| 1. |
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| 2. |
- Abelev, Betty, et al.
(författare)
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Measurement of prompt J/psi and beauty hadron production cross sections at mid-rapidity in pp collisions at root s=7 TeV
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- The ALICE experiment at the LHC has studied J/psi production at mid-rapidity in pp collisions at root s = 7 TeV through its electron pair decay on a data sample corresponding to an integrated luminosity L-int = 5.6 nb(-1). The fraction of J/psi from the decay of long-lived beauty hadrons was determined for J/psi candidates with transverse momentum p(t) > 1,3 GeV/c and rapidity vertical bar y vertical bar < 0.9. The cross section for prompt J/psi mesons, i.e. directly produced J/psi and prompt decays of heavier charmonium states such as the psi(2S) and chi(c) resonances, is sigma(prompt J/psi) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 8.3 +/- 0.8(stat.) +/- 1.1 (syst.)(-1.4)(+1.5) (syst. pol.) mu b. The cross section for the production of b-hadrons decaying to J/psi with p(t) > 1.3 GeV/c and vertical bar y vertical bar < 0.9 is a sigma(J/psi <- hB) (p(t) > 1.3 GeV/c, vertical bar y vertical bar < 0.9) = 1.46 +/- 0.38 (stat.)(-0.32)(+0.26) (syst.) mu b. The results are compared to QCD model predictions. The shape of the p(t) and y distributions of b-quarks predicted by perturbative QCD model calculations are used to extrapolate the measured cross section to derive the b (b) over bar pair total cross section and d sigma/dy at mid-rapidity.
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| 3. |
- Abelev, Betty, et al.
(författare)
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Underlying Event measurements in pp collisions at root s=0.9 and 7 TeV with the ALICE experiment at the LHC
- 2012
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Ingår i: Journal of High Energy Physics. - 1029-8479. ; :7
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Tidskriftsartikel (refereegranskat)abstract
- We present measurements of Underlying Event observables in pp collisions at root s = 0 : 9 and 7 TeV. The analysis is performed as a function of the highest charged-particle transverse momentum p(T),L-T in the event. Different regions are defined with respect to the azimuthal direction of the leading (highest transverse momentum) track: Toward, Transverse and Away. The Toward and Away regions collect the fragmentation products of the hardest partonic interaction. The Transverse region is expected to be most sensitive to the Underlying Event activity. The study is performed with charged particles above three different p(T) thresholds: 0.15, 0.5 and 1.0 GeV/c. In the Transverse region we observe an increase in the multiplicity of a factor 2-3 between the lower and higher collision energies, depending on the track p(T) threshold considered. Data are compared to PYTHIA 6.4, PYTHIA 8.1 and PHOJET. On average, all models considered underestimate the multiplicity and summed p(T) in the Transverse region by about 10-30%.
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| 4. |
- Beal, Jacob, et al.
(författare)
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Robust estimation of bacterial cell count from optical density
- 2020
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Ingår i: Communications Biology. - : Springer Science and Business Media LLC. - 2399-3642. ; 3:1
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Tidskriftsartikel (refereegranskat)abstract
- Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data.
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| 5. |
- Klionsky, Daniel J., et al.
(författare)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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Ingår i: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Forskningsöversikt (refereegranskat)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 6. |
- Kanai, M, et al.
(författare)
-
- 2023
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swepub:Mat__t
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| 7. |
- Abolfathi, Bela, et al.
(författare)
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The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment
- 2018
-
Ingår i: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2
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Tidskriftsartikel (refereegranskat)abstract
- The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
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| 8. |
- Aguilar, Edgar A., et al.
(författare)
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Certifying an Irreducible 1024-Dimensional Photonic State Using Refined Dimension Witnesses
- 2018
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Ingår i: Physical Review Letters. - : AMER PHYSICAL SOC. - 0031-9007 .- 1079-7114. ; 120:23
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Tidskriftsartikel (refereegranskat)abstract
- We report on a new class of dimension witnesses, based on quantum random access codes, which are a function of the recorded statistics and that have different bounds for all possible decompositions of a high-dimensional physical system. Thus, it certifies the dimension of the system and has the new distinct feature of identifying whether the high-dimensional system is decomposable in terms of lower dimensional subsystems. To demonstrate the practicability of this technique, we used it to experimentally certify the generation of an irreducible 1024-dimensional photonic quantum state. Therefore, certifying that the state is not multipartite or encoded using noncoupled different degrees of freedom of a single photon. Our protocol should find applications in a broad class of modern quantum information experiments addressing the generation of high-dimensional quantum systems, where quantum tomography may become intractable.
