Cardiolipins(CLs),the mitochondria-specific class of phospholipids,are crucial to energy metabolism,cristae structure,and cell apoptosis.CLs present significant challenges in lipidomics analysis due to their structura...Cardiolipins(CLs),the mitochondria-specific class of phospholipids,are crucial to energy metabolism,cristae structure,and cell apoptosis.CLs present significant challenges in lipidomics analysis due to their structural diversity with up to four fatty acyl side chains.In this study,we developed CLAN(Cardio Lipin ANalysis),a comprehensive computational pipeline designed to improve the accuracy and coverage of cardiolipin identification.CLAN integrates three innovative modules:A cardiolipin identification module that utilizes specific fragmentation rules for precise characterization of CLs and their acyl side chains;a false positives detection module that employs retention time(RT)criteria to reduce false positives;and a prediction module that constructs regression models to identify CLs lacking authentic MS/MS spectra.CLAN achieved better identification accuracy and the highest recall rate for potential CL identification compared to the existing lipid identification tools.Furthermore,we applied CLAN program to an intermittent fasting mouse model,delineating tissue-specific CL alterations across 10 tissues.Every-other-day fasting(EODF)can partially counteract the disruption of the CL atlas across multiple tissues caused by high-fat-high-sugar diet feeding,providing novel insights into mitochondrial lipid metabolism under dietary interventions.Taken together,this work not only advances CL identification methodology but also underscores CLAN's potential in comprehensive analysis of CL atlas in the EODF animal model.CLAN is freely accessible on Git Hub.展开更多
Peanut seedlings develop from seeds by hypocotyl elongation and differentiation.However,the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown.In t...Peanut seedlings develop from seeds by hypocotyl elongation and differentiation.However,the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown.In this study,a single-nucleus gene expression landscape in peanut seedlings was initially developed from diverse tissues,including stems,roots,leaves,and hypocotyls.Core transcription factor interaction networks driving developmental trajectories were identified to decipher hypocotyl cell heterogeneity.Jasmonic acid and cytokinin regulate peanut hypocotyl expansion and differentiation based on the number and size of cortex cells and hormone levels between the hypocotyl at 3 and 7 d after germination.We further demonstrated that AhBHLH143 potentially represses hypocotyl elongation by promoting the JA pathway and inhibiting the cytokinin pathway.The single-nucleus transcriptomic atlas of peanut seedlings reveals new insights into hypocotyl development and provides a valuable resource for future investigations of seedling development.展开更多
Objective To develop a multimodal imaging atlas of a rat brain-computer interface(BCI)that incorporates brain,arterial,bone tissue and a BCI device using mixed reality(MR)for three-dimensional(3D)visualization.Methods...Objective To develop a multimodal imaging atlas of a rat brain-computer interface(BCI)that incorporates brain,arterial,bone tissue and a BCI device using mixed reality(MR)for three-dimensional(3D)visualization.Methods An invasive BCI was implanted in the left visual cortex of 4-week-old Sprague–Dawley rats.Multimodal imaging techniques,including micro-CT and 9.0 T MRI,were used to acquire images of the rat cranial bone structure,vascular distribution,brain tissue functional zones,and BCI device before and after implantation.Using 3D-slicer software,the images were fused through spatial transformations,followed by image segmentation and 3D model reconstruction.The HoloLens platform was employed for MR visualization.Results This study constructed a multimodal imaging atlas for rats that included the skull,brain tissue,arterial tissue,and BCI device coupled with MR technology to create an interactive 3D anatomical model.Conclusions This multimodal 3D atlas provides an objective and stable reference for exploring complex relationships between brain tissue structure and function,enhancing the understanding of the operational principles of BCIs.This is the first multimodal 3D imaging atlas related to a BCI created using Sprague–Dawley rats.展开更多
