Separable projection integrals for higher-order correlators of the cosmic microwave sky: Acceleration by factors exceeding 100

© 2016. We present a case study describing efforts to optimise and modernise "Modal", the simulation and analysis pipeline used by the Planck satellite experiment for constraining general non-Gaussian models of the early universe via the bispectrum (or three-point correlator) of the cosmic microwave background radiation. We focus on one particular element of the code: the projection of bispectra from the end of inflation to the spherical shell at decoupling, which defines the CMB we observe today. This code involves a three-dimensional inner product between two functions, one of which requires an integral, on a non-rectangular domain containing a sparse grid. We show that by employing separable methods this calculation can be reduced to a one-dimensional summation plus two integrations, reducing the overall dimensionality from four to three. The introduction of separable functions also solves the issue of the non-rectangular sparse grid. This separable method can become unstable in certain scenarios and so the slower non-separable integral must be calculated instead. We present a discussion of the optimisation of both approaches.We demonstrate significant speed-ups of ≈100×, arising from a combination of algorithmic improvements and architecture-aware optimisations targeted at improving thread and vectorisation behaviour. The resulting MPI/OpenMP hybrid code is capable of executing on clusters containing processors and/or coprocessors, with strong-scaling efficiency of 98.6% on up to 16 nodes. We find that a single coprocessor outperforms two processor sockets by a factor of 1.3× and that running the same code across a combination of both microarchitectures improves performance-per-node by a factor of 3.38×. By making bispectrum calculations competitive with those for the power spectrum (or two-point correlator) we are now able to consider joint analysis for cosmological science exploitation of new data.This research is supported by an STFC consolidated grant ST/L000636/1, and funded in part by the Intel R Parallel Computing Centre program. This work was undertaken on the COSMOS Shared Memory system at DAMTP, University of Cambridge operated on behalf of the STFC DiRAC HPC Facility. This equipment is funded by BIS National E-infrastructure capital grant ST/J005673/1 and STFC grants ST/H008586/1, ST/K00333X/1

An exploration of familial associations of two movement pattern-derived subgroups of chronic disabling low back pain; a cross-sectional cohort study

© 2016 Elsevier Ltd. Background: Altered movement patterns with pain have been demonstrated in children, adolescents and adults with chronic disabling low back pain (CDLBP). A previously developed classification system has identified different subgroups including active extension and multidirectional patterns in patients with CDLBP. While familial associations have been identified for certain spinal postures in standing, it is unknown whether a familial relationship might exist between movement pattern-derived subgroups in families with CDLBP. Objectives: This study explored whether familial associations in movement pattern-derived subgroups within and between members of families with CDLBP existed. Design: Cross-sectional cohort study. Method: 33 parents and 28 children with CDLBP were classified into two subgroups based on clinical analysis of video footage of postures and functional movements, combined with aggravating factors obtained from Oswestry Disability Questionnaire. Prevalence of subgroups within family members was determined, associations between parent and child's subgroup membership was evaluated using Fisher's exact test, and spearman's correlation coefficient was used to determine the strength of association between familial dyads. Results: The majority of parents were classified as active extenders, sons predominately multidirectional and daughters were evenly distributed between the two subgroups. No significant association was found when comparing subgroups in nine parent-child relationships. Conclusions: The exploration of a small cohort of family dyads in this study demonstrated that children's movement pattern-derived subgroups could not be explained by their parents' subgroup membership. These results cannot be generalised to the CLBP population due to this study's small sample. Larger sample studies are needed to further elucidate this issue

Intricate Correlation between Body Posture, Personality Trait and Incidence of Body Pain: A Cross-Referential Study Report

