47 research outputs found
A reporting format for leaf-level gas exchange data and metadata
- Author
- Agarwal DA
- Ainsworth EA
- Albert LP
- Ali A
- Anderson J
- Aspinwall MJ
- Bellasio C
- Bernacchi C
- Bonnage S
- Buckley TN
- Bunce J
- Burnett AC
- Busch FA
- Cavanagh A
- Cernusak LA
- Crystal-Ornelas R
- Damerow J
- Davidson KJ
- De Kauwe MG
- Dietze MC
- Domingues TF
- Dusenge ME
- Ellsworth DS
- Ely KS
- Evans JR
- Gauthier PPG
- Gimenez BO
- Gordon EP
- Gough CM
- Halbritter AH
- Hanson DT
- Heskel M
- Hogan JA
- Hupp JR
- Jardine K
- Kattge J
- Keenan T
- Kromdijk J
- Kumarathunge DP
- Lamour J
- Leakey ADB
- LeBauer DS
- Li Q
- Lundgren MR
- McDowell N
- Meacham-Hensold K
- Medlyn BE
- Moore DJP
- NegrĂłn-JuĂĄrez R
- Niinemets Ă
- Osborne CP
- Pivovaroff AL
- Poorter H
- Reed SC
- Rogers A
- Ryu Y
- Sanz-Saez A
- Schmiege SC
- Serbin SP
- Sharkey TD
- Slot M
- Smith NG
- Sonawane BV
- South PF
- Souza DC
- Stinziano JR
- Stuart-Haëntjens E
- Taylor SH
- Tejera MD
- Uddling J
- Vandvik V
- Varadharajan C
- Walker AP
- Walker BJ
- Warren JM
- Way DA
- Wolfe BT
- Wu J
- Wullschleger SD
- Xu C
- Yan Z
- Yang D
- Publication venue
- Ecological Informatics
- Publication date
- 01/01/2021
- Field of study
Leaf-level gas exchange data support the mechanistic understanding of plant fluxes of carbon and water. These fluxes inform our understanding of ecosystem function, are an important constraint on parameterization of terrestrial biosphere models, are necessary to understand the response of plants to global environmental change, and are integral to efforts to improve crop production. Collection of these data using gas analyzers can be both technically challenging and time consuming, and individual studies generally focus on a small range of species, restricted time periods, or limited geographic regions. The high value of these data is exemplified by the many publications that reuse and synthesize gas exchange data, however the lack of metadata and data reporting conventions make full and efficient use of these data difficult. Here we propose a reporting format for leaf-level gas exchange data and metadata to provide guidance to data contributors on how to store data in repositories to maximize their discoverability, facilitate their efficient reuse, and add value to individual datasets. For data users, the reporting format will better allow data repositories to optimize data search and extraction, and more readily integrate similar data into harmonized synthesis products. The reporting format specifies data table variable naming and unit conventions, as well as metadata characterizing experimental conditions and protocols. For common data types that were the focus of this initial version of the reporting format, i.e., survey measurements, dark respiration, carbon dioxide and light response curves, and parameters derived from those measurements, we took a further step of defining required additional data and metadata that would maximize the potential reuse of those data types. To aid data contributors and the development of data ingest tools by data repositories we provided a translation table comparing the outputs of common gas exchange instruments. Extensive consultation with data collectors, data users, instrument manufacturers, and data scientists was undertaken in order to ensure that the reporting format met community needs. The reporting format presented here is intended to form a foundation for future development that will incorporate additional data types and variables as gas exchange systems and measurement approaches advance in the future. The reporting format is published in the U.S. Department of Energy's ESS-DIVE data repository, with documentation and future development efforts being maintained in a version control system
Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.
