Cache-Integrated Network Interfaces: Flexible On-Chip Communication and Synchronization for Large-Scale CMPs

Per-core scratchpad memories (or local stores) allow direct inter-core communication, with latency and energy advantages over coherent cache-based communication, especially as CMP architectures become more distributed. We have designed cache-integrated network interfaces, appropriate for scalable multicores, that combine the best of two worlds – the flexibility of caches and the efficiency of scratchpad memories: on-chip SRAM is configurably shared among caching, scratchpad, and virtualized network interface (NI) functions. This paper presents our architecture, which provides local and remote scratchpad access, to either individual words or multiword blocks through RDMA copy. Furthermore, we introduce event responses, as a technique that enables software configurable communication and synchronization primitives. We present three event response mechanisms that expose NI functionality to software, for multiword transfer initiation, completion notifications for software selected sets of arbitrary size transfers, and multi-party synchronization queues. We implemented these mechanisms in a four-core FPGA prototype, and measure the logic overhead over a cache-only design for basic NI functionality to be less than 20%. We also evaluate the on-chip communication performance on the prototype, as well as the performance of synchronization functions with simulation of CMPs with up to 128 cores. We demonstrate efficient synchronization, low-overhead communication, and amortized-overhead bulk transfers, which allow parallelization gains for fine-grain tasks, and efficient exploitation of the hardware bandwidth.

Bagging statistical network inference from large-scale gene expression data.

Modern biology and medicine aim at hunting molecular and cellular causes of biological functions and diseases. Gene regulatory networks (GRN) inferred from gene expression data are considered an important aid for this research by providing a map of molecular interactions. Hence, GRNs have the potential enabling and enhancing basic as well as applied research in the life sciences. In this paper, we introduce a new method called BC3NET for inferring causal gene regulatory networks from large-scale gene expression data. BC3NET is an ensemble method that is based on bagging the C3NET algorithm, which means it corresponds to a Bayesian approach with noninformative priors. In this study we demonstrate for a variety of simulated and biological gene expression data from S. cerevisiae that BC3NET is an important enhancement over other inference methods that is capable of capturing biochemical interactions from transcription regulation and protein-protein interaction sensibly. An implementation of BC3NET is freely available as an R package from the CRAN repository. © 2012 de Matos Simoes, Emmert-Streib.

Large‐scale wind deployment, social acceptance

The public is typically in agreement with the renewable energy targets established in many national states and generally supports the idea of increased reliance on wind energy. Nevertheless, many specific wind power projects face significant local opposition. A key question for the wind energy sector is, therefore, how to better engage local people to foster support for specific projects. IEA Wind Task 28 on Social Acceptance of Wind Energy Projects aims to facilitate wind energy development by reviewing current practices, emerging ideas, and exchanging successful practices among the participating countries. It also aims to disseminate the insights of leading research to a nontechnical audience, including project developers, local planning officials, and the general public. The interdisciplinary approach adopted by Task 28 enables an in-depth understanding of the nature of opposition to wind projects and a critical assessment of emerging strategies for social acceptance. Task 28 has analyzed a range of key issues related to social acceptance of wind energy, including the impacts on landscapes and ecosystems, on standard of living and well-being, the implementation of energy policy and spatial planning, the distribution of costs and benefits, and procedural justice. It is clear that although wind energy has many benefits; however, specific projects do impact local communities. As such the concerns of the affected people have to be taken seriously. Moreover, as opposition is rarely without foundation, it is in the interests of developers and advocates to engage local people and to improve projects for the benefit of all.

2DRMP-G: Migrating a large-scale numerical mathematical application to a grid environment

We report on the migration of a traditional, single architecture application to a grid application using heterogeneous resources. We focus on the use of the UK e-Science Level 2 grid (UKL2G) which provides a heterogeneous collection of resources distributed within the UK. We discuss the solution architecture, the performance of our application, its future development as a grid-based application and comment on the lessons we have learned in using a grid infrastructure for large-scale numerical problems.

The analysis of large-scale turbulence characteristics in the Indonesian seas derived from a regional model based on the Princeton Ocean Model

