Intracranial aneurysm(IA)is a prevalent cerebrovascular disease associated with high mortality and disability rates upon rupture.The hemodynamics of IA,which are significantly influenced by geometric parameters,direct...Intracranial aneurysm(IA)is a prevalent cerebrovascular disease associated with high mortality and disability rates upon rupture.The hemodynamics of IA,which are significantly influenced by geometric parameters,directly impact its rupture.This study focuses on investigating the transient flow characteristics in saccular IA models fabricated using a water droplet-based method,specifically examining the influence of neck widths.Particle image velocimetry technique and numerical simulation were employed to investigate the dynamic evolution of flow structures within three IA models.The results reveal that neck width(W)has a substantial effect on flow characteristics in the neck region,subsequently impacting the deep flow inside the sac.Three distinct patterns were observed during flow evolution inside the sac:for W=2 mm,two vortices occur and then disappear with relatively low average flow velocity;for W=4 mm,enhanced effects of a high-speed jet result in periodic pulsatile flow velocity distribution while maintaining stable vortex core position;for W=6 mm,significant changes in flow velocity occur due to size expansion and intensity increase of vortices.These findings demonstrate that neck widths play a complex role in influencing transient flow characteristics within IAs.Overall,this research contributes to further understanding transient flow behaviors in IAs.展开更多
Mesh smoothing is an essential technique for the improvement of mesh quality in finite element analysis,due to the fact that mesh quality has a large impact on the convergence of the computational scheme and the accur...Mesh smoothing is an essential technique for the improvement of mesh quality in finite element analysis,due to the fact that mesh quality has a large impact on the convergence of the computational scheme and the accuracy of the numerical results.A novel mesh smoothing method based on regular-position-guided operations is presented in this paper.The method introduced here contains two main stages:The first stage computes the regular position of each vertex based on the shape of the element and conducts regular-position-oriented-based element transformations independently;the second stage determines the finial position of each vertex according to its surrounding elements with an assembly strategy.This method is not limited to planar triangular mesh,but applicable to surface polygonal mesh.Numerical experiments on various mesh models demonstrate the effectiveness and potential of this method.展开更多
Hyper-and multi-spectral image fusion is an important technology to produce hyper-spectral and hyper-resolution images,which always depends on the spectral response function andthe point spread function.However,few wo...Hyper-and multi-spectral image fusion is an important technology to produce hyper-spectral and hyper-resolution images,which always depends on the spectral response function andthe point spread function.However,few works have been payed on the estimation of the two degra-dation functions.To learn the two functions from image pairs to be fused,we propose a Dirichletnetwork,where both functions are properly constrained.Specifically,the spatial response function isconstrained with positivity,while the Dirichlet distribution along with a total variation is imposedon the point spread function.To the best of our knowledge,the neural network and the Dirichlet regularization are exclusively investigated,for the first time,to estimate the degradation functions.Both image degradation and fusion experiments demonstrate the effectiveness and superiority of theproposed Dirichlet network.展开更多
Immunosuppressive cells are pivotal players in tumor progression by affecting the efficacy of conventional therapies and the prognosis of cancer patients.Visualization and real-time evaluation of these cells are very ...Immunosuppressive cells are pivotal players in tumor progression by affecting the efficacy of conventional therapies and the prognosis of cancer patients.Visualization and real-time evaluation of these cells are very important to achieve patient-oriented precision oncological medicine.Noninvasive imaging techniques are excellent tools for this purpose,and various molecular imaging probes have been developed to monitor these protumoral immunosuppressive cells in the tumor microenvironment.In this review,we provide a brief update on the biology of immunosuppressive cells and outline recent progress in their visualization.展开更多
