247 research outputs found
Recombining Low Homology, Functionally Rich Regions of Bacterial Subtilisins by Combinatorial Fragment Exchange
- Author
- A Andreeva
- AM Simm
- Annalisa Pastore
- AV Teplyakov
- AY Lee
- C Betzel
- C Chothia
- C Neylon
- CA Smith
- CS Wright
- D. Dafydd Jones
- DD Jones
- DD Jones
- DJ Neidhart
- H Gron
- H Zhao
- HS Toogood
- IS Povolotskaya
- J Eder
- J Minshull
- J Vevodova
- JA Wells
- JA Wells
- JE Ness
- JJ Perona
- KM Stott
- MA DePristo
- ME Glasner
- MM Meyer
- N Guex
- N Tindbaek
- N Tokuriki
- NC Rockwell
- P Carter
- P Carter
- PN Bryan
- PN Bryan
- R Bott
- R Gupta
- RJ Siezen
- S Bershtein
- S Ewert
- SC Jain
- W Stemmer
- Publication venue
- Public Library of Science
- Publication date
- 01/01/2011
- Field of study
Combinatorial fragment exchange was utilised to recombine key structural and functional low homology regions of bacilli subtilisins to generate new active hybrid proteases with altered substrate profiles. Up to six different regions comprising mostly of loop residues from the commercially important subtilisin Savinase were exchanged with the structurally equivalent regions of six other subtilisins. The six additional subtilisins derive from diverse origins and included thermophilic and intracellular subtilisins as well as other academically and commercially relevant subtilisins. Savinase was largely tolerant to fragment exchange; rational replacement of all six regions with 5 of 6 donating subtilisin sequences preserved activity, albeit reduced compared to Savinase. A combinatorial approach was used to generate hybrid Savinase variants in which the sequences derived from all seven subtilisins at each region were recombined to generate new region combinations. Variants with different substrate profiles and with greater apparent activity compared to Savinase and the rational fragment exchange variants were generated with the substrate profile exhibited by variants dependent on the sequence combination at each region
Uncovering the Dynamics of Cardiac Systems Using Stochastic Pacing and Frequency Domain Analyses
- Author
- A Vinet
- AG Kléber
- Andrew D. McCulloch
- AR Cram
- B Echebarria
- BR Choi
- C Cabo
- D Sato
- DR Chialvo
- DR Chialvo
- E Chudin
- E Cytrynbaum
- E de Lange
- EG Tolkacheva
- EG Tolkacheva
- EM Cherry
- EM Cherry
- Enno de Lange
- GW Beeler
- H Press
- HM Hastings
- Jan P. Kucera
- JB Nolasco
- JJ Fox
- JM Pastore
- JN Weiss
- L Ljung
- M Li
- M Zaniboni
- MA Watanabe
- Mathieu Lemay
- ME Diaz
- MH Hayes
- MR Guevara
- NF Otani
- PN Jordan
- PN Jordan
- R Wu
- R Wu
- R Wu
- SS Kalb
- SS Kalb
- T Lewis
- V Elharrar
- Y Shiferaw
- Z Qu
- Z Qu
- Publication venue
- Public Library of Science
- Publication date
- 01/01/2011
- Field of study
Alternans of cardiac action potential duration (APD) is a well-known arrhythmogenic mechanism which results from dynamical instabilities. The propensity to alternans is classically investigated by examining APD restitution and by deriving APD restitution slopes as predictive markers. However, experiments have shown that such markers are not always accurate for the prediction of alternans. Using a mathematical ventricular cell model known to exhibit unstable dynamics of both membrane potential and Ca2+ cycling, we demonstrate that an accurate marker can be obtained by pacing at cycle lengths (CLs) varying randomly around a basic CL (BCL) and by evaluating the transfer function between the time series of CLs and APDs using an autoregressive-moving-average (ARMA) model. The first pole of this transfer function corresponds to the eigenvalue (λalt) of the dominant eigenmode of the cardiac system, which predicts that alternans occurs when λalt≤−1. For different BCLs, control values of λalt were obtained using eigenmode analysis and compared to the first pole of the transfer function estimated using ARMA model fitting in simulations of random pacing protocols. In all versions of the cell model, this pole provided an accurate estimation of λalt. Furthermore, during slow ramp decreases of BCL or simulated drug application, this approach predicted the onset of alternans by extrapolating the time course of the estimated λalt. In conclusion, stochastic pacing and ARMA model identification represents a novel approach to predict alternans without making any assumptions about its ionic mechanisms. It should therefore be applicable experimentally for any type of myocardial cell
Jet energy measurement with the ATLAS detector in proton-proton collisions at root s=7 TeV
- Author
- Aad G
- Abbott B
- Abdallah J
- Abdelalim AA
- Abdesselam A
- Abdinov O
- Abi B
- Abolins M
- Abramowicz H
- Abreu H
- Acerbi E
- Acharya BS
