Pub Date : 2024-08-14DOI: 10.1016/j.xinn.2024.100685
Yi Shi
{"title":"Drug development in the AI era: AlphaFold 3 is coming!","authors":"Yi Shi","doi":"10.1016/j.xinn.2024.100685","DOIUrl":"https://doi.org/10.1016/j.xinn.2024.100685","url":null,"abstract":"","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"4 1","pages":""},"PeriodicalIF":32.1,"publicationDate":"2024-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142205059","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}
Pub Date : 2024-07-31DOI: 10.1016/j.xinn.2024.100681
Xin Fan, Lei Chen, Min Chen, Na Zhang, Hong Chang, Mingjie He, Zhenghao Shen, Lanyue Zhang, Hao Ding, Yuyan Xie, Yemei Huang, Weixin Ke, Meng Xiao, Xuelei Zang, Heping Xu, Wenxia Fang, Shaojie Li, Cunwei Cao, Yingchun Xu, Shiguang Shan, Wenjuan Wu, Changbin Chen, Xinying Xue, Linqi Wang
Strains from the species complex (CGSC) have caused the Pacific Northwest cryptococcosis outbreak, the largest cluster of life-threatening fungal infections in otherwise healthy human hosts known to date. In this study, we utilized a pan-phenome-based method to assess the fitness outcomes of CGSC strains under 31 stress conditions, providing a comprehensive overview of 2,821 phenotype-strain associations within this pathogenic clade. Phenotypic clustering analysis revealed a strong correlation between distinct types of stress phenotypes in a subset of CGSC strains, suggesting that shared determinants coordinate their adaptations to various stresses. Notably, a specific group of strains, including the outbreak isolates, exhibited a remarkable ability to adapt to all three of the most commonly used antifungal drugs for treating cryptococcosis (amphotericin B, 5-fluorocytosine, and fluconazole). By integrating pan-genomic and pan-transcriptomic analyses, we identified previously unrecognized genes that play crucial roles in conferring multidrug resistance in an outbreak strain with high multidrug adaptation. From these genes, we identified biomarkers that enable the accurate prediction of highly multidrug-adapted CGSC strains, achieving maximum accuracy and area under the curve (AUC) of 0.79 and 0.86, respectively, using machine learning algorithms. Overall, we developed a pan-omic approach to identify cryptococcal multidrug resistance determinants and predict highly multidrug-adapted CGSC strains that may pose significant clinical concern.
{"title":"Pan-omics-based characterization and prediction of highly multidrug-adapted strains from an outbreak fungal species complex","authors":"Xin Fan, Lei Chen, Min Chen, Na Zhang, Hong Chang, Mingjie He, Zhenghao Shen, Lanyue Zhang, Hao Ding, Yuyan Xie, Yemei Huang, Weixin Ke, Meng Xiao, Xuelei Zang, Heping Xu, Wenxia Fang, Shaojie Li, Cunwei Cao, Yingchun Xu, Shiguang Shan, Wenjuan Wu, Changbin Chen, Xinying Xue, Linqi Wang","doi":"10.1016/j.xinn.2024.100681","DOIUrl":"https://doi.org/10.1016/j.xinn.2024.100681","url":null,"abstract":"Strains from the species complex (CGSC) have caused the Pacific Northwest cryptococcosis outbreak, the largest cluster of life-threatening fungal infections in otherwise healthy human hosts known to date. In this study, we utilized a pan-phenome-based method to assess the fitness outcomes of CGSC strains under 31 stress conditions, providing a comprehensive overview of 2,821 phenotype-strain associations within this pathogenic clade. Phenotypic clustering analysis revealed a strong correlation between distinct types of stress phenotypes in a subset of CGSC strains, suggesting that shared determinants coordinate their adaptations to various stresses. Notably, a specific group of strains, including the outbreak isolates, exhibited a remarkable ability to adapt to all three of the most commonly used antifungal drugs for treating cryptococcosis (amphotericin B, 5-fluorocytosine, and fluconazole). By integrating pan-genomic and pan-transcriptomic analyses, we identified previously unrecognized genes that play crucial roles in conferring multidrug resistance in an outbreak strain with high multidrug adaptation. From these genes, we identified biomarkers that enable the accurate prediction of highly multidrug-adapted CGSC strains, achieving maximum accuracy and area under the curve (AUC) of 0.79 and 0.86, respectively, using machine learning algorithms. Overall, we developed a pan-omic approach to identify cryptococcal multidrug resistance determinants and predict highly multidrug-adapted CGSC strains that may pose significant clinical concern.","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"18 1","pages":""},"PeriodicalIF":32.1,"publicationDate":"2024-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141969450","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}
Pub Date : 2024-06-29DOI: 10.1016/j.xinn.2024.100671
