses, and reflection and emission from planets to be detectable in up to ~100 systems in both VIS and NISP- H . Transits of ~500 planetary-radius companions will be characterized with two-colour photometry and ~40 with four-colour photometry (VIS, YJH ), and the albedo of (and emission from) a large sample of hot Jupiters in the H band can be explored statistically.

Description: Motivated by the picture of a thin accretion disc around a black hole, radiating mainly in the direction perpendicular to its plane, we study the motion of test particles interacting with a test geodesic radiation flux originating in the equatorial plane of a Schwarzschild space–time and propagating initially in the perpendicular direction. We assume that the interaction with the test particles is modelled by an effective term corresponding to the Thomson-type interaction which governs the Poynting–Robertson effect. After approximating the individual photon trajectories adequately, we solve the continuity equation approximately in order to find a consistent flux density with a certain plausible prescribed equatorial profile. The combined effects of gravity and radiation are illustrated in several typical figures which confirm that the particles are generically strongly influenced by the flux. In particular, they are both collimated and accelerated in the direction perpendicular to the disc, but this acceleration is not enough to explain highly relativistic outflows emanating from some black hole–disc sources. The model can however be improved in a number of ways before posing further questions which are summarized in concluding remarks.

Description: Off-axis electron holography can be used to measure the inner potential of a specimen from its reconstructed phase image and is thus a powerful technique for materials scientists. However, abrupt reversals of contrast from white to black may sometimes occur in a digitally reconstructed phase image, which results in inaccurate information. Such phase distortion is mainly due to the digital reconstruction process and weak electron wave amplitude in some areas of the specimen. Therefore, digital image processing can be applied to the reconstruction and restoration of phase images. In this paper, fringe reconnection processing is applied to phase image restoration of a crystal structure image. The disconnection and wrong connection of interference fringes in the hologram that directly cause a 2 phase jump imperfection are correctly reconnected. Experimental results show that the phase distortion is significantly reduced after the processing. The quality of the reconstructed phase image was improved by the removal of imperfections in the final phase.

Description: Diabetes causes oxidative stress, which in turn generates excessive free radicals resulting in cellular damage. Vitamin C is an antioxidant that protects tissues and organs from oxidative stress. The thymus is one of the most important lymphoid organs, which regulates T-lymphocyte proliferation and maturation. The aim of this study is to investigate the protective effects of vitamin C on the thymus of streptozotocin (STZ)-induced diabetic rats. The mitotic activity and cell integrity of thymic lymphocytes were explored. Wistar Albino rats were divided into three groups: control (Group 1), STZ-diabetes (Group 2) and vitamin C-treated STZ-diabetics (Group 3). Rats received a single intraperitoneal injection of 45 mg/kg STZ to induce diabetes. Vitamin C (20 mg/kg) was administered intragastrically. Semithin and ultrathin sections were examined under a light or an electron microscope, respectively. Considerable numbers of mitotic lymphocytes were observed in the thymus of control rats. In the diabetic rats, however, numbers of mitotic lymphocytes decreased to ~57% of controls, and cell division abnormalities were observed. Additionally, diabetic rats showed degeneration in the structure of the thymus including trabecular thickening, accumulation of lipid vacuoles, heterochromatic nuclei and loss of mitochondrial cristae. Degradation of medullar and cortical integrity was also detected. In the vitamin C-treated STZ-diabetic group, the structure of the thymus and mitotic activity of the lymphocytes were similar to the control group. These results suggest that vitamin C protects the thymus against injury caused by diabetes and restores thymocyte mitotic activity.

Description: We investigated the stability of Pd/ZnO polar interfaces formed by internal oxidation of Pd–Zn alloys by using high-resolution transmission electron microscopy, electron energy-loss spectroscopy and convergent-beam electron diffraction. At 1273 K, a $$(111{)}_{\mathrm{Pd}}/(000\overline{2}{)}_{\mathrm{ZnO}}$$ polar interface defaceted and transformed into a curved interface, while another (111) Pd /(0002) ZnO polar interface retained its flatness. The $$(111{)}_{\mathrm{Pd}}/(000\overline{2}{)}_{\mathrm{ZnO}}$$ polar interface lost some stability over non-polar interfaces at 1273 K, while the (111) Pd /(0002) ZnO polar interface remained stable.

