Array languages and the N-body problem

This paper is a description of the contributions to the SICSA multicore challenge on many body planetary simulation made by a compiler group at the University of Glasgow. Our group is part of the Computer Vision and Graphics research group and we have for some years been developing array compilers because we think these are a good tool both for expressing graphics algorithms and for exploiting the parallelism that computer vision applications require. We shall describe experiments using two languages on two different platforms and we shall compare the performance of these with reference C implementations running on the same platforms. Finally we shall draw conclusions both about the viability of the array language approach as compared to other approaches used in the challenge and also about the strengths and weaknesses of the two, very different, processor architectures we used

Mainstream parallel array programming on cell

We present the E] compiler and runtime library for the ‘F’ subset of the Fortran 95 programming language. ‘F’ provides first-class support for arrays, allowing E] to implicitly evaluate array expressions in parallel using the SPU coprocessors of the Cell Broadband Engine. We present performance results from four benchmarks that all demonstrate absolute speedups over equivalent ‘C’ or Fortran versions running on the PPU host processor. A significant benefit of this straightforward approach is that a serial implementation of any code is always available, providing code longevity, and a familiar development paradigm

Pulmonary vasospasm in systemic sclerosis: noninvasive techniques for detection

In a subgroup of patients with systemic sclerosis (SSc), vasospasm affecting the pulmonary circulation may contribute to worsening respiratory symptoms, including dyspnea. Noninvasive assessment of pulmonary blood flow (PBF), utilizing inert-gas rebreathing (IGR) and dual-energy computed-tomography pulmonary angiography (DE-CTPA), may be useful for identifying pulmonary vasospasm. Thirty-one participants (22 SSc patients and 9 healthy volunteers) underwent PBF assessment with IGR and DE-CTPA at baseline and after provocation with a cold-air inhalation challenge (CACh). Before the study investigations, participants were assigned to subgroups: group A included SSc patients who reported increased breathlessness after exposure to cold air (n = 11), group B included SSc patients without cold-air sensitivity (n = 11), and group C patients included the healthy volunteers. Median change in PBF from baseline was compared between groups A, B, and C after CACh. Compared with groups B and C, in group A there was a significant decline in median PBF from baseline at 10 minutes (−10%; range: −52.2% to 4.0%; P < 0.01), 20 minutes (−17.4%; −27.9% to 0.0%; P < 0.01), and 30 minutes (−8.5%; −34.4% to 2.0%; P < 0.01) after CACh. There was no significant difference in median PBF change between groups B or C at any time point and no change in pulmonary perfusion on DE-CTPA. Reduction in pulmonary blood flow following CACh suggests that pulmonary vasospasm may be present in a subgroup of patients with SSc and may contribute to worsening dyspnea on exposure to cold

Treatment response in relation to inflammatory and axonal surrogate marker in multiple sclerosis

BACKGROUND: This study aimed to investigate if treatment response could retrospectively be related to inflammatory or axonal pathology as measured by plasma surrogate markers. METHODS: In this 1-year observational study 30 multiple sclerosis (MS) patients with relapsing-remitting disease were treated with intramuscular IFNbeta-1a or subcutaneous IFNbeta-1b. Responders and nonresponders were defined according to clinical and magnetic resonance imaging criteria. The control group consisted of 14 healthy subjects. Plasma levels of surrogate markers for inflammation (nitric oxide metabolites (NOx)), astrocytic activation (S100B) and axonal damage (NfH(SM135)) were measured using standard assays. RESULTS: There were 11 nonresponders and 19 responders to IFNbeta treatment. Median S100B levels were elevated in a higher proportion of treatment responders (63%, 42.9 pg/mL) compared to nonresponders (18%, 11.7 pg/mL, P < 0.05, Fisher's exact test) and controls (0%, 2 pg/mL, P < 0.001). Levels of NOx were found to be more frequently elevated in nonresponders (72%, 39 microM) compared to healthy controls (0%, 37 microM, P < 0.05). Levels of NfH(SM135) were more frequently elevated in responders (58%, 300 pg/mL, P < 0.001) and nonresponders (72%, 500 pg/mL, P < 0.001) compared to controls (0%, 4.5 pg/mL). CONCLUSION: Patients with relapsing-remitting MS who had surrogate marker supported evidence for astrocytic activation responded more frequently to treatment with IFNbeta

