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| 2. |
- Klionsky, Daniel J., et al.
(author)
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Guidelines for the use and interpretation of assays for monitoring autophagy
- 2012
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In: Autophagy. - : Informa UK Limited. - 1554-8635 .- 1554-8627. ; 8:4, s. 445-544
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Research review (peer-reviewed)abstract
- In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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| 3. |
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- 2019
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Journal article (peer-reviewed)
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| 4. |
- Ariyawansa, Hiran A., et al.
(author)
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Fungal diversity notes 111–252—taxonomic and phylogenetic contributions to fungal taxa
- 2015
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In: Fungal diversity. - : Springer Science and Business Media LLC. - 1560-2745 .- 1878-9129. ; 75, s. 27-274
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Journal article (peer-reviewed)abstract
- This paper is a compilation of notes on 142 fungal taxa, including five new families, 20 new genera, and 100 new species, representing a wide taxonomic and geographic range. The new families, Ascocylindricaceae, Caryosporaceae and Wicklowiaceae (Ascomycota) are introduced based on their distinct lineages and unique morphology. The new Dothideomycete genera Pseudomassariosphaeria (Amniculicolaceae), Heracleicola, Neodidymella and P s e u d o m i c ros p h a e r i o p s i s ( D id y m e l l a c e a e ) , P s e u d o p i t h o m y c e s ( D i d y m o s p h a e r i a c e a e ) , Brunneoclavispora, Neolophiostoma and Sulcosporium (Halotthiaceae), Lophiohelichrysum (Lophiostomataceae), G a l l i i c o l a , Popul o c re s c e n t i a a nd Va g i c o l a (Phaeosphaeriaceae), Ascocylindrica (Ascocylindricaceae), E l o n g a t o p e d i c e l l a t a ( R o u s s o e l l a c e a e ) , Pseudoasteromassaria (Latoruaceae) and Pseudomonodictys (Macrodiplodiopsidaceae) are introduced. The newly described species of Dothideomycetes (Ascomycota) are Pseudomassariosphaeria bromicola (Amniculicolaceae), Flammeascoma lignicola (Anteagloniaceae), Ascocylindrica marina (Ascocylindricaceae) , Lembosia xyliae (Asterinaceae), Diplodia crataegicola and Diplodia galiicola ( B o t r yosphae r i a cea e ) , Caryospor a aquat i c a (Caryosporaceae), Heracleicola premilcurensis and Neodi dymell a thai landi cum (Didymellaceae) , Pseudopithomyces palmicola (Didymosphaeriaceae), Floricola viticola (Floricolaceae), Brunneoclavispora bambusae, Neolophiostoma pigmentatum and Sulcosporium thailandica (Halotthiaceae), Pseudoasteromassaria fagi (Latoruaceae), Keissleriella dactylidicola (Lentitheciaceae), Lophiohelichrysum helichrysi (Lophiostomataceae), Aquasubmersa japonica (Lophiotremataceae) , Pseudomonodictys tectonae (Macrodiplodiopsidaceae), Microthyrium buxicola and Tumidispora shoreae (Microthyriaceae), Alloleptosphaeria clematidis, Allophaeosphaer i a c y t i s i , Allophaeosphae r i a subcylindrospora, Dematiopleospora luzulae, Entodesmium artemisiae, Galiicola pseudophaeosphaeria, Loratospora(Basidiomycota) are introduced together with a new genus Neoantrodiella (Neoantrodiellaceae), here based on both morphology coupled with molecular data. In the class Agaricomycetes, Agaricus pseudolangei, Agaricus haematinus, Agaricus atrodiscus and Agaricus exilissimus (Agaricaceae) , Amanita m e l l e i a l b a , Amanita pseudosychnopyramis and Amanita subparvipantherina (Amanitaceae), Entoloma calabrum, Cora barbulata, Dictyonema gomezianum and Inocybe granulosa (Inocybaceae), Xerocomellus sarnarii (Boletaceae), Cantharellus eucalyptorum, Cantharellus nigrescens, Cantharellus tricolor and Cantharellus variabilicolor (Cantharellaceae), Cortinarius alboamarescens, Cortinarius brunneoalbus, Cortinarius ochroamarus, Cortinarius putorius and Cortinarius seidlii (Cortinariaceae), Hymenochaete micropora and Hymenochaete subporioides (Hymenochaetaceae), Xylodon ramicida (Schizoporaceae), Colospora andalasii (Polyporaceae), Russula guangxiensis and Russula hakkae (Russulaceae), Tremella dirinariae, Tremella graphidis and Tremella pyrenulae (Tremellaceae) are introduced. Four new combinations Neoantrodiella gypsea, Neoantrodiella thujae (Neoantrodiellaceae), Punctulariopsis cremeoalbida, Punctulariopsis efibulata (Punctulariaceae) are also introduced here for the division Basidiomycota. Furthermore Absidia caatinguensis, Absidia koreana and Gongronella koreana (Cunninghamellaceae), Mortierella pisiformis and Mortierella formosana (Mortierellaceae) are newly introduced in the Zygomycota, while Neocallimastix cameroonii and Piromyces irregularis (Neocallimastigaceae) ar e i n t roduced i n the Neocallimastigomycota. Reference specimens or changes in classification and notes are provided for Alternaria ethzedia, Cucurbitaria ephedricola, Austropleospora, Austropleospora archidendri, Byssosphaeria rhodomphala, Lophiostoma caulium, Pseudopithomyces maydicus, Massariosphaeria, Neomassariosphaeria and Pestalotiopsis montellica.
