| 1. |
- Aad, G., et al.
(författare)
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- 2010
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swepub:Mat__t
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| 2. |
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| 3. |
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| 4. |
- Aad, G., et al.
(författare)
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- 2010
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swepub:Mat__t
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| 5. |
- Aad, G., et al.
(författare)
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The ATLAS Simulation Infrastructure
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 823-874
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Tidskriftsartikel (refereegranskat)abstract
- The simulation software for the ATLAS Experiment at the Large Hadron Collider is being used for large-scale production of events on the LHC Computing Grid. This simulation requires many components, from the generators that simulate particle collisions, through packages simulating the response of the various detectors and triggers. All of these components come together under the ATLAS simulation infrastructure. In this paper, that infrastructure is discussed, including that supporting the detector description, interfacing the event generation, and combining the GEANT4 simulation of the response of the individual detectors. Also described are the tools allowing the software validation, performance testing, and the validation of the simulated output against known physics processes.
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| 6. |
- Aad, G., et al.
(författare)
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Commissioning of the ATLAS Muon Spectrometer with cosmic rays
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 70:3, s. 875-916
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Tidskriftsartikel (refereegranskat)abstract
- The ATLAS detector at the Large Hadron Collider has collected several hundred million cosmic ray events during 2008 and 2009. These data were used to commission the Muon Spectrometer and to study the performance of the trigger and tracking chambers, their alignment, the detector control system, the data acquisition and the analysis programs. We present the performance in the relevant parameters that determine the quality of the muon measurement. We discuss the single element efficiency, resolution and noise rates, the calibration method of the detector response and of the alignment system, the track reconstruction efficiency and the momentum measurement. The results show that the detector is close to the design performance and that the Muon Spectrometer is ready to detect muons produced in high energy proton-proton collisions.
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| 7. |
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| 8. |
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| 9. |
- Accomando, E., et al.
(författare)
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Physics with e + e - linear colliders
- 1998
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Ingår i: Physics Reports. - 0370-1573. ; 299:1, s. 1-78
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Tidskriftsartikel (refereegranskat)abstract
- The physics potential of e + e - linear colliders is summarized in this report. These machines are planned to operate in the first phase at a center-of-mass energy of 500 GeV, before being scaled up to about 1 TeV. In the second phase of the operation, a final energy of about 2 TeV is expected. The machines will allow us to perform precision tests of the heavy particles in the Standard Model, the top quark and the electroweak bosons. They are ideal facilities for exploring the properties of Higgs particles, in particular in the intermediate mass range. New vector bosons and novel matter particles in extended gauge theories can be searched for and studied thoroughly. The machines provide unique opportunities for the discovery of particles in supersymmetric extensions of the Standard Model, the spectrum of Higgs particles, the supersymmetric partners of the electroweak gauge and Higgs bosons, and of the matter particles. High precision analyses of their properties and interactions will allow for extrapolations to energy scales close to the Planck scale where gravity becomes significant. In alternative scenarios, i.e. compositeness models, novel matter particles and interactions can be discovered and investigated in the energy range above the existing colliders up to the TeV scale. Whatever scenario is realized in Nature, the discovery potential of e + e - linear colliders and the high precision with which the properties of particles and their interactions can be analyzed, define an exciting physics program complementary to hadron machines.
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| 10. |
- Moortgat-Pick, G., et al.
(författare)
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Physics at the e(+) e(-) linear collider
- 2015
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Ingår i: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 75:8
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Forskningsöversikt (refereegranskat)abstract
- A comprehensive review of physics at an e(+) e(-) linear collider in the energy range of root s = 92 GeV-3 TeV is presented in view of recent and expected LHC results, experiments from low-energy as well as astroparticle physics. The report focusses in particular on Higgs-boson, top-quark and electroweak precision physics, but also discusses several models of beyond the standard model physics such as super-symmetry, little Higgs models and extra gauge bosons. The connection to cosmology has been analysed as well.
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| 11. |
- Moortgat-Pick, G., et al.
