Pub Date : 2026-01-01Epub Date: 2024-05-28DOI: 10.1016/j.fmre.2024.05.010
Jie Zang , Zhipeng Lin , Chaowei Ding , DongXiao Bian , Junjun Pan , Xiaodong Tang
Background
Due to the considerable risk of trauma, traditional open surgery has been gradually replaced by minimally invasive surgery using tunnel screws. However, during minimally invasive pelvic surgery, surgical navigation can be improved by effectively using the augmented reality technique. This can further improve the accuracy of the surgery and reduce risks.
Methods
This study adopts a registration approach based on the patient coordinate system and uses a specific manual setting comparison method to select the suitable 3D corner detection parameters.
Results
After experiments, this strategy can effectively improve the accuracy of positioning during surgery. It achieves a balance in detection time and accuracy, which further reduces risks and injuries during surgery.
Conclusions
Our technique can achieve more precise and safer results during minimally invasive pelvic surgery, which shows its great value and potential in the clinic.
{"title":"Augmented reality navigation for precise implantation of LC2 pelvic tunnel screws in minimally invasive surgery","authors":"Jie Zang , Zhipeng Lin , Chaowei Ding , DongXiao Bian , Junjun Pan , Xiaodong Tang","doi":"10.1016/j.fmre.2024.05.010","DOIUrl":"10.1016/j.fmre.2024.05.010","url":null,"abstract":"<div><h3>Background</h3><div>Due to the considerable risk of trauma, traditional open surgery has been gradually replaced by minimally invasive surgery using tunnel screws. However, during minimally invasive pelvic surgery, surgical navigation can be improved by effectively using the augmented reality technique. This can further improve the accuracy of the surgery and reduce risks.</div></div><div><h3>Methods</h3><div>This study adopts a registration approach based on the patient coordinate system and uses a specific manual setting comparison method to select the suitable 3D corner detection parameters.</div></div><div><h3>Results</h3><div>After experiments, this strategy can effectively improve the accuracy of positioning during surgery. It achieves a balance in detection time and accuracy, which further reduces risks and injuries during surgery.</div></div><div><h3>Conclusions</h3><div>Our technique can achieve more precise and safer results during minimally invasive pelvic surgery, which shows its great value and potential in the clinic.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 338-346"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057354","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 : 2026-01-01Epub Date: 2023-11-02DOI: 10.1016/j.fmre.2023.09.004
Xiong Chen , Runnan Shen , Lin Lv , Dongxi Zhu , Guochang You , Zhenluan Tian , Jinwei Chen , Shen Lin , Jiatang Xu , Guibin Hong , Hu Li , Mingli Luo , Lin Cao , Shaoxu Wu , Kai Huang
Cancer can educate platelets by altering transcriptome profiles. However, the exact education mechanism remains unclear, and the variability of tumor-educated platelet (TEP) transcriptome has not been investigated. In this study, we aimed to build a stratification system for TEP based on machine learning (ML) data-driven patterns and platelet transcriptome profiles. This study included platelet samples from 1,628 cancer participants from European and United States populations, including 18 different and most prevalent types of cancer. Gaussian mixture model (GMM) was used to identify robust clusters and similar education pattern. While extreme gradient boosting (XGBoost) was used to precisely predict the clusters. Three clusters were eventually identified. The cluster results showed robustness and generality, reflected by comparable patterns of important gene expression, cancer type prevalence, and biological annotation across derivation, evaluation and validation cohorts. Cluster 1 (n = 346), mainly participated in drug metabolism cytochrome P450, metabolism of xenobiotics by cytochrome P450, and glutathione metabolism. Cluster 2 (n = 538) mainly participated in ribosome, spliceosome, and primary immunodeficiency. Cluster 3 (n = 744) mainly participated in gap junction and focal adhesion. Based on this novel cluster system, further observational study can investigate the association between these clusters and cancer progression, prognosis, cancer associated thrombosis, treatment resistance (both chemotherapy and immunotherapy), and immune cell infiltration. Overall, in this study, we built the first pan-cancer TEP stratification system based on data-driven patterns of ML and platelet transcriptional profiles. These clusters could help us better understand the variability of the pan-cancer education mechanism.
