| 1. |
- Brown, Richard J. P., et al.
(författare)
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Liver-expressed Cd302 and Cr1l limit hepatitis C virus cross-species transmission to mice
- 2020
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Ingår i: Science Advances. - : American Association for the Advancement of Science. - 2375-2548. ; 6:45
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Tidskriftsartikel (refereegranskat)abstract
- Hepatitis C virus (HCV) has no animal reservoir, infecting only humans. To investigate species barrier determinants limiting infection of rodents, murine liver complementary DNA library screening was performed, identifying transmembrane proteins Cd302 and Cr1l as potent restrictors of HCV propagation. Combined ectopic expression in human hepatoma cells impeded HCV uptake and cooperatively mediated transcriptional dysregulation of a noncanonical program of immunity genes. Murine hepatocyte expression of both factors was constitutive and not interferon inducible, while differences in liver expression and the ability to restrict HCV were observed between the murine orthologs and their human counterparts. Genetic ablation of endogenous Cd302 expression in human HCV entry factor transgenic mice increased hepatocyte permissiveness for an adapted HCV strain and dysregulated expression of metabolic process and host defense genes. These findings highlight human-mouse differences in liver-intrinsic antiviral immunity and facilitate the development of next-generation murine models for preclinical testing of HCV vaccine candidates.
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| 2. |
- Schoch, Conrad L., et al.
(författare)
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Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi
- 2014
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Ingår i: Database: The Journal of Biological Databases and Curation. - : Oxford University Press (OUP). - 1758-0463. ; 2014:bau061, s. 1-21
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Tidskriftsartikel (refereegranskat)abstract
- DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.
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| 17. |
- Abulaiti, Yiming, et al.
(författare)
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Search for the Standard Model Higgs boson produced by vector-boson fusion and decaying to bottom quarks in root s=8TeV pp collisions with the ATLAS detector
- 2016
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Ingår i: Journal of High Energy Physics (JHEP). - : Springer. - 1126-6708 .- 1029-8479. ; :11
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Tidskriftsartikel (refereegranskat)abstract
- A search with the ATLAS detector is presented for the Standard Model Higgs boson produced by vector-boson fusion and decaying to a pair of bottom quarks, using 20.2 fb(-1) of LHC proton-proton collision data at root s - 8 TeV. The signal is searched for as a resonance in the invariant mass distribution of a pair of jets containing b-hadrons in vector-boson-fusion candidate events. The yield is measured to be -0.8 +/- 2.3 times the Standard Model cross-section for a Higgs boson mass of 125 GeV. The upper limit on the cross-section times the branching ratio is found to be 4.4 times the Standard Model cross-section at the 95% confidence level, consistent with the expected limit value of 5.4 (5.7) in the background-only (Standard Model production) hypothesis.
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| 18. |
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| 19. |
- Charpentier Ljungqvist, Fredrik, 1982-, et al.
(författare)
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Regional Patterns of Late Medieval and Early Modern European Building Activity Revealed by Felling Dates
- 2022
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Ingår i: Frontiers in Ecology and Evolution. - : Frontiers Media SA. - 2296-701X. ; 9
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Tidskriftsartikel (refereegranskat)abstract
- Although variations in building activity are a useful indicator of societal well-being and demographic development, historical datasets for larger regions and longer periods are still rare. Here, we present 54,045 annually precise dendrochronological felling dates from historical construction timber from across most of Europe between 1250 and 1699 CE to infer variations in building activity. We use geostatistical techniques to compare spatiotemporal dynamics in past European building activity against independent demographic, economic, social and climatic data. We show that the felling dates capture major geographical patterns of demographic trends, especially in regions with dense data coverage. A particularly strong negative association is found between grain prices and the number of felling dates. In addition, a significant positive association is found between the number of felling dates and mining activity. These strong associations, with well-known macro-economic indicators from pre-industrial Europe, corroborate the use of felling dates as an independent source for exploring large-scale fluctuations of societal well-being and demographic development. Three prominent examples are the building boom in the Hanseatic League region of northeastern Germany during the 13th century, the onset of the Late Medieval Crisis in much of Europec. 1300, and the cessation of building activity in large parts of central Europe during armed conflicts such as the Thirty Years’ War (1618–1648 CE). Despite new insights gained from our European-wide felling date inventory, further studies are needed to investigate changes in construction activity of high versus low status buildings, and of urban versus rural buildings, and to compare those results with a variety of historical documentary sources and natural proxy archives.
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| 20. |
- Claussnitzer, Melina, et al.
(författare)
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Leveraging cross-species transcription factor binding site patterns: from diabetes risk Loci to disease mechanisms.
