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SpaGRA:Graph augmentation facilitates domain identification for spatially resolved transcriptomics

Journal of Genetics and Genomics 2025年第1期52卷 93-104页

作者： Xue Sun Wei Zhang Wenrui Li Na Yu Daoliang Zhang Qi Zou Qiongye Dong Xianglin Zhang Zhiping Liu Zhiyuan Yuan Rui Gao Center of Intelligent Medicine School of Control Science and EngineeringShandong UniversityJinanShandong 250061China MOE Key Lab of Bioinformatics and Bioinformatics Division of BNRIST Department of AutomationTsinghua UniversityBeijing 100084China Institute of Precision Medicine Peking University Shenzhen HospitalShenzhenGuangdong 518036China Department of Clinical Laboratory The Second HospitalCheeloo College of MedicineShandong UniversityJinanShandong 250033China Institute of Science and Technology for Brain-Inspired Intelligence Center for Medical Research and InnovationShanghai Pudong HospitalFudan University Pudong Medical CenterFudan UniversityShanghai 200433China

Recent advances in spatially resolved transcriptomics(SRT)have provided new opportunities for characterizing spatial structures of various ***-based geometric deep learning has gained widespread adoption for spatial domain identification ***,most methods define adjacency relation between cells or spots by their spatial distance in SRT data,which overlooks key biological interactions like gene expression similarities,and leads to inaccuracies in spatial domain *** tackle this challenge,we propose a novel method,SpaGRA(https://***/sunxue-yy/SpaGRA),for automatic multi-relationship construction based on graph *** uses spatial distance as prior knowledge and dynamically adjusts edge weights with multi-head graph attention networks(GATs).This helps SpaGRA to uncover diverse node relationships and enhance message passing in geometric contrastive ***,SpaGRA uses these multi-view relationships to construct negative samples,addressing sampling bias posed by random *** results show that SpaGRA presents superior domain identification performance on multiple datasets generated from different *** SpaGRA,we analyze the functional regions in the mouse hypothalamus,identify key genes related to heart development in mouse embryos,and observe cancer-associated fibroblasts enveloping cancer cells in the latest Visium HD ***,SpaGRA can effectively characterize spatial structures across diverse SRT datasets.

关键词： Spatial domain identification Spatially resolved transcriptomics Multi-head graph attention networks Graph augmentation Geometric contrastive learning

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Surfactant-mediated transport of polyvinyl chloride nanoplastics in porous media: Influence of natural organic matter, natural inorganic ligands and electrolytes

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Journal of Contaminant Hydrology 2025年 273卷 104597页

作者： Wang, Yujue Wu, Ming Hao, Yanru Li, Hui Mo, Cehui Guangdong Provincial Research Center for Environment Pollution Control and Remediation Materials Engineering Research Center of Tropical and Subtropical Aquatic Ecological Engineering Ministry of Education College of Life Science and Technology Jinan University Guangzhou510632 China

This study investigates the transport behavior of polyvinyl chloride nanoplastics (PVC-NPs) in porous media under surfactant-mediated conditions through a combination of column experiments, numerical simulations, and extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) interaction energy analysis. The effects of different surfactant types, ionic species, ionic strength, humic acid (HA), and phosphate were examined. Results indicate that surfactants enhance the transport of PVC-NPs, with anionic surfactants exhibiting a stronger enhancement effect than cationic ones. Generally, the addition of cations inhibited PVC-NPs transport, with divalent Ca2+ exhibiting a stronger inhibitory effect than monovalent Na+. Interestingly, at low ionic strengths, Na+ had a stronger inhibitory effect than Ca2+. In the presence of anionic surfactants, higher Na+ concentrations promoted PVC-NPs transport. In contrast, both HA and phosphate inhibited PVC-NPs transport under cationic surfactants, with the degree of inhibition positively correlated with their concentrations. However, under anionic surfactants, high concentrations of HA inhibited PVC-NPs transport, while lower concentrations had no significant impact. Phosphate, under anionic surfactant conditions, initially inhibited but subsequently promoted PVC-NPs transport. This study provides a comprehensive understanding of the natural transport and transformation mechanisms of PVC-NPs in the environment under surfactant influence, offering a solid data foundation and theoretical framework for accurately assessing the potential ecological and human health risks posed by nanomaterials. © 2025 Elsevier B.V.

