| 11. |
- Buckley, Andy, et al.
(författare)
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Rivet user manual
- 2013
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Ingår i: Computer Physics Communications. - : Elsevier BV. - 0010-4655. ; 184:12, s. 2803-2819
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Tidskriftsartikel (refereegranskat)abstract
- This is the manual and user guide for the Rivet system for the validation and tuning of Monte Carlo event generators. As well as the core Rivet library, this manual describes the usage of the rivet program and the AGILe generator interface library. The depth and level of description is chosen for users of the system, starting with the basics of using validation code written by others, and then covering sufficient details to write new Rivet analyses and calculational components. Program summary Program title: Rivet Catalogue identifier: AEPS_v1_0 Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEPS_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 571126 No. of bytes in distributed program, including test data, etc.: 4717522 Distribution format: tar.gz Programming language: C++, Python. Computer: PC running Linux, Mac. Operating system: Linux, Mac OS. RAM: 20 MB Classification: 11.9, 11.2. External routines: HepMC (https://savannah.cern.ch/projects/hepmc/), GSL (http://www.gnu.org/software/gsl/manual/gsl-ref.html), FastJet (http://fastjet.fr/), Python (http://www.python.org/), Swig (http://www.swig.org/), Boost (http://www.boostsoftware.com/), YAML (http://www.yaml.org/spec/1.2/spec.html) Nature of problem: Experimental measurements from high-energy particle colliders should be defined and stored in a general framework such that it is simple to compare theory predictions to them. Rivet is such a framework, and contains at the same time a large collection of existing measurements. Solution method: Rivet is based on HepMC events, a standardised output format provided by many theory simulation tools. Events are processed by Rivet to generate histograms for the requested list of analyses, incorporating all experimental phase space cuts and histogram definitions. Restrictions: Cannot calculate statistical errors for correlated events as they appear in NLO calculations. Unusual features: It is possible for the user to implement and use their own custom analysis as a module without having to modify the main Rivet code/installation. Running time: Depends on the number and complexity of analyses being applied, but typically a few hundred events per second. (C) 2013 Elsevier B.V. All rights reserved.
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| 12. |
- Buckley, Andy, et al.
(författare)
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Systematic event generator tuning for the LHC
- 2010
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Ingår i: European Physical Journal C. Particles and Fields. - : Springer Science and Business Media LLC. - 1434-6044. ; 65:1-2, s. 331-357
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Tidskriftsartikel (refereegranskat)abstract
- Abstract in UndeterminedIn this article we describe Professor, a new program for tuning model parameters of Monte Carlo event generators to experimental data by parameterising the per-bin generator response to parameter variations and numerically optimising the parameterised behaviour. Simulated experimental analysis data is obtained using the Rivet analysis toolkit. This paper presents the Professor procedure and implementation, illustrated with the application of the method to tunes of the Pythia 6 event generator to data from the LEP/SLD and Tevatron experiments. These tunes are substantial improvements on existing standard choices, and are recommended as base tunes for LHC experiments, to be themselves systematically improved upon when early LHC data is available.
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| 13. |
- Bustamante, Mariona, et al.
(författare)
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A genome-wide association meta-analysis of diarrhoeal disease in young children identifies FUT2 locus and provides plausible biological pathways.
- 2016
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Ingår i: Human molecular genetics. - : Oxford University Press (OUP). - 1460-2083 .- 0964-6906. ; 25:18, s. 4127-4142
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Tidskriftsartikel (refereegranskat)abstract
- More than a million childhood diarrhoeal episodes occur worldwide each year, and in developed countries a considerable part of them are caused by viral infections. In this study, we aimed to search for genetic variants associated with diarrhoeal disease in young children by meta-analyzing genome-wide association studies, and to elucidate plausible biological mechanisms. The study was conducted in the context of the Early Genetics and Lifecourse Epidemiology (EAGLE) consortium. Data about diarrhoeal disease in two time windows (around 1 year of age and around 2 years of age) was obtained via parental questionnaires, doctor interviews or medical records. Standard quality control and statistical tests were applied to the 1000 Genomes imputed genotypic data. The meta-analysis (N=5758) followed by replication (N=3784) identified a genome-wide significant association between rs8111874 and diarrhoea at age 1 year. Conditional analysis suggested that the causal variant could be rs601338 (W154X) in the FUT2 gene. Children with the A allele, which results in a truncated FUT2 protein, had lower risk of diarrhoea. FUT2 participates in the production of histo-blood group antigens and has previously been implicated in the susceptibility to infections, including Rotavirus and Norovirus Gene-set enrichment analysis suggested pathways related to the histo-blood group antigen production, and the regulation of ion transport and blood pressure. Among others, the gastrointestinal tract, and the immune and neuro-secretory systems were detected as relevant organs. In summary, this genome-wide association meta-analysis suggests the implication of the FUT2 gene in diarrhoeal disease in young children from the general population.
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| 14. |
- Delgado, Luis Fernando, et al.
