In this paper, we firstly identify the functional modules enriched with differentially expressed genes (DEGs) and characterized by biological processes in specific cellular locations, based on gene ontology (GO) a...In this paper, we firstly identify the functional modules enriched with differentially expressed genes (DEGs) and characterized by biological processes in specific cellular locations, based on gene ontology (GO) and microarray data. Then, we further define and filter disease relevant signature modules according to the ranking of the disease discriminating abilities of the pre-selected functional modules. At last, we analyze the potential way by which they cooperate towards human disease. Application of the proposed method to the analysis of a liver cancer dataset shows that, using the same false discovery rate ( FDR ) threshold, we can find more biologically meaningful and detailed processes by using the cellular localization information. Some biological evidences support the relevancy of our biological modules to the disease mechanism.展开更多
Selecting differentially expressed genes(DEGs) is one of the most important tasks in microarray applications for studying multi-factor diseases including cancers.However,the small samples typically used in current mic...Selecting differentially expressed genes(DEGs) is one of the most important tasks in microarray applications for studying multi-factor diseases including cancers.However,the small samples typically used in current microarray studies may only partially reflect the widely altered gene expressions in complex diseases,which would introduce low reproducibility of gene lists selected by statistical methods.Here,by analyzing seven cancer datasets,we showed that,in each cancer,a wide range of functional modules have altered gene expressions and thus have high disease classification abilities.The results also showed that seven modules are shared across diverse cancers,suggesting hints about the common mechanisms of cancers.Therefore,instead of relying on a few individual genes whose selection is hardly reproducible in current microarray experiments,we may use functional modules as functional signatures to study core mechanisms of cancers and build robust diagnostic classifiers.展开更多
Computational analysis is essential for transforming the masses of microarray datainto a mechanistic understanding of cancer. Here we present a method for findinggene functional modules of cancer from microarray data ...Computational analysis is essential for transforming the masses of microarray datainto a mechanistic understanding of cancer. Here we present a method for findinggene functional modules of cancer from microarray data and have applied it tocolon cancer. First, a colon cancer gene network and a normal colon tissue genenetwork were constructed using correlations between the genes. Then the modulesthat tended to have a homogeneous functional composition were identified by split-ting up the network. Analysis of both networks revealed that they are scale-free.Comparison of the gene functional modules for colon cancer and normal tissuesshowed that the modules’ functions changed with their structures.展开更多
To extract and display the significant information of combat systems,this paper introduces the methodology of functional cartography into combat networks and proposes an integrated framework named“functional cartogra...To extract and display the significant information of combat systems,this paper introduces the methodology of functional cartography into combat networks and proposes an integrated framework named“functional cartography of heterogeneous combat networks based on the operational chain”(FCBOC).In this framework,a functional module detection algorithm named operational chain-based label propagation algorithm(OCLPA),which considers the cooperation and interactions among combat entities and can thus naturally tackle network heterogeneity,is proposed to identify the functional modules of the network.Then,the nodes and their modules are classified into different roles according to their properties.A case study shows that FCBOC can provide a simplified description of disorderly information of combat networks and enable us to identify their functional and structural network characteristics.The results provide useful information to help commanders make precise and accurate decisions regarding the protection,disintegration or optimization of combat networks.Three algorithms are also compared with OCLPA to show that FCBOC can most effectively find functional modules with practical meaning.展开更多
Coronary artery disease (CAD) is a complex human disease, involving multiple genes and their nonlinear interactions, which often act in a modular fashion. Genome-wide single nucleotide polymorphism (SNP) profiling...Coronary artery disease (CAD) is a complex human disease, involving multiple genes and their nonlinear interactions, which often act in a modular fashion. Genome-wide single nucleotide polymorphism (SNP) profiling provides an effective technique to unravel these underlying genetic interplays or their functional involvements for CAD. This study aimed to identify the susceptible pathways and modules for CAD based on SNP omics. First, the Wellcome Trust Case Control Consortium (WTCCC) SNP datasets of CAD and control samples were used to assess the joint effect of multiple genetic variants at the pathway level, using logistic kernel machine regression model. Then, an expanded genetic network was constructed by integrating statistical gene-gene interactions involved in these susceptible pathways with their protein protein interaction (PPI) knowledge. Finally, risk functional modules were identified by decomposition of the network. Of 276 KEGG pathways analyzed, 6 pathways were found to have a significant effect on CAD. Other than glycerolipid metabolism, glycosaminoglycan biosynthesis, and cardiac muscle contraction pathways, three pathways related to other diseases were also revealed, including Alzheimer's disease, non-alcoholic fatty liver disease, and Huntington's disease. A genetic epistatic network of 95 genes was further constructed using the abovementioned integrative approach. Of 10 functional modules derived from the network, 6 have been annotated to phospholipase C activity and cell adhesion molecule binding, which also have known functional involvement in Alzheimer's disease. These findings indicate an overlap of the underlying molecular mechanisms between CAD and Alzheimer's disease, thus providing new insights into the molecular basis for CAD and its molecular relationships with other diseases.展开更多
The organization of biological neuronal networks into functional modules has intrigued scientists and inspired engineers to develop artificial systems.These networks are characterized by two key properties.First,they ...The organization of biological neuronal networks into functional modules has intrigued scientists and inspired engineers to develop artificial systems.These networks are characterized by two key properties.First,they exhibit dense interconnectivity(Braitenburg and Schüz,1998;Campagnola et al.,2022).The strength and probability of connectivity depend on cell type,inter-neuronal distance,and species.Still,every cortical neuron receives input from thousands of other neurons while transmitting output to a similar number of neurons.Second,communication between neurons occurs primarily via chemical or electrical synapses.展开更多
