77 research outputs found
A framework for protein structure classification and identification of novel protein structures
- Author
- Publication venue
- BioMed Central
- Publication date
- 01/01/2006
- Field of study
BACKGROUND: Protein structure classification plays a central role in understanding the function of a protein molecule with respect to all known proteins in a structure database. With the rapid increase in the number of new protein structures, the need for automated and accurate methods for protein classification is increasingly important. RESULTS: In this paper we present a unified framework for protein structure classification and identification of novel protein structures. The framework consists of a set of components for comparing, classifying, and clustering protein structures. These components allow us to accurately classify proteins into known folds, to detect new protein folds, and to provide a way of clustering the new folds. In our evaluation with SCOP 1.69, our method correctly classifies 86.0%, 87.7%, and 90.5% of new domains at family, superfamily, and fold levels. Furthermore, for protein domains that belong to new domain families, our method is able to produce clusters that closely correspond to the new families in SCOP 1.69. As a result, our method can also be used to suggest new classification groups that contain novel folds. CONCLUSION: We have developed a method called proCC for automatically classifying and clustering domains. The method is effective in classifying new domains and suggesting new domain families, and it is also very efficient. A web site offering access to proCC is freely available a
Hidden Markov model speed heuristic and iterative HMM search procedure
- Author
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC
- Author
- Abi B
- Abud A Abed
- Acciarri R
- Acero MA
- Adames MR
- Adamov G
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- Aguilar J
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- Alonso MJ Rodriguez
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- Wu W
- Wu W
- Xiao Y
- Xie F
- Yaeggy B
- Yandel E
- Yang G
- Yang K
- Yang T
- Yankelevich A
- Yershov N
- Yonehara K
- Yoon YS
- Young T
- Yu B
- Yu H
- Yu H
- Yu J
- Yu Y
- Yuan W
- Zaki R
- Zalesak J
- Zambelli L
- Zamorano B
- Zani A
- Zazueta L
- Zeller GP
- Zennamo J
- Zeug K
- Zhang C
- Zhang S
- Zhang Y
- Zhao M
- Zhivun E
- Zhu G
- Zimmerman ED
- Zucchelli S
- Zuklin J
- Zutshi V
- Zwaska R
- Publication venue
- 'Springer Fachmedien Wiesbaden GmbH'
- Publication date
- 16/07/2022
- Field of study
DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6Â Ă Â 6Â Ă Â 6Â m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7Â m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties
Targeting the glycoproteome
- Author
- A Chiba
- A Halim
- A Harazono
- A Harazono
- A Imberty
- A Imberty
- A Kobata
- A Kobata
- A Lee
- A Varki
- A Zougman
- AA Gooley
- Adnan Halim
- AM Wu
- Ammi Grahn
- BP Peters
- C Krisp
- C Sihlbom
- C Sihlbom
- C Slawson
- C Steentoft
- CA Cooper
- CIA Balog
- CS Chu
- CS Wang
- D Kolarich
- D Wang
- DJ Gill
- DJ Harvey
- DJ Moloney
- E Mirgorodskaya
- E Mirgorodskaya
- E Mirgorodskaya
- E Mohorko
- E Portelius
- E Portelius
- E Portelius
- E Tian
- ED Dodds
- F Hanisch
- F Kjeldsen
- F Maley
- F Schwarz
- G Palmisano
- G Palmisano
- G Zauner
- Göran Larson
- H Geyer
- H Kaji
- H Maeda
- H Schachter
- H Zhang
- H-J Gabius
- HJ Gabius
- HJ Gabius
- I Perdivara
- J Bunkenborg
- J Escribano
- J Nilsson
- J Nilsson
- J Tang
- J Zhao
- JD Marth
- JJ Coon
- JM Hogan
- JM Strub
- Jonas Nilsson
- JU Baenziger
- JV Olsen
- K Akasaka-Manya