OBJECTIVE: Occupational back pain is a disorder that commonly affects the working population, resulting in disability, health-care utilization, and a heavy socioeconomic burden. Although the etiology of occupational pain remains largely unsolved, anecdotal evidence exists for the contribution of personality and posture to long-term pain management, pointing to a direct contribution of the mind-body axis. In the current study, we have conducted an extensive evaluation into the relationships between posture and personality. METHOD: We have sampled a random population of 100 subjects (50 men and 50 women) in the age range of 13-82 years based on their personality and biomechanical profiles. All subjects were French-Canadian, living in Canada between the Québec and Sorel-Tracy areas. The Biotonix analyses and report were used on the subjects being tested in order to distinguish postural deviations. Personality was determined by using the Myers-Briggs Type Indicator questionnaire. RESULTS: We establish a correlation between ideal and kyphosis-lordosis postures and extraverted personalities. Conversely, our studies establish a correlative relationship between flat back and sway-back postures with introverted personalities. CONCLUSION: Overall, our studies establish a novel correlative relationship between personality, posture and pain

Superficial simplicity of the 2010 El Mayor–Cucapah earthquake of Baja California in Mexico

The geometry of faults is usually thought to be more complicated at the surface than at depth and to control the initiation, propagation and arrest of seismic ruptures. The fault system that runs from southern California into Mexico is a simple strike-slip boundary: the west side of California and Mexico moves northwards with respect to the east. However, the M_w 7.2 2010 El Mayor–Cucapah earthquake on this fault system produced a pattern of seismic waves that indicates a far more complex source than slip on a planar strike-slip fault. Here we use geodetic, remote-sensing and seismological data to reconstruct the fault geometry and history of slip during this earthquake. We find that the earthquake produced a straight 120-km-long fault trace that cut through the Cucapah mountain range and across the Colorado River delta. However, at depth, the fault is made up of two different segments connected by a small extensional fault. Both segments strike N130° E, but dip in opposite directions. The earthquake was initiated on the connecting extensional fault and 15 s later ruptured the two main segments with dominantly strike-slip motion. We show that complexities in the fault geometry at depth explain well the complex pattern of radiated seismic waves. We conclude that the location and detailed characteristics of the earthquake could not have been anticipated on the basis of observations of surface geology alone

Temporal Patterns of Nucleotide Misincorporations and DNA Fragmentation in Ancient DNA

DNA that survives in museum specimens, bones and other tissues recovered by archaeologists is invariably fragmented and chemically modified. The extent to which such modifications accumulate over time is largely unknown but could potentially be used to differentiate between endogenous old DNA and present-day DNA contaminating specimens and experiments. Here we examine mitochondrial DNA sequences from tissue remains that vary in age between 18 and 60,000 years with respect to three molecular features: fragment length, base composition at strand breaks, and apparent C to T substitutions. We find that fragment length does not decrease consistently over time and that strand breaks occur preferentially before purine residues by what may be at least two different molecular mechanisms that are not yet understood. In contrast, the frequency of apparent C to T substitutions towards the 5′-ends of molecules tends to increase over time. These nucleotide misincorporations are thus a useful tool to distinguish recent from ancient DNA sources in specimens that have not been subjected to unusual or harsh treatments

Application and comparison of large-scale solution-based DNA capture-enrichment methods on ancient DNA

The development of second-generation sequencing technologies has greatly benefitted the field of ancient DNA (aDNA). Its application can be further exploited by the use of targeted capture-enrichment methods to overcome restrictions posed by low endogenous and contaminating DNA in ancient samples. We tested the performance of Agilent's SureSelect and Mycroarray's MySelect in-solution capture systems on Illumina sequencing libraries built from ancient maize to identify key factors influencing aDNA capture experiments. High levels of clonality as well as the presence of multiple-copy sequences in the capture targets led to biases in the data regardless of the capture method. Neither method consistently outperformed the other in terms of average target enrichment, and no obvious difference was observed either when two tiling designs were compared. In addition to demonstrating the plausibility of capturing aDNA from ancient plant material, our results also enable us to provide useful recommendations for those planning targeted-sequencing on aDNA

A revision of the status of Lepadogaster lepadogaster (Teleostei : Gobiesocidae): sympatric subspecies or a long misunderstood blend of species?