Turbulence characteristics in the Indonesian seas on the horizontal scale of order of 100 km were calculated with a regional model of the Indonesian seas circulation in the area based on the Princeton Ocean Model (POM). As is well known, the POM incorporates the Mellor–Yamada turbulence closure scheme. The calculated characteristics are: twice the turbulence kinetic energy per unit mass, <i>q</i>²; the turbulence master scale, &ell;; mixing coefficients of momentum, <i>K</i>_M; and temperature and salinity, <i>K</i>_H; etc. The analyzed turbulence has been generated essentially by the shear of large-scale ocean currents and by the large-scale wind turbulence. We focused on the analysis of turbulence around important topographic features, such as the Lifamatola Sill, the North Sangihe Ridge, the Dewakang Sill, and the North and South Halmahera Sea Sills. In general, the structure of turbulence characteristics in these regions turned out to be similar. For this reason, we have carried out a detailed analysis of the Lifamatola Sill region because dynamically this region is very important and some estimates of mixing coefficients in this area are available. <br><br> Briefly, the main results are as follows. The distribution of <i>q</i>² is quite adequately reproduced by the model. To the north of the Lifamatola Sill (in the Maluku Sea) and to the south of the Sill (in the Seram Sea), large values of <i>q</i>² occur in the deep layer extending several hundred meters above the bottom. The observed increase of <i>q</i>² near the very bottom is probably due to the increase of velocity shear and the corresponding shear production of <i>q</i>² very close to the bottom. The turbulence master scale, &ell;, was found to be constant in the main depth of the ocean, while &ell; rapidly decreases close to the bottom, as one would expect. However, in deep profiles away from the sill, the effect of topography results in the &ell; structure being unreasonably complicated as one moves towards the bottom. Values of 15 to 20 × 10^&minus;4 m² s^-1 were obtained for <i>K</i>_M and <i>K</i>_H in deep water in the vicinity of the Lifamatola Sill. These estimates agree well with basin-scale averaged values of 13.3 × 10^&minus;4 m² s^-1 found diagnostically for <i>K</i>_H in the deep Banda and Seram Seas (Gordon et al., 2003) and a value of 9.0 × 10^&minus;4 m² s^-1 found diagnostically for <i>K</i>_H for the deep Banda Sea system (van Aken et al., 1988). The somewhat higher simulated values can be explained by the presence of steep topography around the sill.

Preliminary results from follow-up of a large-scale population survey of antibodies to gliadin, reticulin and endomysium

Coeliac disease is often under-diagnosed, particularly in cases which are atypical or asymptomatic.

Cognitive, global, and functional benefits of donepezil in Alzheimer's disease and vascular dementia:results from large-scale clinical trials

Alzheimer's disease (AD) and vascular dementia (VaD) are both associated with deficits in cholinergic neurotransmission that are amenable to therapeutic intervention. The cholinesterase inhibitor, donepezil, is clinically effective in both AD and VaD. Results from a 10-study metaanalysis of donepezil (5 or 10 mg/day) in AD and a two-study combined analysis of donepezil (5 or 10 mg/day) in VaD are presented to compare patient characteristics and donepezil treatment outcomes. The analyzed studies were randomized, placebo-controlled, and of up to 24 weeks duration. In both AD and VaD, donepezil provided significant benefits compared with placebo on measures of cognition and global function. Placebo-treated AD patients showed a decline in cognition and global function, whereas placebo-treated VaD patients remained stable, suggesting treatment effects of donepezil in VaD were driven by improvement rather than stabilization or reduced decline. More VaD patients than AD patients received concomitant medications. Cardiovascular adverse events were more common in VaD than AD patients but were not increased by donepezil. In conclusion, although there are differences between AD and VaD patients in comorbid conditions and concomitant medications, donepezil is effective and well tolerated in both types of dementia.

Polycyclic aromatic hydrocarbon (PAH) dispersion and deposition to vegetation and soil following a large scale chemical fire

Polycyclic aromatic hydrocarbons (PAHs) were determined in soil and vegetation following a large scale chemical fire involving 10,000 ton of polypropylene. In comparison with sites outside the plume from the fire, PAH concentrations were elevated in grass shoots (by up to 70-fold) and in soil (by up to 370-fold). The pattern of PAH dispersion under the plume was dependent on the physical-chemical properties of individual PAHs. The lighter, least hydrophobic PAHs were dispersed into the environment at greater distances than heavier, more hydrophobic PAHs. At the most distant sampling point (4.5 km) under the plume, the low molecular weight PAHs were still considerably elevated in vegetation samples compared to control sites. Dispersion appeared to be regulated by the compounds partitioning between the vapour and particulate phase, with dry particulate deposition occurring closer to the fire source than gaseous deposition. For all PAHs, the fire resulted in greater contamination of soils compared to grasses, with the relative ratio of plant/soil contamination decreasing as hydrophobicity increased.

Dioxin and furan residues in wood mice (Apodemus sylvaticus) following a large scale polyvinyl chloride (PVC) fire

A forest ecosystem was contaminated as a result of a fire involving 600 t of PVC. A wide range of 2,3,7,8-substituted dioxin and furan congeners were elevated (by up to 4-fold) on soil adjacent to the factory compared to a site 200 m from the factory perimeter. Livers of wood mice (Apodemus sylvaticus) caught on these areas were also analysed for dioxins and furans. Toxic equivalents (TEQs) were 9-fold higher in wood mice caught on the site 10 m from the factory perimeter compared with the site 200 m from the perimeter, with individual 2,3,7,8-substituted congeners being elevated by up to 30-fold. Wood mouse liver TEQs were found to be highly correlated with cadmium kidney concentrations, cadmium also being found at elevated concentrations at the accident site. There was also a significant positive correlation between wood mouse liver TEQs and relative liver weights (wet weights expressed as a percentage of total body weight). The results of this study are discussed in the wider context of dioxin contamination in the environment.

