| 1. |
- Correa, D. F., et al.
(författare)
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Geographic patterns of tree dispersal modes in Amazonia and their ecological correlates
- 2023
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Ingår i: Global Ecology and Biogeography. - : Wiley. - 1466-822X .- 1466-8238. ; 32:1, s. 49-69
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Tidskriftsartikel (refereegranskat)abstract
- Aim To investigate the geographic patterns and ecological correlates in the geographic distribution of the most common tree dispersal modes in Amazonia (endozoochory, synzoochory, anemochory and hydrochory). We examined if the proportional abundance of these dispersal modes could be explained by the availability of dispersal agents (disperser-availability hypothesis) and/or the availability of resources for constructing zoochorous fruits (resource-availability hypothesis). Time period Tree-inventory plots established between 1934 and 2019. Major taxa studied Trees with a diameter at breast height (DBH) >= 9.55 cm. Location Amazonia, here defined as the lowland rain forests of the Amazon River basin and the Guiana Shield. Methods We assigned dispersal modes to a total of 5433 species and morphospecies within 1877 tree-inventory plots across terra-firme, seasonally flooded, and permanently flooded forests. We investigated geographic patterns in the proportional abundance of dispersal modes. We performed an abundance-weighted mean pairwise distance (MPD) test and fit generalized linear models (GLMs) to explain the geographic distribution of dispersal modes. Results Anemochory was significantly, positively associated with mean annual wind speed, and hydrochory was significantly higher in flooded forests. Dispersal modes did not consistently show significant associations with the availability of resources for constructing zoochorous fruits. A lower dissimilarity in dispersal modes, resulting from a higher dominance of endozoochory, occurred in terra-firme forests (excluding podzols) compared to flooded forests. Main conclusions The disperser-availability hypothesis was well supported for abiotic dispersal modes (anemochory and hydrochory). The availability of resources for constructing zoochorous fruits seems an unlikely explanation for the distribution of dispersal modes in Amazonia. The association between frugivores and the proportional abundance of zoochory requires further research, as tree recruitment not only depends on dispersal vectors but also on conditions that favour or limit seedling recruitment across forest types.
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| 2. |
- Abbasi, R., et al.
(författare)
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Characterization of the astrophysical diffuse neutrino flux using starting track events in IceCube
- 2024
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Ingår i: Physical Review D - Particles, Fields, Gravitation and Cosmology. - 2470-0010 .- 2470-0029. ; 110:2
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Tidskriftsartikel (refereegranskat)abstract
- A measurement of the diffuse astrophysical neutrino spectrum is presented using IceCube data collected from 2011-2022 (10.3 years). We developed novel detection techniques to search for events with a contained vertex and exiting track induced by muon neutrinos undergoing a charged-current interaction. Searching for these starting track events allows us to not only more effectively reject atmospheric muons but also atmospheric neutrino backgrounds in the southern sky, opening a new window to the sub-100 TeV astrophysical neutrino sky. The event selection is constructed using a dynamic starting track veto and machine learning algorithms. We use this data to measure the astrophysical diffuse flux as a single power law flux (SPL) with a best-fit spectral index of γ=2.58-0.09+0.10 and per-flavor normalization of φper-flavorAstro=1.68-0.22+0.19×10-18×GeV-1 cm-2 s-1 sr-1 (at 100 TeV). The sensitive energy range for this dataset is 3-550 TeV under the SPL assumption. This data was also used to measure the flux under a broken power law, however we did not find any evidence of a low energy cutoff.
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| 3. |
- Abbasi, R., et al.
(författare)
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Citizen science for IceCube: Name that Neutrino
- 2024
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Ingår i: European Physical Journal Plus. - 2190-5444. ; 139:6
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Tidskriftsartikel (refereegranskat)abstract
- Name that Neutrino is a citizen science project where volunteers aid in classification of events for the IceCube Neutrino Observatory, an immense particle detector at the geographic South Pole. From March 2023 to September 2023, volunteers did classifications of videos produced from simulated data of both neutrino signal and background interactions. Name that Neutrino obtained more than 128,000 classifications by over 1800 registered volunteers that were compared to results obtained by a deep neural network machine-learning algorithm. Possible improvements for both Name that Neutrino and the deep neural network are discussed.
