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Kiwimagi KA, Letendre JH, Weinberg BH, Wang J, Chen M, Watanabe L, Myers CJ, Beal J, Wong WW, Weiss R. Quantitative characterization of recombinase-based digitizer circuits enables predictable amplification of biological signals. Commun Biol 2021; 4:875. [PMID: 34267310 PMCID: PMC8282836 DOI: 10.1038/s42003-021-02325-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 05/24/2021] [Indexed: 12/24/2022] Open
Abstract
Many synthetic gene circuits are restricted to single-use applications or require iterative refinement for incorporation into complex systems. One example is the recombinase-based digitizer circuit, which has been used to improve weak or leaky biological signals. Here we present a workflow to quantitatively define digitizer performance and predict responses to different input signals. Using a combination of signal-to-noise ratio (SNR), area under a receiver operating characteristic curve (AUC), and fold change (FC), we evaluate three small-molecule inducible digitizer designs demonstrating FC up to 508x and SNR up to 3.77 dB. To study their behavior further and improve modularity, we develop a mixed phenotypic/mechanistic model capable of predicting digitizer configurations that amplify a synNotch cell-to-cell communication signal (Δ SNR up to 2.8 dB). We hope the metrics and modeling approaches here will facilitate incorporation of these digitizers into other systems while providing an improved workflow for gene circuit characterization.
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Acharya S, Adamová D, Adler A, Adolfsson J, Aggarwal MM, Aglieri Rinella G, Agnello M, Agrawal N, Ahammed Z, Ahmad S, Ahn SU, Akbar Z, Akindinov A, Al-Turany M, Alam SN, Albuquerque DSD, Aleksandrov D, Alessandro B, Alfanda HM, Alfaro Molina R, Ali B, Ali Y, Alici A, Alizadehvandchali N, Alkin A, Alme J, Alt T, Altenkamper L, Altsybeev I, Anaam MN, Andrei C, Andreou D, Andronic A, Angeletti M, Anguelov V, Anson C, Antičić T, Antinori F, Antonioli P, Apadula N, Aphecetche L, Appelshäuser H, Arcelli S, Arnaldi R, Arratia M, Arsene IC, Arslandok M, Augustinus A, Averbeck R, Aziz S, Azmi MD, Badalà A, Baek YW, Bagnasco S, Bai X, Bailhache R, Bala R, Balbino A, Baldisseri A, Ball M, Balouza S, Banerjee D, Barbera R, Barioglio L, Barnaföldi GG, Barnby LS, Barret V, Bartalini P, Bartels C, Barth K, Bartsch E, Baruffaldi F, Bastid N, Basu S, Batigne G, Batyunya B, Bauri D, Bazo Alba JL, Bearden IG, Beattie C, Bedda C, Behera NK, Belikov I, Bell Hechavarria ADC, Bellini F, Bellwied R, Belyaev V, Bencedi G, Beole S, Bercuci A, Berdnikov Y, Berenyi D, Bertens RA, Berzano D, Besoiu MG, Betev L, Bhasin A, Bhat IR, Bhat MA, Bhatt H, Bhattacharjee B, Bianchi A, Bianchi L, Bianchi N, Bielčík J, Bielčíková J, Bilandzic A, Biro G, Biswas R, Biswas S, Blair JT, Blau D, Blume C, Boca G, Bock F, Bogdanov A, Boi S, Bok J, Boldizsár L, Bolozdynya A, Bombara M, Bonomi G, Borel H, Borissov A, Bossi H, Botta E, Bratrud L, Braun-Munzinger P, Bregant M, Broz M, Bruna E, Bruno GE, Buckland MD, Budnikov D, Buesching H, Bufalino S, Bugnon O, Buhler P, Buncic P, Buthelezi Z, Butt JB, Bysiak SA, Caffarri D, Caliva A, Calvo Villar E, Camacho JMM, Camacho RS, Camerini P, Canedo FDM, Capon AA, Carnesecchi F, Caron R, Castillo Castellanos J, Castro AJ, Casula EAR, Catalano F, Ceballos Sanchez C, Chakraborty P, Chandra S, Chang W, Chapeland S, Chartier M, Chattopadhyay S, Chattopadhyay S, Chauvin A, Cheshkov C, Cheynis B, Chibante Barroso V, Chinellato DD, Cho S, Chochula P, Chowdhury T, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Cicalo C, Cifarelli L, Cilladi LD, Cindolo F, Ciupek MR, Clai G, Cleymans J, Colamaria F, Colella D, Collu A, Colocci M, Concas M, Conesa Balbastre G, Conesa Del Valle Z, Contin G, Contreras JG, Cormier TM, Corrales Morales Y, Cortese P, Cosentino MR, Costa F, Costanza S, Crochet P, Cuautle E, Cui P, Cunqueiro L, Dabrowski D, Dahms T, Dainese A, Damas FPA, Danisch MC, Danu A, Das D, Das I, Das P, Das P, Das S, Dash A, Dash S, De S, De Caro A, de Cataldo G, de Cuveland J, De Falco A, De Gruttola D, De Marco N, De Pasquale S, Deb S, Degenhardt HF, Deja KR, Deloff A, Delsanto S, Deng W, Dhankher P, Di Bari D, Di Mauro A, Diaz RA, Dietel T, Dillenseger P, Ding Y, Divià R, Dixit DU, Djuvsland Ø, Dmitrieva U, Dobrin A, Dönigus B, Dordic O, Dubey AK, Dubla A, Dudi S, Dukhishyam M, Dupieux P, Ehlers RJ, Eikeland VN, Elia D, Erazmus B, Erhardt F, Erokhin A, Ersdal MR, Espagnon B, Eulisse G, Evans D, Evdokimov S, Fabbietti L, Faggin M, Faivre J, Fan F, Fantoni A, Fasel M, Fecchio P, Feliciello A, Feofilov G, Fernández Téllez A, Ferrero A, Ferretti A, Festanti A, Feuillard VJG, Figiel J, Filchagin S, Finogeev D, Fionda FM, Fiorenza G, Flor F, Flores AN, Foertsch S, Foka P, Fokin S, Fragiacomo E, Frankenfeld U, Fuchs U, Furget C, Furs A, Fusco Girard M, Gaardhøje JJ, Gagliardi M, Gago AM, Gal A, Galvan CD, Ganoti P, Garabatos C, Garcia JRA, Garcia-Solis E, Garg K, Gargiulo C, Garibli A, Garner K, Gasik P, Gauger EF, Gay Ducati MB, Germain M, Ghosh J, Ghosh P, Ghosh SK, Giacalone M, Gianotti P, Giubellino P, Giubilato P, Glaenzer AMC, Glässel P, Gomez Ramirez A, Gonzalez V, González-Trueba LH, Gorbunov S, Görlich L, Goswami A, Gotovac S, Grabski V, Graczykowski LK, Graham KL, Greiner L, Grelli A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Groettvik OS, Grosa F, Grosse-Oetringhaus JF, Grosso R, Guernane R, Guittiere M, Gulbrandsen K, Gunji T, Gupta A, Gupta R, Guzman IB, Haake R, Habib MK, Hadjidakis C, Hamagaki H, Hamar G, Hamid M, Hannigan R, Haque MR, Harlenderova A, Harris JW, Harton A, Hasenbichler JA, Hassan H, Hassan QU, Hatzifotiadou D, Hauer P, Havener LB, Hayashi S, Heckel ST, Hellbär E, Helstrup H, Herghelegiu A, Herman T, Hernandez EG, Herrera Corral G, Herrmann F, Hetland KF, Hillemanns H, Hills C, Hippolyte B, Hohlweger B, Honermann J, Horak D, Hornung A, Hornung S, Hosokawa R, Hristov P, Huang C, Hughes C, Huhn P, Humanic TJ, Hushnud H, Husova LA, Hussain N, Hussain SA, Hutter D, Iddon JP, Ilkaev R, Ilyas H, Inaba M, Innocenti GM, Ippolitov M, Isakov A, Islam MS, Ivanov M, Ivanov V, Izucheev V, Jacak B, Jacazio N, Jacobs PM, Jadlovska S, Jadlovsky J, Jaelani S, Jahnke C, Jakubowska MJ, Janik MA, Janson T, Jercic M, Jevons O, Jin M, Jonas F, Jones PG, Jung J, Jung M, Jusko A, Kalinak P, Kalweit A, Kaplin V, Kar S, Karasu Uysal A, Karatovic D, Karavichev O, Karavicheva T, Karczmarczyk P, Karpechev E, Kazantsev A, Kebschull U, Keidel R, Keil M, Ketzer B, Khabanova Z, Khan AM, Khan S, Khanzadeev A, Kharlov Y, Khatun A, Khuntia A, Kileng B, Kim B, Kim B, Kim D, Kim DJ, Kim EJ, Kim H, Kim J, Kim JS, Kim J, Kim J, Kim J, Kim M, Kim S, Kim T, Kim T, Kirsch S, Kisel I, Kiselev S, Kisiel A, Klay JL, Klein C, Klein J, Klein S, Klein-Bösing C, Kleiner M, Kluge A, Knichel ML, Knospe AG, Kobdaj C, Köhler MK, Kollegger T, Kondratyev A, Kondratyeva N, Kondratyuk E, Konig J, Konigstorfer SA, Konopka PJ, Kornakov G, Koska L, Kovalenko O, Kovalenko V, Kowalski M, Králik I, Kravčáková A, Kreis L, Krivda M, Krizek F, Krizkova Gajdosova K, Krüger M, Kryshen E, Krzewicki M, Kubera AM, Kučera V, Kuhn C, Kuijer PG, Kumar L, Kundu S, Kurashvili P, Kurepin A, Kurepin AB, Kuryakin A, Kushpil S, Kvapil J, Kweon MJ, Kwon JY, Kwon Y, La Pointe SL, La Rocca P, Lai YS, Lamanna M, Langoy R, Lapidus K, Lardeux A, Larionov P, Laudi E, Lavicka R, Lazareva T, Lea R, Leardini L, Lee J, Lee S, Lehner S, Lehrbach J, Lemmon RC, León Monzón I, Lesser ED, Lettrich M, Lévai P, Li X, Li XL, Lien J, Lietava R, Lim B, Lindenstruth V, Lindner A, Lippmann C, Lisa MA, Liu A, Liu J, Liu S, Llope WJ, Lofnes IM, Loginov V, Loizides C, Loncar P, Lopez JA, Lopez X, López Torres E, Luhder JR, Lunardon M, Luparello G, Ma YG, Maevskaya A, Mager M, Mahmood SM, Mahmoud T, Maire A, Majka RD, Malaev M, Malik QW, Malinina L, Mal'Kevich D, Malzacher P, Mandaglio G, Manko V, Manso F, Manzari V, Mao Y, Marchisone M, Mareš J, Margagliotti GV, Margotti A, Marín A, Markert C, Marquard M, Martin CD, Martin NA, Martinengo P, Martinez JL, Martínez MI, Martínez García G, Masciocchi S, Masera M, Masoni A, Massacrier L, Masson E, Mastroserio A, Mathis AM, Matonoha O, Matuoka PFT, Matyja A, Mayer C, Mazzaschi F, Mazzilli M, Mazzoni MA, Mechler AF, Meddi F, Melikyan Y, Menchaca-Rocha A, Mengke C, Meninno E, Menon AS, Meres M, Mhlanga S, Miake Y, Micheletti L, Migliorin LC, Mihaylov DL, Mikhaylov K, Mishra AN, Miśkowiec D, Modak A, Mohammadi N, Mohanty AP, Mohanty B, Khan MM, Moravcova Z, Mordasini C, Moreira De Godoy DA, Moreno LAP, Morozov I, Morsch A, Mrnjavac T, Muccifora V, Mudnic E, Mühlheim D, Muhuri S, Mulligan JD, Mulliri A, Munhoz MG, Munzer RH, Murakami H, Murray S, Musa L, Musinsky J, Myers CJ, Myrcha JW, Naik B, Nair R, Nandi BK, Nania R, Nappi E, Naru MU, Nassirpour AF, Nattrass C, Nayak R, Nayak TK, Nazarenko S, Neagu A, Negrao De Oliveira RA, Nellen L, Nesbo SV, Neskovic G, Nesterov D, Neumann LT, Nielsen BS, Nikolaev S, Nikulin S, Nikulin V, Noferini F, Nomokonov P, Norman J, Novitzky N, Nowakowski P, Nyanin A, Nystrand J, Ogino M, Ohlson A, Oleniacz J, Oliveira Da Silva AC, Oliver MH, Oppedisano C, Ortiz Velasquez A, Oskarsson A, Otwinowski J, Oyama K, Pachmayer Y, Pacik V, Padhan S, Pagano D, Paić G, Pan J, Panebianco S, Pareek P, Park J, Parkkila JE, Parmar S, Pathak SP, Paul B, Pazzini J, Pei H, Peitzmann T, Peng X, Pereira LG, Pereira Da Costa H, Peresunko D, Perez GM, Perrin S, Pestov Y, Petráček V, Petrovici M, Pezzi RP, Piano S, Pikna M, Pillot P, Pinazza O, Pinsky L, Pinto C, Pisano S, Pistone D, Płoskoń M, Planinic M, Pliquett F, Poghosyan MG, Polichtchouk B, Poljak N, Pop A, Porteboeuf-Houssais S, Pozdniakov V, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Putschke J, Qiu S, Quaglia L, Quishpe RE, Ragoni S, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Ramirez SAR, Raniwala R, Raniwala S, Räsänen SS, Rath R, Ratza V, Ravasenga I, Read KF, Redelbach AR, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Rescakova Z, Reygers K, Riabov A, Riabov V, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rode SP, Rodríguez Cahuantzi M, Røed K, Rogalev R, Rogochaya E, Rohr D, Röhrich D, Rojas PF, Rokita PS, Ronchetti F, Rosano A, Rosas ED, Roslon K, Rossi A, Rotondi A, Roy A, Roy P, Rueda OV, Rui R, Rumyantsev B, Rustamov A, Ryabinkin E, Ryabov Y, Rybicki A, Rytkonen H, Saarimaki OAM, Sadek R, Sadhu S, Sadovsky S, Šafařík K, Saha SK, Sahoo B, Sahoo P, Sahoo R, Sahoo S, Sahu PK, Saini J, Sakai S, Sambyal S, Samsonov V, Sarkar D, Sarkar N, Sarma P, Sarti VM, Sas MHP, Scapparone E, Schambach J, Scheid HS, Schiaua C, Schicker R, Schmah A, Schmidt C, Schmidt HR, Schmidt MO, Schmidt M, Schmidt NV, Schmier AR, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Seger JE, Sekiguchi Y, Sekihata D, Selyuzhenkov I, Senyukov S, Serebryakov D, Sevcenco A, Shabanov A, Shabetai A, Shahoyan R, Shaikh W, Shangaraev A, Sharma A, Sharma A, Sharma H, Sharma M, Sharma N, Sharma S, Sheibani O, Shigaki K, Shimomura M, Shirinkin S, Shou Q, Sibiriak Y, Siddhanta S, Siemiarczuk T, Silvermyr D, Simatovic G, Simonetti G, Singh B, Singh R, Singh R, Singh R, Singh VK, Singhal V, Sinha T, Sitar B, Sitta M, Skaali TB, Slupecki M, Smirnov N, Snellings RJM, Soncco C, Song J, Songmoolnak A, Soramel F, Sorensen S, Sputowska I, Stachel J, Stan I, Steffanic PJ, Stenlund E, Stiefelmaier SF, Stocco D, Storetvedt MM, Stritto LD, Suaide AAP, Sugitate T, Suire C, Suleymanov M, Suljic M, Sultanov R, Šumbera M, Sumberia V, Sumowidagdo S, Swain S, Szabo A, Szarka I, Tabassam U, Taghavi SF, Taillepied G, Takahashi J, Tambave GJ, Tang S, Tarhini M, Tarzila MG, Tauro A, Tejeda Muñoz G, Telesca A, Terlizzi L, Terrevoli C, Thakur D, Thakur S, Thomas D, Thoresen F, Tieulent R, Tikhonov A, Timmins AR, Toia A, Topilskaya N, Toppi M, Torales-Acosta F, Torres SR, Trifiró A, Tripathy S, Tripathy T, Trogolo S, Trombetta G, Tropp L, Trubnikov V, Trzaska WH, Trzcinski TP, Trzeciak BA, Tumkin A, Turrisi R, Tveter TS, Ullaland K, Umaka EN, Uras A, Usai GL, Vala M, Valle N, Vallero S, van der Kolk N, van Doremalen LVR, van Leeuwen M, Vande Vyvre P, Varga D, Varga Z, Varga-Kofarago M, Vargas A, Vasileiou M, Vasiliev A, Vázquez Doce O, Vechernin V, Vercellin E, Vergara Limón S, Vermunt L, Vernet R, Vértesi R, Vickovic L, Vilakazi Z, Villalobos Baillie O, Vino G, Vinogradov A, Virgili T, Vislavicius V, Vodopyanov A, Volkel B, Völkl MA, Voloshin K, Voloshin SA, Volpe G, von Haller B, Vorobyev I, Voscek D, Vrláková J, Wagner B, Weber M, Weber SG, Wegrzynek A, Wenzel SC, Wessels JP, Wiechula J, Wikne J, Wilk G, Wilkinson J, Willems GA, Willsher E, Windelband B, Winn M, Witt WE, Wright JR, Wu Y, Xu R, Yalcin S, Yamaguchi Y, Yamakawa K, Yang S, Yano S, Yin Z, Yokoyama H, Yoo IK, Yoon JH, Yuan S, Yuncu A, Yurchenko V, Zaccolo V, Zaman A, Zampolli C, Zanoli HJC, Zardoshti N, Zarochentsev A, Závada P, Zaviyalov N, Zbroszczyk H, Zhalov M, Zhang S, Zhang X, Zhang Z, Zherebchevskii V, Zhi Y, Zhou D, Zhou Y, Zhou Z, Zhu J, Zhu Y, Zichichi A, Zinovjev G, Zurlo N. Elliptic Flow of Electrons from Beauty-Hadron Decays in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV. PHYSICAL REVIEW LETTERS 2021; 126:162001. [PMID: 33961482 DOI: 10.1103/physrevlett.126.162001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 01/27/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
The elliptic flow of electrons from beauty hadron decays at midrapidity (|y|<0.8) is measured in Pb-Pb collisions at sqrt[s_{NN}]=5.02 TeV with the ALICE detector at the LHC. The azimuthal distribution of the particles produced in the collisions can be parametrized with a Fourier expansion, in which the second harmonic coefficient represents the elliptic flow, v_{2}. The v_{2} coefficient of electrons from beauty hadron decays is measured for the first time in the transverse momentum (p_{T}) range 1.3-6 GeV/c in the centrality class 30%-50%. The measurement of electrons from beauty-hadron decays exploits their larger mean proper decay length cτ≈500 μm compared to that of charm hadrons and most of the other background sources. The v_{2} of electrons from beauty hadron decays at midrapidity is found to be positive with a significance of 3.75 σ. The results provide insights into the degree of thermalization of beauty quarks in the medium. A model assuming full thermalization of beauty quarks is strongly disfavored by the measurement at high p_{T}, but is in agreement with the results at low p_{T}. Transport models including substantial interactions of beauty quarks with an expanding strongly interacting medium describe the measurement within uncertainties.
