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Book ; Online: R-Judge

Yuan, Tongxin / He, Zhiwei / Dong, Lingzhong / Wang, Yiming / Zhao, Ruijie / Xia, Tian / Xu, Lizhen / Zhou, Binglin / Li, Fangqi / Zhang, Zhuosheng / Wang, Rui / Liu, Gongshen

Benchmarking Safety Risk Awareness for LLM Agents

2024

Abstract: ... within diverse environments. We introduce R-Judge, a benchmark crafted to evaluate the proficiency of LLMs ... in judging safety risks given agent interaction records. R-Judge comprises 162 agent interaction records ... consensus on safety with annotated safety risk labels and high-quality risk descriptions. Utilizing R-Judge ...

Abstract	Large language models (LLMs) have exhibited great potential in autonomously completing tasks across real-world applications. Despite this, these LLM agents introduce unexpected safety risks when operating in interactive environments. Instead of centering on LLM-generated content safety in most prior studies, this work addresses the imperative need for benchmarking the behavioral safety of LLM agents within diverse environments. We introduce R-Judge, a benchmark crafted to evaluate the proficiency of LLMs in judging safety risks given agent interaction records. R-Judge comprises 162 agent interaction records, encompassing 27 key risk scenarios among 7 application categories and 10 risk types. It incorporates human consensus on safety with annotated safety risk labels and high-quality risk descriptions. Utilizing R-Judge, we conduct a comprehensive evaluation of 8 prominent LLMs commonly employed as the backbone for agents. The best-performing model, GPT-4, achieves 72.29% in contrast to the human score of 89.38%, showing considerable room for enhancing the risk awareness of LLMs. Notably, leveraging risk descriptions as environment feedback significantly improves model performance, revealing the importance of salient safety risk feedback. Furthermore, we design an effective chain of safety analysis technique to help the judgment of safety risks and conduct an in-depth case study to facilitate future research. R-Judge is publicly available at https://github.com/Lordog/R-Judge.
Keywords	Computer Science - Computation and Language ; Computer Science - Artificial Intelligence
Publishing date	2024-01-18
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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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, 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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 / 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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
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Article ; Online: Platelet Membrane-Coated r-SAK Improves Thrombolytic Efficacy by Targeting Thrombus.

Hua, Rui / Li, Mingxi / Lin, Qingxia / Dong, Mengying / Gong, Xiaoxuan / Lin, Zhenyu / Li, Yule / Li, Chen / Wu, Tian / Tan, Chunyue / Zhang, Wenhao / Wang, Qin / Wu, Tianyu / Zhou, Xiaoyu / Yang, Fang / Li, Chunjian

ACS applied materials & interfaces

2024

Abstract: ... and consequently restricted indications. Recombinant staphylokinase (r-SAK) is a third-generation ... pathological thrombosis, we developed a platelet membrane (PM)-coated r-SAK (PM-r-SAK). Results ... from animal experiments and human in vitro studies showed that the PM-r-SAK had a thrombolytic efficacy equal to or better ...

Abstract	Thrombolytic therapy is one of the most effective treatments for thrombus dissolution and recanalization of blocked vessels in thrombotic diseases. However, the application of the thrombolytic strategy has been limited due to unsatisfactory thrombolytic efficacy, relatively higher bleeding complications, and consequently restricted indications. Recombinant staphylokinase (r-SAK) is a third-generation thrombolytic agent produced by genetic engineering technology, which exhibits a better thrombolytic efficacy than urokinase and recombinant streptokinase. Inspired by the natural affinity of platelets in hemostasis and pathological thrombosis, we developed a platelet membrane (PM)-coated r-SAK (PM-r-SAK). Results from animal experiments and human in vitro studies showed that the PM-r-SAK had a thrombolytic efficacy equal to or better than its 4-fold dose of r-SAK. In a totally occluded rabbit femoral artery thrombosis model, the PM-r-SAK significantly shortened the initial recanalization time compared to the same dose and 4-fold dose of r-SAK. Regarding the recanalized vessels, the PM-r-SAK prolonged the time of reperfusion compared to the same dose and 4-fold dose of r-SAK, though the differences were not significant. An in vitro thrombolytic experiment demonstrated that the thrombolytic efficacy of PM-r-SAK could be inhibited by platelet-poor plasma from patients taking aspirin and ticagrelor. PM coating significantly improves the thrombolytic efficacy of r-SAK, which is related to the thrombus-targeting activity of the PM-r-SAK and can be inhibited by aspirin- and ticagrelor-treated plasma.
Language	English
Publishing date	2024-04-16
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.3c18402
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Article: Residues R

