SOAP3-dp: Fast, Accurate and Sensitive GPU-based Short Read Aligner

To tackle the exponentially increasing throughput of Next-Generation Sequencing (NGS), most of the existing short-read aligners can be configured to favor speed in trade of accuracy and sensitivity. SOAP3-dp, through leveraging the computational power of both CPU and GPU with optimized algorithms, delivers high speed and sensitivity simultaneously. Compared with widely adopted aligners including BWA, Bowtie2, SeqAlto, GEM and GPU-based aligners including BarraCUDA and CUSHAW, SOAP3-dp is two to tens of times faster, while maintaining the highest sensitivity and lowest false discovery rate (FDR) on Illumina reads with different lengths. Transcending its predecessor SOAP3, which does not allow gapped alignment, SOAP3-dp by default tolerates alignment similarity as low as 60 percent. Real data evaluation using human genome demonstrates SOAP3-dp's power to enable more authentic variants and longer Indels to be discovered. Fosmid sequencing shows a 9.1 percent FDR on newly discovered deletions. SOAP3-dp natively supports BAM file format and provides a scoring scheme same as BWA, which enables it to be integrated into existing analysis pipelines. SOAP3-dp has been deployed on Amazon-EC2, NIH-Biowulf and Tianhe-1A.Comment: 21 pages, 6 figures, submitted to PLoS ONE, additional files available at "https://www.dropbox.com/sh/bhclhxpoiubh371/O5CO_CkXQE". Comments most welcom

AMaχoS—Abstract Machine for Xcerpt

Web query languages promise convenient and efficient access to Web data such as XML, RDF, or Topic Maps. Xcerpt is one such Web query language with strong emphasis on novel high-level constructs for effective and convenient query authoring, particularly tailored to versatile access to data in different Web formats such as XML or RDF. However, so far it lacks an efficient implementation to supplement the convenient language features. AMaχoS is an abstract machine implementation for Xcerpt that aims at efficiency and ease of deployment. It strictly separates compilation and execution of queries: Queries are compiled once to abstract machine code that consists in (1) a code segment with instructions for evaluating each rule and (2) a hint segment that provides the abstract machine with optimization hints derived by the query compilation. This article summarizes the motivation and principles behind AMaχoS and discusses how its current architecture realizes these principles

Four Lessons in Versatility or How Query Languages Adapt to the Web

Exposing not only human-centered information, but machine-processable data on the Web is one of the commonalities of recent Web trends. It has enabled a new kind of applications and businesses where the data is used in ways not foreseen by the data providers. Yet this exposition has fractured the Web into islands of data, each in different Web formats: Some providers choose XML, others RDF, again others JSON or OWL, for their data, even in similar domains. This fracturing stifles innovation as application builders have to cope not only with one Web stack (e.g., XML technology) but with several ones, each of considerable complexity. With Xcerpt we have developed a rule- and pattern based query language that aims to give shield application builders from much of this complexity: In a single query language XML and RDF data can be accessed, processed, combined, and re-published. Though the need for combined access to XML and RDF data has been recognized in previous work (including the W3C’s GRDDL), our approach differs in four main aspects: (1) We provide a single language (rather than two separate or embedded languages), thus minimizing the conceptual overhead of dealing with disparate data formats. (2) Both the declarative (logic-based) and the operational semantics are unified in that they apply for querying XML and RDF in the same way. (3) We show that the resulting query language can be implemented reusing traditional database technology, if desirable. Nevertheless, we also give a unified evaluation approach based on interval labelings of graphs that is at least as fast as existing approaches for tree-shaped XML data, yet provides linear time and space querying also for many RDF graphs. We believe that Web query languages are the right tool for declarative data access in Web applications and that Xcerpt is a significant step towards a more convenient, yet highly efficient data access in a “Web of Data”

sgsR: a structurally guided sampling toolbox for LiDAR-based forest inventories

Establishing field inventories can be labor intensive, logistically challenging and expensive. Optimizing a sample to derive accurate forest attribute predictions is a key management-level inventory objective. Traditional sampling designs involving pre-defined, interpreted strata could result in poor selection of within-strata sampling intensities, leading to inaccurate estimates of forest structural variables. The use of airborne laser scanning (ALS) data as an applied forest inventory tool continues to improve understanding of the composition and spatial distribution of vegetation structure across forested landscapes. The increased availability of wall-to-wall ALS data is promoting the concept of structurally guided sampling (SGS), where ALS metrics are used as an auxiliary data source driving stratification and sampling within management-level forest inventories. In this manuscript, we present an open-source R package named sgsR that provides a robust toolbox for implementing various SGS approaches. The goal of this package is to provide a toolkit to facilitate better optimized allocation of sample units and sample size, as well as to assess and augment existing plot networks by accounting for current forest structural conditions. Here, we first provide justification for SGS approaches and the creation of the sgsR toolbox. We then briefly describe key functions and workflows the package offers and provide two reproducible examples. Avenues to implement SGS protocols according to auxiliary data needs are presented

Impact of physical activity, sedentary behaviour and muscle strength on bone stiffness in 2-10-year-old children-cross-sectional results from the IDEFICS study

Background: Physical activity (PA), weight-bearing exercises (WBE) and muscle strength contribute to skeletal development, while sedentary behaviour (SB) adversely affects bone health. Previous studies examined the isolated effect of PA, SB or muscle strength on bone health, which was usually assessed by x-ray methods, in children. Little is known about the combined effects of these factors on bone stiffness (SI) assessed by quantitative ultrasound. We investigated the joint association of PA, SB and muscle strength on SI in children. Methods: In 1512 preschool (2- < 6 years) and 2953 school children (6-10 years), data on calcaneal SI as well as on accelerometer-based sedentary time (SED), light (LPA), moderate (MPA) and vigorous PA (VPA) were available. Parents reported sports (WBE versus no WBE), leisure time PA and screen time of their children. Jumping distance and handgrip strength served as indicators for muscle strength. The association of PA, SB and muscle strength with SI was estimated by multivariate linear regression, stratified by age group. Models were adjusted for age, sex, country, fat-free mass, daylight duration, consumption of dairy products and PA, or respectively SB. Results: Mean SI was similar in preschool (79.5 +/- 15.0) and school children (81.3 +/- 12.1). In both age groups, an additional 10 min/day in MPA or VPA increased the SI on average by 1 or 2 %, respectively (p = .05). The negative association of SED with SI decreased after controlling for MVPA. LPA was not associated with SI. Furthermore, participation in WBE led to a 3 and 2 % higher SI in preschool (p = 0.003) and school children (p < .001), respectively. Although muscle strength significantly contributed to SI, it did not affect the associations of PA with SI. In contrast to objectively assessed PA, reported leisure time PA and screen time showed no remarkable association with SI. Conclusion: This study suggests that already an additional 10 min/day of MPA or VPA or the participation in WBE may result in a relevant increase in SI in children, taking muscle strength and SB into account. Our results support the importance of assessing accelerometer-based PA in large-scale studies. This may be important when deriving dose-response relationships between PA and bone health in children

How HRM affects corporate financial performance. Evidence from Belgian SMEs. Paper.

Employment; Expected; Managers; Studies; Management; Performance;