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Acharya S, Adamová D, Adler A, Adolfsson J, Aggarwal MM, Aglieri Rinella G, Agnello M, Agrawal N, Ahammed Z, Ahmad S, Ahn SU, Akbar Z, Akindinov A, Al-Turany M, Alam SN, Albuquerque DSD, Aleksandrov D, Alessandro B, Alfanda HM, Alfaro Molina R, Ali B, Ali Y, Alici A, Alizadehvandchali N, Alkin A, Alme J, Alt T, Altenkamper L, Altsybeev I, Anaam MN, Andrei C, Andreou D, Andronic A, Angeletti M, Anguelov V, Anson C, Antičić T, Antinori F, Antonioli P, Apadula N, Aphecetche L, Appelshäuser H, Arcelli S, Arnaldi R, Arratia M, Arsene IC, Arslandok M, Augustinus A, Averbeck R, Aziz S, Azmi MD, Badalà A, Baek YW, Bagnasco S, Bai X, Bailhache R, Bala R, Balbino A, Baldisseri A, Ball M, Balouza S, Banerjee D, Barbera R, Barioglio L, Barnaföldi GG, Barnby LS, Barret V, Bartalini P, Bartels C, Barth K, Bartsch E, Baruffaldi F, Bastid N, Basu S, Batigne G, Batyunya B, Bauri D, Bazo Alba JL, Bearden IG, Beattie C, Bedda C, Behera NK, Belikov I, Bell Hechavarria ADC, Bellini F, Bellwied R, Belyaev V, Bencedi G, Beole S, Bercuci A, Berdnikov Y, Berenyi D, Bertens RA, Berzano D, Besoiu MG, Betev L, Bhasin A, Bhat IR, Bhat MA, Bhatt H, Bhattacharjee B, Bianchi A, Bianchi L, Bianchi N, Bielčík J, Bielčíková J, Bilandzic A, Biro G, Biswas R, Biswas S, Blair JT, Blau D, Blume C, Boca G, Bock F, Bogdanov A, Boi S, Bok J, Boldizsár L, Bolozdynya A, Bombara M, Bonomi G, Borel H, Borissov A, Bossi H, Botta E, Bratrud L, Braun-Munzinger P, Bregant M, Broz M, Bruna E, Bruno GE, Buckland MD, Budnikov D, Buesching H, Bufalino S, Bugnon O, Buhler P, Buncic P, Buthelezi Z, Butt JB, Bysiak SA, Caffarri D, Caliva A, Calvo Villar E, Camacho JMM, Camacho RS, Camerini P, Canedo FDM, Capon AA, Carnesecchi F, Caron R, Castillo Castellanos J, Castro AJ, Casula EAR, Catalano F, Ceballos Sanchez C, Chakraborty P, Chandra S, Chang W, Chapeland S, Chartier M, Chattopadhyay S, Chattopadhyay S, Chauvin A, Cheshkov C, Cheynis B, Chibante Barroso V, Chinellato DD, Cho S, Chochula P, Chowdhury T, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Cicalo C, Cifarelli L, Cilladi LD, Cindolo F, Ciupek MR, Clai G, Cleymans J, Colamaria F, Colella D, Collu A, Colocci M, Concas M, Conesa Balbastre G, Conesa Del Valle Z, Contin G, Contreras JG, Cormier TM, Corrales Morales Y, Cortese P, Cosentino MR, Costa F, Costanza S, Crochet P, Cuautle E, Cui P, Cunqueiro L, Dabrowski D, Dahms T, Dainese A, Damas FPA, Danisch MC, Danu A, Das D, Das I, Das P, Das P, Das S, Dash A, Dash S, De S, De Caro A, de Cataldo G, de Cuveland J, De Falco A, De Gruttola D, De Marco N, De Pasquale S, Deb S, Degenhardt HF, Deja KR, Deloff A, Delsanto S, Deng W, Dhankher P, Di Bari D, Di Mauro A, Diaz RA, Dietel T, Dillenseger P, Ding Y, Divià R, Dixit DU, Djuvsland Ø, Dmitrieva U, Dobrin A, Dönigus B, Dordic O, Dubey AK, Dubla A, Dudi S, Dukhishyam M, Dupieux P, Ehlers RJ, Eikeland VN, Elia D, Erazmus B, Erhardt F, Erokhin A, Ersdal MR, Espagnon B, Eulisse G, Evans D, Evdokimov S, Fabbietti L, Faggin M, Faivre J, Fan F, Fantoni A, Fasel M, Fecchio P, Feliciello A, Feofilov G, Fernández Téllez A, Ferrero A, Ferretti A, Festanti A, Feuillard VJG, Figiel J, Filchagin S, Finogeev D, Fionda FM, Fiorenza G, Flor F, Flores AN, Foertsch S, Foka P, Fokin S, Fragiacomo E, Frankenfeld U, Fuchs U, Furget C, Furs A, Fusco Girard M, Gaardhøje JJ, Gagliardi M, Gago AM, Gal A, Galvan CD, Ganoti P, Garabatos C, Garcia JRA, Garcia-Solis E, Garg K, Gargiulo C, Garibli A, Garner K, Gasik P, Gauger EF, Gay Ducati MB, Germain M, Ghosh J, Ghosh P, Ghosh SK, Giacalone M, Gianotti P, Giubellino P, Giubilato P, Glaenzer AMC, Glässel P, Gomez Ramirez A, Gonzalez V, González-Trueba LH, Gorbunov S, Görlich L, Goswami A, Gotovac S, Grabski V, Graczykowski LK, Graham KL, Greiner L, Grelli A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Groettvik OS, Grosa F, Grosse-Oetringhaus JF, Grosso R, Guernane R, Guittiere M, Gulbrandsen K, Gunji T, Gupta A, Gupta R, Guzman IB, Haake R, Habib MK, Hadjidakis C, Hamagaki H, Hamar G, Hamid M, Hannigan R, Haque MR, Harlenderova A, Harris JW, Harton A, Hasenbichler JA, Hassan H, Hassan QU, Hatzifotiadou D, Hauer P, Havener LB, Hayashi S, Heckel ST, Hellbär E, Helstrup H, Herghelegiu A, Herman T, Hernandez EG, Herrera Corral G, Herrmann F, Hetland KF, Hillemanns H, Hills C, Hippolyte B, Hohlweger B, Honermann J, Horak D, Hornung A, Hornung S, Hosokawa R, Hristov P, Huang C, Hughes C, Huhn P, Humanic TJ, Hushnud H, Husova LA, Hussain N, Hussain SA, Hutter D, Iddon JP, Ilkaev R, Ilyas H, Inaba M, Innocenti GM, Ippolitov M, Isakov A, Islam MS, Ivanov M, Ivanov V, Izucheev V, Jacak B, Jacazio N, Jacobs PM, Jadlovska S, Jadlovsky J, Jaelani S, Jahnke C, Jakubowska MJ, Janik MA, Janson T, Jercic M, Jevons O, Jin M, Jonas F, Jones PG, Jung J, Jung M, Jusko A, Kalinak P, Kalweit A, Kaplin V, Kar S, Karasu Uysal A, Karatovic D, Karavichev O, Karavicheva T, Karczmarczyk P, Karpechev E, Kazantsev A, Kebschull U, Keidel R, Keil M, Ketzer B, Khabanova Z, Khan AM, Khan S, Khanzadeev A, Kharlov Y, Khatun A, Khuntia A, Kileng B, Kim B, Kim B, Kim D, Kim DJ, Kim EJ, Kim H, Kim J, Kim JS, Kim J, Kim J, Kim J, Kim M, Kim S, Kim T, Kim T, Kirsch S, Kisel I, Kiselev S, Kisiel A, Klay JL, Klein C, Klein J, Klein S, Klein-Bösing C, Kleiner M, Kluge A, Knichel ML, Knospe AG, Kobdaj C, Köhler MK, Kollegger T, Kondratyev A, Kondratyeva N, Kondratyuk E, Konig J, Konigstorfer SA, Konopka PJ, Kornakov G, Koska L, Kovalenko O, Kovalenko V, Kowalski M, Králik I, Kravčáková A, Kreis L, Krivda M, Krizek F, Krizkova Gajdosova K, Krüger M, Kryshen E, Krzewicki M, Kubera AM, Kučera V, Kuhn C, Kuijer PG, Kumar L, Kundu S, Kurashvili P, Kurepin A, Kurepin AB, Kuryakin A, Kushpil S, Kvapil J, Kweon MJ, Kwon JY, Kwon Y, La Pointe SL, La Rocca P, Lai YS, Lamanna M, Langoy R, Lapidus K, Lardeux A, Larionov P, Laudi E, Lavicka R, Lazareva T, Lea R, Leardini L, Lee J, Lee S, Lehner S, Lehrbach J, Lemmon RC, León Monzón I, Lesser ED, Lettrich M, Lévai P, Li X, Li XL, Lien J, Lietava R, Lim B, Lindenstruth V, Lindner A, Lippmann C, Lisa MA, Liu A, Liu J, Liu S, Llope WJ, Lofnes IM, Loginov V, Loizides C, Loncar P, Lopez JA, Lopez X, López Torres E, Luhder JR, Lunardon M, Luparello G, Ma YG, Maevskaya A, Mager M, Mahmood SM, Mahmoud T, Maire A, Majka RD, Malaev M, Malik QW, Malinina L, Mal'Kevich D, Malzacher P, Mandaglio G, Manko V, Manso F, Manzari V, Mao Y, Marchisone M, Mareš J, Margagliotti GV, Margotti A, Marín A, Markert C, Marquard M, Martin CD, Martin NA, Martinengo P, Martinez JL, Martínez MI, Martínez García G, Masciocchi S, Masera M, Masoni A, Massacrier L, Masson E, Mastroserio A, Mathis AM, Matonoha O, Matuoka PFT, Matyja A, Mayer C, Mazzaschi F, Mazzilli M, Mazzoni MA, Mechler AF, Meddi F, Melikyan Y, Menchaca-Rocha A, Mengke C, Meninno E, Menon AS, Meres M, Mhlanga S, Miake Y, Micheletti L, Migliorin LC, Mihaylov DL, Mikhaylov K, Mishra AN, Miśkowiec D, Modak A, Mohammadi N, Mohanty AP, Mohanty B, Mohisin Khan M, Moravcova Z, Mordasini C, Moreira De Godoy DA, Moreno LAP, Morozov I, Morsch A, Mrnjavac T, Muccifora V, Mudnic E, Mühlheim D, Muhuri S, Mulligan JD, Mulliri A, Munhoz MG, Munzer RH, Murakami H, Murray S, Musa L, Musinsky J, Myers CJ, Myrcha JW, Naik B, Nair R, Nandi BK, Nania R, Nappi E, Naru MU, Nassirpour AF, Nattrass C, Nayak R, Nayak TK, Nazarenko S, Neagu A, Negrao De Oliveira RA, Nellen L, Nesbo SV, Neskovic G, Nesterov D, Neumann LT, Nielsen BS, Nikolaev S, Nikulin S, Nikulin V, Noferini F, Nomokonov P, Norman J, Novitzky N, Nowakowski P, Nyanin A, Nystrand J, Ogino M, Ohlson A, Oleniacz J, Oliveira Da Silva AC, Oliver MH, Oppedisano C, Ortiz Velasquez A, Oskarsson A, Otwinowski J, Oyama K, Pachmayer Y, Pacik V, Padhan S, Pagano D, Paić G, Pan J, Panebianco S, Pareek P, Park J, Parkkila JE, Parmar S, Pathak SP, Paul B, Pazzini J, Pei H, Peitzmann T, Peng X, Pereira LG, Pereira Da Costa H, Peresunko D, Perez GM, Perrin S, Pestov Y, Petráček V, Petrovici M, Pezzi RP, Piano S, Pikna M, Pillot P, Pinazza O, Pinsky L, Pinto C, Pisano S, Pistone D, Płoskoń M, Planinic M, Pliquett F, Poghosyan MG, Polichtchouk B, Poljak N, Pop A, Porteboeuf-Houssais S, Pozdniakov V, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Putschke J, Qiu S, Quaglia L, Quishpe RE, Ragoni S, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Ramirez SAR, Raniwala R, Raniwala S, Räsänen SS, Rath R, Ratza V, Ravasenga I, Read KF, Redelbach AR, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Rescakova Z, Reygers K, Riabov A, Riabov V, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rode SP, Rodríguez Cahuantzi M, Røed K, Rogalev R, Rogochaya E, Rohr D, Röhrich D, Rojas PF, Rokita PS, Ronchetti F, Rosano A, Rosas ED, Roslon K, Rossi A, Rotondi A, Roy A, Roy P, Rueda OV, Rui R, Rumyantsev B, Rustamov A, Ryabinkin E, Ryabov Y, Rybicki A, Rytkonen H, Saarimaki OAM, Sadek R, Sadhu S, Sadovsky S, Šafařík K, Saha SK, Sahoo B, Sahoo P, Sahoo R, Sahoo S, Sahu PK, Saini J, Sakai S, Sambyal S, Samsonov V, Sarkar D, Sarkar N, Sarma P, Sarti VM, Sas MHP, Scapparone E, Schambach J, Scheid HS, Schiaua C, Schicker R, Schmah A, Schmidt C, Schmidt HR, Schmidt MO, Schmidt M, Schmidt NV, Schmier AR, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Seger JE, Sekiguchi Y, Sekihata D, Selyuzhenkov I, Senyukov S, Serebryakov D, Sevcenco A, Shabanov A, Shabetai A, Shahoyan R, Shaikh W, Shangaraev A, Sharma A, Sharma A, Sharma H, Sharma M, Sharma N, Sharma S, Sheibani O, Shigaki K, Shimomura M, Shirinkin S, Shou Q, Sibiriak Y, Siddhanta S, Siemiarczuk T, Silvermyr D, Simatovic G, Simonetti G, Singh B, Singh R, Singh R, Singh R, Singh VK, Singhal V, Sinha T, Sitar B, Sitta M, Skaali TB, Slupecki M, Smirnov N, Snellings RJM, Soncco C, Song J, Songmoolnak A, Soramel F, Sorensen S, Sputowska I, Stachel J, Stan I, Steffanic PJ, Stenlund E, Stiefelmaier SF, Stocco D, Storetvedt MM, Stritto LD, Suaide AAP, Sugitate T, Suire C, Suleymanov M, Suljic M, Sultanov R, Šumbera M, Sumberia V, Sumowidagdo S, Swain S, Szabo A, Szarka I, Tabassam U, Taghavi SF, Taillepied G, Takahashi J, Tambave GJ, Tang S, Tarhini M, Tarzila MG, Tauro A, Tejeda Muñoz G, Telesca A, Terlizzi L, Terrevoli C, Thakur D, Thakur S, Thomas D, Thoresen F, Tieulent R, Tikhonov A, Timmins AR, Toia A, Topilskaya N, Toppi M, Torales-Acosta F, Torres SR, Trifiró A, Tripathy S, Tripathy T, Trogolo S, Trombetta G, Tropp L, Trubnikov V, Trzaska WH, Trzcinski TP, Trzeciak BA, Tumkin A, Turrisi R, Tveter TS, Ullaland K, Umaka EN, Uras A, Usai GL, Vala M, Valle N, Vallero S, van der Kolk N, van Doremalen LVR, van Leeuwen M, Vande Vyvre P, Varga D, Varga Z, Varga-Kofarago M, Vargas A, Vasileiou M, Vasiliev A, Vázquez Doce O, Vechernin V, Vercellin E, Vergara Limón S, Vermunt L, Vernet R, Vértesi R, Vickovic L, Vilakazi Z, Villalobos Baillie O, Vino G, Vinogradov A, Virgili T, Vislavicius V, Vodopyanov A, Volkel B, Völkl MA, Voloshin K, Voloshin SA, Volpe G, von Haller B, Vorobyev I, Voscek D, Vrláková J, Wagner B, Weber M, Weber SG, Wegrzynek A, Wenzel SC, Wessels JP, Wiechula J, Wikne J, Wilk G, Wilkinson J, Willems GA, Willsher E, Windelband B, Winn M, Witt WE, Wright JR, Wu Y, Xu R, Yalcin S, Yamaguchi Y, Yamakawa K, Yang S, Yano S, Yin Z, Yokoyama H, Yoo IK, Yoon JH, Yuan S, Yuncu A, Yurchenko V, Zaccolo V, Zaman A, Zampolli C, Zanoli HJC, Zardoshti N, Zarochentsev A, Závada P, Zaviyalov N, Zbroszczyk H, Zhalov M, Zhang S, Zhang X, Zhang Z, Zherebchevskii V, Zhi Y, Zhou D, Zhou Y, Zhou Z, Zhu J, Zhu Y, Zichichi A, Zinovjev G, Zurlo N. Measurement of the Low-Energy Antideuteron Inelastic Cross Section. PHYSICAL REVIEW LETTERS 2020; 125:162001. [PMID: 33124836 DOI: 10.1103/physrevlett.125.162001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/10/2020] [Accepted: 09/09/2020] [Indexed: 06/11/2023]
Abstract
In this Letter, we report the first measurement of the inelastic cross section for antideuteron-nucleus interactions at low particle momenta, covering a range of 0.3≤p<4 GeV/c. The measurement is carried out using p-Pb collisions at a center-of-mass energy per nucleon-nucleon pair of sqrt[s_{NN}]=5.02 TeV, recorded with the ALICE detector at the CERN LHC and utilizing the detector material as an absorber for antideuterons and antiprotons. The extracted raw primary antiparticle-to-particle ratios are compared to the results from detailed ALICE simulations based on the geant4 toolkit for the propagation of (anti)particles through the detector material. The analysis of the raw primary (anti)proton spectra serves as a benchmark for this study, since their hadronic interaction cross sections are well constrained experimentally. The first measurement of the inelastic cross section for antideuteron-nucleus interactions averaged over the ALICE detector material with atomic mass numbers ⟨A⟩=17.4 and 31.8 is obtained. The measured inelastic cross section points to a possible excess with respect to the Glauber model parametrization used in geant4 in the lowest momentum interval of 0.3≤p<0.47 GeV/c up to a factor 2.1. This result is relevant for the understanding of antimatter propagation and the contributions to antinuclei production from cosmic ray interactions within the interstellar medium. In addition, the momentum range covered by this measurement is of particular importance to evaluate signal predictions for indirect dark-matter searches.
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McLaughlin JA, Beal J, Mısırlı G, Grünberg R, Bartley BA, Scott-Brown J, Vaidyanathan P, Fontanarrosa P, Oberortner E, Wipat A, Gorochowski TE, Myers CJ. The Synthetic Biology Open Language (SBOL) Version 3: Simplified Data Exchange for Bioengineering. Front Bioeng Biotechnol 2020; 8:1009. [PMID: 33015004 PMCID: PMC7516281 DOI: 10.3389/fbioe.2020.01009] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 07/31/2020] [Indexed: 12/17/2022] Open
Abstract
The Synthetic Biology Open Language (SBOL) is a community-developed data standard that allows knowledge about biological designs to be captured using a machine-tractable, ontology-backed representation that is built using Semantic Web technologies. While early versions of SBOL focused only on the description of DNA-based components and their sub-components, SBOL can now be used to represent knowledge across multiple scales and throughout the entire synthetic biology workflow, from the specification of a single molecule or DNA fragment through to multicellular systems containing multiple interacting genetic circuits. The third major iteration of the SBOL standard, SBOL3, is an effort to streamline and simplify the underlying data model with a focus on real-world applications, based on experience from the deployment of SBOL in a variety of scientific and industrial settings. Here, we introduce the SBOL3 specification both in comparison to previous versions of SBOL and through practical examples of its use.
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Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik‐Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier‐Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M. SBML Level 3: an extensible format for the exchange and reuse of biological models. Mol Syst Biol 2020; 16:e9110. [PMID: 32845085 PMCID: PMC8411907 DOI: 10.15252/msb.20199110] [Citation(s) in RCA: 115] [Impact Index Per Article: 28.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 06/24/2020] [Accepted: 07/09/2020] [Indexed: 12/25/2022] Open
Abstract
Systems biology has experienced dramatic growth in the number, size, and complexity of computational models. To reproduce simulation results and reuse models, researchers must exchange unambiguous model descriptions. We review the latest edition of the Systems Biology Markup Language (SBML), a format designed for this purpose. A community of modelers and software authors developed SBML Level 3 over the past decade. Its modular form consists of a core suited to representing reaction-based models and packages that extend the core with features suited to other model types including constraint-based models, reaction-diffusion models, logical network models, and rule-based models. The format leverages two decades of SBML and a rich software ecosystem that transformed how systems biologists build and interact with models. More recently, the rise of multiscale models of whole cells and organs, and new data sources such as single-cell measurements and live imaging, has precipitated new ways of integrating data with models. We provide our perspectives on the challenges presented by these developments and how SBML Level 3 provides the foundation needed to support this evolution.
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Smith LP, Moodie SL, Bergmann FT, Gillespie C, Keating SM, König M, Myers CJ, Swat MJ, Wilkinson DJ, Hucka M. Systems Biology Markup Language (SBML) Level 3 Package: Distributions, Version 1, Release 1. J Integr Bioinform 2020; 17:jib-2020-0018. [PMID: 32750035 PMCID: PMC7756622 DOI: 10.1515/jib-2020-0018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 04/17/2020] [Indexed: 11/23/2022] Open
Abstract
Biological models often contain elements that have inexact numerical values, since they are based on values that are stochastic in nature or data that contains uncertainty. The Systems Biology Markup Language (SBML) Level 3 Core specification does not include an explicit mechanism to include inexact or stochastic values in a model, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactic constructs. The SBML Distributions package for SBML Level 3 adds the necessary features to allow models to encode information about the distribution and uncertainty of values underlying a quantity.