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| 4. |
- Abbasi, R., et al.
(författare)
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Improved modeling of in-ice particle showers for IceCube event reconstruction
- 2024
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Ingår i: Journal of Instrumentation. - 1748-0221. ; 19:6
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Tidskriftsartikel (refereegranskat)abstract
- The IceCube Neutrino Observatory relies on an array of photomultiplier tubes to detect Cherenkov light produced by charged particles in the South Pole ice. IceCube data analyses depend on an in-depth characterization of the glacial ice, and on novel approaches in event reconstruction that utilize fast approximations of photoelectron yields. Here, a more accurate model is derived for event reconstruction that better captures our current knowledge of ice optical properties. When evaluated on a Monte Carlo simulation set, the median angular resolution for in-ice particle showers improves by over a factor of three compared to a reconstruction based on a simplified model of the ice. The most substantial improvement is obtained when including effects of birefringence due to the polycrystalline structure of the ice. When evaluated on data classified as particle showers in the high-energy starting events sample, a significantly improved description of the events is observed.
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| 5. |
- 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
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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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| 8. |
- Fresard, Laure, et al.
(författare)
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Identification of rare-disease genes using blood transcriptome sequencing and large control cohorts
- 2019
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Ingår i: Nature Medicine. - : NATURE PUBLISHING GROUP. - 1078-8956 .- 1546-170X. ; 25:6, s. 911-919
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Tidskriftsartikel (refereegranskat)abstract
- It is estimated that 350 million individuals worldwide suffer from rare diseases, which are predominantly caused by mutation in a single gene(1). The current molecular diagnostic rate is estimated at 50%, with whole-exome sequencing (WES) among the most successful approaches(2-5). For patients in whom WES is uninformative, RNA sequencing (RNA-seq) has shown diagnostic utility in specific tissues and diseases(6-8). This includes muscle biopsies from patients with undiagnosed rare muscle disorders(6,9), and cultured fibroblasts from patients with mitochondrial disorders(7). However, for many individuals, biopsies are not performed for clinical care, and tissues are difficult to access. We sought to assess the utility of RNA-seq from blood as a diagnostic tool for rare diseases of different pathophysiologies. We generated whole-blood RNA-seq from 94 individuals with undiagnosed rare diseases spanning 16 diverse disease categories. We developed a robust approach to compare data from these individuals with large sets of RNA-seq data for controls (n = 1,594 unrelated controls and n = 49 family members) and demonstrated the impacts of expression, splicing, gene and variant filtering strategies on disease gene identification. Across our cohort, we observed that RNA-seq yields a 7.5% diagnostic rate, and an additional 16.7% with improved candidate gene resolution.
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| 9. |
- Adewumi, Oluseun, et al.
(författare)
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Characterization of human embryonic stem cell lines by the International Stem Cell Initiative
- 2007
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Ingår i: Nature Biotechnology. - : Springer Science and Business Media LLC. - 1087-0156 .- 1546-1696. ; 25:7, s. 803-816
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Tidskriftsartikel (refereegranskat)abstract
- The International Stem Cell Initiative characterized 59 human embryonic stem cell lines from 17 laboratories worldwide. Despite diverse genotypes and different techniques used for derivation and maintenance, all lines exhibited similar expression patterns for several markers of human embryonic stem cells. They expressed the glycolipid antigens SSEA3 and SSEA4, the keratan sulfate antigens TRA-1-60, TRA-1-81, GCTM2 and GCT343, and the protein antigens CD9, Thy1 (also known as CD90), tissue- nonspecific alkaline phosphatase and class 1 HLA, as well as the strongly developmentally regulated genes NANOG, POU5F1 (formerly known as OCT4), TDGF1, DNMT3B, GABRB3 and GDF3. Nevertheless, the lines were not identical: differences in expression of several lineage markers were evident, and several imprinted genes showed generally similar allele-specific expression patterns, but some gene-dependent variation was observed. Also, some female lines expressed readily detectable levels of XIST whereas others did not. No significant contamination of the lines with mycoplasma, bacteria or cytopathic viruses was detected.
