Performance analysis of a parallel, multi-node pipeline for DNA sequencing

Post-sequencing DNA analysis typically consists of read mapping followed by variant calling and is very time-consuming, even on a multi-core machine. Recently, we proposed Halvade, a parallel, multi-node implementation of a DNA sequencing pipeline according to the GATK Best Practices recommendations. The MapReduce programming model is used to distribute the workload among different workers. In this paper, we study the impact of different hardware configurations on the performance of Halvade. Benchmarks indicate that especially the lack of good multithreading capabilities in the existing tools (BWA, SAMtools, Picard, GATK) cause suboptimal scaling behavior. We demonstrate that it is possible to circumvent this bottleneck by using multiprocessing on high-memory machines rather than using multithreading. Using a 15-node cluster with 360 CPU cores in total, this results in a runtime of 1 h 31 min. Compared to a single-threaded runtime of similar to 12 days, this corresponds to an overall parallel efficiency of 53%

Progress in mixed Eulerian-Lagrangian finite element simulation of forming processes

A review is given of a mixed Eulerian-Lagrangian finite element method for simulation of forming processes. This method permits incremental adaptation of nodal point locations independently from the actual material displacements. Hence numerical difficulties due to large element distortions, as may occur when the updated Lagrange method is applied, can be avoided. Movement of (free) surfaces can be taken into account by adapting nodal surface points in a way that they remain on the surface. Hardening and other deformation path dependent properties are determined by incremental treatment of convective terms. A local and a weighed global smoothing procedure is introduced in order to avoid numerical instabilities and numerical diffusion. Prediction of contact phenomena such as gap openning and/or closing and sliding with friction is accomplished by a special contact element. The method is demonstrated by simulations of an upsetting process and a wire drawing process

Strong between-site variation in New Caledonian crows' use of hook-tool-making materials

The study was funded through a BBSRC David Phillips Fellowship (grants BB/G023913/1 and BB/G023913/2 to CR) and doctoral studentships from the BBSRC (BK), JASSO (SS), and the School of Biology, University of St Andrews (JvdW).Functional tool use requires the selection of appropriate raw materials. New Caledonian crows Corvus moneduloides are known for their extraordinary tool-making behaviour, including the crafting of hooked stick tools from branched vegetation. We describe a surprisingly strong between-site difference in the plant materials used by wild crows to manufacture these tools: crows at one study site use branches of the non-native shrub Desmanthus virgatus, whereas only approximately 7 km away, birds apparently ignore this material in favour of the terminal twigs of an as-yet-unidentified tree species. Although it is likely that differences in local plant communities drive this striking pattern, it remains to be determined how and why crows develop such strong site-specific preferences for certain raw materials.Publisher PDFPeer reviewe

Vote choice in one round and two round elections

Nous proposons un modèle de vote stratégique dans lequel la décision de supporter ou non un candidat dépend de B, le bénéfice associé à l'élection de ce candidat, et de V, la viabilité perçue du candidat. Nous testons ce modèle sur des données obtenues lors d'une série d'expériences dans les quelles les participants votaient dans huit élections successives, quatre suivant la règle de vote à un seul tour, et quatre suivant le vote à deux tours. Nous montrons que le même modèle s'applique aux deux systèmes, bien que l'impact de la viabilité soit légèrement plus faible dans le cas des élections à deux tours.Elections, système de vote, comportement stratégique

X-rays from Colliding Stellar Winds: the case of close WR+O binary systems

We have analysed the X-ray emission from a sample of close WR+O binaries using data from the public Chandra and XMM-Newton archives. Global spectral fits show that two-temperature plasma is needed to match the X-ray emission from these objects as the hot component (kT > 2 keV) is an important ingredient of the spectral models. In close WR+O binaries, X-rays likely originate in colliding stellar wind (CSW) shocks driven by the massive winds of the binary components. CSW shocks in these objects are expected to be radiative due to the high density of the plasma in the interaction region. Opposite to this, our analysis shows that the CSW shocks in the sample of close WR+O binaries are adiabatic. This is possible only if the mass-loss rates of the stellar components in the binary are at least one order of magnitude smaller than the values currently accepted. The most likely explanation for the X-ray properties of close WR+O binaries could be that their winds are two-component flows. The more massive component (dense clumps) play role for the optical/UV emission from these objects, while the smooth rarefied component is a key factor for their X-ray emission.Comment: MNRAS, accepted for publication (Feb 6, 2012); 13 pages, 6 figures, 3 table

