Fast Iterative Graph Computation: A Path Centric Approach

Abstract—Large scale graph processing represents an inter-esting challenge due to the lack of locality. This paper presents PathGraph for improving iterative graph computation on graphs with billions of edges. Our system design has three unique features: First, we model a large graph using a collection of tree-based partitions and use an path-centric computation rather than vertex-centric or edge-centric computation. Our parallel computation model significantly improves the memory and disk locality for performing iterative computation algorithms. Second, we design a compact storage that further maximize sequential access and minimize random access on storage media. Third, we implement the path-centric computation model by using a scatter/gather programming model, which parallels the iterative computation at partition tree level and performs sequential updates for vertices in each partition tree. The experimental results show that the path-centric approach outperforms vertex-centric and edge-centric systems on a number of graph algorithms for both in-memory and out-of-core graphs

Does Adjuvant Treatment With Ginkgo Biloba to Statins Have Additional Benefits in Patients With Dyslipidemia?

Objective: Ginkgo biloba are widely used alone or in combination with other lipid-lowering agents in the treatment of dyslipidemia in China. We conducted this meta-analysis to investigate whether adjuvant treatment with ginkgo biloba leaves to statins has incremental benefits in patients with dyslipidemia.Methods: Potential studies were searched from PubMed, EMBASE, Cochrane Library, China National Knowledge Infrastructure, VIP, and Wanfang database up to October 2017. Only randomized controlled trials (RCTs) comparing the efficacy and safety of ginkgo biloba leaves plus statins versus statins alone in patients with dyslipidemia were included.Results: Eight RCTs involving 664 patients were included. Compared with statins therapy alone, combination of statins and ginkgo biloba leaves therapy achieved greater reductions in triglycerides [mean difference (MD) -0.32 mmol/L; 95% confidence interval (CI) -0.43 to -0.20], total cholesterol (MD -0.61 mmol/L; 95% CI -0.90 to -0.33), or low-density lipoprotein cholesterol (LDL-C) (MD -0.32 mmol/L; 95% CI -0.48 to -0.16), and a greater increment in high-density lipoprotein cholesterol (MD 0.26 mmol/L; 95% CI 0.15 to 0.37). Subgroup analyses showed that ginkgo biloba leaves plus simvastatin appeared to achieve a greater reduction in serum levels of triglycerides, total cholesterol, and LDL-C than in combination with atorvastatin therapy.Conclusion: This meta-analysis suggests that adjuvant treatment with ginkgo biloba leaves appears to improve blood lipid parameters than statins therapy alone. More well-designed RCTs are needed to investigate the benefits of the combination of statins and ginkgo biloba leaves

A Comparative Study of Theoretical Graph Models for Characterizing Structural Networks of Human Brain

Previous studies have investigated both structural and functional brain networks via graph-theoretical methods. However, there is an important issue that has not been adequately discussed before: what is the optimal theoretical graph model for describing the structural networks of human brain? In this paper, we perform a comparative study to address this problem. Firstly, large-scale cortical regions of interest (ROIs) are localized by recently developed and validated brain reference system named Dense Individualized Common Connectivity-based Cortical Landmarks (DICCCOL) to address the limitations in the identification of the brain network ROIs in previous studies. Then, we construct structural brain networks based on diffusion tensor imaging (DTI) data. Afterwards, the global and local graph properties of the constructed structural brain networks are measured using the state-of-the-art graph analysis algorithms and tools and are further compared with seven popular theoretical graph models. In addition, we compare the topological properties between two graph models, namely, stickiness-index-based model (STICKY) and scale-free gene duplication model (SF-GD), that have higher similarity with the real structural brain networks in terms of global and local graph properties. Our experimental results suggest that among the seven theoretical graph models compared in this study, STICKY and SF-GD models have better performances in characterizing the structural human brain network