{"title":"Unsupervised and supervised machine learning to identify variability of tumor-educated platelets and association with pan-cancer: A cross-national study","authors":"Xiong Chen , Runnan Shen , Lin Lv , Dongxi Zhu , Guochang You , Zhenluan Tian , Jinwei Chen , Shen Lin , Jiatang Xu , Guibin Hong , Hu Li , Mingli Luo , Lin Cao , Shaoxu Wu , Kai Huang","doi":"10.1016/j.fmre.2023.09.004","DOIUrl":"10.1016/j.fmre.2023.09.004","url":null,"abstract":"<div><div>Cancer can educate platelets by altering transcriptome profiles. However, the exact education mechanism remains unclear, and the variability of tumor-educated platelet (TEP) transcriptome has not been investigated. In this study, we aimed to build a stratification system for TEP based on machine learning (ML) data-driven patterns and platelet transcriptome profiles. This study included platelet samples from 1,628 cancer participants from European and United States populations, including 18 different and most prevalent types of cancer. Gaussian mixture model (GMM) was used to identify robust clusters and similar education pattern. While extreme gradient boosting (XGBoost) was used to precisely predict the clusters. Three clusters were eventually identified. The cluster results showed robustness and generality, reflected by comparable patterns of important gene expression, cancer type prevalence, and biological annotation across derivation, evaluation and validation cohorts. Cluster 1 (<em>n</em> = 346), mainly participated in drug metabolism cytochrome P450, metabolism of xenobiotics by cytochrome P450, and glutathione metabolism. Cluster 2 (<em>n</em> = 538) mainly participated in ribosome, spliceosome, and primary immunodeficiency. Cluster 3 (<em>n</em> = 744) mainly participated in gap junction and focal adhesion. Based on this novel cluster system, further observational study can investigate the association between these clusters and cancer progression, prognosis, cancer associated thrombosis, treatment resistance (both chemotherapy and immunotherapy), and immune cell infiltration. Overall, in this study, we built the first pan-cancer TEP stratification system based on data-driven patterns of ML and platelet transcriptional profiles. These clusters could help us better understand the variability of the pan-cancer education mechanism.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 498-508"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135373145","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}
Wound dressings are highly desirable for mitigating pathogenic bacterial infections. Sterilized cotton fabric is a widely used medical dressing, facilitating wound healing, mitigating pathogenic infections, and reducing treatment expenses. Nevertheless, untreated cotton fabric lacks intrinsic antibacterial properties. In this study, we introduced antibiotics-loaded aminopropyl and octadecyl grafted mesoporous silica nanoparticles onto the surface of hydrophobized cotton fabric. The obtained wound dressing exhibited remarkable antibacterial efficacy against Escherichia coli and Staphylococcus aureus through sustained antibiotic release. In vivo assessments verified that this intelligent cotton fabric dressing accelerates wound healing and prevents adhesion to skin tissues. Additionally, the reusability, hydrophobic nature, and straightforward synthesis methodology collectively provide an alternative solution to smart wound dressings for biomedical applications.
{"title":"Enhancement of antibacterial and wound healing capabilities of cotton fabric through the covalent bonding of antibiotic-loaded hydrophobized mesoporous silica nanoparticles","authors":"Ruiqi Zhang , Chao Yao , Atif Saleem , Yumei Qian , Pengfei Wang , Rui Zhang , Shengcai Qi , Yuezhou Zhang","doi":"10.1016/j.fmre.2023.08.012","DOIUrl":"10.1016/j.fmre.2023.08.012","url":null,"abstract":"<div><div>Wound dressings are highly desirable for mitigating pathogenic bacterial infections. Sterilized cotton fabric is a widely used medical dressing, facilitating wound healing, mitigating pathogenic infections, and reducing treatment expenses. Nevertheless, untreated cotton fabric lacks intrinsic antibacterial properties. In this study, we introduced antibiotics-loaded aminopropyl and octadecyl grafted mesoporous silica nanoparticles onto the surface of hydrophobized cotton fabric. The obtained wound dressing exhibited remarkable antibacterial efficacy against <em>Escherichia coli</em> and <em>Staphylococcus aureus</em> through sustained antibiotic release. <em>In vivo</em> assessments verified that this intelligent cotton fabric dressing accelerates wound healing and prevents adhesion to skin tissues. Additionally, the reusability, hydrophobic nature, and straightforward synthesis methodology collectively provide an alternative solution to smart wound dressings for biomedical applications.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 509-520"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138626128","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 : 2026-01-01Epub Date: 2024-04-18DOI: 10.1016/j.fmre.2024.03.027
Sujuan Duan , Yajun Zeng , Hong-Bin Wang , Hong-Lei Jin
Chloroplasts have their own genomes, as do the nucleus and mitochondria. Coordination between these genomic compartments in plant cells is crucial for plant development and adaptation to the environment. However, little attention has been paid to the coordination of genome stability in the chloroplast and other genomic compartments. Several recent studies have shed light on the regulatory mechanisms governing this coordination, demonstrating the importance of communication between the different genomes to maintain genome stability. Here we review the communication of genome stability between chloroplasts and other compartments in plant cells. We also discuss the challenges and opportunities in this exciting research area.