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Acharya S, Adamová D, Adler A, Adolfsson J, Aggarwal MM, Aglieri Rinella G, Agnello M, Agrawal N, Ahammed Z, Ahmad S, Ahn SU, Akindinov A, Al-Turany M, Alam SN, Albuquerque DSD, Aleksandrov D, Alessandro B, Alfanda HM, Alfaro Molina R, Ali B, Ali Y, Alici A, Alkin A, Alme J, Alt T, Altenkamper L, Altsybeev I, Anaam MN, Andrei C, Andreou D, Andrews HA, Andronic A, Angeletti M, Anguelov V, Anson C, Antičić T, Antinori F, Antonioli P, Anwar R, Apadula N, Aphecetche L, Appelshäuser H, Arcelli S, Arnaldi R, Arratia M, Arsene IC, Arslandok M, Augustinus A, Averbeck R, Aziz S, Azmi MD, Badalà A, Baek YW, Bagnasco S, Bai X, Bailhache R, Bala R, Baldisseri A, Ball M, Balouza S, Barbera R, Barioglio L, Barnaföldi GG, Barnby LS, Barret V, Bartalini P, Barth K, Bartsch E, Baruffaldi F, Bastid N, Basu S, Batigne G, Batyunya B, Bauri D, Bazo Alba JL, Bearden IG, Bedda C, Behera NK, Belikov I, Bell Hechavarria ADC, Bellini F, Bellwied R, Belyaev V, Bencedi G, Beole S, Bercuci A, Berdnikov Y, Berenyi D, Bertens RA, Berzano D, Besoiu MG, Betev L, Bhasin A, Bhat IR, Bhat MA, Bhatt H, Bhattacharjee B, Bianchi A, Bianchi L, Bianchi N, Bielčík J, Bielčíková J, Bilandzic A, Biro G, Biswas R, Biswas S, Blair JT, Blau D, Blume C, Boca G, Bock F, Bogdanov A, Boi S, Boldizsár L, Bolozdynya A, Bombara M, Bonomi G, Borel H, Borissov A, Bossi H, Botta E, Bratrud L, Braun-Munzinger P, Bregant M, Broz M, Brucken EJ, Bruna E, Bruno GE, Buckland MD, Budnikov D, Buesching H, Bufalino S, Bugnon O, Buhler P, Buncic P, Buthelezi Z, Butt JB, Buxton JT, Bysiak SA, Caffarri D, Caliva A, Calvo Villar E, Camacho RS, Camerini P, Capon AA, Carnesecchi F, Caron R, Castillo Castellanos J, Castro AJ, Casula EAR, Catalano F, Ceballos Sanchez C, Chakraborty P, Chandra S, Chang W, Chapeland S, Chartier M, Chattopadhyay S, Chattopadhyay S, Chauvin A, Cheshkov C, Cheynis B, Chibante Barroso V, Chinellato DD, Cho S, Chochula P, Chowdhury T, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Cicalo C, Cifarelli L, Cindolo F, Cleymans J, Colamaria F, Colella D, Collu A, Colocci M, Concas M, Conesa Balbastre G, Conesa Del Valle Z, Contin G, Contreras JG, Cormier TM, Corrales Morales Y, Cortese P, Cosentino MR, Costa F, Costanza S, Crochet P, Cuautle E, Cui P, Cunqueiro L, Dabrowski D, Dahms T, Dainese A, Damas FPA, Danisch MC, Danu A, Das D, Das I, Das P, Das P, Das S, Dash A, Dash S, De S, De Caro A, de Cataldo G, de Cuveland J, De Falco A, De Gruttola D, De Marco N, De Pasquale S, Deb S, Debjani B, Degenhardt HF, Deja KR, Deloff A, Delsanto S, Devetak D, Dhankher P, Di Bari D, Di Mauro A, Diaz RA, Dietel T, Dillenseger P, Ding Y, Divià R, Dixit DU, Djuvsland Ø, Dmitrieva U, Dobrin A, Dönigus B, Dordic O, Dubey AK, Dubla A, Dudi S, Dukhishyam M, Dupieux P, Ehlers RJ, Eikeland VN, Elia D, Engel H, Epple E, Erazmus B, Erhardt F, Erokhin A, Ersdal MR, Espagnon B, Esumi S, Eulisse G, Evans D, Evdokimov S, Fabbietti L, Faggin M, Faivre J, Fan F, Fantoni A, Fasel M, Fecchio P, Feliciello A, Feofilov G, Fernández Téllez A, Ferrero A, Ferretti A, Festanti A, Feuillard VJG, Figiel J, Filchagin S, Finogeev D, Fionda FM, Fiorenza G, Flor F, Foertsch S, Foka P, Fokin S, Fragiacomo E, Frankenfeld U, Fuchs U, Furget C, Furs A, Fusco Girard M, Gaardhøje JJ, Gagliardi M, Gago AM, Gal A, Galvan CD, Ganoti P, Garabatos C, Garcia-Solis E, Garg K, Gargiulo C, Garibli A, Garner K, Gasik P, Gauger EF, Gay Ducati MB, Germain M, Ghosh J, Ghosh P, Ghosh SK, Gianotti P, Giubellino P, Giubilato P, Glässel P, Goméz Coral DM, Gomez Ramirez A, Gonzalez V, González-Zamora P, Gorbunov S, Görlich L, Gotovac S, Grabski V, Graczykowski LK, Graham KL, Greiner L, Grelli A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Groettvik OS, Grosa F, Grosse-Oetringhaus JF, Grosso R, Guernane R, Guittiere M, Gulbrandsen K, Gunji T, Gupta A, Gupta R, Guzman IB, Haake R, Habib MK, Hadjidakis C, Hamagaki H, Hamar G, Hamid M, Hannigan R, Haque MR, Harlenderova A, Harris JW, Harton A, Hasenbichler JA, Hassan H, Hatzifotiadou D, Hauer P, Hayashi S, Heckel ST, Hellbär E, Helstrup H, Herghelegiu A, Herman T, Hernandez EG, Herrera Corral G, Herrmann F, Hetland KF, Hilden TE, Hillemanns H, Hills C, Hippolyte B, Hohlweger B, Horak D, Hornung A, Hornung S, Hosokawa R, Hristov P, Huang C, Hughes C, Huhn P, Humanic TJ, Hushnud H, Husova LA, Hussain N, Hussain SA, Hutter D, Iddon JP, Ilkaev R, Inaba M, Innocenti GM, Ippolitov M, Isakov A, Islam MS, Ivanov M, Ivanov V, Izucheev V, Jacak B, Jacazio N, Jacobs PM, Jadlovska S, Jadlovsky J, Jaelani S, Jahnke C, Jakubowska MJ, Janik MA, Janson T, Jercic M, Jevons O, Jin M, Jonas F, Jones PG, Jung J, Jung M, Jusko A, Kalinak P, Kalweit A, Kaplin V, Kar S, Karasu Uysal A, Karavichev O, Karavicheva T, Karczmarczyk P, Karpechev E, Kazantsev A, Kebschull U, Keidel R, Keil M, Ketzer B, Khabanova Z, Khan AM, Khan S, Khan SA, Khanzadeev A, Kharlov Y, Khatun A, Khuntia A, Kileng B, Kim B, Kim B, Kim D, Kim DJ, Kim EJ, Kim H, Kim J, Kim JS, Kim J, Kim J, Kim J, Kim M, Kim S, Kim T, Kim T, Kirsch S, Kisel I, Kiselev S, Kisiel A, Klay JL, Klein C, Klein J, Klein S, Klein-Bösing C, Kleiner M, Kluge A, Knichel ML, Knospe AG, Kobdaj C, Köhler MK, Kollegger T, Kondratyev A, Kondratyeva N, Kondratyuk E, Konig J, Konopka PJ, Koska L, Kovalenko O, Kovalenko V, Kowalski M, Králik I, Kravčáková A, Kreis L, Krivda M, Krizek F, Krizkova Gajdosova K, Krüger M, Kryshen E, Krzewicki M, Kubera AM, Kučera V, Kuhn C, Kuijer PG, Kumar L, Kumar S, Kundu S, Kurashvili P, Kurepin A, Kurepin AB, Kuryakin A, Kushpil S, Kvapil J, Kweon MJ, Kwon JY, Kwon Y, La Pointe SL, La Rocca P, Lai YS, Langoy R, Lapidus K, Lardeux A, Larionov P, Laudi E, Lavicka R, Lazareva T, Lea R, Leardini L, Lee J, Lee S, Lehas F, Lehner S, Lehrbach J, Lemmon RC, León Monzón I, Lesser ED, Lettrich M, Lévai P, Li X, Li XL, Lien J, Lietava R, Lim B, Lindenstruth V, Lindsay SW, Lippmann C, Lisa MA, Litichevskyi V, Liu A, Liu S, Llope WJ, Lofnes IM, Loginov V, Loizides C, Loncar P, Lopez X, López Torres E, Luhder JR, Lunardon M, Luparello G, Ma Y, Maevskaya A, Mager M, Mahmood SM, Mahmoud T, Maire A, Majka RD, Malaev M, Malik QW, Malinina L, Mal'Kevich D, Malzacher P, Mandaglio G, Manko V, Manso F, Manzari V, Mao Y, Marchisone M, Mareš J, Margagliotti GV, Margotti A, Margutti J, Marín A, Markert C, Marquard M, Martin NA, Martinengo P, Martinez JL, Martínez MI, Martínez García G, Martinez Pedreira M, Masciocchi S, Masera M, Masoni A, Massacrier L, Masson E, Mastroserio A, Mathis AM, Matonoha O, Matuoka PFT, Matyja A, Mayer C, Mazzilli M, Mazzoni MA, Mechler AF, Meddi F, Melikyan Y, Menchaca-Rocha A, Mengke C, Meninno E, Meres M, Mhlanga S, Miake Y, Micheletti L, Mihaylov DL, Mikhaylov K, Mischke A, Mishra AN, Miśkowiec D, Modak A, Mohammadi N, Mohanty AP, Mohanty B, Khan MM, Mordasini C, Moreira De Godoy DA, Moreno LAP, Morozov I, Morsch A, Mrnjavac T, Muccifora V, Mudnic E, Mühlheim D, Muhuri S, Mulligan JD, Munhoz MG, Munzer RH, Murakami H, Murray S, Musa L, Musinsky J, Myers CJ, Myrcha JW, Naik B, Nair R, Nandi BK, Nania R, Nappi E, Naru MU, Nassirpour AF, Nattrass C, Nayak R, Nayak TK, Nazarenko S, Neagu A, Negrao De Oliveira RA, Nellen L, Nesbo SV, Neskovic G, Nesterov D, Neumann LT, Nielsen BS, Nikolaev S, Nikulin S, Nikulin V, Noferini F, Nomokonov P, Norman J, Novitzky N, Nowakowski P, Nyanin A, Nystrand J, Ogino M, Ohlson A, Oleniacz J, Oliveira Da Silva AC, Oliver MH, Oppedisano C, Orava R, Ortiz Velasquez A, Oskarsson A, Otwinowski J, Oyama K, Pachmayer Y, Pacik V, Pagano D, Paić G, Pan J, Pandey AK, Panebianco S, Pareek P, Park J, Parkkila JE, Parmar S, Pathak SP, Patra RN, Paul B, Pei H, Peitzmann T, Peng X, Pereira LG, Pereira Da Costa H, Peresunko D, Perez GM, Perez Lezama E, Peskov V, Pestov Y, Petráček V, Petrovici M, Pezzi RP, Piano S, Pikna M, Pillot P, Pinazza O, Pinsky L, Pinto C, Pisano S, Pistone D, Płoskoń M, Planinic M, Pliquett F, Pluta J, Pochybova S, Poghosyan MG, Polichtchouk B, Poljak N, Pop A, Poppenborg H, Porteboeuf-Houssais S, Pozdniakov V, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Putschke J, Quishpe RE, Ragoni S, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Raniwala R, Raniwala S, Räsänen SS, Rath R, Ratza V, Ravasenga I, Read KF, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Rescakova Z, Revol JP, Reygers K, Riabov V, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rode SP, Rodríguez Cahuantzi M, Røed K, Rogalev R, Rogochaya E, Rohr D, Röhrich D, Rokita PS, Ronchetti F, Rosas ED, Roslon K, Rossi A, Rotondi A, Roy A, Roy P, Rueda OV, Rui R, Rumyantsev B, Rustamov A, Ryabinkin E, Ryabov Y, Rybicki A, Rytkonen H, Saarimaki OAM, Sadhu S, Sadovsky S, Šafařík K, Saha SK, Sahoo B, Sahoo P, Sahoo R, Sahoo S, Sahu PK, Saini J, Sakai S, Sambyal S, Samsonov V, Sarkar D, Sarkar N, Sarma P, Sarti VM, Sas MHP, Scapparone E, Schaefer B, Schambach J, Scheid HS, Schiaua C, Schicker R, Schmah A, Schmidt C, Schmidt HR, Schmidt MO, Schmidt M, Schmidt NV, Schmier AR, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Šefčík M, Seger JE, Sekiguchi Y, Sekihata D, Selyuzhenkov I, Senyukov S, Serebryakov D, Serradilla E, Sevcenco A, Shabanov A, Shabetai A, Shahoyan R, Shaikh W, Shangaraev A, Sharma A, Sharma A, Sharma H, Sharma M, Sharma N, Sheikh AI, Shigaki K, Shimomura M, Shirinkin S, Shou Q, Sibiriak Y, Siddhanta S, Siemiarczuk T, Silvermyr D, Simatovic G, Simonetti G, Singh R, Singh R, Singh R, Singh VK, Singhal V, Sinha T, Sitar B, Sitta M, Skaali TB, Slupecki M, Smirnov N, Snellings RJM, Snellman TW, Soncco C, Song J, Songmoolnak A, Soramel F, Sorensen S, Sputowska I, Stachel J, Stan I, Stankus P, Steffanic PJ, Stenlund E, Stocco D, Storetvedt MM, Stritto LD, Suaide AAP, Sugitate T, Suire C, Suleymanov M, Suljic M, Sultanov R, Šumbera M, Sumowidagdo S, Swain S, Szabo A, Szarka I, Tabassam U, Taillepied G, Takahashi J, Tambave GJ, Tang S, Tarhini M, Tarzila MG, Tauro A, Tejeda Muñoz G, Telesca A, Terrevoli C, Thakur D, Thakur S, Thomas D, Thoresen F, Tieulent R, Tikhonov A, Timmins AR, Toia A, Topilskaya N, Toppi M, Torales-Acosta F, Torres SR, Trifiro A, Tripathy S, Tripathy T, Trogolo S, Trombetta G, Tropp L, Trubnikov V, Trzaska WH, Trzcinski TP, Trzeciak BA, Tsuji T, Tumkin A, Turrisi R, Tveter TS, Ullaland K, Umaka EN, Uras A, Usai GL, Utrobicic A, Vala M, Valle N, Vallero S, van der Kolk N, van Doremalen LVR, van Leeuwen M, Vande Vyvre P, Varga D, Varga Z, Varga-Kofarago M, Vargas A, Vasileiou M, Vasiliev A, Vázquez Doce O, Vechernin V, Veen AM, Vercellin E, Vergara Limón S, Vermunt L, Vernet R, Vértesi R, Vickovic L, Vilakazi Z, Villalobos Baillie O, Villatoro Tello A, Vino G, Vinogradov A, Virgili T, Vislavicius V, Vodopyanov A, Volkel B, Völkl MA, Voloshin K, Voloshin SA, Volpe G, von Haller B, Vorobyev I, Voscek D, Vrláková J, Wagner B, Weber M, Weber SG, Wegrzynek A, Weiser DF, Wenzel SC, Wessels JP, Wiechula J, Wikne J, Wilk G, Wilkinson J, Willems GA, Willsher E, Windelband B, Winn M, Witt WE, Wu Y, Xu R, Yalcin S, Yamakawa K, Yang S, Yano S, Yin Z, Yokoyama H, Yoo IK, Yoon JH, Yuan S, Yuncu A, Yurchenko V, Zaccolo V, Zaman A, Zampolli C, Zanoli HJC, Zardoshti N, Zarochentsev A, Závada P, Zaviyalov N, Zbroszczyk H, Zhalov M, Zhang S, Zhang X, Zhang Z, Zherebchevskii V, Zhou D, Zhou Y, Zhou Z, Zhu J, Zhu Y, Zichichi A, Zimmermann MB, Zinovjev G, Zurlo N. Probing the Effects of Strong Electromagnetic Fields with Charge-Dependent Directed Flow in Pb-Pb Collisions at the LHC. PHYSICAL REVIEW LETTERS 2020; 125:022301. [PMID: 32701333 DOI: 10.1103/physrevlett.125.022301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/22/2020] [Accepted: 05/19/2020] [Indexed: 06/11/2023]
Abstract
The first measurement at the LHC of charge-dependent directed flow (v_{1}) relative to the spectator plane is presented for Pb-Pb collisions at sqrt[s_{NN}]=5.02 TeV. Results are reported for charged hadrons and D^{0} mesons for the transverse momentum intervals p_{T}>0.2 GeV/c and 3<p_{T}<6 GeV/c in the 5%-40% and 10%-40% centrality classes, respectively. The difference between the positively and negatively charged hadron v_{1} has a positive slope as a function of pseudorapidity η, dΔv_{1}/dη=[1.68±0.49(stat)±0.41(syst)]×10^{-4}. The same measurement for D^{0} and D[over ¯]^{0} mesons yields a positive value dΔv_{1}/dη=[4.9±1.7(stat)±0.6(syst)]×10^{-1}, which is about 3 orders of magnitude larger than the one of the charged hadrons. These measurements can provide new insights into the effects of the strong electromagnetic field and the initial tilt of matter created in noncentral heavy ion collisions on the dynamics of light (u, d, and s) and heavy (c) quarks. The large difference between the observed Δv_{1} of charged hadrons and D^{0} mesons may reflect different sensitivity of the charm and light quarks to the early time dynamics of a heavy ion collision. These observations challenge some recent theoretical calculations, which predicted a negative and an order of magnitude smaller value of dΔv_{1}/dη for both light flavor and charmed hadrons.
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Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Putschke J, Quishpe RE, Ragoni S, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Raniwala R, Raniwala S, Räsänen SS, Rath R, Ratza V, Ravasenga I, Read KF, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Rescakova Z, Revol JP, Reygers K, Riabov V, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rode SP, Rodríguez Cahuantzi M, Røed K, Rogalev R, Rogochaya E, Rohr D, Röhrich D, Rokita PS, Ronchetti F, Rosas ED, Roslon K, Rossi A, Rotondi A, Roy A, Roy P, Rueda OV, Rui R, Rumyantsev B, Rustamov A, Ryabinkin E, Ryabov Y, Rybicki A, Rytkonen H, Saarimaki OAM, Sadhu S, Sadovsky S, Šafařík K, Saha SK, Sahoo B, Sahoo P, Sahoo R, Sahoo S, Sahu PK, Saini J, Sakai S, Sambyal S, Samsonov V, Sarkar D, Sarkar N, Sarma P, Sarti VM, Sas MHP, Scapparone E, Schaefer B, Schambach J, Scheid HS, Schiaua C, Schicker R, Schmah A, Schmidt C, Schmidt HR, Schmidt MO, Schmidt M, Schmidt NV, Schmier AR, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Šefčík M, Seger JE, Sekiguchi Y, Sekihata D, Selyuzhenkov I, Senyukov S, Serebryakov D, Serradilla E, Sevcenco A, Shabanov A, Shabetai A, Shahoyan R, Shaikh W, Shangaraev A, Sharma A, Sharma A, Sharma H, Sharma M, Sharma N, Sheikh AI, Shigaki K, Shimomura M, Shirinkin S, Shou Q, Sibiriak Y, Siddhanta S, Siemiarczuk T, Silvermyr D, Simatovic G, Simonetti G, Singh R, Singh R, Singh R, Singh VK, Singhal V, Sinha T, Sitar B, Sitta M, Skaali TB, Slupecki M, Smirnov N, Snellings RJM, Snellman TW, Soncco C, Song J, Songmoolnak A, Soramel F, Sorensen S, Sputowska I, Stachel J, Stan I, Stankus P, Steffanic PJ, Stenlund E, Stocco D, Storetvedt MM, Stritto LD, Suaide AAP, Sugitate T, Suire C, Suleymanov M, Suljic M, Sultanov R, Šumbera M, Sumowidagdo S, Swain S, Szabo A, Szarka I, Tabassam U, Taillepied G, Takahashi J, Tambave GJ, Tang S, Tarhini M, Tarzila MG, Tauro A, Tejeda Muñoz G, Telesca A, Terrevoli C, Thakur D, Thakur S, Thomas D, Thoresen F, Tieulent R, Tikhonov A, Timmins AR, Toia A, Topilskaya N, Toppi M, Torales-Acosta F, Torres SR, Trifiro A, Tripathy S, Tripathy T, Trogolo S, Trombetta G, Tropp L, Trubnikov V, Trzaska WH, Trzcinski TP, Trzeciak BA, Tsuji T, Tumkin A, Turrisi R, Tveter TS, Ullaland K, Umaka EN, Uras A, Usai GL, Utrobicic A, Vala M, Valle N, Vallero S, van der Kolk N, van Doremalen LVR, van Leeuwen M, Vande Vyvre P, Varga D, Varga Z, Varga-Kofarago M, Vargas A, Vasileiou M, Vasiliev A, Vázquez Doce O, Vechernin V, Veen AM, Vercellin E, Vergara Limón S, Vermunt L, Vernet R, Vértesi R, Vickovic L, Vilakazi Z, Villalobos Baillie O, Villatoro Tello A, Vino G, Vinogradov A, Virgili T, Vislavicius V, Vodopyanov A, Volkel B, Völkl MA, Voloshin K, Voloshin SA, Volpe G, von Haller B, Vorobyev I, Voscek D, Vrláková J, Wagner B, Weber M, Weber SG, Wegrzynek A, Weiser DF, Wenzel SC, Wessels JP, Wiechula J, Wikne J, Wilk G, Wilkinson J, Willems GA, Willsher E, Windelband B, Winn M, Witt WE, Wu Y, Xu R, Yalcin S, Yamakawa K, Yang S, Yano S, Yin Z, Yokoyama H, Yoo IK, Yoon JH, Yuan S, Yuncu A, Yurchenko V, Zaccolo V, Zaman A, Zampolli C, Zanoli HJC, Zardoshti N, Zarochentsev A, Závada P, Zaviyalov N, Zbroszczyk H, Zhalov M, Zhang S, Zhang X, Zhang Z, Zherebchevskii V, Zhou D, Zhou Y, Zhou Z, Zhu J, Zhu Y, Zichichi A, Zimmermann MB, Zinovjev G, Zurlo N. Evidence of Spin-Orbital Angular Momentum Interactions in Relativistic Heavy-Ion Collisions. PHYSICAL REVIEW LETTERS 2020; 125:012301. [PMID: 32678650 DOI: 10.1103/physrevlett.125.012301] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 02/25/2020] [Accepted: 05/27/2020] [Indexed: 06/11/2023]
Abstract
The first evidence of spin alignment of vector mesons (K^{*0} and ϕ) in heavy-ion collisions at the Large Hadron Collider (LHC) is reported. The spin density matrix element ρ_{00} is measured at midrapidity (|y|<0.5) in Pb-Pb collisions at a center-of-mass energy (sqrt[s_{NN}]) of 2.76 TeV with the ALICE detector. ρ_{00} values are found to be less than 1/3 (1/3 implies no spin alignment) at low transverse momentum (p_{T}<2 GeV/c) for K^{*0} and ϕ at a level of 3σ and 2σ, respectively. No significant spin alignment is observed for the K_{S}^{0} meson (spin=0) in Pb-Pb collisions and for the vector mesons in pp collisions. The measured spin alignment is unexpectedly large but qualitatively consistent with the expectation from models which attribute it to a polarization of quarks in the presence of angular momentum in heavy-ion collisions and a subsequent hadronization by the process of recombination.
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Waltemath D, Golebiewski M, Blinov ML, Gleeson P, Hermjakob H, Hucka M, Inau ET, Keating SM, König M, Krebs O, Malik-Sheriff RS, Nickerson D, Oberortner E, Sauro HM, Schreiber F, Smith L, Stefan MI, Wittig U, Myers CJ. The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE). J Integr Bioinform 2020; 17:jib-2020-0005. [PMID: 32598315 PMCID: PMC7756615 DOI: 10.1515/jib-2020-0005] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/14/2020] [Indexed: 01/23/2023] Open
Abstract
This paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.
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Baig H, Fontanarrosa P, Kulkarni V, McLaughlin JA, Vaidyanathan P, Bartley B, Beal J, Crowther M, Gorochowski TE, Grünberg R, Misirli G, Scott-Brown J, Oberortner E, Wipat A, Myers CJ. Synthetic biology open language (SBOL) version 3.0.0. J Integr Bioinform 2020; 17:jib-2020-0017. [PMID: 32589605 PMCID: PMC7756618 DOI: 10.1515/jib-2020-0017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 04/16/2020] [Indexed: 11/15/2022] Open
Abstract
Synthetic biology builds upon genetics, molecular biology, and metabolic engineering by applying engineering principles to the design of biological systems. When designing a synthetic system, synthetic biologists need to exchange information about multiple types of molecules, the intended behavior of the system, and actual experimental measurements. The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, following an open community process involving both wet bench scientists and dry scientific modelers and software developers, across academia, industry, and other institutions. This document describes SBOL 3.0.0, which condenses and simplifies previous versions of SBOL based on experiences in deployment across a variety of scientific and industrial settings. In particular, SBOL 3.0.0, (1) separates sequence features from part/sub-part relationships, (2) renames Component Definition/Component to Component/Sub-Component, (3) merges Component and Module classes, (4) ensures consistency between data model and ontology terms, (5) extends the means to define and reference Sub-Components, (6) refines requirements on object URIs, (7) enables graph-based serialization, (8) moves Systems Biology Ontology (SBO) for Component types, (9) makes all sequence associations explicit, (10) makes interfaces explicit, (11) generalizes Sequence Constraints into a general structural Constraint class, and (12) expands the set of allowed constraints.
