Pub Date : 2026-01-01DOI: 10.1016/j.fmre.2023.10.024
Boyi Cheng , Lei Chen , Lichang Zhou , Qingshan Lin , Jinqi Jiang , Hui Lu , Lei Miao , Xiaonan Feng , Zongping Wang , Guanghao Chen , Gang Guo
Biological nutrient (including nitrogen and phosphorus) removal is often hindered by the lack of organic carbon (C) sources, which can result in the excessive growth of glycogen-accumulating organisms (GAOs), even in sulfate-containing wastewater. Elemental sulfur (S0) has been considered as an economical and energy-efficient electron donor to achieve biological nutrient removal from wastewater. In this study, the long-term effects of C/S0 ratios on the competition between sulfur-mediated bacteria (SMB) and GAOs was investigated to explore the feasibility of using S0 to partially replace carbon and suppress the proliferation of GAOs in biological treatment systems. Four parallel bioreactors were continuously operated for approximately 100 days and fed a substrate consisting of 400, 200, 100, and 0 mg acetate-COD/L, in addition to 0.53 g S0/cycle (equal to 400 mg COD/L); the acetate-COD concentrations corresponded to C/S0 ratios of 0.28 (R1), 0.14 (R2), 0.07 (R3), and 0 (R4), respectively. The results showed that a relatively high C/S0 ratio of 0.28 (in R1) and low C/S0 ratios of 0.07 (in R3) and 0 (in R4) enhanced 1) S metabolism, especially anaerobic S0 reduction to form S2−, which was mediated by sulfate/sulfur-reducing bacteria (SRB/S0RB, e.g., Desulfobacter and Desulfuromonas), or 2) S0 oxidation to form sulfate, which was mediated by sulfur-oxidizing bacteria (SOB, e.g., Thiobacillus) to promote their growth over GAOs (e.g., Candidatus_Competibacter). However, when the C/S0 ratio was 0.14 in R2, this reactor displayed a GAO phenotype rather than a SMB phenotype since GAO communities have a higher acetate uptake rate than SMB. Thus, an appropriate amount of S0 addition supported the competitiveness of SMB over GAOs. Finally, the potential mechanism about competition between the two communities (SMB and GAOs) was revealed. This study provides a new mechanistic strategy to promote the proliferation of SMB over GAOs in carbon-deficient wastewater.
{"title":"Sulfur-mediated bacteria outperform glycogen-accumulating organisms in carbon-deficient wastewater: Key role of influent C/S0 ratios","authors":"Boyi Cheng , Lei Chen , Lichang Zhou , Qingshan Lin , Jinqi Jiang , Hui Lu , Lei Miao , Xiaonan Feng , Zongping Wang , Guanghao Chen , Gang Guo","doi":"10.1016/j.fmre.2023.10.024","DOIUrl":"10.1016/j.fmre.2023.10.024","url":null,"abstract":"<div><div>Biological nutrient (including nitrogen and phosphorus) removal is often hindered by the lack of organic carbon (C) sources, which can result in the excessive growth of glycogen-accumulating organisms (GAOs), even in sulfate-containing wastewater. Elemental sulfur (S<sup>0</sup>) has been considered as an economical and energy-efficient electron donor to achieve biological nutrient removal from wastewater. In this study, the long-term effects of C/S<sup>0</sup> ratios on the competition between sulfur-mediated bacteria (SMB) and GAOs was investigated to explore the feasibility of using S<sup>0</sup> to partially replace carbon and suppress the proliferation of GAOs in biological treatment systems. Four parallel bioreactors were continuously operated for approximately 100 days and fed a substrate consisting of 400, 200, 100, and 0 mg acetate-COD/L, in addition to 0.53 g S<sup>0</sup>/cycle (equal to 400 mg COD/L); the acetate-COD concentrations corresponded to C/S<sup>0</sup> ratios of 0.28 (R1), 0.14 (R2), 0.07 (R3), and 0 (R4), respectively. The results showed that a relatively high C/S<sup>0</sup> ratio of 0.28 (in R1) and low C/S<sup>0</sup> ratios of 0.07 (in R3) and 0 (in R4) enhanced 1) S metabolism, especially anaerobic S<sup>0</sup> reduction to form S<sup>2−</sup>, which was mediated by sulfate/sulfur-reducing bacteria (SRB/S<sup>0</sup>RB, e.g., <em>Desulfobacter and Desulfuromonas</em>), or 2) S<sup>0</sup> oxidation to form sulfate, which was mediated by sulfur-oxidizing bacteria (SOB, e.g<em>., Thiobacillus</em>) to promote their growth over GAOs (e.g., <em>Candidatus_Competibacter</em>). However, when the C/S<sup>0</sup> ratio was 0.14 in R2, this reactor displayed a GAO phenotype rather than a SMB phenotype since GAO communities have a higher acetate uptake rate than SMB. Thus, an appropriate amount of S<sup>0</sup> addition supported the competitiveness of SMB over GAOs. Finally, the potential mechanism about competition between the two communities (SMB and GAOs) was revealed. This study provides a new mechanistic strategy to promote the proliferation of SMB over GAOs in carbon-deficient wastewater.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 212-222"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139539045","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2026-01-01DOI: 10.1016/j.fmre.2024.03.004