- Adams DL
- Addy TN
- Adelman J
- Aderholz M
- Adomeit S
- Adragna P
- Adye T
- Aefsky S
- Aguilar-Saavedra JA
- Aharrouche M
- Ahlen SP
- Ahles F
- Ahmad A
- Ahsan M
- Aielli G
- Akdogana T
- Akesson TPA
- Akimoto G
- Akimov AV
- Akiyama A
- Aktas A
- Alam MA
- Alam MS
- Albert J
- Albrand S
- Aleksa M
- Aleksandrov IN
- Alessandria F
- Alexa C
- Alexander G
- Alexandre G
- Alexopoulos T
- Alhroob M
- Aliev M
- Alimonti G
- Alison J
- Aliyev M
- Allport PP
- Allwood-Spiers SE
- Almenar CC
- Almond J
- Aloisio A
- Alon R
- Alonso A
- Alviggi MG
- Amako K
- Amaral P
- Amelung C
- Ammosov VV
- Amorim A
- Amoros G
- Amram N
- Anastopoulos C
- Ancu LS
- Andari N
- Andeen T
- Anders CF
- Anders G
- Anderson KJ
- Andreazza A
- Andrei V
- Andrieux M-L
- Anduaga XS
- Angerami A
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- Anh TV
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- Anulli F
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- Aracena I
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- Aranda CP
- Arce ATH
- Archambault JP
- Arfaoui S
- Arguin J-F
- Arik E
- Arik M
- Armbruster AJ
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- Arnault C
- Artamonov A
- Artoni G
- Arutinov D
- Asai S
- Asfandiyarov R
- Ask S
- Asman B
- Asner D
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- Yilmaz M
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- Zarzhitsky P
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- Zhemchugov A
- Zheng S
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- Zieminska D
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- Zitoun R
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- Zwalinski L
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/03/2013
- Field of study
The jet energy scale and its systematic uncertainty are determined for jets measured with the ATLAS detector at the LHC in proton-proton collision data at a centre-of-mass energy of √s = 7TeV corresponding to an integrated luminosity of 38 pb-1. Jets are reconstructed with the anti-kt algorithm with distance parameters R=0. 4 or R=0. 6. Jet energy and angle corrections are determined from Monte Carlo simulations to calibrate jets with transverse momenta pT≥20 GeV and pseudorapidities {pipe}η{pipe}<4. 5. The jet energy systematic uncertainty is estimated using the single isolated hadron response measured in situ and in test-beams, exploiting the transverse momentum balance between central and forward jets in events with dijet topologies and studying systematic variations in Monte Carlo simulations. The jet energy uncertainty is less than 2. 5 % in the central calorimeter region ({pipe}η{pipe}<0. 8) for jets with 60≤pT<800 GeV, and is maximally 14 % for pT<30 GeV in the most forward region 3. 2≤{pipe}η{pipe}<4. 5. The jet energy is validated for jet transverse momenta up to 1 TeV to the level of a few percent using several in situ techniques by comparing a well-known reference such as the recoiling photon pT, the sum of the transverse momenta of tracks associated to the jet, or a system of low-pT jets recoiling against a high-pT jet. More sophisticated jet calibration schemes are presented based on calorimeter cell energy density weighting or hadronic properties of jets, aiming for an improved jet energy resolution and a reduced flavour dependence of the jet response. The systematic uncertainty of the jet energy determined from a combination of in situ techniques is consistent with the one derived from single hadron response measurements over a wide kinematic range. The nominal corrections and uncertainties are derived for isolated jets in an inclusive sample of high-pT jets. Special cases such as event topologies with close-by jets, or selections of samples with an enhanced content of jets originating from light quarks, heavy quarks or gluons are also discussed and the corresponding uncertainties are determined. © 2013 CERN for the benefit of the ATLAS collaboration
Measurement of the inclusive and dijet cross-sections of b-jets in pp collisions at sqrt(s) = 7 TeV with the ATLAS detector
- Author
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- Abbott B
- Abdallah J
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- Abdesselam A
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- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 31/12/2010
- Field of study
The inclusive and dijet production cross-sections have been measured for jets
containing b-hadrons (b-jets) in proton-proton collisions at a centre-of-mass
energy of sqrt(s) = 7 TeV, using the ATLAS detector at the LHC. The
measurements use data corresponding to an integrated luminosity of 34 pb^-1.