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Abstract
Standardizing the visual representation of genetic parts and circuits is essential for unambiguously creating and interpreting genetic designs. To this end, an increasing number of tools are adopting well-defined glyphs from the Synthetic Biology Open Language (SBOL) Visual standard to represent various genetic parts and their relationships. However, the implementation and maintenance of the relationships between biological elements or concepts and their associated glyphs has up to now been left up to tool developers. We address this need with the SBOL Visual 2 Ontology, a machine-accessible resource that provides rules for mapping from genetic parts, molecules, and interactions between them, to agreed SBOL Visual glyphs. This resource, together with a web service, can be used as a library to simplify the development of visualization tools, as a stand-alone resource to computationally search for suitable glyphs, and to help facilitate integration with existing biological ontologies and standards in synthetic biology.
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Acharya S, Adamová D, Adhya SP, Adler A, Adolfsson J, Aggarwal MM, Aglieri Rinella G, Agnello M, Agrawal N, Ahammed Z, Ahmad S, Ahn SU, Aiola S, Akindinov A, Al-Turany M, Alam SN, Albuquerque DSD, Aleksandrov D, Alessandro B, Alfanda HM, Alfaro Molina R, Ali B, Ali Y, Alici A, Alkin A, Alme J, Alt T, Altenkamper L, Altsybeev I, Anaam MN, Andrei C, Andreou D, Andrews HA, Andronic A, Angeletti M, Anguelov V, Anson C, Antičić T, Antinori F, Antonioli P, Anwar R, Apadula N, Aphecetche L, Appelshäuser H, Arcelli S, Arnaldi R, Arratia M, Arsene IC, Arslandok M, Augustinus A, Averbeck R, Aziz S, Azmi MD, Badalà A, Baek YW, Bagnasco S, Bailhache R, Bala R, Baldisseri A, Ball M, Baral RC, Barbera R, Barioglio L, Barnaföldi GG, Barnby LS, Barret V, Bartalini P, Barth K, Bartsch E, Baruffaldi F, Bastid N, Basu S, Batigne G, Batyunya B, Batzing PC, Bauri D, Bazo Alba JL, Bearden IG, Bedda C, Behera NK, Belikov I, Bellini F, Bellwied R, Belyaev V, Bencedi G, Beole S, Bercuci A, Berdnikov Y, Berenyi D, Bertens RA, Berzano D, Betev L, Bhasin A, Bhat IR, Bhatt H, Bhattacharjee B, Bianchi A, Bianchi L, Bianchi N, Bielčík J, Bielčíková J, Bilandzic A, Biro G, Biswas R, Biswas S, Blair JT, Blau D, Blume C, Boca G, Bock F, Bogdanov A, Boldizsár L, Bolozdynya A, Bombara M, Bonomi G, Bonora M, Borel H, Borissov A, Borri M, Bossi H, Botta E, Bourjau C, Bratrud L, Braun-Munzinger P, Bregant M, Broker TA, Broz M, Brucken EJ, Bruna E, Bruno GE, Buckland MD, Budnikov D, Buesching H, Bufalino S, Bugnon O, Buhler P, Buncic P, Busch O, Buthelezi Z, Butt JB, Buxton JT, Caffarri D, Caliva A, Calvo Villar E, Camacho RS, Camerini P, Capon AA, Carnesecchi F, Castillo Castellanos J, Castro AJ, Casula EAR, Catalano F, Ceballos Sanchez C, Chakraborty P, Chandra S, Chang B, Chang W, Chapeland S, Chartier M, Chattopadhyay S, Chattopadhyay S, Chauvin A, Cheshkov C, Cheynis B, Chibante Barroso V, Chinellato DD, Cho S, Chochula P, Chowdhury T, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Cicalo C, Cifarelli L, Cindolo F, Cleymans J, Colamaria F, Colella D, Collu A, Colocci M, Concas M, Conesa Balbastre G, Conesa Del Valle Z, Contin G, Contreras JG, Cormier TM, Corrales Morales Y, Cortese P, Cosentino MR, Costa F, Costanza S, Crkovská J, Crochet P, Cuautle E, Cunqueiro L, Dabrowski D, Dahms T, Dainese A, Damas FPA, Dani S, Danisch MC, Danu A, Das D, Das I, Das S, Dash A, Dash S, Dashi A, De S, De Caro A, de Cataldo G, de Conti C, de Cuveland J, De Falco A, De Gruttola D, De Marco N, De Pasquale S, De Souza RD, Deb S, Degenhardt HF, Deisting A, Deja KR, Deloff A, Delsanto S, Dhankher P, Di Bari D, Di Mauro A, Diaz RA, Dietel T, Dillenseger P, Ding Y, Divià R, Djuvsland Ø, Dmitrieva U, Dobrin A, Dönigus B, Dordic O, Dubey AK, Dubla A, Dudi S, Duggal AK, Dukhishyam M, Dupieux P, Ehlers RJ, Elia D, Engel H, Epple E, Erazmus B, Erhardt F, Erokhin A, Ersdal MR, Espagnon B, Eulisse G, Eum J, Evans D, Evdokimov S, Fabbietti L, Faggin M, Faivre J, Fantoni A, Fasel M, Fecchio P, Feldkamp L, Feliciello A, Feofilov G, Fernández Téllez A, Ferrero A, Ferretti A, Festanti A, Feuillard VJG, Figiel J, Filchagin S, Finogeev D, Fionda FM, Fiorenza G, Flor F, Foertsch S, Foka P, Fokin S, Fragiacomo E, Francisco A, Frankenfeld U, Fronze GG, Fuchs U, Furget C, Furs A, Fusco Girard M, Gaardhøje JJ, Gagliardi M, Gago AM, Gal A, Galvan CD, Ganoti P, Garabatos C, Garcia-Solis E, Garg K, Gargiulo C, Garner K, Gasik P, Gauger EF, Gay Ducati MB, Germain M, Ghosh J, Ghosh P, Ghosh SK, Gianotti P, Giubellino P, Giubilato P, Glässel P, Goméz Coral DM, Gomez Ramirez A, Gonzalez V, González-Zamora P, Gorbunov S, Görlich L, Gotovac S, Grabski V, Graczykowski LK, Graham KL, Greiner L, Grelli A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Groettvik OS, Gronefeld JM, Grosa F, Grosse-Oetringhaus JF, Grosso R, Guernane R, Guerzoni B, Guittiere M, Gulbrandsen K, Gunji T, Gupta A, Gupta R, Guzman IB, Haake R, Habib MK, Hadjidakis C, Hamagaki H, Hamar G, Hamid M, Hamon JC, Hannigan R, Haque MR, Harlenderova A, Harris JW, Harton A, Hassan H, Hatzifotiadou D, Hauer P, Hayashi S, Heckel ST, Hellbär E, Helstrup H, Herghelegiu A, Hernandez EG, Herrera Corral G, Herrmann F, Hetland KF, Hilden TE, Hillemanns H, Hills C, Hippolyte B, Hohlweger B, Horak D, Hornung S, Hosokawa R, Hristov P, Huang C, Hughes C, Huhn P, Humanic TJ, Hushnud H, Husova LA, Hussain N, Hussain SA, Hussain T, Hutter D, Hwang DS, Iddon JP, Ilkaev R, Inaba M, Ippolitov M, Islam MS, Ivanov M, Ivanov V, Izucheev V, Jacak B, Jacazio N, Jacobs PM, Jadhav MB, Jadlovska S, Jadlovsky J, Jaelani S, Jahnke C, Jakubowska MJ, Janik MA, Jercic M, Jevons O, Jimenez Bustamante RT, Jin M, Jonas F, Jones PG, Jusko A, Kalinak P, Kalweit A, Kang JH, Kaplin V, Kar S, Karasu Uysal A, Karavichev O, Karavicheva T, Karczmarczyk P, Karpechev E, Kebschull U, Keidel R, Keil M, Ketzer B, Khabanova Z, Khan AM, Khan S, Khan SA, Khanzadeev A, Kharlov Y, Khatun A, Khuntia A, Kileng B, Kim B, Kim B, Kim D, Kim DJ, Kim EJ, Kim H, Kim JS, Kim J, Kim J, Kim J, Kim M, Kim S, Kim T, Kim T, Kindra K, Kirsch S, Kisel I, Kiselev S, Kisiel A, Klay JL, Klein C, Klein J, Klein S, Klein-Bösing C, Klewin S, Kluge A, Knichel ML, Knospe AG, Kobdaj C, Köhler MK, Kollegger T, Kondratyev A, Kondratyeva N, Kondratyuk E, Konopka PJ, Koska L, Kovalenko O, Kovalenko V, Kowalski M, Králik I, Kravčáková A, Kreis L, Krivda M, Krizek F, Krizkova Gajdosova K, Krüger M, Kryshen E, Krzewicki M, Kubera AM, Kučera V, Kuhn C, Kuijer PG, Kumar L, Kumar S, Kundu S, Kurashvili P, Kurepin A, Kurepin AB, Kushpil S, Kvapil J, Kweon MJ, Kwon Y, La Pointe SL, La Rocca P, Lai YS, Langoy R, Lapidus K, Lardeux A, Larionov P, Laudi E, Lavicka R, Lazareva T, Lea R, Leardini L, Lee S, Lehas F, Lehner S, Lehrbach J, Lemmon RC, León Monzón I, Lesser ED, Lettrich M, Lévai P, Li X, Li XL, Lien J, Lietava R, Lim B, Lindal S, Lindenstruth V, Lindsay SW, Lippmann C, Lisa MA, Litichevskyi V, Liu A, Liu S, Ljunggren HM, Llope WJ, Lofnes IM, Loginov V, Loizides C, Loncar P, Lopez X, López Torres E, Luettig P, Luhder JR, Lunardon M, Luparello G, Lupi M, Maevskaya A, Mager M, Mahmood SM, Mahmoud T, Maire A, Majka RD, Malaev M, Malik QW, Malinina L, Mal'Kevich D, Malzacher P, Mamonov A, Manko V, Manso F, Manzari V, Mao Y, Marchisone M, Mareš J, Margagliotti GV, Margotti A, Margutti J, Marín A, Markert C, Marquard M, Martin NA, Martinengo P, Martinez JL, Martínez MI, Martínez García G, Martinez Pedreira M, Masciocchi S, Masera M, Masoni A, Massacrier L, Masson E, Mastroserio A, Mathis AM, Matuoka PFT, Matyja A, Mayer C, Mazzilli M, Mazzoni MA, Mechler AF, Meddi F, Melikyan Y, Menchaca-Rocha A, Meninno E, Meres M, Mhlanga S, Miake Y, Micheletti L, Mieskolainen MM, Mihaylov DL, Mikhaylov K, Mischke A, Mishra AN, Miśkowiec D, Mitu CM, Mohammadi N, Mohanty AP, Mohanty B, Mohisin Khan M, Mondal M, Mondal MM, Mordasini C, Moreira De Godoy DA, Moreno LAP, Moretto S, Morreale A, Morsch A, Mrnjavac T, Muccifora V, Mudnic E, Mühlheim D, Muhuri S, Mulligan JD, Munhoz MG, Münning K, Munzer RH, Murakami H, Murray S, Musa L, Musinsky J, Myers CJ, Myrcha JW, Naik B, Nair R, Nandi BK, Nania R, Nappi E, Naru MU, Nassirpour AF, Natal da Luz H, Nattrass C, Nayak R, Nayak TK, Nazarenko S, Negrao De Oliveira RA, Nellen L, Nesbo SV, Neskovic G, Nielsen BS, Nikolaev S, Nikulin S, Nikulin V, Noferini F, Nomokonov P, Nooren G, Norman J, Nowakowski P, Nyanin A, Nystrand J, Ogino M, Ohlson A, Oleniacz J, Oliveira Da Silva AC, Oliver MH, Onderwaater J, Oppedisano C, Orava R, Ortiz Velasquez A, Oskarsson A, Otwinowski J, Oyama K, Pachmayer Y, Pacik V, Pagano D, Paić G, Palni P, Pan J, Pandey AK, Panebianco S, Papikyan V, Pareek P, Park J, Parkkila JE, Parmar S, Passfeld A, Pathak SP, Patra RN, Paul B, Pei H, Peitzmann T, Peng X, Pereira LG, Pereira Da Costa H, Peresunko D, Perez GM, Perez Lezama E, Peskov V, Pestov Y, Petráček V, Petrovici M, Pezzi RP, Piano S, Pikna M, Pillot P, Pimentel LODL, Pinazza O, Pinsky L, Pisano S, Piyarathna DB, Płoskoń M, Planinic M, Pliquett F, Pluta J, Pochybova S, Poghosyan MG, Polichtchouk B, Poljak N, Poonsawat W, Pop A, Poppenborg H, Porteboeuf-Houssais S, Pozdniakov V, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Punin V, Puranapanda K, Putschke J, Quishpe RE, Ragoni S, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Raniwala R, Raniwala S, Räsänen SS, Rascanu BT, Rath R, Ratza V, Ravasenga I, Read KF, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Reshetin A, Revol JP, Reygers K, Riabov V, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rode SP, Rodríguez Cahuantzi M, Røed K, Rogalev R, Rogochaya E, Rohr D, Röhrich D, Rokita PS, Ronchetti F, Rosas ED, Roslon K, Rosnet P, Rossi A, Rotondi A, Roukoutakis F, Roy A, Roy P, Rueda OV, Rui R, Rumyantsev B, Rustamov A, Ryabinkin E, Ryabov Y, Rybicki A, Rytkonen H, Saarinen S, Sadhu S, Sadovsky S, Šafařík K, Saha SK, Sahoo B, Sahoo P, Sahoo R, Sahoo S, Sahu PK, Saini J, Sakai S, Sambyal S, Samsonov V, Sandoval A, Sarkar A, Sarkar D, Sarkar N, Sarma P, Sarti VM, Sas MHP, Scapparone E, Schaefer B, Schambach J, Scheid HS, Schiaua C, Schicker R, Schmah A, Schmidt C, Schmidt HR, Schmidt MO, Schmidt M, Schmidt NV, Schmier AR, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Šefčík M, Seger JE, Sekiguchi Y, Sekihata D, Selyuzhenkov I, Senyukov S, Serradilla E, Sett P, Sevcenco A, Shabanov A, Shabetai A, Shahoyan R, Shaikh W, Shangaraev A, Sharma A, Sharma A, Sharma M, Sharma N, Sheikh AI, Shigaki K, Shimomura M, Shirinkin S, Shou Q, Sibiriak Y, Siddhanta S, Siemiarczuk T, Silvermyr D, Simatovic G, Simonetti G, Singh R, Singh R, Singh VK, Singhal V, Sinha T, Sitar B, Sitta M, Skaali TB, Slupecki M, Smirnov N, Snellings RJM, Snellman TW, Sochan J, Soncco C, Song J, Songmoolnak A, Soramel F, Sorensen S, Sputowska I, Stachel J, Stan I, Stankus P, Steffanic PJ, Stenlund E, Stocco D, Storetvedt MM, Strmen P, Suaide AAP, Sugitate T, Suire C, Suleymanov M, Suljic M, Sultanov R, Šumbera M, Sumowidagdo S, Suzuki K, Swain S, Szabo A, Szarka I, Tabassam U, Taillepied G, Takahashi J, Tambave GJ, Tang S, Tarhini M, Tarzila MG, Tauro A, Tejeda Muñoz G, Telesca A, Terrevoli C, Thakur D, Thakur S, Thomas D, Thoresen F, Tieulent R, Tikhonov A, Timmins AR, Toia A, Topilskaya N, Toppi M, Torales-Acosta F, Torres SR, Tripathy S, Tripathy T, Trogolo S, Trombetta G, Tropp L, Trubnikov V, Trzaska WH, Trzcinski TP, Trzeciak BA, Tsuji T, Tumkin A, Turrisi R, Tveter TS, Ullaland K, Umaka EN, Uras A, Usai GL, Utrobicic A, Vala M, Valle N, Vallero S, van der Kolk N, van Doremalen LVR, van Leeuwen M, Vande Vyvre P, Varga D, Varga-Kofarago M, Vargas A, Vargyas M, Varma R, Vasileiou M, Vasiliev A, Vázquez Doce O, Vechernin V, Veen AM, Vercellin E, Vergara Limón S, Vermunt L, Vernet R, Vértesi R, Vickovic L, Viinikainen J, Vilakazi Z, Villalobos Baillie O, Villatoro Tello A, Vino G, Vinogradov A, Virgili T, Vislavicius V, Vodopyanov A, Volkel B, Völkl MA, Voloshin K, Voloshin SA, Volpe G, von Haller B, Vorobyev I, Voscek D, Vrláková J, Wagner B, Watanabe Y, Weber M, Weber SG, Wegrzynek A, Weiser DF, Wenzel SC, Wessels JP, Westerhoff U, Whitehead AM, Widmann E, Wiechula J, Wikne J, Wilk G, Wilkinson J, Willems GA, Willsher E, Windelband B, Witt WE, Wu Y, Xu R, Yalcin S, Yamakawa K, Yang S, Yano S, Yin Z, Yokoyama H, Yoo IK, Yoon JH, Yuan S, Yuncu A, Yurchenko V, Zaccolo V, Zaman A, Zampolli C, Zanoli HJC, Zardoshti N, Zarochentsev A, Závada P, Zaviyalov N, Zbroszczyk H, Zhalov M, Zhang X, Zhang Z, Zhao C, Zherebchevskii V, Zhigareva N, Zhou D, Zhou Y, Zhou Z, Zhu J, Zhu Y, Zichichi A, Zimmermann MB, Zinovjev G, Zurlo N. Scattering Studies with Low-Energy Kaon-Proton Femtoscopy in Proton-Proton Collisions at the LHC. PHYSICAL REVIEW LETTERS 2020; 124:092301. [PMID: 32202883 DOI: 10.1103/physrevlett.124.092301] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 12/03/2019] [Accepted: 02/11/2020] [Indexed: 06/10/2023]
Abstract
The study of the strength and behavior of the antikaon-nucleon (K[over ¯]N) interaction constitutes one of the key focuses of the strangeness sector in low-energy quantum chromodynamics (QCD). In this Letter a unique high-precision measurement of the strong interaction between kaons and protons, close and above the kinematic threshold, is presented. The femtoscopic measurements of the correlation function at low pair-frame relative momentum of (K^{+}p⊕K^{-}p[over ¯]) and (K^{-}p⊕K^{+}p[over ¯]) pairs measured in pp collisions at sqrt[s]=5, 7, and 13 TeV are reported. A structure observed around a relative momentum of 58 MeV/c in the measured correlation function of (K^{-}p⊕K^{+}p[over ¯]) with a significance of 4.4σ constitutes the first experimental evidence for the opening of the (K[over ¯]^{0}n⊕K^{0}n[over ¯]) isospin breaking channel due to the mass difference between charged and neutral kaons. The measured correlation functions have been compared to Jülich and Kyoto models in addition to the Coulomb potential. The high-precision data at low relative momenta presented in this work prove femtoscopy to be a powerful complementary tool to scattering experiments and provide new constraints above the K[over ¯]N threshold for low-energy QCD chiral models.
