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- 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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| 8. |
- 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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| 9. |
- Schael, S, et al.
(författare)
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Precision electroweak measurements on the Z resonance
- 2006
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Ingår i: Physics Reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 427:5-6, s. 257-454
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Forskningsöversikt (refereegranskat)abstract
- We report on the final electroweak measurements performed with data taken at the Z resonance by the experiments operating at the electron-positron colliders SLC and LEP. The data consist of 17 million Z decays accumulated by the ALEPH, DELPHI, L3 and OPAL experiments at LEP, and 600 thousand Z decays by the SLID experiment using a polarised beam at SLC. The measurements include cross-sections, forward-backward asymmetries and polarised asymmetries. The mass and width of the Z boson, m(Z) and Gamma(Z), and its couplings to fermions, for example the p parameter and the effective electroweak mixing angle for leptons, are precisely measured: m(Z) = 91.1875 +/- 0.0021 GeV, Gamma(Z) = 2.4952 +/- 0.0023 GeV, rho(l) = 1.0050 +/- 0.0010, sin(2)theta(eff)(lept) = 0.23153 +/- 0.00016. The number of light neutrino species is determined to be 2.9840 +/- 0.0082, in agreement with the three observed generations of fundamental fermions. The results are compared to the predictions of the Standard Model (SM). At the Z-pole, electroweak radiative corrections beyond the running of the QED and QCD coupling constants are observed with a significance of five standard deviations, and in agreement with the Standard Model. Of the many Z-pole measurements, the forward-backward asymmetry in b-quark production shows the largest difference with respect to its SM expectation, at the level of 2.8 standard deviations. Through radiative corrections evaluated in the framework of the Standard Model, the Z-pole data are also used to predict the mass of the top quark, m(t) = 173(+10)(+13) GeV, and the mass of the W boson, m(W) = 80.363 +/- 0.032 GeV. These indirect constraints are compared to the direct measurements, providing a stringent test of the SM. Using in addition the direct measurements of m(t) and m(W), the mass of the as yet unobserved SM Higgs boson is predicted with a relative uncertainty of about 50% and found to be less than 285 GeV at 95% confidence level. (c) 2006 Elsevier B.V. All rights reserved.
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- Aad, G., et al.
(författare)
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- 2015
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Tidskriftsartikel (refereegranskat)
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