The b-jets are identified using either a lifetime-based method, where secondary
decay vertices of b-hadrons in jets are reconstructed using information from
the tracking detectors, or a muon-based method where the presence of a muon is
used to identify semileptonic decays of b-hadrons inside jets. The inclusive
b-jet cross-section is measured as a function of transverse momentum in the
range 20 < pT < 400 GeV and rapidity in the range |y| < 2.1. The bbbar-dijet
cross-section is measured as a function of the dijet invariant mass in the
range 110 < m_jj < 760 GeV, the azimuthal angle difference between the two jets
and the angular variable chi in two dijet mass regions. The results are
compared with next-to-leading-order QCD predictions. Good agreement is observed
between the measured cross-sections and the predictions obtained using POWHEG +
Pythia. MC@NLO + Herwig shows good agreement with the measured bbbar-dijet
cross-section. However, it does not reproduce the measured inclusive
cross-section well, particularly for central b-jets with large transverse
momenta.Comment: 10 pages plus author list (21 pages total), 8 figures, 1 table, final
version published in European Physical Journal
Measurement of the cross-section for b-jets produced in association with a Z boson at root s=7 TeV with the ATLAS detector ATLAS Collaboration
- Author
- Aad G
- Abbott B
- Abdallah J
- Abdelalim AA
- Abdesselam A
- Abdinov O
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- Abolins M
- Abramowicz H
- Abreu H
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- Aleksa M
- Aleksandrov IN
- Alessandria F
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- Alexandre G
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- Yilmaz M
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- Zaidan R
- Zaitsev AM
- Zajacova Z
- Zalite YK
- Zanello L
- Zarzhitsky P
- Zaytsev A
- Zeitnitz C
- Zeller M
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- Zemla A
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- Zenin O
- Zenis T
- Zenonos Z
- Zenz S
- Zerwas D
- Zhan Z
- Zhang D
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- Zhang Z
- Zhao L
- Zhao T
- Zhao Z
- Zhemchugov A
- Zheng S
- Zhong J
- Zhou B
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- Zhu CG
- Zhu H
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- Zhu Y
- Zhuang X
- Zhuravlov V
- Zieminska D
- Zimmermann R
- Zimmermann S
- Zimmermann S
- Ziolkowski M
- Zitoun R
- Zivkovic L
- Zmouchko VV
- Zobernig G
- Zoccoli A
- Zolnierowski Y
- Zsenei A
- zur Nedden M
- Zutshi V
- Zwalinski L
- Publication venue
- 'Elsevier BV'
- Publication date
- 01/01/2011
- Field of study
A measurement is presented of the inclusive cross-section for b-jet production in association with a Z boson in pp collisions at a centre-of-mass energy of root s = 7 TeV. The analysis uses the data sample collected by the ATLAS experiment in 2010, corresponding to an integrated luminosity of approximately 36 pb(-1). The event selection requires a Z boson decaying into high P-T electrons or muons, and at least one b-jet, identified by its displaced vertex, with transverse momentum p(T) > 25 GeV and rapidity vertical bar y vertical bar < 2.1. After subtraction of background processes, the yield is extracted from the vertex mass distribution of the candidate b-jets. The ratio of this cross-section to the inclusive Z cross-section (the average number of b-jets per Z event) is also measured. Both results are found to be in good agreement with perturbative QCD predictions at next-to-leading order
Observation and branching fraction measurement of the decay Ξb- → Λ0 bπ -
- Author
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- Abdelmotteleb ASW
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- Abudinen F
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- Adeva B
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- Aidala CA
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- Wyllie K
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- Zunica G
- Publication venue
- Publication date
- 01/01/2023
- Field of study
Precision measurement of CP violation in the penguin-mediated decay Bs0→ϕϕ
- Author
- Aaij R
- Abdelmotteleb ASW
- Abellan Beteta C
- Abudinén F
- Ackernley T
- Adeva B
- Adinolfi M
- Adlarson P
- Afsharnia H
- Agapopoulou C
- Aidala CA
- Ajaltouni Z
- Akar S
- Akiba K
- Albicocco P
- Albrecht J
- Alessio F
- Alexander M
- Alfonso Albero A
- Aliouche Z
- Alvarez Cartelle P
- Amalric R