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| 11. |
- Kristan, Matej, et al.
(author)
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The Visual Object Tracking VOT2015 challenge results
- 2015
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In: Proceedings 2015 IEEE International Conference on Computer Vision Workshops ICCVW 2015. - : IEEE. - 9780769557205 ; , s. 564-586
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Conference paper (peer-reviewed)abstract
- The Visual Object Tracking challenge 2015, VOT2015, aims at comparing short-term single-object visual trackers that do not apply pre-learned models of object appearance. Results of 62 trackers are presented. The number of tested trackers makes VOT 2015 the largest benchmark on short-term tracking to date. For each participating tracker, a short description is provided in the appendix. Features of the VOT2015 challenge that go beyond its VOT2014 predecessor are: (i) a new VOT2015 dataset twice as large as in VOT2014 with full annotation of targets by rotated bounding boxes and per-frame attribute, (ii) extensions of the VOT2014 evaluation methodology by introduction of a new performance measure. The dataset, the evaluation kit as well as the results are publicly available at the challenge website(1).
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| 12. |
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| 13. |
- Tang, Ting-Ting, et al.
(author)
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Impaired thymic export and apoptosis contribute to regulatory T-cell defects in patients with chronic heart failure.
- 2011
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In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203 .- 1932-6203. ; 6:9, s. e24272-
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Journal article (peer-reviewed)abstract
- Animal studies suggest that regulatory T (T(reg)) cells play a beneficial role in ventricular remodeling and our previous data have demonstrated defects of T(reg) cells in patients with chronic heart failure (CHF). However, the mechanisms behind T(reg-)cell defects remained unknown. We here sought to elucidate the mechanism of T(reg-)cell defects in CHF patients.
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| 14. |
- Wang, Zhaoming, et al.
(author)
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Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33
- 2014
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In: Human Molecular Genetics. - : Oxford University Press (OUP). - 0964-6906 .- 1460-2083. ; 23:24, s. 6616-6633
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Journal article (peer-reviewed)abstract
- Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10(-39); Region 3: rs2853677, P = 3.30 × 10(-36) and PConditional = 2.36 × 10(-8); Region 4: rs2736098, P = 3.87 × 10(-12) and PConditional = 5.19 × 10(-6), Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10(-6); and Region 6: rs10069690, P = 7.49 × 10(-15) and PConditional = 5.35 × 10(-7)) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10(-18) and PConditional = 7.06 × 10(-16)). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
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| 15. |
- Zhu, Ri Jia, et al.
(author)
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Magnetotransport properties of graphene layers decorated with colloid quantum dots
- 2019
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In: Chinese Physics B. - : IOP Publishing. - 1674-1056. ; 28:6
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Journal article (peer-reviewed)abstract
- The hybrid graphene-quantum dot devices can potentially be used to tailor the electronic, optical, and chemical properties of graphene. Here, the low temperature electronic transport properties of bilayer graphene decorated with PbS colloid quantum dots (CQDs) have been investigated in the weak or strong magnetic fields. The presence of the CQDs introduces additional scattering potentials that alter the magnetotransport properties of the graphene layers, leading to the observation of a new set of magnetoconductance oscillations near zero magnetic field as well as the high-field quantum Hall regime. The results bring about a new strategy for exploring the quantum interference effects in two-dimensional materials which are sensitive to the surrounding electrostatic environment, and open up a new gateway for exploring the graphene sensing with quantum interference effects.
