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Multiple valence states of Fe boosting SERS activity of Fe_(3)O_(4) nanoparticles and enabling effective SERS-MRI bimodal cancer imaging

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Fundamental research 2024年第4期4卷 858-867页

作者： Jie Lin Xuehua Ma Anran Li Ozioma Udochukwu Akakuru Chunshu Pan Meng He Chenyang Yao Wenzhi Ren Yanying Li Dinghu Zhang Yi Cao Tianxiang Chen Aiguo Wu Cixi institute of biomedical Engineering International Cooperation Base of Biomedical Materials Technology and ApplicationChinese Academy of Science Key Laboratory of Magnetic Materials and DevicesZhejiang Engineering Research Center for Biomedical MaterialsNingbo Institute of Materials Technology and EngineeringCASNingbo315201China School of Engineering Medicine Key Laboratory of Big Data-Based Precision Medicine(Beihang University)Ministry of Industry and Information TechnologyBeihang UniversityBeijing100191China Advanced Energy Science and Technology Guangdong laboratory Huizhou 516000China University of Chinese Academy of Sciences Bejing 100049China

Developing novel nanoparticle-based bioprobes utilized in clinical settings with imaging resolutions ranging from cell to tissue levels is a major challenge for tumor diagnosis and ***,an optimized strategy for designing a Fe_(3)O_(4)-based bioprobe for dual-modal cancer imaging based on surface-enhanced Raman scattering(SERS)and magnetic resonance imaging(MRI)is *** SERS activity of ultrasmall Fe_(3)O_(4) nanoparticles(NPs)was discovered,and a 5×10^(-9)M limit of detection for crystal violet molecules was successfully *** high-efficiency interfacial photon-induced charge transfer in Fe_(3)O_(4) NPs was promoted by multiple electronic energy levels ascribed to the multiple valence states of Fe,which was observed using ultraviolet-visible diffuse reflectance *** functional theory calculations were utilized to reveal that the narrow band gap and high electron density of states of ultrasmall Fe_(3)O_(4) NPs significantly boosted the vibronic coupling resonances in the SERS system upon *** subtypes of cancer cells were accurately recognized via high-resolution SERS imaging in vitro using the prepared Feg Og-based bioprobe with high sensitivity and good ***,Fe_(3)O_(4)-based bioprobes simultaneously exhibited T,-weighted MRI contrast enhancement with an active targeting capability for tumors in *** the best of our knowledge,this is the first report on the use of pure semiconductor-based SERS-MRI dual-modal nanoprobes in tumor imaging in vivo and in vitro,which has been previously realized only using semiconductor-metal complex *** non-metallic materials with SERS-MRI dual-modal imaging established in this report are a promising cancer diagnostic platform,which not only showed excellent performance in early tumor diagnosis but also possesses great potential for image-guided tumor treatment.

关键词： Fe_(3)O_(4)NPs SERS-MRI dual-modal nanoprobes PICT Multiple valence states Cancer diagnosis

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Transcriptomic analysis of Andrias davidianus meat and experimental validation for exploring its bioactive components as functional foods

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Food Science and Human Wellness 2024年第1期13卷 166-172页

作者： Changge Guan Zhenglin Tan Shucheng Li Yi Wang Naoyuki Yamamoto Chong Zhang Songjun Wang Junjie Chen Xinhui Xing Key laboratory for Industrial Biocatalysis Ministry of Education of ChinaDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China School of Life Science and Technology Tokyo Institute of TechnologyYokohama 226-0026Japan Sensing System research center National Institute of Advanced Industrial Science and TechnologyTsukuba 305-8565Japan center for Synthetic and Systems Biology Tsinghua UniversityBeijing 100084China Henan Giant Salamander Protection and Development Association Luoyang 471000China Intelligent Computing research center Harbin Institute of TechnologyShenzhen 518071China institute of Biopharmaceutical and Health Engineering Tsinghua Shenzhen International Graduate SchoolShenzhen 518055China institute of biomedical Health Technology and Engineering Shenzhen Bay LaboratoryShenzhen 518067China