Molecular (partial mitochondrial 12S ribosomal DNA sequences), morphological and meristic analysis of Lepadogaster lepadogaster lepadogaster, L. l. purpurea and L. zebrina were performed to investigate the relationships between these taxa. On the western shore of mainland Portugal, where the two subspecies of L. lepadogaster occur sympatrically, they differ in microhabitat preferences and their breeding seasons are largely out of phase. This information, combined with data on distribution patterns, led to the following conclusions: Lepadogaster l. purpurea is considered to be a valid species, L. purpurea (Bonnaterre, 1788), different from L. l. lepadogaster, now designated L. lepadogaster (Bonnaterre, 1788). L. zebrina was found to be a synonym of L. lepadogaster. The two newly defined species were found to be in sympatry at Madeira and the Canary islands, the Atlantic coast of the Iberian Peninsula, and the Mediterranean at least as far as Genoa (Italy). Diagnostic characters and a list of synonyms are provided. (C) 2002 The Linnean Society of London, Biological Journal of the Linnean Society, 2002, 76, 327-338

Assessing methods for dealing with treatment switching in clinical trials: A follow-up simulation study

When patients randomised to the control group of a randomised controlled trial are allowed to switch onto the experimental treatment, intention-to-treat analyses of the treatment effect are confounded because the separation of randomised groups is lost. Previous research has investigated statistical methods that aim to estimate the treatment effect that would have been observed had this treatment switching not occurred and has demonstrated their performance in a limited set of scenarios. Here, we investigate these methods in a new range of realistic scenarios, allowing conclusions to be made based upon a broader evidence base. We simulated randomised controlled trials incorporating prognosis-related treatment switching and investigated the impact of sample size, reduced switching proportions, disease severity, and alternative data-generating models on the performance of adjustment methods, assessed through a comparison of bias, mean squared error, and coverage, related to the estimation of true restricted mean survival in the absence of switching in the control group. Rank preserving structural failure time models, inverse probability of censoring weights, and two-stage methods consistently produced less bias than the intentionto-treat analysis. The switching proportion was confirmed to be a key determinant of bias: sample size and censoring proportion were relatively less important. It is critical to determine the size of the treatment effect in terms of an acceleration factor (rather than a hazard ratio) to provide information on the likely bias associated with rank-preserving structural failure time model adjustments. In general, inverse probability of censoring weight methods are more volatile than other adjustment methods

Negotiation in strategy making teams : group support systems and the process of cognitive change

This paper reports on the use of a Group Support System (GSS) to explore at a micro level some of the processes manifested when a group is negotiating strategy-processes of social and psychological negotiation. It is based on data from a series of interventions with senior management teams of three operating companies comprising a multi-national organization, and with a joint meeting subsequently involving all of the previous participants. The meetings were concerned with negotiating a new strategy for the global organization. The research involved the analysis of detailed time series data logs that exist as a result of using a GSS that is a reflection of cognitive theory

Massive migration from the steppe is a source for Indo-European languages in Europe

We generated genome-wide data from 69 Europeans who lived between 8,000-3,000 years ago by enriching ancient DNA libraries for a target set of almost four hundred thousand polymorphisms. Enrichment of these positions decreases the sequencing required for genome-wide ancient DNA analysis by a median of around 250-fold, allowing us to study an order of magnitude more individuals than previous studies and to obtain new insights about the past. We show that the populations of western and far eastern Europe followed opposite trajectories between 8,000-5,000 years ago. At the beginning of the Neolithic period in Europe, ~8,000-7,000 years ago, closely related groups of early farmers appeared in Germany, Hungary, and Spain, different from indigenous hunter-gatherers, whereas Russia was inhabited by a distinctive population of hunter-gatherers with high affinity to a ~24,000 year old Siberian6 . By ~6,000-5,000 years ago, a resurgence of hunter-gatherer ancestry had occurred throughout much of Europe, but in Russia, the Yamnaya steppe herders of this time were descended not only from the preceding eastern European hunter-gatherers, but from a population of Near Eastern ancestry. Western and Eastern Europe came into contact ~4,500 years ago, as the Late Neolithic Corded Ware people from Germany traced ~3/4 of their ancestry to the Yamnaya, documenting a massive migration into the heartland of Europe from its eastern periphery. This steppe ancestry persisted in all sampled central Europeans until at least ~3,000 years ago, and is ubiquitous in present-day Europeans. These results provide support for the theory of a steppe origin of at least some of the Indo-European languages of Europe