Metal-organic frameworks(MOFs)with tunable structures provide a versatile platform for exploring active sites and show great potential in enzyme-like catalysis.In this study,arginine was employed as a modulator to syn...Metal-organic frameworks(MOFs)with tunable structures provide a versatile platform for exploring active sites and show great potential in enzyme-like catalysis.In this study,arginine was employed as a modulator to synthesize an arginine-copper metal-organic framework(Arg-Cu-MOF),which demonstrated superior peroxidase-like activity and stability in comparison to unmodified Cu-MOF.The improved activity resulted from an increased density of Cu+active sites,facilitating efficient·OH generation through H2O2 decomposition.Glyphosate interacts with the copper sites in a way that affects·OH generation and chromogenic substrate oxidation,leading to detectable colorimetric changes.By integrating Arg-Cu-MOF into a needle sensor,we allowed sample handling,reagent mixing,and signal readout,enabling both precise instrumental measurements and semi-quantitative visual detection of glyphosate.This sensor offers a detection range of 0.05-200μg/mL with a detection limit of 0.049μg/m L.This work highlights the potential of MOF modulation strategies and integrated detection platforms to enhance analytical performance,improve user-friendliness,and expand the application scope of biomimetic nanomaterials.展开更多
●AIM:To compare the changes of pupil parameters and visual quality after cataract surgery and explore their potential correlations.●METHODS:This retrospective cohort study analyzed clinical data of Han Chinese patie...●AIM:To compare the changes of pupil parameters and visual quality after cataract surgery and explore their potential correlations.●METHODS:This retrospective cohort study analyzed clinical data of Han Chinese patients who received cataract surgery from June 2016 to October 2016.Visual acuity,pupil size,pupil shift,wavefront aberrations,point spread function(PSF),and modulation transfer function(MTF)were detected preoperatively,1d and 1mo postoperatively.Pupil parameters and visual outcomes were compared across the three time points.●RESULTS:A total of 110 eyes from 110 patients(42 males and 68 females)were enrolled,with a mean age of 66.8±7.9y(range:53–88y).Under both photopic and mesopic conditions,pupil diameter and pupil shift at 1d and 1mo after surgery were significantly lower than baseline levels.Corneal aberrations decreased postoperatively.Photopic and mesopic modulation transfer function derived from higher-order(HO)aberrations increased significantly from postoperative day 1 to postoperative month 1.Pupil size was positively correlated with wavefront aberrations,and negatively correlated with total PSF and HO-PSF.Significant correlations were identified between preoperative pupil diameter and 1-month postoperative visual quality indicators(including aberrations,PSF and modulation transfer function).A preoperative mesopic pupil diameter over 5.60 mm effectively predicted poor 1-month postoperative visual quality(HO aberrations>0.5μm),with an area under the curve(AUC)of 0.71.●CONCLUSION:Pupil parameters and visual quality alter significantly after cataract surgery,and moderate correlations exist between pupil diameter and visual quality at each time point.Preoperative pupil diameter is correlated with 1-month postoperative visual quality.展开更多
Objective:This study explores the role of methoxy polyethylene glycol@Elabela-11(mPEG@ELA-11),a pHresponsive ELA-11 conjugate,in modulating macrophage function and attenuating atherosclerosis,focusing on the protein k...Objective:This study explores the role of methoxy polyethylene glycol@Elabela-11(mPEG@ELA-11),a pHresponsive ELA-11 conjugate,in modulating macrophage function and attenuating atherosclerosis,focusing on the protein kinase B(AKT)-mediated endoplasmic reticulum(ER)stress pathway as a molecular target.Impact Statement:We reveal that ELA-11 alleviates atherosclerosis by suppressing macrophage foam cell formation,M1 polarization,and apoptosis via the AKT-ER stress pathway.We also develop mPEG@ELA-11,a novel pH-responsive nanocarrier,to enhance targeted drug delivery and therapeutic efficacy,offering a breakthrough for peptide-based cardiovascular nanomedicine.Introduction:Atherosclerosis,driven by macrophage dysfunction and lipid accumulation,is a major global killer.ELA-11,a fragment of Elabela peptide,shows cardiovascular protective effects,but its role in atherosclerosis and optimal delivery remain unstudied.Methods:Elabela mRNA(APELA)expression was analyzed in human carotid atherosclerotic plaques using real-time quantitative PCR analysis,and serum ELA levels were quantified via enzyme-linked immunosorbent assay in patients with carotid stenosis.In vitro studies on RAW264.7 macrophages evaluated mPEG@ELA-11 effects on oxidized low-density lipoprotein-induced foam cell formation,polarization,and apoptosis.In vivo efficacy was tested in ApoE-/-mice,comparing mPEG@ELA-11 with free ELA-11,and its pH-responsive release mechanism was characterized.Results:APELA was downregulated in human atherosclerotic plaques,especially unstable lesions.mPEG@ELA-11 suppressed foam cell formation,M1 polarization,and apoptosis by inhibiting the AKT-ER stress pathway in vitro.In mice,it reduced plaque area more effectively than free ELA-11 attributed to pH-triggered release.Conclusion:The pH-responsive mPEG@ELA-11 alleviates atherosclerosis by modulating macrophages via the AKT-ER stress pathway,with favorable targeting and safety,representing a promising targeted peptide nanomedicine for atherosclerosis.展开更多
A novel parameter identification method for magnetic levitation bearing rotor systems is proposed,based on the modulation function method.The fundamental principle of the modulation function method for parameter ident...A novel parameter identification method for magnetic levitation bearing rotor systems is proposed,based on the modulation function method.The fundamental principle of the modulation function method for parameter identification is derived on the basis of the characteristics of the modulation function.The transformation of the differential equation model of a continuous system into a general algebraic equation model is effectively achieved,thereby avoiding the influence of errors introduced by the initial value and differential derivation of the system.Modulation function method parameter identification models have been established for single-degree-of-freedom and multi-degree-of-freedom magnetic levitation bearing rotor systems.The influence of different parameters of Hartley modulation function on the accuracy of system parameter identification has been investigated,thus providing a basis for the design of Hartley modulation function parameters.Simulation and experimental results demonstrate that the modulation function method can effectively identify system parameters despite the presence of system noise.展开更多