Zeyu Du, Feng Qiao, Liping Tong, Wentai Zhang, Xiaohui Mou, Xin Zhao, Manfred F. Maitz, Huaiyu Wang, Nan Huang, Zhilu Yang
Universal coatings with versatile surface adhesion, good mechanochemical robustness, and the capacity for secondary modification are of great scientific interest. However, incorporating these advantages into a system is still a great challenge. Here, we report a series of catechol-decorated polyallylamines (CPAs), denoted as pseudo- foot protein 5 (-Mefp-5), that mimic not only the catechol and amine groups but also the backbone of Mefp-5. CPAs can fabricate highly adhesive, robust, multifunctional polyCPA (PCPA) coatings based on synergetic catechol-polyamine chemistry as universal building blocks. Due to the interpenetrating entangled network architectures, these coatings exhibit high chemical robustness against harsh conditions (HCl, pH 1; NaOH, pH 14; HO, 30%), good mechanical robustness, and wear resistance. In addition, PCPA coatings provide abundant grafting sites, enabling the fabrication of various functional surfaces through secondary modification. Furthermore, the versatility, multifaceted robustness, and scalability of PCPA coatings indicate their great potential for surface engineering, especially for withstanding harsh conditions in multipurpose biomedical applications.
{"title":"Mimicking Mytilus edulis foot protein: A versatile strategy for robust biomedical coatings","authors":"Zeyu Du, Feng Qiao, Liping Tong, Wentai Zhang, Xiaohui Mou, Xin Zhao, Manfred F. Maitz, Huaiyu Wang, Nan Huang, Zhilu Yang","doi":"10.1016/j.xinn.2024.100671","DOIUrl":"https://doi.org/10.1016/j.xinn.2024.100671","url":null,"abstract":"Universal coatings with versatile surface adhesion, good mechanochemical robustness, and the capacity for secondary modification are of great scientific interest. However, incorporating these advantages into a system is still a great challenge. Here, we report a series of catechol-decorated polyallylamines (CPAs), denoted as pseudo- foot protein 5 (-Mefp-5), that mimic not only the catechol and amine groups but also the backbone of Mefp-5. CPAs can fabricate highly adhesive, robust, multifunctional polyCPA (PCPA) coatings based on synergetic catechol-polyamine chemistry as universal building blocks. Due to the interpenetrating entangled network architectures, these coatings exhibit high chemical robustness against harsh conditions (HCl, pH 1; NaOH, pH 14; HO, 30%), good mechanical robustness, and wear resistance. In addition, PCPA coatings provide abundant grafting sites, enabling the fabrication of various functional surfaces through secondary modification. Furthermore, the versatility, multifaceted robustness, and scalability of PCPA coatings indicate their great potential for surface engineering, especially for withstanding harsh conditions in multipurpose biomedical applications.","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"1 1","pages":""},"PeriodicalIF":32.1,"publicationDate":"2024-06-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141778578","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}
Research on returned samples can provide ground truth for the study of the geological evolution history of the Moon. However, previous missions all collected samples from the near side of the Moon, which is significantly different from the far side of the Moon in terms of the thickness of the lunar crust, magma activity, and composition. Therefore, the samples from the far side of the Moon are of great significance for a comprehensive understanding of the history of the Moon. China’s Chang’e-6 (CE-6) probe has successfully landed on the lunar far side and will return samples in the coming days. With the precise location of the CE-6 landing site, a detailed analysis of the geological background is conducted in this research. The landing site of CE-6 is within the Apollo crater, which is inside the largest impact basin on the Moon, i.e., the South Pole-Aitken (SPA) basin. According to the numerical simulation of the formation process of the SPA basin, CE-6 landed at the edge of the SPA impact melting zone, which is presumably composed of impact melt of the lunar mantle. The Apollo crater subsequently excavated deep material again, which constitutes the basement of the CE-6 landing area. Later, erupted basalt covered these basement rocks, and they also constitute the main source of the CE-6 samples. Based on the dating method of crater size-frequency distribution, we find that the basalt is ∼2.50 Ga. The CE-6 samples also possibly contain basement rocks as excavated and ejected by craters, and they can provide crucial information for our understanding of lunar geological history along with the basalt samples.
