{"title":"An automatic annotation tool and reference database for T cell subtypes and states at single-cell resolution.","authors":"Wen-Kang Shen, Chu-Yu Zhang, Yi-Min Gu, Tao Luo, Si-Yi Chen, Tao Yue, Gui-Yan Xie, Yu Liao, Yong Yuan, Qian Lei, An-Yuan Guo","doi":"10.1016/j.scib.2025.02.043","DOIUrl":"https://doi.org/10.1016/j.scib.2025.02.043","url":null,"abstract":"<p><p>T cells have various subtypes and states with different functions. However, a reference list and automated annotation tool for T cell subtypes and states are lacking, which is critical for analyzing and comparing T cells under various conditions. We constructed the largest human T cell reference, containing 1,348,268 T cells from 35 conditions and 16 tissues. We classified T cells into 33 subtypes and further stratified them into 68 categories according to subtype and state. Based on this reference, we developed a tool named STCAT to automatically annotate T cells from scRNA-seq data by hierarchical models and marker correction. The accuracy of STCAT was 28% higher than that of existing tools validated on six independent datasets, including cancer and healthy samples. Using STCAT, we consistently discovered that CD4<sup>+</sup> Th17 cells were enriched in late-stage lung cancer patients in multiple datasets, whereas MAIT cells were prevalent in milder-stage COVID-19 patients. We also confirmed a decrease in Treg cytotoxicity in post-treatment ovarian cancer. Systematic landscape analyses of CD4<sup>+</sup> and CD8<sup>+</sup> T cell references revealed that CD4<sup>+</sup> Treg cells were enriched in tumor samples and that CD8<sup>+</sup> naive-related cells were abundant in healthy individuals. Finally, we deposited all the T cell references and annotations into a TCellAtlas (https://guolab.wchscu.cn/TCellAtlas) database, which allows users to browse T cell expression profiles and analyze customized scRNA-seq data by STCAT. In conclusion, comprehensive human T cell subtypes and states reference, automated annotation tool, and database will greatly facilitate research on T cell immunity and tumor immunology.</p>","PeriodicalId":421,"journal":{"name":"Science Bulletin","volume":" ","pages":""},"PeriodicalIF":18.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741819","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Science BulletinPub Date : 2025-03-17DOI: 10.1016/j.scib.2024.12.054
Yansui Liu, Cong Ou, Yaqun Liu, Zhi Cao, Guy M Robinson, Xunhuan Li
{"title":"Unequal impacts of global urban-rural settlement construction on cropland and production over the past three decades.","authors":"Yansui Liu, Cong Ou, Yaqun Liu, Zhi Cao, Guy M Robinson, Xunhuan Li","doi":"10.1016/j.scib.2024.12.054","DOIUrl":"https://doi.org/10.1016/j.scib.2024.12.054","url":null,"abstract":"<p><p>The world has experienced a rapid expansion of human settlements in both urban and rural areas in recent decades, yet the unequal impacts of this construction on global food security remain unclear. In this study, we delineated the global-scale expansion of urban-rural settlements at a fine resolution from 1985 to 2020 and quantified their uneven impacts on food security, focusing on the relationships between settlement types, cropland categories, and disparities in crop production. Our results showed that despite dramatic urbanization, rural settlements still constituted the majority of human settlement areas in 2020. Globally, cropland loss due to the expansion of rural settlements was 1.2 times greater than that caused by urbanization, while the associated yield loss was 1.5 times higher. Notably, urban-rural settlement expansion in Asia accounted for 61% of cropland loss and 64% of yield loss. Moreover, future scenarios predicted that Asia's urban-rural settlement expansion will continue to have the most significant impacts on the loss of cropland and yield throughout the 2030s. These results provide systematic evidence of the unequal impacts of urban-rural settlement construction on global cropland and food security.</p>","PeriodicalId":421,"journal":{"name":"Science Bulletin","volume":" ","pages":""},"PeriodicalIF":18.8,"publicationDate":"2025-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Science BulletinPub Date : 2025-03-15DOI: 10.1016/j.scib.2025.03.031
Xianyong Cao
{"title":"Stability of Holocene pollen assemblages in eastern China disturbed by human activities over the last two millennia.","authors":"Xianyong Cao","doi":"10.1016/j.scib.2025.03.031","DOIUrl":"https://doi.org/10.1016/j.scib.2025.03.031","url":null,"abstract":"","PeriodicalId":421,"journal":{"name":"Science Bulletin","volume":" ","pages":""},"PeriodicalIF":18.8,"publicationDate":"2025-03-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690363","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Science BulletinPub Date : 2025-03-13DOI: 10.1016/j.scib.2025.02.042
Xiangzhen Deng, Qiaoling Zhao, Han Zhang, Fengjuan Zhang, Huaibin Shen
{"title":"Bright and efficient green ZnSeTe-based quantum-dot light-emitting diodes with EQE exceeding 20.","authors":"Xiangzhen Deng, Qiaoling Zhao, Han Zhang, Fengjuan Zhang, Huaibin Shen","doi":"10.1016/j.scib.2025.02.042","DOIUrl":"https://doi.org/10.1016/j.scib.2025.02.042","url":null,"abstract":"<p><p>Ternary ZnSeTe quantum dots (QDs) are recognized as promising eco-friendly emitters for blue quantum-dot light-emitting diodes (QD-LEDs) and are capable of extending their emission range to green or even red light. Although extensive investigations have enabled significant advances in the external quantum efficiency of blue ZnSeTe QD-LEDs, unfortunately, the lack of effective defect passivation strategies for green and red ZnSeTe QDs poses difficulties in improving device performance, thereby impeding their development. Here, we propose to enhance the luminescence performance of green ZnSeTe devices by inserting an ultrathin ZnSeS interlayer to fabricate efficient QDs. This strategy enables us to achieve gradient thick-shell QD structures, thereby alleviating lattice mismatch at the shell-shell interface and passivating surface defects. These improvements result in enhanced quantum efficiency, improved optical stability, and elevated band position. These combined features enhance exciton recombination and promote charge injection balance, leading to a record-breaking external quantum efficiency of 20.6% and a high brightness of 106,054 cd m<sup>-2</sup>, accompanied by an improved operational stability.</p>","PeriodicalId":421,"journal":{"name":"Science Bulletin","volume":" ","pages":""},"PeriodicalIF":18.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143690432","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Science BulletinPub Date : 2025-03-13DOI: 10.1016/j.scib.2025.03.022
Lei Zhang, Federico Abbate, Di Li, Andrea Possenti, Matthew Bailes, Alessandro Ridolfi, Paulo C C Freire, Scott M Ransom, Yong-Kun Zhang, Meng Guo, Meng-Meng Ni, Jia-Le Hu, Yi Feng, Pei Wang, Jie Zhang, Qi-Jun Zhi
{"title":"Probing globular cluster with MeerKAT and FAST: A pulsar polarization census.","authors":"Lei Zhang, Federico Abbate, Di Li, Andrea Possenti, Matthew Bailes, Alessandro Ridolfi, Paulo C C Freire, Scott M Ransom, Yong-Kun Zhang, Meng Guo, Meng-Meng Ni, Jia-Le Hu, Yi Feng, Pei Wang, Jie Zhang, Qi-Jun Zhi","doi":"10.1016/j.scib.2025.03.022","DOIUrl":"https://doi.org/10.1016/j.scib.2025.03.022","url":null,"abstract":"","PeriodicalId":421,"journal":{"name":"Science Bulletin","volume":" ","pages":""},"PeriodicalIF":18.8,"publicationDate":"2025-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143741893","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}