(författare)
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Phylogeny-based comparative genomics of Vibrio vulnificus links genetic traits to pathogenicity
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Vibrio vulnificus is a natural part of the microbiome of brackish waters worldwide. It is also an opportunistic pathogen that can cause severe infections and septicemia via consumption of seafood or through wound infections. The species possess diverse virulence factors, yet its precise disease mechanism remains undefined. Comparative genomics between clinical and environmental isolates offers a means to identify key virulence genes, but the scarcity of environmental isolates for V. vulnificus has constituted a significant limitation. Here we sequenced genomes of 82 V. vulnificus isolates from water, sediment and seagrass surface from stations along the Baltic Sea coast and complemented these with 208 and 117 previously sequenced clinical and environmental genomes, respectively, in a comparative analysis. Phylogenetic reconstruction corroborated earlier analysis with four main lineages forming within the species. Strains from the Baltic Sea region were confined to certain phylogenetic lineages (L4 and sublineages L2c and L2e) whereas clinical and environmental strains were found in all lineages, indicting that the phylogenetic structure of V. vulnificus reflects adaptations to specific environmental conditions rather than pathogenicity. Employing orthologue enrichment analysis in a phylogenetic framework using the PhyloBOTL pipeline developed in this work revealed 58 significantly enriched orthologs in clinical compared to environmental isolates. These orthologs were grouped into 18 co-localisation clusters based on the corresponding genes’ proximity in the genomes. The co-localisation clusters entailed clusters with 1 genes previously linked with pathogenicity in V. vulnificus, such as genes for capsular polysaccharide (CPS) synthesis and biofilm formation, but also clusters with genes not previously associated with virulence in the species. Examples of the latter were genes for pilus biosynthesis of the usher-chaperone (CU) pathway, for spermidine synthesis, and for effector proteins of the Type VI secretion system. Finally we leveraged on the clinically enriched genes to design PCR primers for detection and surveillance of pathogenic V. vulnificus strains.
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| 15. |
- Ekeberg, Tomas, 1983-, et al.
(författare)
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Three-dimensional structure determination with an X-ray laser
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Three-dimensional structure determination of a non-crystalline virus has been achieved from a set of randomly oriented continuous diffraction patterns captured with an X-ray laser. Intense, ultra-short X-ray pulses intercepted a beam of single mimivirus particles, producing single particle X-ray diffraction patterns that are assembled into a three-dimensional amplitude distribution based on statistical consistency. Phases are directly retrieved from the assembled Fourier distribution to synthesize a three-dimensional image. The resulting electron density reveals a pseudo-icosahedral asymmetric virion structure with a compartmentalized interior, within which the DNA genome occupies only about a fifth of the volume enclosed by the capsid. Additional electron microscopy data indicate the genome has a chromatin-like fiber structure that has not previously been observed in a virus.
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| 16. |
- Fieg, Max, et al.
(författare)
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Tuning pythia for forward physics experiments
- 2024
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Ingår i: Physical Review D. - 2470-0010. ; 109:1
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Tidskriftsartikel (refereegranskat)abstract
- Event generators like pythia play an important role in physics studies at the Large Hadron Collider (LHC). While they make accurate predictions in the central region, i.e., at pseudorapidities η<5, a disagreement between pythia and measurements in the forward region η>7 has been observed. We introduce a dedicated forward physics tune for the pythia event generator to be used for forward physics studies at the LHC, which uses a more flexible modeling of beam remnant hadronization and is tuned to available particle spectra measured by LHCf. Furthermore, we provide an uncertainty estimate on the new tune in a data-driven way which can be used as a means of flux uncertainty for future forward physics studies. We demonstrate an application of our tune by showing the updated neutrino and dark photon spectra at the FASER experiment.
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| 17. |
- Flexeder, Claudia, et al.
(författare)
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Second-hand smoke exposure in adulthood and lower respiratory health during 20 year follow up in the European Community Respiratory Health Survey
- 2019
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Ingår i: Respiratory Research. - : BioMed Central. - 1465-9921 .- 1465-993X. ; 20
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Tidskriftsartikel (refereegranskat)abstract
- Early life exposure to tobacco smoke has been extensively studied but the role of second-hand smoke (SHS) for new-onset respiratory symptoms and lung function decline in adulthood has not been widely investigated in longitudinal studies. Our aim is to investigate the associations of exposure to SHS in adults with respiratory symptoms, respiratory conditions and lung function over 20 years. We used information from 3011 adults from 26 centres in 12 countries who participated in the European Community Respiratory Health Surveys I-III and were never or former smokers at all three surveys. Associations of SHS exposure with respiratory health (asthma symptom score, asthma, chronic bronchitis, COPD) were analysed using generalised linear mixed-effects models adjusted for confounding factors (including sex, age, smoking status, socioeconomic status and allergic sensitisation). Linear mixed-effects models with additional adjustment for height were used to assess the relationships between SHS exposure and lung function levels and decline. Reported exposure to SHS decreased in all 26 study centres over time. The prevalence of SHS exposure was 38.7% at baseline (1990-1994) and 7.1% after the 20-year follow-up (2008-2011). On average 2.4% of the study participants were not exposed at the first, but were exposed at the third examination. An increase in SHS exposure over time was associated with doctor-diagnosed asthma (odds ratio (OR): 2.7; 95% confidence interval (95%-CI): 1.2-5.9), chronic bronchitis (OR: 4.8; 95%-CI: 1.6-15.0), asthma symptom score (count ratio (CR): 1.9; 95%-CI: 1.2-2.9) and dyspnoea (OR: 2.7; 95%-CI: 1.1-6.7) compared to never exposed to SHS. Associations between increase in SHS exposure and incidence of COPD (OR: 2.0; 95%-CI: 0.6-6.0) or lung function (beta: - 49 ml; 95%-CI: -132, 35 for FEV1 and beta: - 62 ml; 95%-CI: -165, 40 for FVC) were not apparent. Exposure to second-hand smoke may lead to respiratory symptoms, but this is not accompanied by lung function changes.