The deposition characteristics of nasal formulations directly determine the efficacy of the drugs,whilst the complexity of human nasal airway structure encumbers quantitative evaluation of nasal spatial deposition.Mal...The deposition characteristics of nasal formulations directly determine the efficacy of the drugs,whilst the complexity of human nasal airway structure encumbers quantitative evaluation of nasal spatial deposition.Male and female standard nasal airway structure models were calculated from computed tomography data of 128 Chinese Han nationality using statistical shape model.The deposition evaluation devices were further designed,and an imaging method was then employed to obtain drug deposition information.Furthermore,drug spatial deposition atlases were proposed by UV unwrapping,a mathematical mapping procedure flattening three-dimensional(3D)information to two-dimension bidirectionally,to achieve quantification of drug deposition fractions in the regions of interest.Moreover,the feasibility and universality of this method were verified by correlating it with the chemical quantitative results and computational fluid dynamic simulation of drug deposition of mometasone furoate nasal spray and hydroxypropyl methylcellulose nasal powder,respectively.Finally,the unique drug spatial deposition atlases of these two formulations in the male and female evaluation devices were generated,respectively.In summary,the standard nasal airway structure models of the Chinese Han nationality and the drug spatial deposition atlases provide scientific tools for the formulation optimization and quality control of nasal formulations.展开更多
The Southern Atlas front of Tunisia(SAFT),which includes the Gantass structure,is part of the wide fold and thrust belt that developed along the North African margin.In the present work,an integrated geological and ge...The Southern Atlas front of Tunisia(SAFT),which includes the Gantass structure,is part of the wide fold and thrust belt that developed along the North African margin.In the present work,an integrated geological and geophysical study has been conducted using geological maps,drillhole and seismic data to shed lights on the tectono-sedimentary evolution of the SAFT,with particular focus on the Gantass structure.Seismic data has been calibrated using well data and interpreted to reconstruct the preexisting architecture of the region,revealing a Turonian carbonate platform to the south,which passes into a deep basin northwards.Notably,reef constructions have been identified along the platform margin.In addition,we reconstruct the main evolutionary stages of the region:(1)post-rift subsidence from Cenomanian to Campanian,following Early Jurassic rifting,(2)uplift of the Campanian-Maastrichtian carbonate platform during Late Cretaceous compression,(3)successive compressional phases marked by unconformities reflecting middle-to late Eocene,Tortonian and early Pleistocene periods.Our analysis demonstrates that the nucleation of the Gantass structure is not only controlled by pre-existing faults but also by stratigraphic heterogeneity.While most of the regional structures have been shaped by these successive tectonic phases,the Gantass structure,which we interpret as an incipient fault-propagation fold,developed during the latest compression stage.From an economic perspective,this study proves the presence of new reserves of phosphate deposits and highlights potential stratigraphic traps for future hydrocarbon exploration in the region.展开更多
Electronic atlas project (E-atlas project) plays a n important role in the procedure of popularizing maps and is diversifying its a pplication widely in China. Practice for E-atlas projects is a basic approach f or ac...Electronic atlas project (E-atlas project) plays a n important role in the procedure of popularizing maps and is diversifying its a pplication widely in China. Practice for E-atlas projects is a basic approach f or achieving public accessibility to national spatial data infrastructure (N SDI) and meets people’s inherent needs of updated maps. This paper provides a d escription and assessment of an integration of E-atlas projects, analyzes curre nt progress and characters of E-atlas project, summarizes basic guide rules, an d provides solution and interpretation. It depicts a conceptual framework of an authoring toolkit that is driven by application of E-atlas on the basis of succ essful instances. The toolkit which improves interactive interface, decreases op erational difficulties is developed in Visual C++ and used widely in China.展开更多