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Acharya S, Adamová D, Adhya SP, Adler A, Adolfsson J, Aggarwal MM, Aglieri Rinella G, Agnello M, Agrawal N, Ahammed Z, Ahmad S, Ahn SU, Akindinov A, Al-Turany M, Alam SN, Albuquerque DSD, Aleksandrov D, Alessandro B, Alfanda HM, Alfaro Molina R, Ali B, Ali Y, Alici A, Alkin A, Alme J, Alt T, Altenkamper L, Altsybeev I, Anaam MN, Andrei C, Andreou D, Andrews HA, Andronic A, Angeletti M, Anguelov V, Anson C, Antičić T, Antinori F, Antonioli P, Anwar R, Apadula N, Aphecetche L, Appelshäuser H, Arcelli S, Arnaldi R, Arratia M, Arsene IC, Arslandok M, Augustinus A, Averbeck R, Aziz S, Azmi MD, Badalà A, Baek YW, Bagnasco S, Bai X, Bailhache R, Bala R, Baldisseri A, Ball M, Balouza S, Baral RC, Barbera R, Barioglio L, Barnaföldi GG, Barnby LS, Barret V, Bartalini P, Barth K, Bartsch E, Baruffaldi F, Bastid N, Basu S, Batigne G, Batyunya B, Batzing PC, Bauri D, Bazo Alba JL, Bearden IG, Bedda C, Behera NK, Belikov I, Bellini F, Bellwied R, Belyaev V, Bencedi G, Beole S, Bercuci A, Berdnikov Y, Berenyi D, Bertens RA, Berzano D, Besoiu MG, Betev L, Bhasin A, Bhat IR, Bhat MA, Bhatt H, Bhattacharjee B, Bianchi A, Bianchi L, Bianchi N, Bielčík J, Bielčíková J, Bilandzic A, Biro G, Biswas R, Biswas S, Blair JT, Blau D, Blume C, Boca G, Bock F, Bogdanov A, Boldizsár L, Bolozdynya A, Bombara M, Bonomi G, Borel H, Borissov A, Borri M, Bossi H, Botta E, Bratrud L, Braun-Munzinger P, Bregant M, Broker TA, Broz M, Brucken EJ, Bruna E, Bruno GE, Buckland MD, Budnikov D, Buesching H, Bufalino S, Bugnon O, Buhler P, Buncic P, Buthelezi Z, Butt JB, Buxton JT, Bysiak SA, Caffarri D, Caliva A, Calvo Villar E, Camacho RS, Camerini P, Capon AA, Carnesecchi F, Caron R, Castillo Castellanos J, Castro AJ, Casula EAR, Catalano F, Ceballos Sanchez C, Chakraborty P, Chandra S, Chang B, Chang W, Chapeland S, Chartier M, Chattopadhyay S, Chattopadhyay S, Chauvin A, Cheshkov C, Cheynis B, Chibante Barroso V, Chinellato DD, Cho S, Chochula P, Chowdhury T, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Cicalo C, Cifarelli L, Cindolo F, Cleymans J, Colamaria F, Colella D, Collu A, Colocci M, Concas M, Conesa Balbastre G, Conesa Del Valle Z, Contin G, Contreras JG, Cormier TM, Corrales Morales Y, Cortese P, Cosentino MR, Costa F, Costanza S, Crkovská J, Crochet P, Cuautle E, Cunqueiro L, Dabrowski D, Dahms T, Dainese A, Damas FPA, Dani S, Danisch MC, Danu A, Das D, Das I, Das P, Das S, Dash A, Dash S, Dashi A, De S, De Caro A, de Cataldo G, de Conti C, de Cuveland J, De Falco A, De Gruttola D, De Marco N, De Pasquale S, De Souza RD, Deb S, Degenhardt HF, Deja KR, Deloff A, Delsanto S, Devetak D, Dhankher P, Di Bari D, Di Mauro A, Diaz RA, Dietel T, Dillenseger P, Ding Y, Divià R, Djuvsland Ø, Dmitrieva U, Dobrin A, Dönigus B, Dordic O, Dubey AK, Dubla A, Dudi S, Dukhishyam M, Dupieux P, Ehlers RJ, Elia D, Engel H, Epple E, Erazmus B, Erhardt F, Erokhin A, Ersdal MR, Espagnon B, Eulisse G, Eum J, Evans D, Evdokimov S, Fabbietti L, Faggin M, Faivre J, Fantoni A, Fasel M, Fecchio P, Feliciello A, Feofilov G, Fernández Téllez A, Ferrero A, Ferretti A, Festanti A, Feuillard VJG, Figiel J, Filchagin S, Finogeev D, Fionda FM, Fiorenza G, Flor F, Foertsch S, Foka P, Fokin S, Fragiacomo E, Frankenfeld U, Fronze GG, Fuchs U, Furget C, Furs A, Fusco Girard M, Gaardhøje JJ, Gagliardi M, Gago AM, Gal A, Galvan CD, Ganoti P, Garabatos C, Garcia-Solis E, Garg K, Gargiulo C, Garibli A, Garner K, Gasik P, Gauger EF, Gay Ducati MB, Germain M, Ghosh J, Ghosh P, Ghosh SK, Gianotti P, Giubellino P, Giubilato P, Glässel P, Goméz Coral DM, Gomez Ramirez A, Gonzalez V, González-Zamora P, Gorbunov S, Görlich L, Gotovac S, Grabski V, Graczykowski LK, Graham KL, Greiner L, Grelli A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Groettvik OS, Gronefeld JM, Grosa F, Grosse-Oetringhaus JF, Grosso R, Guernane R, Guerzoni B, Guittiere M, Gulbrandsen K, Gunji T, Gupta A, Gupta R, Guzman IB, Haake R, Habib MK, Hadjidakis C, Hamagaki H, Hamar G, Hamid M, Hannigan R, Haque MR, Harlenderova A, Harris JW, Harton A, Hasenbichler JA, Hassan H, Hatzifotiadou D, Hauer P, Hayashi S, Hechavarria ADLB, Heckel ST, Hellbär E, Helstrup H, Herghelegiu A, Hernandez EG, Herrera Corral G, Herrmann F, Hetland KF, Hilden TE, Hillemanns H, Hills C, Hippolyte B, Hohlweger B, Horak D, Hornung S, Hosokawa R, Hristov P, Huang C, Hughes C, Huhn P, Humanic TJ, Hushnud H, Husova LA, Hussain N, Hussain SA, Hussain T, Hutter D, Hwang DS, Iddon JP, Ilkaev R, Inaba M, Ippolitov M, Islam MS, Ivanov M, Ivanov V, Izucheev V, Jacak B, Jacazio N, Jacobs PM, Jadhav MB, Jadlovska S, Jadlovsky J, Jaelani S, Jahnke C, Jakubowska MJ, Janik MA, Jercic M, Jevons O, Jimenez Bustamante RT, Jin M, Jonas F, Jones PG, Jusko A, Kalinak P, Kalweit A, Kang JH, Kaplin V, Kar S, Karasu Uysal A, Karavichev O, Karavicheva T, Karczmarczyk P, Karpechev E, Kebschull U, Keidel R, Keil M, Ketzer B, Khabanova Z, Khan AM, Khan S, Khan SA, Khanzadeev A, Kharlov Y, Khatun A, Khuntia A, Kileng B, Kim B, Kim B, Kim D, Kim DJ, Kim EJ, Kim H, Kim J, Kim JS, Kim J, Kim J, Kim J, Kim M, Kim S, Kim T, Kim T, Kirsch S, Kisel I, Kiselev S, Kisiel A, Klay JL, Klein C, Klein J, Klein S, Klein-Bösing C, Klewin S, Kluge A, Knichel ML, Knospe AG, Kobdaj C, Köhler MK, Kollegger T, Kondratyev A, Kondratyeva N, Kondratyuk E, Konopka PJ, Koska L, Kovalenko O, Kovalenko V, Kowalski M, Králik I, Kravčáková A, Kreis L, Krivda M, Krizek F, Krizkova Gajdosova K, Krüger M, Kryshen E, Krzewicki M, Kubera AM, Kučera V, Kuhn C, Kuijer PG, Kumar L, Kumar S, Kundu S, Kurashvili P, Kurepin A, Kurepin AB, Kuryakin A, Kushpil S, Kvapil J, Kweon MJ, Kwon JY, Kwon Y, La Pointe SL, La Rocca P, Lai YS, Langoy R, Lapidus K, Lardeux A, Larionov P, Laudi E, Lavicka R, Lazareva T, Lea R, Leardini L, Lee S, Lehas F, Lehner S, Lehrbach J, Lemmon RC, León Monzón I, Lesser ED, Lettrich M, Lévai P, Li X, Li XL, Lien J, Lietava R, Lim B, Lindal S, Lindenstruth V, Lindsay SW, Lippmann C, Lisa MA, Litichevskyi V, Liu A, Liu S, Llope WJ, Lofnes IM, Loginov V, Loizides C, Loncar P, Lopez X, López Torres E, Luettig P, Luhder JR, Lunardon M, Luparello G, Lupi M, Maevskaya A, Mager M, Mahmood SM, Mahmoud T, Maire A, Majka RD, Malaev M, Malik QW, Malinina L, Mal'Kevich D, Malzacher P, Mamonov A, Mandaglio G, Manko V, Manso F, Manzari V, Mao Y, Marchisone M, Mareš J, Margagliotti GV, Margotti A, Margutti J, Marín A, Markert C, Marquard M, Martin NA, Martinengo P, Martinez JL, Martínez MI, Martínez García G, Martinez Pedreira M, Masciocchi S, Masera M, Masoni A, Massacrier L, Masson E, Mastroserio A, Mathis AM, Matonoha O, Matuoka PFT, Matyja A, Mayer C, Mazzilli M, Mazzoni MA, Mechler AF, Meddi F, Melikyan Y, Menchaca-Rocha A, Meninno E, Meres M, Mhlanga S, Miake Y, Micheletti L, Mieskolainen MM, Mihaylov DL, Mikhaylov K, Mischke A, Mishra AN, Miśkowiec D, Mitu CM, Modak A, Mohammadi N, Mohanty AP, Mohanty B, Khan MM, Mondal M, Mondal MM, Mordasini C, Moreira De Godoy DA, Moreno LAP, Moretto S, Morreale A, Morsch A, Mrnjavac T, Muccifora V, Mudnic E, Mühlheim D, Muhuri S, Mulligan JD, Munhoz MG, Münning K, Munzer RH, Murakami H, Murray S, Musa L, Musinsky J, Myers CJ, Myrcha JW, Naik B, Nair R, Nandi BK, Nania R, Nappi E, Naru MU, Nassirpour AF, Natal da Luz H, Nattrass C, Nayak R, Nayak TK, Nazarenko S, Negrao De Oliveira RA, Nellen L, Nesbo SV, Neskovic G, Nesterov D, Nielsen BS, Nikolaev S, Nikulin S, Nikulin V, Noferini F, Nomokonov P, Nooren G, Norman J, Novitzky N, Nowakowski P, Nyanin A, Nystrand J, Ogino M, Ohlson A, Oleniacz J, Oliveira Da Silva AC, Oliver MH, Oppedisano C, Orava R, Ortiz Velasquez A, Oskarsson A, Otwinowski J, Oyama K, Pachmayer Y, Pacik V, Pagano D, Paić G, Palni P, Pan J, Pandey AK, Panebianco S, Papikyan V, Pareek P, Park J, Parkkila JE, Parmar S, Passfeld A, Pathak SP, Patra RN, Paul B, Pei H, Peitzmann T, Peng X, Pereira LG, Pereira Da Costa H, Peresunko D, Perez GM, Perez Lezama E, Peskov V, Pestov Y, Petráček V, Petrovici M, Pezzi RP, Piano S, Pikna M, Pillot P, Pimentel LODL, Pinazza O, Pinsky L, Pinto C, Pisano S, Pistone D, Piyarathna DB, Płoskoń M, Planinic M, Pliquett F, Pluta J, Pochybova S, Poghosyan MG, Polichtchouk B, Poljak N, Poonsawat W, Pop A, Poppenborg H, Porteboeuf-Houssais S, Pozdniakov V, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Punin V, Puranapanda K, Putschke J, Quishpe RE, Ragoni S, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Raniwala R, Raniwala S, Räsänen SS, Rascanu BT, Rath R, Ratza V, Ravasenga I, Read KF, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Reshetin A, Revol JP, Reygers K, Riabov V, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rode SP, Rodríguez Cahuantzi M, Røed K, Rogalev R, Rogochaya E, Rohr D, Röhrich D, Rokita PS, Ronchetti F, Rosas ED, Roslon K, Rosnet P, Rossi A, Rotondi A, Roukoutakis F, Roy A, Roy P, Rueda OV, Rui R, Rumyantsev B, Rustamov A, Ryabinkin E, Ryabov Y, Rybicki A, Rytkonen H, Sadhu S, Sadovsky S, Šafařík K, Saha SK, Sahoo B, Sahoo P, Sahoo R, Sahoo S, Sahu PK, Saini J, Sakai S, Sambyal S, Samsonov V, Sanchez FR, Sandoval A, Sarkar A, Sarkar D, Sarkar N, Sarma P, Sarti VM, Sas MHP, Scapparone E, Schaefer B, Schambach J, Scheid HS, Schiaua C, Schicker R, Schmah A, Schmidt C, Schmidt HR, Schmidt MO, Schmidt M, Schmidt NV, Schmier AR, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Šefčík M, Seger JE, Sekiguchi Y, Sekihata D, Selyuzhenkov I, Senyukov S, Serebryakov D, Serradilla E, Sett P, Sevcenco A, Shabanov A, Shabetai A, Shahoyan R, Shaikh W, Shangaraev A, Sharma A, Sharma A, Sharma H, Sharma M, Sharma N, Sheikh AI, Shigaki K, Shimomura M, Shirinkin S, Shou Q, Sibiriak Y, Siddhanta S, Siemiarczuk T, Silvermyr D, Silvestre C, Simatovic G, Simonetti G, Singh R, Singh R, Singh VK, Singhal V, Sinha T, Sitar B, Sitta M, Skaali TB, Slupecki M, Smirnov N, Snellings RJM, Snellman TW, Sochan J, Soncco C, Song J, Songmoolnak A, Soramel F, Sorensen S, Sputowska I, Stachel J, Stan I, Stankus P, Steffanic PJ, Stenlund E, Stocco D, Storetvedt MM, Strmen P, Suaide AAP, Sugitate T, Suire C, Suleymanov M, Suljic M, Sultanov R, Šumbera M, Sumowidagdo S, Suzuki K, Swain S, Szabo A, Szarka I, Tabassam U, Taillepied G, Takahashi J, Tambave GJ, Tang S, Tarhini M, Tarzila MG, Tauro A, Tejeda Muñoz G, Telesca A, Terrevoli C, Thakur D, Thakur S, Thomas D, Thoresen F, Tieulent R, Tikhonov A, Timmins AR, Toia A, Topilskaya N, Toppi M, Torales-Acosta F, Torres SR, Trifiro A, Tripathy S, Tripathy T, Trogolo S, Trombetta G, Tropp L, Trubnikov V, Trzaska WH, Trzcinski TP, Trzeciak BA, Tsuji T, Tumkin A, Turrisi R, Tveter TS, Ullaland K, Umaka EN, Uras A, Usai GL, Utrobicic A, Vala M, Valle N, Vallero S, van der Kolk N, van Doremalen LVR, van Leeuwen M, Vande Vyvre P, Varga D, Varga Z, Varga-Kofarago M, Vargas A, Vargyas M, Varma R, Vasileiou M, Vasiliev A, Vázquez Doce O, Vechernin V, Veen AM, Vercellin E, Vergara Limón S, Vermunt L, Vernet R, Vértesi R, Vicencio MGDLC, Vickovic L, Viinikainen J, Vilakazi Z, Villalobos Baillie O, Villatoro Tello A, Vino G, Vinogradov A, Virgili T, Vislavicius V, Vodopyanov A, Volkel B, Völkl MA, Voloshin K, Voloshin SA, Volpe G, von Haller B, Vorobyev I, Voscek D, Vrláková J, Wagner B, Weber M, Weber SG, Wegrzynek A, Weiser DF, Wenzel SC, Wessels JP, Widmann E, Wiechula J, Wikne J, Wilk G, Wilkinson J, Willems GA, Willsher E, Windelband B, Witt WE, Winn M, Wu Y, Xu R, Yalcin S, Yamakawa K, Yang S, Yano S, Yin Z, Yokoyama H, Yoo IK, Yoon JH, Yuan S, Yuncu A, Yurchenko V, Zaccolo V, Zaman A, Zampolli C, Zanoli HJC, Zardoshti N, Zarochentsev A, Závada P, Zaviyalov N, Zbroszczyk H, Zhalov M, Zhang X, Zhang Z, Zhao C, Zherebchevskii V, Zhigareva N, Zhou D, Zhou Y, Zhou Z, Zhu J, Zhu Y, Zichichi A, Zimmermann MB, Zinovjev G, Zurlo N. Measurement of ϒ(1S) Elliptic Flow at Forward Rapidity in Pb-Pb Collisions at sqrt[s_{NN}]=5.02 TeV. PHYSICAL REVIEW LETTERS 2019; 123:192301. [PMID: 31765217 DOI: 10.1103/physrevlett.123.192301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 09/09/2019] [Indexed: 06/10/2023]
Abstract
The first measurement of the ϒ(1S) elliptic flow coefficient (v_{2}) is performed at forward rapidity (2.5<y<4) in Pb-Pb collisions at sqrt[s_{NN}]=5.02 TeV with the ALICE detector at the LHC. The results are obtained with the scalar product method and are reported as a function of transverse momentum (p_{T}) up to 15 GeV/c in the 5%-60% centrality interval. The measured ϒ(1S)v_{2} is consistent with 0 and with the small positive values predicted by transport models within uncertainties. The v_{2} coefficient in 2<p_{T}<15 GeV/c is lower than that of inclusive J/ψ mesons in the same p_{T} interval by 2.6 standard deviations. These results, combined with earlier suppression measurements, are in agreement with a scenario in which the ϒ(1S) production in Pb-Pb collisions at LHC energies is dominated by dissociation limited to the early stage of the collision, whereas in the J/ψ case there is substantial experimental evidence of an additional regeneration component.
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Zhang M, Zundel Z, Myers CJ. SBOLExplorer: Data Infrastructure and Data Mining for Genetic Design Repositories. ACS Synth Biol 2019; 8:2287-2294. [PMID: 31532640 DOI: 10.1021/acssynbio.9b00089] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
This paper describes SBOLExplorer, a system that is used to provide intuitive searching within the SynBioHub genetic design repository. SynBioHub stores genetic constructs encoded in the SBOL data format. These constructs can represent genetic parts, circuits, and sequences. These constructs are often numerous, exist in various states of completeness and documentation, and do not lend themselves to simple searching and discovery. In particular, this paper focuses on improving the search capabilities of SynBioHub. Inspiration is drawn from the techniques used to organize and search over the World Wide Web, a linked data set with many of the same properties of the SBOL data in SynBioHub. SBOLExplorer integrates these methods into SynBioHub's data representation and search, providing significant improvement over the previous search implementation based on pattern-matching.
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Acharya S, Adamová D, Adhya SP, Adler A, Adolfsson J, Aggarwal MM, Aglieri Rinella G, Agnello M, Agrawal N, Ahammed Z, Ahmad S, Ahn SU, Aiola S, Akindinov A, Al-Turany M, Alam SN, Albuquerque DSD, Aleksandrov D, Alessandro B, Alfanda HM, Alfaro Molina R, Ali B, Ali Y, Alici A, Alkin A, Alme J, Alt T, Altenkamper L, Altsybeev I, Anaam MN, Andrei C, Andreou D, Andrews HA, Andronic A, Angeletti M, Anguelov V, Anson C, Antičić T, Antinori F, Antonioli P, Anwar R, Apadula N, Aphecetche L, Appelshäuser H, Arcelli S, Arnaldi R, Arratia M, Arsene IC, Arslandok M, Augustinus A, Averbeck R, Aziz S, Azmi MD, Badalà A, Baek YW, Bagnasco S, Bailhache R, Bala R, Baldisseri A, Ball M, Baral RC, Barbera R, Barioglio L, Barnaföldi GG, Barnby LS, Barret V, Bartalini P, Barth K, Bartsch E, Bastid N, Basu S, Batigne G, Batyunya B, Batzing PC, Bauri D, Bazo Alba JL, Bearden IG, Bedda C, Behera NK, Belikov I, Bellini F, Bellwied R, Beltran LGE, Belyaev V, Bencedi G, Beole S, Bercuci A, Berdnikov Y, Berenyi D, Bertens RA, Berzano D, Betev L, Bhasin A, Bhat IR, Bhatt H, Bhattacharjee B, Bianchi A, Bianchi L, Bianchi N, Bielčík J, Bielčíková J, Bilandzic A, Biro G, Biswas R, Biswas S, Blair JT, Blau D, Blume C, Boca G, Bock F, Bogdanov A, Boldizsár L, Bolozdynya A, Bombara M, Bonomi G, Bonora M, Borel H, Borissov A, Borri M, Botta E, Bourjau C, Bratrud L, Braun-Munzinger P, Bregant M, Broker TA, Broz M, Brucken EJ, Bruna E, Bruno GE, Buckland MD, Budnikov D, Buesching H, Bufalino S, Buhler P, Buncic P, Busch O, Buthelezi Z, Butt JB, Buxton JT, Caffarri D, Caines H, Caliva A, Calvo Villar E, Camacho RS, Camerini P, Capon AA, Carnesecchi F, Castillo Castellanos J, Castro AJ, Casula EAR, Catalano F, Ceballos Sanchez C, Chakraborty P, Chandra S, Chang B, Chang W, Chapeland S, Chartier M, Chattopadhyay S, Chattopadhyay S, Chauvin A, Cheshkov C, Cheynis B, Chibante Barroso V, Chinellato DD, Cho S, Chochula P, Chowdhury T, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Cicalo C, Cifarelli L, Cindolo F, Cleymans J, Colamaria F, Colella D, Collu A, Colocci M, Concas M, Conesa Balbastre G, Conesa Del Valle Z, Contin G, Contreras JG, Cormier TM, Corrales Morales Y, Cortese P, Cosentino MR, Costa F, Costanza S, Crkovská J, Crochet P, Cuautle E, Cunqueiro L, Dabrowski D, Dahms T, Dainese A, Damas FPA, Dani S, Danisch MC, Danu A, Das D, Das I, Das S, Dash A, Dash S, Dashi A, De S, De Caro A, de Cataldo G, de Conti C, de Cuveland J, De Falco A, De Gruttola D, De Marco N, De Pasquale S, De Souza RD, Deb S, Degenhardt HF, Deisting A, Deja KR, Deloff A, Delsanto S, Dhankher P, Di Bari D, Di Mauro A, Diaz RA, Dietel T, Dillenseger P, Ding Y, Divià R, Djuvsland Ø, Dmitrieva U, Dobrin A, Domenicis Gimenez D, Dönigus B, Dordic O, Dubey AK, Dubla A, Dudi S, Duggal AK, Dukhishyam M, Dupieux P, Ehlers RJ, Elia D, Engel H, Epple E, Erazmus B, Erhardt F, Erokhin A, Ersdal MR, Espagnon B, Eulisse G, Eum J, Evans D, Evdokimov S, Fabbietti L, Faggin M, Faivre J, Fantoni A, Fasel M, Fecchio P, Feldkamp L, Feliciello A, Feofilov G, Fernández Téllez A, Ferrero A, Ferretti A, Festanti A, Feuillard VJG, Figiel J, Filchagin S, Finogeev D, Fionda FM, Fiorenza G, Flor F, Foertsch S, Foka P, Fokin S, Fragiacomo E, Francisco A, Frankenfeld U, Fronze GG, Fuchs U, Furget C, Furs A, Fusco Girard M, Gaardhøje JJ, Gagliardi M, Gago AM, Gal A, Galvan CD, Ganoti P, Garabatos C, Garcia-Solis E, Garg K, Gargiulo C, Garner K, Gasik P, Gauger EF, Gay Ducati MB, Germain M, Ghosh J, Ghosh P, Ghosh SK, Gianotti P, Giubellino P, Giubilato P, Glässel P, Goméz Coral DM, Gomez Ramirez A, Gonzalez V, González-Zamora P, Gorbunov S, Görlich L, Gotovac S, Grabski V, Graczykowski LK, Graham KL, Greiner L, Grelli A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Groettvik OS, Gronefeld JM, Grosa F, Grosse-Oetringhaus JF, Grosso R, Guernane R, Guerzoni B, Guittiere M, Gulbrandsen K, Gunji T, Gupta A, Gupta R, Guzman IB, Haake R, Habib MK, Hadjidakis C, Hamagaki H, Hamar G, Hamid M, Hamon JC, Hannigan R, Haque MR, Harlenderova A, Harris JW, Harton A, Hassan H, Hatzifotiadou D, Hauer P, Hayashi S, Heckel ST, Hellbär E, Helstrup H, Herghelegiu A, Hernandez EG, Herrera Corral G, Herrmann F, Hetland KF, Hilden TE, Hillemanns H, Hills C, Hippolyte B, Hohlweger B, Horak D, Hornung S, Hosokawa R, Hristov P, Huang C, Hughes C, Huhn P, Humanic TJ, Hushnud H, Husova LA, Hussain N, Hussain SA, Hussain T, Hutter D, Hwang DS, Iddon JP, Ilkaev R, Inaba M, Ippolitov M, Islam MS, Ivanov M, Ivanov V, Izucheev V, Jacak B, Jacazio N, Jacobs PM, Jadhav MB, Jadlovska S, Jadlovsky J, Jaelani S, Jahnke C, Jakubowska MJ, Janik MA, Jercic M, Jevons O, Jimenez Bustamante RT, Jin M, Jonas F, Jones PG, Jusko A, Kalinak P, Kalweit A, Kang JH, Kaplin V, Kar S, Karasu Uysal A, Karavichev O, Karavicheva T, Karczmarczyk P, Karpechev E, Kebschull U, Keidel