Yan, Zhi-Yong / Xu, Xiao-Jie / Fang, Le / Cheng, De-Jie / Tian, Yan-Ping / Geng, Chao / Li, Xiang-Dong / Valkonen, Jari P T

Molecular plant-microbe interactions : MPMI

2021 Volume 34, Issue 6, Page(s) 658–668

Abstract: ... in the CP RNA-binding pocket. Substitutions of the two basic residues at positions 192 and 225 (R ...

Abstract	Potyviruses move to neighboring cells in the form of virus particles or a coat protein (CP)-containing ribonucleoprotein complex. However, the precise roles of RNA-binding residues in potyviral CP in viral cell-to-cell movement remain to be elucidated. In this study, we predicted the three-dimensional model of tobacco vein banding mosaic virus (TVBMV)-encoded CP and found nine residues presumably located in the CP RNA-binding pocket. Substitutions of the two basic residues at positions 192 and 225 (R
MeSH term(s)	Capsid Proteins/genetics ; Potyvirus ; RNA, Viral/genetics ; Nicotiana/genetics ; Virus Replication
Chemical Substances	Capsid Proteins ; RNA, Viral
Language	English
Publishing date	2021-07-21
Publishing country	United States
Document type	Journal Article
ZDB-ID	743331-1
ISSN	1943-7706 ; 0894-0282
ISSN (online)	1943-7706
ISSN	0894-0282
DOI	10.1094/MPMI-09-20-0265-R
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Article ; Online: R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation.

Lin, Ruoyao / Zhong, Xiaoming / Zhou, Yongli / Geng, Huichao / Hu, Qingxi / Huang, Zhihao / Hu, Jun / Fu, Xiang-Dong / Chen, Liang / Chen, Jia-Yu

Nucleic acids research

2021 Volume 50, Issue D1, Page(s) D303–D315

Abstract: R-loops play versatile roles in many physiological and pathological processes, and are of great ... incomplete understanding of their regulatory network raise great challenges for R-loop research. Here ... we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues ...

Abstract	R-loops play versatile roles in many physiological and pathological processes, and are of great interest to scientists in multiple fields. However, controversy about their genomic localization and incomplete understanding of their regulatory network raise great challenges for R-loop research. Here, we present R-loopBase (https://rloopbase.nju.edu.cn) to tackle these pressing issues by systematic integration of genomics and literature data. First, based on 107 high-quality genome-wide R-loop mapping datasets generated by 11 different technologies, we present a reference set of human R-loop zones for high-confidence R-loop localization, and spot conservative genomic features associated with R-loop formation. Second, through literature mining and multi-omics analyses, we curate the most comprehensive list of R-loop regulatory proteins and their targeted R-loops in multiple species to date. These efforts help reveal a global regulatory network of R-loop dynamics and its potential links to the development of cancers and neurological diseases. Finally, we integrate billions of functional genomic annotations, and develop interactive interfaces to search, visualize, download and analyze R-loops and R-loop regulators in a well-annotated genomic context. R-loopBase allows all users, including those with little bioinformatics background to utilize these data for their own research. We anticipate R-loopBase will become a one-stop resource for the R-loop community.
MeSH term(s)	Cell Line, Tumor ; Chromosome Mapping ; Computational Biology/methods ; DNA/chemistry ; DNA/genetics ; DNA/metabolism ; Databases, Nucleic Acid ; Datasets as Topic ; Gene Regulatory Networks ; Genome ; Genomic Instability ; HEK293 Cells ; Humans ; Internet ; Molecular Sequence Annotation ; Neoplasms/genetics ; Neoplasms/metabolism ; Neoplasms/pathology ; Nervous System Diseases/genetics ; Nervous System Diseases/metabolism ; Nervous System Diseases/pathology ; Protein Interaction Mapping/methods ; R-Loop Structures ; RNA/chemistry ; RNA/genetics ; RNA/metabolism ; Software ; Transcription, Genetic
Chemical Substances	RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2021-12-16
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/gkab1103
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Zs.A 1067: Show issues

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Article ; Online: Synthesis of (Deoxy)difluoromethylated Phosphines by Reaction of R

Yang, Xiaogang / Lu, Dong / Guan, Wenjian / Yin, Shuang-Feng / Kambe, Nobuaki / Qiu, Renhua

The Journal of organic chemistry

2022 Volume 87, Issue 12, Page(s) 7720–7733

Abstract: R ...