Andrias davidianus(Chinese giant salamander,CGS)is the largest and oldest extant amphibian species in the world and is a source of prospective functional food in ***,the progress of functional peptides mining was slow due to lack of reference genome and protein sequence *** this study,we illustrated full-length transcriptome sequencing to interpret the proteome of CGS meat and obtain 10703 coding DNA *** functional annotation and amino acid composition analysis,we have discovered various genes related to signal transduction,and 16 genes related to *** have also found vast variety of functional peptides through protein coding sequence(CDS)analysis by comparing the data obtained with the functional peptide ***-Pro-Ile predicted by the CDS analysis was released from the CGS meat through enzymatic hydrolysis,suggesting that our approach is *** study suggested that transcriptomic analysis can be used as a reference to guide polypeptide mining in CGS meat,thereby providing a powerful mining strategy for the bioresources with unknown genomic and proteomic sequences.

关键词： Chinese giant salamander Transcriptomic analysis Bioactive components Functional peptides mining

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Comparative transcriptome analysis between rhesus macaques(Macaca mulatta) and crab-eating macaques(M. fascicularis)

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Zoological research 2024年第2期45卷 299-310页

作者： Yu-Xiang Mao Yamei Li Zikun Yang Ning Xu Shilong Zhang Xuankai Wang Xiangyu Yang Qiang Sun Yafei Mao institute of Neuroscience State Key Laboratory of NeuroscienceCenter for Excellence in Brain Science&Intelligence TechnologyChinese Academy of SciencesShanghai 200031China Shanghai center for Brain Science and Brain-Inspired Intelligence Technology Shanghai 201210China University of Chinese Academy of Sciences Beijing 100049China Key laboratory of Genetic Evolution&Animal Models Chinese Academy of SciencesKunmingYunnan 650201China Bio-X institutes Key Laboratory for the Genetics of Developmental and Neuropsychiatric DisordersMinistry of EducationShanghai Jiao Tong UniversityShanghai 200030China Zhiyuan College Shanghai Jiao Tong UniversityShanghai 200240China center for Genomic research International Institutes of MedicineFourth Affiliated HospitalZhejiang UniversityYiwuZhejiang 322000China

Understanding gene expression variations between species is pivotal for deciphering the evolutionary diversity in phenotypes. Rhesus macaques(Macaca mulatta, MMU)and crab-eating macaques(M. fascicularis, MFA) serve as crucial nonhuman primate biomedical models with different phenotypes. To date, however, large-scale comparative transcriptome research between these two species has not yet been fully explored. Here, we conducted systematic comparisons utilizing newly sequenced RNA-seq data from84 samples(41 MFA samples and 43 MMU samples)encompassing 14 common tissues. Our findings revealed a small fraction of genes(3.7%) with differential expression between the two species, as well as 36.5% of genes with tissue-specific expression in both macaques. Comparison of gene expression between macaques and humans indicated that 22.6% of orthologous genes displayed differential expression in at least two tissues. Moreover,19.41% of genes that overlapped with macaque-specific structural variants showed differential expression between humans and macaques. Of these, the FAM220A gene exhibited elevated expression in humans compared to macaques due to lineage-specific duplication. In summary,this study presents a large-scale transcriptomic comparison between MMU and MFA and between macaques and humans. The discovery of gene expression variations not only enhances the biomedical utility of macaque models but also contributes to the wider field of primate genomics.

关键词： Crab-eating macaques Rhesus macaques Comparative transcriptomics biomedical models Nonhuman primates RNA-seq Duplicated genes

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IMPROVED HARMONIC INCOMPATIBILITY REMOVAL FOR SUSCEPTIBILITY MAPPING VIA REDUCTION OF BASIS MISMATCH

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Journal of Computational Mathematics 2022年第6期40卷 913-935页

作者： Chenglong Bao Jianfeng Cai Jae Kyu Choi Bin Dong Ke Wei Yau mathematical Sciences center Tsinghua UniversityBeijing 100084China Department of Mathematics The Hong Kong University of Science and TechnologyHongkongChina School of mathematical Sciences Tongji UniversityShanghai 200092China beijing international center for mathematical research and laboratory for biomedical image analysis beijing institute of big data research Peking UniversityBeijing 100871China School of data Science Fudan UniversityShanghai 200433China

In quantitative susceptibility mapping(QSM),the background field removal is an essential data acquisition step because it has a significant effect on the restoration quality by generating a harmonic incompatibility in the measured local field *** though the sparsity based first generation harmonic incompatibility removal(1GHIRE)model has achieved the performance gain over the traditional approaches,the 1GHIRE model has to be further improved as there is a basis mismatch underlying in numerically solving Poisson’s equation for the background *** this paper,we propose the second generation harmonic incompatibility removal(2GHIRE)model to reduce a basis mismatch,inspired by the balanced approach in the tight frame based image *** results shows the superiority of the proposed 2GHIRE model both in the restoration qualities and the computational efficiency.