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| 9. |
- Aguilar, Helena, et al.
(författare)
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VAV3 mediates resistance to breast cancer endocrine therapy
- 2014
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Ingår i: Breast Cancer Research. - : BioMed Central. - 1465-5411 .- 1465-542X. ; 16:3, s. R53-
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Tidskriftsartikel (refereegranskat)abstract
- INTRODUCTION: Endocrine therapies targeting cell proliferation and survival mediated by estrogen receptor alpha (ERalpha) are among the most effective systemic treatments for ERalpha-positive breast cancer. However, most tumors initially responsive to these therapies acquire resistance through mechanisms that involve ERalpha transcriptional regulatory plasticity. Here, we identify VAV3 as a critical component in this process.METHODS: A cell-based chemical compound screen was carried out to identify therapeutic strategies against resistance to endocrine therapy. Binding to ERalpha was evaluated by molecular docking analyses, an agonist fluoligand assay, and short-hairpin (sh) RNA-mediated protein depletion. Microarray analyses were performed to identify altered gene expression. Western blot of signaling and proliferation markers and shRNA-mediated protein depletion in viability and clonogenic assays were performed to delineate the role of VAV3. Genetic variation in VAV3 was assessed for association with the response to tamoxifen. Immunohistochemical analyses of VAV3 were carried out to determine the association with therapy response and different tumor markers. An analysis of gene expression association with drug sensitivity was carried out to identify a potential therapeutic approach based on differential VAV3 expression.RESULTS: The compound YC-1 was found to comparatively reduce the viability of cell models of acquired resistance. This effect was probably not due to activation of its canonical target (soluble guanylyl cyclase) but instead a result of binding to ERalpha. VAV3 was selectively reduced upon exposure to YC-1 or ERalpha depletion and, accordingly, VAV3 depletion comparatively reduced the viability of cell models of acquired resistance. In the clinical scenario, germline variation in VAV3 was associated with response to tamoxifen in Japanese breast cancer patients (rs10494071 combined P value = 8.4 x 10-4). The allele association combined with gene expression analyses indicated that low VAV3 expression predicts better clinical outcome. Conversely, high nuclear VAV3 expression in tumor cells was associated with poorer endocrine therapy response. Based on VAV3 expression levels and the response to erlotinib in cancer cell lines, targeting EGFR signaling may be a promising therapeutic strategy.CONCLUSIONS: This study proposes VAV3 as a biomarker and rationale signaling target to prevent and/or overcome resistance to endocrine therapy in breast cancer.
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| 10. |
- Aguilar, Xavier, et al.
(författare)
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A Deep Learning-Based Particle-in-Cell Method for Plasma Simulations
- 2021
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Ingår i: 2021 IEEE International Conference On Cluster Computing (CLUSTER 2021). - : Institute of Electrical and Electronics Engineers (IEEE). ; , s. 692-697
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Konferensbidrag (refereegranskat)abstract
- We design and develop a new Particle-in-Cell (PIC) method for plasma simulations using Deep-Learning (DL) to calculate the electric field from the electron phase space. We train a Multilayer Perceptron (MLP) and a Convolutional Neural Network (CNN) to solve the two-stream instability test. We verify that the DL-based MLP PIC method produces the correct results using the two-stream instability: the DL-based PIC provides the expected growth rate of the two-stream instability. The DL-based PIC does not conserve the total energy and momentum. However, the DL-based PIC method is stable against the cold-beam instability, affecting traditional PIC methods. This work shows that integrating DL technologies into traditional computational methods is a viable approach for developing next-generation PIC algorithms.
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| 11. |
- Aguilar, Xavier, et al.
(författare)
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An On-Line Performance Introspection Framework for Task-Based Runtime Systems
- 2019
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Ingår i: 19th International Conference on Computational Science, ICCS 2019. - Cham : Springer Verlag. - 9783030227333 ; , s. 238-252
-
Konferensbidrag (refereegranskat)abstract
- The expected high levels of parallelism together with the heterogeneity and complexity of new computing systems pose many challenges to current software. New programming approaches and runtime systems that can simplify the development of parallel applications are needed. Task-based runtime systems have emerged as a good solution to cope with high levels of parallelism, while providing software portability, and easing program development. However, these runtime systems require real-time information on the state of the system to properly orchestrate program execution and optimise resource utilisation. In this paper, we present a lightweight monitoring infrastructure developed within the AllScale Runtime System, a task-based runtime system for extreme scale. This monitoring component provides real-time introspection capabilities that help the runtime scheduler in its decision-making process and adaptation, while introducing minimum overhead. In addition, the monitoring component provides several post-mortem reports as well as real-time data visualisation that can be of great help in the task of performance debugging.