Flexible and Bendable Acoustofluidics for Particle and Cell Patterning

Surface acoustic wave (SAW) based microfluidic devices provide active techniques to manipulate fluid and particles, which can be used for precise and controllable patterning of microparticles and biological cells, with a high efficiency in a non-invasive and contact-free manner. This paper investigates flexible and bendable SAW microfluidic devices and explores the effects of bending and twisting of SAW devices on microparticle and cell patterning, using both experimental and numerical modelling. We showed that bending flexible SAW devices changes the distribution of particle pattern lines significantly. In devices with concave bending the particle pattern lines converge towards the centre of the curvature, whereas for devices with convex bending, they diverge away from it. Comparing the particle patterning using Lamb and Rayleigh wave devices with concave bending, we found that particle alignment is more efficient in the flexural mode Lamb wave device, whereas for the devices with convex bending, the particle patterning is more clear and regular when Rayleigh waves are used. We further investigated the effects of twisting the flexible SAW devices and observed that the particles are patterned into lines parallel to the deformed interdigital transducers (IDTs). We finally patterned yeast cells using our flexible SAW devices, and demonstrated the possibility of using our flexible acoustofluidic device for biomechanical systems such as body conforming technologies, wearable bio-sensors, and flexible point-of-care devices for personalized health monitoring

DICCCOL: Dense Individualized and Common Connectivity-Based Cortical Landmarks

Is there a common structural and functional cortical architecture that can be quantitatively encoded and precisely reproduced across individuals and populations? This question is still largely unanswered due to the vast complexity, variability, and nonlinearity of the cerebral cortex. Here, we hypothesize that the common cortical architecture can be effectively represented by group-wise consistent structural fiber connections and take a novel data-driven approach to explore the cortical architecture. We report a dense and consistent map of 358 cortical landmarks, named Dense Individualized and Common Connectivity–based Cortical Landmarks (DICCCOLs). Each DICCCOL is defined by group-wise consistent white-matter fiber connection patterns derived from diffusion tensor imaging (DTI) data. Our results have shown that these 358 landmarks are remarkably reproducible over more than one hundred human brains and possess accurate intrinsically established structural and functional cross-subject correspondences validated by large-scale functional magnetic resonance imaging data. In particular, these 358 cortical landmarks can be accurately and efficiently predicted in a new single brain with DTI data. Thus, this set of 358 DICCCOL landmarks comprehensively encodes the common structural and functional cortical architectures, providing opportunities for many applications in brain science including mapping human brain connectomes, as demonstrated in this work

The Genomes of Oryza sativa: A History of Duplications

We report improved whole-genome shotgun sequences for the genomes of indica and japonica rice, both with multimegabase contiguity, or almost 1,000-fold improvement over the drafts of 2002. Tested against a nonredundant collection of 19,079 full-length cDNAs, 97.7% of the genes are aligned, without fragmentation, to the mapped super-scaffolds of one or the other genome. We introduce a gene identification procedure for plants that does not rely on similarity to known genes to remove erroneous predictions resulting from transposable elements. Using the available EST data to adjust for residual errors in the predictions, the estimated gene count is at least 38,000–40,000. Only 2%–3% of the genes are unique to any one subspecies, comparable to the amount of sequence that might still be missing. Despite this lack of variation in gene content, there is enormous variation in the intergenic regions. At least a quarter of the two sequences could not be aligned, and where they could be aligned, single nucleotide polymorphism (SNP) rates varied from as little as 3.0 SNP/kb in the coding regions to 27.6 SNP/kb in the transposable elements. A more inclusive new approach for analyzing duplication history is introduced here. It reveals an ancient whole-genome duplication, a recent segmental duplication on Chromosomes 11 and 12, and massive ongoing individual gene duplications. We find 18 distinct pairs of duplicated segments that cover 65.7% of the genome; 17 of these pairs date back to a common time before the divergence of the grasses. More important, ongoing individual gene duplications provide a never-ending source of raw material for gene genesis and are major contributors to the differences between members of the grass family

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Characterization of the complete chloroplast genome of the Pohlia nutans M211 from Antarctica

The Antarctic Pohlia nutans M211 complete chloroplast (cp) genome, sequenced using Illumina NovaSeq PE150, was 125,199 bp in length. It contained 19,836 bp of inverted repeat (IR) regions that separated a large single-copy region (LSC) of 86,738 bp and a small single-copy region (SSC) of 18,580 bp. The whole-genome encodes 132 genes (80 protein-coding genes, 36 tRNA genes, and 8 rRNA genes) and had 29.5% GC content. The M211 was congruent with Sanionia uncinata (KM111545.1) according to the Phylogenetic tree analyses