Description: Transmission electron microscope (TEM) observation of light metal hydrides is complicated by the instability of these materials under electron irradiation. In this study, the electron kinetic energy dependences of the interactions of incident electrons with lithium, sodium and magnesium hydrides, as well as the constituting element effect on the interactions, were theoretically discussed, and electron irradiation damage to these hydrides was examined using in situ TEM. The results indicate that high incident electron kinetic energy helps alleviate the irradiation damage resulting from inelastic or elastic scattering of the incident electrons in the TEM. Therefore, observations and characterizations of these materials would benefit from increased, instead decreased, TEM operating voltage.

Description: Synaptic plasticity is the process by which long-lasting changes take place at synaptic connections. The phenomenon itself is complex and can involve many levels of organization. Some authors separate forms into adaptations that have positive or negative consequences for the individual. It has been hypothesized that an increase in the number of synapses may represent a structural basis for the enduring expression of synaptic plasticity during some events that involve memory and learning; also, it has been suggested that perforated synapses increase in number after some diseases and experimental situations. The aim of this study was to analyze whether dopamine depletion induces changes in the synaptology of the corpus striatum of rats after the unilateral injection of 6-OHDA. The findings suggest that after the lesion, both contralateral and ipsilateral striata exhibit an increased length of the synaptic ending in ipsilateral (since third day) and contralateral striatum (since Day 20), loss of axospinous synapses in ipsilateral striatum and a significant increment in the number of perforated synapses, suggesting brain plasticity that might be deleterious for the spines, because this type of synaptic contacts are presumably excitatory, and in the absence of the modulatory effects of dopamine, the neuron could die through excitotoxic mechanisms. Thus, we can conclude that the presence of perforated synapses after striatal dopamine depletion might be a form of maladaptive synaptic plasticity.

Description: Unlike in vitro protein dynamics, intracellular protein dynamics are intricately regulated by protein–protein interactions or interactions between proteins and other cellular components, including nucleic acids, the plasma membrane and the cytoskeleton. Alteration of these dynamics plays a crucial role in physiological phenomena such as gene expression and cell division. Live-cell imaging via microscopy with the inherent properties of fluorescent proteins, i.e. photobleaching and photoconversion, or fluorescence correlation spectroscopy, provides insight into the movement of proteins and their interactions with cellular components. This article reviews techniques based on photo-induced changes in the physicochemical properties of fluorescent proteins to measure protein dynamics inside living cells, and it also discusses the strengths and weaknesses of these techniques.

Description: We have developed a method of atomic force microscopy (AFM)-assisted scanning tunneling spectroscopy (STS) under ambient conditions. An AFM function is used for rapid access to a selected position prior to performing STS. The AFM feedback is further used to suppress vertical thermal drift of the tip–sample distance during spectroscopy, enabling flexible and stable spectroscopy measurements at room temperature.

Description: To elucidate high-temperature plastic deformation (creep) mechanism in materials, it is essential to observe dislocation motion under tensile loading. There are many reports on in situ transmission electron microscopy (TEM) observations in the literature; however, the relationship between the dislocation motion and shear stress in 9Cr steel is still not clear. In this study, in order to evaluate this relationship quantitatively, in situ TEM observations were carried out in conjunction with finite element method (FEM) analysis. A tensile test sample was strained at an elevated temperature (903 K) inside a transmission electron microscope, and the stress distribution in the strained sample was analyzed by FEM. The dislocation behavior was clearly found to depend on the shear stress. At a shear stress of 66 MPa, both the dislocation velocity and mobile dislocation density were low. However, a high shear stress level of 95 MPa caused a noticeable increase in the dislocation velocity and mobile dislocation density. Furthermore, in this article, we discuss the dependence of the dislocation behavior on stress. The results presented here also indicate that the relationship between the microstructure and the strength of materials can be revealed by the methods used in this work.