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- Abdel-Aziz AK
- Abdelfatah S
- Abdellatif M
- Abdoli A
- Abel S
- Abeliovich H
- Abildgaard MH
- Abudu YP
- Acevedo-Arozena A
- Adamopoulos IE
- Adeli K
- Adolph TE
- Adornetto A
- Aflaki E
- Agam G
- Agarwal A
- Aggarwal BB
- Agnello M
- Agostinis P
- Agrewala JN
- Agrotis A
- Aguilar PV
- Ahmad ST
- Ahmed ZM
- Ahumada-Castro U
- Aits S
- Aizawa S
- Akkoc Y
- Akoumianaki T
- Akpinar HA
- Al-Abd AM
- Al-Akra L
- Al-Gharaibeh A
- Alaoui-Jamali MA
- Alberti S
- Alcocer-GĂłmez E
- Alessandri C
- Ali M
- Alim Al-Bari MA
- Aliwaini S
- Alizadeh J
- Almacellas E
- Almasan A
- Alonso A
- Alonso GD
- Altan-Bonnet N
- Altieri DC
- Alves da Costa C
- Alves S
- Alzaharna MM
- Amadio M
- Amantini C
- Amaral C
- Ambrosio S
- Amer AO
- Ammanathan V
- An Z
- Andersen SU
- Andrabi SA
- Andrade-Silva M
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- Ălvarez ĂMC
- Ăvalos Y
- Ănal G
- ĂstĂŒn S
- ÄoliÄ M
- ÄokiÄ J
- Ćœerovnik E
- Publication venue
- 'Informa UK Limited'
- Publication date
- 01/01/2021
- Field of study
In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field
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- Author
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- Aarup Petersen H
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- Yusuff I
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- Zuolo D
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- Publication venue
- Elsevier
- Publication date
- 02/02/2024
- Field of study
Data availability:
Release and preservation of data used by the CMS Collaboration as the basis for publications is guided by the CMS policy as stated in âCMS data preservation, re-use and open access policyâ available online at: https://cms-docdb.cern.ch/cgi-bin/PublicDocDB/RetrieveFile?docid=6032&filename=CMSDataPolicyV1.2.pdf&version=2 .A preprint of this article is available online at arXiv:2311.03261v2 [hep-ex] https://arxiv.org/abs/2311.03261v2 . Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/TOP-22-010 (CMS Public Pages)A search is presented for new Higgs bosons in proton-proton (pp) collision events in which a same-sign top quark pair is produced in association with a jet, via the pp â tH/A â ttÂŻc and pp â tH/A â ttÂŻu processes. Here, H and A represent the extra scalar and pseudoscalar boson, respectively, of the second Higgs doublet in the generalized two-Higgs-doublet model (g2HDM). The search is based on pp collision data collected at a center-of-mass energy of 13 TeV with the CMS detector at the LHC, corresponding to an integrated luminosity of 138 fbâ1. Final states with a same-sign lepton pair in association with jets and missing transverse momentum are considered. New Higgs bosons in the 200-1000 GeV mass range and new Yukawa couplings between 0.1 and 1.0 are targeted in the search, for scenarios in which either H or A appear alone, or in which they coexist and interfere. No significant excess above the standard model prediction is observed. Exclusion limits are derived in the context of the g2HDM.SCOAP3
Recommended from our members
Measurement of the Higgs boson production via vector boson fusion and its decay into bottom quarks in proton-proton collisions at sâ = 13 TeV
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- Publication venue
- Springer Nature on behalf of SISSA
- Publication date
- 30/01/2024
- Field of study
A preprint version of the article is available at arXiv:2308.01253v2 [hep-ex], https://arxiv.org/abs/2308.01253v2 . Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/HIG-22-009 (CMS Public Pages). Report number: CMS-HIG-22-009, CERN-EP-2023-110.A measurement of the Higgs boson (H) production via vector boson fusion (VBF) and its decay into a bottom quark-antiquark pair (bbÂŻ) is presented using proton-proton collision data recorded by the CMS experiment at sâ = 13 TeV and corresponding to an integrated luminosity of 90.8 fbâ1. Treating the gluon-gluon fusion process as a background and constraining its rate to the value expected in the standard model (SM) within uncertainties, the signal strength of the VBF process, defined as the ratio of the observed signal rate to that predicted by the SM, is measured to be ÎŒqqHHbbÂŻ = 1.01 +0.55â0.46. The VBF signal is observed with a significance of 2.4 standard deviations relative to the background prediction, while the expected significance is 2.7 standard deviations. Considering inclusive Higgs boson production and decay into bottom quarks, the signal strength is measured to be ÎŒincl.HbbÂŻ = 0.99 +0.48â0.41, corresponding to an observed (expected) significance of 2.6 (2.9) standard deviations.SCOAP3, STFC; Marie-Curie program and the European Research Council and Horizon 2020 Gran
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- Aarup Petersen H
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- Ălvarez FernĂĄndez A
- Publication venue
- Springer Nature on behalf of SISSA
- Publication date
- 15/02/2024
- Field of study
A preprint version of the article is available at arXiv:2311.11370v2 [nucl-ex], https://arxiv.org/abs/2311.11370 .
Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/HIN-21-010 (CMS Public Pages).The hydrodynamic flow-like behavior of charged hadrons in high-energy lead-lead collisions is studied through multiparticle correlations. The elliptic anisotropy values based on different orders of multiparticle cumulants, v2{2k}, are measured up to the tenth order (k = 5) as functions of the collision centrality at a nucleon-nucleon center-of-mass energy of âsNN = 5.02 TeV. The data were recorded by the CMS experiment at the LHC and correspond to an integrated luminosity of 0.607 nbâ1. A hierarchy is observed between the coefficients, with v2{2}>v2{4}âłv2{6}âłv2{8}âłv2{10}. Based on these results, centrality-dependent moments for the fluctuation-driven event-by-event v2 distribution are determined, including the skewness, kurtosis and, for the first time, superskewness. Assuming a hydrodynamic expansion of the produced medium, these moments directly probe the initial-state geometry in high-energy nucleus-nucleus collisions.SCOAP3
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- Author
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- Publication venue
- Springer Nature on behalf of SISSA
- Publication date
- 13/12/2023
- Field of study
A preprint version of the article is available at arXiv:2305.07998v2 [hep-ex], https://arxiv.org/abs/2305.07998v2 . Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/EXO-20-012 (CMS Public Pages). Report number: CMS-EXO-20-012, CERN-EP-2023-064.A search for resonances in events with the Îł+jet final state has been performed using proton-proton collision data collected at âs = 13 TeV by the CMS experiment at the LHC. The total data analyzed correspond to an integrated luminosity of 138 fbâ1. Models of excited quarks and quantum black holes are considered. Using a wide-jet reconstruction for the candidate jet, the Îł+jet invariant mass spectrum measured in data is examined for the presence of resonances over the standard model continuum background. The background is estimated by fitting the mass distribution with a functional form. The data exhibit no statistically significant deviations from the expected standard model background. Exclusion limits at 95% confidence level on the resonance mass and other parameters are set. Excited light-flavor quarks (excited bottom quarks) are excluded up to a mass of 6.0 (3.8) TeV. Quantum black hole production is excluded for masses up to 7.5 (5.2) TeV in the Arkani-Hamed-Dimopoulos-Dvali (Randall-Sundrum) model. These lower mass bounds are the most stringent to date among those obtained in the Îł+jet final state.SCOAP3
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Search for long-lived particles using out-of-time trackless jets in proton-proton collisions at âs =13TeV
- Author
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- Aarup Petersen H
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- Yockey H
- Yohay R
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- Yumiceva F
- Yusuff I
- Zabi A
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- Zalewski P
- Zanetti M
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- Zecchinelli AG
- Zeinali M
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- Zhizhin I
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- Zimermmane Castro Santos A
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- Zygala L
- Publication venue
- Springer Science and Business Media LLC
- Publication date
- 27/07/2023
- Field of study
A search for long-lived particles decaying in the outer regions of the CMS silicon tracker or in the calorimeters is presented. The search is based on a data sample of proton-proton collisions at âs = 13 TeV recorded with the CMS detector at the LHC in 2016â2018, corresponding to an integrated luminosity of 138 fbâ1. A novel technique, using nearly trackless and out-of-time jet information combined in a deep neural network discriminator, is employed to identify decays of long-lived particles. The results are interpreted in a simplified model of chargino-neutralino production, where the neutralino is the next-to-lightest supersymmetric particle, is long-lived, and decays to a gravitino and either a Higgs or Z boson. This search is most sensitive to neutralino proper decay lengths of approximately 0.5 m, for which masses up to 1.18 TeV are excluded at 95% confidence level. The current search is the best result to date in the mass range from the kinematic limit imposed by the Higgs boson mass up to 1.8 TeV.SCOAP
Recommended from our members
Search for long-lived heavy neutral leptons with lepton flavour conserving or violating decays to a jet and a charged lepton
- Author
- Aarrestad TK
- Aarup Petersen H
- Abbaneo D
- Abbiendi G
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- Publication venue
- Springer Nature on behalf of SISSA
- Publication date
- 19/03/2024
- Field of study
