On the design and implementation of broadcast and global combine operations using the postal model

There are a number of models that were proposed in recent years for message passing parallel systems. Examples are the postal model and its generalization the LogP model. In the postal model a parameter λ is used to model the communication latency of the message-passing system. Each node during each round can send a fixed-size message and, simultaneously, receive a message of the same size. Furthermore, a message sent out during round r will incur a latency of hand will arrive at the receiving node at round r + λ - 1. Our goal in this paper is to bridge the gap between the theoretical modeling and the practical implementation. In particular, we investigate a number of practical issues related to the design and implementation of two collective communication operations, namely, the broadcast operation and the global combine operation. Those practical issues include, for example, 1) techniques for measurement of the value of λ on a given machine, 2) creating efficient broadcast algorithms that get the latency hand the number of nodes n as parameters and 3) creating efficient global combine algorithms for parallel machines with λ which is not an integer. We propose solutions that address those practical issues and present results of an experimental study of the new algorithms on the Intel Delta machine. Our main conclusion is that the postal model can help in performance prediction and tuning, for example, a properly tuned broadcast improves the known implementation by more than 20%

Fluctuating asymmetry and environmental stress : understanding the role of trait history

While fluctuating asymmetry (FA; small, random deviations from perfect symmetry in bilaterally symmetrical traits) is widely regarded as a proxy for environmental and genetic stress effects, empirical associations between FA and stress are often weak or heterogeneous among traits. A conceptually important source of heterogeneity in relationships with FA is variation in the selection history of the trait(s) under study, i.e. traits that experienced a (recent) history of directional change are predicted to be developmentally less stable, potentially through the loss of canalizing modifiers. Here we applied X-ray photography on museum specimens and live captures to test to what extent the magnitude of FA and FA-stress relationships covary with directional shifts in traits related to the flight apparatus of four East-African rainforest birds that underwent recent shifts in habitat quality and landscape connectivity. Both the magnitude and direction of phenotypic change varied among species, with some traits increasing in size while others decreased or maintained their original size. In three of the four species, traits that underwent larger directional changes were less strongly buffered against random perturbations during their development, and traits that increased in size over time developed more asymmetrically than those that decreased. As we believe that spurious relationships due to biased comparisons of historic (museum specimens) and current (field captures) samples can be ruled out, these results support the largely untested hypothesis that directional shifts may increase the sensitivity of developing traits to random perturbations of environmental or genetic origin

The calcium dynamics of human dental pulp stem cells stimulated with tricalcium silicate-based cements determine their differentiation and mineralization outcome

Calcium (Ca2+) signalling plays an indispensable role in dental pulp and dentin regeneration, but the Ca2+ responses of human dental pulp stem cells (hDPSCs) stimulated with tricalcium silicate-based (TCS-based) dental biomaterials remains largely unexplored. The objective of the present study was to identify and correlate extracellular Ca2+ concentration, intracellular Ca2+ dynamics, pH, cytotoxicity, gene expression and mineralization ability of human dental pulp stem cells (hDPSCs) stimulated with two different TCS-based biomaterials: Biodentine and ProRoot white MTA. The hDPSCs were exposed to the biomaterials, brought in contact with the overlaying medium, with subsequent measurements of extracellular Ca2+ and pH, and intracellular Ca2+ changes. Messenger RNA expression (BGLAP, TGF-β, MMP1 and BMP2), cytotoxicity (MTT and TUNEL) and mineralization potential (Alizarin red and Von Kossa staining) were then evaluated. Biodentine released significantly more Ca2+ in the α-MEM medium than ProRoot WMTA but this had no cytotoxic impact on hDPSCs. The larger Biodentine-linked Ca2+ release resulted in altered intracellular Ca2+ dynamics, which attained a higher maximum amplitude, faster rise time and increased area under the curve of the Ca2+ changes compared to ProRoot WMTA. Experiments with intracellular Ca2+ chelation, demonstrated that the biomaterial-triggered Ca2+ dynamics affected stem cell-related gene expression, cellular differentiation and mineralization potential. In conclusion, biomaterial-specific Ca2+ dynamics in hDPSCs determine differentiation and mineralization outcomes, with increased Ca2+ dynamics enhancing mineralization

Environmentally and behaviourally mediated co-occurrence of functional traits in bird communities of tropical forest fragments

Two major theories of community assembly - based on the assumption of limiting similarity' or 'habitat filtering', respectively - predict contrasting patterns in the spatial arrangement of functional traits. Previous analyses have made progress in testing these predictions and identifying underlying processes, but have also pointed to theoretical as well as methodological shortcomings. Here we applied a recently developed methodology for spatially explicit analysis of phylogenetic meta-community structure to study the pattern of co-occurrence of functional traits in Afrotropical and Neotropical bird species inhabiting forest fragments. Focusing separately on locomotory, dietary, and dispersal traits, we tested whether environmental filtering causes spatial clustering, or competition leads to spatial segregation as predicted by limiting similarity theory. We detected significant segregation of species co-occurrences in African fragments, but not in the Neotropical ones. Interspecific competition had a higher impact on trait co-occurrence than filter effects, yet no single functional trait was able to explain the observed degree of spatial segregation among species. Despite high regional variability spanning from spatial segregation to aggregation, we found a consistent tendency for a clustered spatial patterning of functional traits among communities in fragmented landscapes, particularly in non-territorial species. Overall, we show that behavioural effects, such as territoriality, and environmental effects, such as the area of forest remnants or properties of the landscape matrix in which they are embedded, can strongly affect the pattern of trait co-occurrence. Our findings suggest that trait-based analyses of community structure should include behavioural and environmental covariates, and we here provide an appropriate method for linking functional traits, species ecology and environmental conditions to clarify the drivers underlying spatial patterns of species co-occurrence

The BLLAST field experiment: Boundary-Layer late afternoon and sunset turbulence

Due to the major role of the sun in heating the earth's surface, the atmospheric planetary boundary layer over land is inherently marked by a diurnal cycle. The afternoon transition, the period of the day that connects the daytime dry convective boundary layer to the night-time stable boundary layer, still has a number of unanswered scientific questions. This phase of the diurnal cycle is challenging from both modelling and observational perspectives: it is transitory, most of the forcings are small or null and the turbulence regime changes from fully convective, close to homogeneous and isotropic, toward a more heterogeneous and intermittent state. These issues motivated the BLLAST (Boundary-Layer Late Afternoon and Sunset Turbulence) field campaign that was conducted from 14 June to 8 July 2011 in southern France, in an area of complex and heterogeneous terrain. A wide range of instrumented platforms including full-size aircraft, remotely piloted aircraft systems, remote-sensing instruments, radiosoundings, tethered balloons, surface flux stations and various meteorological towers were deployed over different surface types. The boundary layer, from the earth's surface to the free troposphere, was probed during the entire day, with a focus and intense observation periods that were conducted from midday until sunset. The BLLAST field campaign also provided an opportunity to test innovative measurement systems, such as new miniaturized sensors, and a new technique for frequent radiosoundings of the low troposphere. Twelve fair weather days displaying various meteorological conditions were extensively documented during the field experiment. The boundary-layer growth varied from one day to another depending on many contributions including stability, advection, subsidence, the state of the previous day's residual layer, as well as local, meso- or synoptic scale conditions. Ground-based measurements combined with tethered-balloon and airborne observations captured the turbulence decay from the surface throughout the whole boundary layer and documented the evolution of the turbulence characteristic length scales during the transition period. Closely integrated with the field experiment, numerical studies are now underway with a complete hierarchy of models to support the data interpretation and improve the model representations.publishedVersio