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| 10. |
- Bonamy, AKE, et al.
(författare)
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Wide variation in severe neonatal morbidity among very preterm infants in European regions
- 2019
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Ingår i: Archives of disease in childhood. Fetal and neonatal edition. - : BMJ. - 1468-2052 .- 1359-2998. ; 104:1, s. F36-F45
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Tidskriftsartikel (refereegranskat)abstract
- To investigate the variation in severe neonatal morbidity among very preterm (VPT) infants across European regions and whether morbidity rates are higher in regions with low compared with high mortality rates.DesignArea-based cohort study of all births before 32 weeks of gestational age.Setting16 regions in 11 European countries in 2011/2012.PatientsSurvivors to discharge from neonatal care (n=6422).Main outcome measuresSevere neonatal morbidity was defined as intraventricular haemorrhage grades III and IV, cystic periventricular leukomalacia, surgical necrotizing enterocolitis and retinopathy of prematurity grades ≥3. A secondary outcome included severe bronchopulmonary dysplasia (BPD), data available in 14 regions. Common definitions for neonatal morbidities were established before data abstraction from medical records. Regional severe neonatal morbidity rates were correlated with regional in-hospital mortality rates for live births after adjustment on maternal and neonatal characteristics.Results10.6% of survivors had a severe neonatal morbidity without severe BPD (regional range 6.4%–23.5%) and 13.8% including severe BPD (regional range 10.0%–23.5%). Adjusted inhospital mortality was 13.7% (regional range 8.4%–18.8%). Differences between regions remained significant after consideration of maternal and neonatal characteristics (P<0.001) and severe neonatal morbidity rates were not correlated with mortality rates (P=0.50).ConclusionSevere neonatal morbidity rates for VPT survivors varied widely across European regions and were independent of mortality rates.
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| 11. |
- Cuttini, M, et al.
(författare)
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Breastfeeding outcomes in European NICUs: impact of parental visiting policies
- 2019
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Ingår i: Archives of disease in childhood. Fetal and neonatal edition. - : BMJ. - 1468-2052 .- 1359-2998. ; 104:2, s. F151-
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Tidskriftsartikel (refereegranskat)abstract
- The documented benefits of maternal milk for very preterm infants have raised interest in hospital policies that promote breastfeeding. We investigated the hypothesis that more liberal parental policies are associated with increased breastfeeding at discharge from the neonatal unit.DesignProspective area-based cohort study.SettingNeonatal intensive care units (NICUs) in 19 regions of 11 European countries.PatientsAll very preterm infants discharged alive in participating regions in 2011–2012 after spending >70% of their hospital stay in the same NICU (n=4407).Main outcome measuresWe assessed four feeding outcomes at hospital discharge: any and exclusive maternal milk feeding, independent of feeding method; any and exclusive direct breastfeeding, defined as sucking at the breast. We computed a neonatal unit Parental Presence Score (PPS) based on policies regarding parental visiting in the intensive care area (range 1–10, with higher values indicating more liberal policies), and we used multivariable multilevel modified Poisson regression analysis to assess the relation between unit PPS and outcomes.ResultsPolicies regarding visiting hours, duration of visits and possibility for parents to stay during medical rounds and spend the night in unit differed within and across countries. After adjustment for potential confounders, infants cared for in units with liberal parental policies (PPS≥7) were about twofold significantly more likely to be discharged with exclusive maternal milk feeding and exclusive direct breastfeeding.ConclusionUnit policies promoting parental presence and involvement in care may increase the likelihood of successful breastfeeding at discharge for very preterm infants.
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| 17. |
- Callaghan, D. A., et al.