Large Scale Verification of MPI Programs Using Lamport Clocks with Lazy Update

We propose a dynamic verification approach for large-scale message passing programs to locate correctness bugs caused by unforeseen nondeterministic interactions. This approach hinges on an efficient protocol to track the causality between nondeterministic message receive operations and potentially matching send operations. We show that causality tracking protocols that rely solely on logical clocks fail to capture all nuances of MPI program behavior, including the variety of ways in which nonblocking calls can complete. Our approach is hinged on formally defining the matches-before relation underlying the MPI standard, and devising lazy update logical clock based algorithms that can correctly discover all potential outcomes of nondeterministic receives in practice. can achieve the same coverage as a vector clock based algorithm while maintaining good scalability. LLCP allows us to analyze realistic MPI programs involving a thousand MPI processes, incurring only modest overheads in terms of communication bandwidth, latency, and memory consumption. © 2011 IEEE.

Collectives of diagnostic biomarkers identify high-risk subpopulations of hematuria patients: exploiting heterogeneity in large-scale biomarker data

Background: Ineffective risk stratification can delay diagnosis of serious disease in patients with hematuria. We applied a systems biology approach to analyze clinical, demographic and biomarker measurements (n = 29) collected from 157 hematuric patients: 80 urothelial cancer (UC) and 77 controls with confounding pathologies.

Methods: On the basis of biomarkers, we conducted agglomerative hierarchical clustering to identify patient and biomarker clusters. We then explored the relationship between the patient clusters and clinical characteristics using Chi-square analyses. We determined classification errors and areas under the receiver operating curve of Random Forest Classifiers (RFC) for patient subpopulations using the biomarker clusters to reduce the dimensionality of the data.

Results: Agglomerative clustering identified five patient clusters and seven biomarker clusters. Final diagnoses categories were non-randomly distributed across the five patient clusters. In addition, two of the patient clusters were enriched with patients with ‘low cancer-risk’ characteristics. The biomarkers which contributed to the diagnostic classifiers for these two patient clusters were similar. In contrast, three of the patient clusters were significantly enriched with patients harboring ‘high cancer-risk” characteristics including proteinuria, aggressive pathological stage and grade, and malignant cytology. Patients in these three clusters included controls, that is, patients with other serious disease and patients with cancers other than UC. Biomarkers which contributed to the diagnostic classifiers for the largest ‘high cancer- risk’ cluster were different than those contributing to the classifiers for the ‘low cancer-risk’ clusters. Biomarkers which contributed to subpopulations that were split according to smoking status, gender and medication were different.

Conclusions: The systems biology approach applied in this study allowed the hematuric patients to cluster naturally on the basis of the heterogeneity within their biomarker data, into five distinct risk subpopulations. Our findings highlight an approach with the promise to unlock the potential of biomarkers. This will be especially valuable in the field of diagnostic bladder cancer where biomarkers are urgently required. Clinicians could interpret risk classification scores in the context of clinical parameters at the time of triage. This could reduce cystoscopies and enable priority diagnosis of aggressive diseases, leading to improved patient outcomes at reduced costs. © 2013 Emmert-Streib et al; licensee BioMed Central Ltd.

Large-scale spatial patterns in the distribution of Collembola (Hexapoda) species in Antarctic terrestrial ecosystems

We tested whether the distribution of three common springtail species (Gressittacantha terranova, Gomphiocephalus hodgsoni and Friesea grisea) in Victoria Land (Antarctica) could be modelled as a function of latitude, longitude, altitude and distance from the sea.

Victoria Land, Ross Dependency, Antarctica.

Generalized linear models were constructed using species presence/absence data relative to geographical features (latitude, longitude, altitude, distance from sea) across the species' entire ranges. Model results were then integrated with the known phylogeography of each species and hypotheses were generated on the role of climate as a major driver of Antarctic springtail distribution.

Based on model selection using Akaike's information criterion, the species' distributions were: hump-shaped relative to longitude and monotonic with altitude for Gressittacantha terranova; hump-shaped relative to latitude and monotonic with altitude for Gomphiocephalus hodgsoni; and hump-shaped relative to longitude and monotonic with latitude, altitude and distance from the sea for Friesea grisea.

No single distributional pattern was shared by the three species. While distributions were partially a response to climatic spatial clines, the patterns observed strongly suggest that past geological events have influenced the observed distributions. Accordingly, present-day spatial patterns are likely to have arisen from the interaction of historical and environmental drivers. Future studies will need to integrate a range of spatial and temporal scales to further quantify their respective roles.

Coordinated Design of Phase Measurement Unit and Power System Stabilisers in Large Scale Power System

This paper presents a case-study of a PMU application with PSS support in a real large scale Chinese power system to suppress inter-area oscillations. The paper uses PMU measured feedback signals from a PSS input signal for dynamic torque analysis (DTA). In the paper, a mathematical model of multi-machine power system is described, followed by formation of the residue and DTA indices. Simulations of the model are used with a large-scale power system model to demonstrate the role of PSS and the equivalence of DTA residue indices.