关键词： Cationic surfactants

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DMHFR:Decoder with Multi-Head Feature Receptors for Tract Image Segmentation

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Computers, Materials & Continua 2025年第3期82卷 4841-4862页

作者： Jianuo Huang Bohan Lai Weiye Qiu Caixu Xu Jie He Department of Endoscopy Center Zhongshan Hospital(Xiamen)Fudan UniversityXiamen361015China School of Computing and Data Science Xiamen University MalaysiaSepang43900Malaysia School of Computer Science and Techonology Tongji UniversityShanghai200092China Guangxi Key Laboratory of Machine Vision and Intelligent Control Wuzhou UniversityWuzhou543002China Xiamen Clinical Research Center for Cancer Therapy Xiamen361015China

The self-attention mechanism of Transformers,which captures long-range contextual information,has demonstrated significant potential in image ***,their ability to learn local,contextual relationships between pixels requires further *** methods face challenges in efficiently managing multi-scale fea-tures of different granularities from the encoder backbone,leaving room for improvement in their global representation and feature extraction *** address these challenges,we propose a novel Decoder with Multi-Head Feature Receptors(DMHFR),which receives multi-scale features from the encoder backbone and organizes them into three feature groups with different granularities:coarse,fine-grained,and full *** groups are subsequently processed by Multi-Head Feature Receptors(MHFRs)after feature capture and modeling *** include two Three-Head Feature Receptors(THFRs)and one Four-Head Feature Receptor(FHFR).Each group of features is passed through these MHFRs and then fed into axial transformers,which help the model capture long-range dependencies within the *** three MHFRs produce three distinct feature *** output from the FHFR serves as auxiliary auxiliary features in the prediction head,and the prediction output and their losses will eventually be *** results show that the Transformer using DMHFR outperforms 15 state of the arts(SOTA)methods on five public ***,it achieved significant improvements in mean DICE scores over the classic Parallel Reverse Attention Network(PraNet)method,with gains of 4.1%,2.2%,1.4%,8.9%,and 16.3%on the CVC-ClinicDB,Kvasir-SEG,CVC-T,CVC-ColonDB,and ETIS-LaribPolypDB datasets,respectively.

关键词： Medical image segmentation feature exploration feature aggregation deep learning multi-head feature receptor

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Substrate cultivation system improved the quality of ‘Hongyan’ strawberry fruits compared with the soil cultivation system

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Food Chemistry 2025年 485卷 144430页

作者： Xu, Su Shi, Dajuan Chen, Haijiang Ma, Fengwei Tao, Guangcan Wu, Wenneng Lin, Dong Wu, Siyao Fei, Qiang Hu, Yan Meng, Lingshuai College of Food Science and Engineering Guizhou Engineering Research Center for Characteristic Flavor Perception and Quality Control of Dual-Food Homologous Resources Guiyang University Guiyang550005 China

This study explored the influence of substrate cultivation system on the quality of ‘Hongyan’ strawberry through physicochemical and sensory evaluation, E-nose, GC–MS, and GC-IMS. Results revealed that substrate cultivation system significantly enhanced the formation of total acids, vitamin C, total phenols, and volatile esters, alcohols, and acids in strawberries. Additionally, it improved the hardness, acidity, aroma intensity, and color of the fruit. ROAV analysis of VOCs demonstrated that substrate cultivation system promoted green, floral, citrus, and wood aromatic notes, while introducing unique caramel and mint flavors. Through VIP values, three key physicochemical parameters and several vital volatile esters, alcohols, and aldehydes were identified as essential biomarkers for distinguishing strawberries grown under substrate cultivation system versus soil cultivation system. Correlation analysis underscored significant relationships between VOCs, particularly esters, aldehydes, and alcohols, and a notable positive correlation between ambient temperature, substrate temperature, fertilization frequency, and the physicochemical properties and characteristic VOCs. © 2025 Elsevier Ltd

关键词： Phenols

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The impacts of PVC microplastics on physiology and transcriptomic responses of pearl oyster Pinctada fucata martensii

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Journal of Oceanology and Limnology 2025年第2期43卷 589-613页

作者： Robert MKUYE Luomin HUANG Chuangye YANG Xiuyan YANG Fortunatus MASANJA Salifu IBRAHIM Fenglan LU Shaojie ZHU Hailing WU Yuewen DENG Fisheries College Guangdong Ocean UniversityZhanjiang 524088China Guangdong Science and Innovation Center for Pearl Culture Zhanjiang 524088China Pearl Breeding and Processing Engineering Technology Research Centre of Guangdong Province Zhanjiang 524088China Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture Zhanjiang 524088China Guangdong Marine Ecology Early Warning and Monitoring Laboratory Zhanjiang 524088China

