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  1. Article ; Online: Measurement of the Ratios of Branching Fractions R(D^{*}) and R(D^{0}).

    Aaij, R / Abdelmotteleb, A S W / Abellan Beteta, C / Abudinén, F / Ackernley, T / Adeva, B / Adinolfi, M / Adlarson, P / Afsharnia, H / Agapopoulou, C / Aidala, C A / Ajaltouni, Z / Akar, S / Akiba, K / Albicocco, P / Albrecht, J / Alessio, F / Alexander, M / Alfonso Albero, A /
    Aliouche, Z / Alvarez Cartelle, P / Amalric, R / Amato, S / Amey, J L / Amhis, Y / An, L / Anderlini, L / Andersson, M / Andreianov, A / Andreotti, M / Andreou, D / Ao, D / Archilli, F / Artamonov, A / Artuso, M / Aslanides, E / Atzeni, M / Audurier, B / Bachiller Perea, I B / Bachmann, S / Bachmayer, M / Back, J J / Bailly-Reyre, A / Baladron Rodriguez, P / Balagura, V / Baldini, W / Baptista de Souza Leite, J / Barbetti, M / Barlow, R J / Barsuk, S / Barter, W / Bartolini, M / Baryshnikov, F / Basels, J M / Bassi, G / Batsukh, B / Battig, A / Bay, A / Beck, A / Becker, M / Bedeschi, F / Bediaga, I B / Beiter, A / Belin, S / Bellee, V / Belous, K / Belov, I / Belyaev, I / Benane, G / Bencivenni, G / Ben-Haim, E / Berezhnoy, A / Bernet, R / Bernet Andres, S / Berninghoff, D / Bernstein, H C / Bertella, C / Bertolin, A / Betancourt, C / Betti, F / Bezshyiko, Ia / Bhasin, S / Bhom, J / Bian, L / Bieker, M S / Biesuz, N V / Billoir, P / Biolchini, A / Birch, M / Bishop, F C R / Bitadze, A / Bizzeti, A / Blago, M P / Blake, T / Blanc, F / Blank, J E / Blusk, S / Bobulska, D / Boelhauve, J A / Boente Garcia, O / Boettcher, T / Boldyrev, A / Bolognani, C S / Bolzonella, R / Bondar, N / Borgato, F / Borghi, S / Borsato, M / Borsuk, J T / Bouchiba, S A / Bowcock, T J V / Boyer, A / Bozzi, C / Bradley, M J / Braun, S / Brea Rodriguez, A / Brodzicka, J / Brossa Gonzalo, A / Brown, J / Brundu, D / Buonaura, A / Buonincontri, L / Burke, A T / Burr, C / Bursche, A / Butkevich, A / Butter, J S / Buytaert, J / Byczynski, W / Cadeddu, S / Cai, H / Calabrese, R / Calefice, L / Cali, S / Calvi, M / Calvo Gomez, M / Campana, P / Campora Perez, D H / Campoverde Quezada, A F / Capelli, S / Capriotti, L / Carbone, A / Cardinale, R / Cardini, A / Carniti, P / Carus, L / Casais Vidal, A / Caspary, R / Casse, G / Cattaneo, M / Cavallero, G / Cavallini, V / Celani, S / Cerasoli, J / Cervenkov, D / Chadwick, A J / Chahrour, I / Chapman, M G / Charles, M / Charpentier, Ph / Chavez Barajas, C A / Chefdeville, M / Chen, C / Chen, S / Chernov, A / Chernyshenko, S / Chobanova, V / Cholak, S / Chrzaszcz, M / Chubykin, A / Chulikov, V / Ciambrone, P / Cicala, M F / Cid Vidal, X / Ciezarek, G / Cifra, P / Ciullo, G / Clarke, P E L / Clemencic, M / Cliff, H V / Closier, J / Cobbledick, J L / Coco, V / Coelho, J A B / Cogan, J / Cogneras, E / Cojocariu, L / Collins, P / Colombo, T / Congedo, L / Contu, A / Cooke, N / Corredoira, I / Corti, G / Couturier, B / Craik, D C / Cruz Torres, M / Currie, R / Da Silva, C L / Dadabaev, S / Dai, L / Dai, X / Dall'Occo, E / Dalseno, J / D'Ambrosio, C / Daniel, J / Danilina, A / d'Argent, P / Davies, J E / Davis, A / De Aguiar Francisco, O / de Boer, J / De Bruyn, K / De Capua, S / De Cian, M / De Freitas Carneiro Da Graca, U / De Lucia, E / De Miranda, J M / De Paula, L / De Serio, M / De Simone, D / De Simone, P / De Vellis, F / de Vries, J A / Dean, C T / Debernardis, F / Decamp, D / Dedu, V / Del Buono, L / Delaney, B / Dembinski, H-P / Denysenko, V / Deschamps, O / Dettori, F / Dey, B / Di Nezza, P / Diachkov, I / Didenko, S / Dieste Maronas, L / Ding, S / Dobishuk, V / Dolmatov, A / Dong, C / Donohoe, A M / Dordei, F / Dos Reis, A C / Douglas, L / Downes, A G / Duda, P / Dudek, M W / Dufour, L / Duk, V / Durante, P / Duras, M M / Durham, J M / Dutta, D / Dziurda, A / Dzyuba, A / Easo, S / Egede, U / Egorychev, V / Eirea Orro, C / Eisenhardt, S / Ejopu, E / Ek-In, S / Eklund, L / Elashri, M E / Ellbracht, J / Ely, S / Ene, A / Epple, E / Escher, S / Eschle, J / Esen, S / Evans, T / Fabiano, F / Falcao, L N / Fan, Y / Fang, B / Fantini, L / Faria, M / Farry, S / Fazzini, D / Felkowski, L F / Feo, M / Fernandez Gomez, M / Fernez, A D / Ferrari, F / Ferreira Lopes, L / Ferreira Rodrigues, F / Ferreres Sole, S / Ferrillo, M / Ferro-Luzzi, M / Filippov, S / Fini, R A / Fiorini, M / Firlej, M / Fischer, K M / Fitzgerald, D S / Fitzpatrick, C / Fiutowski, T / Fleuret, F / Fontana, M / Fontanelli, F / Forty, R / Foulds-Holt, D / Franco Lima, V / Franco Sevilla, M / Frank, M / Franzoso, E / Frau, G / Frei, C / Friday, D A / Frontini, L / Fu, J / Fuehring, Q / Fulghesu, T / Gabriel, E / Galati, G / Galati, M D / Gallas Torreira, A / Galli, D / Gambetta, S / Gandelman, M / Gandini, P / Gao, Y / Garau, M / Garcia Martin, L M / Garcia Moreno, P / García Pardiñas, J / Garcia Plana, B / Garcia Rosales, F A / Garrido, L / Gaspar, C / Geertsema, R E / Gerick, D / Gerken, L L / Gersabeck, E / Gersabeck, M / Gershon, T / Giambastiani, L / Gibson, V / Giemza, H K / Gilman, A L / Giovannetti, M / Gioventù, A / Gironella Gironell, P / Giugliano, C / Giza, M A / Gizdov, K / Gkougkousis, E L / Gligorov, V V / Göbel, C / Golobardes, E / Golubkov, D / Golutvin, A / Gomes, A / Gomez Fernandez, S / Goncalves Abrantes, F / Goncerz, M / Gong, G / Gorelov, I V / Gotti, C / Grabowski, J P / Grammatico, T / Granado Cardoso, L A / Graugés, E / Graverini, E / Graziani, G / Grecu, A T / Greeven, L M / Grieser, N A / Grillo, L / Gromov, S / Gruberg Cazon, B R / Gu, C / Guarise, M / Guittiere, M / Günther, P A / Gushchin, E / Guth, A / Guz, Y / Gys, T / Hadavizadeh, T / Hadjivasiliou, C / Haefeli, G / Haen, C / Haimberger, J / Haines, S C / Halewood-Leagas, T / Halvorsen, M M / Hamilton, P M / Hammerich, J / Han, Q / Han, X / Hansen, E B / Hansmann-Menzemer, S / Hao, L / Harnew, N / Harrison, T / Hasse, C / Hatch, M / He, J / Heijhoff, K / Hemmer, F H / Henderson, C / Henderson, R D L / Hennequin, A M / Hennessy, K / Henry, L / Herd, J / Heuel, J / Hicheur, A / Hill, D / Hilton, M / Hollitt, S E / Horswill, J / Hou, R / Hou, Y / Hu, J / Hu, W / Hu, X / Huang, W / Huang, X / Hulsbergen, W / Hunter, R J / Hushchyn, M / Hutchcroft, D / Ibis, P / Idzik, M / Ilin, D / Ilten, P / Inglessi, A / Iniukhin, A / Ishteev, A / Ivshin, K / Jacobsson, R / Jage, H / Jaimes Elles, S J / Jakobsen, S / Jans, E / Jashal, B K / Jawahery, A / Jevtic, V / Jiang, E / Jiang, X / Jiang, Y / John, M / Johnson, D / Jones, C R / Jones, T P / Jost, B / Jurik, N / Juszczak, I / Kandybei, S / Kang, Y / Karacson, M / Karpenkov, D / Karpov, M / Kautz, J W / Keizer, F / Keller, D M / Kenzie, M / Ketel, T / Khanji, B / Kharisova, A / Kholodenko, S / Khreich, G / Kirn, T / Kirsebom, V S / Kitouni, O / Klaver, S / Kleijne, N / Klimaszewski, K / Kmiec, M R / Koliiev, S / Kolk, L / Kondybayeva, A / Konoplyannikov, A / Kopciewicz, P / Kopecna, R / Koppenburg, P / Korolev, M / Kostiuk, I / Kot, O / Kotriakhova, S / Kozachuk, A / Kravchenko, P / Kravchuk, L / Krawczyk, R D / Kreps, M / Kretzschmar, S / Krokovny, P / Krupa, W / Krzemien, W / Kubat, J / Kubis, S / Kucewicz, W / Kucharczyk, M / Kudryavtsev, V / Kulikova, E K / Kupsc, A / Lacarrere, D / Lafferty, G / Lai, A / Lampis, A / Lancierini, D / Landesa Gomez, C / Lane, J J / Lane, R / Langenbruch, C / Langer, J / Lantwin, O / Latham, T / Lazzari, F / Lazzaroni, M / Le Gac, R / Lee, S H / Lefèvre, R / Leflat, A / Legotin, S / Lenisa, P / Leroy, O / Lesiak, T / Leverington, B / Li, A / Li, H / Li, K / Li, P / Li, P-R / Li, S / Li, T / Li, Y / Li, Z / Liang, X / Lin, C / Lin, T / Lindner, R / Lisovskyi, V / Litvinov, R / Liu, G / Liu, H / Liu, Q / Liu, S / Lobo Salvia, A / Loi, A / Lollini, R / Lomba Castro, J / Longstaff, I / Lopes, J H / Lopez Huertas, A / López Soliño, S / Lovell, G H / Lu, Y / Lucarelli, C / Lucchesi, D / Luchuk, S / Lucio Martinez, M / Lukashenko, V / Luo, Y / Lupato, A / Luppi, E / Lusiani, A / Lynch, K / Lyu, X-R / Ma, R / Maccolini, S / Machefert, F / Maciuc, F / Mackay, I / Macko, V / Madhan Mohan, L R / Maevskiy, A / Maisuzenko, D / Majewski, M W / Malczewski, J J / Malde, S / Malecki, B / Malinin, A / Maltsev, T / Manca, G / Mancinelli, G / Mancuso, C / Manera Escalero, R / Manuzzi, D / Manzari, C A / Marangotto, D / Marchand, J F / Marconi, U / Mariani, S / Marin Benito, C / Marks, J / Marshall, A M / Marshall, P J / Martelli, G / Martellotti, G / Martinazzoli, L / Martinelli, M / Martinez Santos, D / Martinez Vidal, F / Massafferri, A / Materok, M / Matev, R / Mathad, A / Matiunin, V / Matteuzzi, C / Mattioli, K R / Mauri, A / Maurice, E / Mauricio, J / Mazurek, M / McCann, M / Mcconnell, L / McGrath, T H / McHugh, N T / McNab, A / McNulty, R / Mead, J V / Meadows, B / Meier, G / Melnychuk, D / Meloni, S / Merk, M / Merli, A / Meyer Garcia, L / Miao, D / Mikhasenko, M / Milanes, D A / Millard, E / Milovanovic, M / Minard, M-N / Minotti, A / Miralles, T / Mitchell, S E / Mitreska, B / Mitzel, D S / Mödden, A / Mohammed, R A / Moise, R D / Mokhnenko, S / Mombächer, T / Monk, M / Monroy, I A / Monteil, S / Morello, G / Morello, M J / Morgenthaler, M P / Moron, J / Morris, A B / Morris, A G / Mountain, R / Mu, H / Muhammad, E / Muheim, F / Mulder, M / Müller, K / Murphy, C H / Murray, D / Murta, R / Muzzetto, P / Naik, P / Nakada, T / Nandakumar, R / Nanut, T / Nasteva, I / Needham, M / Neri, N / Neubert, S / Neufeld, N / Neustroev, P / Newcombe, R / Nicolini, J / Nicotra, D / Niel, E M / Nieswand, S / Nikitin, N / Nolte, N S / Normand, C / Novoa Fernandez, J / Nowak, G N / Nunez, C / Oblakowska-Mucha, A / Obraztsov, V / Oeser, T / Okamura, S / Oldeman, R / Oliva, F / Onderwater, C J G / O'Neil, R H / Otalora Goicochea, J M / Ovsiannikova, T / Owen, P / Oyanguren, A / Ozcelik, O / Padeken, K O / Pagare, B / Pais, P R / Pajero, T / Palano, A / Palutan, M / Pan, Y / Panshin, G / Paolucci, L / Papanestis, A / Pappagallo, M / Pappalardo, L L / Pappenheimer, C / Parker, W / Parkes, C / Passalacqua, B / Passaleva, G / Pastore, A / Patel, M / Patrignani, C / Pawley, C J / Pellegrino, A / Pepe Altarelli, M / Perazzini, S / Pereima, D / Pereiro Castro, A / Perret, P / Petridis, K / Petrolini, A / Petrov, A / Petrucci, S / Petruzzo, M / Pham, H / Philippov, A / Piandani, R / Pica, L / Piccini, M / Pietrzyk, B / Pietrzyk, G / Pili, M / Pinci, D / Pisani, F / Pizzichemi, M / Placinta, V / Plews, J / Plo Casasus, M / Polci, F / Poli Lener, M / Poluektov, A / Polukhina, N / Polyakov, I / Polycarpo, E / Ponce, S / Popov, D / Poslavskii, S / Prasanth, K / Promberger, L / Prouve, C / Pugatch, V / Puill, V / Punzi, G / Qi, H R / Qian, W / Qin, N / Qu, S / Quagliani, R / Raab, N V / Rachwal, B / Rademacker, J H / Rajagopalan, R / Rama, M / Ramos Pernas, M / Rangel, M S / Ratnikov, F / Raven, G / Rebollo De Miguel, M / Redi, F / Reich, J / Reiss, F / Remon Alepuz, C / Ren, Z / Resmi, P K / Ribatti, R / Ricci, A M / Ricciardi, S / Richardson, K / Richardson-Slipper, M / Rinnert, K / Robbe, P / Robertson, G / Rodrigues, A B / Rodrigues, E / Rodriguez Fernandez, E / Rodriguez Lopez, J A / Rodriguez Rodriguez, E / Rolf, D L / Rollings, A / Roloff, P / Romanovskiy, V / Romero Lamas, M / Romero Vidal, A / Roth, J D / Rotondo, M / Rudolph, M S / Ruf, T / Ruiz Fernandez, R A / Ruiz Vidal, J / Ryzhikov, A / Ryzka, J / Saborido Silva, J J / Sagidova, N / Sahoo, N / Saitta, B / Salomoni, M / Sanchez Gras, C / Sanderswood, I / Santacesaria, R / Santamarina Rios, C / Santimaria, M / Santovetti, E / Saranin, D / Sarpis, G / Sarpis, M / Sarti, A / Satriano, C / Satta, A / Saur, M / Savrina, D / Sazak, H / Scantlebury Smead, L G / Scarabotto, A / Schael, S / Scherl, S / Schiller, M / Schindler, H / Schmelling, M / Schmidt, B / Schmitt, S / Schneider, O / Schopper, A / Schubiger, M / Schulte, S / Schune, M H / Schwemmer, R / Sciascia, B / Sciuccati, A / Sellam, S / Semennikov, A / Senghi Soares, M / Sergi, A / Serra, N / Sestini, L / Seuthe, A / Shang, Y / Shangase, D M / Shapkin, M / Shchemerov, I / Shchutska, L / Shears, T / Shekhtman, L / Shen, Z / Sheng, S / Shevchenko, V / Shi, B / Shields, E B / Shimizu, Y / Shmanin, E / Shorkin, R / Shupperd, J D / Siddi, B G / Silva Coutinho, R / Simi, G / Simone, S / Singla, M / Skidmore, N / Skuza, R / Skwarnicki, T / Slater, M W / Smallwood, J C / Smeaton, J G / Smith, E / Smith, K / Smith, M / Snoch, A / Soares Lavra, L / Sokoloff, M D / Soler, F J P / Solomin, A / Solovev, A / Solovyev, I / Song, R / Souza De Almeida, F L / Souza De Paula, B / Spaan, B / Spadaro Norella, E / Spedicato, E / Spiridenkov, E / Spradlin, P / Sriskaran, V / Stagni, F / Stahl, M / Stahl, S / Stanislaus, S / Stein, E N / Steinkamp, O / Stenyakin, O / Stevens, H / Stone, S / Strekalina, D / Su, Y S / Suljik, F / Sun, J / Sun, L / Sun, Y / Svihra, P / Swallow, P N / Swientek, K / Szabelski, A / Szumlak, T / Szymanski, M / Tan, Y / Taneja, S / Tat, M D / Terentev, A / Teubert, F / Thomas, E / Thompson, D J D / Thomson, K A / Tilquin, H / Tisserand, V / T'Jampens, S / Tobin, M / Tomassetti, L / Tonani, G / Tong, X / Torres Machado, D / Tou, D Y / Trilov, S M / Trippl, C / Tuci, G / Tuning, N / Ukleja, A / Unverzagt, D J / Usachov, A / Ustyuzhanin, A / Uwer, U / Vagner, A / Vagnoni, V / Valassi, A / Valenti, G / Valls Canudas, N / Van Dijk, M / Van Hecke, H / van Herwijnen, E / Van Hulse, C B / van Veghel, M / Vazquez Gomez, R / Vazquez Regueiro, P / Vázquez Sierra, C / Vecchi, S / Velthuis, J J / Veltri, M / Venkateswaran, A / Veronesi, M / Vesterinen, M / Vieira, D / Vieites Diaz, M / Vilasis-Cardona, X / Vilella Figueras, E / Villa, A / Vincent, P / Volle, F C / Vom Bruch, D / Vorobyev, A / Vorobyev, V / Voropaev, N / Vos, K / Vrahas, C / Walsh, J / Walton, E J / Wan, G / Wang, C / Wang, G / Wang, J / Wang, M / Wang, R / Wang, X / Wang, Y / Wang, Z / Ward, J A / Watson, N K / Websdale, D / Wei, Y / Westhenry, B D C / White, D J / Whitehead, M / Wiederhold, A R / Wiedner, D / Wilkinson, G / Wilkinson, M K / Williams, I / Williams, M / Williams, M R J / Williams, R / Wilson, F F / Wislicki, W / Witek, M / Witola, L / Wong, C P / Wormser, G / Wotton, S A / Wu, H / Wu, J / Wyllie, K / Xiang, Z / Xie, Y / Xu, A / Xu, J / Xu, L / Xu, M / Xu, Q / Xu, Z / Yang, D / Yang, S / Yang, X / Yang, Y / Yang, Z / Yeomans, L E / Yeroshenko, V / Yeung, H / Yin, H / Yu, J / Yuan, X / Zaffaroni, E / Zavertyaev, M / Zdybal, M / Zeng, M / Zhang, C / Zhang, D / Zhang, L / Zhang, S / Zhang, Y / Zhao, Y / Zharkova, A / Zhelezov, A / Zheng, Y / Zhou, T / Zhou, X / Zhou, Y / Zhovkovska, V / Zhu, X / Zhu, Z / Zhukov, V / Zou, Q / Zucchelli, S / Zuliani, D / Zunica, G