Mengjie Hao , Yinghui Xie , Zhongshan Chen , Hui Yang , Geoffrey I.N. Waterhouse , Shengqian Ma , Xiangke Wang
Uranium extraction from seawater is a promising approach for ensuring continued uranium fuel supply to the nuclear power industry. However, extracting uranium by this route is challenging due to the low concentration of uranium, high ionic strength, and marine micro-organisms in seawater. Recently, a range of novel porous adsorbent materials have been developed for uranium extraction from ocean water. These adsorbents rely on specific pore characteristics and functional groups (hydroxyl, carboxyl, amidoxime, phosphate, etc.) to achieve a high affinity and selectivity for uranyl ions (UO22+) relative to other ions. Relying strongly on coordination principles, specific binding sites for uranium are assembled in these porous materials, with cooperative actions of several functional groups often used to achieve strong uranium capture and adsorption selectivity. In addition to traditional adsorbents, adsorption-photocatalytic and adsorption-electrocatalytic materials are also being pursued, which include both specific adsorption sites and photocatalytic or electrocatalytic moieties in their frameworks. These innovative strategies allow the conversion of uranyl ions into harvestable solid products (such as UO2 or Na2O(UO3·H2O)x) and result in high extraction efficiencies together with good biofouling resistance. This perspective aims to capture some of the recent breakthroughs in the design of porous materials for selective uranium extraction from seawater.
{"title":"Promising porous materials for uranium extraction from seawater","authors":"Mengjie Hao , Yinghui Xie , Zhongshan Chen , Hui Yang , Geoffrey I.N. Waterhouse , Shengqian Ma , Xiangke Wang","doi":"10.1016/j.fmre.2024.03.004","DOIUrl":"10.1016/j.fmre.2024.03.004","url":null,"abstract":"<div><div>Uranium extraction from seawater is a promising approach for ensuring continued uranium fuel supply to the nuclear power industry. However, extracting uranium by this route is challenging due to the low concentration of uranium, high ionic strength, and marine micro-organisms in seawater. Recently, a range of novel porous adsorbent materials have been developed for uranium extraction from ocean water. These adsorbents rely on specific pore characteristics and functional groups (hydroxyl, carboxyl, amidoxime, phosphate, etc.) to achieve a high affinity and selectivity for uranyl ions (UO<sub>2</sub><sup>2+</sup>) relative to other ions. Relying strongly on coordination principles, specific binding sites for uranium are assembled in these porous materials, with cooperative actions of several functional groups often used to achieve strong uranium capture and adsorption selectivity. In addition to traditional adsorbents, adsorption-photocatalytic and adsorption-electrocatalytic materials are also being pursued, which include both specific adsorption sites and photocatalytic or electrocatalytic moieties in their frameworks. These innovative strategies allow the conversion of uranyl ions into harvestable solid products (such as UO<sub>2</sub> or Na<sub>2</sub>O(UO<sub>3</sub>·H<sub>2</sub>O)<sub>x</sub>) and result in high extraction efficiencies together with good biofouling resistance. This perspective aims to capture some of the recent breakthroughs in the design of porous materials for selective uranium extraction from seawater.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 170-172"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140281154","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2026-01-01DOI: 10.1016/j.fmre.2023.06.016
Qi Zhang , Chenyang Hu , Xuan Pang
Stemming from the simultaneous activation among multiple metal centers, many multinuclear catalysts show markedly higher reaction rate and selectivity on a wide array of reactions. Inspired by these seminal discoveries, there has been a recent surge of interest in developing polymerization catalysts with three or more metal centers to achieve high activity, stereoselectivity and sequence controllability. In the multinuclear catalysts, the electron-absorbing effect between neighboring Lewis acid atoms was discovered to significantly enhance a multitude of catalytic properties. At the same time, the modification of the organic ligand structure can dramatically change the catalytic activity of the catalyst, widen the scope of copolymerization systems and simplify the catalytic system. In this review, the state-of-the-art design strategies, successful applications and catalytic performance of multinuclear organometallic catalysts are overviewed.