Microplastics(MPs),particularly polyvinyl chloride microplastics(PVC MPs)have become a notable environmental pollutant that affect various marine organisms such as Pinctada fucata *** filter feeders,these bivalves consume significant volumes of water containing MPs,leading to contact with and ingestion of ***,given the ecological and economic importance of *** in artificial pearl production,investigating the effects of PVC MPs exposure is *** study aimed to investigate the effects of PVC MPs exposure on nucleus retention,pearl formation,oxidative stress by examining superoxide dismutase(SOD)activity,catalase(CAT)activity,lipid peroxidation(LPO),and total antioxidant capacity(TAOC)of ***,while also exploring transcriptomic changes at different concentrations and exposure time points,including a recovery *** pearl oysters were exposed to PVC MPs at concentrations of 1-,2.5-,and 5-mg PVC MPs/L for 10 d followed by 6 d of *** 1-,4-,10-d of exposure,and additional 6 d of recovery,samples were taken and *** revealed that only prolonged exposure(10 d)to PVC MPs affected SOD activity,while CAT activity,LPO,and TAOC remained unaffected throughout the ***,SOD activity was restored during the 6-d recovery *** analysis highlighted significant gene alterations linked to various pathways,affecting cellular processes,environmental information processing,genetic information processing,metabolism,and organismal systems,with an increase in pathway-related genes during recovery,implying a potential role of PVC MPs as gene *** study provided insights into the effects of PVC MPs on ***,shedding light on pearl retention,oxidative systems,and molecular pathways influenced by PVC ***,it contributed novel information on potential MPs exposure biomarkers,particularly relevant to marine organisms like ***.

关键词： microplastic(MP) Pinctada fucata martensii oxidative stress transcriptome

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Electric control of excitons in van der Waals antiferromagnet NiPS_(3)

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science China Materials 2025年第3期68卷 928-932页

作者： Han Wang Zhiyong Chen Bo Peng National Engineering Research Center of Electromagnetic Radiation Control Materials School of Electronic Science and EngineeringUniversity of Electronic Science and Technology of ChinaChengdu 611731China Key Laboratory of Multi Spectral Absorbing Materials and Structures of Ministry of Education University of Electronic Science and Technology of ChinaChengdu 611731China

The discovery of ferromagnetic two-dimensional(2D)materials has opened up new avenues for manipulating the spin of single atomic layer or a few atomic layers[1-5],and the magneto-optical coupling has played an important role in revealing the physical phenomena of magnetism at the nanoscale limit[5-8].Among them,excitons coupled to magnetic sequences have garnered significant research interest.

关键词： ferromagnetic limit atomic

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Effect of acid fracturing fluid modifying coal microstructure stimulated by ultrasonic

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International Journal of Mining science and Technology 2025年第2期35卷 275-293页

作者： Shaojie Zuo Rui Gan Zhijie Wen Liang Zhang Zhizhong Jiang Fuping Zhao Chengwei Liu Kun Li Zhiyuan Xu College of Mining Guizhou UniversityGuiyang 550025China Shandong Key Laboratory of Mining Disaster Prevention and Control Shandong University of Science and TechnologyQingdao 266590China School of Emergency Management Xihua UniversityChengdu 610039China Guizhou Research Institute of Oil&Gas Exploration and Development Engineering Guiyang 550022China Liupanshui Normal University Liupanshui 553000China

The combination of ultrasonic and acid fracturing fluid can strengthen the modification effect on the micropore structure of the coal matrix,thereby enhancing the efficiency of the acid fracturing *** this research,acetic acid was utilized to formulate acid fracturing fluids with varying concentrations,and the evolutionary traits of both the acid fracturing fluids and ultrasonic waves in relation to coal samples were *** functional group structure,mineral composition,micropore structure and surface morphology of coal samples were characterized by FTIR,XRD,N_(2)adsorption at low temperature and *** results showed that aromatics(I)and branching parameters(CH_(2)/CH_(3))were reduced by 81.58%and 88.67%,respectively,after 9%acetic acid *** acid can dissolve carbonates and clay minerals in coal,create new pores,and increase porosity,pore volume and pore fractal *** modification by 7%acetic acid,the pore volume increased by 5.7 *** observation shows that the diameter of coal surface holes increases,EDS scanning shows that the content of mineral elements in coal decreases,the connectivity of coal holes increases,and the holes *** findings of this research offer theoretical direction for optimizing ultrasonic-enhanced acid fracturing fluid modification.

关键词： Acidic fracturing fluid Ultrasonic Coalbed methane Microstructure

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Learning from N-tuple similarities and unlabeled data

IEEE Transactions on Artificial Intelligence

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IEEE Transactions on Artificial Intelligence 2025年

作者： Li, Junpeng Huang, Shuying Hua, Changchun Yang, Yana Yanshan University Engineering Research Center Ministry of Education for Intelligent Control System and Intelligent Equipment Qinhuangdao China

Learning from pairwise similarity and unlabeled data (SU) is a recently emerging weakly-supervised learning method, which learns a classifier from similar data pairs (two instances belong to the same class) and unlabeled data. However, this framework is insoluble for triplet similarities and unlabeled data. To address this limitation, this paper develops a framework for learning from triplet similarities (three instances belonging to the same class) and unlabeled data points, denoted as TSU. This framework not only showcases the feasibility of constructing a TSU classifier but also serves as an inspiration to explore the broader challenge of addressing N-tuple similarities (N ≥ 2) and unlabeled data points. To tackle this more generalized problem, the present paper develop an advancing weakly-supervision framework of learning from N-tuple similarities (N instances belong to the same class) and unlabeled data points, named NSU. This framework provides a solid foundation for handling diverse similarity scenarios. Based on these findings, we propose empirical risk minimization estimators for both TSU and NSU classification. The estimation error bounds are also established for the proposed methods. Finally, experiments are performed to verify the effectiveness of the proposed algorithm. © 2020 IEEE.