AIM:To investigate how angles kappa and alpha affect postoperative visual quality in patients with multifocal intraocular lens(mIOLs)implantation.METHODS:Retrospective cases series.A total of 46 patients(46 eyes)who u...AIM:To investigate how angles kappa and alpha affect postoperative visual quality in patients with multifocal intraocular lens(mIOLs)implantation.METHODS:Retrospective cases series.A total of 46 patients(46 eyes)who underwent phacoemulsification were subsumed.The correlation between Preoperative angles kappa and alpha,wave-front aberrations and objective visual quality of cornea,internal,and total eye after surgery were analyzed using iTrace.RESULTS:The magnitude of angle kappa was negatively correlated with internal and total modulation transfer function(MTF)at 3 mm;the magnitude of angle kappa was positively correlated with astigmatism,trefoil,higher-order aberrations(HOAs)of both internal and total eye at 3 mm.The magnitude of angle alpha was negatively correlated with total MTF and total Strehl ratio at 3 mm.The magnitude of angle alpha was positively correlated with corneal coma at 5 mm,internal astigmatism at both 3 mm and 5 mm,and total spherical aberration(SA)at 3 mm.Multivariate linear regression analysis showed that,among candidate independent variables(kappa,alpha,astigmatism,SA,coma,trefoil,and HOAs),astigmatism is the only independent factor for altering corneal MTF at 3 mm and 5 mm;astigmatism and HOAs emerged as independent factors for altering internal MTF at 3 mm and 5 mm,and total MTF at 3 mm;astigmatism,SA and HOAs emerged as independent factors for altering total MTF at 5 mm.CONCLUSION:With greater preoperative angle kappa or angle alpha,patients who accept mIOL implantation tend to have larger internal astigmatism and HOAs,which resulting in poor visual quality,especially those with small pupil size.展开更多
The 2009 swine-origin influenza virus(S-OIV,H1N1 subtype)has developed into a new pandemic influenza as announced by the World Health Organization.In order to uncover clues about the determinants for virulence and pat...The 2009 swine-origin influenza virus(S-OIV,H1N1 subtype)has developed into a new pandemic influenza as announced by the World Health Organization.In order to uncover clues about the determinants for virulence and pathogenicity of the virus,we characterized the functional modules of the surface glycoprotein hemagglutinin(HA),the most important protein in molecular epidemiology and pathogenesis of influenza viruses.We analyzed receptor binding sites,basic patch,neutralization antibody epitopes and T cell epitopes in the HA protein of the current S-OIV according to the corresponding functional and structural modules previously characterized in other H1 HA molecules or HA molecules of other subtypes.We compared their differences and similarities systematically.Based on the amino acids defined as the functional and structural modules,the HA protein of 2009 S-OIV should specifically bind to the human 2,6-receptor.The D225G/E mutation in HA,which is found in some isolates,may confer dual binding specificity to the 2,3and 2,6-receptor based on previously reported work.This HA variant contains two basic patches,one of which results in increased basicity,suggesting enhanced membrane fusion function.The 2009 S-OIV HA also has an extra glycosylation site at position 276.Four of the five antibody neutralization epitopes identified in A/RP/8/34(H1N1)were exposed,but the other was hidden by a glycosylation site.The previously identified cytotoxic T cell epitopes in various HA molecules were summarized and their corresponding sequences in 2009 S-OIV HA were defined.These results are critical for understanding the pathogenicity of the virus and host immune response against the virus.展开更多
Continuing advancement in astronomy,space exploration,and scientific detection,has increased demand for infrared multi-band detection systems.Traditional three-band optical systems,designed to simultaneously image at ...Continuing advancement in astronomy,space exploration,and scientific detection,has increased demand for infrared multi-band detection systems.Traditional three-band optical systems,designed to simultaneously image at infrared short-wave,mid-wave,and long-wave bands typically rely on dispersive elements,leading to bulky sizes,complex system architectures,low efficiency,and challenges in rapid assembly.To overcome these obstacles,in combination with the latest third-generation infrared detectors,we propose a design for a compact and lightweight three-band optical system,with infrared capabilities in all three required bands.The core of this approach is an integrated design philosophy that emphasizes the high steepness of mirror surfaces.This design achieves uniform correction and optimization of chromatic aberration and off-axis aberration across the spectral range.We introduce a novel integration of optical and mechanical elements to replace traditional assembly,reducing manufacturing and assembly errors,and degrees of freedom,associated with high-power optical elements.Confirming the effectiveness through a combination of simulations and experimental comparisons,the measured mid-wave full-field transfer function exceeds 0.405 at 17 lp/mm,satisfying the imaging requirements of the system.The optical system is lightweight and compact,with a total mass under 408 g and a compact volume of justΦ112 mm×117 mm.This serves as a valuable reference for the engineering application of high-performance,compact multi-band infrared composite detection systems for astronomy and space exploration.展开更多
Niche theory is one of the most important ecological theories.It is widely applied to analyzing such phenomena as competition among,and evolution of,urban ecosystem functional modules.This paper describes a study conc...Niche theory is one of the most important ecological theories.It is widely applied to analyzing such phenomena as competition among,and evolution of,urban ecosystem functional modules.This paper describes a study concerning'different functional modules of Kaifeng city urban ecosystem.Niche theory and techniques were used to analyze the changes of these functional modules in the period 1994-2003.The results showed that,in the period 1994-2003:(1)Niche value of the atmospheric environment and urban virescence modules increased,while niche value of the water environment and sound environment modules decreased;(2)niche value of the tertiary industry module increased,niche value of the secondary industry module decreased,while niche value of the primary industry module showed little change;and(3)niche value of the infrastructure,resource distribution,and production&social security modules increased,while niche value of the population module decreased.This study may contribute to macroscopic planning of urban functional modules,economic development,and environmental protection.展开更多
The association between miRNA and disease has attracted more and more attention.Until now,existing methods for identifying miRNA related disease mainly rely on top-ranked association model,which may not provide a full...The association between miRNA and disease has attracted more and more attention.Until now,existing methods for identifying miRNA related disease mainly rely on top-ranked association model,which may not provide a full landscape of association between miRNA and disease.Hence there is strong need of new computational method to identify the associations from miRNA group view.In this paper,we proposed a framework,MDA-TOEPGA,to identify miRNAdisease association based on two-objective evolutionary programming genetic algorithm,which identifies latent miRNAdisease associations from the view of functional module.To understand the miRNA functional module in diseases,the case study is presented.We have been compared MDA-TOEPGA with several state-of-the-art functional module algorithm.Experimental results showed that our method cannot only outperform classical algorithms,such as K-means,IK-means,MCODE,HC-PIN,and ClusterONE,but can also achieve an ideal overall performance in terms of a composite score consisting of f1,Sensitivity,and Accuracy.Altogether,our study showed that MDA-TOEPGA is a promising method to investigate miRNA-disease association from the landscapes of functional module.展开更多