(författare)
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Geographic range and population size of the habitat specialist Codonoblepharon forsteri in a changing climate
- 2022
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Ingår i: Journal of Bryology. - 0373-6687 .- 1743-2820. ; 44:1, s. 35-40
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Tidskriftsartikel (refereegranskat)abstract
- Introduction: Codonoblepharon forsteri is a rare epiphytic moss characteristically associated with water-filled holes in trees. This study aims to review its range and population and assess effects of climate change.Methods: An inventory of sites from where C. forsteri has been recorded was compiled. Extent of Occurrence (EOO) and Area of Occupancy (AOO) were calculated. Population size was estimated, using an occupied tree as an ‘individual-equivalent’ of the moss. Climatic conditions of its current distribution were characterised, and an ensemble model of its distribution generated. The latter was projected onto present and future climatic layers.Results: C. forsteri has been recorded from 205 sites in 18 countries, in Europe, N Africa and SW Asia. It has been undergoing an overall decline. Most sites have few occupied trees, and a world population of 1000–10,000 individual-equivalents is estimated. Model projections suggest the species will experience a range increase of +0.27–0.78 by 2050 and +0.34–0.97 by 2070, especially in the NW, in particular across France and the UK. Range loss is predicted to be -0.16–0.23 in 2050 and -0.18–0.32 in 2070, affecting the driest areas of the current range around the Mediterranean, especially in N Africa.Conclusions: C. forsteri has a relatively large EOO but a relatively small AOO, likely the product of its habitat specialism. A major reason for recent declines appears to be widespread abandonment of traditional ‘pollarding’ of trees. The potential climatic range of the species will shift significantly northwards over the next few decades
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| 18. |
- Cederwall, Bo, et al.
(författare)
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NEW FEATURES OF SUPERDEFORMED BANDS IN HG-194
- 1994
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Ingår i: Physical Review Letters. - 0031-9007 .- 1079-7114. ; 72:20, s. 3150-3153
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Tidskriftsartikel (refereegranskat)abstract
- Two new features of superdeformed (SD) bands in the A almost-equal-to 190 region emerge from a study of Hg-194 with the Gammasphere detector array. A decrease of the dynamic moment of inertia is observed for rotational frequencies HBARomega greater-than-or-equal-to 0.4 MeV, confirming long standing expectations based on mean field calculations with pairing. Evidence for a small staggering in the SD transition energies is also observed, suggesting the presence of terms with fourfold symmetry in the SD Hamiltonian.
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| 19. |
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| 20. |
- Gepner, B. D., et al.
(författare)
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Comparison of human body models in frontal crashes with reclined seatback
- 2019
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Ingår i: Conference proceedings International Research Council on the Biomechanics of Injury, IRCOBI. - 2235-3151. ; , s. 293-307
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Konferensbidrag (refereegranskat)abstract
- Reclined seating configurations, relevant to the future of Autonomous Driving Systems is likely to challenge the current state-of-the-art restraint systems. Human body models (HBM) offer an attractive tool to support the design process, however their validity in the reclined scenario remains questionable. The goal of this study is to compare the response of selected HBMs in the frontal, reclined scenario, while utilizing a new prototype restraint system. A sled model with a generic seat, 50 deg seatback recline angle and a prototype 3-point belt system was used in this study. Four different male HBMs were compared, the Global Human Body Model Consortium (GHBMC) simplified occupant model (GHBMC-S), the GHBMC detailed model (GHBMC-D), Total Human Model for Safety SAFER (THUMS-S) model, and THUMS-v5 model. All HBMs showed good pelvis engagement, except GHBMC-D that submarined under the lap belt. Additionally, large differences were observed in pelvis and lumbar spine response between GHBMC and THUMS family models. Since no relevant PMHS data is currently available, it is impossible to evaluate the biofidelity of these models in the reclined scenarios. Evaluating the relative biofidelity of these models can only be accomplished with experimental data capturing detailed 3D skeletal kinematics and all the boundary forces necessary for model evaluation.
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| 21. |
- Hohenschurz-Schmidt, David, et al.
(författare)
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Recommendations for the development, implementation, and reporting of control interventions in efficacy and mechanistic trials of physical, psychological, and self-management therapies : the CoPPS Statement
- 2023
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Ingår i: BMJ. British Medical Journal. - : BMJ Publishing Group Ltd. - 0959-8146 .- 0959-535X. ; 381, s. e072108-
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Tidskriftsartikel (refereegranskat)abstract
- Control interventions (often called "sham," "placebo," or "attention controls") are essential for studying the efficacy or mechanism of physical, psychological, and self-management interventions in clinical trials. This article presents core recommendations for designing, conducting, and reporting control interventions to establish a quality standard in non-pharmacological intervention research. A framework of additional considerations supports researchers' decision making in this context. We also provide a reporting checklist for control interventions to enhance research transparency, usefulness, and rigour.