{"title":"Multinuclear catalyst: An efficient tool for the synthesis of polyesters and polycarbonates by ring-opening polymerization","authors":"Qi Zhang , Chenyang Hu , Xuan Pang","doi":"10.1016/j.fmre.2023.06.016","DOIUrl":"10.1016/j.fmre.2023.06.016","url":null,"abstract":"<div><div>Stemming from the simultaneous activation among multiple metal centers, many multinuclear catalysts show markedly higher reaction rate and selectivity on a wide array of reactions. Inspired by these seminal discoveries, there has been a recent surge of interest in developing polymerization catalysts with three or more metal centers to achieve high activity, stereoselectivity and sequence controllability. In the multinuclear catalysts, the electron-absorbing effect between neighboring Lewis acid atoms was discovered to significantly enhance a multitude of catalytic properties. At the same time, the modification of the organic ligand structure can dramatically change the catalytic activity of the catalyst, widen the scope of copolymerization systems and simplify the catalytic system. In this review, the state-of-the-art design strategies, successful applications and catalytic performance of multinuclear organometallic catalysts are overviewed.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 184-200"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135761662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2026-01-01DOI: 10.1016/j.fmre.2025.07.014
Gang Xu, Tong Guo, Ai-Qun Li
Most structural design frameworks remain rooted in outdated assumptions: that hazards occur in isolation, materials do not degrade, and failure can be prevented through overdesign. In an era marked by accelerating climate volatility, cascading disasters, and mounting carbon constraints, such logic is increasingly untenable. From earthquake–flood sequences to heat-induced corrosion and permafrost collapse, modern infrastructure faces compound and evolving risks that current codes fail to anticipate. At the same time, conventional approaches often achieve safety through carbon-intensive construction, exacerbating the very environmental crises they must endure. This rethinking aligns with emerging paradigms in resilience engineering, disaster risk reduction, and adaptive infrastructure design, which similarly emphasize systems thinking, robustness, and long–term functionality under uncertainty. We argue for a fundamental redefinition of structural safety—one that prioritizes resilience over resistance, adaptability over rigidity, and sustainability over excess. This requires innovative tools (AI-driven diagnostics, lifecycle modeling frameworks), new materials (durable, repairable, low-carbon-footprint systems), and quantifiable metrics (recovery duration, embodied carbon emissions, residual functionality assessment). Structural engineers must now lead as strategists of climate-ready, socially responsive infrastructure. The goal of the next generation of design is not merely to ensure that structures survive,but that they serve, recover, and regenerate in a volatile century.