- K Hakansson
- K Kubota
- K Ohtsubo
- K Sparbier
- K Sparbier
- K Sparbier
- K Ueda
- KA Stumpo
- KD Greis
- KG Hagen Ten
- KJ Brown
- KT-BG Schjoldager
- L Wells
- L Wells
- LA Breci
- LA Tabak
- M Frank
- M Kurogochi
- M Kurogochi
- M Ly
- M Madera
- M Mormann
- M Thaysen-Andersen
- M Wuhrer
- M Wuhrer
- M Wuhrer
- MA Tarp
- MB Renfrow
- MB Renfrow
- ME Wernette-Hammond
- MHJ Selman
- MJ Huddleston
- MR Larsen
- MR Larsen
- MT Mazur
- N Hashii
- N Sharon
- N Shibuya
- NE Scott
- P Hao
- P HĂ€gglund
- P PĂ„hlsson
- PH Jensen
- R Richter
- R Uematsu
- RA Laine
- RN Knibbs
- S Henning
- S Mysling
- S Mysling
- S Selvaraju
- SH Stalnaker
- T Lea
- T Liu
- T LĂŒtteke
- T Pacchiarotta
- T Yoshida-Moriguchi
- TA Gerken
- TH Plummer Jr
- U Lewandrowski
- W Sun
- WR Alley Jr
- Y Ito
- Y Lee
- Y Maeda
- Y Nagata
- Y Santiago
- Y Sato
- Y Takegawa
- Y Wada
- Y Wada
- Y Wang
- Y Wang
- Y Xu
- Z Darula
- Z Darula
- Z Darula
- Z Lei
- Z Yang
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- Field of study
Design, construction and operation of the ProtoDUNE-SP Liquid Argon TPC
- Author
- Abi B
- Abud AA
- Acciarri R
- Acero MA
- Adames MR
- Adamov G
- Adams D
- Adinolfi M
- Aduszkiewicz A
- Aguilar J
- Ahmad Z
- Ahmed J
- Alba JLB
- Ali-Mohammadzadeh B
- Alion T
- Allison K
- Almeida RMD
- Alonso MJR
- Alrashed M
- Alt C
- Alton A
- Amedo P
- Anderson J
- Andreopoulos C
- Andreotti M
- Andrews MP
- Andrianala F
- Andringa S
- Anfimov N
- Ankowski A
- Antoniassi M
- Antonova M
- Antoshkin A
- Antusch S
- Aranda-Fernandez A
- Ariga A
- Arnold LO
- Arroyave MA
- Asaadi J
- Asquith L
- Astiz ILDI
- Aurisano A
- Aushev V
- Autiero D
- Ayala-Torres M
- Azfar F
- B ACG
- Back A
- Back H
- Back JJ
- Backhouse C
- Baesso P
- Bagaturia I
- Bagby L
- Balashov N
- Balasubramanian S
- Baldi P
- Baller B
- Bambah B
- Barao F
- Barenboim G
- Barker GJ
- Barkhouse W
- Barnes C
- Barr G
- Barros A
- Barros N
- Barrow JL
- Basharina-Freshville A
- Bashyal A
- Basque V
- Battat JBR
- Battisti F
- Bay F
- Bazetto MCQ
- Beacom JF
- Bechetoille E
- Behera B
- Belchior E
- Bellantoni L
- Bellettini G
- Bellini V
- Beltramello O
- Belver D
- Benekos N
- Berg RV
- Berger J
- Berkman S
- Bermeo LVG
- Bernardini P
- Berner RM
- Berns H
- Bertolucci S
- Betancourt M
- Bevan A
- Bezerra TJC
- Bhattacharjee M
- Bhuller S
- Bhuyan B
- Biagi S
- Bian J
- Biassoni M
- Biery K
- Bilki B
- Bishai M
- Bitadze A
- Blake A
- Blaszczyk FDM
- Blazey GC
- Blucher E
- Boissevain J
- Bolognesi S
- Bolton T
- Bomben L
- Bonesini M
- Bongrand M
- Bonilla ER
- Bonini F
- Bonis ID
- Booth A
- Booth C
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- Bordoni S
- Borkum A
- Boschi T
- Bostan N
- Bour P
- Bourgeois C
- Boyd SB
- Boyden D
- Bracinik J
- Braga D
- Brailsford D
- Branca A
- Brandt A
- Bremer J
- Brew C
- Brianne E
- Brice SJ
- Brizzolari C
- Bromberg C
- Brooijmans G
- Brooke J
- Bross A
- Brunetti G
- Brunetti M
- Buchanan N
- Budd H
- Bueno LM
- Butorov I
- Cagnoli I
- Caicedo DAM
- Caiulo D
- Calabrese R
- Calafiura P
- Calcutt J
- Calin M
- Calvez S
- Calvo E
- Caminata A
- Campanelli M
- Campo AOD
- Cankocak K
- Caratelli D
- Carini G
- Carlus B
- Carneiro MF
- Carniti P
- Carranza H
- Carroll T
- Casta JF
- Castillo A
- Castromonte C
- Catano-Mur E
- Cattadori C
- Cavalier F
- Cavanna F
- Centro S
- Cerati G
- Cervelli A
- Chalifour M
- Chappell A
- Chardonnet E
- Charitonidis N
- Chatterjee A
- Chattopadhyay S
- Chen H
- Chen K
- Chen M
- Chen Y
- Chen Z
- Cheon Y
- Cherdack D
- Chi C
- Childress S
- Chiriacescu A
- Chisnall G
- Cho K
- Choate S
- Chokheli D
- Chong PS
- Choubey S
- Christensen A
