Gotowa bibliografia na temat „Shuang chong guo ji”

Abstract The accuracy of current deconvolution methods largely relies on the quality of cell-type expression references. However, single-cell (sc) and single-nuclei (sn) RNA-seq data used for building the reference are usually generated from independent studies that are distinct from the bulk RNA-seq data to be deconvolved. This study design inherently introduces technical confounding factors as unwanted variations, which is not fully addressed by current methods. To evaluate the impact of this variation on deconvolution accuracy, we generated a benchmark dataset where bulk and snRNA-seq profiling were performed from the same aliquot of single-nuclei that were extracted from 24 healthy retina samples. All donor eye samples were collected within six hours post-mortem and were absent of any disease. This study design guarantees the matched sequencing data to present the same cell-type compositions, so that cross-platform technical artifacts become the remaining confounding factor. We used the benchmark dataset to evaluate the performance of seven current deconvolution methods and found they performed much worse in matched real-bulk data than in matched pseudo-bulks that were summations of the single-cell data. This finding suggests that none of these methods have fully addressed the major technical artifacts between bulk and single-cell sequencing platforms. We therefore propose DeMix.SC, a new deconvolution framework that optimizes deconvolution parameters using a small set of matched bulk and sc/snRNA-seq data from the same tissue type. DeMix.SC includes two major steps. First, we measure the technical variations across genes and across platforms using the benchmark data. Second, we introduce a new weight function for each gene that produces a ranking order that accounts for both the platform-specific technical variations and cell-type specific expressions at gene level. Using the benchmark data for retina, we applied DeMix.SC to previously published human retinal RNA-seq data from 523 individuals with different stages of age-related macular degeneration (AMD). We observed that DeMix.SC can accurately capture the cell-type composition shifts in the AMD retina. DeMix.SC revealed a significant drop of rod cells as well as increased astrocytes, bipolar cells, and Müller cells in the AMD retina compared to the non-AMD group. The proportion changes of the later three minor cell types were not identified by other methods, while DeMix.SC could reveal such tendency. In summary, DeMix.SC integrates benchmark data to improve the deconvolution accuracy in retina samples. Our method is generic and can be applied to other disease conditions, such as deciphering the cell-type heterogeneity in cancer. We expect DeMix.SC will help revolutionize the downstream cell-type specific analysis of bulk RNA-seq data and identify cellular targets of human diseases. Citation Format: Shuai Guo, Xuesen Cheng, Andrew Koval, Shuangxi Ji, Qingnan Liang, Yumei Li, Leah A. Owen, Ivana K. Kim, John Weinstein, Scott Kopetz, John Paul Shen, Margaret M. DeAngelis, Rui Chen, Wenyi Wang. Integration with benchmark data of paired bulk and single-cell RNA sequencing data substantially improves the accuracy of bulk tissue deconvolution. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4273.

Committee I.1: Environment Alexander Babanin (Chair); Mariana Bernardino; Franz von Bock und Polach; Ricardo Campos,; Jun Ding; Sanne van Essen; Tomaso Gaggero; Maryam Haroutunian; Vanessa Katsardi; Alexander Nilva; Arttu Polojarvi; Erik Vanem; Jungyong Wang; Huidong Zhang; Tingyao Zhu Floor Discussers: Florian Sprenger; Carlos Guedes Soares; Henk den Besten Committee I.2: Loads Ole Andreas Hermundstad (Chair); Shuhong Chai; Guillaume de Hauteclocque; Sheng Dong; Chih-Chung Fang; Thomas B. Johannessen; Celso Morooka; Masayoshi Oka; Jasna Prpić-Oršić; Alessandro Sacchet; Mahmud Sazidy; Bahadir Ugurlu; Roberto Vettor; Peter Wellens Official Discusser: Hayden Marcollo Committee II-1: Quasi-Static Response James Underwood (Chair); Erick Alley; Jerolim Andrić Dario Boote; Zhen Gao; Ad Van Hoeve; Jasmin Jelovica; Yasumi Kawamura; Yooil Kim; Jian Hu Liu; Sime Malenica; Heikki Remes; Asokendu Samanta; Krzysztof Woloszyk; Deqing Yang Official Discusser: Prof. T. Yoshikwa Committee II.2: Dynamic Response Gaute Storhaug (Chair); Daniele Dessi; Sharad Dhavalikar; Ingo Drummen; Michael Holtmann; Young-Cheol Huh; Lorenzo Moro; Andre Paiva; Svein Sævik; Rong-Juin Shyu; Shan Wang; Sue Wang; WenWei Wu; Yasuhira Yamada; Guiyong Zhang Floor Discussers: Ling Zhu; Tomoki Takami; Anriette (Annie) Bekker; Bruce Quinton; Robert Sielski Committee III.1: Ultimate Strength Paul E. Hess (Chair); Chen An; Lars Brubak; Xiao Chen; Jinn Tong Chiu; Jurek Czujko; Ionel Darie; Guoqing Feng; Marco Gaiotti; Beom Seon Jang; Adnan Kefal; Sukron Makmun; Jonas Ringsberg; Jani Romanoff; Saad Saad-Eldeen; Ingrid Schipperen; Kristjan Tabri; Yikun Wang; Daisuke Yanagihara Official Discusser: Jørgen Amdahl Committee III.2: Fatigue and Fracture Yordan Garbatov (Chair); Sigmund K Ås; Henk Den Besten; Philipp Haselbach; Adrian Kahl; Dale Karr; Myung Hyun Kim; Junjie Liu; Marcelo Igor Lourenço de Souza; Wengang Mao; Eeva Mikkola; Naoki Osawa; Fredhi Agung Prasetyo; Mauro Sicchiero; Suhas Vhanmane; Marta Vicente del Amo; Jingxia Yue Official Discusser Weicheng Cui Floor Discussers: Robert Sielski; Sören Ehlers; Stephane Paboeuf; Teresa Magoga Committee IV.1: Design Principles and Criteria Matthew Collette (Chair); Piero Caridis; Petar Georgiev; Torfinn Hørte; Han Koo Jeong; Rafet emek Kurt; Igor Ilnytskiy; Tetsuo Okada; Charles Randall; Zbigniew Sekulski; Matteo Sidari; Zhihu Zhan; Ling Zhu Official Discusser: Enrico Rizzuto Committee IV.2: Design Methods Andrea Ivaldi (Chair); Abbas Bayatfar; Jean-David Caprace; Gennadiy Egorov; Svein Erling Heggelund; Shinichi Hirakawa; Jung Min Kwon; Dan Mcgreer; Pero Prebeg; Robert Sielski; Mark Slagmolen; Adam Sobey; Wenyong Tang; Jiameng Wu Official Discusser: Mario Dogliani Committee V.1: Accidental Limit States Bruce Quinton; Gaetano De Luca; Topan Firmandha; Mihkel Körgesaar; Hervé Le Sourne; Ken Nahshon; Gabriele Notaro; Kourosh Parsa; Smiljko Rudan; Katsuyuki Suzuki; Osiris Valdez Banda; CareyWalters; Deyu Wang; Zhaolong Yu Official Discusser: Manolis Samuelides Committee V.2: Experimental Methods Sören Ehlers (Chair); Nagi Abdussamie; Kim Branner; ShiXiao Fu; Martijn Hoogeland; Kari Kolari; Paul Lara; Constantine Michailides; Hideaki Murayama; Cesare Rizzo; Jung Kwan Seo; Patrick Kaeding Official Discusser: Giles Thomas Committee V.3: Materials and Fabrication Technology Lennart Josefson (Chair); Konstantinos Anyfantis; Bianca de Carvalho Pinheiro; Bai-Qiao Chen; Pingsha Dong; Nicole Ferrari; Koji Gotoh; James Huang; Matthias Krause; Kun Liu; Stephane Paboeuf; Stephen van Duin; Fang Wang; Albert Zamarin Official Discusser: Frank Roland Floor Discussers Alessandro Caleo; Agnes Marie Horn; Krzysztof Woloszyk; Robert Sielski Committee V.4: Offshore Renewable Energy Atanasios Kolios (Chair); Kyong-Hwan Kim; Chen Hsing Cheng; Elif Oguz; Pablo Morato; Freeman Ralph; Chuang Fang; Chunyan Ji; Marc Le Boulluec; Thomas Choisnet; Luca Greco; Tomoaki Utsunomiya; Kourosh Rezanejad; Charles Rawson; Jose Miguel Rodrigues Official Discusser: Amy Robertson Committee V.5: Special Vessels Darren Truelock (Chair); Jason Lavroff; Dustin Pearson; Zbigniew (Jan) Czaban; Hanbing Luo; Fuhua Wang; Ivan Catipovic; Ermina Begovic; Yukichi Takaoka; Claudia Loureiro; Chang Yong Song; Esther Garcia; Alexander Egorov; Jean-Baptiste Souppez; Pradeep Sensharma; Rachel Nicholls-Lee Official Discusser: Jaye Falls Floor Discussers: Jasmin Jelovica; Stephane Paboeuf; Sören Ehlers Committee V.6: Ocean Space Utilization Sebastian Schreier (Chair); Felice Arena; Harry Bingham; Nuno Fonseca; Zhiqiang Hu; Debabrata Karmakar; Ekaterina Kim; Hui Li; Pengfei Liu; Motohiko Murai; Spiro J Pahos; Chao Tian; George Wang Official Discusser: Hideyuki Suzuki Floor Discussers: Robert Sielski; Sue Wang; Sarat Mohapatra; Gaute Storhaug; Henk den Besten Committee V.7: Structural Longevity Iraklis Lazakis (Chair); Bernt Leira; Nianzhong Chen; Geovana Drumond; Chi-Fang Lee; Paul Jurisic; Bin Liu; Alysson Mondoro; Pooria Pahlavan; Xinghua Shi; Ha Cheol Song; Tadashi Sugimura; Christian Jochum; Tommaso Coppola Official Discusser: Timo de Beer Floor Discusser: Krzysztof Woloszyk Committee V.8: Subsea Technology Agnes Marie Horn (Chair); Tauhid Rahman; Ilson Pasqualino; Menglan Duan; Zhuang Kang; Michael Rye Andersen; Yoshihiro Konno; Chunsik Shim; Angelo Teixeira; Selda Oterkus; Blair Thornton; Brajendra Mishra Official Discusser: Segen F. 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