R, Keil M, Ketzer B, Khabanova Z, Khan AM, Khan S, Khan SA, Khanzadeev A, Kharlov Y, Khatun A, Khuntia A, Kileng B, Kim B, Kim B, Kim D, Kim DJ, Kim EJ, Kim H, Kim JS, Kim J, Kim J, Kim J, Kim M, Kim S, Kim T, Kim T, Kindra K, Kirsch S, Kisel I, Kiselev S, Kisiel A, Klay JL, Klein C, Klein J, Klein S, Klein-Bösing C, Klewin S, Kluge A, Knichel ML, Knospe AG, Kobdaj C, Kofarago M, Köhler MK, Kollegger T, Kondratyev A, Kondratyeva N, Kondratyuk E, Konopka PJ, Konyushikhin M, Koska L, Kovalenko O, Kovalenko V, Kowalski M, Králik I, Kravčáková A, Kreis L, Krivda M, Krizek F, Krizkova Gajdosova K, Krüger M, Kryshen E, Krzewicki M, Kubera AM, Kučera V, Kuhn C, Kuijer PG, Kumar L, Kumar S, Kundu S, Kurashvili P, Kurepin A, Kurepin AB, Kushpil S, Kvapil J, Kweon MJ, Kwon Y, La Pointe SL, La Rocca P, Lai YS, Langoy R, Lapidus K, Lardeux A, Larionov P, Laudi E, Lavicka R, Lazareva T, Lea R, Leardini L, Lee S, Lehas F, Lehner S, Lehrbach J, Lemmon RC, León Monzón I, Lettrich M, Lévai P, Li X, Li XL, Lien J, Lietava R, Lim B, Lindal S, Lindenstruth V, Lindsay SW, Lippmann C, Lisa MA, Litichevskyi V, Liu A, Liu S, Ljunggren HM, Llope WJ, Lodato DF, Loginov V, Loizides C, Loncar P, Lopez X, López Torres E, Luettig P, Luhder JR, Lunardon M, Luparello G, Lupi M, Maevskaya A, Mager M, Mahmood SM, Mahmoud T, Maire A, Majka RD, Malaev M, Malik QW, Malinina L, Mal'Kevich D, Malzacher P, Mamonov A, Manko V, Manso F, Manzari V, Mao Y, Marchisone M, Mareš J, Margagliotti GV, Margotti A, Margutti J, Marín A, Markert C, Marquard M, Martin NA, Martinengo P, Martinez JL, Martínez MI, Martínez García G, Martinez Pedreira M, Masciocchi S, Masera M, Masoni A, Massacrier L, Masson E, Mastroserio A, Mathis AM, Matuoka PFT, Matyja A, Mayer C, Mazzilli M, Mazzoni MA, Mechler AF, Meddi F, Melikyan Y, Menchaca-Rocha A, Meninno E, Meres M, Mhlanga S, Miake Y, Micheletti L, Mieskolainen MM, Mihaylov DL, Mikhaylov K, Mischke A, Mishra AN, Miśkowiec D, Mitu CM, Mohammadi N, Mohanty AP, Mohanty B, Khan MM, Mondal MM, Mordasini C, Moreira De Godoy DA, Moreno LAP, Moretto S, Morreale A, Morsch A, Mrnjavac T, Muccifora V, Mudnic E, Mühlheim D, Muhuri S, Mulligan JD, Munhoz MG, Münning K, Munzer RH, Murakami H, Murray S, Musa L, Musinsky J, Myers CJ, Myrcha JW, Naik B, Nair R, Nandi BK, Nania R, Nappi E, Naru MU, Nassirpour AF, Natal da Luz H, Nattrass C, Nayak K, Nayak R, Nayak TK, Nazarenko S, Negrao De Oliveira RA, Nellen L, Nesbo SV, Neskovic G, Ng F, Nielsen BS, Nikolaev S, Nikulin S, Nikulin V, Noferini F, Nomokonov P, Nooren G, Noris JCC, Norman J, Nowakowski P, Nyanin A, Nystrand J, Ogino M, Ohlson A, Oleniacz J, Oliveira Da Silva AC, Oliver MH, Onderwaater J, Oppedisano C, Orava R, Ortiz Velasquez A, Oskarsson A, Otwinowski J, Oyama K, Pachmayer Y, Pacik V, Pagano D, Paić G, Palni P, Pan J, Pandey AK, Panebianco S, Papikyan V, Pareek P, Park J, Parkkila JE, Parmar S, Passfeld A, Pathak SP, Patra RN, Paul B, Pei H, Peitzmann T, Peng X, Pereira LG, Pereira Da Costa H, Peresunko D, Perez GM, Perez Lezama E, Peskov V, Pestov Y, Petráček V, Petrovici M, Pezzi RP, Piano S, Pikna M, Pillot P, Pimentel LODL, Pinazza O, Pinsky L, Pisano S, Piyarathna DB, Płoskoń M, Planinic M, Pliquett F, Pluta J, Pochybova S, Poghosyan MG, Polichtchouk B, Poljak N, Poonsawat W, Pop A, Poppenborg H, Porteboeuf-Houssais S, Pozdniakov V, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Punin V, Puranapanda K, Putschke J, Quishpe RE, Ragoni S, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Raniwala R, Raniwala S, Räsänen SS, Rascanu BT, Rath R, Ratza V, Ravasenga I, Read KF, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Reshetin A, Revol JP, Reygers K, Riabov V, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rode SP, Rodríguez Cahuantzi M, Røed K, Rogalev R, Rogochaya E, Rohr D, Röhrich D, Rokita PS, Ronchetti F, Rosas ED, Roslon K, Rosnet P, Rossi A, Rotondi A, Roukoutakis F, Roy A, Roy P, Rueda OV, Rui R, Rumyantsev B, Rustamov A, Ryabinkin E, Ryabov Y, Rybicki A, Rytkonen H, Saarinen S, Sadhu S, Sadovsky S, Šafařík K, Saha SK, Sahoo B, Sahoo P, Sahoo R, Sahoo S, Sahu PK, Saini J, Sakai S, Sambyal S, Samsonov V, Sandoval A, Sarkar A, Sarkar D, Sarkar N, Sarma P, Sarti VM, Sas MHP, Scapparone E, Schaefer B, Schambach J, Scheid HS, Schiaua C, Schicker R, Schmah A, Schmidt C, Schmidt HR, Schmidt MO, Schmidt M, Schmidt NV, Schmier AR, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Šefčík M, Seger JE, Sekiguchi Y, Sekihata D, Selyuzhenkov I, Senyukov S, Serradilla E, Sett P, Sevcenco A, Shabanov A, Shabetai A, Shahoyan R, Shaikh W, Shangaraev A, Sharma A, Sharma A, Sharma M, Sharma N, Sheikh AI, Shigaki K, Shimomura M, Shirinkin S, Shou Q, Sibiriak Y, Siddhanta S, Siemiarczuk T, Silvermyr D, Simatovic G, Simonetti G, Singh R, Singh R, Singh VK, Singhal V, Sinha T, Sitar B, Sitta M, Skaali TB, Slupecki M, Smirnov N, Snellings RJM, Snellman TW, Sochan J, Soncco C, Song J, Songmoolnak A, Soramel F, Sorensen S, Sputowska I, Stachel J, Stan I, Stankus P, Steffanic PJ, Stenlund E, Stocco D, Storetvedt MM, Strmen P, Suaide AAP, Sugitate T, Suire C, Suleymanov M, Suljic M, Sultanov R, Šumbera M, Sumowidagdo S, Suzuki K, Swain S, Szabo A, Szarka I, Tabassam U, Taillepied G, Takahashi J, Tambave GJ, Tang S, Tarhini M, Tarzila MG, Tauro A, Tejeda Muñoz G, Telesca A, Terrevoli C, Thakur D, Thakur S, Thomas D, Thoresen F, Tieulent R, Tikhonov A, Timmins AR, Toia A, Topilskaya N, Toppi M, Torales-Acosta F, Torres SR, Tripathy S, Tripathy T, Trogolo S, Trombetta G, Tropp L, Trubnikov V, Trzaska WH, Trzcinski TP, Trzeciak BA, Tsuji T, Tumkin A, Turrisi R, Tveter TS, Ullaland K, Umaka EN, Uras A, Usai GL, Utrobicic A, Vala M, Valle N, van der Kolk N, van Doremalen LVR, van Leeuwen M, Vande Vyvre P, Varga D, Vargas A, Vargyas M, Varma R, Vasileiou M, Vasiliev A, Vázquez Doce O, Vechernin V, Veen AM, Vercellin E, Vergara Limón S, Vermunt L, Vernet R, Vértesi R, Vickovic L, Viinikainen J, Vilakazi Z, Villalobos Baillie O, Villatoro Tello A, Vino G, Vinogradov A, Virgili T, Vislavicius V, Vodopyanov A, Volkel B, Völkl MA, Voloshin K, Voloshin SA, Volpe G, von Haller B, Vorobyev I, Voscek D, Vrláková J, Wagner B, Wang M, Watanabe Y, Weber M, Weber SG, Wegrzynek A, Weiser DF, Wenzel SC, Wessels JP, Westerhoff U, Whitehead AM, Widmann E, Wiechula J, Wikne J, Wilk G, Wilkinson J, Willems GA, Willsher E, Windelband B, Witt WE, Wu Y, Xu R, Yalcin S, Yamakawa K, Yang S, Yano S, Yin Z, Yokoyama H, Yoo IK, Yoon JH, Yuan S, Yuncu A, Yurchenko V, Zaccolo V, Zaman A, Zampolli C, Zanoli HJC, Zardoshti N, Zarochentsev A, Závada P, Zaviyalov N, Zbroszczyk H, Zhalov M, Zhang X, Zhang Y, Zhang Z, Zhao C, Zherebchevskii V, Zhigareva N, Zhou D, Zhou Y, Zhou Z, Zhu H, Zhu J, Zhu Y, Zichichi A, Zimmermann MB, Zinovjev G, Zurlo N. Investigations of Anisotropic Flow Using Multiparticle Azimuthal Correlations in pp, p-Pb, Xe-Xe, and Pb-Pb Collisions at the LHC. PHYSICAL REVIEW LETTERS 2019; 123:142301. [PMID: 31702212 DOI: 10.1103/physrevlett.123.142301] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Indexed: 06/10/2023]
Abstract
Measurements of anisotropic flow coefficients (v_{n}) and their cross-correlations using two- and multiparticle cumulant methods are reported in collisions of pp at sqrt[s]=13 TeV, p-Pb at a center-of-mass energy per nucleon pair sqrt[s_{NN}]=5.02 TeV, Xe-Xe at sqrt[s_{NN}]=5.44 TeV, and Pb-Pb at sqrt[s_{NN}]=5.02 TeV recorded with the ALICE detector. The multiplicity dependence of v_{n} is studied in a very wide range from 20 to 3000 particles produced in the midrapidity region |η|<0.8 for the transverse momentum range 0.2<p_{T}<3.0 GeV/c. An ordering of the coefficients v_{2}>v_{3}>v_{4} is found in pp and p-Pb collisions, similar to that seen in large collision systems, while a weak v_{2} multiplicity dependence is observed relative to nucleus-nucleus collisions in the same multiplicity range. Using a novel subevent method, v_{2} measured with four-particle cumulants is found to be compatible with that from six-particle cumulants in pp and p-Pb collisions. The magnitude of the correlation between v_{n}^{2} and v_{m}^{2}, evaluated with the symmetric cumulants SC(m,n) is observed to be positive at all multiplicities for v_{2} and v_{4}, while for v_{2} and v_{3} it is negative and changes sign for multiplicities below 100, which may indicate a different v_{n} fluctuation pattern in this multiplicity range. The observed long-range multiparticle azimuthal correlations in high multiplicity pp and p-Pb collisions can neither be described by pythia 8 nor by impact-parameter-Glasma, music, and ultrarelativistic quantum molecular dynamics model calculations, and hence, provide new insights into the understanding of collective effects in small collision systems.
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Acharya S, Adamová D, Adhya SP, Adler A, Adolfsson J, Aggarwal MM, Aglieri Rinella G, Agnello M, Agrawal N, Ahammed Z, Ahmad S, Ahn SU, Aiola S, Akindinov A, Al-Turany M, Alam SN, Albuquerque DSD, Aleksandrov D, Alessandro B, Alfanda HM, Alfaro Molina R, Ali B, Ali Y, Alici A, Alkin A, Alme J, Alt T, Altenkamper L, Altsybeev I, Anaam MN, Andrei C, Andreou D, Andrews HA, Andronic A, Angeletti M, Anguelov V, Anson C, Antičić T, Antinori F, Antonioli P, Anwar R, Apadula N, Aphecetche L, Appelshäuser H, Arcelli S, Arnaldi R, Arratia M, Arsene IC, Arslandok M, Augustinus A, Averbeck R, Aziz S, Azmi MD, Badalà A, Baek YW, Bagnasco S, Bailhache R, Bala R, Baldisseri A, Ball M, Baral RC, Barbera R, Barioglio L, Barnaföldi GG, Barnby LS, Barret V, Bartalini P, Barth K, Bartsch E, Baruffaldi F, Bastid N, Basu S, Batigne G, Batyunya B, Batzing PC, Bauri D, Bazo Alba JL, Bearden IG, Bedda C, Behera NK, Belikov I, Bellini F, Bellwied R, Belyaev V, Bencedi G, Beole S, Bercuci A, Berdnikov Y, Berenyi D, Bertens RA, Berzano D, Betev L, Bhasin A, Bhat IR, Bhatt H, Bhattacharjee B, Bianchi A, Bianchi L, Bianchi N, Bielčík J, Bielčíková J, Bilandzic A, Biro G, Biswas R, Biswas S, Blair JT, Blau D, Blume C, Boca G, Bock F, Bogdanov A, Boldizsár L, Bolozdynya A, Bombara M, Bonomi G, Bonora M, Borel H, Borissov A, Borri M, Bossi H, Botta E, Bourjau C, Bratrud L, Braun-Munzinger P, Bregant M, Broker TA, Broz M, Brucken EJ, Bruna E, Bruno GE, Buckland MD, Budnikov D, Buesching H, Bufalino S, Bugnon O, Buhler P, Buncic P, Busch O, Buthelezi Z, Butt JB, Buxton JT, Caffarri D, Caliva A, Calvo Villar E, Camacho RS, Camerini P, Capon AA, Carnesecchi F, Castillo Castellanos J, Castro AJ, Casula EAR, Catalano F, Ceballos Sanchez C, Chakraborty P, Chandra S, Chang B, Chang W, Chapeland S, Chartier M, Chattopadhyay S, Chattopadhyay S, Chauvin A, Cheshkov C, Cheynis B, Chibante Barroso V, Chinellato DD, Cho S, Chochula P, Chowdhury T, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Cicalo C, Cifarelli L, Cindolo F, Cleymans J, Colamaria F, Colella D, Collu A, Colocci M, Concas M, Conesa Balbastre G, Conesa Del Valle Z, Contin G, Contreras JG, Cormier TM, Corrales Morales Y, Cortese P, Cosentino MR, Costa F, Costanza S, Crkovská J, Crochet P, Cuautle E, Cunqueiro L, Dabrowski D, Dahms T, Dainese A, Damas FPA, Dani S, Danisch MC, Danu A, Das D, Das I, Das S, Dash A, Dash S, Dashi A, De S, De Caro A, de Cataldo G, de Conti C, de Cuveland J, De Falco A, De Gruttola D, De Marco N, De Pasquale S, De Souza RD, Deb S, Degenhardt HF, Deisting A, Deja KR, Deloff A, Delsanto S, Dhankher P, Di Bari D, Di Mauro A, Diaz RA, Dietel T, Dillenseger P, Ding Y, Divià R, Djuvsland Ø, Dmitrieva U, Dobrin A, Dönigus B, Dordic O, Dubey AK, Dubla A, Dudi S, Duggal AK, Dukhishyam M, Dupieux P, Ehlers RJ, Elia D, Engel H, Epple E, Erazmus B, Erhardt F, Erokhin A, Ersdal MR, Espagnon B, Eulisse G, Eum J, Evans D, Evdokimov S, Fabbietti L, Faggin M, Faivre J, Fantoni A, Fasel M, Fecchio P, Feldkamp L, Feliciello A, Feofilov G, Fernández Téllez A, Ferrero A, Ferretti A, Festanti A, Feuillard VJG, Figiel J, Filchagin S, Finogeev D, Fionda FM, Fiorenza G, Flor F, Foertsch S, Foka P, Fokin S, Fragiacomo E, Francisco A, Frankenfeld U, Fronze GG, Fuchs U, Furget C, Furs A, Fusco Girard M, Gaardhøje JJ, Gagliardi M, Gago AM, Gal A, Galvan CD, Ganoti P, Garabatos C, Garcia-Solis E, Garg K, Gargiulo C, Garner K, Gasik P, Gauger EF, Gay Ducati MB, Germain M, Ghosh J, Ghosh P, Ghosh SK, Gianotti P, Giubellino P, Giubilato P, Glässel P, Goméz Coral DM, Gomez Ramirez A, Gonzalez V, González-Zamora P, Gorbunov S, Görlich L, Gotovac S, Grabski V, Graczykowski LK, Graham KL, Greiner L, Grelli A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Groettvik OS, Gronefeld JM, Grosa F, Grosse-Oetringhaus JF, Grosso R, Guernane R, Guerzoni B, Guittiere M, Gulbrandsen K, Gunji T, Gupta A, Gupta R, Guzman IB, Haake R, Habib MK, Hadjidakis C, Hamagaki H, Hamar G, Hamid M, Hamon JC, Hannigan R, Haque MR, Harlenderova A, Harris JW, Harton A, Hassan H, Hatzifotiadou D, Hauer P, Hayashi S, Heckel ST, Hellbär E, Helstrup H, Herghelegiu A, Hernandez EG, Herrera Corral G, Herrmann F, Hetland KF, Hilden TE, Hillemanns H, Hills C, Hippolyte B, Hohlweger B, Horak D, Hornung S, Hosokawa R, Hristov P, Huang C, Hughes C, Huhn P, Humanic TJ, Hushnud H, Husova LA, Hussain N, Hussain SA, Hussain T, Hutter D, Hwang DS, Iddon JP, Ilkaev R, Inaba M, Ippolitov M, Islam MS, Ivanov M, Ivanov V, Izucheev V, Jacak B, Jacazio N, Jacobs PM, Jadhav MB, Jadlovska S, Jadlovsky J, Jaelani S, Jahnke C, Jakubowska MJ, Janik MA, Jercic M, Jevons O, Jimenez Bustamante RT, Jin M, Jonas F, Jones PG, Jusko A, Kalinak P, Kalweit A, Kang JH, Kaplin V, Kar S, Karasu Uysal A, Karavichev O, Karavicheva T, Karczmarczyk P, Karpechev E, Kebschull U, Keidel R, Keil M, Ketzer B, Khabanova Z, Khan AM, Khan S, Khan SA, Khanzadeev A, Kharlov Y, Khatun A, Khuntia A, Kileng B, Kim B, Kim B, Kim D, Kim DJ, Kim EJ, Kim H, Kim JS, Kim J, Kim J, Kim J, Kim M, Kim S, Kim T, Kim T, Kindra K, Kirsch S, Kisel I, Kiselev S, Kisiel A, Klay JL, Klein C, Klein J, Klein S, Klein-Bösing C, Klewin S, Kluge A, Knichel ML, Knospe AG, Kobdaj C, Köhler MK, Kollegger T, Kondratyev A, Kondratyeva N, Kondratyuk E, Konopka PJ, Koska L, Kovalenko O, Kovalenko V, Kowalski M, Králik I, Kravčáková A, Kreis L, Krivda M, Krizek F, Krizkova Gajdosova K, Krüger M, Kryshen E, Krzewicki M, Kubera AM, Kučera V, Kuhn C, Kuijer PG, Kumar L, Kumar S, Kundu S, Kurashvili P, Kurepin A, Kurepin AB, Kushpil S, Kvapil J, Kweon MJ, Kwon Y, La Pointe SL, La Rocca P, Lai YS, Langoy R, Lapidus K, Lardeux A, Larionov P, Laudi E, Lavicka R, Lazareva T, Lea R, Leardini L, Lee S, Lehas F, Lehner S, Lehrbach J, Lemmon RC, León Monzón I, Lesser ED, Lettrich M, Lévai P, Li X, Li XL, Lien J, Lietava R, Lim B, Lindal S, Lindenstruth V, Lindsay SW, Lippmann C, Lisa MA, Litichevskyi V, Liu A, Liu S, Ljunggren HM, Llope WJ, Lofnes IM, Loginov V, Loizides C, Loncar P, Lopez X, López Torres E, Luettig P, Luhder JR, Lunardon M, Luparello G, Lupi M, Maevskaya A, Mager M, Mahmood SM, Mahmoud T, Maire A, Majka RD, Malaev M, Malik QW, Malinina L, Mal'Kevich D, Malzacher P, Mamonov A, Manko V, Manso F, Manzari V, Mao Y, Marchisone M, Mareš J, Margagliotti GV, Margotti A, Margutti J, Marín A, Markert C, Marquard M, Martin NA, Martinengo P, Martinez JL, Martínez MI, Martínez García G, Martinez Pedreira M, Masciocchi S, Masera M, Masoni A, Massacrier L, Masson E, Mastroserio A, Mathis AM, Matuoka PFT, Matyja A, Mayer C, Mazzilli M, Mazzoni MA, Mechler AF, Meddi F, Melikyan Y, Menchaca-Rocha A, Meninno E, Meres M, Mhlanga S, Miake Y, Micheletti L, Mieskolainen MM, Mihaylov DL, Mikhaylov K, Mischke A, Mishra AN, Miśkowiec D, Mitu CM, Mohammadi N, Mohanty AP, Mohanty B, Mohisin Khan M, Mondal M, Mondal MM, Mordasini C, Moreira De Godoy DA, Moreno LAP, Moretto S, Morreale A, Morsch A, Mrnjavac T, Muccifora V, Mudnic E, Mühlheim D, Muhuri S, Mulligan JD, Munhoz MG, Münning K, Munzer RH, Murakami H, Murray S, Musa L, Musinsky J, Myers CJ, Myrcha JW, Naik B, Nair R, Nandi BK, Nania R, Nappi E, Naru MU, Nassirpour AF, Natal da Luz H, Nattrass C, Nayak R, Nayak TK, Nazarenko S, Negrao De Oliveira RA, Nellen L, Nesbo SV, Neskovic G, Nielsen BS, Nikolaev S, Nikulin S, Nikulin V, Noferini F, Nomokonov P, Nooren G, Norman J, Nowakowski P, Nyanin A, Nystrand J, Ogino M, Ohlson A, Oleniacz J, Oliveira Da Silva AC, Oliver MH, Onderwaater J, Oppedisano C, Orava R, Ortiz Velasquez A, Oskarsson A, Otwinowski J, Oyama K, Pachmayer Y, Pacik V, Pagano D, Paić G, Palni P, Pan J, Pandey AK, Panebianco S, Papikyan V, Pareek P, Park J, Parkkila JE, Parmar S, Passfeld A, Pathak SP, Patra RN, Paul B, Pei H, Peitzmann T, Peng X, Pereira LG, Pereira Da Costa H, Peresunko D, Perez GM, Perez Lezama E, Peskov V, Pestov Y, Petráček V, Petrovici M, Pezzi RP, Piano S, Pikna M, Pillot P, Pimentel LODL, Pinazza O, Pinsky L, Pisano S, Piyarathna DB, Płoskoń M, Planinic M, Pliquett F, Pluta J, Pochybova S, Poghosyan MG, Polichtchouk B, Poljak N, Poonsawat W, Pop A, Poppenborg H, Porteboeuf-Houssais S, Pozdniakov V, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Punin V, Puranapanda K, Putschke J, Quishpe RE, Ragoni S, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Raniwala R, Raniwala S, Räsänen SS, Rascanu BT, Rath R, Ratza V, Ravasenga I, Read KF, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Reshetin A, Revol JP, Reygers K, Riabov V, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rode SP, Rodríguez Cahuantzi M, Røed K, Rogalev R, Rogochaya E, Rohr D, Röhrich D, Rokita PS, Ronchetti F, Rosas ED, Roslon K, Rosnet P, Rossi A, Rotondi A, Roukoutakis F, Roy A, Roy P, Rueda OV, Rui R, Rumyantsev B, Rustamov A, Ryabinkin E, Ryabov Y, Rybicki A, Rytkonen H, Saarinen S, Sadhu S, Sadovsky S, Šafařík K, Saha SK, Sahoo B, Sahoo P, Sahoo R, Sahoo S, Sahu PK, Saini J, Sakai S, Sambyal S, Samsonov V, Sandoval A, Sarkar A, Sarkar D, Sarkar N, Sarma P, Sarti VM, Sas MHP, Scapparone E, Schaefer B, Schambach J, Scheid HS, Schiaua C, Schicker R, Schmah A, Schmidt C, Schmidt HR, Schmidt MO, Schmidt M, Schmidt NV, Schmier AR, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Šefčík M, Seger JE, Sekiguchi Y, Sekihata D, Selyuzhenkov I, Senyukov S, Serradilla E, Sett P, Sevcenco A, Shabanov A, Shabetai A, Shahoyan R, Shaikh W, Shangaraev A, Sharma A, Sharma A, Sharma M, Sharma N, Sheikh AI, Shigaki K, Shimomura M, Shirinkin S, Shou Q, Sibiriak Y, Siddhanta S, Siemiarczuk T, Silvermyr D, Simatovic G, Simonetti G, Singh R, Singh R, Singh VK, Singhal V, Sinha T, Sitar B, Sitta M, Skaali TB, Slupecki M, Smirnov N, Snellings RJM, Snellman TW, Sochan J, Soncco C, Song J, Songmoolnak A, Soramel F, Sorensen S, Sputowska I, Stachel J, Stan I, Stankus P, Steffanic PJ, Stenlund E, Stocco D, Storetvedt MM, Strmen P, Suaide AAP, Sugitate T, Suire C, Suleymanov M, Suljic M, Sultanov R, Šumbera M, Sumowidagdo S, Suzuki K, Swain S, Szabo A, Szarka I, Tabassam U, Taillepied G, Takahashi J, Tambave GJ, Tang S, Tarhini M, Tarzila MG, Tauro A, Tejeda Muñoz G, Telesca A, Terrevoli C, Thakur D, Thakur S, Thomas D, Thoresen F, Tieulent R, Tikhonov A, Timmins AR, Toia A, Topilskaya N, Toppi M, Torales-Acosta F, Torres SR, Tripathy S, Tripathy T, Trogolo S, Trombetta G, Tropp L, Trubnikov V, Trzaska WH, Trzcinski TP, Trzeciak BA, Tsuji T, Tumkin A, Turrisi R, Tveter TS, Ullaland K, Umaka EN, Uras A, Usai GL, Utrobicic A, Vala M, Valle N, Vallero S, van der Kolk N, van Doremalen LVR, van Leeuwen M, Vande Vyvre P, Varga D, Varga-Kofarago M, Vargas A, Vargyas M, Varma R, Vasileiou M, Vasiliev A, Vázquez Doce O, Vechernin V, Veen AM, Vercellin E, Vergara Limón S, Vermunt L, Vernet R, Vértesi R, Vickovic L, Viinikainen J, Vilakazi Z, Villalobos Baillie O, Villatoro Tello A, Vino G, Vinogradov A, Virgili T, Vislavicius V, Vodopyanov A, Volkel B, Völkl MA, Voloshin K, Voloshin SA, Volpe G, von Haller B, Vorobyev I, Voscek D, Vrláková J, Wagner B, Watanabe Y, Weber M, Weber SG, Wegrzynek A, Weiser DF, Wenzel SC, Wessels JP, Westerhoff U, Whitehead AM, Widmann E, Wiechula J, Wikne J, Wilk G, Wilkinson J, Willems GA, Willsher E, Windelband B, Witt WE, Wu Y, Xu R, Yalcin S, Yamakawa K, Yang S, Yano S, Yin Z, Yokoyama H, Yoo IK, Yoon JH, Yuan S, Yuncu A, Yurchenko V, Zaccolo V, Zaman A, Zampolli C, Zanoli HJC, Zardoshti N, Zarochentsev A, Závada P, Zaviyalov N, Zbroszczyk H, Zhalov M, Zhang X, Zhang Z, Zhao C, Zherebchevskii V, Zhigareva N, Zhou D, Zhou Y, Zhou Z, Zhu J, Zhu Y, Zichichi A, Zimmermann MB, Zinovjev G, Zurlo N. First Observation of an Attractive Interaction between a Proton and a Cascade Baryon. PHYSICAL REVIEW LETTERS 2019; 123:112002. [PMID: 31573229 DOI: 10.1103/physrevlett.123.112002] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Revised: 06/28/2019] [Indexed: 06/10/2023]