Abstract	R
MeSH term(s)	Alkynes ; Catalysis ; Hydrocarbons, Fluorinated ; Iodides ; Ligands ; Palladium ; Phosphines ; Silanes
Chemical Substances	Alkynes ; Hydrocarbons, Fluorinated ; Iodides ; Ligands ; Phosphines ; Silanes ; Palladium (5TWQ1V240M) ; trimethyl(trifluoromethyl)silane (A009786QPJ)
Language	English
Publishing date	2022-05-27
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	123490-0
ISSN	1520-6904 ; 0022-3263
ISSN (online)	1520-6904
ISSN	0022-3263
DOI	10.1021/acs.joc.2c00308
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Article ; Online: Measurement of R(D) and R(D^{*}) with a Semileptonic Tagging Method.

Caria, G / Urquijo, P / Adachi, I / Aihara, H / Al Said, S / Asner, D M / Atmacan, H / Aushev, T / Babu, V / Badhrees, I / Bahinipati, S / Bakich, A M / Behera, P / Beleño, C / Bennett, J / Bhuyan, B / Bilka, T / Biswal, J / Bozek, A /

Bračko, M / Browder, T E / Campajola, M / Červenkov, D / Chang, P / Cheaib, R / Chekelian, V / Chen, A / Cheon, B G / Chilikin, K / Cho, H E / Cho, K / Choi, Y / Choudhury, S / Cinabro, D / Cunliffe, S / Dash, N / De Nardo, G / Di Capua, F / Di Carlo, S / Doležal, Z / Dong, T V / Eidelman, S / Epifanov, D / Fast, J E / Ferber, T / Ferlewicz, D / Fulsom, B G / Garg, R / Gaur, V / Gabyshev, N / Garmash, A / Giri, A / Goldenzweig, P / Greenwald, D / Grzymkowska, O / Guan, Y / Hartbrich, O / Hayasaka, K / Hayashii, H / Higuchi, T / Hou, W-S / Hsu, C-L / Iijima, T / Inami, K / Inguglia, G / Ishikawa, A / Itoh, R / Iwasaki, M / Iwasaki, Y / Jacobs, W W / Jeon, H B / Jia, S / Jin, Y / Joffe, D / Joo, K K / Kaliyar, A B / Kang, K H / Karyan, G / Kawasaki, T / Kichimi, H / Kim, C H / Kim, D Y / Kim, H J / Kim, K T / Kim, S H / Kinoshita, K / Kodyš, P / Korpar, S / Kotchetkov, D / Križan, P / Kroeger, R / Krohn, J-F / Krokovny, P / Kuhr, T / Kumar, R / Kwon, Y-J / Lange, J S / Lee, I S / Lee, J K / Lee, S C / Li, L K / Li, Y B / Li Gioi, L / Libby, J / Lieret, K / Liventsev, D / Luo, T / MacQueen, C / Masuda, M / Matsuda, T / Matvienko, D / Merola, M / Metzner, F / Miyabayashi, K / Mohanty, G B / Moon, T J / Mori, T / Mussa, R / Nakamura, K R / Nakao, M / Nath, K J / Nayak, M / Nisar, N K / Nishida, S / Nishimura, K / Ogawa, K / Ono, H / Onuki, Y / Oskin, P / Pakhlov, P / Pakhlova, G / Pal, B / Pang, T / Park, H / Park, S-H / Patra, S / Paul, S / Pedlar, T K / Pestotnik, R / Piilonen, L E / Popov, V / Prencipe, E / Prim, M T / Rabusov, A / Resmi, P K / Ritter, M / Rozanska, M / Russo, G / Sahoo, D / Sakai, Y / Sandilya, S / Santelj, L / Sanuki, T / Savinov, V / Schneider, O / Schnell, G / Schueler, J / Schwanda, C / Schwartz, A J / Seino, Y / Senyo, K / Sevior, M E / Shebalin, V / Shiu, J-G / Shwartz, B / Simon, F / Sokolov, A / Solovieva, E / Starič, M / Stottler, Z S / Sumiyoshi, T / Sutcliffe, W / Takizawa, M / Tamponi, U / Tanida, K / Tenchini, F / Trabelsi, K / Uchida, M / Uglov, T / Uno, S / Usov, Y / Vahsen, S E / Van Tonder, R / Varner, G / Varvell, K E / Vossen, A / Waheed, E / Wang, B / Wang, C H / Wang, M-Z / Wang, P / Wang, X L / Watanuki, S / Wiechczynski, J / Won, E / Yamamoto, H / Yang, S B / Ye, H / Yin, J H / Yuan, C Z / Zhang, Z P / Zhilich, V / Zhukova, V / Zhulanov, V