关键词： Quantitative susceptibility mapping Magnetic resonance imaging Deconvolution Partial differential equation Harmonic incompatibility removal (Tight)wavelet frames Sparse approximation

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Landscape of global urban environmental resistome and its association with local socioeconomic and medical status

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Science China(Life Sciences) 2024年第6期67卷 1292-1301页

作者： Jun Wu Yige Hu Michael H Perlin David Danko Jun Lu Manuela Oliveira Johannes Werner Maria M Zambrano Maria A Sierra Olayinka O Osuolale Paweł Łabaj Nicolás Rascovan Nur Hazlin Hazrin-Chong Soojin Jang Haruo Suzuki Marina Nieto-Caballero Bharath Prithiviraj Patrick K H Lee Agnieszka Chmielarczyk Anna Różańska Yongxiang Zhao Lan Wang Christopher E Mason Tieliu Shi center for Bioinformatics and Computational Biology and the Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China Department of Biology Program on Disease EvolutionUniversity of LouisvilleLouisville 40292USA Weill Cornell Medicine New York 10065USA The Bin Talal Bin Abdulaziz Alsaud institute for Computational Biomedicine New York 10065USA Department of Pulmonary Medicine Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghai 200025China i3S-Instituto de Investiga玢o e Inova玢o em Saúde Universidade do PortoPorto 4050-290Portugal Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto 4200-465Portugal Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPorto 4050-290Portugal High Performance and Cloud Computing Group Zentrum für Datenverarbeitung(ZDV)Eberhard Karls University of TübingenW鋍hterstra遝7672074TübingenGermany Corporación Corpogen research center Bogotá110311Colombia Applied Environmental Metagenomics and Infectious Diseases research(AEMIDR) Department of Biological SciencesElizade UniversityIlara-Mokin 340271Nigeria Maopolska Centre of Biotechnology Jagiellonian UniversityKraków 30-005Poland Aix-Marseille Université Mediterranean Institute of OceanologyUniversitéde ToulonCNRSIRDUM 110Marseille 83041France Department of Biological Sciences and Biotechnology Faculty of Science and TechnologyUniversiti Kebangsaan Malaysia43600 UKM BangiSelangor Institut Pasteur Korea Seoul 13488Republic of Korea Faculty of Environment and Information Studies Keio UniversityFujisawaKanagawa 252-0882Japan University of Colorado at Boulder CivilEnvironmental and Architectural DepartmentBoulder 80303USA Brooklyn College of the City University of New York Brooklyn 11210USA School of Energy and Environment City University of Hong KongHong Kong 999077China Department of Microbiology Faculty of MedicineJagiellonian UniversityKraków 30-005Poland Biological Targeting Diagnosis and The

Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban *** address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB international Consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based *** findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical *** also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environment represents a rich source of novel *** study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

关键词： urban environment metagenome antibiotic resistance resistance diversity biosynthetic gene clusters

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High-resolution spatio-temporal analysis of snowmelt over Antarctic Peninsula ice shelves from 2015 to 2021 using SAR images

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international Journal of Digital Earth 2023年第1期16卷 825-846页

作者： Qi Zhu Huadong Guo Lu Zhang Dong Liang Xuting Liu Heng Zhou Yiting Gou Key laboratory of Digital Earth Science Aerospace Information Research InstituteChinese Academy of SciencesBeijingPeople’s Republic of China international research center of big data for Sustainable Development Goals BeijingPeople’s Republic of China University of Chinese Academy of Sciences BeijingPeople’s Republic of China