{"title":"Rethinking structural safety for a volatile century","authors":"Gang Xu, Tong Guo, Ai-Qun Li","doi":"10.1016/j.fmre.2025.07.014","DOIUrl":"10.1016/j.fmre.2025.07.014","url":null,"abstract":"<div><div>Most structural design frameworks remain rooted in outdated assumptions: that hazards occur in isolation, materials do not degrade, and failure can be prevented through overdesign. In an era marked by accelerating climate volatility, cascading disasters, and mounting carbon constraints, such logic is increasingly untenable. From earthquake–flood sequences to heat-induced corrosion and permafrost collapse, modern infrastructure faces compound and evolving risks that current codes fail to anticipate. At the same time, conventional approaches often achieve safety through carbon-intensive construction, exacerbating the very environmental crises they must endure. This rethinking aligns with emerging paradigms in resilience engineering, disaster risk reduction, and adaptive infrastructure design, which similarly emphasize systems thinking, robustness, and long–term functionality under uncertainty. We argue for a fundamental redefinition of structural safety—one that prioritizes resilience over resistance, adaptability over rigidity, and sustainability over excess. This requires innovative tools (AI-driven diagnostics, lifecycle modeling frameworks), new materials (durable, repairable, low-carbon-footprint systems), and quantifiable metrics (recovery duration, embodied carbon emissions, residual functionality assessment). Structural engineers must now lead as strategists of climate-ready, socially responsive infrastructure. The goal of the next generation of design is not merely to ensure that structures survive,but that they serve, recover, and regenerate in a volatile century.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 335-337"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057287","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2026-01-01DOI: 10.1016/j.fmre.2024.11.026
Fangkun Sun , Zhilin Guo , Yangfan Lu , Jiang Li , Tian-Nan Ye , Hideo Hosono , Jiazhen Wu
Electrides are emerging materials that exhibit a unique electronic structure, where electrons, unbound to specific atomic nuclei, act as anions within periodic lattice vacancies. The most characteristic feature of an electride is its low work function (ΦWF < ∼3.5 eV), comparable to alkali metals, making it a highly promising electron donor in chemical reactions. In this paper, we summarized recent applications of variable electrides in various reactions, especially as catalysts. We thoroughly explored their unique behaviors and demonstrated their broad applicability in multiple reactions, such as selective hydrogenation, carbon-carbon coupling reactions, and electrocatalysis. In addition, we discussed the current challenges of electrides with active electron anions and highlighted their substantial potential for application in future advancements. This review provides fundamental guidance for utilizing high-performance electride-based materials in various chemical reactions, mainly focusing on heterogeneous catalysis.
{"title":"Electrides: Emerging electronic materials for catalysis","authors":"Fangkun Sun , Zhilin Guo , Yangfan Lu , Jiang Li , Tian-Nan Ye , Hideo Hosono , Jiazhen Wu","doi":"10.1016/j.fmre.2024.11.026","DOIUrl":"10.1016/j.fmre.2024.11.026","url":null,"abstract":"<div><div>Electrides are emerging materials that exhibit a unique electronic structure, where electrons, unbound to specific atomic nuclei, act as anions within periodic lattice vacancies. The most characteristic feature of an electride is its low work function (Φ<sub>WF</sub> < ∼3.5 eV), comparable to alkali metals, making it a highly promising electron donor in chemical reactions. In this paper, we summarized recent applications of variable electrides in various reactions, especially as catalysts. We thoroughly explored their unique behaviors and demonstrated their broad applicability in multiple reactions, such as selective hydrogenation, carbon-carbon coupling reactions, and electrocatalysis. In addition, we discussed the current challenges of electrides with active electron anions and highlighted their substantial potential for application in future advancements. This review provides fundamental guidance for utilizing high-performance electride-based materials in various chemical reactions, mainly focusing on heterogeneous catalysis.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 400-415"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057373","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Immunotherapy has revolutionized cancer treatment by leveraging the immune system to target tumors. However, its efficacy is often limited by the immunosuppressive tumor microenvironment and the development of resistance, leading to response rates of only 20%–30%. Ultrasound-targeted nanobubbles (UTN) combined with cancer immunotherapy present a promising solution to the limitations of current treatments. By utilizing the mechanical and biological effects of ultrasound, UTN improve drug delivery, reduce systemic toxicity, and modulate immune responses within the tumor microenvironment. Preclinical studies have shown that UTN combined with cancer immunotherapy can significantly increase the use of checkpoint inhibitors, tumor vaccines, and gene-based therapies, resulting in better tumor control. This article reviews the latest advancements, applications, and challenges of UTN combined with cancer immunotherapy, emphasizing the potential of UTN to overcome current therapeutic barriers and providing a forward-looking perspective on its translation into clinical practice.