{"title":"Coordination of genome stability: Novel communication pathways between chloroplasts and other compartments in plant cells","authors":"Sujuan Duan , Yajun Zeng , Hong-Bin Wang , Hong-Lei Jin","doi":"10.1016/j.fmre.2024.03.027","DOIUrl":"10.1016/j.fmre.2024.03.027","url":null,"abstract":"<div><div>Chloroplasts have their own genomes, as do the nucleus and mitochondria. Coordination between these genomic compartments in plant cells is crucial for plant development and adaptation to the environment. However, little attention has been paid to the coordination of genome stability in the chloroplast and other genomic compartments. Several recent studies have shed light on the regulatory mechanisms governing this coordination, demonstrating the importance of communication between the different genomes to maintain genome stability. Here we review the communication of genome stability between chloroplasts and other compartments in plant cells. We also discuss the challenges and opportunities in this exciting research area.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 242-245"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140772306","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 : 2026-01-01Epub Date: 2024-01-11DOI: 10.1016/j.fmre.2024.01.002
Guanyu Zhang , Chang Xu , Dong Sun , Qinsheng Wang , Guowei Lu , Qihuang Gong
Photodetection, the conversion of optical signals to electrical signals, plays a pivotal role in optical communication, sensing, and computing. However, with the advent of novel applications such as quantum computing, intelligent driving, high-speed communication, and augmented reality, traditional photodetectors encounter challenges associated with miniaturization, the assurance of high performance, and the need for multifunctionality. These demands have prompted the development of novel photodetectors. One particularly promising avenue involves integrating conventional photodetection with metasurfaces. Metasurfaces facilitate highly localized field manipulation and versatile modes control at the subwavelength scale via plasmon resonance or Mie scattering, thereby enabling superior performance and multifunctionality detection. Consequently, metasurface-enhanced photodetectors have garnered significant attention in recent years. This review provides an overview of the unique roles played by metasurfaces in photodetection and summarizes notable breakthroughs in recent years.
{"title":"Metasurface-tuned light-matter interactions for high-performance photodetectors","authors":"Guanyu Zhang , Chang Xu , Dong Sun , Qinsheng Wang , Guowei Lu , Qihuang Gong","doi":"10.1016/j.fmre.2024.01.002","DOIUrl":"10.1016/j.fmre.2024.01.002","url":null,"abstract":"<div><div>Photodetection, the conversion of optical signals to electrical signals, plays a pivotal role in optical communication, sensing, and computing. However, with the advent of novel applications such as quantum computing, intelligent driving, high-speed communication, and augmented reality, traditional photodetectors encounter challenges associated with miniaturization, the assurance of high performance, and the need for multifunctionality. These demands have prompted the development of novel photodetectors. One particularly promising avenue involves integrating conventional photodetection with metasurfaces. Metasurfaces facilitate highly localized field manipulation and versatile modes control at the subwavelength scale via plasmon resonance or Mie scattering, thereby enabling superior performance and multifunctionality detection. Consequently, metasurface-enhanced photodetectors have garnered significant attention in recent years. This review provides an overview of the unique roles played by metasurfaces in photodetection and summarizes notable breakthroughs in recent years.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 111-125"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139631419","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 : 2026-01-01Epub Date: 2024-05-11DOI: 10.1016/j.fmre.2024.05.002
Changchun Song , Alain N. Rousseau , Yanyu Song , Yang Ou , Ning Chen , Xianwei Wang , Li Sun , Yuedong Guo , Hao Zhang , Zhengang Zhang , Zhuohang Xin
Permafrost wetlands are closely related to potential greenhouse gas emissions under climate warming. In recent decades, climate change and human activities have induced extensive permafrost degradation, severely influencing the stability of wetlands in permafrost regions. The widely observed significant changes in vegetation cover, hydrological conditions, and soil carbon stability are strongly affecting the carbon cycle and the carbon sources/sinks of permafrost wetlands. In this review, research progress on the response and feedback mechanisms of wetland ecological processes to permafrost degradation under the influences of climate change is first explored, including the impacts of permafrost degradation on the vegetation dynamics, hydrological processes, soil carbon decomposition, greenhouse gas emissions, and carbon feedback. In addition, several questions regarding recent advances are raised and some suggestions are provided for future related research pertaining to the following issues: (i) linkages and response relationships between permafrost degradation and the vegetation-hydrology-carbon cycle in permafrost wetlands, (ii) stabilization mechanisms of their carbon sink function, (iii) accurate estimation of the carbon sequestration rate and sink potential, and (iv) carbon feedback in permafrost wetlands under future climate change scenarios. The findings will provide critical scientific evidence and data support for protecting wetland ecosystems in permafrost regions under changing climate conditions and the implementation of carbon peaking and carbon neutrality strategies.