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| 12. |
- Aguilar, Xavier, et al.
(författare)
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Automatic On-Line Detection of MPI Application Structure with Event Flow Graphs
- 2015
-
Ingår i: EURO-PAR 2015. - Berlin, Heidelberg : Springer Berlin/Heidelberg. - 9783662480960 - 9783662480953 ; , s. 70-81
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Konferensbidrag (refereegranskat)abstract
- The deployment of larger and larger HPC systems challenges the scalability of both applications and analysis tools. Performance analysis toolsets provide users with means to spot bottlenecks in their applications by either collecting aggregated statistics or generating loss-less time-stamped traces. While obtaining detailed trace information is the best method to examine the behavior of an application in detail, it is infeasible at extreme scales due to the huge volume of data generated. In this context, knowing the application structure, and particularly the nesting of loops in iterative applications is of great importance as it allows, among other things, to reduce the amount of data collected by focusing on important sections of the code. In this paper we demonstrate how the loop nesting structure of an MPI application can be extracted on-line from its event flow graph without the need of any explicit source code instrumentation. We show how this knowledge on the application structure can be used to compute postmortem statistics as well as to reduce the amount of redundant data collected. To that end, we present a usage scenario where this structure information is utilized on-line (while the application runs) to intelligently collect fine-grained data for only a few iterations of an application, considerably reducing the amount of data gathered.
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| 13. |
- Aguilar, Xavier, et al.
(författare)
-
MPI Trace Compression Using Event Flow Graphs
- 2014
-
Konferensbidrag (refereegranskat)abstract
- Understanding how parallel applications behave is crucial for using high-performance computing (HPC) resources efficiently. However, the task of performance analysis is becoming increasingly difficult due to the growing complexity of scientific codes and the size of machines. Even though many tools have been developed over the past years to help in this task, current approaches either only offer an overview of the application discarding temporal information, or they generate huge trace files that are often difficult to handle.In this paper we propose the use of event flow graphs for monitoring MPI applications, a new and different approach that balances the low overhead of profiling tools with the abundance of information available from tracers. Event flow graphs are captured with very low overhead, require orders of magnitude less storage than standard trace files, and can still recover the full sequence of events in the application. We test this new approach with the NERSC-8/Trinity Benchmark suite and achieve compression ratios up to 119x.
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| 14. |
- Aguilar, Xavier, et al.
(författare)
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Online MPI trace compression using event flow graphs and wavelets
- 2016
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Ingår i: Procedia Computer Science. - : Elsevier. - 1877-0509. ; , s. 1497-1506
-
Konferensbidrag (refereegranskat)abstract
- Performance analysis of scientific parallel applications is essential to use High Performance Computing (HPC) infrastructures efficiently. Nevertheless, collecting detailed data of large-scale parallel programs and long-running applications is infeasible due to the huge amount of performance information generated. Even though there are no technological constraints in storing Terabytes of performance data, the constant flushing of such data to disk introduces a massive overhead into the application that makes the performance measurements worthless. This paper explores the use of Event flow graphs together with wavelet analysis and EZW-encoding to provide MPI event traces that are orders of magnitude smaller while preserving accurate information on timestamped events. Our mechanism compresses the performance data online while the application runs, thus, reducing the pressure put on the I/O system due to buffer flushing. As a result, we achieve lower application perturbation, reduced performance data output, and the possibility to monitor longer application runs.
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| 15. |
- Aguilar, Xavier, et al.
(författare)
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Online Performance Data Introspection with IPM
- 2014
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Ingår i: Proceedings of the 15th IEEE International Conference on High Performance Computing and Communications (HPCC 2013). - : IEEE Computer Society. - 9780769550886 ; , s. 728-734
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Konferensbidrag (refereegranskat)abstract
- Exascale systems will be heterogeneous architectures with multiple levels of concurrency and energy constraints. In such a complex scenario, performance monitoring and runtime systems play a major role to obtain good application performance and scalability. Furthermore, online access to performance data becomes a necessity to decide how to schedule resources and orchestrate computational elements: processes, threads, tasks, etc. We present the Performance Introspection API, an extension of the IPM tool that provides online runtime access to performance data from an application while it runs. We describe its design and implementation and show its overhead on several test benchmarks. We also present a real test case using the Performance Introspection API in conjunction with processor frequency scaling to reduce power consumption.
