Principles for automated and reproducible benchmarking

The diversity in processor technology used by High Performance Computing (HPC) facilities is growing, and so applications must be written in such a way that they can attain high levels of performance across a range of different CPUs, GPUs, and other accelerators. Measuring application performance across this wide range of platforms becomes crucial, but there are significant challenges to do this rigorously, in a time efficient way, whilst assuring results are scientifically meaningful, reproducible, and actionable. This paper presents a methodology for measuring and analysing the performance portability of a parallel application and shares a software framework which combines and extends adopted technologies to provide a usable benchmarking tool. We demonstrate the flexibility and effectiveness of the methodology and benchmarking framework by showcasing a variety of benchmarking case studies which utilise a stable of supercomputing resources at a national scale

Limiting Similarity Revisited

We reinvestigate the validity of the limiting similarity principle via numerical simulations of the Lotka-Volterra model. A Gaussian competition kernel is employed to describe decreasing competition with increasing difference in a one-dimensional phenotype variable. The simulations are initiated by a large number of species, evenly distributed along the phenotype axis. Exceptionally, the Gaussian carrying capacity supports coexistence of all species, initially present. In case of any other, distinctly different, carrying capacity functions, competition resulted in extinction of all, but a few species. A comprehensive study of classes of fractal-like carrying capacity functions with different fractal exponents was carried out. The average phenotype differences between surviving species were found to be roughly equal to the competition width. We conclude that, despite the existence of exceptional cases, the classical picture of limiting similarity and niche segregation is a good rule of thumb for practical purposes

Newsletter Networks in the Feminist History and Archives Movement

This article examines how networks have been critical to the construction of feminist histories. The author examines the publication Matrices: A Lesbian/Feminist Research Newsletter (1977–1996), to argue that a feminist network mode can be traced through the examination of small-scale print newsletters that draw on the language and function of networks. Publications such as Matrices emerge into wide production and circulation in the 1970s alongside feminist community archives, and newsletters and archives work together as interconnected social movement technologies. Newsletters enabled activist-researchers writing feminist histories to share difficult-to-access information, resources, and primary sources via photocopying and other modes of print reproduction.  Looking from the present, the author examines how network thinking has been a feature of feminist activism and knowledge production since before the Internet, suggesting that publications such as Matrices are part of a longer history of networked communications media in feminist contexts

Cyclic competition of four species: domains and interfaces

We study numerically domain growth and interface fluctuations in one- and two-dimensional lattice systems composed of four species that interact in a cyclic way. Particle mobility is implemented through exchanges of particles located on neighboring lattice sites. For the chain we find that domain growth strongly depends on the mobility, with a higher mobility yielding a larger domain growth exponent. In two space dimensions, when also exchanges between mutually neutral particles are possible, both domain growth and interface fluctuations display universal regimes that are independent of the predation and exchange rates.Comment: 14 pages, 7 figures, version accepted for publication in J. Stat. Mec

Co-Swarming and Local Collapse: Quorum Sensing Conveys Resilience to Bacterial Communities by Localizing Cheater Mutants in Pseudomonas aeruginosa

Background: Members of swarming bacterial consortia compete for nutrients but also use a co-operation mechanism called quorum sensing (QS) that relies on chemical signals as well as other secreted products (‘‘public goods’’) necessary for swarming. Deleting various genes of this machinery leads to cheater mutants impaired in various aspects of swarming cooperation. Methodology/Principal Findings: Pairwise consortia made of Pseudomonas aeruginosa, its QS mutants as well as B. cepacia cells show that a interspecies consortium can ‘‘combine the skills’ ’ of its participants so that the strains can cross together barriers that they could not cross alone. In contrast, deleterious mutants are excluded from consortia either by competition or by local population collapse. According to modeling, both scenarios are the consequence of the QS signalling mechanism itself. Conclusion/Significance: The results indirectly explain why it is an advantage for bacteria to maintain QS systems that can cross-talk among different species, and conversely, why certain QS mutants which can be abundant in isolated niches

Microelectrode records from a cockroach thoracic ganglion: Synaptic potentials and temporal patterns of spike activity

1. 1. E.p.s.p.s and i.p.s.p.s + were recorded from cells in the cockroach third thoracic ganglion, using microcapillary electrodes filled with 3 M KCl.2. 2. Spike response patterns indicating complex integrative activities at the single cell level were also recorded.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/32924/1/0000306.pd

