| 1. |
- Bottai, Matteo, et al.
(author)
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EULAR/ACR classification criteria for adult and juvenile idiopathic inflammatory myopathies and their major subgroups : a methodology report
- 2017
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In: RMD Open. - : BMJ. - 2056-5933. ; 3:2
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Journal article (peer-reviewed)abstract
- Objective To describe the methodology used to develop new classification criteria for adult and juvenile idiopathic inflammatory myopathies (IIMs) and their major subgroups.Methods An international, multidisciplinary group of myositis experts produced a set of 93 potentially relevant variables to be tested for inclusion in the criteria. Rheumatology, dermatology, neurology and paediatric clinics worldwide collected data on 976 IIM cases (74% adults, 26% children) and 624 non-IIM comparator cases with mimicking conditions (82% adults, 18% children). The participating clinicians classified each case as IIM or non-IIM. Generally, the classification of any given patient was based on few variables, leaving remaining variables unmeasured. We investigated the strength of the association between all variables and between these and the disease status as determined by the physician. We considered three approaches: (1) a probability-score approach, (2) a sum-of-items approach criteria and (3) a classification-tree approach.Results The approaches yielded several candidate models that were scrutinised with respect to statistical performance and clinical relevance. The probability-score approach showed superior statistical performance and clinical practicability and was therefore preferred over the others. We developed a classification tree for subclassification of patients with IIM. A calculator for electronic devices, such as computers and smartphones, facilitates the use of the European League Against Rheumatism/American College of Rheumatology (EULAR/ACR) classification criteria.Conclusions The new EULAR/ACR classification criteria provide a patient's probability of having IIM for use in clinical and research settings. The probability is based on a score obtained by summing the weights associated with a set of criteria items.
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| 2. |
- Carpenter, Stephen R., et al.
(author)
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Accelerate Synthesis in Ecology and Environmental Sciences
- 2009
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In: BioScience. - : Oxford University Press (OUP). - 0006-3568 .- 1525-3244. ; 59:8, s. 699-701
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Journal article (peer-reviewed)abstract
- Ecology is a leading discipline in the synthesis of diverse knowledge. Ecologists have had considerable experience in bringing together diverse, multinational data sets, disciplines, and cultural perspectives to address a wide range of issues in basic and applied science. Now is the time to build on this foundation and invest in ecological synthesis through new national or international programs. While synthesis takes place through many mechanisms, including individual efforts, working groups, and research networks, centers are extraordinarily effective institutional settings for advancing synthesis projects.
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| 3. |
- Deans, Andrew R, et al.
(author)
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Finding Our Way through Phenotypes.
- 2015
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In: PLoS Biology. - : Public Library of Science (PLoS). - 1545-7885. ; 13:1
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Journal article (peer-reviewed)abstract
- Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.
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| 4. |
- Notarnicola, A., et al.
(author)
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Autoantibodies against a subunit of mitochondrial respiratory chain complex I in inclusion body myositis
- 2023
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In: Annals of the Rheumatic Diseases. - : BMJ. - 0003-4967 .- 1468-2060. ; 82, s. 574-574
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Journal article (peer-reviewed)abstract
- Background Autoantibodies are found in up to 80% of patients with idiopathic inflammatory myopathies (IIM) and are associated with distinct clinical phenotypes [1]. Autoantibodies targeting cytosolic 5´-nucleotidase 1A (anti-cN1A) are currently the only known serum biomarker for the subgroup inclusion body myositis (IBM) (2), although detected even in other autoimmune diseases.Objectives To identify new autoimmune targets in IIM by antigen bead array assay.Methods In a first cross-sectional exploratory study, 357 antigens representing 268 proteins were incubated with plasma samples from 219 IIM (108 Polymyositis (PM), 80 Dermatomyositis (DM) and 31 IBM) patients, 349 Systemic Lupus Erythematosus (SLE) patients and 306 population controls for screening of IgG reactivity by antigen bead array. All samples were identified in the local biobank of the Rheumatology clinic, Karolinska University Hospital. Interesting results obtained for the IBM subgroup were then validated in an independent larger cohort of 287 patients with IBM followed at nine European rheumatological or