{"title":"Research progress and perspectives on ecological processes and carbon feedback in permafrost wetlands under changing climate conditions","authors":"Changchun Song , Alain N. Rousseau , Yanyu Song , Yang Ou , Ning Chen , Xianwei Wang , Li Sun , Yuedong Guo , Hao Zhang , Zhengang Zhang , Zhuohang Xin","doi":"10.1016/j.fmre.2024.05.002","DOIUrl":"10.1016/j.fmre.2024.05.002","url":null,"abstract":"<div><div>Permafrost wetlands are closely related to potential greenhouse gas emissions under climate warming. In recent decades, climate change and human activities have induced extensive permafrost degradation, severely influencing the stability of wetlands in permafrost regions. The widely observed significant changes in vegetation cover, hydrological conditions, and soil carbon stability are strongly affecting the carbon cycle and the carbon sources/sinks of permafrost wetlands. In this review, research progress on the response and feedback mechanisms of wetland ecological processes to permafrost degradation under the influences of climate change is first explored, including the impacts of permafrost degradation on the vegetation dynamics, hydrological processes, soil carbon decomposition, greenhouse gas emissions, and carbon feedback. In addition, several questions regarding recent advances are raised and some suggestions are provided for future related research pertaining to the following issues: (i) linkages and response relationships between permafrost degradation and the vegetation-hydrology-carbon cycle in permafrost wetlands, (ii) stabilization mechanisms of their carbon sink function, (iii) accurate estimation of the carbon sequestration rate and sink potential, and (iv) carbon feedback in permafrost wetlands under future climate change scenarios. The findings will provide critical scientific evidence and data support for protecting wetland ecosystems in permafrost regions under changing climate conditions and the implementation of carbon peaking and carbon neutrality strategies.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 270-280"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141051418","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 : 2026-01-01Epub Date: 2025-03-08DOI: 10.1016/j.fmre.2025.03.001
Yufei Zhang , Yanyan Guo , Hangxing Jia , Huijing Ma , Shengjun Tan , Yong E. Zhang
As a Nobel Prize-winning discovery, transposable elements, or “jumping genes”, have attracted significant interest due to their roles in providing functional coding and regulatory sequences. A longstanding hypothesis suggests that somatic transposition may preferentially occur in the mammalian brain, contributing to neuronal diversity. Here, we aim to provide the latest overview of somatic transposition studies in the human brain. We first introduce the historical context and the limited studies on the functionality of somatic transposition, indicating its pathogenic role. We then highlight the wide variability in somatic transposition rate estimates across studies, discussing the complexities—such as artificial chimeras and the multicopy nature—that contribute to false positive and negative results. We also review the evolving experimental and computational methods designed to mitigate these challenges and briefly cover studies estimating germline transposition rate. Finally, we suggest that advances in single-cell genome amplification methods, coupled with deep learning-based software, could pave the way for more definitive studies on the prevalence and functional role of somatic transposition in the human brain.
