ALBERT

Description: We have studied the impact of dust feedback on the survival and structure of vortices in protoplanetary discs using 2D shearing box simulations with Lagrangian dust particles. We consider dust with a variety of sizes (stopping time t s  = 10 –2 –1 –10 2 –1 ), from fully coupled with the gas to the decoupling limit. We find that a vortex is destroyed by dust feedback when the total dust-to-gas mass ratio within the vortex is larger than 30–50 per cent, independent of the dust size. The dust distribution can still be asymmetric in some cases after the vortex has been destroyed. With smaller amounts of dust, a vortex can survive for at least 100 orbits, and the maximum dust surface density within the vortex can be more than 100 times larger than the gas surface density, potentially facilitating planetesimal formation. On the other hand, in these stable vortices, small ( t s  〈  –1 ) and large ( t s –1 ) dust grains concentrate differently and affect the gas dynamics in different ways. The distribution of large dust is more elongated than that of small dust. Large dust ( t s –1 ) concentrates in the centre of the vortex and feedback leads to turn-over in vorticity towards the centre, forming a quiescent region within an anticyclonic vortex. Such a turn-over is absent if the vortex is loaded with small grains. We demonstrate that, in protoplanetary discs where both large and small dust grains are present and under the right condition, the concentration of large dust towards the vortex centre can lead to a quiescent centre, repelling the small dust and forming a small dust ring around the vortex centre. Such anticorrelations between small and large dust within vortices may explain the discrepancy between Atacama Large Millimeter Array and near-IR scattered light observations in the asymmetric region of transitional discs.

Description: We use 118 strong gravitational lenses observed by the SLACS, BOSS emission-line lens survey (BELLS), LSD and SL2S surveys to constrain the total mass profile and the profile of luminosity density of stars (light tracers) in elliptical galaxies up to redshift z ~ 1. Assuming power-law density profiles for the total mass density, = 0 ( r / r 0 ) –α , and luminosity density, = 0 ( r / r 0 ) – , we investigate the power-law index and its first derivative with respect to the redshift. Using Monte Carlo simulations of the posterior likelihood taking the Planck 's best-fitting cosmology as a prior, we find = 2.132 ± 0.055 with a mild trend / z l = –0.067 ± 0.119 when α = = , suggesting that the total density profile of massive galaxies could have become slightly steeper over cosmic time. Furthermore, similar analyses performed on sub-samples defined by different lens redshifts and velocity dispersions indicate the need of treating low-, intermediate- and high-mass galaxies separately. Allowing to be a free parameter, we obtain α = 2.070 ± 0.031, α/ z l = –0.121 ± 0.078 and = 2.710 ± 0.143. The model in which mass traces light is rejected at 〉95 per cent confidence, and our analysis robustly indicates the presence of dark matter in the form of a mass component that is differently spatially extended than the light. In this case, intermediate-mass elliptical galaxies (200 km s –1 〈 ap ≤ 300 km s –1 ) show the best consistency with the singular isothermal sphere as an effective model of galactic lenses.

Description: Restriction endonucleases are highly specific in recognizing the particular DNA sequence they act on. However, their activity is affected by sequence context, enzyme concentration and buffer composition. Changes in these factors may lead to either ineffective cleavage at the cognate restriction site or relaxed specificity allowing cleavage of degenerate ‘star’ sites. Additionally, uncharacterized restriction endonucleases and engineered variants present novel activities. Traditionally, restriction endonuclease activity is assayed on simple substrates such as plasmids and synthesized oligonucleotides. We present and use high-throughput Illumina sequencing-based strategies to assay the sequence specificity and flanking sequence preference of restriction endonucleases. The techniques use fragmented DNA from sequenced genomes to quantify restriction endonuclease cleavage on a complex genomic DNA substrate in a single reaction. By mapping millions of restriction site–flanking reads back to the Escherichia coli and Drosophila melanogaster genomes we were able to quantitatively characterize the cognate and star site activity of EcoRI and MfeI and demonstrate genome-wide decreases in star activity with engineered high-fidelity variants EcoRI-HF and MfeI-HF, as well as quantify the influence on MfeI cleavage conferred by flanking nucleotides. The methods presented are readily applicable to all type II restriction endonucleases that cleave both strands of double-stranded DNA.

Description: Although the Matuyama–Brunhes boundary (MBB) in the Chinese Loess Plateau (CLP) is very important in reliably correlating Quaternary loess with other sediments in the world, particularly with marine and polar ice cores, its exact stratigraphic position remains controversial. Previous investigations usually placed the MBB between paleosol unit S8 and loess unit L8 in various locations. To better understand the spatial differences in the MBB position, a high-resolution paleomagnetic study was conducted in a loess section of the Lantian Basin at the southern margin of the CLP. The results show that the MBB is situated in the middle of the relatively weak paleosol unit S7, consistent with a recent report on the MBB based on a 10 Be study from the Xifeng and Luochuan loess sections of the central CLP. However, the regional anomalously low magnetic susceptibility in paleosols S7 and S8 indicates that it is more reliable to determine the paleoclimate boundaries between loess and paleosol horizons of this segment with median grain size. Then, the MBB in the Yushan section can be correlated with the bottom of paleosol S7, corresponding to the older part of interglacial marine isotope stage 19. This result temporally reconciles the striking discrepancy of the position of the MBB recorded in between loess and other typical sedimentary sequences, and further confirms that the stratigraphic position of the MBB could spatially vary to a certain extent due to regional sedimentary or paleoclimatic conditions in the marginal areas of the CLP. In the Yushan section, the high-frequency variations of paleomagnetic directions during a long period of ~31 ka before the MBB, however, could not be attributed to a genuine response to the true geomagnetic behaviour. Moreover, the climate offset defined by the magnetic susceptibility and median grain size of the section can be preliminarily attributed to the regional geology and paleoenvironment background. A multiproxy-based stratigraphic division is considered very necessary when paleomagnetic and climatic boundaries are defined exactly in a specific area of the southern CLP.