Description: A dual-axis 360° rotation specimen holder was developed for use in reconstructing the three-dimensional (3D) distribution of a magnetic field using a combination of electron holography and tomography. Pillar-shaped specimens are used to obtain accurate reconstruction without a missing angle. The holder's rotation rod can be turned 〉360°; the pillar is set ±45° to the azimuth for both x - and y -axis rotation. Two rotation series of holograms in individual axes are recorded for vector field tomography. The two vector components of the magnetic field are reconstructed directly from the two series of holograms, and the remaining component is calculated using Maxwell's equation, div B = 0. As a result, all 3D magnetic fields are reconstructed.

Description: A new type of electrochemical cell was developed for in situ transmission electron microscopy observation that enables the electrode materials to be conveniently changed. The electrochemical cell was used to observe the electrochemical growth or dissolution of copper islands on a gold film with simultaneous cyclic voltammetry measurements. The copper islands could be explained by three-dimensional growing model.

Description: We report the detection of Ne viii in a z abs = 0.599 61 absorber towards the QSO PG1407+265 ( z em = 0.94). Besides Ne viii , absorption from H i Lyman series lines (H i  1025–915), several other low (C ii , N ii , O ii and S ii ), intermediate (C iii , N iii , N iv , O iii , S iv and S v ) and high (S vi , O vi and Ne viii ) ionization metal lines are detected. Disparity in the absorption line kinematics between different ions implies that the absorbing gas comprises of multiple ionization phases. The low and the intermediate ions (except S v ) trace a compact (~410 pc), metal-rich ( Z  ~ Z ) and overdense (log n H  ~ –2.6) photoionized region that sustained star formation for a prolonged period. The high ions, Ne viii and O vi , can be explained as arising in a low density (–5.3 ≤ log n H ≤ –5.0), metal-rich ( Z Z ) and diffuse (~180 kpc) photoionized gas. The S v , S vi and C iv [detected in the Faint Object Spectrograph (FOS) spectrum] require an intermediate photoionization phase with –4.2 〈 log n H  〈 –3.5. Alternatively, a pure collisional ionization model, as used to explain the previous known Ne viii absorbers, with 5.65 〈 log T  〈 5.72, can reproduce the S vi , O vi and Ne viii column densities simultaneously in a single phase. However, even such models require an intermediate phase to reproduce any observable S v and/or C iv . Therefore, we conclude that when multiple phases are present, the presence of Ne viii is not necessarily an unambiguous indication of collisionally ionized hot gas.

Description: Radiation fields emitted by O- and B-type stars or young stellar populations (SPs) are generally considered as significant central ionizing sources (CISs) of classic H  ii regions. In our previous studies, we showed that the inclusion of binary interactions in stellar population synthesis models can significantly increase the ultraviolet spectrum hardness and the number of ionizing photons of intermediate-age (IA) SPs (7 log( t /yr) 8). In this work, we present photoionization models of H  ii regions ionized by radiation fields emitted by IA SPs, including binary systems, and show that these fields are in theory possible candidates for significant CISs of classic H  ii regions. When radiation fields of IA SPs comprising binary systems are used as the CISs of classic H  ii regions, the theoretical strengths of a number of lines (such as [O  iii ] 4959 ' , [S  ii ] 6716 ' , etc.), which are weaker than observations, are increased; the border or selection-criterion lines between star-forming galaxies and active galactic nuclei (AGNs) in the diagnostic diagrams (for example, [N  ii ] 6583/Hα versus [O  iii ] 5007/Hβ), move into the region occupied originally by AGNs; and the He  ii 1640 line, observed in Lyman break and high-redshift gravitationally lensed galaxies, also can be produced.

Description: We reformulate rotation measure (RM) synthesis for data sets with discrete frequency channels and an arbitrary channel response function. The most commonly used version of the formalism by Brentjens & De Bruyn assumes a top-hat response function in wavelength squared, while real data sets can often be approximated better with a top-hat in frequency. We simulate mock data sets for various source geometries, using a top-hat response function in frequency, and we compare the quality of the RM spectra that are found with both formalisms. We include the response function of the simulated data to calculate exact RM spectra using our formalism. We show that the formalism by Brentjens & De Bruyn produces accurate results even if depolarization at the lowest frequencies in the observing band is severe. If RMs are large, our formalism reconstructs the emitted signal more accurately, with a higher amplitude and (in most cases) a narrower RM spread function. Our formalism can also detect sources with larger (absolute) RMs for a given sensitivity level of the observations.