Dear Editor,Angiogenesis,the process of forming new blood vessels,is closely linked to osteogenesis,the formation of new bone tissue,which is important for bone development and homeostasis(Kusumbe et al.,2014).Recent ...Dear Editor,Angiogenesis,the process of forming new blood vessels,is closely linked to osteogenesis,the formation of new bone tissue,which is important for bone development and homeostasis(Kusumbe et al.,2014).Recent studies have established that Endothelial-to-Osteoblast Conversion(EC-to-OSB),mediated by Endothelial-to-Mesenchymal Transition and subsequent osteogenesis,plays a crucial role ectopic ossification during cancer bone metastasis(Lin et al.,2017;Medici et al.,2010).Moreover,research suggests that endothelial cells are one of the sources of bone marrow mesenchymal stem cells(BMSCs)which contribute to the reconstruction of the bone marrow niche during bone marrow transplantation(Kenswil et al.,2021).However,this view remains controversial,as other studies(Cao et al.,2023).Since it remains unclear whether and how EC-to-OSB regulates bone formation and homeostasis under physiological or aged conditions.Therefore,further research on the pathogenesis of osteoporosis(OP)is urgent.展开更多
The sole use of single modality data often fails to capture the complex heterogeneity among patients,including the variability in resistance to anti-HER2 therapy and outcomes of combined treatment regimens,for the tre...The sole use of single modality data often fails to capture the complex heterogeneity among patients,including the variability in resistance to anti-HER2 therapy and outcomes of combined treatment regimens,for the treatment of HER2-positive gastric cancer(GC).This modality deficit has not been fully considered in many studies.Furthermore,the application of artificial intelligence in predicting the treatment response,particularly in complex diseases such as GC,is still in its infancy.Therefore,this study aimed to use a comprehensive analytic approach to accurately predict treatment responses to anti-HER2 therapy or anti-HER2 combined immunotherapy in patients with HER2-positive GC.We collected multi-modal data,comprising radiology,pathology,and clinical information from a cohort of 429 patients:310 treated with anti-HER2 therapy and 119 treated with a combination of anti-HER2 and anti-PD-1/PD-L1 inhibitors immunotherapy.We introduced a deep learning model,called the Multi-Modal model(MuMo),that integrates these data to make precise treatment response predictions.MuMo achieved an area under the curve score of 0.821 for anti-HER2 therapy and 0.914 for combined immunotherapy.Moreover,patients classified as low-risk by MuMo exhibited significantly prolonged progression-free survival and overall survival(log-rank test,P<0.05).These findings not only highlight the significance of multi-modal data analysis in enhancing treatment evaluation and personalized medicine for HER2-positive gastric cancer,but also the potential and clinical value of our model.展开更多
Efficient and reliable profiling methods are essential to study epigenetics.Tn5,one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency,is widely adopted in different gen...Efficient and reliable profiling methods are essential to study epigenetics.Tn5,one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency,is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome.Based on Tn5,the Assay for Transposase-Accessible Chromatin using sequencing(ATAC-seq)and the Cleavage Under Targets and Tagmentation(CUT&Tag)were developed to measure chromatin accessibility and detect DNA–protein interactions.These methodologies can be applied to large amounts of biological samples with low-input levels,such as rare tissues,embryos,and sorted single cells.However,fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly.Furthermore,inappropriate data analysis can generate biased or misleading conclusions.Therefore,it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools,many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing(ChIP-seq)data.Here,we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag data.We compared the sensitivity,specificity,and peak width distribution for both narrow-type and broad-type peak calling.We also tested the influence of the availability of control IgG input in CUT&Tag data analysis.Finally,we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag data.Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies,which were implemented into Docker/Singularity images for streamlined data analysis.展开更多
Rubber plantations have increased signifcantly under unprecedented economic growth in tropical areas,which leads to soil degradation and thereby alters soil hydrological processes.However,our understanding of how fore...Rubber plantations have increased signifcantly under unprecedented economic growth in tropical areas,which leads to soil degradation and thereby alters soil hydrological processes.However,our understanding of how forest conversion affects soil hydrological processes remains unclear.Here,we collected soil samples from secondary forests(SF)and rubber plantations(RP)to determine the soil hydrological characteristics.We found the topsoil(0-20 cm)water retention in SF was higher than that of RP but displayed the contrast pattern in a deeper soil layer(20-60 cm).Meanwhile,the soil infltration rates among the two vegetation types decreased signifcantly with infltration time,with higher