Generating optimized Fourier interpolation routines for density function theory using SPIRAL

© 2015 IEEE.Upsampling of a multi-dimensional data-set is an operation with wide application in image processing and quantum mechanical calculations using density functional theory. For small up sampling factors as seen in the quantum chemistry code ONETEP, a time-shift based implementation that shifts samples by a fraction of the original grid spacing to fill in the intermediate values using a frequency domain Fourier property can be a good choice. Readily available highly optimized multidimensional FFT implementations are leveraged at the expense of extra passes through the entire working set. In this paper we present an optimized variant of the time-shift based up sampling. Since ONETEP handles threading, we address the memory hierarchy and SIMD vectorization, and focus on problem dimensions relevant for ONETEP. We present a formalization of this operation within the SPIRAL framework and demonstrate auto-generated and auto-tuned interpolation libraries. We compare the performance of our generated code against the previous best implementations using highly optimized FFT libraries (FFTW and MKL). We demonstrate speed-ups in isolation averaging 3x and within ONETEP of up to 15%

Exploiting the chaotic behaviour of atmospheric models with reconfigurable architectures

Reconfigurable architectures are becoming mainstream: Amazon, Microsoft and IBM are supporting such architectures in their data centres. The computationally intensive nature of atmospheric modelling is an attractive target for hardware acceleration using reconfigurable computing. Performance of hardware designs can be improved through the use of reduced-precision arithmetic, but maintaining appropriate accuracy is essential. We explore reduced-precision optimisation for simulating chaotic systems, targeting atmospheric modelling, in which even minor changes in arithmetic behaviour will cause simulations to diverge quickly. The possibility of equally valid simulations having differing outcomes means that standard techniques for comparing numerical accuracy are inappropriate. We use the Hellinger distance to compare statistical behaviour between reduced-precision CPU implementations to guide reconfigurable designs of a chaotic system, then analyse accuracy, performance and power efficiency of the resulting implementations. Our results show that with only a limited loss in accuracy corresponding to less than 10% uncertainty in input parameters, the throughput and energy efficiency of a single-precision chaotic system implemented on a Xilinx Virtex-6 SX475T Field Programmable Gate Array (FPGA) can be more than doubled

The bearable lightness of being

How are philosophical questions about what kinds of things there are to be understood and how are they to be answered? This paper defends broadly Fregean answers to these questions. Ontological categories-such as object, property, and relation-are explained in terms of a prior logical categorization of expressions, as singular terms, predicates of varying degree and level, etc. Questions about what kinds of object, property, etc., there are are, on this approach, reduce to questions about truth and logical form: for example, the question whether there are numbers is the question whether there are true atomic statements in which expressions function as singular terms which, if they have reference at all, stand for numbers, and the question whether there are properties of a given type is a question about whether there are meaningful predicates of an appropriate degree and level. This approach is defended against the objection that it must be wrong because makes what there depend on us or our language. Some problems confronting the Fregean approach-including Frege's notorious paradox of the concept horse-are addressed. It is argued that the approach results in a modest and sober deflationary understanding of ontological commitments

Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain

Protein-protein interactions, particularly weak and transient ones, are often mediated by peptide recognition domains, such as Src Homology 2 and 3 (SH2 and SH3) domains, which bind to specific sequence and structural motifs. It is important but challenging to determine the binding specificity of these domains accurately and to predict their physiological interacting partners. In this study, the interactions between 35 peptide ligands (15 binders and 20 non-binders) and the Abl SH3 domain were analyzed using molecular dynamics simulation and the Molecular Mechanics/Poisson-Boltzmann Solvent Area method. The calculated binding free energies correlated well with the rank order of the binding peptides and clearly distinguished binders from non-binders. Free energy component analysis revealed that the van der Waals interactions dictate the binding strength of peptides, whereas the binding specificity is determined by the electrostatic interaction and the polar contribution of desolvation. The binding motif of the Abl SH3 domain was then determined by a virtual mutagenesis method, which mutates the residue at each position of the template peptide relative to all other 19 amino acids and calculates the binding free energy difference between the template and the mutated peptides using the Molecular Mechanics/Poisson-Boltzmann Solvent Area method. A single position mutation free energy profile was thus established and used as a scoring matrix to search peptides recognized by the Abl SH3 domain in the human genome. Our approach successfully picked ten out of 13 experimentally determined binding partners of the Abl SH3 domain among the top 600 candidates from the 218,540 decapeptides with the PXXP motif in the SWISS-PROT database. We expect that this physical-principle based method can be applied to other protein domains as well