{"title":"Jumping in the human brain: A review on somatic transposition","authors":"Yufei Zhang , Yanyan Guo , Hangxing Jia , Huijing Ma , Shengjun Tan , Yong E. Zhang","doi":"10.1016/j.fmre.2025.03.001","DOIUrl":"10.1016/j.fmre.2025.03.001","url":null,"abstract":"<div><div>As a Nobel Prize-winning discovery, transposable elements, or “jumping genes”, have attracted significant interest due to their roles in providing functional coding and regulatory sequences. A longstanding hypothesis suggests that somatic transposition may preferentially occur in the mammalian brain, contributing to neuronal diversity. Here, we aim to provide the latest overview of somatic transposition studies in the human brain. We first introduce the historical context and the limited studies on the functionality of somatic transposition, indicating its pathogenic role. We then highlight the wide variability in somatic transposition rate estimates across studies, discussing the complexities—such as artificial chimeras and the multicopy nature—that contribute to false positive and negative results. We also review the evolving experimental and computational methods designed to mitigate these challenges and briefly cover studies estimating germline transposition rate. Finally, we suggest that advances in single-cell genome amplification methods, coupled with deep learning-based software, could pave the way for more definitive studies on the prevalence and functional role of somatic transposition in the human brain.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 11-19"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057284","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 : 2026-01-01Epub Date: 2024-09-17DOI: 10.1016/j.fmre.2024.06.016
Xiu-Shen Wei , He-Yang Xu , Ye Wu , Xiaoming Liu , Ruru Gao , Jiacheng Liu , Bowen Du
Survival analysis is a critical tool for cancer research, yet handling censored data remains challenging due to supervision bias and inaccurate hazard estimates. To address these issues, we propose a simple but effective method termed KD, which employs knowledge distillation using uncensored data to rectify the supervision bias in censored data. This approach leverages the combined power of both rectified censored data and uncensored data to improve survival prediction accuracy. Remarkably, our KD method not only effectively harnesses censored data but also better reflects clinical reality, demonstrating its immense value in survival analysis. We applied our KD method to 19 target cancer sites using The Cancer Genome Atlas (TCGA) dataset. Our results consistently outperform traditional machine learning and deep learning-based methods across both target cancer sites and independent cancer cohorts. More importantly, our data-driven approach enables the model to extract hidden information from censored data, leading to conclusions that align more closely with clinical knowledge and scenarios. This validation of our KD method’s effectiveness highlights the substantial value of rational censored data usage, providing valuable insights for cancer research and clinical decisions. All data and codes are freely available at: https://datatellstruth.github.io/.
{"title":"Data tells the truth: A Knowledge distillation method for genomic survival analysis by handling censoring","authors":"Xiu-Shen Wei , He-Yang Xu , Ye Wu , Xiaoming Liu , Ruru Gao , Jiacheng Liu , Bowen Du","doi":"10.1016/j.fmre.2024.06.016","DOIUrl":"10.1016/j.fmre.2024.06.016","url":null,"abstract":"<div><div>Survival analysis is a critical tool for cancer research, yet handling censored data remains challenging due to supervision bias and inaccurate hazard estimates. To address these issues, we propose a simple but effective method termed KD, which employs knowledge distillation using uncensored data to rectify the supervision bias in censored data. This approach leverages the combined power of both rectified censored data and uncensored data to improve survival prediction accuracy. Remarkably, our KD method not only effectively harnesses censored data but also better reflects clinical reality, demonstrating its immense value in survival analysis. We applied our KD method to 19 target cancer sites using The Cancer Genome Atlas (TCGA) dataset. Our results consistently outperform traditional machine learning and deep learning-based methods across both target cancer sites and independent cancer cohorts. More importantly, our data-driven approach enables the model to extract hidden information from censored data, leading to conclusions that align more closely with clinical knowledge and scenarios. This validation of our KD method’s effectiveness highlights the substantial value of rational censored data usage, providing valuable insights for cancer research and clinical decisions. All data and codes are freely available at: <span><span>https://datatellstruth.github.io/</span><svg><path></path></svg></span>.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 432-440"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057376","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}
Vortex-induced vibration (VIV) of a bluff body is well known as a canonical phenomenon in complex fluid–structure interactions (FSI). However, our understanding and physical theories of this phenomenon are still restricted to a lower Reynolds number (Re) range owing to the limitations of experimental fluid mechanics. Herein, we describe a virtual physical framework (VPF) capable of editing and controlling the physical parameters of an actual physical system with high fidelity by combining numerical disciplinary and mechanical actuators. We demonstrated the effectiveness of applying a VPF to address the experimental fluid mechanical challenges of VIV for a bluff body at a high Re by virtualizing a large, flexibly mounted rigid cylindrical system. We observed the VIV evolution of the bluff body at different Re values. Notably, the VIV appears in its “soar” stages with unexpected amplitudes of 2.4 D, nearly 200% higher than the traditionally acknowledged value at approximately Re = 2.0E5, while suddenly entering into its “death” stages with no vibrations over the critical Re region. The dissynchrony changes in the energy dissipation and input with Re caused by drag and excitation forces in the fluid system were further found to result in these VIV phenomena. This discovery upsets previous perceptions of VIVs and raises profound questions regarding related engineering projects. The VPF also opens a promising paradigm in experimental research for accelerating scientific discovery and investigating unaddressed classical physical phenomena.