AIM:To describe the characteristics of modulation transfer function(MTF)of anterior corneal surface,and obtain the the normal reference range of MTF at different spatial frequencies and optical zones of the anterior c...AIM:To describe the characteristics of modulation transfer function(MTF)of anterior corneal surface,and obtain the the normal reference range of MTF at different spatial frequencies and optical zones of the anterior corneal surface in myopes.METHODS:Four hundred eyes from 200 patients were examined under SIRIUS corneal topography system.Phoenis analysis software was applied to simulate the MTF curves of anterior corneal surface at vertical and horizontal meridians at the 3,4,5,6,7mm optical zones of cornea.The MTF values at spatial frequencies of 5,10,15,20,25,30,35,40,45,50,55 and 60 cycles/degree(c/d)were selected.RESULTS:The MTF curve of anterior corneal surface decreased rapidly from low to intermediate frequency(0-15cpd)at various optical zones of cornea,the value decreased to 0 slowly at higher frequency(>15cpd).With the increase of the optical zones of cornea,MTF curve decreased gradually.3)In the range of 3 mm-6 mm optical zones of the cornea,the MTF values measured at horizontal meridian were greater than the corresponding values at horizontal meridian of each spatial frequency,the difference was statistically significant(P<0.05).At 7 mm optical zones of cornea,the MTF values measured at horizontal meridian were less than the corresponding values at vertical meridian at 10-60 spatial frequencies(cpd),and the difference was statistically significant in 25,30,35,40,45,50 cpd(P<0.05).CONCLUSION:MTF can be used to describe the imaging quality of optical systems at anterior corneal surface objectively in detail.展开更多
When imaging ocean surface waves by X-band marine radar, the radar backscatter from the sea surface is modulated by the long surface gravity waves. The modulation transfer function (MTF) comprises tilt, hydrodynamic...When imaging ocean surface waves by X-band marine radar, the radar backscatter from the sea surface is modulated by the long surface gravity waves. The modulation transfer function (MTF) comprises tilt, hydrodynamic, and shadowing modulations. A conventional linear MTF was derived using HH-polarized radar observations under conditions of deep water. In this study, we propose a new quadratic polynomial MTF based on W-polarized radar measurements taken from heterogeneous nearshore wave fields. This new MTF is obtained using a radar-observed image spectrum and in situ buoy-measured wave frequency spectrum. We validate the MTF by comparing peak and mean wave periods retrieved from X-band marine radar image sequences with those measured by the buoy. It is shown that the retrieval accuracies of peak and mean wave periods of the new MTF are better than the conventional MTF. The results also show that the bias and root mean square errors of the peak and mean wave periods of the new MTF are 0.05 and 0.88 s, and 0.32 and 0.53 s, respectively, while those of the conventional MTF are 0.61 and 0.98 s, and 1.39 and 1.48 s, respectively. Moreover, it is also shown that the retrieval results are insensitive to the coefficients in the proposed MTF.展开更多
The atmospheric scattering optical transfer function (OTF) is solved by applying the multi-coupled single scattering (MCSS) method to the three-dimensional radiative transfer equation (RTE) under the periodic gr...The atmospheric scattering optical transfer function (OTF) is solved by applying the multi-coupled single scattering (MCSS) method to the three-dimensional radiative transfer equation (RTE) under the periodic ground condition. This approach is a direct hit to the atmospheric scattering OTF using the same original context of modulation transfer function (MTF) measurement, i.e., images of sinusoidal grating at different spatial frequencies. Both the amplitude and phase shift of the OTF at various zenith and azimuth angles can be obtained at an arbitrary spatial frequency.展开更多
The resolution characteristic can be obtained by the modulation transfer function (MTF) of a GaAs/GaA1As photocathode. After establishing the theoretical model of GaAs(100)-oriented atomic configuration and the fo...The resolution characteristic can be obtained by the modulation transfer function (MTF) of a GaAs/GaA1As photocathode. After establishing the theoretical model of GaAs(100)-oriented atomic configuration and the formula for the ionized impurity scattering of the non-equilibrium carriers, this paper calculates the trajectories of photoelectrons in a photocathode. Thus the distribution of photoelectron spots on the emit-face is obtained, which is namely the point spread function. The MTF is obtained by Fourier transfer of the line spread function obtained from the point spread function. The MTF obtained from these calculations is shown to depend heavily on the electron diffusion length, and enhanced considerably by decreasing the electron diffusion length and increasing the doping concentration. Furthermore, the resolution is enhanced considerably by increasing the active-layer thickness, especially at high spatial frequencies. The best spatial resolution is 860 lp/mm, for the GaAs photocathode of doping concentration 1 ×10^19 cm 3 electron diffusion length 3.6 μm and the active-layer thickness 2 μm, under the 633-nm light irradiated. This research will contribute to the future improvement of the cathode's resolution for preparing a high performance GaAs photocathode, and improve the resolution of a low light level image intensifier.展开更多
The temporal characteristics of GaAs NEA and alkali metal photocathodes are studied using Monte Carlo simulation method. The electron transit time and its distribution functions in the photocathodes are calculated. Ba...The temporal characteristics of GaAs NEA and alkali metal photocathodes are studied using Monte Carlo simulation method. The electron transit time and its distribution functions in the photocathodes are calculated. Based on the results, the time modulation transfer functions and temporal resolutions of the photocathodes are obtained. The results show that the response time and temporal resolution of alkali metal photocathode is in femitosecond order and those of GaAs NEA photocathode are in picosecond order.展开更多
基金the National High Technology Research and Development Programme of China(No.2003AA2Z20512002AA2Z2052)+1 种基金the National Natural Science Foundation of China(No.3017051530370388)
摘要In this paper, we firstly identify the functional modules enriched with differentially expressed genes (DEGs) and characterized by biological processes in specific cellular locations, based on gene ontology (GO) and microarray data. Then, we further define and filter disease relevant signature modules according to the ranking of the disease discriminating abilities of the pre-selected functional modules. At last, we analyze the potential way by which they cooperate towards human disease. Application of the proposed method to the analysis of a liver cancer dataset shows that, using the same false discovery rate ( FDR ) threshold, we can find more biologically meaningful and detailed processes by using the cellular localization information. Some biological evidences support the relevancy of our biological modules to the disease mechanism.