- 2014
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Ingår i: Cell. - : Elsevier BV. - 1097-4172 .- 0092-8674. ; 156:1-2, s. 343-358
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Tidskriftsartikel (refereegranskat)abstract
- Genome-wide association studies have revealed numerous risk loci associated with diverse diseases. However, identification of disease-causing variants within association loci remains a major challenge. Divergence in gene expression due to cis-regulatory variants in noncoding regions is central to disease susceptibility. We show that integrative computational analysis of phylogenetic conservation with a complexity assessment of co-occurring transcription factor binding sites (TFBS) can identify cis-regulatory variants and elucidate their mechanistic role in disease. Analysis of established type 2 diabetes risk loci revealed a striking clustering of distinct homeobox TFBS. We identified the PRRX1 homeobox factor as a repressor of PPARG2 expression in adipose cells and demonstrate its adverse effect on lipid metabolism and systemic insulin sensitivity, dependent on the rs4684847 risk allele that triggers PRRX1 binding. Thus, cross-species conservation analysis at the level of co-occurring TFBS provides a valuable contribution to the translation of genetic association signals to disease-related molecular mechanisms.
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| 21. |
- Grossmann, Igor, et al.
(författare)
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Insights into the accuracy of social scientists' forecasts of societal change
- 2023
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Ingår i: Nature Human Behaviour. - : Springer Nature. - 2397-3374. ; 7, s. 484-501
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Tidskriftsartikel (refereegranskat)abstract
- How well can social scientists predict societal change, and what processes underlie their predictions? To answer these questions, we ran two forecasting tournaments testing the accuracy of predictions of societal change in domains commonly studied in the social sciences: ideological preferences, political polarization, life satisfaction, sentiment on social media, and gender-career and racial bias. After we provided them with historical trend data on the relevant domain, social scientists submitted pre-registered monthly forecasts for a year (Tournament 1; N = 86 teams and 359 forecasts), with an opportunity to update forecasts on the basis of new data six months later (Tournament 2; N = 120 teams and 546 forecasts). Benchmarking forecasting accuracy revealed that social scientists' forecasts were on average no more accurate than those of simple statistical models (historical means, random walks or linear regressions) or the aggregate forecasts of a sample from the general public (N = 802). However, scientists were more accurate if they had scientific expertise in a prediction domain, were interdisciplinary, used simpler models and based predictions on prior data. How accurate are social scientists in predicting societal change, and what processes underlie their predictions? Grossmann et al. report the findings of two forecasting tournaments. Social scientists' forecasts were on average no more accurate than those of simple statistical models.
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| 22. |
- Seifert, Frank, et al.
(författare)
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Tempo Induction by Stream-Based Evaluation of Musical Events
- 2006
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Ingår i: ISMIR 2006. ; , s. 344-345
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Konferensbidrag (refereegranskat)abstract
- We present an approach for tempo induction that is based on a more perception-oriented analysis of inter-onset intervals. Therefore we utilize auditory grouping concepts and define some rules for their formation. Finally, we show preliminary results that confirm our aim of improving the quality of tempo induction by reducing the amount of perceptually irrelevant data.
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| 23. |
- Seifert, Michael, et al.
(författare)
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Exploiting prior knowledge and gene distances in the analysis of tumor expression profiles with extended Hidden Markov Models.
- 2011
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Ingår i: Bioinformatics (Oxford, England). - : Oxford University Press (OUP). - 1367-4811 .- 1367-4803. ; 27:12, s. 1645-52
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Tidskriftsartikel (refereegranskat)abstract
- Changes in gene expression levels play a central role in tumors. Additional information about the distribution of gene expression levels and distances between adjacent genes on chromosomes should be integrated into the analysis of tumor expression profiles.We use a Hidden Markov Model with distance-scaled transition matrices (DSHMM) to incorporate chromosomal distances of adjacent genes on chromosomes into the identification of differentially expressed genes in breast cancer. We train the DSHMM by integrating prior knowledge about potential distributions of expression levels of differentially expressed and unchanged genes in tumor. We find that especially the combination of these data and to a lesser extent the modeling of distances between adjacent genes contribute to a substantial improvement of the identification of differentially expressed genes in comparison to other existing methods. This performance benefit is also supported by the identification of genes well known to be associated with breast cancer. That suggests applications of DSHMMs for screening of other tumor expression profiles.The DSHMM is available as part of the open-source Java library Jstacs (www.jstacs.de/index.php/DSHMM).
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| 24. |
- Weber, Manuel, et al.