stable soil infltration rates in SF than those in RP.Moreover,soil properties were also impacted by the forest conversion,such as the topsoil capillary porosity(CP)and total porosity(TP)in SF were higher than those of RP but contrasted in a deep soil layer.In comparison,the topsoil bulk density(BD)in SF was lower than that of RP,but contrasted in the deep soil layer and reached a signifcant level in the 0-10 and 40-50 cm(P<0.05).Overall,the soil water retention was mainly determined by the CP,which could explain 31.56%of the total variance in soil water retention,followed by TP(26.57%)and soil BD(26.47%),whereas soil texture exerts a weak effect on soil water retention.Therefore,we can conclude that the conversion of tropical rainforest into rubber plantations may accelerate soil erosion owing to its lower topsoil water retention and soil infltration rates.展开更多
Palladium-based alloy is a kind of material with a high glass forming ability and can be easily formed into an amorphous state. After an annealing process, it can also be maintained at a crystallized state. To study t...Palladium-based alloy is a kind of material with a high glass forming ability and can be easily formed into an amorphous state. After an annealing process, it can also be maintained at a crystallized state. To study the thermal and electrical transport properties of crystallized palladium-based alloys, the steady-state T-type method, standard four-probe method, and AC heating-DC detecting T-type method were used to measure the thermal conductivity, electrical conductivity, and Seebeck coeffi- cient of crystallized Pd4oNiloCu3oP2o and Pd43Nilo- Cu27P2o alloys respectively. The results show that compared to amorphous samples, the thermal conductivity and electrical conductivity of crystallized palladium-based alloys are significantly higher, while the Seebeck coeffi- cient is lower. The ratio of crystallized and amorphous thermal conductivity is higher for Pd43Ni10Cu27P2o alloy fiber which has a higher glass forming ability, while the ratio of electronic thermal conductivity almost remains constant for both alloy fibers. The results also show that the slope of electrical resistivity to temperature is a function of elemental composition for crystallized quaternary palla- dium-based alloy fibers. The sensitivity of thermal conductivity and electrical conductivity to the composition is high, while the correlation between Seebeck coefficient and composition is relatively weak.展开更多
基金supported by the National Natural Science Foundation of China(Grant Nos.12172017 and 11872083)Project of Beijing Municipal Education Commission(Grant Nos.KZ202210005006 and KZ202110005007).
文摘Intracranial aneurysm(IA)is a prevalent cerebrovascular disease associated with high mortality and disability rates upon rupture.The hemodynamics of IA,which are significantly influenced by geometric parameters,directly impact its rupture.This study focuses on investigating the transient flow characteristics in saccular IA models fabricated using a water droplet-based method,specifically examining the influence of neck widths.Particle image velocimetry technique and numerical simulation were employed to investigate the dynamic evolution of flow structures within three IA models.The results reveal that neck width(W)has a substantial effect on flow characteristics in the neck region,subsequently impacting the deep flow inside the sac.Three distinct patterns were observed during flow evolution inside the sac:for W=2 mm,two vortices occur and then disappear with relatively low average flow velocity;for W=4 mm,enhanced effects of a high-speed jet result in periodic pulsatile flow velocity distribution while maintaining stable vortex core position;for W=6 mm,significant changes in flow velocity occur due to size expansion and intensity increase of vortices.These findings demonstrate that neck widths play a complex role in influencing transient flow characteristics within IAs.Overall,this research contributes to further understanding transient flow behaviors in IAs.
文摘Mesh smoothing is an essential technique for the improvement of mesh quality in finite element analysis,due to the fact that mesh quality has a large impact on the convergence of the computational scheme and the accuracy of the numerical results.A novel mesh smoothing method based on regular-position-guided operations is presented in this paper.The method introduced here contains two main stages:The first stage computes the regular position of each vertex based on the shape of the element and conducts regular-position-oriented-based element transformations independently;the second stage determines the finial position of each vertex according to its surrounding elements with an assembly strategy.This method is not limited to planar triangular mesh,but applicable to surface polygonal mesh.Numerical experiments on various mesh models demonstrate the effectiveness and potential of this method.
基金the Postdoctoral ScienceFoundation of China(No.2023M730156)the NationalNatural Foundation of China(No.62301012).