目的:探讨基于Atlas实施宫颈癌危及器官自动勾画时图谱库入库病例数的增加对自动勾画结果的影响,以期得到最优图谱库病例数。方法:运用MIM软件建立4组宫颈癌图谱库(入库病例数目分别为30、60、90、120例)。随机选择图谱库外10例宫颈癌...目的:探讨基于Atlas实施宫颈癌危及器官自动勾画时图谱库入库病例数的增加对自动勾画结果的影响,以期得到最优图谱库病例数。方法:运用MIM软件建立4组宫颈癌图谱库(入库病例数目分别为30、60、90、120例)。随机选择图谱库外10例宫颈癌患者图像,由一名临床经验丰富的医生进行危及器官(膀胱、直肠和双侧股骨头)的手动勾画,将其定义为参考勾画,并对该10例患者图像进行危及器官自动勾画,勾画匹配数目分别选择为3和9。通过定量评价勾画时间、相似性系数(DSC)、敏感性指数(SI)、包容性指数、质心偏差、Jaccard系数(JAC)、Hausdorff距离(HD),将自动勾画结果与参考勾画进行单因素方差分析,从而探讨不同图谱库病例数对自动勾画结果的影响。结果:勾画匹配数目选择为3时,4组模板中平均自动勾画时间小于手动勾画(1.31/1.33/1.35/1.39min vs 10.25min),匹配数目选9时具有同样的趋势(5.07/5.24/5.14/5.24min vs 10.25min),但各组间没有差异性。匹配数目为3时膀胱SI(P=0.018)、直肠SI(P=0.010)、直肠DSC(P=0.016)、直肠JAC(P=0.013)、直肠HD(P=0.042),以及匹配数目为9时直肠HD(P=0.002)均具有统计学差异,其他参数没有统计学意义。结论:基于Atlas实施危及器官自动勾画能够节省勾画时间,模板数目的增加不会影响勾画效率,30例图谱库勾画时整体结果较差,60例以上的图谱库略有优势,提高膀胱、直肠的勾画准确性,但考虑时间成本,对于宫颈癌的勾画建议采用60例作为临床模板库病例数。展开更多
基金supported by grants from the National Key Research and Development Program of China(No.2022YFE0205800)the National Natural Science Foundation of China(No.21974114)+5 种基金Major Science and Technology Special Project of Fujian Province(No.2022YZ036012)the Fundamental Research Funds for the Central Universities(No.20720220003)Project“111”sponsored by the State Bureau of Foreign Experts and Ministry of Education of China(No.BP0618017)to S.-H.LinNatural Science Foundation of Fujian Province of China(No.2022J01330)Natural Science Foundation of Xiamen City of China(No.3502Z20227208)the China Scholarship Council(No.202308350047)to J.Zeng。
文摘Cardiolipins(CLs),the mitochondria-specific class of phospholipids,are crucial to energy metabolism,cristae structure,and cell apoptosis.CLs present significant challenges in lipidomics analysis due to their structural diversity with up to four fatty acyl side chains.In this study,we developed CLAN(Cardio Lipin ANalysis),a comprehensive computational pipeline designed to improve the accuracy and coverage of cardiolipin identification.CLAN integrates three innovative modules:A cardiolipin identification module that utilizes specific fragmentation rules for precise characterization of CLs and their acyl side chains;a false positives detection module that employs retention time(RT)criteria to reduce false positives;and a prediction module that constructs regression models to identify CLs lacking authentic MS/MS spectra.CLAN achieved better identification accuracy and the highest recall rate for potential CL identification compared to the existing lipid identification tools.Furthermore,we applied CLAN program to an intermittent fasting mouse model,delineating tissue-specific CL alterations across 10 tissues.Every-other-day fasting(EODF)can partially counteract the disruption of the CL atlas across multiple tissues caused by high-fat-high-sugar diet feeding,providing novel insights into mitochondrial lipid metabolism under dietary interventions.Taken together,this work not only advances CL identification methodology but also underscores CLAN's potential in comprehensive analysis of CL atlas in the EODF animal model.CLAN is freely accessible on Git Hub.
基金supported by the Guangdong Provincial Key Research and Development Program-Modern Seed Industry(2022B0202060004)National Key Research and Development Project(2023YFD1202800)+9 种基金National Natural Science Foundation of China(32272121,32172051,32301869,32000471)Guangdong Science and Technology Plan Project(2023B1212060038)Guangdong Basic and Applied Basic Research Foundation(2021A1515010811,2023A1515010098,2023A1515010569)China Agriculture Research System of MOF and MARA(CARS-13)Guangzhou Basic and Applied Basic Research Foundation(2023A04J0776)Special Fund for Scientific Innovation Strategy-Construction of High Level Academy of Agriculture Science(R2020PY-JX004,R2020PY-JG005,R2021PY-QY003,R2022YJYB3025)the Foundation of the Director of Crop Research Institute of Guangdong Academy of Agriculture Sciences(202201,202306)Special Funds for the Revitalization of Agriculture through Seed Industry under the Provincial Rural Revitalization Strategy(2022-NPY-00-022)the Project of Collaborative Innovation Center of GDAAS(XTXM202203)Science and Technology Planning Project of Heyuan City(Heyuan She Nong Da Zhuan Xiang 2022002).