- Amato S
- Amey JL
- Amhis Y
- An L
- Anderlini L
- Andersson M
- Andreianov A
- Andreotti M
- Andreou D
- Ao D
- Archilli F
- Artamonov A
- Artuso M
- Aslanides E
- Atzeni M
- Audurier B
- Bachiller Perea IB
- Bachmann S
- Bachmayer M
- Back JJ
- Bailly-Reyre A
- Baladron Rodriguez P
- Balagura V
- Baldini W
- Baptista de Souza Leite J
- Barbetti M
- Barlow RJ
- Barsuk S
- Barter W
- Bartolini M
- Baryshnikov F
- Basels JM
- Bassi G
- Batozskaya V
- Batsukh B
- Battig A
- Bay A
- Beck A
- Becker M
- Bedeschi F
- Bediaga IB
- Beiter A
- Belin S
- Bellee V
- Belous K
- Belov I
- Belyaev I
- Ben-Haim E
- Benane G
- Bencivenni G
- Berezhnoy A
- Bernet Andres S
- Bernet R
- Berninghoff D
- Bernstein HC
- Bertella C
- Bertolin A
- Betancourt C
- Betti F
- Bezshyiko Ia
- Bhom J
- Bian L
- Bieker MS
- Biesuz NV
- Billoir P
- Biolchini A
- Birch M
- Bishop FCR
- Bitadze A
- Bizzeti A
- Blago MP
- Blake T
- Blanc F
- Blank JE
- Blusk S
- Bobulska D
- Bocharnikov VB
- Boelhauve JA
- Boente Garcia O
- Boettcher T
- Boldyrev A
- Bolognani CS
- Bolzonella R
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- Bowcock TJV
- Boyer A
- Bozzi C
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- Braun S
- Brea Rodriguez A
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- Brodzicka J
- Brossa Gonzalo A
- Brown J
- Brundu D
- Buonaura A
- Buonincontri L
- Burke AT
- Burr C
- Bursche A
- Butkevich A
- Butter JS
- Buytaert J
- Byczynski W
- Cadeddu S
- Cai H
- Calabrese R
- Calefice L
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- Calvo Gomez M
- Campana P
- Campora Perez DH
- Campoverde Quezada AF
- Capelli S
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- Chefdeville M
- Chen C
- Chen S
- Chernov A
- Chernyshenko S
- Chobanova V
- Cholak S
- Chrzaszcz M
- Chubykin A
- Chulikov V
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- Cicala MF
- Cid Vidal X
- Ciezarek G
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- Clarke PEL
- Clemencic M
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- Corredoira I
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- Craik DC
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- Da Silva CL
- Dadabaev S
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- Dai X
- Dall'Occo E
- Dalseno J
- Daniel J
- Danilina A
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- Davis A
- De Aguiar Francisco O
- de Boer J
- De Bruyn K
- De Capua S
- De Cian M
- De Freitas Carneiro Da Graca U
- De Lucia E
- De Miranda JM
- De Paula L
- De Serio M
- De Simone D
- De Simone P
- De Vellis F
- de Vries JA
- Dean CT
- Debernardis F
- Decamp D
- Dedu V
- Del Buono L
- Delaney B
- Dembinski H-P
- Denysenko V
- Deschamps O
- Dettori F
- Dey B
- Di Nezza P
- Diachkov I
- Didenko S
- Dieste Maronas L
- Ding S
- Dobishuk V
- Dolmatov A
- Dong C
- Donohoe AM
- Dordei F
- Dos Reis AC
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- Downes AG
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- Dudek MW
- Dufour L
- Duk V
- Durante P
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- Dziurda A
- Dzyuba A
- Easo S
- Egede U
- Egorychev A
- Egorychev V
- Eirea Orro C
- Eisenhardt S
- Ejopu E
- Ek-In S
- Eklund L
- Elashri ME
- Ellbracht J
- Ely S
- Ene A
- Epple E
- Escher S
- Eschle J
- Esen S
- Evans T
- Fabiano F
- Falcao LN
- Fan Y
- Fang B
- Fantini L
- Faria M
- Farry S
- Fazzini D
- Felkowski LF
- Feo M
- Fernandez Gomez M
- Fernez AD
- Ferrari F
- Ferreira Lopes L
- Ferreira Rodrigues F
- Ferreres Sole S
- Ferrillo M
- Ferro-Luzzi M
- Filippov S
- Fini RA
- Fiorini M
- Firlej M
- Fischer KM
- Fitzgerald DS
- Fitzpatrick C
- Fiutowski T
- Fleuret F
- Fontana M
- Fontanelli F
- Forty R
- Foulds-Holt D
- Franco Lima V
- Franco Sevilla M
- Frank M
- Franzoso E
- Frau G
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- Gabriel E
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- Galli D
- Gambetta S
- Gandelman M
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- Gao R
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- Garcia Moreno P
- Garcia Plana B
- Garcia Rosales FA
- García Pardiñas J
- Garrido L
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- Gerick D
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- Gershon T
- Giambastiani L
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- Giemza HK
- Gilman AL
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- Gioventù A
- Gironella Gironell P
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- Publication venue