文摘Hyper-and multi-spectral image fusion is an important technology to produce hyper-spectral and hyper-resolution images,which always depends on the spectral response function andthe point spread function.However,few works have been payed on the estimation of the two degra-dation functions.To learn the two functions from image pairs to be fused,we propose a Dirichletnetwork,where both functions are properly constrained.Specifically,the spatial response function isconstrained with positivity,while the Dirichlet distribution along with a total variation is imposedon the point spread function.To the best of our knowledge,the neural network and the Dirichlet regularization are exclusively investigated,for the first time,to estimate the degradation functions.Both image degradation and fusion experiments demonstrate the effectiveness and superiority of theproposed Dirichlet network.
基金National Natural Science Foundation of China,Grant/Award Numbers:91959119,81873903,82001871,82272041。
文摘Immunosuppressive cells are pivotal players in tumor progression by affecting the efficacy of conventional therapies and the prognosis of cancer patients.Visualization and real-time evaluation of these cells are very important to achieve patient-oriented precision oncological medicine.Noninvasive imaging techniques are excellent tools for this purpose,and various molecular imaging probes have been developed to monitor these protumoral immunosuppressive cells in the tumor microenvironment.In this review,we provide a brief update on the biology of immunosuppressive cells and outline recent progress in their visualization.
基金supported,in part,by the National Key Research and Development Program of China Grants(2019YFA0906001)the National Natural Science Foundation of China Grants(82372476 and 82350710800)Guangdong Provincial Science and Technology Innovation Council Grant(2017B030301018)。
文摘Dear Editor,Angiogenesis,the process of forming new blood vessels,is closely linked to osteogenesis,the formation of new bone tissue,which is important for bone development and homeostasis(Kusumbe et al.,2014).Recent studies have established that Endothelial-to-Osteoblast Conversion(EC-to-OSB),mediated by Endothelial-to-Mesenchymal Transition and subsequent osteogenesis,plays a crucial role ectopic ossification during cancer bone metastasis(Lin et al.,2017;Medici et al.,2010).Moreover,research suggests that endothelial cells are one of the sources of bone marrow mesenchymal stem cells(BMSCs)which contribute to the reconstruction of the bone marrow niche during bone marrow transplantation(Kenswil et al.,2021).However,this view remains controversial,as other studies(Cao et al.,2023).Since it remains unclear whether and how EC-to-OSB regulates bone formation and homeostasis under physiological or aged conditions.Therefore,further research on the pathogenesis of osteoporosis(OP)is urgent.
基金supported by the National Natural Science Foundation of China(91959205 to L.S.,U22A20327 to L.S.,82203881 to Y.C.,82272627 to XT.Z.,7232018 to Y.S.,12090022 to B.D.,11831002 to B.D.,81801778 to L.Z.)Beijing Natural Science Foundation(7222021 to Y.C.,Z200015 to XT.Z.)+1 种基金Beijing Hospitals Authority Youth Programme(QML20231115 to Y.C.)Clinical Medicine Plus X-Young Scholars Project of Peking University(PKU2023LCXQ041 to Y.C.and L.Z.).
文摘The sole use of single modality data often fails to capture the complex heterogeneity among patients,including the variability in resistance to anti-HER2 therapy and outcomes of combined treatment regimens,for the treatment of HER2-positive gastric cancer(GC).This modality deficit has not been fully considered in many studies.Furthermore,the application of artificial intelligence in predicting the treatment response,particularly in complex diseases such as GC,is still in its infancy.Therefore,this study aimed to use a comprehensive analytic approach to accurately predict treatment responses to anti-HER2 therapy or anti-HER2 combined immunotherapy in patients with HER2-positive GC.We collected multi-modal data,comprising radiology,pathology,and clinical information from a cohort of 429 patients:310 treated with anti-HER2 therapy and 119 treated with a combination of anti-HER2 and anti-PD-1/PD-L1 inhibitors immunotherapy.We introduced a deep learning model,called the Multi-Modal model(MuMo),that integrates these data to make precise treatment response predictions.MuMo achieved an area under the curve score of 0.821 for anti-HER2 therapy and 0.914 for combined immunotherapy.Moreover,patients classified as low-risk by MuMo exhibited significantly prolonged progression-free survival and overall survival(log-rank test,P<0.05).These findings not only highlight the significance of multi-modal data analysis in enhancing treatment evaluation and personalized medicine for HER2-positive gastric cancer,but also the potential and clinical value of our model.