{"title":"Virtual physical framework reveals vortex-induced vibration “Soar” and “Death” for a bluff body at high Reynolds numbers","authors":"Haojie Ren , Shixiao Fu , Mengmeng Zhang , Yuwang Xu , Hao Ren","doi":"10.1016/j.fmre.2024.05.011","DOIUrl":"10.1016/j.fmre.2024.05.011","url":null,"abstract":"<div><div>Vortex-induced vibration (VIV) of a bluff body is well known as a canonical phenomenon in complex fluid–structure interactions (FSI). However, our understanding and physical theories of this phenomenon are still restricted to a lower Reynolds number (<em>Re</em>) range owing to the limitations of experimental fluid mechanics. Herein, we describe a virtual physical framework (VPF) capable of editing and controlling the physical parameters of an actual physical system with high fidelity by combining numerical disciplinary and mechanical actuators. We demonstrated the effectiveness of applying a VPF to address the experimental fluid mechanical challenges of VIV for a bluff body at a high <em>Re</em> by virtualizing a large, flexibly mounted rigid cylindrical system. We observed the VIV evolution of the bluff body at different <em>Re</em> values. Notably, the VIV appears in its “soar” stages with unexpected amplitudes of 2.4 D, nearly 200% higher than the traditionally acknowledged value at approximately <em>Re</em> = 2.0E5, while suddenly entering into its “death” stages with no vibrations over the critical <em>Re</em> region. The dissynchrony changes in the energy dissipation and input with <em>Re</em> caused by drag and excitation forces in the fluid system were further found to result in these VIV phenomena. This discovery upsets previous perceptions of VIVs and raises profound questions regarding related engineering projects. The VPF also opens a promising paradigm in experimental research for accelerating scientific discovery and investigating unaddressed classical physical phenomena.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 347-357"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057355","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 : 2026-01-01Epub Date: 2024-12-20DOI: 10.1016/j.fmre.2024.11.027
Nianzu Yang , Huaijin Wu , Kaipeng Zeng , Yang Li , Siyuan Bao , Junchi Yan
Machine learning, particularly graph learning, is gaining increasing recognition for its transformative impact across various fields. One such promising application is in the realm of molecule design and discovery, notably within the pharmaceutical industry. Our survey offers a comprehensive overview of state-of-the-art methods in molecule design, particularly focusing on de novo drug design, which incorporates (deep) graph learning techniques. We categorize these methods into three distinct groups: i) all-at-once, ii) fragment-based, and iii) node-by-node. Additionally, we introduce some key public datasets and outline the commonly used evaluation metrics for both the generation and optimization of molecules. In the end, we discuss the existing challenges in this field and suggest potential directions for future research.
{"title":"Molecule generation for drug design: A graph learning perspective","authors":"Nianzu Yang , Huaijin Wu , Kaipeng Zeng , Yang Li , Siyuan Bao , Junchi Yan","doi":"10.1016/j.fmre.2024.11.027","DOIUrl":"10.1016/j.fmre.2024.11.027","url":null,"abstract":"<div><div>Machine learning, particularly graph learning, is gaining increasing recognition for its transformative impact across various fields. One such promising application is in the realm of molecule design and discovery, notably within the pharmaceutical industry. Our survey offers a comprehensive overview of state-of-the-art methods in molecule design, particularly focusing on <em>de novo</em> drug design, which incorporates (deep) graph learning techniques. We categorize these methods into three distinct groups: <em>i) all-at-once, ii) fragment-based</em>, and <em>iii) node-by-node</em>. Additionally, we introduce some key public datasets and outline the commonly used evaluation metrics for both the generation and optimization of molecules. In the end, we discuss the existing challenges in this field and suggest potential directions for future research.</div></div>","PeriodicalId":34602,"journal":{"name":"Fundamental Research","volume":"6 1","pages":"Pages 40-52"},"PeriodicalIF":6.3,"publicationDate":"2026-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146057567","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}
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