Abstract
This Letter presents the first experimental observation of the attractive strong interaction between a proton and a multistrange baryon (hyperon) Ξ^{-}. The result is extracted from two-particle correlations of combined p-Ξ^{-}⊕p[over ¯]-Ξ[over ¯]^{+} pairs measured in p-Pb collisions at sqrt[s_{NN}]=5.02 TeV at the LHC with ALICE. The measured correlation function is compared with the prediction obtained assuming only an attractive Coulomb interaction and a standard deviation in the range [3.6, 5.3] is found. Since the measured p-Ξ^{-}⊕p[over ¯]-Ξ[over ¯]^{+} correlation is significantly enhanced with respect to the Coulomb prediction, the presence of an additional, strong, attractive interaction is evident. The data are compatible with recent lattice calculations by the HAL-QCD Collaboration, with a standard deviation in the range [1.8, 3.7]. The lattice potential predicts a shallow repulsive Ξ^{-} interaction within pure neutron matter and this implies stiffer equations of state for neutron-rich matter including hyperons. Implications of the strong interaction for the modeling of neutron stars are discussed.
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Bartley BA, Choi K, Samineni M, Zundel Z, Nguyen T, Myers CJ, Sauro HM. pySBOL: A Python Package for Genetic Design Automation and Standardization. ACS Synth Biol 2019; 8:1515-1518. [PMID: 30424601 DOI: 10.1021/acssynbio.8b00336] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
This paper presents pySBOL, a software library for computer-aided design of synthetic biological systems in the Python scripting language. This library provides an easy-to-use, object-oriented, application programming interface (API) with low barrier of entry for synthetic biology application developers. The pySBOL library enables reuse of genetic parts and designs through standardized data exchange with biological parts repositories and software tools that communicate using the Synthetic Biology Open Language (SBOL). In addition, pySBOL supports data management of design-build-test-learn workflows for individual laboratories as well as large, distributed teams of synthetic biologists. PySBOL also lets users add custom data to SBOL files to support the specific data requirements of their research. This extensibility helps users integrate software tool chains and develop workflows for new applications. These features and others make the pySBOL library a valuable tool for supporting engineering practices in synthetic biology. Documentation and installation instructions can be found at pysbol2.readthedocs.io .
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Roehner N, Bartley B, Beal J, McLaughlin J, Pocock M, Zhang M, Zundel Z, Myers CJ. Specifying Combinatorial Designs with the Synthetic Biology Open Language (SBOL). ACS Synth Biol 2019; 8:1519-1523. [PMID: 31260271 DOI: 10.1021/acssynbio.9b00092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
As improvements in DNA synthesis technology and assembly methods make combinatorial assembly of genetic constructs increasingly accessible, methods for representing genetic constructs likewise need to improve to handle the exponential growth of combinatorial design space. To this end, we present a community accepted extension of the SBOL data standard that allows for the efficient and flexible encoding of combinatorial designs. This extension includes data structures for representing genetic designs with "variable" components that can be implemented by choosing one of many linked designs for existing genetic parts or constructs. We demonstrate the representational power of the SBOL combinatorial design extension through case studies on metabolic pathway design and genetic circuit design, and we report the expansion of the SBOLDesigner software tool to support users in creating and modifying combinatorial designs in SBOL.
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Hucka M, Bergmann FT, Chaouiya C, Dräger A, Hoops S, Keating SM, König M, Novère NL, Myers CJ, Olivier BG, Sahle S, Schaff JC, Sheriff R, Smith LP, Waltemath D, Wilkinson DJ, Zhang F. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2. J Integr Bioinform 2019; 16:/j/jib.ahead-of-print/jib-2019-0021/jib-2019-0021.xml. [PMID: 31219795 PMCID: PMC6798823 DOI: 10.1515/jib-2019-0021] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 05/20/2019] [Indexed: 11/15/2022] Open
Abstract
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project website at http://sbml.org/.
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Acharya S, Adamová D, Adolfsson J, Aggarwal MM, Aglieri Rinella G, Agnello M, Agrawal N, Ahammed Z, Ahn SU, Aiola S, Akindinov A, Al-Turany M, Alam SN, Albuquerque DSD, Aleksandrov D, Alessandro B, Alfaro Molina R, Ali Y, Alici A, Alkin A, Alme J, Alt T, Altenkamper L, Altsybeev I, Anaam MN, Andrei C, Andreou D, Andrews HA, Andronic A, Angeletti M, Anguelov V, Anson C, Antičić T, Antinori F, Antonioli P, Anwar R, Apadula N, Aphecetche L, Appelshäuser H, Arcelli S, Arnaldi R, Arnold OW, Arsene IC, Arslandok M, Augustinus A, Averbeck R, Azmi MD, Badalà A, Baek YW, Bagnasco S, Bailhache R, Bala R, Baldisseri A, Ball M, Baral RC, Barbano AM, Barbera R, Barile F, Barioglio L, Barnaföldi GG, Barnby LS, Barret V, Bartalini P, Barth K, Bartsch E, Bastid N, Basu S, Batigne G, Batyunya B, Batzing PC, Bazo Alba JL, Bearden IG, Beck H, Bedda C, Behera NK, Belikov I, Bellini F, Bello Martinez H, Bellwied R, Beltran LGE, Belyaev V, Bencedi G, Beole S, Bercuci A, Berdnikov Y, Berenyi D, Bertens RA, Berzano D, Betev L, Bhaduri PP, Bhasin A, Bhat IR, Bhatt H, Bhattacharjee B, Bhom J, Bianchi A, Bianchi L, Bianchi N, Bielčík J, Bielčíková J, Bilandzic A, Biro G, Biswas R, Biswas S, Blair JT, Blau D, Blume C, Boca G, Bock F, Bogdanov A, Boldizsár L, Bombara M, Bonomi G, Bonora M, Borel H, Borissov A, Borri M, Botta E, Bourjau C, Bratrud L, Braun-Munzinger P, Bregant M, Broker TA, Broz M, Brucken EJ, Bruna E, Bruno GE, Budnikov D, Buesching H, Bufalino S, Buhler P, Buncic P, Busch O, Buthelezi Z, Butt JB, Buxton JT, Cabala J, Caffarri D, Caines H, Caliva A, Calvo Villar E, Camacho RS, Camerini P, Capon AA, Carena F, Carena W, Carnesecchi F, Castillo Castellanos J, Castro AJ, Casula EAR, Ceballos Sanchez C, Chandra S, Chang B, Chang W, Chapeland S, Chartier M, Chattopadhyay S, Chattopadhyay S, Chauvin A, Cheshkov C, Cheynis B, Chibante Barroso V, Chinellato DD, Cho S, Chochula P, Chowdhury T, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Chung SU, Cicalo C, Cifarelli L, Cindolo F, Cleymans J, Colamaria F, Colella D, Collu A, Colocci M, Concas M, Conesa Balbastre G, Conesa Del Valle Z, Contreras JG, Cormier TM, Corrales Morales Y, Cortese P, Cosentino MR, Costa F, Costanza S, Crkovská J, Crochet P, Cuautle E, Cunqueiro L, Dahms T, Dainese A, Dani S, Danisch MC, Danu A, Das D, Das I, Das S, Dash A, Dash S, De S, De Caro A, de Cataldo G, de Conti C, de Cuveland J, De Falco A, De Gruttola D, De Marco N, De Pasquale S, De Souza RD, Degenhardt HF, Deisting A, Deloff A, Delsanto S, Deplano C, Dhankher P, Di Bari D, Di Mauro A, Di Ruzza B, Diaz RA, Dietel T, Dillenseger P, Ding Y, Divià R, Djuvsland Ø, Dobrin A, Domenicis Gimenez D, Dönigus B, Dordic O, Doremalen LVR, Dubey AK, Dubla A, Ducroux L, Dudi S, Duggal AK, Dukhishyam M, Dupieux P, Ehlers RJ, Elia D, Endress E, Engel H, Epple E, Erazmus B, Erhardt F, Ersdal MR, Espagnon B, Eulisse G, Eum J, Evans D, Evdokimov S, Fabbietti L, Faggin M, Faivre J, Fantoni A, Fasel M, Feldkamp L, Feliciello A, Feofilov G, Fernández Téllez A, Ferretti A, Festanti A, Feuillard VJG, Figiel J, Figueredo MAS, Filchagin S, Finogeev D, Fionda FM, Fiorenza G, Flor F, Floris M, Foertsch S, Foka P, Fokin S, Fragiacomo E, Francescon A, Francisco A, Frankenfeld U, Fronze GG, Fuchs U, Furget C, Furs A, Fusco Girard M, Gaardhøje JJ, Gagliardi M, Gago AM, Gajdosova K, Gallio M, Galvan CD, Ganoti P, Garabatos C, Garcia-Solis E, Garg K, Gargiulo C, Gasik P, Gauger EF, Gay Ducati MB, Germain M, Ghosh J, Ghosh P, Ghosh SK, Gianotti P, Giubellino P, Giubilato P, Glässel P, Goméz Coral DM, Gomez Ramirez A, Gonzalez V, González-Zamora P, Gorbunov S, Görlich L, Gotovac S, Grabski V, Graczykowski LK, Graham KL, Greiner L, Grelli A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Gronefeld JM, Grosa F, Grosse-Oetringhaus JF, Grosso R, Guernane R, Guerzoni B, Guittiere M, Gulbrandsen K, Gunji T, Gupta A, Gupta R, Guzman IB, Haake R, Habib MK, Hadjidakis C, Hamagaki H, Hamar G, Hamid M, Hamon JC, Hannigan R, Haque MR, Harlenderova A, Harris JW, Harton A, Hassan H, Hatzifotiadou D, Hayashi S, Heckel ST, Hellbär E, Helstrup H, Herghelegiu A, Hernandez EG, Herrera Corral G, Herrmann F, Hetland KF, Hilden TE, Hillemanns H, Hills C, Hippolyte B, Hohlweger B, Horak D, Hornung S, Hosokawa R, Hota J, Hristov P, Huang C, Hughes C, Huhn P, Humanic TJ, Hushnud H, Hussain N, Hussain T, Hutter D, Hwang DS, Iddon JP, Iga Buitron SA, Ilkaev R, Inaba M, Ippolitov M, Islam MS, Ivanov M, Ivanov V, Izucheev V, Jacak B, Jacazio N, Jacobs PM, Jadhav MB, Jadlovska S, Jadlovsky J, Jaelani S, Jahnke C, Jakubowska MJ, Janik MA, Jena C, Jercic M, Jevons O, Jimenez Bustamante RT, Jin M, Jones PG, Jusko A, Kalinak P, Kalweit A, Kang JH, Kaplin V, Kar S, Karasu Uysal A, Karavichev O, Karavicheva T, Karczmarczyk P, Karpechev E, Kebschull U, Keidel R, Keijdener DLD, Keil M, Ketzer B, Khabanova Z, Khan AM, Khan S, Khan SA, Khanzadeev A, Kharlov Y, Khatun A, Khuntia A, Kielbowicz MM, Kileng B, Kim B, Kim D, Kim DJ, Kim EJ, Kim H, Kim JS, Kim J, Kim M, Kim S, Kim T, Kim T, Kirsch S, Kisel I, Kiselev S, Kisiel A, Klay JL, Klein C, Klein J, Klein-Bösing C, Klewin S, Kluge A, Knichel ML, Knospe AG, Kobdaj C, Kofarago M, Köhler MK, Kollegger T, Kondratyeva N, Kondratyuk E, Konevskikh A, Konopka PJ, Konyushikhin M, Kovalenko O, Kovalenko V, Kowalski M, Králik I, Kravčáková A, Kreis L, Krivda M, Krizek F, Krüger M, Kryshen E, Krzewicki M, Kubera AM, Kučera V, Kuhn C, Kuijer PG, Kumar J, Kumar L, Kumar S, Kundu S, Kurashvili P, Kurepin A, Kurepin AB, Kuryakin A, Kushpil S, Kvapil J, Kweon MJ, Kwon Y, La Pointe SL, La Rocca P, Lai YS, Lakomov I, Langoy R, Lapidus K, Lardeux A, Larionov P, Laudi E, Lavicka R, Lea R, Leardini L, Lee S, Lehas F, Lehner S, Lehrbach J, Lemmon RC, León Monzón I, Lévai P, Li X, Li XL, Lien J, Lietava R, Lim B, Lindal S, Lindenstruth V, Lindsay SW, Lippmann C, Lisa MA, Litichevskyi V, Liu A, Ljunggren HM, Llope WJ, Lodato DF, Loginov V, Loizides C, Loncar P, Lopez X, López Torres E, Lowe A, Luettig P, Luhder JR, Lunardon M, Luparello G, Lupi M, Maevskaya A, Mager M, Mahmood SM, Maire A, Majka RD, Malaev M, Malik QW, Malinina L, Mal'Kevich D, Malzacher P, Mamonov A, Manko V, Manso F, Manzari V, Mao Y, Marchisone M, Mareš J, Margagliotti GV, Margotti A, Margutti J, Marín A, Markert C, Marquard M, Martin NA, Martinengo P, Martinez JL, Martínez MI, Martínez García G, Martinez Pedreira M, Masciocchi S, Masera M, Masoni A, Massacrier L, Masson E, Mastroserio A, Mathis AM, Matuoka PFT, Matyja A, Mayer C, Mazzilli M, Mazzoni MA, Meddi F, Melikyan Y, Menchaca-Rocha A, Meninno E, Mercado Pérez J, Meres M, Meza CS, Mhlanga S, Miake Y, Micheletti L, Mieskolainen MM, Mihaylov DL, Mikhaylov K, Mischke A, Mishra AN, Miśkowiec D, Mitra J, Mitu CM, Mohammadi N, Mohanty AP, Mohanty B, Mohisin Khan M, Moreira De Godoy DA, Moreno LAP, Moretto S, Morreale A, Morsch A, Mrnjavac T, Muccifora V, Mudnic E, Mühlheim D, Muhuri S, Mukherjee M, Mulligan JD, Munhoz MG, Münning K, Munoz MIA, Munzer RH, Murakami H, Murray S, Musa L, Musinsky J, Myers CJ, Myrcha JW, Naik B, Nair R, Nandi BK, Nania R, Nappi E, Narayan A, Naru MU, Nassirpour AF, Natal da Luz H, Nattrass C, Navarro SR, Nayak K, Nayak R, Nayak TK, Nazarenko S, Negrao De Oliveira RA, Nellen L, Nesbo SV, Neskovic G, Ng F, Nicassio M, Niedziela J, Nielsen BS, Nikolaev S, Nikulin S, Nikulin V, Noferini F, Nomokonov P, Nooren G, Noris JCC, Norman J, Nyanin A, Nystrand J, Oh H, Ohlson A, Oleniacz J, Oliveira Da Silva AC, Oliver MH, Onderwaater J, Oppedisano C, Orava R, Oravec M, Ortiz Velasquez A, Oskarsson A, Otwinowski J, Oyama K, Pachmayer Y, Pacik V, Pagano D, Paić G, Palni P, Pan J, Pandey AK, Panebianco S, Papikyan V, Pareek P, Park J, Parkkila JE, Parmar S, Passfeld A, Pathak SP, Patra RN, Paul B, Pei H, Peitzmann T, Peng X, Pereira LG, Pereira Da Costa H, Peresunko D, Perez Lezama E, Peskov V, Pestov Y, Petráček V, Petrovici M, Petta C, Pezzi RP, Piano S, Pikna M, Pillot P, Pimentel LODL, Pinazza O, Pinsky L, Pisano S, Piyarathna DB, Płoskoń M, Planinic M, Pliquett F, Pluta J, Pochybova S, Podesta-Lerma PLM, Poghosyan MG, Polichtchouk B, Poljak N, Poonsawat W, Pop A, Poppenborg H, Porteboeuf-Houssais S, Pozdniakov V, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Punin V, Putschke J, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Raniwala R, Raniwala S, Räsänen SS, Rascanu BT, Ratza V, Ravasenga I, Read KF, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Reshetin A, Revol JP, Reygers K, Riabov V, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rode SP, Rodríguez Cahuantzi M, Røed K, Rogalev R, Rogochaya E, Rohr D, Röhrich D, Rokita PS, Ronchetti F, Rosas ED, Roslon K, Rosnet P, Rossi A, Rotondi A, Roukoutakis F, Roy C, Roy P, Rueda OV, Rui R, Rumyantsev B, Rustamov A, Ryabinkin E, Ryabov Y, Rybicki A, Saarinen S, Sadhu S, Sadovsky S, Šafařík K, Saha SK, Sahoo B, Sahoo P, Sahoo R, Sahoo S, Sahu PK, Saini J, Sakai S, Saleh MA, Sambyal S, Samsonov V, Sandoval A, Sarkar A, Sarkar D, Sarkar N, Sarma P, Sas MHP, Scapparone E, Scarlassara F, Schaefer B, Scheid HS, Schiaua C, Schicker R, Schmidt C, Schmidt HR, Schmidt MO, Schmidt M, Schmidt NV, Schukraft J, Schutz Y, Schwarz K, Schweda K, Scioli G, Scomparin E, Šefčík M, Seger JE, Sekiguchi Y, Sekihata D, Selyuzhenkov I, Senyukov S, Serradilla E, Sett P, Sevcenco A, Shabanov A, Shabetai A, Shahoyan R, Shaikh W, Shangaraev A, Sharma A, Sharma A, Sharma M, Sharma N, Sheikh AI, Shigaki K, Shimomura M, Shirinkin S, Shou Q, Shtejer K, Sibiriak Y, Siddhanta S, Sielewicz KM, Siemiarczuk T, Silvermyr D, Simatovic G, Simonetti G, Singaraju R, Singh R, Singh R, Singhal V, Sinha T, Sitar B, Sitta M, Skaali TB, Slupecki M, Smirnov N, Snellings RJM, Snellman TW, Song J, Soramel F, Sorensen S, Sozzi F, Sputowska I, Stachel J, Stan I, Stankus P, Stenlund E, Stocco D, Storetvedt MM, Strmen P, Suaide AAP, Sugitate T, Suire C, Suleymanov M, Suljic M, Sultanov R, Šumbera M, Sumowidagdo S, Suzuki K, Swain S, Szabo A, Szarka I, Tabassam U, Takahashi J, Tambave GJ, Tanaka N, Tarhini M, Tariq M, Tarzila MG, Tauro A, Tejeda Muñoz G, Telesca A, Terrevoli C, Teyssier B, Thakur D, Thakur S, Thomas D, Thoresen F, Tieulent R, Tikhonov A, Timmins AR, Toia A, Topilskaya N, Toppi M, Torales-Acosta F, Torres SR, Tripathy S, Trogolo S, Trombetta G, Tropp L, Trubnikov V, Trzaska WH, Trzcinski TP, Trzeciak BA, Tsuji T, Tumkin A, Turrisi R, Tveter TS, Ullaland K, Umaka EN, Uras A, Usai GL, Utrobicic A, Vala M, Van Hoorne JW, van Leeuwen M, Vande Vyvre P, Varga D, Vargas A, Vargyas M, Varma R, Vasileiou M, Vasiliev A, Vauthier A, Vázquez Doce O, Vechernin V, Veen AM, Vercellin E, Vergara Limón S, Vermunt L, Vernet R, Vértesi R, Vickovic L, Viinikainen J, Vilakazi Z, Villalobos Baillie O, Villatoro Tello A, Vinogradov A, Virgili T, Vislavicius V, Vodopyanov A, Völkl MA, Voloshin K, Voloshin SA, Volpe G, von Haller B, Vorobyev I, Voscek D, Vranic D, Vrláková J, Wagner B, Wang H, Wang M, Watanabe Y, Weber M, Weber SG, Wegrzynek A, Weiser DF, Wenzel SC, Wessels JP, Westerhoff U, Whitehead AM, Wiechula J, Wikne J, Wilk G, Wilkinson J, Willems GA, Williams MCS, Willsher E, Windelband B, Witt WE, Xu R, Yalcin S, Yamakawa K, Yano S, Yin Z, Yokoyama H, Yoo IK, Yoon JH, Yurchenko V, Zaccolo V, Zaman A, Zampolli C, Zanoli HJC, Zardoshti N, Zarochentsev A, Závada P, Zaviyalov N, Zbroszczyk H, Zhalov M, Zhang X, Zhang Y, Zhang Z, Zhao C, Zherebchevskii V, Zhigareva N, Zhou D, Zhou Y, Zhou Z, Zhu H, Zhu J, Zhu Y, Zichichi A, Zimmermann MB, Zinovjev G, Zmeskal J, Zou S. Azimuthal Anisotropy of Heavy-Flavor Decay Electrons in p-Pb Collisions at sqrt[s_{NN}]=5.02 TeV. PHYSICAL REVIEW LETTERS 2019; 122:072301. [PMID: 30848618 DOI: 10.1103/physrevlett.122.072301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 10/16/2018] [Indexed: 06/09/2023]
Abstract
Angular correlations between heavy-flavor decay electrons and charged particles at midrapidity (|η|<0.8) are measured in p-Pb collisions at sqrt[s_{NN}]=5.02 TeV. The analysis is carried out for the 0%-20% (high) and 60%-100% (low) multiplicity ranges. The jet contribution in the correlation distribution from high-multiplicity events is removed by subtracting the distribution from low-multiplicity events. An azimuthal modulation remains after removing the jet contribution, similar to previous observations in two-particle angular correlation measurements for light-flavor hadrons. A Fourier decomposition of the modulation results in a positive second-order coefficient (v_{2}) for heavy-flavor decay electrons in the transverse momentum interval 1.5<p_{T}<4 GeV/c in high-multiplicity events, with a significance larger than 5σ. The results are compared with those of charged particles at midrapidity and those of inclusive muons at forward rapidity. The v_{2} measurement of open heavy-flavor particles at midrapidity in small collision systems could provide crucial information to help interpret the anisotropies observed in such systems.