Description: Depopulation of metastable He(2 3 S) and He(2 1 S) by radiative association with helium ions resulting in the formation of the He $_{2}^{+}$ molecular ions is investigated. Rate coefficients for spontaneous radiative association of the He $_{2}^{+}$ molecular ion on the spin-doublet manifold are presented as functions of temperature from 10 up to 500 000 K considering the association to rotational-vibrational bound states of the lowest doublet electronic states $X^{2}\Sigma ^{+}_{u}$ and $A^{2}\Sigma ^{+}_{g}$ from the continuum states of the excited doublet electronic states $B^{2}\Sigma ^{+}_{u}$ and $D^{2}\Sigma ^{+}_{u}$ . The dipole-driven processes B -〉 A and D -〉 A are compared to the quadrupole-driven processes B -〉 X and D -〉 X . For all considered temperatures, the dipole-driven process D -〉 A dominates over the other processes. The rate coefficient for the quadrupole-driven process B -〉 X is at least three orders of magnitude larger than the rate coefficient of the dipole-driven process B -〉 A .

Description: We present the results of a new analysis of the X-ray selected active galactic nuclei (AGN) population residing in and behind 135 of the most massive galaxy clusters in the redshift range of 0.2 〈  z  〈 0.9 observed with Chandra . With a sample of more than 11 000 X-ray point sources, we are able to measure, for the first time, evidence for evolution in the cluster AGN population beyond the expected evolution of field AGN. Our analysis shows that overall number density of cluster AGN scales with the cluster mass as ~ M 500 – 1.2 . There is no evidence for the overall number density of cluster member X-ray AGN depending on the cluster redshift in a manner different than field AGN, nor is there any evidence that the spatial distribution of cluster AGN (given in units of the cluster overdensity radius r 500 ) strongly depends on the cluster mass or redshift. The M –1.2 ± 0.7 scaling relation we measure is consistent with theoretical predictions of the galaxy merger rate in clusters, which is expected to scale with the cluster velocity dispersion, , as ~ –3 or ~ M –1 . This consistency suggests that galaxy mergers may be an important contributor to the cluster AGN population, a result that is further corroborated by visual inspection of Hubble images for 23 spectroscopically confirmed cluster member AGN in our sample. A merger-driven scenario for the triggering of X-ray AGN is not strongly favoured by studies of field galaxies, however, suggesting that different mechanisms may be primarily responsible for the triggering of cluster and field X-ray AGN.

Description: Motivation : Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent ‘third-generation’ sequencing technologies provide single-molecule templates and longer sequencing reads, but at the cost of higher per-nucleotide error rates. Results : We present MultiBreak-SV, an algorithm to detect structural variants (SVs) from single molecule sequencing data, paired read sequencing data, or a combination of sequencing data from different platforms. We demonstrate that combining low-coverage third-generation data from Pacific Biosciences (PacBio) with high-coverage paired read data is advantageous on simulated chromosomes. We apply MultiBreak-SV to PacBio data from four human fosmids and show that it detects known SVs with high sensitivity and specificity. Finally, we perform a whole-genome analysis on PacBio data from a complete hydatidiform mole cell line and predict 1002 high-probability SVs, over half of which are confirmed by an Illumina-based assembly. Availability and implementation : MultiBreak-SV is available at http://compbio.cs.brown.edu/software/ . Contact : annaritz@vt.edu or braphael@cs.brown.edu Supplementary information: Supplementary data are available at Bioinformatics online.

Description: Motivation: Insertions play an important role in genome evolution. However, such variants are difficult to detect from short-read sequencing data, especially when they exceed the paired-end insert size. Many approaches have been proposed to call short insertion variants based on paired-end mapping. However, there remains a lack of practical methods to detect and assemble long variants. Results: We propose here an original method, called M ind T he G ap , for the integrated detection and assembly of insertion variants from re-sequencing data. Importantly, it is designed to call insertions of any size, whether they are novel or duplicated, homozygous or heterozygous in the donor genome. M ind T he G ap uses an efficient k -mer-based method to detect insertion sites in a reference genome, and subsequently assemble them from the donor reads. M ind T he G ap showed high recall and precision on simulated datasets of various genome complexities. When applied to real Caenorhabditis elegans and human NA12878 datasets, M ind T he G ap detected and correctly assembled insertions 〉1 kb, using at most 14 GB of memory. Availability and implementation: http://mindthegap.genouest.org Contact: guillaume.rizk@inria.fr or claire.lemaitre@inria.fr