- Christian D
- Christodoulou G
- Chukanov A
- Chung M
- Church E
- Cicero V
- Clarke P
- Coan TE
- Cocco AG
- Coelho JAB
- Collaboration DUNE
- Conley E
- Conley R
- Conrad JM
- Convery M
- Copello S
- Corwin L
- Cremaldi L
- Cremonesi L
- Crespo-Anadon JI
- Crisler M
- Cristaldo E
- Cross R
- Cudd A
- Cuesta C
- Cui Y
- Cussans D
- Dabrowski M
- Dalager O
- David C
- David Q
- Davies GS
- Davini S
- Dawson J
- De K
- Debbins P
- Decowski MP
- Deisting A
- Delbart A
- Delepine D
- Delgado M
- Delgado MAR
- Dell'Acqua A
- DeMuth DM
- Dennis S
- Densham C
- Deptuch GW
- Devi R
- Dharmapalan R
- Dias M
- Diaz DG
- Diaz F
- Diaz JS
- Ding P
- Distefano C
- Diurba R
- Diwan M
- Djurcic Z
- Doering D
- Dolan S
- Dolek F
- Dolinski MJ
- Domine L
- Domizio SD
- Douglas D
- Douillet D
- Drake G
- Drielsma F
- Duarte L
- Duchesneau D
- Duffy K
- Dunne P
- Durkin T
- Duyang H
- Dvornikov O
- Dwyer DA
- Dyshkant AS
- Eads M
- Earle A
- Edmunds D
- Eisch J
- Emberger L
- Emery S
- Ereditato A
- Erjavec T
- Escobar CO
- Eurin G
- Evans JJ
- Ewart E
- Ezeribe AC
- Fahey K
- Fajardo LSG
- Falcone A
- FanĂ M
- Farnese C
- Farzan Y
- Fedoseev D
- Felix J
- Feng Y
- Fernandez-Martinez E
- Ferraro F
- Fields L
- Filip P
- Filthaut F
- Fiorentini A
- Fiorini M
- Fitzpatrick RS
- Flanagan W
- Fleming B
- Flight R
- Forero DV
- Fowler J
- Fox W
- Franc J
- Francis K
- Franco D
- Freeman J
- Freestone J
- Fried J
- Friedland A
- Fuess S
- Furic I
- Furmanski AP
- Gabrielli A
- Gago A
- Gallagher H
- Gallas A
- Gallego-Ros A
- Gallice N
- Galymov V
- Gamberini E
- Gamble T
- Ganacim F
- Gandhi R
- Gandrajula R
- Gao F
- Gao S
- Garcia-Gamez D
- GarcĂa-Peris MA
- Gardiner S
- Gastler D
- Gauvreau J
- Ge G
- Gelli B
- Gendotti A
- Gent S
- Ghorbani-Moghaddam Z
- Giammaria P
- Giammaria T
- Gibin D
- Gil-Botella I
- Gilligan S
- Girerd C
- Giri AK
- Giulio LD
- Gnani D
- Gogota O
- Gold M
- Gollapinni S
- Gollwitzer K
- Gomes RA
- Gonnella F
- Gonzalez-Cuevas JA
- Gonzalez-Lopez M
- Goodman MC
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- Gotti C
- Goudzovski E
- Gouvea AD
- Grace C
- Graham M
- Gran R
- Granados E
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- Grant A
- Grant C
- Gratieri D
- Green P
- Greenler L
- Greer J
- Grenard J
- Griffith WC
- Groh M
- Grudzinski J
- Grzelak K
- Gu W
- Guardincerri E
- Guarino V
- Guarise M
- Guenette R
- Guerard E
- Guerzoni M
- Guglielmi A
- Guo B
- Guthikonda KK
- Gutierrez R
- Guzowski P
- Guzzo MM
- Gwon S
- Ha C
- Habig A
- Hadavand H
- Haenni R
- Hahn A
- Haiston J
- Hamacher-Baumann P
- Hamernik T
- Hamilton P
- Han J
- Harris DA
- Hartnell J
- Harton J
- Hasegawa T
- Hasnip C
- Hatcher R
- Hatfield KW
- Hatzikoutelis A
- Hayes C
- Hayrapetyan K
- Hays J
- Hazen E
- He M
- Heavey A
- Heeger KM
- Heise J
- Hennessy K
- Henry S
- Herner K
- Hertel L
- Hewes J
- Higuera A
- Hill T
- Hillier SJ
- Himmel A
- Hirsch LR
- Ho J
- Hoff J
- Holanda PCD
- Holin A
- Hoppe E
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- Hostert M
- Hourlier A
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- Hronek MS
- Huang J
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- Iliescu AM
- Illingworth R
- Ingratta G
- Ioannisian A
- Isenhower L
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- Jackson CM
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- Kadenko I
- Kakorin I
- Kalitkina A
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- Karcher A
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- Kashur L
- Kazaryan N
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- Keener P
- Kelly KJ
- Kemp E