(författare)
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Polarized positrons and electrons at the linear collider
- 2008
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Ingår i: Physics reports. - : Elsevier BV. - 0370-1573 .- 1873-6270. ; 460:4-5, s. 131-243
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Forskningsöversikt (refereegranskat)abstract
- The proposed International Linear Collider (ILC) is well-suited for discovering physics beyond the Standard Model and for precisely unraveling the structure of the underlying physics. The physics return can be maximized by the use of polarized beams. This report shows the paramount role of polarized beams and summarizes the benefits obtained from polarizing the positron beam, as well as the electron beam. The physics case for this option is illustrated explicitly by analyzing reference reactions in different physics scenarios. The results show that positron polarization, combined with the clean experimental environment provided by the linear collider, allows to improve strongly the potential of searches for new particles and the identification of their dynamics, which opens the road to resolve shortcomings of the Standard Model. The report also presents an overview of possible designs for polarizing both beams at the ILC, as well as for measuring their polarization.
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| 12. |
- Aevarsson, Arnthór, et al.
(författare)
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Going to extremes - a metagenomic journey into the dark matter of life
- 2021
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press (OUP). - 1574-6968. ; 368:12
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Forskningsöversikt (refereegranskat)abstract
- The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.
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| 13. |
- 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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| 14. |
- Behle, Anna, et al.
(författare)
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Manipulation of topoisomerase expression inhibits cell division but not growth and reveals a distinctive promoter structure in Synechocystis
- 2022
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 50:22, s. 12790-12808
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Tidskriftsartikel (refereegranskat)abstract
- In cyanobacteria DNA supercoiling varies over the diurnal cycle and is integrated with temporal programs of transcription and replication. We manipulated DNA supercoiling in Synechocystis sp. PCC 6803 by CRISPRi-based knockdown of gyrase subunits and overexpression of topoisomerase I (TopoI). Cell division was blocked but cell growth continued in all strains. The small endogenous plasmids were only transiently relaxed, then became strongly supercoiled in the TopoI overexpression strain. Transcript abundances showed a pronounced 5'/3' gradient along transcription units, incl. the rRNA genes, in the gyrase knockdown strains. These observations are consistent with the basic tenets of the homeostasis and twin-domain models of supercoiling in bacteria. TopoI induction initially led to downregulation of G+C-rich and upregulation of A+T-rich genes. The transcriptional response quickly bifurcated into six groups which overlap with diurnally co-expressed gene groups. Each group shows distinct deviations from a common core promoter structure, where helically phased A-tracts are in phase with the transcription start site. Together, our data show that major co-expression groups (regulons) in Synechocystis all respond differentially to DNA supercoiling, and suggest to re-evaluate the long-standing question of the role of A-tracts in bacterial promoters.
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| 15. |
- Brenner, Richard, et al.
(författare)
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The ATLAS tau trigger and planned trigger efficiency studies with early data
- 2009
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Ingår i: Proceedings of CHarged2008. - Trieste : Proceedings of Science. ; , s. 1-7
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Konferensbidrag (refereegranskat)abstract
- The tau trigger system of the ATLAS detector has been developed to increase the sensitivity ofthe detector to the Higgs boson and searches for physics beyond the Standard Model. A trigger system split in three levels has been designed for hadronically decaying tau leptons optimized for efficiency and good background rejection. At the first level the trigger uses only information from the calorimeters while the other two levels include also information from the tracking. Both energy and shape variables for the hadronic tau jets are used in the trigger algorithms. The very intense QCD background, however, makes it a challenge to develop an efficient trigger with high purity at low transverse momentum. Thus the tau trigger is best used in combination with other trigger variables such as missing transverse energy or jets. Before the tau trigger can be used in searches, it has to be commissioned with data and the efficiency and background rejectionof QCD has to be studied in detail.
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| 16. |
- Casado, M. P., et al.
(författare)
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The ATLAS tau trigger
- 2009
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Ingår i: Nuclear physics B, Proceedings supplements. - : Elsevier BV. - 0920-5632 .- 1873-3832. ; 189, s. 291-298
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Tidskriftsartikel (refereegranskat)abstract
- The implementation of a trigger for hadronically decaying tau leptons at the Large Hadronic Collider (LHC) is challenging due to the high background rate, on the other hand it increases tremendously the discovery potential of ATLAS in searches for Standard Model (SM) or Supersymmetric (SUSY) Higgs or other more exotic final states. In this paper we describe the ATLAS tau trigger system, focusing on the early data taking period, and present results from studies based oil GEANT 4 simulated events, including trigger rates and the acceptance of tau leptons from SM processes. In order to cope with the rate and optimize the efficiency of important physics channels, the results of the current simulation studies indicate that ATLAS tau triggers should include either relatively high transverse momentum single tau signatures, or low transverse momentum tau signatures in combination with other signatures, such as missing transverse energy, leptons, or jets.