{"title":"Recent advances in ultrasound-targeted nanobubbles combined with cancer immunotherapy: Mechanisms, applications, and challenges","authors":"Xueqin Chen , Lifan Xu , Chen Chen , Qizhao Huang , Jianjun Hu","doi":"10.1016/j.fmre.2024.10.017","DOIUrl":"10.1016/j.fmre.2024.10.017","url":null,"abstract":"<div><div>Immunotherapy has revolutionized cancer treatment by leveraging the immune system to target tumors. However, its efficacy is often limited by the immunosuppressive tumor microenvironment and the development of resistance, leading to response rates of only 20%–30%. Ultrasound-targeted nanobubbles (UTN) combined with cancer immunotherapy present a promising solution to the limitations of current treatments. By utilizing the mechanical and biological effects of ultrasound, UTN improve drug delivery, reduce systemic toxicity, and modulate immune responses within the tumor microenvironment. Preclinical studies have shown that UTN combined with cancer immunotherapy can significantly increase the use of checkpoint inhibitors, tumor vaccines, and gene-based therapies, resulting in better tumor control. This article reviews the latest advancements, applications, and challenges of UTN combined with cancer immunotherapy, emphasizing the potential of UTN to overcome current therapeutic barriers and providing a forward-looking perspective on its translation into clinical practice.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 489-497"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057380","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2026-01-01DOI: 10.1016/j.fmre.2025.07.007
Shao-Zhen Jiang , Liu-Bing Yu , Beilei Shen , Jie Pan , Xiao-Wei Li , Rong-Bo Luo , Ling-Jun Fan , Bing-Shuo Qian , Yunkai Zhu , Ziqiao Wang , Yu Liu , Tingting Li , Xin-Ran Zhang , Yu Yu , Wen Xue , Tian Xia , Hong Cai , Qiu-Ying Han , Kai Wang , Xin Xu , Tao Li
The formation of liquid condensates by nucleocapsid (N) protein and viral RNA is a critical and highly conserved event in the life cycle of numerous viruses. Targeting this process emerges as a possible strategy to combat viral infections. Here, we discover that punicalagin, a natural compound derived from Punica granatum, exhibits potent pan-antiviral activity. Through a screening of 2799 compounds, we identified that punicalagin inhibits the formation of N-RNA condensations at nanomolar concentrations, resulting in significant inhibition of viral replication. The oral administration of punicalagin effectively dampens the viral load in tissues of mice infected with various viruses, such as SARS-CoV-2, vesicular stomatitis virus (VSV) and influenza A virus (IAV). Moreover, we show that punicalagin also blocks the virus-stimulated inflammation by targeting mitochondrial antiviral signaling protein (MAVS), thereby alleviating tissue damage and lethality in the infected animals. Thus, by reporting that punicalagin targets the conserved process across different viruses, our work suggests a new paradigm for developing antiviral therapies against both current and future viral threats.
{"title":"Disruption of the nucleocapsid-RNA condensation by punicalagin is a broad-spectrum antiviral approach","authors":"Shao-Zhen Jiang , Liu-Bing Yu , Beilei Shen , Jie Pan , Xiao-Wei Li , Rong-Bo Luo , Ling-Jun Fan , Bing-Shuo Qian , Yunkai Zhu , Ziqiao Wang , Yu Liu , Tingting Li , Xin-Ran Zhang , Yu Yu , Wen Xue , Tian Xia , Hong Cai , Qiu-Ying Han , Kai Wang , Xin Xu , Tao Li","doi":"10.1016/j.fmre.2025.07.007","DOIUrl":"10.1016/j.fmre.2025.07.007","url":null,"abstract":"<div><div>The formation of liquid condensates by nucleocapsid (N) protein and viral RNA is a critical and highly conserved event in the life cycle of numerous viruses. Targeting this process emerges as a possible strategy to combat viral infections. Here, we discover that punicalagin, a natural compound derived from Punica granatum, exhibits potent pan-antiviral activity. Through a screening of 2799 compounds, we identified that punicalagin inhibits the formation of N-RNA condensations at nanomolar concentrations, resulting in significant inhibition of viral replication. The oral administration of punicalagin effectively dampens the viral load in tissues of mice infected with various viruses, such as SARS-CoV-2, vesicular stomatitis virus (VSV) and influenza A virus (IAV). Moreover, we show that punicalagin also blocks the virus-stimulated inflammation by targeting mitochondrial antiviral signaling protein (MAVS), thereby alleviating tissue damage and lethality in the infected animals. Thus, by reporting that punicalagin targets the conserved process across different viruses, our work suggests a new paradigm for developing antiviral therapies against both current and future viral threats.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 535-547"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"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 : 2026-01-01DOI: 10.1016/j.fmre.2025.08.009
Shiwei Cao , Junwei Liu , Yixue Li
Immune checkpoint blockade (ICB) therapies have revolutionized cancer treatment, showing success across various cancer types. However, there is variability in response rates among different cancers and individual patients. This highlights the critical need for precise patient stratification. Machine Learning and Deep Learning models are increasingly utilized to predict ICB responses by integrating multi-omics data, such as clinical, genomic, radiomic, and transcriptomic information. This review outlines the key methodologies of these predictive models. It underscores their role in enhancing response prediction. We delve into the advanced mechanisms of ICB response and discuss the biological foundations that inform these models. This demonstrates how basic research informs clinical application. We aim to offer comprehensive insights into how artificial intelligence can optimize patient stratification for ICB therapy.