Physical review letters

2020 Volume 124, Issue 16, Page(s) 161803

Abstract: The experimental results on the ratios of branching fractions R(D)=B(B[over ¯]→Dτ^{-}ν[over ¯]_{τ ... B(B[over ¯]→Dℓ^{-}ν[over ¯]_{ℓ}) and R(D^{*})=B(B[over ¯]→D^{*}τ^{-}ν[over ¯]_{τ})/B(B[over ¯]→D^ ... simultaneous measurement of R(D) and R(D^{*}), based on a data sample containing 772×10^{6} BB[over ¯] events ...

Abstract	The experimental results on the ratios of branching fractions R(D)=B(B[over ¯]→Dτ^{-}ν[over ¯]_{τ})/B(B[over ¯]→Dℓ^{-}ν[over ¯]_{ℓ}) and R(D^{})=B(B[over ¯]→D^{}τ^{-}ν[over ¯]_{τ})/B(B[over ¯]→D^{}ℓ^{-}ν[over ¯]_{ℓ}), where ℓ denotes an electron or a muon, show a long-standing discrepancy with the standard model predictions, and might hint at a violation of lepton flavor universality. We report a new simultaneous measurement of R(D) and R(D^{}), based on a data sample containing 772×10^{6} BB[over ¯] events recorded at the ϒ(4S) resonance with the Belle detector at the KEKB e^{+}e^{-} collider. In this analysis the tag-side B meson is reconstructed in a semileptonic decay mode and the signal-side τ is reconstructed in a purely leptonic decay. The measured values are R(D)=0.307±0.037±0.016 and R(D^{})=0.283±0.018±0.014, where the first uncertainties are statistical and the second are systematic. These results are in agreement with the standard model predictions within 0.2, 1.1, and 0.8 standard deviations for R(D), R(D^{}), and their combination, respectively. This work constitutes the most precise measurements of R(D) and R(D^{*}) performed to date as well as the first result for R(D) based on a semileptonic tagging method.
Language	English
Publishing date	2020-05-08
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.124.161803
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Article ; Online: RespirAnalyzer: an R package for analyzing data from continuous monitoring of respiratory signals.

Zhang, Teng / Dong, Xinzheng / Wang, Dandan / Huang, Chen / Zhang, Xiaohua Douglas

Bioinformatics advances

2024 Volume 4, Issue 1, Page(s) vbae003

Abstract: ... scientific understanding in the field of respiratory health.: Results: The R package : Availability and ... implementation: The package for Windows is available from both Comprehensive R Archive Network (CRAN): https ... cran.r-project.org/web/packages/RespirAnalyzer/index.html and GitHub: https://github.com/dongxinzheng ...

Abstract	Motivation: The analysis of data obtained from continuous monitoring of respiratory signals (CMRS) holds significant importance in improving patient care, optimizing sports performance, and advancing scientific understanding in the field of respiratory health. Results: The R package Availability and implementation: The package for Windows is available from both Comprehensive R Archive Network (CRAN): https://cran.r-project.org/web/packages/RespirAnalyzer/index.html and GitHub: https://github.com/dongxinzheng/RespirAnalyzer.
Language	English
Publishing date	2024-01-13
Publishing country	England
Document type	Journal Article
ISSN	2635-0041
ISSN (online)	2635-0041
DOI	10.1093/bioadv/vbae003
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Article ; Online: Mapping R-Loops Using Catalytically Inactive RNaseH1 (R-ChIP).