Ice shelves play an essential role in the dynamics of the Antarctic ice *** surface meltwater is important,as it can irreversibly weaken ice shelves by exerting additional hydrostatic ***,high-resolution snowmelt products are urgently needed to accurately analyze melting patterns of ice shelves and further estimate mass *** this study,a new high-resolution(40 m)snowmelt dataset over all of the Antarctic Peninsula ice shelves larger than 100 km^(2) was developed based on the modified snowmelt detection framework by using a co-orbit normalization *** dataset provides detailed snowmelt information on each ice shelf,including the image coverage,melting area and melting ratio every 5 *** melting patterns of three typical ice shelves(George VI,Wilkins and Larsen C Ice Shelves)and the spatio-temporal melting distribution of the Antarctic Peninsula(AP)were further *** snowmelt information indicates that both the extent and duration of snowmelt have been increasing in the Antarctic Peninsula from 2015 to 2021,and we found that the snowmelt on the Antarctic Peninsula showed a spatial pattern of significantly intense snowmelt on the western *** believe this study will provide essential data for ice shelf investigation to support otherfields of polar research.

关键词： Surface snowmelt ice shelf sentinel-1 imagery Antarctic Peninsula high resolution

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Path PPI: an integrated dataset of human pathways and protein-protein interactions

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Science China(Life Sciences) 2015年第6期58卷 579-589页

作者： TANG HaiLin ZHONG Fan LIU Wei HE FuChu XIE HongWei College of Mechanical & Electronic Engineering and Automatization National University of Defense Technology institutes of biomedical Sciences Fudan University State Key laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine

Integration of pathway and protein-protein interaction(PPI) data can provide more information that could lead to new biological insights. PPIs are usually represented by a simple binary model, whereas pathways are represented by more complicated models. We developed a series of rules for transforming protein interactions from pathway to binary model, and the protein interactions from seven pathway databases, including PID, Bio Carta, Reactome, Net Path, INOH, SPIKE and KEGG, were transformed based on these rules. These pathway-derived binary protein interactions were integrated with PPIs from other five PPI databases including HPRD, Int Act, Bio GRID, MINT and DIP, to develop integrated dataset(named Path PPI). More detailed interaction type and modification information on protein interactions can be preserved in Path PPI than other existing datasets. Comparison analysis results indicate that most of the interaction overlaps values(OAB) among these pathway databases were less than 5%, and these databases must be used conjunctively. The Path PPI data was provided at http://proteomeview. ***/Path PPI/Path ***.

关键词： databases integration pathway protein-protein interaction proteomics

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Fast extraction of winter wheat planting area in Huang-Huai-Hai Plain using high-resolution satellite imagery on a cloud computing platform

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international Journal of Agricultural and Biological Engineering 2022年第1期15卷 241-250页

作者： Dongyan Zhang Mengru Zhang Fenfang Lin Zhenggao Pan Fei Jiang Liang He Hang Yang Ning Jin National Engineering research center for Agro-Ecological big data analysis&Application Anhui UniversityHefei 230601China Key laboratory of Geospatial Technology for Middle and Lower Yellow River Regions(Henan University) Ministry of EducationKaifeng 475004HenanChina School of Informatics and Engineering Suzhou UniversitySuzhou 234000AnhuiChina National Meteorological center Beijing 100081China Aerospace Information research institute Chinese Academy of ScienceBeijing 100101China

To extract regional winter wheat planting area using higher-resolution satellite imagery still faces many challenges due to large data size and long processing time in traditional remote sensing *** Earth Engine(GEE),a cloud computing analysis platform based on global geospatial analysis,provides a new opportunity for rapid analysis of remote sensing *** this study,high-quality Landsat-8 imagery was used to extract the winter wheat planting area from the Huang-Huai-Hai Plain in *** random forest algorithm was used to identify and map the winter wheat sown in 2019 and harvested in 2020,and Sentinel-2 imagery was used to verify the *** spectral indices,texture,and terrain features of the image were derived,and their contribution to the classification accuracy of winter wheat was evaluated by *** the top nine features were selected to form an optimal feature *** the set of thirty-four features and the optimized feature subset as the input variables of the random forest classifier,the results show that the accuracy difference between the two feature classification schemes is small,but the classification effect of all feature sets is slightly better than the optimal feature *** overall classification accuracy of sample plots verification was 86%-95%,the Kappa coefficient was between 0.7 and 0.85,and the percentage error of the total area was 5.42%.The research demonstrates a reliable method for mapping a wide range of winter wheat planting area,and provides a good prospect for exploring the precise mapping of other crops,which is of great significance to crop monitoring and agricultural development.