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| 17. |
- Herrera-Belaroussi, Aude, et al.
(författare)
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Candidatus Frankia nodulisporulans sp. nov., an Alnus glutinosa-infective Frankia species unable to grow in pure culture and able to sporulate in-planta
- 2020
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Ingår i: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020 .- 1618-0984. ; 43:6
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Tidskriftsartikel (refereegranskat)abstract
- We describe a new Frankia species, for three non-isolated strains obtained from Alnus glutinosa in France and Sweden, respectively. These strains can nodulate several Alnus species (A. glutinosa, A. incana, A. alno-betula), they form hyphae, vesicles and sporangia in the root nodule cortex but have resisted all attempts at isolation in pure culture. Their genomes have been sequenced, they are significantly smaller than those of other Alnus-infective species (5 Mb instead of 7.5 Mb) and are very closely related to one another (ANI of 100%). The name Candidatus Frankia nodulisporulans is proposed.
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| 18. |
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| 19. |
- Ralph, P., et al.
(författare)
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Pandemic programming: How COVID-19 affects software developers and how their organizations can help
- 2020
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Ingår i: Empirical Software Engineering. - : Springer Science and Business Media LLC. - 1382-3256 .- 1573-7616. ; 25, s. 4927-4961
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Tidskriftsartikel (refereegranskat)abstract
- Context As a novel coronavirus swept the world in early 2020, thousands of software developers began working from home. Many did so on short notice, under difficult and stressful conditions. Objective This study investigates the effects of the pandemic on developers' wellbeing and productivity. Method A questionnaire survey was created mainly from existing, validated scales and translated into 12 languages. The data was analyzed using non-parametric inferential statistics and structural equation modeling. Results The questionnaire received 2225 usable responses from 53 countries. Factor analysis supported the validity of the scales and the structural model achieved a good fit (CFI = 0.961, RMSEA = 0.051, SRMR = 0.067). Confirmatory results include: (1) the pandemic has had a negative effect on developers' wellbeing and productivity; (2) productivity and wellbeing are closely related; (3) disaster preparedness, fear related to the pandemic and home office ergonomics all affect wellbeing or productivity. Exploratory analysis suggests that: (1) women, parents and people with disabilities may be disproportionately affected; (2) different people need different kinds of support. Conclusions To improve employee productivity, software companies should focus on maximizing employee wellbeing and improving the ergonomics of employees' home offices. Women, parents and disabled persons may require extra support.
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| 20. |
- Wibberg, Daniel, et al.
(författare)
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Frankia-Enriched Metagenomes from the Earliest Diverging Symbiotic Frankia Cluster : They Come in Teams
- 2019
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Ingår i: Genome Biology and Evolution. - : Oxford University Press (OUP). - 1759-6653. ; 11:8, s. 2273-2291
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Tidskriftsartikel (refereegranskat)abstract
- Frankia strains induce the formation of nitrogen-fixing nodules on roots of actinorhizal plants. Phylogenetically, Frankia strains can be grouped in four clusters. The earliest divergent cluster, cluster-2, has a particularly wide host range. The analysis of cluster-2 strains has been hampered by the fact that with two exceptions, they could never be cultured. In this study, 12 Frankia-enriched metagenomes of Frankia cluster-2 strains or strain assemblages were sequenced based on seven inoculum sources. Sequences obtained via DNA isolated from whole nodules were compared with those of DNA isolated from fractionated preparations enhanced in the Frankia symbiotic structures. The results show that cluster-2 inocula represent groups of strains, and that strains not represented in symbiotic structures, that is, unable to performsymbiotic nitrogen fixation, may still be able to colonize nodules. Transposase gene abundance was compared in the different Frankia-enriched metagenomes with the result that NorthAmerican strains contain more transposase genes than Eurasian strains. An analysis of the evolution and distribution of the host plants indicated that bursts of transposition may have coincided with niche competition with other cluster-2 Frankia strains. The first genome of an inoculum from the Southern Hemisphere, obtained from nodules of Coriaria papuana in Papua NewGuinea, represents a novel species, postulated as Candidatus Frankiameridionalis. All Frankia-enrichedmetagenomes obtained in this study contained homologs of the canonical nod genes nodABC; the North American genomes also contained the sulfotransferase gene nodH, while the genome from the Southern Hemisphere only contained nodC and a truncated copy of nodB.
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