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- Khabibullin M
- Khotjantsev A
- Khvedelidze A
- Kim D
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- Koehler K
- Koerner LW
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- Lawrence A
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- Lurgio PD
- Lurkin N
- Lux T
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- Machado AA
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- Marchionni A
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- Marshak M
- Marshall CM
- Marshall J
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- Miedema T
- Mikola V
- Milincic R
- Miller G
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- Zilberman P
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- Zucchelli S
- Zuklin J
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- Publication venue
- 'IOP Publishing'
- Publication date
- 04/08/2021
- Field of study
The ProtoDUNE-SP detector is a single-phase liquid argon time projection chamber (LArTPC) that was constructed and operated in the CERN North Area at the end of the H4 beamline. This detector is a prototype for the first far detector module of the Deep Underground Neutrino Experiment (DUNE), which will be constructed at the Sandford Underground Research Facility (SURF) in Lead, South Dakota, U.S.A. The ProtoDUNE-SP detector incorporates full-size components as designed for DUNE and has an active volume of 7 Ă 6 Ă 7.2 m3. The H4 beam delivers incident particles with well-measured momenta and high-purity particle identification. ProtoDUNE-SP's successful operation between 2018 and 2020 demonstrates the effectiveness of the single-phase far detector design. This paper describes the design, construction, assembly and operation of the detector components
Separation of track- and shower-like energy deposits in ProtoDUNE-SP using a convolutional neural network
- Author
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- Publication venue
- Publication date
- 01/01/2022
- Field of study
Liquid argon time projection chamber detector technology provides high spatial and calorimetric resolutions on the charged particles traversing liquid argon. As a result, the technology has been used in a number of recent neutrino experiments, and is the technology of choice for the Deep Underground Neutrino Experiment (DUNE). In order to perform high precision measurements of neutrinos in the detector, final state particles need to be effectively identified, and their energy accurately reconstructed. This article proposes an algorithm based on a convolutional neural network to perform the classification of energy deposits and reconstructed particles as track-like or arising from electromagnetic cascades. Results from testing the algorithm on data from ProtoDUNE-SP, a prototype of the DUNE far detector, are presented. The network identifies track- and shower-like particles, as well as Michel electrons, with high efficiency. The performance of the algorithm is consistent between data and simulation
Separation of track- and shower-like energy deposits in ProtoDUNE-SP using a convolutional neural network
- Author
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- Zimmerman ED
- Zucchelli S
- Zuklin J
- Zutshi V
- Zwaska R
- Publication venue
- 'Springer Science and Business Media LLC'
- Publication date
- 01/01/2022
- Field of study