Zhang, Xuan / Hao, Yajing / Fu, Xiang-Dong

Methods in molecular biology (Clifton, N.J.)

2022 Volume 2528, Page(s) 359–372

Abstract: R-loops, three-stranded structures containing double-stranded DNA invaded by single-stranded RNA ... regulation of R-loops is thus a gateway to address many fundamental questions in regulatory biology ... which requires the elucidation of the R-loop landscape at the genome scale. To aid in such efforts, this article ...

Abstract	R-loops, three-stranded structures containing double-stranded DNA invaded by single-stranded RNA, have been linked to diverse biological processes. They play important roles in regulating gene regulation and DNA repair, contributing to a wide range of diseases. Understanding the formation and dynamic regulation of R-loops is thus a gateway to address many fundamental questions in regulatory biology, which requires the elucidation of the R-loop landscape at the genome scale. To aid in such efforts, this article provides an overview on R-loop mapping strategies along with a detailed protocol based on the use of catalytically inactive RNaseH1, an evolutionarily conserved protein responsible for R-loop recognition and resolution.
MeSH term(s)	DNA/genetics ; DNA Repair ; Genome ; R-Loop Structures ; RNA/genetics ; Transcription, Genetic
Chemical Substances	RNA (63231-63-0) ; DNA (9007-49-2)
Language	English
Publishing date	2022-06-15
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-2477-7_24
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Article: RNA helicase DDX5 is involved in R-loop dynamics of preimplantation embryos.

Lee, Hyeonji / Han, Dong Wook / Yoo, Seonho / Kwon, Ohbeom / La, Hyeonwoo / Park, Chanhyeok / Lee, Heeji / Kang, Kiye / Uhm, Sang Jun / Song, Hyuk / Do, Jeong Tae / Choi, Youngsok / Hong, Kwonho

Animal bioscience

2024

Abstract: Objective: R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated ... by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is ... responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been ...

Abstract	Objective: R-loops are DNA:RNA triplex hybrids, and their metabolism is tightly regulated by transcriptional regulation, DNA damage response, and chromatin structure dynamics. R-loop homeostasis is dynamically regulated and closely associated with gene transcription in mouse zygotes. However, the factors responsible for regulating these dynamic changes in the R-loops of fertilized mouse eggs have not yet been investigated. This study examined the functions of candidate factors that interact with R-loops during zygotic gene activation. Methods: In this study, we used publicly available next-generation sequencing datasets, including low-input ribosome profiling analysis and polymerase II chromatin immunoprecipitation-sequencing (ChIP-seq), to identify potential regulators of R-loop dynamics in zygotes. These datasets were downloaded, reanalyzed, and compared with mass spectrometry data to identify candidate factors involved in regulating R-loop dynamics. To validate the functions of these candidate factors, we treated mouse zygotes with chemical inhibitors using in vitro fertilization. Immunofluorescence with an anti-R-loop antibody was then performed to quantify changes in R-loop metabolism. Results: We identified DEAD-box-5 (DDX5) and histone deacetylase-2 (HDAC2) as candidates that potentially regulate R-loop metabolism in oocytes, zygotes and two-cell embryos based on change of their gene translation. Our analysis revealed that the DDX5 inhibition of activity led to decreased R-loop accumulation in pronuclei, indicating its involvement in regulating R-loop dynamics. However, the inhibition of histone deacetylase-2 activity did not significantly affect R-loop levels in pronuclei. Conclusion: These findings suggest that dynamic changes in R-loops during mouse zygote development are likely regulated by RNA helicases, particularly DDX5, in conjunction with transcriptional processes. Our study provides compelling evidence for the involvement of these factors in regulating R-loop dynamics during early embryonic development.
Language	English
Publishing date	2024-02-22
Publishing country	Korea (South)
Document type	Journal Article
ISSN	2765-0189
ISSN	2765-0189
DOI	10.5713/ab.23.0401
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