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| 22. |
- Koistinen, Ville Mikael, et al.
(författare)
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Metabolic changes in response to varying whole-grain wheat and rye intake
- 2024
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Ingår i: npj Science of Food. - 2396-8370. ; 8:1
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Tidskriftsartikel (refereegranskat)abstract
- Epidemiological studies have shown associations between whole-grain intake and lowered disease risk. A sufficient level of whole-grain intake to reach the health benefits has not been established, and there is limited knowledge about the impact of whole-grain intake on metabolite levels. In this clinical intervention study, we aimed to identify plasma and urine metabolites associated with two different intake levels of whole-grain wheat and rye and to correlate them with clinical plasma biomarkers. Healthy volunteers (N = 68) were divided into two groups receiving either whole-grain wheat or whole-grain rye in two four-week interventions with 48 and 96 g/d of whole grains consumed. The metabolomics of the plasma samples was performed with UPLC–QTOF-MS. Plasma alkylresorcinols were quantified with GC-MS and plasma and urinary mammalian lignans with HPLC-ECD. The high-dose intervention impacted the metabolite profile, including microbial metabolites, more in the rye-enriched diet compared with wheat. Among the increased metabolites were alkylresorcinol glucuronides, sinapyl alcohol, and pipecolic acid betaine, while the decreased metabolites included acylcarnitines and ether lipids. Plasma alkylresorcinols, urinary enterolactone, and total mammalian lignans reflected the study diets in a dose-dependent manner. Several key metabolites linked with whole-grain consumption and gut microbial metabolism increased in a linear manner between the two interventions. The results reveal that an increase in whole-grain intake, particularly rye, is strongly reflected in the metabolite profile, is correlated with clinical variables, and suggests that a diet rich in whole grains promotes the growth and/or metabolism of microbes producing potentially beneficial microbial metabolites.
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| 23. |
- Schaller, Matthieu, et al.
(författare)
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Swift : a modern highly parallel gravity and smoothed particle hydrodynamics solver for astrophysical and cosmological applications
- 2024
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Ingår i: Monthly notices of the Royal Astronomical Society. - 0035-8711 .- 1365-2966. ; 530:2, s. 2378-2419
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Tidskriftsartikel (refereegranskat)abstract
- Numerical simulations have become one of the key tools used by theorists in all the fields of astrophysics and cosmology. The development of modern tools that target the largest existing computing systems and exploit state-of-the-art numerical methods and algorithms is thus crucial. In this paper, we introduce the fully open-source highly-parallel, versatile, and modular coupled hydrodynamics, gravity, cosmology, and galaxy-formation code SWIFT. The software package exploits hybrid shared- and distributed-memory task-based parallelism, asynchronous communications, and domain-decomposition algorithms based on balancing the workload, rather than the data, to efficiently exploit modern high-performance computing cluster architectures. Gravity is solved for using a fast-multipole-method, optionally coupled to a particle mesh solver in Fourier space to handle periodic volumes. For gas evolution, multiple modern flavours of Smoothed Particle Hydrodynamics are implemented. SWIFT also evolves neutrinos using a state-of-the-art particle-based method. Two complementary networks of sub-grid models for galaxy formation as well as extensions to simulate planetary physics are also released as part of the code. An extensive set of output options, including snapshots, light-cones, power spectra, and a coupling to structure finders are also included. We describe the overall code architecture, summarize the consistency and accuracy tests that were performed, and demonstrate the excellent weak-scaling performance of the code using a representative cosmological hydrodynamical problem with ≈300 billion particles. The code is released to the community alongside extensive documentation for both users and developers, a large selection of example test problems, and a suite of tools to aid in the analysis of large simulations run with SWIFT.
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| 26. |
- Zeitlin, J, et al.
(författare)
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Authors' reply to Page and Rafi
- 2016
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Ingår i: BMJ (Clinical research ed.). - : BMJ. - 1756-1833. ; 354, s. i4671-
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)
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| 27. |
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