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| 16. |
- Aguilar, Xavier
(författare)
-
Performance Monitoring, Analysis, and Real-Time Introspection on Large-Scale Parallel Systems
- 2020
-
Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- High-Performance Computing (HPC) has become an important scientific driver. A wide variety of research ranging for example from drug design to climate modelling is nowadays performed in HPC systems. Furthermore, the tremendous computer power of such HPC systems allows scientists to simulate problems that were unimaginable a few years ago. However, the continuous increase in size and complexity of HPC systems is turning the development of efficient parallel software into a difficult task. Therefore, the use of per- formance monitoring and analysis is a must in order to unveil inefficiencies in parallel software. Nevertheless, performance tools also face challenges as a result of the size of HPC systems, for example, coping with huge amounts of performance data generated.In this thesis, we propose a new model for performance characterisation of MPI applications that tackles the challenge of big performance data sets. Our approach uses Event Flow Graphs to balance the scalability of profiling techniques (generating performance reports with aggregated metrics) with the richness of information of tracing methods (generating files with sequences of time-stamped events). In other words, graphs allow to encode ordered se- quences of events without storing the whole sequence of such events, and therefore, they need much less memory and disk space, and are more scal- able. We demonstrate in this thesis how our Event Flow Graph model can be used as a trace compression method. Furthermore, we propose a method to automatically detect the structure of MPI applications using our Event Flow Graphs. This knowledge can afterwards be used to collect performance data in a smarter way, reducing for example the amount of redundant data collected. Finally, we demonstrate that our graphs can be used beyond trace compression and automatic analysis of performance data. We propose a new methodology to use Event Flow Graphs in the task of visual performance data exploration.In addition to the Event Flow Graph model, we also explore in this thesis the design and use of performance data introspection frameworks. Future HPC systems will be very dynamic environments providing extreme levels of parallelism, but with energy constraints, considerable resource sharing, and heterogeneous hardware. Thus, the use of real-time performance data to or- chestrate program execution in such a complex and dynamic environment will be a necessity. This thesis presents two different performance data introspec- tion frameworks that we have implemented. These introspection frameworks are easy to use, and provide performance data in real time with very low overhead. We demonstrate, among other things, how our approach can be used to reduce in real time the energy consumed by the system.The approaches proposed in this thesis have been validated in different HPC systems using multiple scientific kernels as well as real scientific applica- tions. The experiments show that our approaches in performance character- isation and performance data introspection are not intrusive at all, and can be a valuable contribution to help in the performance monitoring of future HPC systems.
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| 17. |
- Aguilar, Xavier, et al.
(författare)
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Scalability analysis of Dalton, a molecular structure program
- 2013
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Ingår i: Future Generation Computer Systems. - : Elsevier BV. - 0167-739X .- 1872-7115. ; 29:8, s. 2197-2204
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Tidskriftsartikel (refereegranskat)abstract
- Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a performance characterization and optimization of Dalton. We also propose a solution to avoid the master/worker design of Dalton to become a performance bottleneck for larger process numbers. With these improvements we obtain speedups of 4x, increasing the parallel efficiency of the code and being able to run in it in a much bigger number of cores.
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| 18. |
- Aguilar, Xavier, et al.
(författare)
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Scaling Dalton, a molecular electronic structure program
- 2011
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Ingår i: Seventh International Conference on e-Science, e-Science 2011, 5-8 December 2011, Stockholm, Sweden. - : IEEE conference proceedings. - 9781457721632 ; , s. 256-262
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Konferensbidrag (refereegranskat)abstract
- Dalton is a molecular electronic structure program featuring common methods of computational chemistry that are based on pure quantum mechanics (QM) as well as hybrid quantum mechanics/molecular mechanics (QM/MM). It is specialized and has a leading position in calculation of molecular properties with a large world-wide user community (over 2000 licenses issued). In this paper, we present a characterization and performance optimization of Dalton that increases the scalability and parallel efficiency of the application. We also propose asolution that helps to avoid the master/worker design of Daltonto become a performance bottleneck for larger process numbers and increase the parallel efficiency.