    Physical review letters

    2023  Volume 131, Issue 11, Page(s) 111802

    Abstract: The ratios of branching fractions R(D^{*})≡B(B[over ¯]→D^{*}τ^{-}ν[over ¯]_{τ})/B(B[over ¯]→D^{*}μ^ ... ν[over ¯]_{μ}) and R(D^{0})≡B(B^{-}→D^{0}τ^{-}ν[over ¯]_{τ})/B(B^{-}→D^{0}μ^{-}ν[over ¯]_{μ}) are ... is identified in the decay mode τ^{-}→μ^{-}ν_{τ}ν[over ¯]_{μ}. The measured values are R(D^{*})=0 ...

    Abstract The ratios of branching fractions R(D^{*})≡B(B[over ¯]→D^{*}τ^{-}ν[over ¯]_{τ})/B(B[over ¯]→D^{*}μ^{-}ν[over ¯]_{μ}) and R(D^{0})≡B(B^{-}→D^{0}τ^{-}ν[over ¯]_{τ})/B(B^{-}→D^{0}μ^{-}ν[over ¯]_{μ}) are measured, assuming isospin symmetry, using a sample of proton-proton collision data corresponding to 3.0  fb^{-1} of integrated luminosity recorded by the LHCb experiment during 2011 and 2012. The tau lepton is identified in the decay mode τ^{-}→μ^{-}ν_{τ}ν[over ¯]_{μ}. The measured values are R(D^{*})=0.281±0.018±0.024 and R(D^{0})=0.441±0.060±0.066, where the first uncertainty is statistical and the second is systematic. The correlation between these measurements is ρ=-0.43. The results are consistent with the current average of these quantities and are at a combined 1.9 standard deviations from the predictions based on lepton flavor universality in the standard model.
    Language English
    Publishing date 2023-09-29
    Publishing country United States
    Document type Journal Article
    ZDB-ID 208853-8
    ISSN 1079-7114 ; 0031-9007
    ISSN (online) 1079-7114
    ISSN 0031-9007
    DOI 10.1103/PhysRevLett.131.111802
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: rWCVP: a companion R package for the World Checklist of Vascular Plants.

    Brown, Matilda J M / Walker, Barnaby E / Black, Nicholas / Govaerts, Rafaël H A / Ondo, Ian / Turner, Robert / Nic Lughadha, Eimear

    The New phytologist

    2023  Volume 240, Issue 4, Page(s) 1355–1365

    Abstract: ... we present rWCVP, an open-source R package that aims to facilitate the use of the WCVP by providing clear ...

    Abstract The World Checklist of Vascular Plants (WCVP) is an extremely valuable resource that is being used to address many fundamental and applied questions in plant science, conservation, ecology and evolution. However, databases of this size require data manipulation skills that pose a barrier to many potential users. Here, we present rWCVP, an open-source R package that aims to facilitate the use of the WCVP by providing clear, intuitive functions to execute many common tasks. These functions include taxonomic name reconciliation, geospatial integration, mapping and generation of multiple different summaries of the WCVP in both data and report format. We have included extensive documentation and tutorials, providing step-by-step guides that are accessible even to users with minimal programming experience. rWCVP is available on cran and GitHub.
    MeSH term(s) Software ; Checklist ; Tracheophyta ; Plants ; Databases, Factual
    Language English
    Publishing date 2023-05-11
    Publishing country England
    Document type Journal Article
    ZDB-ID 208885-x
    ISSN 1469-8137 ; 0028-646X
    ISSN (online) 1469-8137
    ISSN 0028-646X
    DOI 10.1111/nph.18919
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  3. Article ; Online: APOBEC3B regulates R-loops and promotes transcription-associated mutagenesis in cancer.

    McCann, Jennifer L / Cristini, Agnese / Law, Emily K / Lee, Seo Yun / Tellier, Michael / Carpenter, Michael A / Beghè, Chiara / Kim, Jae Jin / Sanchez, Anthony / Jarvis, Matthew C / Stefanovska, Bojana / Temiz, Nuri A / Bergstrom, Erik N / Salamango, Daniel J / Brown, Margaret R / Murphy, Shona / Alexandrov, Ludmil B / Miller, Kyle M / Gromak, Natalia /
    Harris, Reuben S

    Nature genetics

    2023  Volume 55, Issue 10, Page(s) 1721–1734

    Abstract: ... interactions with a surprising number of R-loop factors. Biochemical experiments show APOBEC3B binding to R ... loops in cells and in vitro. Genetic experiments demonstrate R-loop increases in cells lacking APOBEC3B ... landscape of physiological and stimulus-induced R-loops with thousands of differentially altered regions ...

    Abstract The single-stranded DNA cytosine-to-uracil deaminase APOBEC3B is an antiviral protein implicated in cancer. However, its substrates in cells are not fully delineated. Here APOBEC3B proteomics reveal interactions with a surprising number of R-loop factors. Biochemical experiments show APOBEC3B binding to R-loops in cells and in vitro. Genetic experiments demonstrate R-loop increases in cells lacking APOBEC3B and decreases in cells overexpressing APOBEC3B. Genome-wide analyses show major changes in the overall landscape of physiological and stimulus-induced R-loops with thousands of differentially altered regions, as well as binding of APOBEC3B to many of these sites. APOBEC3 mutagenesis impacts genes overexpressed in tumors and splice factor mutant tumors preferentially, and APOBEC3-attributed kataegis are enriched in RTCW motifs consistent with APOBEC3B deamination. Taken together with the fact that APOBEC3B binds single-stranded DNA and RNA and preferentially deaminates DNA, these results support a mechanism in which APOBEC3B regulates R-loops and contributes to R-loop mutagenesis in cancer.
    MeSH term(s) Humans ; R-Loop Structures ; DNA, Single-Stranded/genetics ; Genome-Wide Association Study ; Mutagenesis ; Neoplasms/genetics ; Neoplasms/pathology ; Cytidine Deaminase/genetics ; Minor Histocompatibility Antigens/genetics ; Minor Histocompatibility Antigens/metabolism
    Chemical Substances DNA, Single-Stranded ; Cytidine Deaminase (EC 3.5.4.5) ; Minor Histocompatibility Antigens ; APOBEC3B protein, human (EC 3.5.4.5)
    Language English
    Publishing date 2023-09-21
    Publishing country United States
    Document type Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 1108734-1
    ISSN 1546-1718 ; 1061-4036
    ISSN (online) 1546-1718
    ISSN 1061-4036
    DOI 10.1038/s41588-023-01504-w
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  4. Article ; Online: Longitudinal comparison of the self-administered ALSFRS-RSE and ALSFRS-R as functional outcome measures in ALS.