基金supported by the National Natural Science Foundation of China (Grant Nos. 30170515,30370388 and 30970668)
摘要Selecting differentially expressed genes(DEGs) is one of the most important tasks in microarray applications for studying multi-factor diseases including cancers.However,the small samples typically used in current microarray studies may only partially reflect the widely altered gene expressions in complex diseases,which would introduce low reproducibility of gene lists selected by statistical methods.Here,by analyzing seven cancer datasets,we showed that,in each cancer,a wide range of functional modules have altered gene expressions and thus have high disease classification abilities.The results also showed that seven modules are shared across diverse cancers,suggesting hints about the common mechanisms of cancers.Therefore,instead of relying on a few individual genes whose selection is hardly reproducible in current microarray experiments,we may use functional modules as functional signatures to study core mechanisms of cancers and build robust diagnostic classifiers.
基金the National Natural Science Foundation of China (Grant No. 60234020).
摘要Computational analysis is essential for transforming the masses of microarray datainto a mechanistic understanding of cancer. Here we present a method for findinggene functional modules of cancer from microarray data and have applied it tocolon cancer. First, a colon cancer gene network and a normal colon tissue genenetwork were constructed using correlations between the genes. Then the modulesthat tended to have a homogeneous functional composition were identified by split-ting up the network. Analysis of both networks revealed that they are scale-free.Comparison of the gene functional modules for colon cancer and normal tissuesshowed that the modules’ functions changed with their structures.
摘要To extract and display the significant information of combat systems,this paper introduces the methodology of functional cartography into combat networks and proposes an integrated framework named“functional cartography of heterogeneous combat networks based on the operational chain”(FCBOC).In this framework,a functional module detection algorithm named operational chain-based label propagation algorithm(OCLPA),which considers the cooperation and interactions among combat entities and can thus naturally tackle network heterogeneity,is proposed to identify the functional modules of the network.Then,the nodes and their modules are classified into different roles according to their properties.A case study shows that FCBOC can provide a simplified description of disorderly information of combat networks and enable us to identify their functional and structural network characteristics.The results provide useful information to help commanders make precise and accurate decisions regarding the protection,disintegration or optimization of combat networks.Three algorithms are also compared with OCLPA to show that FCBOC can most effectively find functional modules with practical meaning.
基金supported in part by the National Natural Science Foundation of China(Grant Nos.31071166 and 81373085)Natural Science Foundation of Guangdong Province,China(Grant No.8251008901000007)+2 种基金Science and Technology Planning Project of Guangdong Province(Grant No.2009A030301004)Dongguan Science and Technology Project,Guangdong,China(Grant No.2011108101015)the funds from Guangdong Medical College,China(Grant Nos.XG1001,JB1214,XZ1105,STIF201122,M2011024,and M2011010)
摘要Coronary artery disease (CAD) is a complex human disease, involving multiple genes and their nonlinear interactions, which often act in a modular fashion. Genome-wide single nucleotide polymorphism (SNP) profiling provides an effective technique to unravel these underlying genetic interplays or their functional involvements for CAD. This study aimed to identify the susceptible pathways and modules for CAD based on SNP omics. First, the Wellcome Trust Case Control Consortium (WTCCC) SNP datasets of CAD and control samples were used to assess the joint effect of multiple genetic variants at the pathway level, using logistic kernel machine regression model. Then, an expanded genetic network was constructed by integrating statistical gene-gene interactions involved in these susceptible pathways with their protein protein interaction (PPI) knowledge. Finally, risk functional modules were identified by decomposition of the network. Of 276 KEGG pathways analyzed, 6 pathways were found to have a significant effect on CAD. Other than glycerolipid metabolism, glycosaminoglycan biosynthesis, and cardiac muscle contraction pathways, three pathways related to other diseases were also revealed, including Alzheimer's disease, non-alcoholic fatty liver disease, and Huntington's disease. A genetic epistatic network of 95 genes was further constructed using the abovementioned integrative approach. Of 10 functional modules derived from the network, 6 have been annotated to phospholipase C activity and cell adhesion molecule binding, which also have known functional involvement in Alzheimer's disease. These findings indicate an overlap of the underlying molecular mechanisms between CAD and Alzheimer's disease, thus providing new insights into the molecular basis for CAD and its molecular relationships with other diseases.