neurological centers. IBM serum samples were explored by antigen bead array and results validated by western blot. As controls, serum samples from 30 patients with PM and 30 with DM, HLA-matched with the IBM Swedish cohort, were included. Demographics, laboratory, clinical, and muscle biopsy data of the IBM cohort was retrieved.Results In the exploratory study IgG reactivity towards NADH dehydrogenase 1 α subcomplex 11 (NDUFA11), a subunit of the membrane-bound mitochondrial respiratory chain complex I, was discovered with higher frequency in the IBM (9,7%) than PM (2,8%) and DM samples (2,5%), although the difference was not statistically significant. Anti-NDUFA11 IgG was also found in 2,3% of SLE and 2,6% of population control samples. In the validation study anti-NDUFA11 autoantibodies were detected in 11/287 IBM patients (3,8%), 0/30 PM and 0/30 DM patients. Reactivity against NDUFA11 could be confirmed by western blot (Table 1, Figure 1). The eleven anti-NDUFA11 positive patients showed a trend of lower frequency of wheelchair/walker ever use and higher creatine kinase levels at time of IBM diagnosis compared to the anti-NDUFA11 negative group. Ragged red fibers were significantly more prevalent in anti-NDUFA11 positive than negative patients (p=0.04). Anti-cN1A autoantibodies were detected in 98/287 (34,1%) of IBM, 3/30 (10%) DM and 9/29 (31%) PM patients, p=0.03. Coexistence of anti NDUFA11 and anti-cN1A antibodies was observed in 3 IBM patients.Conclusion Our results reveal a new autoimmune target in the mitochondrial respiratory chain complex I that might be specifically associated with IBM. This is of particular interest as mitochondrial abnormalities are known histological findings in muscle biopsies of IBM patients.References [1]Galindo-Feria AS, Wang G, Lundberg IE. Autoantibodies: Pathogenic or epiphenomenon. Best Pract Res Clin Rheumatol. 2022;36(2):101767.[2]Herbert MK,et al. Disease specificity of autoantibodies to cytosolic 5’-nucleotidase 1A in sporadic inclusion body myositis versus known autoimmune diseases. Ann Rheum Dis. 2016;75(4):696-701.
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| 5. |
- Abulaiti, Yiming, et al.
(author)
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Determination of the strong coupling constant alpha(s) from transverse energy-energy correlations in multijet events at root s=8 TeV using the ATLAS detector
- 2017
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In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 77:12
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Journal article (peer-reviewed)abstract
- Measurements of transverse energy-energy correlations and their associated asymmetries in multi-jet events using the ATLAS detector at the LHC are presented. The data used correspond to vs = 8 TeV proton-proton collisions with an integrated luminosity of 20.2 fb(-1). The results are presented in bins of the scalar sum of the transverse momenta of the two leading jets, unfolded to the particle level and compared to the predictions from Monte Carlo simulations. A comparison with next-to-leading-order perturbative QCD is also performed, showing excellent agreement within the uncertainties. From this comparison, the value of the strong coupling constant is extracted for different energy regimes, thus testing the running of alpha(s)(mu) predicted in QCD up to scales over 1 TeV. A global fit to the transverse energy-energy correlation distributions yields alpha(s)(m(Z)) = 0.1162 +/- 0.0011 (exp.)(-0.0070)(+0.0084) (theo.), while a global fit to the asymmetry distributions yields a value of alpha(s)(m(Z)) = 0.1196 +/- 0.0013 (exp.)(-0.0045)(+0.0075) (theo.).
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| 6. |
- Abulaiti, Yiming, et al.
(author)
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Measurement of jet fragmentation in Pb plus Pb and pp collisions at root s(NN)=2.76 TeV with the ATLAS detector at the LHC
- 2017
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In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 77:6
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Journal article (peer-reviewed)abstract
- The distributions of transverse momentum and longitudinal momentum fraction of charged particles in jets are measured in Pb+Pb and pp collisions with the ATLAS detector at the LHC. The distributions are measured as a function of jet transverse momentum and rapidity. The analysis utilises an integrated luminosity of 0.14 nb(-1) of Pb+Pb data and 4.0 pb(-1) of pp data collected in 2011 and 2013, respectively, at the same centre-of-mass energy of 2.76 TeV per colliding nucleon pair. The distributions measured in pp collisions are used as a reference for those measured in Pb+Pb collisions in order to evaluate the impact on the internal structure of jets from the jet energy loss of fast partons propagating through the hot, dense medium created in heavy-ion collisions. Modest but significant centrality-dependent modifications of fragmentation functions in Pb+Pb collisions with respect to those in pp collisions are seen. No significant dependence of modifications on jet p(T) and rapidity selections is observed except for the fragments with the highest transverse momenta for which some reduction of yields is observed for more forward jets.
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| 7. |
- Abulaiti, Yiming, et al.