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| 19. |
- Aguilar, Xavier
(författare)
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Towards Scalable Performance Analysis of MPI Parallel Applications
- 2015
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- A considerably fraction of science discovery is nowadays relying on computer simulations. High Performance Computing (HPC) provides scientists with the means to simulate processes ranging from climate modeling to protein folding. However, achieving good application performance and making an optimal use of HPC resources is a heroic task due to the complexity of parallel software. Therefore, performance tools and runtime systems that help users to execute applications in the most optimal way are of utmost importance in the landscape of HPC. In this thesis, we explore different techniques to tackle the challenges of collecting, storing, and using fine-grained performance data. First, we investigate the automatic use of real-time performance data in order to run applications in an optimal way. To that end, we present a prototype of an adaptive task-based runtime system that uses real-time performance data for task scheduling. This runtime system has a performance monitoring component that provides real-time access to the performance behavior of anapplication while it runs. The implementation of this monitoring component is presented and evaluated within this thesis. Secondly, we explore lossless compression approaches for MPI monitoring. One of the main problems that performance tools face is the huge amount of fine-grained data that can be generated from an instrumented application. Collecting fine-grained data from a program is the best method to uncover the root causes of performance bottlenecks, however, it is unfeasible with extremely parallel applications or applications with long execution times. On the other hand, collecting coarse-grained data is scalable but sometimes not enough to discern the root cause of a performance problem. Thus, we propose a new method for performance monitoring of MPI programs using event flow graphs. Event flow graphs provide very low overhead in terms of execution time and storage size, and can be used to reconstruct fine-grained trace files of application events ordered in time.
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| 20. |
- Aguilar, Xavier, et al.
(författare)
-
Visual MPI Performance Analysis using Event Flow Graphs
- 2015
-
Ingår i: Procedia Computer Science. - : Elsevier. - 1877-0509. ; 51, s. 1353-1362
-
Tidskriftsartikel (refereegranskat)abstract
- Event flow graphs used in the context of performance monitoring combine the scalability and low overhead of profiling methods with lossless information recording of tracing tools. In other words, they capture statistics on the performance behavior of parallel applications while pre- serving the temporal ordering of events. Event flow graphs require significantly less storage than regular event traces and can still be used to recover the full ordered sequence of events performed by the application. In this paper we explore the usage of event flow graphs in the context of visual performance analysis. We show that graphs can be used to quickly spot performance problems, helping to better understand the behavior of an application. We demonstrate our performance analysis approach with MiniFE, a mini-application that mimics the key performance aspects of finite- element applications in High Performance Computing (HPC).
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| 21. |
- Gonzales-Alvares, G, et al.
(författare)
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Drug design on the cell BE
- 2010
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Ingår i: Scientific Computing with Multicore and Accelerators. - : CRC Press. - 9781439825365 - 9781439825372 ; , s. 331-350
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Bokkapitel (refereegranskat)
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| 22. |
- Hudson, Lawrence N, et al.
(författare)
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The database of the PREDICTS (Projecting Responses of Ecological Diversity In Changing Terrestrial Systems) project
- 2017
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Ingår i: Ecology and Evolution. - : John Wiley & Sons. - 2045-7758. ; 7:1, s. 145-188
-
Tidskriftsartikel (refereegranskat)abstract
- The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.
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| 23. |
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| 24. |
- Jung, Christian, et al.
(författare)
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A comparison of very old patients admitted to intensive care unit after acute versus elective surgery or intervention
- 2019
-
Ingår i: Journal of critical care. - : W B SAUNDERS CO-ELSEVIER INC. - 0883-9441 .- 1557-8615. ; 52, s. 141-148
-
Tidskriftsartikel (refereegranskat)abstract
- Background: We aimed to evaluate differences in outcome between patients admitted to intensive care unit (ICU) after elective versus acute surgery in a multinational cohort of very old patients (80 years; VIP). Predictors of mortality, with special emphasis on frailty, were assessed.Methods: In total, 5063 VIPs were induded in this analysis, 922 were admitted after elective surgery or intervention, 4141 acutely, with 402 after acute surgery. Differences were calculated using Mann-Whitney-U test and Wilcoxon test. Univariate and multivariable logistic regression were used to assess associations with mortality.Results: Compared patients admitted after acute surgery, patients admitted after elective surgery suffered less often from frailty as defined as CFS (28% vs 46%; p < 0.001), evidenced lower SOFA scores (4 +/- 5 vs 7 +/- 7; p < 0.001). Presence of frailty (CFS >4) was associated with significantly increased mortality both in elective surgery patients (7% vs 12%; p = 0.01), in acute surgery (7% vs 12%; p = 0.02).Conclusions: VIPs admitted to ICU after elective surgery evidenced favorable outcome over patients after acute surgery even after correction for relevant confounders. Frailty might be used to guide clinicians in risk stratification in both patients admitted after elective and acute surgery.
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| 25. |
- Labarta, Jesús, et al.