文摘Peanut seedlings develop from seeds by hypocotyl elongation and differentiation.However,the intricate gene regulatory networks and molecular crosstalk underlying hypocotyl growth in peanuts remain largely unknown.In this study,a single-nucleus gene expression landscape in peanut seedlings was initially developed from diverse tissues,including stems,roots,leaves,and hypocotyls.Core transcription factor interaction networks driving developmental trajectories were identified to decipher hypocotyl cell heterogeneity.Jasmonic acid and cytokinin regulate peanut hypocotyl expansion and differentiation based on the number and size of cortex cells and hormone levels between the hypocotyl at 3 and 7 d after germination.We further demonstrated that AhBHLH143 potentially represses hypocotyl elongation by promoting the JA pathway and inhibiting the cytokinin pathway.The single-nucleus transcriptomic atlas of peanut seedlings reveals new insights into hypocotyl development and provides a valuable resource for future investigations of seedling development.
基金supported by the National Natural Science Foundation of China(No.82172524 and No.81974355)National Innovation Platform Development Program(No.2020021105012440),China+3 种基金Major Program of Hubei Province(No.2021BEA161),ChinaMajor Key Project of Hubei Province(No.JD2023BAA005),ChinaWuhan Union Hospital Free Innovation Preliminary Research Fund(No.2024XHYN047),ChinaJoint Funds for the Innovation of Science and Technology(No.2024Y9062),Fujian Province,China.
文摘Objective To develop a multimodal imaging atlas of a rat brain-computer interface(BCI)that incorporates brain,arterial,bone tissue and a BCI device using mixed reality(MR)for three-dimensional(3D)visualization.Methods An invasive BCI was implanted in the left visual cortex of 4-week-old Sprague–Dawley rats.Multimodal imaging techniques,including micro-CT and 9.0 T MRI,were used to acquire images of the rat cranial bone structure,vascular distribution,brain tissue functional zones,and BCI device before and after implantation.Using 3D-slicer software,the images were fused through spatial transformations,followed by image segmentation and 3D model reconstruction.The HoloLens platform was employed for MR visualization.Results This study constructed a multimodal imaging atlas for rats that included the skull,brain tissue,arterial tissue,and BCI device coupled with MR technology to create an interactive 3D anatomical model.Conclusions This multimodal 3D atlas provides an objective and stable reference for exploring complex relationships between brain tissue structure and function,enhancing the understanding of the operational principles of BCIs.This is the first multimodal 3D imaging atlas related to a BCI created using Sprague–Dawley rats.
基金funded by the National Natural Science Foundation of China(No.82273863).
文摘The deposition characteristics of nasal formulations directly determine the efficacy of the drugs,whilst the complexity of human nasal airway structure encumbers quantitative evaluation of nasal spatial deposition.Male and female standard nasal airway structure models were calculated from computed tomography data of 128 Chinese Han nationality using statistical shape model.The deposition evaluation devices were further designed,and an imaging method was then employed to obtain drug deposition information.Furthermore,drug spatial deposition atlases were proposed by UV unwrapping,a mathematical mapping procedure flattening three-dimensional(3D)information to two-dimension bidirectionally,to achieve quantification of drug deposition fractions in the regions of interest.Moreover,the feasibility and universality of this method were verified by correlating it with the chemical quantitative results and computational fluid dynamic simulation of drug deposition of mometasone furoate nasal spray and hydroxypropyl methylcellulose nasal powder,respectively.Finally,the unique drug spatial deposition atlases of these two formulations in the male and female evaluation devices were generated,respectively.In summary,the standard nasal airway structure models of the Chinese Han nationality and the drug spatial deposition atlases provide scientific tools for the formulation optimization and quality control of nasal formulations.