(författare)
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Changes in Tumor-to-Blood Ratio as a prognostic marker for progression-free survival and overall survival in neuroendocrine tumor patients undergoing PRRT
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Background:Historically, patient selection for peptide receptor radionuclide therapy (PRRT) has been performed by virtue of somatostatin-receptor scintigraphy (SRS). In recent years, somatostatin-receptor positron emission tomography (SSTR-PET) has gradually replaced SRS because of its improved diagnostic capacity, creating an unmet need for SSTR-PET-based selection criteria for PRRT. Tumor-to-Blood-ratio (TBR) measurements have shown high correlation with the net influx rate Ki, reflecting the tumor somatostatin-receptor expression, to a higher degree than standardized uptake value (SUV) measurements. TBR may therefore predict treatment response to PRRT. In addition, changes in semiquantitative SSTR-PET parameters have been shown to predate morphological changes, making them a suitable metric for response assessment. Methods:The institutional database of the Department of Nuclear Medicine (University Hospital Essen) was searched for NET patients undergoing ≥2 PRRT cycles with available baseline and follow-up SSTR-PET. Two blinded independent readers reported the occurrence of new lesions quantified tumor uptake of up to 9 lesions per-patient using SUV, TBR, and tumor-spleen ratio (TSR). The association between baseline TBR and changes in uptake / occurrence of new lesions with progression-free survival (PFS) and overall survival (OS) was tested by use of a Cox regression model and log-rank test. Results: Patients with baseline TBR in the 1st quartile had a shorter PFS (14.4 months) than those in the 3rd (23.7 months; p=0.03) and 4th (24.1 months; p=0.02) quartile. Similarly, these patients had significantly shorter OS (32.5 months) than those with baseline TBR in the 2nd (41.8 months; p=0.03), 3rd (69.2 months; p<0.01), and 4th (42.7 months; p=0.03) quartile. Baseline to follow-up increases in TBR were independently associated with shorter PFS when accounting for prognostic markers, e.g. RECIST response (Hazard Ratio=3.29[95%CI= 1.62-6.68]; p<0.01). This was confirmed with regards to OS (Hazard Ratio=1.94[95%CI= 1.14-3.32]; p=0.02). Changes in TSR and SUVmean were not associated with PFS or OS. Conclusions: Baseline TBR as well as changes in TBR were significantly associated with PFS and OS and may improve patient selection and morphological response assessment. Future trials need to assess the role of TBR for therapy monitoring also during PRRT, and prospectively explore TBR as a predictive marker for patient selection.
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| 25. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review C (Nuclear Physics). - 0556-2813 .- 1089-490X. ; 92:3
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Tidskriftsartikel (refereegranskat)
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| 26. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: The European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6052. ; 75:7
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Tidskriftsartikel (refereegranskat)
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| 27. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: The European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6052. ; 75:7
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Tidskriftsartikel (refereegranskat)
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| 28. |
- Aad, G., et al.
(författare)
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- 2015
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Tidskriftsartikel (refereegranskat)
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| 29. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: The European Physical Journal C. - : Springer Science and Business Media LLC. - 1434-6052. ; 75:9
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Tidskriftsartikel (refereegranskat)
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| 30. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368 .- 1550-7998. ; 91:11, s. 112011-
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Tidskriftsartikel (refereegranskat)
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| 31. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 115:9
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Tidskriftsartikel (refereegranskat)
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| 32. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Journal of High Energy Physics. - : Springer-Verlag New York. - 1029-8479 .- 1126-6708. ; :9
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Tidskriftsartikel (refereegranskat)
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| 33. |
- Aad, G., et al.
(författare)
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- 2015
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Tidskriftsartikel (refereegranskat)
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| 34. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368 .- 1550-7998. ; 92:1
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| 35. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Journal of High Energy Physics. - : Springer. - 1029-8479 .- 1126-6708. ; :12
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Tidskriftsartikel (refereegranskat)
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| 36. |
- Aad, G., et al.
(författare)
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- 2015
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Tidskriftsartikel (refereegranskat)
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| 37. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Journal of High Energy Physics. - : Societa Italiana di Fisica. - 1029-8479 .- 1126-6708. ; :8
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Tidskriftsartikel (refereegranskat)
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| 38. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Journal of High Energy Physics. - : Societa Italiana di Fisica. - 1029-8479 .- 1126-6708. ; :9
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Tidskriftsartikel (refereegranskat)
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| 39. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review Letters. - : American Physical Society. - 1079-7114 .- 0031-9007. ; 114:23
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Tidskriftsartikel (refereegranskat)
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| 40. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review Letters. - : American Physical Society. - 1079-7114 .- 0031-9007. ; 114:22
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Tidskriftsartikel (refereegranskat)
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| 41. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :8
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Tidskriftsartikel (refereegranskat)
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| 42. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review D (Particles, Fields, Gravitation and Cosmology). - 1550-2368 .- 1550-7998. ; 92:9
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Tidskriftsartikel (refereegranskat)
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| 43. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 115:13
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Tidskriftsartikel (refereegranskat)
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| 44. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 115:3
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Tidskriftsartikel (refereegranskat)
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| 45. |
- Aad, G., et al.
(författare)
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- 2015
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Tidskriftsartikel (refereegranskat)
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| 46. |
- Aad, G., et al.
(författare)
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- 2015
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Ingår i: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 115:3
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