(författare)
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Scalability of tracing and visualization tools
- 2005
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Ingår i: Parallel Computing: Current & Future Issues of High-End Computing. - Jülich : Central Institute for Applied Mathematics. - 3000173528 ; , s. 869-876
-
Konferensbidrag (refereegranskat)abstract
- Extending the capability of performance tools to deal with the larger and larger machines being deployed is necessary in order to understand their actual behavior and identify how to achieve per- formance expectations in the frequent case these are not met at a first try. Trace based tools such as Paraver provide extremely powerful and flexible analysis capabilities to identify performance problems not detectable by profile based tools. Scaling up the usability of trace based tools requires new techniques in both the acquisition and visualization phases. The CEPBA-tools approach distributes the functionalities required to tackle large systems in three different levels. Different acquisition techniques are used in the instrumen- tation package to control the data captured and maximize the ratio of information to file size. An intermediate level set of tools are used to summarize the generated Paraver traces into smaller traces, with the same format, but where some of the information has been summarized. Examples of filter functionalities at this level include summarization of certain events in periodic software counters and selection of specific time intervals or events. At the final level, different rendering techniques have been introduced in Paraver to visualize traces of many processes while still being able to con- vey to the analyst the information relevant to identify problems at very coarse level as well as the capabilities to dig down to very detailed levels. The paper describes in detail the techniques being used along those lines in the CEPBA-tools environment in order to support the analysis of applications run on large systems.
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| 26. |
- Markidis, Stefano, et al.
(författare)
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Paving the path to exascale computing with CRESTA development environment
- 2013
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The development and implementation of efficient computer codes for exascale supercomputers will require combined advancement of all development environment components: compilers, automatic tuning frameworks, run-time systems, debuggers and performance monitoring and analysis tools. The exascale era poses unprecedented challenges. Because the presence of accelerators is more and more common among the fastest supercomputer and will play a role in exascale computing, compilers will need to support hybrid computer architectures and generate efficient code hiding the complexity of programming accelerators. Hand optimization of the code will be very difficult on exascale machine and will be increasingly assisted by automatic tuners. Application tuning will be more focus on parallel aspects of the computation because of large amount of available parallelism. The application workload will be distributed over million of processes, and to implement ad-hoc strategies directly in the application will be probably unfeasible while an adaptive run-time system will provide automatic load balancing. Debuggers and performance monitoring tools will deal with million processes and with huge amount of data from application and hardware counters, but they will still be required to minimize the overhead and retain scalability. In this talk, we present how the development environment of the CRESTA exascale EC project meets all these challenges by advancing the state of the art in the field.An investigation of compiler support for hybrid GPU programming, the design concepts, and the main characteristics of the alpha prototype implementation of the CRESTA development environment components for exascale computing are presented. A performance study of OpenACC compiler directives has been carried out, showing very promising results and indicating OpenACC as viable approach for programming hybrid exascale supercomputer. A new Domain-Specific Language (DSL) has been defined for the expression of parallel auto-tuning at very large scale. The focus of on the extension of the auto-tuning approach into the parallel domain to enable tuning of communication-related aspects of application. A new adaptive run-time system has been designed to schedule processes depending on the resource availability, on the workload, and on the run-time analysis of the application performance. The Allinea DDT debugger and the Dresden University of Technology MUST MPI correctness checker are being extended to provide a unified interface, to improve scalability, and to include new disruptive technology based on statistical analysis of run-time behavior of the application for anomalies detection. The new exascale prototypes of the Dresden University of Technology Vampir, VampirTrace and Score-P performance monitoring and analysis tools have been released. The new features include the possibility of applying filtering technique before loading performance data to drastically reduce memory needs during the performance analysis. The initial evaluation study of the development environment is targeted on the CRESTA project applications to determine how the development environment could be coupled into a production suite for exascale computing.
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| 27. |
- Meijer, Tomas, 1980-, et al.
(författare)
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Endoparasites in the endangered Fennoscandian population of arctic foxes (Vulpes lagopus)
- 2011
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Ingår i: European Journal of Wildlife Research. - : Springer Science and Business Media LLC. - 1612-4642 .- 1439-0574. ; 57:4, s. 923-927
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Tidskriftsartikel (refereegranskat)abstract
- The Fennoscandian arctic fox (Vulpes lagopus) population is endangered due to overharvest and competition with the larger red fox (Vulpes vulpes). In this study, we have screened the population in Sweden for endoparasites by analysis of non-invasively faecal samples collected at reproductive dens during two summers, one with low food abundance (2008) and the other with high food abundance (2010). Eggs, larvae and oocysts of a total of 14 different endoparasites were identified with a species richness per inhabited den of 3.2 (CI95% +/- 0.48) in 2008 and 2.7 (CI95% +/- 0.72) in 2010. Capillariidae-like eggs was identified at 59% of the dens in 2008 and 57% in 2010 and Toxocara canis with 7% (2008) and 30% (2010); Toxascaris leonina with 93% (2008) and 65% (2010); Uncinaria stenocephala 65% (2008) and 39% (2010); Crenosoma vulpis 3% (2008) and 4% (2010); Trichuris sp. 7% (2008) and 4% (2010); Cystoisospora canis-like oocysts 28% (2008) and 26% (2010); Cystoisospora ohiensis-like oocysts 38% (2008) and 4% (2010); Eimeria sp. 7% (2008) and 9% (2010); Sarcocystis sp. 3% (2008) and 9% (2010); Taenia sp. 10% (2008) and 4% (2010); Mesocestoides sp. 3% (2008) and 0% (2010); Balantidium sp. 0% (2008) and 9% (2010) and Spiruroidea-like eggs 0% (2008) and 4% (2010). To our knowledge, Balantidium sp., Sarcocystis sp. and Trichuris sp. has never been described before in wild arctic foxes.