New distance measures for classifying X-ray astronomy data into stellar classes

The classification of the X-ray sources into classes (such as extragalactic sources, background stars, ...) is an essential task in astronomy. Typically, one of the classes corresponds to extragalactic radiation, whose photon emission behaviour is well characterized by a homogeneous Poisson process. We propose to use normalized versions of the Wasserstein and Zolotarev distances to quantify the deviation of the distribution of photon interarrival times from the exponential class. Our main motivation is the analysis of a massive dataset from X-ray astronomy obtained by the Chandra Orion Ultradeep Project (COUP). This project yielded a large catalog of 1616 X-ray cosmic sources in the Orion Nebula region, with their series of photon arrival times and associated energies. We consider the plug-in estimators of these metrics, determine their asymptotic distributions, and illustrate their finite-sample performance with a Monte Carlo study. We estimate these metrics for each COUP source from three different classes. We conclude that our proposal provides a striking amount of information on the nature of the photon emitting sources. Further, these variables have the ability to identify X-ray sources wrongly catalogued before. As an appealing conclusion, we show that some sources, previously classified as extragalactic emissions, have a much higher probability of being young stars in Orion Nebula.Comment: 29 page

Evaluation of a Participatory Ergonomics Intervention in Small Commercial Construction Firms

BACKGROUND: Work-related musculoskeletal disorders (WMSD) among construction workers remain high. Participatory ergonomics (PE) interventions that engage workers and employers in reducing work injury risks have shown mixed results. METHODS: Eight-six workers from seven contractors participated in a PE program. A logic model guided the process evaluation and summative evaluation of short term and intermediate impacts and long term outcomes from surveys and field records. RESULTS: Process measures showed good delivery of training, high worker engagement, and low contractor participation. Workers’ knowledge improved and workers reported changes to work practices and tools used; contractor provision of appropriate equipment was low (33%). No changes were seen in symptoms or reported physical effort. CONCLUSIONS: The PE program produced many worker-identified ergonomic solutions, but lacked needed support from contractors. Future interventions should engage higher levels of the construction organizational system to improve contractor involvement for reducing WMSD

On the Impact of Link Layer Retransmissions on TCP for Aeronautical Communications

In this article, we evaluate the impact of link layer retransmissions on the performance of TCP in the context of aeronautical communications.We present the architecture of aeronautical networks, which is manly driven by an important channel access delay, and the various retransmission strategies that can be implemented at both link and transport layers. We consider a worst case scenario to illustrate the benefits provided by the ARQ scheme at the link layer in terms of transmission delay.We evaluate the trade-off between allowing a fast data transmission and a low usage of satellite capacity by adjusting link layer parameters

Mass-Loss Rate Determination for the Massive Binary V444 Cyg using 3-D Monte-Carlo Simulations of Line and Polarization Variability

A newly developed 3-D Monte Carlo model is used, in conjunction with a multi-line non-LTE radiative transfer model, to determine the mass-loss rate of the Wolf-Rayet (W-R) star in the massive binary \object{V444 Cyg} (WN5+O6). This independent estimate of mass-loss rate is attained by fitting the observed \HeI (5876) \AA and \HeII (5412) \AA line profiles, and the continuum light curves of three Stokes parameters ((I, Q, U)) in the (V) band simultaneously. The high accuracy of our determination arises from the use of many observational constraints, and the sensitivity of the continuum polarization to the mass-loss rate. Our best fit model suggests that the mass-loss rate of the system is (\dot{M}_{\WR}=0.6(\pm 0.2) \times 10^{-5} M_{\sun} \mathrm{yr}^{-1} ), and is independent of the assumed distance to \object{V444 Cyg}. The fits did not allow a unique value for the radius of the W-R star to be derived. The range of the volume filling factor for the W-R star atmosphere is estimated to be in the range of 0.050 (for R_{\WR}=5.0 R_{\sun}) to 0.075 (for R_{\WR}=2.5 R_{\sun}). We also found that the blue-side of \HeI (5876 ) \AA and \HeII (5412) \AA lines at phase 0.8 is relatively unaffected by the emission from the wind-wind interaction zone and the absorption by the O-star atmosphere; hence, the profiles at this phase are suitable for spectral line fittings using a spherical radiative transfer model.Comment: 18 pages, 17 figures: Accepeted for publication in A&

Cognitive flexibility predicts early reading skills

International audienceAn important aspect of learning to read is efficiency in accessing different kinds of linguistic information (orthographic, phonological, and semantic) about written words. The present study investigates whether, in addition to the integrity of such linguistic skills, early progress in reading may require a degree of cognitive flexibility in order to manage the coordination of this information effectively. Our study will look for evidence of a link between flexibility and both word reading and passage reading comprehension, and examine whether any such link involves domain-general or reading-specific flexibility. As the only previous support for a predictive relationship between flexibility and early reading comes from studies of reading comprehension in the opaque English orthography, another possibility is that this relationship may be largely orthography-dependent, only coming into play when mappings between representations are complex and polyvalent. To investigate these questions, 60 second-graders learning to read the more transparent French orthography were presented with two multiple classification tasks involving reading-specific cognitive flexibility (based on words) and non-specific flexibility (based on pictures). Reading skills were assessed by word reading, pseudo-word decoding, and passage reading comprehension measures. Flexibility was found to contribute significant unique variance to passage reading comprehension even in the less opaque French orthography. More interestingly, the data also show that flexibility is critical in accounting for one of the core components of reading comprehension, namely, the reading of words in isolation. Finally, the results constrain the debate over whether flexibility has to be reading-specific to be critically involved in reading