Description: The analysis of SOlar and Heliospheric Observatory ( SOHO ) Solar Wind ANisotropies (SWAN) data for backscattered solar Lyman α radiation performed by Lallement et al. showed for the first time that the average direction of interstellar hydrogen flow in the heliosphere is deflected by several degrees relative to the original direction of the interstellar wind outside the heliosphere. This deflection is caused by the indirect influence of the interstellar magnetic field (IsMF) through charge exchange between hydrogen atoms and interstellar protons deflected by the IsMF in the region of interaction between the solar wind and the local interstellar medium (LISM). Thus, measurements of the backscattered Lyman α radiation at the Earth's orbit can be used as a remote IsMF diagnostic. However, the direction of interstellar hydrogen flow in the vicinity of the Sun may be influenced by other effects such as the solar radiation pressure, gravitation and ionization and kinetic non-Maxwellian properties of the hydrogen distribution and also may depend on other LISM parameters besides IsMF. In this work, we perform a theoretical modelling of the backscattered solar Lyman α radiation seen at 1 au from the Sun and analyse the direction of hydrogen flow in the heliosphere, which can be obtained from the spectral properties of the backscattered radiation. The influence of different effects mentioned above is investigated. Also we compare our results obtained by means of a state-of-art 3D time-dependent kinetic model of the hydrogen distribution with the SWAN data of 1996.

Description: Type Ia supernovae (SNe Ia) are often used as the standard candles to probe the anisotropic expansion of the Universe. In this paper, we make a comprehensive comparison between the hemisphere comparison (HC) method and dipole-fitting (DF) method in searching for the cosmological preferred direction using the Union2 data set, a compilation of 557 well-calibrated SNe Ia. We find that the directions of the faintest SNe Ia derived from these two methods are approximately opposite. Monte Carlo simulations show that the results of the HC method strongly depend on the distribution of the data points in the sky. The coincidence that the HC method and DF method give two completely opposite directions may be due to the extremely non-uniform distribution of the Union2 data set.

Description: We show that if young low-mass stars are subject to vigorous X-ray driven disc winds, then such winds may be rendered detectable in cluster environments through their interaction with ionizing radiation from massive stars. In particular we argue that in the Orion nebula cluster (ONC) one expects to see of order tens of ‘X-ray proplyds’ (i.e. objects with offset ionization fronts detectable through optical imaging) in the range 0.3–0.6 pc from 1 C Ori (the dominant O star in the ONC). Objects at this distance lie outside the central ‘FUV zone’ in the ONC where proplyd structures are instead well explained by neutral winds driven by external far-ultraviolet (FUV) emission from 1 C Ori. We show that the predicted numbers and sizes of X-ray proplyds in this region are compatible with the numbers of proplyds observed and that this may also provide an explanation for at least some of the far flung proplyds observed in the Carina nebula. We compare the sizes of observed proplyds outside the FUV region of the ONC with model predictions based on the current observed X-ray luminosities of these sources (bearing in mind that the current size is actually set by the X-ray luminosity a few hundred years previously, corresponding to the flow time to the ionization front). We discuss whether variability on this time-scale can plausibly explain the proplyd size data on a case-by-case basis. We also calculate the predicted radio free–free emission signature of X-ray proplyds and show that this is readily detectable. Monitoring is, however, required in order to distinguish such emission from non-thermal radio emission from active coronae. We also predict that it is only at distances more than a parsec from 1 C Ori that the free–free emission signature of such offset ionized structures would be clearly distinguishable from an externally driven ionized disc wind. We argue that the fortuitous proximity of massive stars in the ONC can be used as a beacon to light up internally driven X-ray winds and that this represents a promising avenue for observational tests of the X-ray photoevaporation scenario.