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| 28. |
- O'Donncha, F., et al.
(författare)
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AllScale toolchain pilot applications : PDE based solvers using a parallel development environment
- 2019
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Ingår i: Computer Physics Communications. - : Elsevier B.V.. - 0010-4655 .- 1879-2944.
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Tidskriftsartikel (refereegranskat)abstract
- AllScale is a programming environment targeting simplified development of highly scalable parallel applications by dividing development responsibilities into silos. The front-end AllScale API provides a simple C++ development environment through a suite of parallel constructs expressions denoting tasks operating concurrently. This interfaces with the other components of the toolchain (core-level API, compiler and runtime) which manages tasks related to the machine and system level, hidden to the user. The paper describes the development of two large-scale parallel applications within the AllScale API, namely, an advection– diffusion model with data assimilation and a Lagrangian space-weather simulation model based on a particle-in-cell method. We present mathematical formulations and implementations and evaluate parallel constructs developed using the AllScale API. The performance of the applications from the perspective of both parallel scalability, and more importantly productivity are assessed. We demonstrate how the AllScale API can greatly improve developer productivity while maintaining parallel performance in two applications with distinct numerical characteristics. Code complexity metrics demonstrate reduction in application specific implementations of up to 30% while performance tests on three different compute systems demonstrate comparable parallel scalability to an MPI version of the code.
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| 29. |
- Osterman Lind, Eva, et al.
(författare)
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Pearsonema (syn Capillaria) plica associated cystitis in a Fennoscandian arctic fox (Vulpes lagopus: a case report
- 2010
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Ingår i: Acta Veterinaria Scandinavica. - : Springer Science and Business Media LLC. - 0044-605X .- 1751-0147. ; 52
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Tidskriftsartikel (refereegranskat)abstract
- The bladderworm Pearsonema (syn Capillaria) plica affects domestic dogs and wild carnivores worldwide. A high prevalence in red foxes (Vulpes vulpes) has been reported in many European countries. P. plica inhabits the lower urinary tract and is considered to be of low pathogenic significance in dogs mostly causing asymptomatic infections. However, a higher level of pathogenicity has been reported in foxes. A severe cystitis associated with numerous bladderworms was found in a captive arctic fox (Vulpes lagopus) originating from the endangered Fennoscandian arctic fox population. To our knowledge this is the first description of P. plica infection in an arctic fox.
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| 30. |
- Pons, Carles, et al.
(författare)
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Cell-Dock : high-performance protein-protein docking
- 2012
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 28:18, s. 2394-2396
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Tidskriftsartikel (refereegranskat)abstract
- The application of docking to large-scale experiments or the explicit treatment of protein flexibility are part of the new challenges in structural bioinformatics that will require large computer resources and more efficient algorithms. Highly optimized fast Fourier transform (FFT) approaches are broadly used in docking programs but their optimal code implementation leaves hardware acceleration as the only option to significantly reduce the computational cost of these tools. In this work we present Cell-Dock, an FFT-based docking algorithm adapted to the Cell BE processor. We show that Cell-Dock runs faster than FTDock with maximum speedups of above 200x, while achieving results of similar quality.
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| 31. |
- Schliephake, Michael, et al.
(författare)
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Design and Implementation of a Runtime System for Parallel Numerical Simulations on Large-Scale Clusters
- 2011
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Ingår i: Proceedings Of The International Conference On Computational Science (ICCS). - : Elsevier. ; , s. 2105-2114
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Konferensbidrag (refereegranskat)abstract
- The execution of scientific codes will introduce a number of new challenges and intensify some old ones on new high-performance computing infrastructures. Petascale computers are large systems with complex designs using heterogeneous technologies that make the programming and porting of applications difficult, particularly if one wants to use the maximum peak performance of the system. In this paper we present the design and first prototype of a runtime system for parallel numerical simulations on large-scale systems. The proposed runtime system addresses the challenges of performance, scalability, and programmability of large-scale HPC systems. We also present initial results of our prototype implementation using a molecular dynamics application kernel.