{"title":"Harnessing multi-omics and machine learning for predicting immune checkpoint blockade responses: Advances, challenges, and future directions","authors":"Shiwei Cao , Junwei Liu , Yixue Li","doi":"10.1016/j.fmre.2025.08.009","DOIUrl":"10.1016/j.fmre.2025.08.009","url":null,"abstract":"<div><div>Immune checkpoint blockade (ICB) therapies have revolutionized cancer treatment, showing success across various cancer types. However, there is variability in response rates among different cancers and individual patients. This highlights the critical need for precise patient stratification. Machine Learning and Deep Learning models are increasingly utilized to predict ICB responses by integrating multi-omics data, such as clinical, genomic, radiomic, and transcriptomic information. This review outlines the key methodologies of these predictive models. It underscores their role in enhancing response prediction. We delve into the advanced mechanisms of ICB response and discuss the biological foundations that inform these models. This demonstrates how basic research informs clinical application. We aim to offer comprehensive insights into how artificial intelligence can optimize patient stratification for ICB therapy.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 62-76"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057569","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Multi-omics cancer data provides complementary views of tumorigenesis and progression. Technical challenges exist in integrating these heterogeneous data into deep learning models to better understand tumorigenesis and predict cancer recurrence. We herein propose a novel end-to-end deep learning method (MULGONET) for cancer recurrence prediction and biomarker discovery. First, MULGONET can effectively solve the curse of dimensionality and the lack of model interpretability in multi-omics data integration. Second, it explores interactions and regulatory relationships between genes and GO terms, thus providing biological insights. Benchmark results show that MULGONET outperforms other contemporary classification methods. It achieves AUPRs of 0.774 ± 0.015, 0.873 ± 0.003 and 0.702 ± 0.011 on the bladder, pancreatic and stomach cancer datasets, respectively. We also show that MULGONET can effectively identify prognostic genes and GO terms associated with cancer recurrence.
{"title":"MULGONET: An interpretable neural network framework to integrate multi-omics data for cancer recurrence prediction and biomarker discovery","authors":"Wei Lan , Zhentao Tang , Haibo Liao , Qingfeng Chen , Yi-Ping Phoebe Chen , Zhaolei Zhang , Jianxin Wang","doi":"10.1016/j.fmre.2025.01.004","DOIUrl":"10.1016/j.fmre.2025.01.004","url":null,"abstract":"<div><div>Multi-omics cancer data provides complementary views of tumorigenesis and progression. Technical challenges exist in integrating these heterogeneous data into deep learning models to better understand tumorigenesis and predict cancer recurrence. We herein propose a novel end-to-end deep learning method (MULGONET) for cancer recurrence prediction and biomarker discovery. First, MULGONET can effectively solve the curse of dimensionality and the lack of model interpretability in multi-omics data integration. Second, it explores interactions and regulatory relationships between genes and GO terms, thus providing biological insights. Benchmark results show that MULGONET outperforms other contemporary classification methods. It achieves AUPRs of 0.774 ± 0.015, 0.873 ± 0.003 and 0.702 ± 0.011 on the bladder, pancreatic and stomach cancer datasets, respectively. We also show that MULGONET can effectively identify prognostic genes and GO terms associated with cancer recurrence.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 99-110"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057572","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"综合性期刊","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}