    Erb, M Kelley / Calcagno, Narghes / Brown, Roland / Burke, Katherine M / Scheier, Zoe A / Iyer, Amrita S / Clark, Alison / Higgins, Max P / Keegan, Mackenzie / Gupta, Anoopum S / Johnson, Stephen A / Chew, Sheena / Berry, James D

    Amyotrophic lateral sclerosis & frontotemporal degeneration

    2024  , Page(s) 1–11

    Abstract: ... ...

    Abstract Objective
    Language English
    Publishing date 2024-03-19
    Publishing country England
    Document type Journal Article
    ZDB-ID 2705049-X
    ISSN 2167-9223 ; 2167-8421
    ISSN (online) 2167-9223
    ISSN 2167-8421
    DOI 10.1080/21678421.2024.2322549
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article: Benchmarking R packages for Calculation of Persistent Homology.

    Somasundaram, Eashwar V / Brown, Shael E / Litzler, Adam / Scott, Jacob G / Wadhwa, Raoul R

    The R journal

    2021  Volume 13, Issue 1, Page(s) 184–193

    Abstract: Several persistent homology software libraries have been implemented in R. Specifically ...

    Abstract Several persistent homology software libraries have been implemented in R. Specifically, the Dionysus, GUDHI, and Ripser libraries have been wrapped by the
    Language English
    Publishing date 2021-06-07
    Publishing country United States
    Document type Journal Article
    ISSN 2073-4859
    ISSN 2073-4859
    DOI 10.32614/RJ-2021-033
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Book ; Online: r-indexing without backward searching

    Ahmed, Omar / Baláž, Andrej / Brown, Nathaniel K. / Depuydt, Lore / Goga, Adrián / Petescia, Alessia / Zakeri, Mohsen / Fostier, Jan / Gagie, Travis / Langmead, Ben / Navarro, Gonzalo / Prezza, Nicola

    2023  

    Abstract: ... Let $\bar{r}$ be the number of runs in the Burrows-Wheeler Transform of the reverse of $T$ ... We can index $T$ in $O (\bar{r} + g)$ space such that, given a pattern $P$ and constant-time access to the Karp ...

    Abstract Suppose we are given a text $T$ of length $n$ and a straight-line program for $T$ with $g$ rules. Let $\bar{r}$ be the number of runs in the Burrows-Wheeler Transform of the reverse of $T$. We can index $T$ in $O (\bar{r} + g)$ space such that, given a pattern $P$ and constant-time access to the Karp-Rabin hashes of the substrings of $P$ and the reverse of $P$, we can find the maximal exact matches of $P$ with respect to $T$ correctly with high probability and using $O (\log n)$ time for each edge we would descend in the suffix tree of $T$ while finding those matches.
    Keywords Computer Science - Data Structures and Algorithms
    Publishing date 2023-12-03
    Publishing country us
    Document type Book ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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  7. Article ; Online: RNF8 ubiquitylation of XRN2 facilitates R-loop resolution and restrains genomic instability in BRCA1 mutant cells.

    Krishnan, Rehna / Lapierre, Mariah / Gautreau, Brandon / Nixon, Kevin C J / El Ghamrasni, Samah / Patel, Parasvi S / Hao, Jun / Yerlici, V Talya / Guturi, Kiran Kumar Naidu / St-Germain, Jonathan / Mateo, Francesca / Saad, Amine / Algouneh, Arash / Earnshaw, Rebecca / Shili, Duan / Seitova, Alma / Miller, Joshua / Khosraviani, Negin / Penn, Adam /
    Ho, Brandon / Sanchez, Otto / Hande, M Prakash / Masson, Jean-Yves / Brown, Grant W / Alaoui-Jamali, Moulay / Reynolds, John J / Arrowsmith, Cheryl / Raught, Brian / Pujana, Miguel A / Mekhail, Karim / Stewart, Grant S / Hakem, Anne / Hakem, Razqallah

    Nucleic acids research

    2023  Volume 51, Issue 19, Page(s) 10484–10505

    Abstract: ... cancer cells was found to promote R-loop accumulation and replication fork instability, leading ... which is crucial for transcription termination and R-loop resolution. We report that RNF8 ubiquitylates ... XRN2 to facilitate its recruitment to R-loop-prone genomic loci and that RNF8 deficiency in BRCA1 ...

    Abstract Breast cancer linked with BRCA1/2 mutations commonly recur and resist current therapies, including PARP inhibitors. Given the lack of effective targeted therapies for BRCA1-mutant cancers, we sought to identify novel targets to selectively kill these cancers. Here, we report that loss of RNF8 significantly protects Brca1-mutant mice against mammary tumorigenesis. RNF8 deficiency in human BRCA1-mutant breast cancer cells was found to promote R-loop accumulation and replication fork instability, leading to increased DNA damage, senescence, and synthetic lethality. Mechanistically, RNF8 interacts with XRN2, which is crucial for transcription termination and R-loop resolution. We report that RNF8 ubiquitylates XRN2 to facilitate its recruitment to R-loop-prone genomic loci and that RNF8 deficiency in BRCA1-mutant breast cancer cells decreases XRN2 occupancy at R-loop-prone sites, thereby promoting R-loop accumulation, transcription-replication collisions, excessive genomic instability, and cancer cell death. Collectively, our work identifies a synthetic lethal interaction between RNF8 and BRCA1, which is mediated by a pathological accumulation of R-loops.
    MeSH term(s) Animals ; Female ; Humans ; Mice ; BRCA1 Protein/metabolism ; BRCA2 Protein/genetics ; Breast Neoplasms/genetics ; DNA Damage ; DNA-Binding Proteins/metabolism ; Exoribonucleases/metabolism ; Genomic Instability ; Neoplasm Recurrence, Local ; R-Loop Structures ; Ubiquitin-Protein Ligases/genetics ; Ubiquitin-Protein Ligases/metabolism ; Ubiquitination
    Chemical Substances BRCA1 Protein ; BRCA1 protein, human ; BRCA2 Protein ; BRCA2 protein, human ; DNA-Binding Proteins ; Exoribonucleases (EC 3.1.-) ; RNF8 protein, human ; Ubiquitin-Protein Ligases (EC 2.3.2.27) ; XRN2 protein, human (EC 3.1.13.1) ; Brca1 protein, mouse ; Rnf8 protein, mouse (EC 2.3.2.27) ; Xrn2 protein, mouse (EC 3.1.11.-)
    Language English
    Publishing date 2023-09-11
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 186809-3
    ISSN 1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
    ISSN (online) 1362-4962 ; 1362-4954
    ISSN 0301-5610 ; 0305-1048
    DOI 10.1093/nar/gkad733
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  8. Article ; Online: Tenascin-R Autoimmunity: Isolated Tremor Reversed with Immunotherapy.