CFTR Functions as a Bicarbonate Channel in Pancreatic Duct Cells

Pancreatic duct epithelium secretes a HCO3−-rich fluid by a mechanism dependent on cystic fibrosis transmembrane conductance regulator (CFTR) in the apical membrane. However, the exact role of CFTR remains unclear. One possibility is that the HCO3− permeability of CFTR provides a pathway for apical HCO3− efflux during maximal secretion. We have therefore attempted to measure electrodiffusive fluxes of HCO3− induced by changes in membrane potential across the apical membrane of interlobular ducts isolated from the guinea pig pancreas. This was done by recording the changes in intracellular pH (pHi) that occurred in luminally perfused ducts when membrane potential was altered by manipulation of bath K+ concentration. Apical HCO3− fluxes activated by cyclic AMP were independent of Cl− and luminal Na+, and substantially inhibited by the CFTR blocker, CFTRinh-172. Furthermore, comparable HCO3− fluxes observed in ducts isolated from wild-type mice were absent in ducts from cystic fibrosis (ΔF) mice. To estimate the HCO3− permeability of the apical membrane under physiological conditions, guinea pig ducts were luminally perfused with a solution containing 125 mM HCO3− and 24 mM Cl− in the presence of 5% CO2. From the changes in pHi, membrane potential, and buffering capacity, the flux and electrochemical gradient of HCO3− across the apical membrane were determined and used to calculate the HCO3− permeability. Our estimate of ∼0.1 µm sec−1 for the apical HCO3− permeability of guinea pig duct cells under these conditions is close to the value required to account for observed rates of HCO3− secretion. This suggests that CFTR functions as a HCO3− channel in pancreatic duct cells, and that it provides a significant pathway for HCO3− transport across the apical membrane

Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP

Disease-associated SNPs detected in large-scale association studies are frequently located in non-coding genomic regions, suggesting that they may be involved in transcriptional regulation. Here we describe a new strategy for detecting regulatory SNPs (rSNPs), by combining computational and experimental approaches. Whole genome ChIP-chip data for USF1 was analyzed using a novel motif finding algorithm called BCRANK. 1754 binding sites were identified and 140 candidate rSNPs were found in the predicted sites. For validating their regulatory function, seven SNPs found to be heterozygous in at least one of four human cell samples were investigated by ChIP and sequence analysis (haploChIP). In four of five cases where the SNP was predicted to affect binding, USF1 was preferentially bound to the allele containing the consensus motif. Allelic differences in binding for other proteins and histone marks further reinforced the SNPs regulatory potential. Moreover, for one of these SNPs, H3K36me3 and POLR2A levels at neighboring heterozygous SNPs indicated effects on transcription. Our strategy, which is entirely based on in vivo data for both the prediction and validation steps, can identify individual binding sites at base pair resolution and predict rSNPs. Overall, this approach can help to pinpoint the causative SNPs in complex disorders where the associated haplotypes are located in regulatory regions. Availability: BCRANK is available from Bioconductor (http://www.bioconductor.org/)

The role of adaptive trans-generational plasticity in biological invasions of plants

High-impact biological invasions often involve establishment and spread in disturbed, high-resource patches followed by establishment and spread in biotically or abiotically stressful areas. Evolutionary change may be required for the second phase of invasion (establishment and spread in stressful areas) to occur. When species have low genetic diversity and short selection history, within-generation phenotypic plasticity is often cited as the mechanism through which spread across multiple habitat types can occur. We show that trans-generational plasticity (TGP) can result in pre-adapted progeny that exhibit traits associated with increased fitness both in high-resource patches and in stressful conditions. In the invasive sedge, Cyperus esculentus, maternal plants growing in nutrient-poor patches can place disproportional number of propagules into nutrient-rich patches. Using the invasive annual grass, Aegilops triuncialis, we show that maternal response to soil conditions can confer greater stress tolerance in seedlings in the form of greater photosynthetic efficiency. We also show TGP for a phenological shift in a low resource environment that results in greater stress tolerance in progeny. These lines of evidence suggest that the maternal environment can have profound effects on offspring success and that TGP may play a significant role in some plant invasions