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McLaughlin JA, Myers CJ, Zundel Z, Wilkinson N, Atallah C, Wipat A. sboljs: Bringing the Synthetic Biology Open Language to the Web Browser. ACS Synth Biol 2019; 8:191-193. [PMID: 30403869 DOI: 10.1021/acssynbio.8b00338] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The Synthetic Biology Open Language (SBOL) is a data standard for the representation of engineered biological systems. SBOL is implemented in the form of software libraries which can be used to add SBOL support to both new and existing software tools. While existing libraries allow for software to be developed that runs on a server or is installed locally, they lack the capability to create SBOL software that runs directly in a Web browser. Here, we address this issue by presenting sboljs, a JavaScript software library for SBOL that is capable of being used both on the server and in the Web browser.
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Waltemath D, Bergmann FT, Chaouiya C, Czauderna T, Gleeson P, Goble C, Golebiewski M, Hucka M, Juty N, Krebs O, Le Novère N, Mi H, Moraru II, Myers CJ, Nickerson D, Olivier BG, Rodriguez N, Schreiber F, Smith L, Zhang F, Bonnet E. Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). Stand Genomic Sci 2018; 13:17. [PMID: 30117501 PMCID: PMC6083578 DOI: 10.1186/s40793-018-0320-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
[This corrects the article DOI: 10.4056/sigs.5279417.].
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Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core. J Integr Bioinform 2018. [PMCID: PMC6167037 DOI: 10.1515/jib-2017-0080] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 1 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. No design changes have been made to the description of models between Release 1 and Release 2; changes are restricted to the format of annotations, the correction of errata and the addition of clarifications. Other materials and software are available from the SBML project website at http://sbml.org/.
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Acharya S, Adamová D, Adolfsson J, Aggarwal MM, Aglieri Rinella G, Agnello M, Agrawal N, Ahammed Z, Ahmad N, Ahn SU, Aiola S, Akindinov A, Alam SN, Alba JLB, Albuquerque DSD, Aleksandrov D, Alessandro B, Alfaro Molina R, Alici A, Alkin A, Alme J, Alt T, Altenkamper L, Altsybeev I, Alves Garcia Prado C, Andrei C, Andreou D, Andrews HA, Andronic A, Anguelov V, Anson C, Antičić T, Antinori F, Antonioli P, Anwar R, Aphecetche L, Appelshäuser H, Arcelli S, Arnaldi R, Arnold OW, Arsene IC, Arslandok M, Audurier B, Augustinus A, Averbeck R, Azmi MD, Badalà A, Baek YW, Bagnasco S, Bailhache R, Bala R, Baldisseri A, Ball M, Baral RC, Barbano AM, Barbera R, Barile F, Barioglio L, Barnaföldi GG, Barnby LS, Barret V, Bartalini P, Barth K, Bartsch E, Basile M, Bastid N, Basu S, Batigne G, Batyunya B, Batzing PC, Bearden IG, Beck H, Bedda C, Behera NK, Belikov I, Bellini F, Bello Martinez H, Bellwied R, Beltran LGE, Belyaev V, Bencedi G, Beole S, Bercuci A, Berdnikov Y, Berenyi D, Bertens RA, Berzano D, Betev L, Bhasin A, Bhat IR, Bhati AK, Bhattacharjee B, Bhom J, Bianchi L, Bianchi N, Bianchin C, Bielčík J, Bielčíková J, Bilandzic A, Biro G, Biswas R, Biswas S, Blair JT, Blau D, Blume C, Boca G, Bock F, Bogdanov A, Boldizsár L, Bombara M, Bonomi G, Bonora M, Book J, Borel H, Borissov A, Borri M, Botta E, Bourjau C, Bratrud L, Braun-Munzinger P, Bregant M, Broker TA, Broz M, Brucken EJ, Bruna E, Bruno GE, Budnikov D, Buesching H, Bufalino S, Buhler P, Buncic P, Busch O, Buthelezi Z, Butt JB, Buxton JT, Cabala J, Caffarri D, Caines H, Caliva A, Calvo Villar E, Camerini P, Capon AA, Carena F, Carena W, Carnesecchi F, Castillo Castellanos J, Castro AJ, Casula EAR, Ceballos Sanchez C, Cerello P, Chandra S, Chang B, Chapeland S, Chartier M, Charvet JL, Chattopadhyay S, Chattopadhyay S, Chauvin A, Cherney M, Cheshkov C, Cheynis B, Chibante Barroso V, Chinellato DD, Cho S, Chochula P, Choi K, Chojnacki M, Choudhury S, Chowdhury T, Christakoglou P, Christensen CH, Christiansen P, Chujo T, Chung SU, Cicalo C, Cifarelli L, Cindolo F, Cleymans J, Colamaria F, Colella D, Collu A, Colocci M, Concas M, Conesa Balbastre G, Conesa Del Valle Z, Connors ME, Contreras JG, Cormier TM, Corrales Morales Y, Cortés Maldonado I, Cortese P, Cosentino MR, Costa F, Costanza S, Crkovská J, Crochet P, Cuautle E, Cunqueiro L, Dahms T, Dainese A, Danisch MC, Danu A, Das D, Das I, Das S, Dash A, Dash S, De S, De Caro A, de Cataldo G, de Conti C, de Cuveland J, De Falco A, De Gruttola D, De Marco N, De Pasquale S, De Souza RD, Degenhardt HF, Deisting A, Deloff A, Deplano C, Dhankher P, Di Bari D, Di Mauro A, Di Nezza P, Di Ruzza B, Diaz Corchero MA, Dietel T, Dillenseger P, Divià R, Djuvsland Ø, Dobrin A, Domenicis Gimenez D, Dönigus B, Dordic O, Doremalen LVV, Dubey AK, Dubla A, Ducroux L, Duggal AK, Dupieux P, Ehlers RJ, Elia D, Endress E, Engel H, Epple E, Erazmus B, Erhardt F, Espagnon B, Esumi S, Eulisse G, Eum J, Evans D, Evdokimov S, Fabbietti L, Faivre J, Fantoni A, Fasel M, Feldkamp L, Feliciello A, Feofilov G, Ferencei J, Fernández Téllez A, Ferreiro EG, Ferretti A, Festanti A, Feuillard VJG, Figiel J, Figueredo MAS, Filchagin S, Finogeev D, Fionda FM, Fiore EM, Floris M, Foertsch S, Foka P, Fokin S, Fragiacomo E, Francescon A, Francisco A, Frankenfeld U, Fronze GG, Fuchs U, Furget C, Furs A, Fusco Girard M, Gaardhøje JJ, Gagliardi M, Gago AM, Gajdosova K, Gallio M, Galvan CD, Ganoti P, Gao C, Garabatos C, Garcia-Solis E, Garg K, Gargiulo C, Gasik P, Gauger EF, Gay Ducati MB, Germain M, Ghosh J, Ghosh P, Ghosh SK, Gianotti P, Giubellino P, Giubilato P, Gladysz-Dziadus E, Glässel P, Goméz Coral DM, Gomez Ramirez A, Gonzalez AS, Gonzalez V, González-Zamora P, Gorbunov S, Görlich L, Gotovac S, Grabski V, Graczykowski LK, Graham KL, Greiner L, Grelli A, Grigoras C, Grigoriev V, Grigoryan A, Grigoryan S, Grion N, Gronefeld JM, Grosa F, Grosse-Oetringhaus JF, Grosso R, Gruber L, Guber F, Guernane R, Guerzoni B, Gulbrandsen K, Gunji T, Gupta A, Gupta R, Guzman IB, Haake R, Hadjidakis C, Hamagaki H, Hamar G, Hamon JC, Haque MR, Harris JW, Harton A, Hassan H, Hatzifotiadou D, Hayashi S, Heckel ST, Hellbär E, Helstrup H, Herghelegiu A, Herrera Corral G, Herrmann F, Hess BA, Hetland KF, Hillemanns H, Hills C, Hippolyte B, Hladky J, Hohlweger B, Horak D, Hornung S, Hosokawa R, Hristov P, Hughes C, Humanic TJ, Hussain N, Hussain T, Hutter D, Hwang DS, Iga Buitron SA, Ilkaev R, Inaba M, Ippolitov M, Irfan M, Isakov V, Ivanov M, Ivanov V, Izucheev V, Jacak B, Jacazio N, Jacobs PM, Jadhav MB, Jadlovsky J, Jaelani S, Jahnke C, Jakubowska MJ, Janik MA, Jayarathna PHSY, Jena C, Jena S, Jercic M, Jimenez Bustamante RT, Jones PG, Jusko A, Kalinak P, Kalweit A, Kang JH, Kaplin V, Kar S, Karasu Uysal A, Karavichev O, Karavicheva T, Karayan L, Karczmarczyk P, Karpechev E, Kebschull U, Keidel R, Keijdener DLD, Keil M, Ketzer B, Khabanova Z, Khan P, Khan SA, Khanzadeev A, Kharlov Y, Khatun A, Khuntia A, Kielbowicz MM, Kileng B, Kim B, Kim D, Kim DJ, Kim H, Kim JS, Kim J, Kim M, Kim M, Kim S, Kim T, Kirsch S, Kisel I, Kiselev S, Kisiel A, Kiss G, Klay JL, Klein C, Klein J, Klein-Bösing C, Klewin S, Kluge A, Knichel ML, Knospe AG, Kobdaj C, Kofarago M, Kollegger T, Kolojvari A, Kondratiev V, Kondratyeva N, Kondratyuk E, Konevskikh A, Konyushikhin M, Kopcik M, Kour M, Kouzinopoulos C, Kovalenko O, Kovalenko V, Kowalski M, Koyithatta Meethaleveedu G, Králik I, Kravčáková A, Krivda M, Krizek F, Kryshen E, Krzewicki M, Kubera AM, Kučera V, Kuhn C, Kuijer PG, Kumar A, Kumar J, Kumar L, Kumar S, Kundu S, Kurashvili P, Kurepin A, Kurepin AB, Kuryakin A, Kushpil S, Kweon MJ, Kwon Y, La Pointe SL, La Rocca P, Lagana Fernandes C, Lai YS, Lakomov I, Langoy R, Lapidus K, Lara C, Lardeux A, Lattuca A, Laudi E, Lavicka R, Lazaridis L, Lea R, Leardini L, Lee S, Lehas F, Lehner S, Lehrbach J, Lemmon RC, Lenti V, Leogrande E, León Monzón I, Lévai P, Li S, Li X, Lien J, Lietava R, Lim B, Lindal S, Lindenstruth V, Lindsay SW, Lippmann C, Lisa MA, Litichevskyi V, Ljunggren HM, Llope WJ, Lodato DF, Loenne PI, Loginov V, Loizides C, Loncar P, Lopez X, López Torres E, Lowe A, Luettig P, Luhder JR, Lunardon M, Luparello G, Lupi M, Lutz TH, Maevskaya A, Mager M, Mahajan S, Mahmood SM, Maire A, Majka RD, Malaev M, Malinina L, Mal'Kevich D, Malzacher P, Mamonov A, Manko V, Manso F, Manzari V, Mao Y, Marchisone M, Mareš J, Margagliotti GV, Margotti A, Margutti J, Marín A, Markert C, Marquard M, Martin NA, Martinengo P, Martinez JAL, Martínez MI, Martínez García G, Martinez Pedreira M, Mas A, Masciocchi S, Masera M, Masoni A, Masson E, Mastroserio A, Mathis AM, Matyja A, Mayer C, Mazer J, Mazzilli M, Mazzoni MA, Meddi F, Melikyan Y, Menchaca-Rocha A, Meninno E, Mercado Pérez J, Meres M, Mhlanga S, Miake Y, Mieskolainen MM, Mihaylov D, Mihaylov DL, Mikhaylov K, Milano L, Milosevic J, Mischke A, Mishra AN, Miśkowiec D, Mitra J, Mitu CM, Mohammadi N, Mohanty B, Mohisin Khan M, Montes E, Moreira De Godoy DA, Moreno LAP, Moretto S, Morreale A, Morsch A, Muccifora V, Mudnic E, Mühlheim D, Muhuri S, Mukherjee M, Mulligan JD, Munhoz MG, Münning K, Munzer RH, Murakami H, Murray S, Musa L, Musinsky J, Myers CJ, Myrcha JW, Naik B, Nair R, Nandi BK, Nania R, Nappi E, Narayan A, Naru MU, Natal da Luz H, Nattrass C, Navarro SR, Nayak K, Nayak R, Nayak TK, Nazarenko S, Nedosekin A, Negrao De Oliveira RA, Nellen L, Nesbo SV, Ng F, Nicassio M, Niculescu M, Niedziela J, Nielsen BS, Nikolaev S, Nikulin S, Nikulin V, Nobuhiro A, Noferini F, Nomokonov P, Nooren G, Noris JCC, Norman J, Nyanin A, Nystrand J, Oeschler H, Oh S, Ohlson A, Okubo T, Olah L, Oleniacz J, Oliveira Da Silva AC, Oliver MH, Onderwaater J, Oppedisano C, Orava R, Oravec M, Ortiz Velasquez A, Oskarsson A, Otwinowski J, Oyama K, Pachmayer Y, Pacik V, Pagano D, Pagano P, Paić G, Palni P, Pan J, Pandey AK, Panebianco S, Papikyan V, Pappalardo GS, Pareek P, Park J, Parmar S, Passfeld A, Pathak SP, Paticchio V, Patra RN, Paul B, Pei H, Peitzmann T, Peng X, Pereira LG, Pereira Da Costa H, Peresunko D, Perez Lezama E, Peskov V, Pestov Y, Petráček V, Petrov V, Petrovici M, Petta C, Pezzi RP, Piano S, Pikna M, Pillot P, Pimentel LODL, Pinazza O, Pinsky L, Piyarathna DB, Płoskoń M, Planinic M, Pliquett F, Pluta J, Pochybova S, Podesta-Lerma PLM, Poghosyan MG, Polichtchouk B, Poljak N, Poonsawat W, Pop A, Poppenborg H, Porteboeuf-Houssais S, Porter J, Pozdniakov V, Prasad SK, Preghenella R, Prino F, Pruneau CA, Pshenichnov I, Puccio M, Puddu G, Pujahari P, Punin V, Putschke J, Rachevski A, Raha S, Rajput S, Rak J, Rakotozafindrabe A, Ramello L, Rami F, Rana DB, Raniwala R, Raniwala S, Räsänen SS, Rascanu BT, Rathee D, Ratza V, Ravasenga I, Read KF, Redlich K, Rehman A, Reichelt P, Reidt F, Ren X, Renfordt R, Reolon AR, Reshetin A, Reygers K, Riabov V, Ricci RA, Richert T, Richter M, Riedler P, Riegler W, Riggi F, Ristea C, Rodríguez Cahuantzi M, Røed K, Rogochaya E, Rohr D, Röhrich D, Rokita PS, Ronchetti F, Rosas ED, Rosnet P, Rossi A, Rotondi A, Roukoutakis F, Roy A, Roy 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D-Meson Azimuthal Anisotropy in Midcentral Pb-Pb Collisions at sqrt[s]_{NN}=5.02 TeV. PHYSICAL REVIEW LETTERS 2018; 120:102301. [PMID: 29570314 DOI: 10.1103/physrevlett.120.102301] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Revised: 11/16/2017] [Indexed: 06/08/2023]
Abstract
The azimuthal anisotropy coefficient v_{2} of prompt D^{0}, D^{+}, D^{*+}, and D_{s}^{+} mesons was measured in midcentral (30%-50% centrality class) Pb-Pb collisions at a center-of-mass energy per nucleon pair sqrt[s_{NN}]=5.02 TeV, with the ALICE detector at the LHC. The D mesons were reconstructed via their hadronic decays at midrapidity, |y|<0.8, in the transverse momentum interval 1<p_{T}<24 GeV/c. The measured D-meson v_{2} has similar values as that of charged pions. The D_{s}^{+} v_{2}, measured for the first time, is found to be compatible with that of nonstrange D mesons. The measurements are compared with theoretical calculations of charm-quark transport in a hydrodynamically expanding medium and have the potential to constrain medium parameters.
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Hucka M, Bergmann FT, Dräger A, Hoops S, Keating SM, Le Novère N, Myers CJ, Olivier BG, Sahle S, Schaff JC, Smith LP, Waltemath D, Wilkinson DJ. The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core. J Integr Bioinform 2018. [PMID: 29522418 PMCID: PMC6167032 DOI: 10.1515/jib-2017-0081] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML, their encoding in XML (the eXtensible Markup Language), validation rules that determine the validity of an SBML document, and examples of models in SBML form. The design of Version 2 differs from Version 1 principally in allowing new MathML constructs, making more child elements optional, and adding identifiers to all SBML elements instead of only selected elements. Other materials and software are available from the SBML project website at http://sbml.org/.
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