Description: : Exhaustive mapping of next-generation sequencing data to a set of relevant reference sequences becomes an important task in pathogen discovery and metagenomic classification. However, the runtime and memory usage increase as the number of reference sequences and the repeat content among these sequences increase. In many applications, read mapping time dominates the entire application. We developed CompMap, a reference-based compression program, to speed up this process. CompMap enables the generation of a non-redundant representative sequence for the input sequences. We have demonstrated that reads can be mapped to this representative sequence with a much reduced time and memory usage, and the mapping to the original reference sequences can be recovered with high accuracy. Availability and implementation : CompMap is implemented in C and freely available at http://csse.szu.edu.cn/staff/zhuzx/CompMap/ . Contact : xiaoyang@broadinstitute.org Supplementary information : Supplementary data are available at Bioinformatics online.

Description: In this paper, assuming the validity of distance duality relation, = D L ( z )(1 + z ) –2 / D A ( z ) = 1, where D A ( z ) and D L ( z ) are the angular and the luminosity distance, respectively, we explore two kinds of gas mass density profiles of clusters: the isothermal β model and the non-isothermal double-β model. In our analysis, performed on 38 massive galaxy clusters observed by Chandra (within the redshift range of 0.14 〈 z 〈 0.89), we use two types of cluster gas mass fraction data corresponding to different mass density profiles fitted to the X-ray data. Using two general parameterizations of ( z ) (phenomenologically allowing for distance duality violation), we find that the non-isothermal double-β model agrees better with the distance duality relation, while the isothermal β model tends to be marginally incompatible with the Etherington theorem at 68.3 per cent confidence level (CL). However, current accuracy of the data does not allow to distinguish between the two models for the gas-density distribution at a significant level.

Description: The prevalence of heterogeneous manycore processors has been shown as a promising alternative to web-based data parallel MapReduce applications. The differences of manycore from multicore raise new challenges to designing and implementing efficient and scalable MapReduce applications, such as memory access congestion. This paper argues that it is more efficient using multiple small groups of cores than using a single group with all cores to address these challenges. We propose a group-based MapReduce implementation, called Grouped-MapReduce (GMR). It uses grouping to align tasks so that the tasks in each group are congestion-free. Further, it uses multiplexing to control the implementation of groups so that multiple groups can efficiently share the limited memory bandwidth without causing serious memory access congestion. We have implemented a prototype of GMR based on Phoenix++, an already highly optimized MapReduce runtime. Experiments on six benchmarks show that GMR implements and scales well on manycore systems and obtains an impressive improvement over Phoenix++ from 1.04x to 1.77x without artificially tuning the existing application code.

Description: Full virtualization technology is highly reusable. Using this property, various types and versions of existing operating systems and drivers can be reused in a virtual machine to customize users’ application environments. However, these environments are threatened by drivers’ write operation faults, which are caused by bugs in reused drivers. Chariot is a reliability architecture that has been developed to solve this problem. This architecture captures a driver's write operations by maintaining the write permissions of shadow pages as read-only to examine their correctness. Nevertheless, this capture method produces many page faults in the virtual machine monitor and has an adverse impact on the performance of isolated drivers. To reduce performance losses, this paper examines two algorithms that cache recently used shadow pages using different structures to avoid frequent page faults. The experimental results show that the performance of isolated drivers can be greatly improved using these shadow page caches without significantly impacting the isolation efficiency of Chariot.

Description: Sex-specific genetic effects have been proposed to be an important source of variation for human complex traits. Here we use two distinct genome-wide methods to estimate the autosomal genetic correlation ( r g ) between men and women for human height and body mass index (BMI), using individual-level ( n = ~44 000) and summary-level ( n = ~133 000) data from genome-wide association studies. Results are consistent and show that the between-sex genetic correlation is not significantly different from unity for both traits. In contrast, we find evidence of genetic heterogeneity between sexes for waist–hip ratio ( r g = ~0.7) and between populations for BMI ( r g = ~0.9 between Europe and the USA) but not for height. The lack of evidence for substantial genetic heterogeneity for body size is consistent with empirical findings across traits and species.

Description: The exponential growth of high-throughput DNA sequence data has posed great challenges to genomic data storage, retrieval and transmission. Compression is a critical tool to address these challenges, where many methods have been developed to reduce the storage size of the genomes and sequencing data (reads, quality scores and metadata). However, genomic data are being generated faster than they could be meaningfully analyzed, leaving a large scope for developing novel compression algorithms that could directly facilitate data analysis beyond data transfer and storage. In this article, we categorize and provide a comprehensive review of the existing compression methods specialized for genomic data and present experimental results on compression ratio, memory usage, time for compression and decompression. We further present the remaining challenges and potential directions for future research.