- Publication date
- 01/01/2023
- Field of study
A flavor-tagged time-dependent angular analysis of the decay
Bs0→ϕϕ is performed using pp collision data collected
by the LHCb experiment at % at s=13 TeV, the center-of-mass energy of
13 TeV, corresponding to an integrated luminosity of 6 fb^{-1}. The
CP-violating phase and direct CP-violation parameter are measured
to be ϕssˉs=−0.042±0.075±0.009 rad and
∣λ∣=1.004±0.030±0.009, respectively, assuming the same values
for all polarization states of the ϕϕ system. In these results, the
first uncertainties are statistical and the second systematic. These parameters
are also determined separately for each polarization state, showing no evidence
for polarization dependence. The results are combined with previous LHCb
measurements using pp collisions at center-of-mass energies of 7 and 8 TeV,
yielding ϕssˉs=−0.074±0.069 rad and ∣lambda∣=1.009±0.030. This is the most precise study of time-dependent CP violation
in a penguin-dominated B meson decay. The results are consistent with
CP symmetry and with the Standard Model predictions.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2023-001.html (LHCb
public pages
Observation of Two New Excited Ξb0 States Decaying to Λb0 K-π+
- Author
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- Abdelmotteleb ASW
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- Zonneveld JB
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- Zunica G
- Publication venue
- 'American Physical Society (APS)'
- Publication date
- 01/01/2022
- Field of study
Two narrow resonant states are observed in the Λb0K-π+ mass spectrum using a data sample of proton-proton collisions at a center-of-mass energy of 13 TeV, collected by the LHCb experiment and corresponding to an integrated luminosity of 6 fb-1. The minimal quark content of the Λb0K-π+ system indicates that these are excited Ξb0 baryons. The masses of the Ξb(6327)0 and Ξb(6333)0 states are m[Ξb(6327)0]=6327.28-0.21+0.23±0.12±0.24 and m[Ξb(6333)0]=6332.69-0.18+0.17±0.03±0.22 MeV, respectively, with a mass splitting of Δm=5.41-0.27+0.26±0.12 MeV, where the uncertainties are statistical, systematic, and due to the Λb0 mass measurement. The measured natural widths of these states are consistent with zero, with upper limits of Γ[Ξb(6327)0]<2.20(2.56) and Γ[Ξb(6333)0]<1.60(1.92) MeV at a 90% (95%) credibility level. The significance of the two-peak hypothesis is larger than nine (five) Gaussian standard deviations compared to the no-peak (one-peak) hypothesis. The masses, widths, and resonant structure of the new states are in good agreement with the expectations for a doublet of 1D Ξb0 resonances
Measurement of the Λb0→Λ(1520)μ+μ− differential branching fraction
- Author
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- Wyllie K
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- Yeroshenko V
- Yeung H
- Yin H
- Yu J
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- Zaffaroni E
- Zavertyaev M
- Zdybal M
- Zeng M
- Zhang C
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- Zhang S
- Zhang Y
- Zhang Y
- Zhao Y
- Zharkova A
- Zhelezov A
- Zheng Y
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- Zhukov V
- Zou Q
- Zucchelli S
- Zuliani D
- Zunica G
- Publication venue
- Publication date
- 01/01/2023
- Field of study
The branching fraction of the rare decay Λb0→Λ(1520)μ+μ− is measured for the first time, in the squared dimuon mass
intervals, q2, excluding the J/ψ and ψ(2S) regions. The data
sample analyzed was collected by the LHCb experiment at center-of-mass energies
of 7, 8, and 13 TeV, corresponding to a total integrated luminosity of $9\
\mathrm{fb}^{-1}.Theresultinthehighestq^{2}interval,q^{2} >15.0\
\mathrm{GeV}^2/c^4$, where theoretical predictions have the smallest model
dependence, agrees with the predictions.Comment: All figures and tables, along with any supplementary material and
additional information, are available at
https://cern.ch/lhcbproject/Publications/p/LHCb-PAPER-2022-050.html (LHCb
public pages
Pan-cancer analysis of whole genomes
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- The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium View Correspondence (jump link)
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- Ó. A. th
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- Publication venue
- Publication date
- 11/12/2019
- Field of study
Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe
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