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| 32. |
- Servat, Harald, et al.
(författare)
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Drug Design Issues on the Cell BE
- 2008
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Ingår i: High Performance Embedded Architectures and Compilers. - Berlin, Heidelberg : Springer. - 9783540775591 ; , s. 176-190
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Konferensbidrag (refereegranskat)abstract
- Structure alignment prediction between proteins (protein docking) is crucial for drug design, and a challenging problem for bioinformatics, pharmaceutics, and current and future processors due to it is a very time consuming process. Here, we analyze a well known protein docking application in the Bioinformatic field, Fourier Transform Docking (FTDock), on a 3.2GHz Cell Broadband Engine (BE) processor. FTDock is a geometry complementary approximation of the protein docking problem, and baseline of several protein docking algorithms currently used. In particular, we measure the performance impact of reducing, tuning and overlapping memory accesses, and the efficiency of different parallelization strategies (SIMD, MPI, OpenMP, etc.) on porting that biomedical application to the Cell BE. Results show the potential of the Cell BE processor for drug design applications, but also that there are important memory and computer architecture aspects that should be considered.
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| 33. |
- Servat, Harald, et al.
(författare)
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Drug Design on the Cell BroadBand Engine
- 2007
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Ingår i: Parallel Architecture and Compilation Techniques. - : IEEE Computer Society. - 9780769529448 ; , s. 425-425
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Konferensbidrag (refereegranskat)abstract
- We evaluate a well known protein docking application in the bioinformatic field, Fourier Transform Docking (FTDock) (Gabb et al., 1997), on a Blade with two 3.2GHz cell broadband engine (BE) processor (Kahle et al., 2005). FTDock is a geometry complementary approximation of the protein docking problem, and uses 3D FFTs to reduce the complexity of the algorithm. FTDock achieves a significant speedup when most time consuming functions are offloaded to SPEs, and vectorized. We show the performance impact evolution of of-loading and vectorizing two functions of FTDock (CM and SC) on 1 SPU. We show total execution time of FTDock when CM and SC run in the PPU (bar 1), CM is off loaded (bar 2), CM is also vectorized (bar 3), SC is offloaded (bar 4) and SC is also vectorized (bar 5). Parallelizing functions that are not offloaded, using OpenMP for instance, on the dual-thread PPE helps to increase the PPEpipeline use and system throughput, and the scalability of the application.
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| 34. |
- Thoman, Peter, et al.
(författare)
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A taxonomy of task-based parallel programming technologies for high-performance computing
- 2018
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Ingår i: Journal of Supercomputing. - : SPRINGER. - 0920-8542 .- 1573-0484. ; 74:4, s. 1422-1434
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Tidskriftsartikel (refereegranskat)abstract
- Task-based programming models for shared memory-such as Cilk Plus and OpenMP 3-are well established and documented. However, with the increase in parallel, many-core, and heterogeneous systems, a number of research-driven projects have developed more diversified task-based support, employing various programming and runtime features. Unfortunately, despite the fact that dozens of different task-based systems exist today and are actively used for parallel and high-performance computing (HPC), no comprehensive overview or classification of task-based technologies for HPC exists. In this paper, we provide an initial task-focused taxonomy for HPC technologies, which covers both programming interfaces and runtime mechanisms. We demonstrate the usefulness of our taxonomy by classifying state-of-the-art task-based environments in use today.
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| 35. |
- Thoman, Peter, et al.
(författare)
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A Taxonomy of Task-Based Technologies for High-Performance Computing
- 2018
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Ingår i: PARALLEL PROCESSING AND APPLIED MATHEMATICS (PPAM 2017), PT II. - Cham : SPRINGER INTERNATIONAL PUBLISHING AG. - 9783319780542 ; , s. 264-274
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Konferensbidrag (refereegranskat)abstract
- Task-based programming models for shared memory - such as Cilk Plus and OpenMP 3 - are well established and documented. However, with the increase in heterogeneous, many-core and parallel systems, a number of research-driven projects have developed more diversified task-based support, employing various programming and runtime features. Unfortunately, despite the fact that dozens of different task-based systems exist today and are actively used for parallel and high-performance computing, no comprehensive overview or classification of task-based technologies for HPC exists. In this paper, we provide an initial task-focused taxonomy for HPC technologies, which covers both programming interfaces and runtime mechanisms. We demonstrate the usefulness of our taxonomy by classifying state-of-the-art task-based environments in use today.
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| 36. |
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| 37. |
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