Description: Cross-correlating the Planck High Frequency Instrument maps against quasars from the Sloan Digital Sky Survey DR7, we estimate the intensity distribution of the cosmic infrared background (CIB) over the redshift range 0 〈  z  〈 5. We detect redshift-dependent spatial cross-correlations between the two data sets using the 857, 545, and 353 GHz channels and we obtain upper limits at 217 GHz consistent with expectations. At all frequencies with detectable signal we infer a redshift distribution peaking around z  ~ 1.2 and find the recovered spectrum to be consistent with emission arising from star-forming galaxies. By assuming simple modified blackbody and Kennicutt relations, we estimate dust and star formation rate density as a function of redshift, finding results consistent with earlier multiwavelength measurements over a large portion of cosmic history. However, we note that, lacking mid-infrared coverage, we are not able to make an accurate determination of the mean temperature for the dust responsible for the CIB. Our results demonstrate that clustering-based redshift inference is a valuable tool for measuring the entire evolution history of the cosmic star formation rate from a single and homogeneous data set.

Description: While wide-field surveys of M31 have revealed much substructure at large radii, understanding the nature and origin of this material is not straightforward from morphology alone. Using deep Hubble Space Telescope /Advanced Camera for Surveys data, we have derived further constraints in the form of quantitative star formation histories (SFHs) for 14 inner halo fields which sample diverse substructures. In agreement with our previous analysis of colour–magnitude diagram morphologies, we find the resultant behaviours can be broadly separated into two categories. The SFHs of ‘disc-like’ fields indicate that most of their mass has formed since z  ~ 1, with one quarter of the mass formed in the last 5 Gyr. We find ‘stream-like’ fields to be on average 1.5 Gyr older, with 10 per cent of their stellar mass formed within the last 5 Gyr. These fields are also characterized by an age–metallicity relation showing rapid chemical enrichment to solar metallicity by z  = 1, suggestive of an early-type progenitor. We confirm a significant burst of star formation 2 Gyr ago, discovered in our previous work, in all the fields studied here. The presence of these young stars in our most remote fields suggests that they have not formed in situ but have been kicked-out from the thin disc through disc heating in the recent past.

Description: The solar analogues 16 Cyg A and B are excellent asteroseismic targets in the Kepler field of view and together with a red dwarf and a Jovian planet form an interesting system. For these more evolved Sun-like stars we cannot detect surface rotation with the current Kepler data but instead use the technique of asteroseimology to determine rotational properties of both 16 Cyg A and B. We find the rotation periods to be $23.8^{+1.5}_{-1.8}$ and $23.2^{+11.5}_{-3.2} \rm \, d$ , and the angles of inclination to be $56^{+6}_{-5} \, ^{\circ }$ and $36^{+17}_{-7} \, ^{\circ }$ , for A and B, respectively. Together with these results we use the published mass and age to suggest that, under the assumption of a solar-like rotation profile, 16 Cyg A could be used when calibrating gyrochronology relations. In addition, we discuss the known 16 Cyg B star–planet eccentricity and measured low obliquity which is consistent with Kozai cycling and tidal theory.

Description: Current wide-area radio surveys are dominated by active galactic nuclei, yet many of these sources have no identified optical counterparts. Here we investigate whether one can constrain the nature and properties of these sources, using Fanaroff–Riley type II (FR II) radio galaxies as probes. These sources are easy to identify since the angular separation of their lobes remains almost constant at some tens of arcseconds for z  〉 1. Using a simple algorithm applied to the Faint Images of the Radio Sky at Twenty-cm survey, we obtain the largest FR II sample to date, containing over 10 4 double-lobed sources. A subset of 459 sources is matched to Sloan Digital Sky Survey quasars. This sample yields a statistically meaningful description of the fraction of quasars with lobes as a function of redshift and luminosity. This relation is combined with the bolometric quasar luminosity function and a disc–lobe correlation to obtain a robust prediction for the density of FR IIs on the radio sky. We find that the observed density can be explained by the population of known quasars, implying that the majority of powerful jets originate from a radiatively efficient accretion flow with a linear jet–disc coupling. Finally, we show that high-redshift jets are more often quenched within 100 kpc, suggesting a higher efficiency of jet-induced feedback into their host galaxies.