{"title":"Geological context of the Chang’e-6 landing area and implications for sample analysis","authors":"Zongyu Yue, Sheng Gou, Shujuan Sun, Wei Yang, Yi Chen, Yexin Wang, Honglei Lin, Kaichang Di, Yangting Lin, Xianhua Li, Fuyuan Wu","doi":"10.1016/j.xinn.2024.100663","DOIUrl":"https://doi.org/10.1016/j.xinn.2024.100663","url":null,"abstract":"Research on returned samples can provide ground truth for the study of the geological evolution history of the Moon. However, previous missions all collected samples from the near side of the Moon, which is significantly different from the far side of the Moon in terms of the thickness of the lunar crust, magma activity, and composition. Therefore, the samples from the far side of the Moon are of great significance for a comprehensive understanding of the history of the Moon. China’s Chang’e-6 (CE-6) probe has successfully landed on the lunar far side and will return samples in the coming days. With the precise location of the CE-6 landing site, a detailed analysis of the geological background is conducted in this research. The landing site of CE-6 is within the Apollo crater, which is inside the largest impact basin on the Moon, i.e., the South Pole-Aitken (SPA) basin. According to the numerical simulation of the formation process of the SPA basin, CE-6 landed at the edge of the SPA impact melting zone, which is presumably composed of impact melt of the lunar mantle. The Apollo crater subsequently excavated deep material again, which constitutes the basement of the CE-6 landing area. Later, erupted basalt covered these basement rocks, and they also constitute the main source of the CE-6 samples. Based on the dating method of crater size-frequency distribution, we find that the basalt is ∼2.50 Ga. The CE-6 samples also possibly contain basement rocks as excavated and ejected by craters, and they can provide crucial information for our understanding of lunar geological history along with the basalt samples.","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"852 1","pages":""},"PeriodicalIF":32.1,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548797","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}
Pub Date : 2024-06-21DOI: 10.1016/j.xinn.2024.100662
Aimei Zhou, Zhecheng Sun, Lei Sun
The past century has witnessed the flourishing of organic radical chemistry. Stable organic radicals are highly valuable for quantum technologies thanks to their inherent room temperature quantum coherence, atomic-level designability, and fine tunability. In this comprehensive review, we highlight the potential of stable organic radicals as high-temperature qubits and explore their applications in quantum information science, which remain largely underexplored. Firstly, we summarize known spin dynamic properties of stable organic radicals and examine factors that influence their electron spin relaxation and decoherence times. This examination reveals their design principles and optimal operating conditions. We further discuss their integration in solid-state materials and surface structures, and present their state-of-the-art applications in quantum computing, quantum memory, and quantum sensing. Finally, we analyze the primary challenges associated with stable organic radical qubits and provide tentative insights to future research directions.
{"title":"Stable organic radical qubits and their applications in quantum information science","authors":"Aimei Zhou, Zhecheng Sun, Lei Sun","doi":"10.1016/j.xinn.2024.100662","DOIUrl":"https://doi.org/10.1016/j.xinn.2024.100662","url":null,"abstract":"The past century has witnessed the flourishing of organic radical chemistry. Stable organic radicals are highly valuable for quantum technologies thanks to their inherent room temperature quantum coherence, atomic-level designability, and fine tunability. In this comprehensive review, we highlight the potential of stable organic radicals as high-temperature qubits and explore their applications in quantum information science, which remain largely underexplored. Firstly, we summarize known spin dynamic properties of stable organic radicals and examine factors that influence their electron spin relaxation and decoherence times. This examination reveals their design principles and optimal operating conditions. We further discuss their integration in solid-state materials and surface structures, and present their state-of-the-art applications in quantum computing, quantum memory, and quantum sensing. Finally, we analyze the primary challenges associated with stable organic radical qubits and provide tentative insights to future research directions.","PeriodicalId":36121,"journal":{"name":"The Innovation","volume":"61 1","pages":""},"PeriodicalIF":32.1,"publicationDate":"2024-06-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141548798","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}
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