基金supported in part by the Rosetrees Trust(#CF-2023-I-2_113)by the Israel Ministry of Innovation,Science,and Technology(#7393)(to ES).
摘要The organization of biological neuronal networks into functional modules has intrigued scientists and inspired engineers to develop artificial systems.These networks are characterized by two key properties.First,they exhibit dense interconnectivity(Braitenburg and Schüz,1998;Campagnola et al.,2022).The strength and probability of connectivity depend on cell type,inter-neuronal distance,and species.Still,every cortical neuron receives input from thousands of other neurons while transmitting output to a similar number of neurons.Second,communication between neurons occurs primarily via chemical or electrical synapses.
基金financial support from a start-up fund of Central China Normal Universitythe Fundamental Research Funds for the Central Universities(Nos.CCNU25QN004,CCNU24JCPT032 and CCNU22JC006)+3 种基金Natural Science Foundation of Hubei Province(No.2023AFB571)Knowledge Innovation Program of Wuhan-Shuguang Project(No.2023020201020441)the Open Research Fund of the Key Laboratory of Ministry of Education,Hangzhou Normal University(No.KFJJ2023009)the Program of Introducing Talents of Discipline to Universities of China(111 program,No.B17019)。
摘要Metal-organic frameworks(MOFs)with tunable structures provide a versatile platform for exploring active sites and show great potential in enzyme-like catalysis.In this study,arginine was employed as a modulator to synthesize an arginine-copper metal-organic framework(Arg-Cu-MOF),which demonstrated superior peroxidase-like activity and stability in comparison to unmodified Cu-MOF.The improved activity resulted from an increased density of Cu+active sites,facilitating efficient·OH generation through H2O2 decomposition.Glyphosate interacts with the copper sites in a way that affects·OH generation and chromogenic substrate oxidation,leading to detectable colorimetric changes.By integrating Arg-Cu-MOF into a needle sensor,we allowed sample handling,reagent mixing,and signal readout,enabling both precise instrumental measurements and semi-quantitative visual detection of glyphosate.This sensor offers a detection range of 0.05-200μg/mL with a detection limit of 0.049μg/m L.This work highlights the potential of MOF modulation strategies and integrated detection platforms to enhance analytical performance,improve user-friendliness,and expand the application scope of biomimetic nanomaterials.
基金Supported by National Natural Science Foundation of China(No.81300747)Natural Science Foundation of Shanghai(Science and Technology Commission of Shanghai Municipality,No.22ZR1410400+8 种基金No.19ZR1408600)the Excellent Young Doctor Training Program of Shanghai(Shanghai Municipal Health Commission,No.2015-2018)the Clinical Research Project of Shanghai Municipal Health Commission(Shanghai Municipal Health Commission,No.202540103)the Shanghai Municipal Health Commission’s Seed Program for Medical New Technology Research and Translation(Shanghai Municipal Health Commission,No.2025ZZ2068)the Scientific Research Program of Shanghai Pudong New Area Health Commission(Shanghai Pudong New Area Health Commission,No.PW2024D-05)Young Clinical Scientist Training Program(Fudan University Shanghai Medical College,No.DGF828019-2/038)the“Medicine+X”Interdisciplinary Research Project(Tongji University,No.2025-0553-YB-07)Vision and Action-Ophthalmology Clinical Research Support Program(the Bethune Foundation,No.BFC-KECS-LC-20251022-01)Shanghai Tenth People’s Hospital Undergraduate Teaching Courses(Tenth People’s Hospital of Tongji University,Funding Type:A:2025 Blended Teaching Courses and B:2025 Demonstration Courses).
摘要●AIM:To compare the changes of pupil parameters and visual quality after cataract surgery and explore their potential correlations.●METHODS:This retrospective cohort study analyzed clinical data of Han Chinese patients who received cataract surgery from June 2016 to October 2016.Visual acuity,pupil size,pupil shift,wavefront aberrations,point spread function(PSF),and modulation transfer function(MTF)were detected preoperatively,1d and 1mo postoperatively.Pupil parameters and visual outcomes were compared across the three time points.●RESULTS:A total of 110 eyes from 110 patients(42 males and 68 females)were enrolled,with a mean age of 66.8±7.9y(range:53–88y).Under both photopic and mesopic conditions,pupil diameter and pupil shift at 1d and 1mo after surgery were significantly lower than baseline levels.Corneal aberrations decreased postoperatively.Photopic and mesopic modulation transfer function derived from higher-order(HO)aberrations increased significantly from postoperative day 1 to postoperative month 1.Pupil size was positively correlated with wavefront aberrations,and negatively correlated with total PSF and HO-PSF.Significant correlations were identified between preoperative pupil diameter and 1-month postoperative visual quality indicators(including aberrations,PSF and modulation transfer function).A preoperative mesopic pupil diameter over 5.60 mm effectively predicted poor 1-month postoperative visual quality(HO aberrations>0.5μm),with an area under the curve(AUC)of 0.71.●CONCLUSION:Pupil parameters and visual quality alter significantly after cataract surgery,and moderate correlations exist between pupil diameter and visual quality at each time point.Preoperative pupil diameter is correlated with 1-month postoperative visual quality.
基金supported by the National Natural Science Foundation of China(82270481,82470481,and 82370498)the Shuang Bai Ren Project of Shanghai Jiao Tong University(JYYJXYS20240821)the Medical Scientific Research Project of Shanghai Hongkou Health Commission(Hongwei 2302-17 and 2302-22).