文摘The Southern Atlas front of Tunisia(SAFT),which includes the Gantass structure,is part of the wide fold and thrust belt that developed along the North African margin.In the present work,an integrated geological and geophysical study has been conducted using geological maps,drillhole and seismic data to shed lights on the tectono-sedimentary evolution of the SAFT,with particular focus on the Gantass structure.Seismic data has been calibrated using well data and interpreted to reconstruct the preexisting architecture of the region,revealing a Turonian carbonate platform to the south,which passes into a deep basin northwards.Notably,reef constructions have been identified along the platform margin.In addition,we reconstruct the main evolutionary stages of the region:(1)post-rift subsidence from Cenomanian to Campanian,following Early Jurassic rifting,(2)uplift of the Campanian-Maastrichtian carbonate platform during Late Cretaceous compression,(3)successive compressional phases marked by unconformities reflecting middle-to late Eocene,Tortonian and early Pleistocene periods.Our analysis demonstrates that the nucleation of the Gantass structure is not only controlled by pre-existing faults but also by stratigraphic heterogeneity.While most of the regional structures have been shaped by these successive tectonic phases,the Gantass structure,which we interpret as an incipient fault-propagation fold,developed during the latest compression stage.From an economic perspective,this study proves the presence of new reserves of phosphate deposits and highlights potential stratigraphic traps for future hydrocarbon exploration in the region.
文摘Electronic atlas project (E-atlas project) plays a n important role in the procedure of popularizing maps and is diversifying its a pplication widely in China. Practice for E-atlas projects is a basic approach f or achieving public accessibility to national spatial data infrastructure (N SDI) and meets people’s inherent needs of updated maps. This paper provides a d escription and assessment of an integration of E-atlas projects, analyzes curre nt progress and characters of E-atlas project, summarizes basic guide rules, an d provides solution and interpretation. It depicts a conceptual framework of an authoring toolkit that is driven by application of E-atlas on the basis of succ essful instances. The toolkit which improves interactive interface, decreases op erational difficulties is developed in Visual C++ and used widely in China.
文摘目的:探讨基于Atlas实施宫颈癌危及器官自动勾画时图谱库入库病例数的增加对自动勾画结果的影响,以期得到最优图谱库病例数。方法:运用MIM软件建立4组宫颈癌图谱库(入库病例数目分别为30、60、90、120例)。随机选择图谱库外10例宫颈癌患者图像,由一名临床经验丰富的医生进行危及器官(膀胱、直肠和双侧股骨头)的手动勾画,将其定义为参考勾画,并对该10例患者图像进行危及器官自动勾画,勾画匹配数目分别选择为3和9。通过定量评价勾画时间、相似性系数(DSC)、敏感性指数(SI)、包容性指数、质心偏差、Jaccard系数(JAC)、Hausdorff距离(HD),将自动勾画结果与参考勾画进行单因素方差分析,从而探讨不同图谱库病例数对自动勾画结果的影响。结果:勾画匹配数目选择为3时,4组模板中平均自动勾画时间小于手动勾画(1.31/1.33/1.35/1.39min vs 10.25min),匹配数目选9时具有同样的趋势(5.07/5.24/5.14/5.24min vs 10.25min),但各组间没有差异性。匹配数目为3时膀胱SI(P=0.018)、直肠SI(P=0.010)、直肠DSC(P=0.016)、直肠JAC(P=0.013)、直肠HD(P=0.042),以及匹配数目为9时直肠HD(P=0.002)均具有统计学差异,其他参数没有统计学意义。结论:基于Atlas实施危及器官自动勾画能够节省勾画时间,模板数目的增加不会影响勾画效率,30例图谱库勾画时整体结果较差,60例以上的图谱库略有优势,提高膀胱、直肠的勾画准确性,但考虑时间成本,对于宫颈癌的勾画建议采用60例作为临床模板库病例数。