Using Stable Isotope Analyses to Assess the Trophic Ecology of Scleractinian Corals

Studies on the trophic ecology of scleractinian corals often include stable isotope analyses of tissue and symbiont carbon and nitrogen. These approaches have provided critical insights into the trophic sources and sinks that are essential to understanding larger-scale carbon and nitrogen budgets on coral reefs. While stable isotopes have identified most shallow water (\u3c30 m) corals as mixotrophic, with variable dependencies on autotrophic versus heterotrophic resources, corals in the mesophotic zone (~30–150 m) transition to heterotrophy with increasing depth because of decreased photosynthetic productivity. Recently, these interpretations of the stable isotope data to distinguish between autotrophy and heterotrophy have been criticized because they are confounded by increased nutrients, reverse translocation of photosynthate, and changes in irradiance that do not influence photosynthate translocation. Here we critically examine the studies that support these criticisms and show that they are contextually not relevant to interpreting the transition to heterotrophy in corals from shallow to mesophotic depths. Additionally, new data and a re-analysis of previously published data show that additional information (e.g., skeletal isotopic analysis) improves the interpretation of bulk stable isotope data in determining when a transition from primary dependence on autotrophy to heterotrophy occurs in scleractinian corals

Stable Isotopes of Water Vapor in the Vadose Zone: A Review of Measurement and Modeling Techniques

Author's manuscript made available in accordance with the publisher's policy.The stable isotopes of soil water vapor can be useful in the study of ecosystem processes. Modeling has historically dominated the measurement of these parameters due to sampling difficulties. We discuss new developments in modeling and measurement, including the implications of including soil water potential in the Craig–Gordon modeling framework. The stable isotopes of soil water vapor are useful tracers of hydrologic processes occurring in the vadose zone. The measurement of soil water vapor isotopic composition (δ18O, δ2H) is challenging due to difficulties inherent in sampling the vadose zone airspace in situ. Historically, these parameters have therefore been modeled, as opposed to directly measured, and typically soil water vapor is treated as being in isotopic equilibrium with liquid soil water. We reviewed the measurement and modeling of soil water vapor isotopes, with implications for studies of the soil–plant–atmosphere continuum. We also investigated a case study with in situ measurements from a soil profile in a semiarid African savanna, which supports the assumption of liquid–vapor isotopic equilibrium. A contribution of this work is to introduce the effect of soil water potential (Ѱ) on kinetic fractionation during soil evaporation within the Craig–Gordon modeling framework. Including Ѱ in these calculations becomes important for relatively dry soils (Ѱ < −10 MPa). Additionally, we assert that the recent development of laser-based isotope analytical systems may allow regular in situ measurement of the vadose zone isotopic composition of water in the vapor phase. Wet soils pose particular sampling difficulties, and novel techniques are being developed to address these issues

Uncertainties in the assessment of the isotopic composition of surface fluxes: A direct comparison of techniques using laser-based water vapor isotope analyzers