基金supported by the National Institutes of Health,USA(Grant Nos.R35GM142917 to Bo Zhang,U24ES026699 to Bo Zhang,R25DA027995 to Bo Zhang,R03AG070474 to Guoyan Zhao,R01NS123571 to Guoyan Zhao,U19NS130607 to Guoyan Zhao,and U24HG012070 to Bo Zhang and Guoyan Zhao)National Institutes of Health,USA.
文摘Efficient and reliable profiling methods are essential to study epigenetics.Tn5,one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency,is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome.Based on Tn5,the Assay for Transposase-Accessible Chromatin using sequencing(ATAC-seq)and the Cleavage Under Targets and Tagmentation(CUT&Tag)were developed to measure chromatin accessibility and detect DNA–protein interactions.These methodologies can be applied to large amounts of biological samples with low-input levels,such as rare tissues,embryos,and sorted single cells.However,fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly.Furthermore,inappropriate data analysis can generate biased or misleading conclusions.Therefore,it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools,many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing(ChIP-seq)data.Here,we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag data.We compared the sensitivity,specificity,and peak width distribution for both narrow-type and broad-type peak calling.We also tested the influence of the availability of control IgG input in CUT&Tag data analysis.Finally,we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag data.Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies,which were implemented into Docker/Singularity images for streamlined data analysis.
基金supported by the Hainan Province South China Sea New Star Science and Technology Innovation Talent Platform Project(NHXXRCXM202303)National Natural Science Foundation of China(42207524)+2 种基金Hainan Provincial Natural Science Foundation of China(422QN264 and 423MS117)Key R&D Program of Hainan(ZDYF2022SHFZ042)start-up funding from Hainan University(KYQD(ZR)-22085).
文摘Rubber plantations have increased signifcantly under unprecedented economic growth in tropical areas,which leads to soil degradation and thereby alters soil hydrological processes.However,our understanding of how forest conversion affects soil hydrological processes remains unclear.Here,we collected soil samples from secondary forests(SF)and rubber plantations(RP)to determine the soil hydrological characteristics.We found the topsoil(0-20 cm)water retention in SF was higher than that of RP but displayed the contrast pattern in a deeper soil layer(20-60 cm).Meanwhile,the soil infltration rates among the two vegetation types decreased signifcantly with infltration time,with higher stable soil infltration rates in SF than those in RP.Moreover,soil properties were also impacted by the forest conversion,such as the topsoil capillary porosity(CP)and total porosity(TP)in SF were higher than those of RP but contrasted in a deep soil layer.In comparison,the topsoil bulk density(BD)in SF was lower than that of RP,but contrasted in the deep soil layer and reached a signifcant level in the 0-10 and 40-50 cm(P<0.05).Overall,the soil water retention was mainly determined by the CP,which could explain 31.56%of the total variance in soil water retention,followed by TP(26.57%)and soil BD(26.47%),whereas soil texture exerts a weak effect on soil water retention.Therefore,we can conclude that the conversion of tropical rainforest into rubber plantations may accelerate soil erosion owing to its lower topsoil water retention and soil infltration rates.
文摘Palladium-based alloy is a kind of material with a high glass forming ability and can be easily formed into an amorphous state. After an annealing process, it can also be maintained at a crystallized state. To study the thermal and electrical transport properties of crystallized palladium-based alloys, the steady-state T-type method, standard four-probe method, and AC heating-DC detecting T-type method were used to measure the thermal conductivity, electrical conductivity, and Seebeck coeffi- cient of crystallized Pd4oNiloCu3oP2o and Pd43Nilo- Cu27P2o alloys respectively. The results show that compared to amorphous samples, the thermal conductivity and electrical conductivity of crystallized palladium-based alloys are significantly higher, while the Seebeck coeffi- cient is lower. The ratio of crystallized and amorphous thermal conductivity is higher for Pd43Ni10Cu27P2o alloy fiber which has a higher glass forming ability, while the ratio of electronic thermal conductivity almost remains constant for both alloy fibers. The results also show that the slope of electrical resistivity to temperature is a function of elemental composition for crystallized quaternary palla- dium-based alloy fibers. The sensitivity of thermal conductivity and electrical conductivity to the composition is high, while the correlation between Seebeck coefficient and composition is relatively weak.