    Yang, Binxia / Brown, Andrew / McKeon, Andrew / Ahlskog, J Eric / Tipton, Philip / Guo, Yong / Lucchinetti, Claudia / Pittock, Sean J / Zekeridou, Anastasia

    Annals of neurology

    2023  Volume 94, Issue 3, Page(s) 502–507

    Abstract: ... by immunoprecipitation and mass spectrometry and confirmed by antigen-specific assays to be specific for tenascin-R ... He was investigated for cancer and diagnosed with follicular lymphoma that expressed tenascin-R ...

    Abstract Autoimmune movement disorders are increasingly recognized, but isolated tremor is extremely rare. We describe a 70-year-old male with rapidly progressive, severe postural and intention tremor and weight loss. His cerebrospinal fluid was inflammatory and harbored a neural tissue-restricted antibody. The autoantigen was identified by immunoprecipitation and mass spectrometry and confirmed by antigen-specific assays to be specific for tenascin-R. He was investigated for cancer and diagnosed with follicular lymphoma that expressed tenascin-R suggesting a paraneoplastic origin; cancer treatment and immunotherapy led to complete recovery. With this individualized patient approach and antibody discovery, we expand the spectrum of antibodies accompanying autoimmune hyperkinetic movement disorders. ANN NEUROL 2023;94:502-507.
    MeSH term(s) Male ; Humans ; Aged ; Tremor ; Autoimmunity ; Autoimmune Diseases ; Autoantibodies ; Immunotherapy
    Chemical Substances tenascin R (147604-77-1) ; Autoantibodies
    Language English
    Publishing date 2023-07-14
    Publishing country United States
    Document type Case Reports ; Journal Article ; Research Support, N.I.H., Extramural
    ZDB-ID 80362-5
    ISSN 1531-8249 ; 0364-5134
    ISSN (online) 1531-8249
    ISSN 0364-5134
    DOI 10.1002/ana.26730
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  9. Article ; Online: Radiation and Dose-densification of R-CHOP in Aggressive B-cell Lymphoma With Intermediate Prognosis: The UNFOLDER Study.

    Thurner, Lorenz / Ziepert, Marita / Berdel, Christian / Schmidt, Christian / Borchmann, Peter / Kaddu-Mulindwa, Dominic / Viardot, Andreas / Witzens-Harig, Mathias / Dierlamm, Judith / Haenel, Mathias / Metzner, Bernd / Wulf, Gerald / Lengfelder, Eva / Keller, Ulrich B / Frickhofen, Norbert / Nickelsen, Maike / Gaska, Tobias / Griesinger, Frank / Mahlberg, Rolf /
    Marks, Reinhard / Shpilberg, Ofer / Lindemann, Hans-Walter / Soekler, Martin / Fischer von Weikersthal, Ludwig / Kiehl, Michael / Roemer, Eva / Bentz, Martin / Krammer-Steiner, Beate / Trappe, Ralf / de Nully Brown, Peter / Federico, Massimo / Merli, Francesco / Engelhard, Marianne / Glass, Bertram / Schmitz, Norbert / Truemper, Lorenz / Bewarder, Moritz / Hartmann, Frank / Murawski, Niels / Stilgenbauer, Stephan / Rosenwald, Andreas / Altmann, Bettina / Schmidberger, Heinz / Fleckenstein, Jochen / Loeffler, Markus / Poeschel, Viola / Held, Gerhard

    HemaSphere

    2023  Volume 7, Issue 7, Page(s) e904

    Abstract: UNFOLDER (Unfavorable Young Low-Risk Densification of R-Chemo Regimens) is an international phase-3 ... factorial design patients were randomized to 6× R-CHOP-14 or 6× R-CHOP-21 (rituximab, cyclophosphamide ... randomized to receive radiotherapy (R-CHOP-21: 155; R-CHOP-14: 150) and 162 to observation (R-CHOP-21: 81, R ...