A preprint version of the article is available at arXiv:2312.07484v3 [hep-ex], https://arxiv.org/abs/2312.07484 . Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/EXO-21-013 (CMS Public Pages)A search for long-lived heavy neutral leptons (HNLs) is presented, which considers the hadronic final state and coupling scenarios involving all three lepton generations in the 2-20 GeV HNL mass range for the first time. Events comprising two leptons (electrons or muons) and jets are analyzed in a data sample of proton-proton collisions, recorded with the CMS experiment at the CERN LHC at a centre-of-mass energy of 13 TeV, corresponding to an integrated luminosity of 138 fbâ1. A novel jet tagger, based on a deep neural network, has been developed to identify jets from an HNL decay using various features of the jet and its constituent particles. The network output can be used as a powerful discriminating tool to probe a broad range of HNL lifetimes and masses. Contributions from background processes are determined from data. No excess of events in data over the expected background is observed. Upper limits on the HNL production cross section are derived as functions of the HNL mass and the three coupling strengths VâN to each lepton generation â and presented as exclusion limits in the coupling-mass plane, as lower limits on the HNL lifetime, and on the HNL mass. In this search, the most stringent limit on the coupling strength is obtained for pure muon coupling scenarios; values of |VÎŒN|2 > 5 (4) Ă 10â7 are excluded for Dirac (Majorana) HNLs with a mass of 10 GeV at a confidence level of 95% that correspond to proper decay lengths of 17 (10) mm.SCOAP3
Recommended from our members
Search for dark matter particles in W+Wâ events with transverse momentum imbalance in proton-proton collisions at âs = 13 TeV
- Author
- Aarrestad TK
- Aarup Petersen H
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- Publication venue
- Springer Nature on behalf of SISSA
- Publication date
- 02/03/2024
- Field of study
A preprint version of the article is available at arXiv:2310.12229v2 [hep-ex], https://arxiv.org/abs/2310.12229v2 . Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/EXO-21-012 (CMS Public Pages).A search for dark matter particles is performed using events with a pair of W bosons and large missing transverse momentum. Candidate events are selected by requiring one or two leptons (â = electrons or muons). The analysis is based on proton-proton collision data collected at a center-of-mass energy of 13 TeV by the CMS experiment at the LHC and corresponding to an integrated luminosity of 138 fbâ1. No significant excess over the expected standard model background is observed in the âÎœqq and 2â2Îœ final states of the W+Wâ boson pair. Limits are set on dark matter production in the context of a simplified dark Higgs model, with a dark Higgs boson mass above the W+Wâ mass threshold. The dark matter phase space is probed in the mass range 100â300 GeV, extending the scope of previous searches. Current exclusion limits are improved in the range of dark Higgs masses from 160 to 250 GeV, for a dark matter mass of 200 GeV.SCOAP3
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Search for direct production of GeV-scale resonances decaying to a pair of muons in proton-proton collisions at sâ = 13 TeV
- Author
- Aarrestad TK
- Aarup Petersen H
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- Publication venue
- Springer Nature on behalf of SISSA
- Publication date
- 30/11/2023
- Field of study
A preprint version of the article is available at arXiv:2309.16003v2 [hep-ex], https://arxiv.org/abs/2309.16003v2 . Comments: Replaced with the published version. Added the journal reference and the DOI. All the figures and tables, including additional supplementary figures, can be found at https://cms-results.web.cern.ch/cms-results/public-results/publications/EXO-21-005 (CMS Public Pages). Report number: CMS-EXO-21-005, CERN-EP-2023-165.A search for direct production of low-mass dimuon resonances is performed using sâ = 13 TeV proton-proton collision data collected by the CMS experiment during the 2017-2018 operation of the CERN LHC with an integrated luminosity of 96.6 fbâ1. The search exploits a dedicated high-rate trigger stream that records events with two muons with transverse momenta as low as 3 GeV but does not include the full event information. The search is performed by looking for narrow peaks in the dimuon mass spectrum in the ranges of 1.1-2.6 GeV and 4.2-7.9 GeV. No significant excess of events above the expectation from the standard model background is observed. Model-independent limits on production rates of dimuon resonances within the experimental fiducial acceptance are set. Competitive or world's best limits are set at 90% confidence level for a minimal dark photon model and for a scenario with two Higgs doublets and an extra complex scalar singlet (2HDM+S). Values of the squared kinetic mixing coefficient Δ2 in the dark photon model above 10â6 are excluded over most of the mass range of the search. In the 2HDM+S, values of the mixing angle sin(ΞH) above 0.08 are excluded over most of the mass range of the search with a fixed ratio of the Higgs doublets vacuum expectation tanÎČ = 0.5.SCOAP3