Accreting Millisecond X-Ray Pulsars

Accreting Millisecond X-Ray Pulsars (AMXPs) are astrophysical laboratories without parallel in the study of extreme physics. In this chapter we review the past fifteen years of discoveries in the field. We summarize the observations of the fifteen known AMXPs, with a particular emphasis on the multi-wavelength observations that have been carried out since the discovery of the first AMXP in 1998. We review accretion torque theory, the pulse formation process, and how AMXP observations have changed our view on the interaction of plasma and magnetic fields in strong gravity. We also explain how the AMXPs have deepened our understanding of the thermonuclear burst process, in particular the phenomenon of burst oscillations. We conclude with a discussion of the open problems that remain to be addressed in the future.Comment: Review to appear in "Timing neutron stars: pulsations, oscillations and explosions", T. Belloni, M. Mendez, C.M. Zhang Eds., ASSL, Springer; [revision with literature updated, several typos removed, 1 new AMXP added

Population health status of South Asian and African-Caribbean communities in the United Kingdom

Population health status scores are routinely used to inform economic evaluation and evaluate the impact of disease and/or treatment on health. It is unclear whether the health status in black and minority ethnic groups are comparable to these population health status data. The aim of this study was to evaluate health-status in South Asian and African-Caribbean populations

Researchers’ attitudes to the 3Rs - An upturned hierarchy?

Animal use in biomedical research is generally justified by its potential benefits to the health of humans, or other animals, or the environment. However, ethical acceptability also requires scientists to limit harm to animals in their research. Training in laboratory animal science (LAS) helps scientists to do this by promoting best practice and the 3Rs. This study evaluated scientists’ awareness and application of the 3Rs, and their approach to other ethical issues in animal research. It was based on an online survey of participants in LAS courses held in eight venues in four European countries: Portugal (Porto, Braga), Germany (Munich, Heidelberg), Switzerland (Basel, Lausanne, Zurich), and Denmark (Copenhagen). The survey questions were designed to assess general attitudes to animal use in biomedical research, Replacement alternatives, Reduction and Refinement conflicts, and harm-benefit analysis. The survey was conducted twice: immediately before the course (‘BC’, N = 310) and as a follow-up six months after the course (‘AC’, N = 127). While courses do appear to raise awareness of the 3Rs, they had no measurable effect on the existing low level of belief that animal experimentation can be fully replaced by non-animal methods. Most researchers acknowledged ethical issues with their work and reported that they discussed these with their peers. The level of an animal’s welfare, and especially the prevention of pain, was regarded as the most pressing ethical issue, and as more important than the number of animals used or the use of animals as such. Refinement was considered more feasible than Replacement, as well as more urgent, and was also favoured over Reduction. Respondents in the survey reversed the ‘hierarchy’ of the 3Rs proposed by their architects, Russell and Burch, prioritizing Refinement over Reduction, and Reduction over Replacement. This ordering may conflict with the expectations of the public and regulators.</div

Increasing genome instability in adrenocortical carcinoma progression with involvement of chromosomes 3, 9 and X at the adenoma stage

The investigation of chromosomal aberrations in adrenocortical tumours has been limited by the difficulties of applying classical cytogenetics to tumours with low levels of proliferation. We have therefore applied the technique of interphase cytogenetics to paraffin-embedded archival specimens of 14 adrenocortical adenomas and 13 carcinomas. Hybridizations were performed using centromere-specific probes to chromosomes 3, 4, 9, 17, 18 and X, which have been shown to be altered in other types of tumours. Chromosomal imbalance was defined on the basis of changes in both chromosome index (CI) and signal distribution (SD). Where only one of these was altered, this was classified as a tendency to gain or loss. On the basis of the analysis of optimal hybridizations, carcinomas showed gains in all chromosomes studied, five of nine showing gains in multiple chromosomes. Gains were most common in chromosomes 3, 9 and, in particular X, eight of 11 showing gain, and one a tendency to gain. Chromosomal gain was seen less commonly in adenomas, but again chromosomes 3, 9 and X were involved. Losses were infrequent, only one carcinoma showing loss of chromosome 18, and adenomas showing a tendency to loss of chromosomes 4 (two cases), 17 (one case) and 18 (two cases). Our data suggest that changes in chromosomes 3, 9 and X are early events in adrenocortical tumorigenesis, and that there is increasing chromosomal instability with tumour progression. © 1999 Cancer Research Campaig