    Abstract UNFOLDER (Unfavorable Young Low-Risk Densification of R-Chemo Regimens) is an international phase-3 trial in patients 18-60 years with aggressive B-cell lymphoma and intermediate prognosis defined by age-adjusted International Prognostic Index (aaIPI) of 0 and bulky disease (≥7.5 cm) or aaIPI of 1. In a 2 × 2 factorial design patients were randomized to 6× R-CHOP-14 or 6× R-CHOP-21 (rituximab, cyclophosphamide, doxorubicin, vincristine, and prediso[lo]ne) and to consolidation radiotherapy to extralymphatic and bulky disease or observation. Response was assessed according to the standardized response criteria published in 1999, not including F-18 fluordesoxyglucose positron emission tomography/computed tomography (FDG-PET). Primary endpoint was event-free survival (EFS). A total of 695 of 700 patients were eligible for the intention-to-treat analysis. Totally 467 patients qualified for radiotherapy of whom 305 patients were randomized to receive radiotherapy (R-CHOP-21: 155; R-CHOP-14: 150) and 162 to observation (R-CHOP-21: 81, R-CHOP-14: 81). Two hundred twenty-eight patients not qualifying for radiotherapy were randomized for R-CHOP-14 versus R-CHOP-21. After a median observation of 66 months 3-year EFS was superior in the radiotherapy-arm versus observation-arm (84% versus 68%;
    Language English
    Publishing date 2023-07-05
    Publishing country United States
    Document type Journal Article
    ISSN 2572-9241
    ISSN (online) 2572-9241
    DOI 10.1097/HS9.0000000000000904
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  10. Article ; Online: Venetoclax plus dose-adjusted R-EPOCH for Richter syndrome.

    Davids, Matthew S / Rogers, Kerry A / Tyekucheva, Svitlana / Wang, Zixu / Pazienza, Samantha / Renner, Sarah K / Montegaard, Josie / Ihuoma, Udochukwu / Lehmberg, Timothy Z / Parry, Erin M / Wu, Catherine J / Jacobson, Caron A / Fisher, David C / Thompson, Philip A / Brown, Jennifer R

    Blood

    2021  Volume 139, Issue 5, Page(s) 686–689

    Abstract: ... doxorubicin (VR-EPOCH) to determine the rate of complete response (CR). Patients received R-EPOCH for 1 cycle ...

    Abstract Richter syndrome (RS) of chronic lymphocytic leukemia (CLL) is typically chemoresistant, with a poor prognosis. We hypothesized that the oral Bcl-2 inhibitor venetoclax could sensitize RS to chemoimmunotherapy and improve outcomes. We conducted a single-arm, investigator-sponsored, phase 2 trial of venetoclax plus dose-adjusted rituximab, etoposide, prednisone, vincristine, cyclophosphamide, and doxorubicin (VR-EPOCH) to determine the rate of complete response (CR). Patients received R-EPOCH for 1 cycle, then after count recovery, accelerated daily venetoclax ramp-up to 400 mg, then VR-EPOCH for up to 5 more 21-day cycles. Responders received venetoclax maintenance or cellular therapy off-study. Twenty-six patients were treated, and 13 of 26 (50%) achieved CR, with 11 achieving undetectable bone marrow minimal residual disease for CLL. Three additional patients achieved partial response (overall response rate, 62%). Median progression-free survival was 10.1 months, and median overall survival was 19.6 months. Hematologic toxicity included grade ≥3 neutropenia (65%) and thrombocytopenia (50%), with febrile neutropenia in 38%. No patients experienced tumor lysis syndrome with daily venetoclax ramp-up. VR-EPOCH is active in RS, with deeper, more durable responses than historical regimens. Toxicities from intensive chemoimmunotherapy and venetoclax were observed. Our data suggest that studies comparing venetoclax with chemoimmunotherapy to chemoimmunotherapy alone are warranted. This trial was registered at www.clinicaltrials.gov as #NCT03054896.
    MeSH term(s) Aged ; Antineoplastic Combined Chemotherapy Protocols/administration & dosage ; Antineoplastic Combined Chemotherapy Protocols/adverse effects ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Bridged Bicyclo Compounds, Heterocyclic/administration & dosage ; Bridged Bicyclo Compounds, Heterocyclic/adverse effects ; Bridged Bicyclo Compounds, Heterocyclic/therapeutic use ; Cyclophosphamide/administration & dosage ; Cyclophosphamide/adverse effects ; Cyclophosphamide/therapeutic use ; Doxorubicin/administration & dosage ; Doxorubicin/adverse effects ; Doxorubicin/therapeutic use ; Etoposide/administration & dosage ; Etoposide/adverse effects ; Etoposide/therapeutic use ; Female ; Humans ; Leukemia, Lymphocytic, Chronic, B-Cell/drug therapy ; Lymphoma, Large B-Cell, Diffuse/drug therapy ; Male ; Middle Aged ; Neutropenia/chemically induced ; Prednisone/administration & dosage ; Prednisone/adverse effects ; Prednisone/therapeutic use ; Progression-Free Survival ; Sulfonamides/administration & dosage ; Sulfonamides/adverse effects ; Sulfonamides/therapeutic use ; Vincristine/administration & dosage ; Vincristine/adverse effects ; Vincristine/therapeutic use
    Chemical Substances Bridged Bicyclo Compounds, Heterocyclic ; Sulfonamides ; Vincristine (5J49Q6B70F) ; Etoposide (6PLQ3CP4P3) ; Doxorubicin (80168379AG) ; Cyclophosphamide (8N3DW7272P) ; venetoclax (N54AIC43PW) ; Prednisone (VB0R961HZT)
    Language English
    Publishing date 2021-11-19
    Publishing country United States
    Document type Clinical Trial, Phase II ; Journal Article ; Multicenter Study ; Research Support, Non-U.S. Gov't
    ZDB-ID 80069-7
    ISSN 1528-0020 ; 0006-4971
    ISSN (online) 1528-0020
    ISSN 0006-4971
    DOI 10.1182/blood.2021011386
    Database MEDical Literature Analysis and Retrieval System OnLINE

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