Author's manuscript made available in accordance with the publisher's policy.The isotopic composition of surface fluxes is a key environmental tracer currently estimated with a variety of methods, including: Keeling mixing models, the flux-gradient technique, and eddy covariance. We present a direct inter-comparison of these three methods used to estimate the isotopic ratio of water vapor in surface fluxes (δET) over half-hour periods, with a focus on the statistical uncertainty of each method image We develop expressions for image a function of instrument precision, sample size, and atmospheric conditions. Uncertainty estimators are validated with high frequency (1 Hz) data from multiple configurations of commercial off-axis integrated cavity output spectroscopy (ICOS) systems. We find measurement techniques utilizing the high frequency capabilities of ICOS system outperform those methods where a single average of the isotopic composition is obtained at each height, with improvements attributed to large sample counts and increased variation in observed concentrations. Analytically, and with supporting data, we show that over 30 minute periods the Keeling plot and flux-gradient techniques produce nearly identicalδET and image values, while eddy covariance calculations always introduce more uncertainty given the same high frequency data. This additional uncertainty is proportional to the reciprocal of the correlation coefficient between vertical wind speed and water vapor mixing ratio. Finally, given the inverse relationship between δET uncertainties and the range of water vapor observed, we propose that experimental designs should attempt to maximize both sample count and the coefficient of variation in atmospheric water vapor

Disease Knowledge Transfer across Neurodegenerative Diseases

We introduce Disease Knowledge Transfer (DKT), a novel technique for transferring biomarker information between related neurodegenerative diseases. DKT infers robust multimodal biomarker trajectories in rare neurodegenerative diseases even when only limited, unimodal data is available, by transferring information from larger multimodal datasets from common neurodegenerative diseases. DKT is a joint-disease generative model of biomarker progressions, which exploits biomarker relationships that are shared across diseases. Our proposed method allows, for the first time, the estimation of plausible, multimodal biomarker trajectories in Posterior Cortical Atrophy (PCA), a rare neurodegenerative disease where only unimodal MRI data is available. For this we train DKT on a combined dataset containing subjects with two distinct diseases and sizes of data available: 1) a larger, multimodal typical AD (tAD) dataset from the TADPOLE Challenge, and 2) a smaller unimodal Posterior Cortical Atrophy (PCA) dataset from the Dementia Research Centre (DRC), for which only a limited number of Magnetic Resonance Imaging (MRI) scans are available. Although validation is challenging due to lack of data in PCA, we validate DKT on synthetic data and two patient datasets (TADPOLE and PCA cohorts), showing it can estimate the ground truth parameters in the simulation and predict unseen biomarkers on the two patient datasets. While we demonstrated DKT on Alzheimer's variants, we note DKT is generalisable to other forms of related neurodegenerative diseases. Source code for DKT is available online: https://github.com/mrazvan22/dkt.Comment: accepted at MICCAI 2019, 13 pages, 5 figures, 2 table

Growth and feeding in the sponge Agelas tubulata from shallow to mesophotic depths on Grand Cayman Island

On Caribbean coral reefs, sponges are important members of the benthic community and play multiple roles in ecosystem structure and function. They have an important role in benthic-pelagic coupling, consuming particulate organic matter (POM) and dissolved organic matter (DOM) and in turn providing food in the form of sponge biomass or the release of detritus for a variety of coral reef organisms. Throughout the Caribbean, sponges show consistent increases in their abundance and growth rates as depth increases into the mesophotic zone (30–150 m). This has been hypothesized to be driven by bottom-up forces, particularly the increased supply of nitrogen-rich POM in mesophotic coral reef ecosystems (MCEs). Here, we tested the hypothesis that the sponge, Agelas tubulata, exhibits increased growth rates on MCEs relative to shallow reefs on Grand Cayman Island and that this is driven by bottom-up forcing. We observed increased growth rates in mesophotic A. tubulata, compared with shallow conspecifics, despite variability in feeding on both POM and DOM. Mesophotic sponges, however, were consistently exposed to greater amounts of POM, which was seasonally variable unlike DOM. Changes in stable isotopic signatures, and higher feeding rates with increasing depth, were consistent with increasing rates of growth in sponges as depth increases. These observations support the hypothesis that mesophotic sponges have higher growth rates due to increased POM availability and consumption over time. The results of this study illustrate the crucial role that bottom-up forcing has in the structuring of sponge communities on both shallow and mesophotic Caribbean coral reefs and the importance of POM as a source of nitrogen in sponge diets