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| 18. |
- Höche, Stefan, et al.
(författare)
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Simulation of vector boson plus many jet final states at the high luminosity LHC
- 2019
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Ingår i: Physical Review D. - 2470-0010. ; 100:1
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Tidskriftsartikel (refereegranskat)abstract
- We present a novel event-generation framework for the efficient simulation of vector boson plus multijet backgrounds at the high-luminosity LHC and at possible future hadron colliders. Message passing interface parallelization of parton-level and particle-level event generation and storage of parton-level event information using the HDF5 data format allow us to obtain leading-order merged Monte Carlo predictions with up to nine jets in the final state. The parton-level event samples generated in this manner correspond to an integrated luminosity of 3 ab-1 and are made publicly available for future phenomenological studies.
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| 19. |
- Imboden, Medea, et al.
(författare)
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Epigenome-wide association study of lung function level and its change
- 2019
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Ingår i: European Respiratory Journal. - : European Respiratory Society. - 0903-1936 .- 1399-3003. ; 54:1
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Tidskriftsartikel (refereegranskat)abstract
- Previous reports link differential DNA methylation (DNAme) to environmental exposures that are associated with lung function. Direct evidence on lung function DNAme is, however, limited. We undertook an agnostic epigenome-wide association study (EWAS) on pre-bronchodilation lung function and its change in adults.In a discovery-replication EWAS design, DNAme in blood and spirometry were measured twice, 6-15 years apart, in the same participants of three adult population-based discovery cohorts (n=2043). Associated DNAme markers (p<5×10-7) were tested in seven replication cohorts (adult: n=3327; childhood: n=420). Technical bias-adjusted residuals of a regression of the normalised absolute β-values on control probe-derived principle components were regressed on level and change of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC) and their ratio (FEV1/FVC) in the covariate-adjusted discovery EWAS. Inverse-variance-weighted meta-analyses were performed on results from discovery and replication samples in all participants and never-smokers.EWAS signals were enriched for smoking-related DNAme. We replicated 57 lung function DNAme markers in adult, but not childhood samples, all previously associated with smoking. Markers not previously associated with smoking failed replication. cg05575921 (AHRR (aryl hydrocarbon receptor repressor)) showed the statistically most significant association with cross-sectional lung function (FEV1/FVC: pdiscovery=3.96×10-21 and pcombined=7.22×10-50). A score combining 10 DNAme markers previously reported to mediate the effect of smoking on lung function was associated with lung function (FEV1/FVC: p=2.65×10-20).Our results reveal that lung function-associated methylation signals in adults are predominantly smoking related, and possibly of clinical utility in identifying poor lung function and accelerated decline. Larger studies with more repeat time-points are needed to identify lung function DNAme in never-smokers and in children.
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| 20. |
- Jackson, Victoria E, et al.
(författare)
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Meta-analysis of exome array data identifies six novel genetic loci for lung function.
- 2018
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Ingår i: Wellcome open research. - : F1000 Research Ltd. - 2398-502X. ; 3
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Tidskriftsartikel (refereegranskat)abstract
- Background: Over 90 regions of the genome have been associated with lung function to date, many of which have also been implicated in chronic obstructive pulmonary disease. Methods: We carried out meta-analyses of exome array data and three lung function measures: forced expiratory volume in one second (FEV 1), forced vital capacity (FVC) and the ratio of FEV 1 to FVC (FEV 1/FVC). These analyses by the SpiroMeta and CHARGE consortia included 60,749 individuals of European ancestry from 23 studies, and 7,721 individuals of African Ancestry from 5 studies in the discovery stage, with follow-up in up to 111,556 independent individuals. Results: We identified significant (P<2·8x10 -7) associations with six SNPs: a nonsynonymous variant in RPAP1, which is predicted to be damaging, three intronic SNPs ( SEC24C, CASC17 and UQCC1) and two intergenic SNPs near to LY86 and FGF10. Expression quantitative trait loci analyses found evidence for regulation of gene expression at three signals and implicated several genes, including TYRO3 and PLAU. Conclusions: Further interrogation of these loci could provide greater understanding of the determinants of lung function and pulmonary disease.
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