摘要Objective:This study explores the role of methoxy polyethylene glycol@Elabela-11(mPEG@ELA-11),a pHresponsive ELA-11 conjugate,in modulating macrophage function and attenuating atherosclerosis,focusing on the protein kinase B(AKT)-mediated endoplasmic reticulum(ER)stress pathway as a molecular target.Impact Statement:We reveal that ELA-11 alleviates atherosclerosis by suppressing macrophage foam cell formation,M1 polarization,and apoptosis via the AKT-ER stress pathway.We also develop mPEG@ELA-11,a novel pH-responsive nanocarrier,to enhance targeted drug delivery and therapeutic efficacy,offering a breakthrough for peptide-based cardiovascular nanomedicine.Introduction:Atherosclerosis,driven by macrophage dysfunction and lipid accumulation,is a major global killer.ELA-11,a fragment of Elabela peptide,shows cardiovascular protective effects,but its role in atherosclerosis and optimal delivery remain unstudied.Methods:Elabela mRNA(APELA)expression was analyzed in human carotid atherosclerotic plaques using real-time quantitative PCR analysis,and serum ELA levels were quantified via enzyme-linked immunosorbent assay in patients with carotid stenosis.In vitro studies on RAW264.7 macrophages evaluated mPEG@ELA-11 effects on oxidized low-density lipoprotein-induced foam cell formation,polarization,and apoptosis.In vivo efficacy was tested in ApoE-/-mice,comparing mPEG@ELA-11 with free ELA-11,and its pH-responsive release mechanism was characterized.Results:APELA was downregulated in human atherosclerotic plaques,especially unstable lesions.mPEG@ELA-11 suppressed foam cell formation,M1 polarization,and apoptosis by inhibiting the AKT-ER stress pathway in vitro.In mice,it reduced plaque area more effectively than free ELA-11 attributed to pH-triggered release.Conclusion:The pH-responsive mPEG@ELA-11 alleviates atherosclerosis by modulating macrophages via the AKT-ER stress pathway,with favorable targeting and safety,representing a promising targeted peptide nanomedicine for atherosclerosis.
基金supported by the National Science and Technology Major Project(Grant No.J2019-Ⅳ-0003-0070).
摘要A novel parameter identification method for magnetic levitation bearing rotor systems is proposed,based on the modulation function method.The fundamental principle of the modulation function method for parameter identification is derived on the basis of the characteristics of the modulation function.The transformation of the differential equation model of a continuous system into a general algebraic equation model is effectively achieved,thereby avoiding the influence of errors introduced by the initial value and differential derivation of the system.Modulation function method parameter identification models have been established for single-degree-of-freedom and multi-degree-of-freedom magnetic levitation bearing rotor systems.The influence of different parameters of Hartley modulation function on the accuracy of system parameter identification has been investigated,thus providing a basis for the design of Hartley modulation function parameters.Simulation and experimental results demonstrate that the modulation function method can effectively identify system parameters despite the presence of system noise.
摘要AIM:To investigate how angles kappa and alpha affect postoperative visual quality in patients with multifocal intraocular lens(mIOLs)implantation.METHODS:Retrospective cases series.A total of 46 patients(46 eyes)who underwent phacoemulsification were subsumed.The correlation between Preoperative angles kappa and alpha,wave-front aberrations and objective visual quality of cornea,internal,and total eye after surgery were analyzed using iTrace.RESULTS:The magnitude of angle kappa was negatively correlated with internal and total modulation transfer function(MTF)at 3 mm;the magnitude of angle kappa was positively correlated with astigmatism,trefoil,higher-order aberrations(HOAs)of both internal and total eye at 3 mm.The magnitude of angle alpha was negatively correlated with total MTF and total Strehl ratio at 3 mm.The magnitude of angle alpha was positively correlated with corneal coma at 5 mm,internal astigmatism at both 3 mm and 5 mm,and total spherical aberration(SA)at 3 mm.Multivariate linear regression analysis showed that,among candidate independent variables(kappa,alpha,astigmatism,SA,coma,trefoil,and HOAs),astigmatism is the only independent factor for altering corneal MTF at 3 mm and 5 mm;astigmatism and HOAs emerged as independent factors for altering internal MTF at 3 mm and 5 mm,and total MTF at 3 mm;astigmatism,SA and HOAs emerged as independent factors for altering total MTF at 5 mm.CONCLUSION:With greater preoperative angle kappa or angle alpha,patients who accept mIOL implantation tend to have larger internal astigmatism and HOAs,which resulting in poor visual quality,especially those with small pupil size.
基金supported by the National Basic Research Program of China(Grant No.2010CB534004)an intramural grant from the Chinese Academy of Sciences(Grant No.KSCX2-YW-R-158)
摘要The 2009 swine-origin influenza virus(S-OIV,H1N1 subtype)has developed into a new pandemic influenza as announced by the World Health Organization.In order to uncover clues about the determinants for virulence and pathogenicity of the virus,we characterized the functional modules of the surface glycoprotein hemagglutinin(HA),the most important protein in molecular epidemiology and pathogenesis of influenza viruses.We analyzed receptor binding sites,basic patch,neutralization antibody epitopes and T cell epitopes in the HA protein of the current S-OIV according to the corresponding functional and structural modules previously characterized in other H1 HA molecules or HA molecules of other subtypes.We compared their differences and similarities systematically.Based on the amino acids defined as the functional and structural modules,the HA protein of 2009 S-OIV should specifically bind to the human 2,6-receptor.The D225G/E mutation in HA,which is found in some isolates,may confer dual binding specificity to the 2,3and 2,6-receptor based on previously reported work.This HA variant contains two basic patches,one of which results in increased basicity,suggesting enhanced membrane fusion function.The 2009 S-OIV HA also has an extra glycosylation site at position 276.Four of the five antibody neutralization epitopes identified in A/RP/8/34(H1N1)were exposed,but the other was hidden by a glycosylation site.The previously identified cytotoxic T cell epitopes in various HA molecules were summarized and their corresponding sequences in 2009 S-OIV HA were defined.These results are critical for understanding the pathogenicity of the virus and host immune response against the virus.