(author)
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Measurement of multi-particle azimuthal correlations in pp, p plus Pb and low-multiplicity Pb plus Pb collisions with the ATLAS detector
- 2017
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In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 77:6
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Journal article (peer-reviewed)abstract
- Multi-particle cumulants and corresponding Fourier harmonics are measured for azimuthal angle distributions of charged particles in pp collisions at root S = 5.02 and 13 TeV and in p + Pb collisions at root S-NN = 5.02 TeV, and compared to the results obtained for low-multiplicity Pb + Pb collisions at root S-NN = 2.76 TeV. These measurements aim to assess the collective nature of particle production. The measurements of multi-particle cumulants confirm the evidence for collective phenomena in p + Pb and low-multiplicity Pb + Pb collisions. On the other hand, the pp results for four-particle cumulants do not demonstrate collective behaviour, indicating that they may be biased by contributions from non-flow correlations. A comparison of multi-particle cumulants and derived Fourier harmonics across different collision systems is presented as a function of the charged-particle multiplicity. For a given multiplicity, the measured Fourier harmonics are largest in Pb + Pb, smaller in p + Pb and smallest in pp collisions. The pp results show no dependence on the collision energy, nor on the multiplicity.
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| 8. |
- Abulaiti, Yiming, et al.
(author)
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Measurement of the cross-section for electroweak production of dijets in association with a Z boson in pp collisions at root s=13 TeV with the ATLAS detector
- 2017
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In: Physics Letters B. - : Elsevier BV. - 0370-2693 .- 1873-2445. ; 775, s. 206-228
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Journal article (peer-reviewed)abstract
- The cross-section for the production of two jets in association with a leptonically decaying Z boson (Zjj) is measured in proton-proton collisions at a centre-of-mass energy of 13 TeV, using data recorded with the ATLAS detector at the Large Hadron Collider, corresponding to an integrated luminosity of 3.2 fb(-1). The electroweak Zjj cross-section is extracted in a fiducial region chosen to enhance the electroweak contribution relative to the dominant Drell-Yan Zjj process, which is constrained using a data-driven approach. The measured fiducial electroweak cross-section is sigma(Zjj)(EW) = 119 +/- 16 (stat.) +/- 20 (syst.) +/- 2 (lumi.) fb for dijet invariant mass greater than 250 GeV, and 34.2 +/- 5.8 (stat.) +/- 5.5 (syst.) +/- 0.7 (lumi.) fb for dijet invariant mass greater than 1 TeV. Standard Model predictions are in agreement with the measurements. The inclusive Zjj cross-section is also measured in six different fiducial regions with varying contributions from electroweak and Drell-Yan Zjj production.
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| 9. |
- Abulaiti, Yiming, et al.
(author)
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Measurement of the inclusive jet cross-sections in proton-proton collisions at root s=8 TeV with the ATLAS detector
- 2017
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In: Journal of High Energy Physics (JHEP). - : SPRINGER. - 1126-6708 .- 1029-8479. ; :9
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Journal article (peer-reviewed)abstract
- Inclusive jet production cross-sections are measured in proton-proton collisions at a centre-of-mass energy of root s = 8 TeV recorded by the ATLAS experiment at the Large Hadron Collider at CERN. The total integrated luminosity of the analysed data set amounts to 20.2 fb(-1). Double-differential cross-sections are measured for jets defined by the anti-k(t) jet clustering algorithm with radius parameters of R = 0.4 and R = 0.6 and are presented as a function of the jet transverse momentum, in the range between 70 GeV and 2.5 TeV and in six bins of the absolute jet rapidity, between 0 and 3.0. The measured cross-sections are compared to predictions of quantum chromodynamics, calculated at next-to-leading order in perturbation theory, and corrected for non-perturbative and electroweak effects. The level of agreement with predictions, using a selection of different parton distribution functions for the proton, is quantified. Tensions between the data and the theory predictions are observed.
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| 10. |
- Abulaiti, Yiming, et al.
(author)
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Measurement of the W-boson mass in pp collisions at root s=7 TeV with the ATLAS detector
- 2018
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In: European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6044 .- 1434-6052. ; 78:2
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Journal article (peer-reviewed)abstract
- A measurement of the mass of the W boson is presented based on proton-proton collision data recorded in 2011 at a centre-of-mass energy of 7 TeV with the ATLAS detector at the LHC, and corresponding to 4.6 fb(-1) of integrated luminosity. The selected data sample consists of 7.8 x 10(6) candidates in the W -> mu nu channel and 5.9 x 10(6) candidates in the W -> e nu channel. The W-boson mass is obtained from template fits to the reconstructed distributions of the charged lepton transverse momentum and of the W boson transverse mass in the electron and muon decay channels, yielding m(W) = 80370 +/- 7 (stat.) +/- 11(exp. syst.) +/- 14 (mod. syst.) MeV = 80370 +/- 19 MeV, where the first uncertainty is statistical, the second corresponds to the experimental systematic uncertainty, and the third to the physics-modelling systematic uncertainty. A measurement of the mass difference between the W+ and W- bosons yields m(W+) - m(W-) = -29 +/- 28 MeV.
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