关键词： Self-supervised learning

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MM-UKAN++: A Novel Kolmogorov–Arnold Network-Based U-Shaped Network for Ultrasound Image Segmentation

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IEEE Transactions on Ultrasonics, Ferroelectrics, and Frequency control 2025年第4期72卷 498-514页

作者： Zhang, Boheng Huang, Haorui Shen, Yi Sun, Mingjian Harbin Institute of Technology Department of Control Science and Engineering Heilongjiang Harbin150001 China Pohang University of Science and Technology Department of Convergence IT Engineering Pohang37673 Korea Republic of Harbin Institute of Technology Suzhou Research Institute Jiangsu Suzhou215000 China Harbin Institute of Technology Department of Information Science and Engineering Shandong Weihai264200 China Harbin Institute of Technology Shandong Weihai264200 China Shandong Laboratory of Advanced Biomaterials and Medical Devices Shandong Weihai264209 China

Ultrasound (US) imaging is an important and commonly used medical imaging modality. Accurate and fast automatic segmentation of regions of interest (ROIs) in US images is essential for enhancing the efficiency of clinical and robot-assisted diagnosis. However, US images suffer from low contrast, fuzzy boundaries, and significant scale variations in ROIs. Existing convolutional neural network (CNN)-based and transformer-based methods struggle with model efficiency and explainability. To address these challenges, we introduce MM-UKAN++, a novel U-shaped network based on Kolmogorov-Arnold networks (KANs). MM-UKAN++ leverages multilevel KAN layers as the encoder and decoder within the U-network architecture and incorporates an innovative multidimensional attention mechanism to refine skip connections by weighting features from frequency-channel and spatial perspectives. In addition, the network effectively integrates multiscale information, fusing outputs from different scale decoders to generate precise segmentation predictions. MM-UKAN++ achieves higher segmentation accuracy with lower computational cost and outperforms other mainstream methods on several open-source datasets for US image segmentation tasks, including achieving 69.42% IoU, 81.30% Dice, and 3.31 mm HD in the BUSI dataset with 3.17 G floating point of operations (FLOPs) and 9.90 M parameters. The excellent performance on our automatic carotid artery US scanning and diagnostic system further proves the speed and accuracy of MM-UKAN++. Besides, the good performance in other medical image segmentation tasks reveals the promising applications of MM-UKAN++. The code is available on GitHub. © 1986-2012 IEEE.

关键词： Image segmentation

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Bifidobacterium breve alleviates gut-liver-axis injury caused by high-fat diet and aflatoxin B_1 in mice

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Food science and Human Wellness 2025年第2期14卷 617-632页

作者： Yongli Ye Tingwei Wang Jian Ji Jia-Sheng Wang Yinzhi Zhang Xiulan Sun International Joint Laboratory on Food Safety Synergetic Innovation Center of Food Safety and Quality ControlSchool of Food Science and TechnologyJiangnan UniversityWuxi 214122China School of Biological and Chemical Engineering Zhejiang University of Science and TechnologyHangzhou 310023China Department of Environmental Health Science College of Public HealthUniversity of GeorgiaAthens 30602USA Yixing Institute of Food and Biotechnology Co. Ltd.Yixing 214200China

Aflatoxin B_1(AFB_1)is a common contaminant in cereals of global concern,and long-term low-dose exposure can adversely affect human ***,we showed that populations with dietary patterns characterized by high-fat diet(HFD)might have an increased risk of exposure to high levels of AFB_*** data indicated that chronic exposure of AFB_1 induced“gut-liver axis”injury in mice under HFD and normal diet(ND)***_1 further aggravated hepatic and intestinal injury,and intestinal microbiota disruption in HFD *** breve BAA-2849 intervention analysis showed that liver injury and lipid disorders caused by AFB_1 exposure were alleviated by regulating the proportions of different gut *** demonstrated through a mice model that the populations with a dietary pattern of HFD might be more susceptible to AFB_1 exposure and adverse effects on the gut-liver axis,and the toxicity of AFB_1 exposure can be alleviated by regulating the gut microbiota.

关键词： Aflatoxin B_1 High-fat diet Lipid metabolism Gut-liver axis Gut microbiota Bifidobacterium breve

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