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| 16. |
- Aad, G., et al.
(author)
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- 2013
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Journal article (peer-reviewed)
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| 17. |
- Aad, G., et al.
(author)
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- 2013
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In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 15
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Journal article (peer-reviewed)
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| 18. |
- Aad, G., et al.
(author)
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- 2015
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Journal article (peer-reviewed)
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| 19. |
- Aad, G., et al.
(author)
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- 2013
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Journal article (peer-reviewed)
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| 20. |
- Aad, G., et al.
(author)
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- 2013
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Journal article (peer-reviewed)
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| 21. |
- Aad, G., et al.
(author)
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- 2013
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Journal article (peer-reviewed)
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| 22. |
- Aad, G., et al.
(author)
-
- 2014
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Journal article (peer-reviewed)
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| 23. |
- Aad, G., et al.
(author)
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- 2013
-
In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 15
-
Journal article (peer-reviewed)
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| 24. |
- Aad, G., et al.
(author)
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- 2013
-
In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 15
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Journal article (peer-reviewed)
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| 25. |
- Aad, G., et al.
(author)
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- 2012
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Journal article (peer-reviewed)
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| 26. |
- Aad, G., et al.
(author)
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- 2013
-
In: New Journal of Physics. - : IOP Publishing. - 1367-2630. ; 15
-
Journal article (peer-reviewed)
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| 27. |
- Aad, G., et al.
(author)
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- 2013
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Journal article (peer-reviewed)
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| 28. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 29. |
- Aad, G., et al.
(author)
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- 2013
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Journal article (peer-reviewed)
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| 30. |
- Aad, G., et al.
(author)
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- 2013
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Journal article (peer-reviewed)
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| 31. |
- Aad, G., et al.
(author)
-
- 2013
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Journal article (peer-reviewed)
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| 32. |
- Aad, G., et al.
(author)
-
- 2014
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Journal article (peer-reviewed)
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| 33. |
- Aad, G., et al.
(author)
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- 2014
-
In: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 112:4
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Journal article (peer-reviewed)
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| 34. |
- Aad, G., et al.
(author)
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- 2013
-
In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :6
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Journal article (peer-reviewed)
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| 35. |
- Aad, G., et al.
(author)
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- 2014
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In: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 112:9
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Journal article (peer-reviewed)
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| 36. |
- Aad, G., et al.
(author)
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- 2013
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :7
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Journal article (peer-reviewed)
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| 37. |
- Aad, G., et al.
(author)
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- 2013
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In: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 111:23
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Journal article (peer-reviewed)
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| 38. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :5
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Journal article (peer-reviewed)
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| 39. |
- Aad, G., et al.
(author)
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- 2014
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :4
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Journal article (peer-reviewed)
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| 40. |
- Aad, G., et al.
(author)
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- 2013
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :10
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Journal article (peer-reviewed)
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| 41. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 42. |
- Aad, G., et al.
(author)
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- 2013
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Journal article (peer-reviewed)
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| 43. |
- Aad, G., et al.
(author)
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- 2014
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In: Physical Review Letters. - 1079-7114 .- 0031-9007. ; 112:20
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Journal article (peer-reviewed)
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| 44. |
- Aad, G., et al.
(author)
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- 2013
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :11
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Journal article (peer-reviewed)
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| 45. |
- Aad, G, et al.
(author)
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- 2015
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swepub:Mat__t
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| 46. |
- Aad, G., et al.
(author)
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- 2013
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :2
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Journal article (peer-reviewed)
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| 47. |
- Aad, G., et al.
(author)
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- 2014
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Journal article (peer-reviewed)
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| 48. |
- Aad, G., et al.
(author)
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- 2013
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :10
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Journal article (peer-reviewed)
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| 49. |
- Aad, G., et al.
(author)
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- 2013
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In: Journal of High Energy Physics. - 1029-8479 .- 1126-6708. ; :4
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Journal article (peer-reviewed)
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| 50. |
- Aad, G., et al.
(author)
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- 2013
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Journal article (peer-reviewed)
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