Liquid argon time projection chamber detector technology provides high spatial and calorimetric resolutions on the charged particles traversing liquid argon. As a result, the technology has been used in a number of recent neutrino experiments, and is the technology of choice for the Deep Underground Neutrino Experiment (DUNE). In order to perform high precision measurements of neutrinos in the detector, final state particles need to be effectively identified, and their energy accurately reconstructed. This article proposes an algorithm based on a convolutional neural network to perform the classification of energy deposits and reconstructed particles as track-like or arising from electromagnetic cascades. Results from testing the algorithm on experimental data from ProtoDUNE-SP, a prototype of the DUNE far detector, are presented. The network identifies track- and shower-like particles, as well as Michel electrons, with high efficiency. The performance of the algorithm is consistent between experimental data and simulation
Low exposure long-baseline neutrino oscillation sensitivity of the DUNE experiment
- Author
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- Publication venue
- Publication date
- Field of study
The Deep Underground Neutrino Experiment (DUNE) will produce world-leading neutrino oscillation measurements over the lifetime of the experiment. In this work, we explore DUNE's sensitivity to observe charge-parity violation (CPV) in the neutrino sector, and to resolve the mass ordering, for exposures of up to 100 kiloton-megawatt-years (kt-MW-yr). The analysis includes detailed uncertainties on the flux prediction, the neutrino interaction model, and detector effects. We demonstrate that DUNE will be able to unambiguously resolve the neutrino mass ordering at a 3Ï (5Ï) level, with a 66 (100) kt-MW-yr far detector exposure, and has the ability to make strong statements at significantly shorter exposures depending on the true value of other oscillation parameters. We also show that DUNE has the potential to make a robust measurement of CPV at a 3Ï level with a 100 kt-MW-yr exposure for the maximally CP-violating values \delta_{\rm CP}} = \pm\pi/2. Additionally, the dependence of DUNE's sensitivity on the exposure taken in neutrino-enhanced and antineutrino-enhanced running is discussed. An equal fraction of exposure taken in each beam mode is found to be close to optimal when considered over the entire space of interest
Searching for solar KDAR with DUNE
- Author
- Abi B
- Abud AA
- Acciarri R
- Acero MA
- Adames MR
- Adamov G
- Adams D
- Adinolfi M
- Aduszkiewicz A
- Aguilar J
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- Tishchenko V
- Todd J
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- Tonazzo A
- Torbunov D
- Torti M
- Tortola M
- Tortorici F
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- Urheim J
- Usher T
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- Vermeulen MA
- Verzocchi M
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- Vignoli C
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- Villanueva AC
- Viren B
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- Waldron AV
- Wallbank M
- Wallis C
- Wang H
- Wang J
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- Wascko MO
- Waters D
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- White A
- Whitehead LH
- Whittington D
- Wilking MJ
- Wilkinson C
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- Wisniewski W
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- Publication venue
- Publication date
- Field of study
Organizational trust in times of COVID-19 : hospitality employeesâ affective responses to managersâ communication
- Publication venue
- 'Elsevier BV'
- Publication date
- 28/02/2024
- Field of study
202105 bcwhNot applicableSelf-fundedPublished36 month
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