关键词： Google Earth Engine regional scale winter wheat rapid mapping

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Plasma biomarker screening for liver fibrosis with the N-terminal isotope tagging strategy

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Science China(Life Sciences) 2011年第5期54卷 393-402页

作者： LI ShuLong LIU Xin WEI Lai WANG HuiFen ZHANG JiYang WEI HanDong QIAN XiaoHong JIANG Ying HE FuChu State Key laboratory of Proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing 102206 China beijing institute of Biotechnology Beijing 100071 China People 's Hospital of Peking University Beijing 100044 China 302 Military Hospital of China Beijing 100039 China institutes of biomedical Sciences Fudan University Shanghai 200032 China Central laboratory Yantai Yu-Huang-Ding Hospital Yantai 264000 China

A non-invasive diagnostic approach is crucial for the evaluation of severity of liver disease,treatment decisions,and assessing drug *** study evaluated plasma proteomic profiling via an N-terminal isotope tagging strategy coupled with liquid chromatography/Fourier transform ion cyclotron resonance mass spectrometry measurement to detect liver fibrosis *** plasma from different liver fibrosis stages,which were assessed in advance by the current gold-standard of liver biopsy,was quantitatively analyzed.A total of 72 plasma proteins were found to be dysregulated during the fibrogenesis process,and this finding constituted a valuable candidate plasma biomarker bank for follow-up *** results of fibronectin by Western blotting reconfirmed the mass-based *** Pathways analysis showed four types of metabolic networks for the functional effect of liver fibrosis disease in chronic hepatitis B ***,quantitative proteomics via the N-terminal acetyl isotope labeling technique provides an effective and useful tool for screening plasma candidate biomarkers for liver *** quantitatively monitored the fibrogenesis process in CHB *** discovered many new valuable candidate biomarkers for the diagnosis of liver fibrosis and also partly identified the mechanism involved in liver fibrosis *** results provide a clearer understanding of liver fibrosis pathophysiology and will also hopefully lead to improvement of clinical diagnosis and treatment.

关键词： quantitative proteomics fiver fibrosis biomarker plasma hepatitis B virus

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Dynamic tear meniscus parameters in complete blinking:insights into dry eye assessment

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international Journal of Ophthalmology(English edition) 2023年第12期16卷 1911-1918页

作者： Ying-Huai Zhang Jun Feng Chen-Yuan Yi Xian-Yu Deng Yong-Jin Zhou Lei Tian Ying Jie Guangdong Key laboratory of biomedical Measurements and Ultrasound Imaging School of Biomedical EngineeringShenzhen University Medical SchoolShenzhen 518060Guangdong ProvinceChina Marshall laboratory of biomedical Engineering Shenzhen 518055Guangdong ProvinceChina beijing Ophthalmology and Visual Sciences Key laboratory Beijing Tongren Eye CenterBeijing Tongren HospitalBeijing Institute of OphthalmologyCapital Medical UniversityBeijing 100730China

AIM:To investigate the relationship between dynamic tear meniscus parameters and dry eye using an automated tear meniscus segmentation ***:The analysis of tear meniscus videos captured within 5s after a complete blink includes data from 38 *** processing video data,several key parameters including the average height of the tear meniscus at different lengths,the curvature of the tear meniscus’s upper boundary,and the total area of the tear meniscus in each frame were *** effective values of these dynamic parameters were then linearly fitted to explore the relationship between their changing trends and dry eye ***:In 94.74%of the samples,the average height of central tear meniscus increased over ***,97.37%of the samples exhibited an increase in the overall tear meniscus height(TMH)and area from the nasal to temporal ***,the central TMH increased at a faster rate compared to the nasal side with the temporal side showing the slowest *** analysis indicates that the upper boundary curvature of the whole tear meniscus as well as the tear meniscus of the nasal side(2,3,and 4 mm)aid in identifying the presence of dry eye and assessing its ***:This study contributes to the understanding of tear meniscus dynamics as potential markers for dry eye,utilizing an automated and non-invasive approach that has implications for clinical assessment.

关键词： dry eye dynamic tear meniscus blinking

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