基金National Natural Science Foundation of China(12073028,12473084).
摘要Continuing advancement in astronomy,space exploration,and scientific detection,has increased demand for infrared multi-band detection systems.Traditional three-band optical systems,designed to simultaneously image at infrared short-wave,mid-wave,and long-wave bands typically rely on dispersive elements,leading to bulky sizes,complex system architectures,low efficiency,and challenges in rapid assembly.To overcome these obstacles,in combination with the latest third-generation infrared detectors,we propose a design for a compact and lightweight three-band optical system,with infrared capabilities in all three required bands.The core of this approach is an integrated design philosophy that emphasizes the high steepness of mirror surfaces.This design achieves uniform correction and optimization of chromatic aberration and off-axis aberration across the spectral range.We introduce a novel integration of optical and mechanical elements to replace traditional assembly,reducing manufacturing and assembly errors,and degrees of freedom,associated with high-power optical elements.Confirming the effectiveness through a combination of simulations and experimental comparisons,the measured mid-wave full-field transfer function exceeds 0.405 at 17 lp/mm,satisfying the imaging requirements of the system.The optical system is lightweight and compact,with a total mass under 408 g and a compact volume of justΦ112 mm×117 mm.This serves as a valuable reference for the engineering application of high-performance,compact multi-band infrared composite detection systems for astronomy and space exploration.
基金National Natural Science Foundation of China,No.30570301,No.40671175
摘要Niche theory is one of the most important ecological theories.It is widely applied to analyzing such phenomena as competition among,and evolution of,urban ecosystem functional modules.This paper describes a study concerning'different functional modules of Kaifeng city urban ecosystem.Niche theory and techniques were used to analyze the changes of these functional modules in the period 1994-2003.The results showed that,in the period 1994-2003:(1)Niche value of the atmospheric environment and urban virescence modules increased,while niche value of the water environment and sound environment modules decreased;(2)niche value of the tertiary industry module increased,niche value of the secondary industry module decreased,while niche value of the primary industry module showed little change;and(3)niche value of the infrastructure,resource distribution,and production&social security modules increased,while niche value of the population module decreased.This study may contribute to macroscopic planning of urban functional modules,economic development,and environmental protection.
基金This work was supported in part by the National Natural Science Foundation of China under Grants 61873089,62032007the Key Project of the Education Department of Hunan Province under Grant 20A087the Innovation Platform Open Fund Project of Hunan Provincial Education Department under Grant 20K025.
摘要The association between miRNA and disease has attracted more and more attention.Until now,existing methods for identifying miRNA related disease mainly rely on top-ranked association model,which may not provide a full landscape of association between miRNA and disease.Hence there is strong need of new computational method to identify the associations from miRNA group view.In this paper,we proposed a framework,MDA-TOEPGA,to identify miRNAdisease association based on two-objective evolutionary programming genetic algorithm,which identifies latent miRNAdisease associations from the view of functional module.To understand the miRNA functional module in diseases,the case study is presented.We have been compared MDA-TOEPGA with several state-of-the-art functional module algorithm.Experimental results showed that our method cannot only outperform classical algorithms,such as K-means,IK-means,MCODE,HC-PIN,and ClusterONE,but can also achieve an ideal overall performance in terms of a composite score consisting of f1,Sensitivity,and Accuracy.Altogether,our study showed that MDA-TOEPGA is a promising method to investigate miRNA-disease association from the landscapes of functional module.
摘要AIM:To describe the characteristics of modulation transfer function(MTF)of anterior corneal surface,and obtain the the normal reference range of MTF at different spatial frequencies and optical zones of the anterior corneal surface in myopes.METHODS:Four hundred eyes from 200 patients were examined under SIRIUS corneal topography system.Phoenis analysis software was applied to simulate the MTF curves of anterior corneal surface at vertical and horizontal meridians at the 3,4,5,6,7mm optical zones of cornea.The MTF values at spatial frequencies of 5,10,15,20,25,30,35,40,45,50,55 and 60 cycles/degree(c/d)were selected.RESULTS:The MTF curve of anterior corneal surface decreased rapidly from low to intermediate frequency(0-15cpd)at various optical zones of cornea,the value decreased to 0 slowly at higher frequency(>15cpd).With the increase of the optical zones of cornea,MTF curve decreased gradually.3)In the range of 3 mm-6 mm optical zones of the cornea,the MTF values measured at horizontal meridian were greater than the corresponding values at horizontal meridian of each spatial frequency,the difference was statistically significant(P<0.05).At 7 mm optical zones of cornea,the MTF values measured at horizontal meridian were less than the corresponding values at vertical meridian at 10-60 spatial frequencies(cpd),and the difference was statistically significant in 25,30,35,40,45,50 cpd(P<0.05).CONCLUSION:MTF can be used to describe the imaging quality of optical systems at anterior corneal surface objectively in detail.
基金Supported by the National High Technology Research and Development Program of China(863 Program)(No.2013AA09A505)the National Natural Science Foundation of China(Nos.41076119,41176160,41476158)+4 种基金the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD)the Natural Science Youth Foundation of Jiangsu Province(No.BK2012467)the Natural Science State Key Foundation of Jiangsu Province(No.BK2011008)the National Natural Science Youth Foundation of China(No.41206171)the Startup Foundation for Introducing Talent of Nanjing University of Information Science and Technology(No.S8113078001)
摘要When imaging ocean surface waves by X-band marine radar, the radar backscatter from the sea surface is modulated by the long surface gravity waves. The modulation transfer function (MTF) comprises tilt, hydrodynamic, and shadowing modulations. A conventional linear MTF was derived using HH-polarized radar observations under conditions of deep water. In this study, we propose a new quadratic polynomial MTF based on W-polarized radar measurements taken from heterogeneous nearshore wave fields. This new MTF is obtained using a radar-observed image spectrum and in situ buoy-measured wave frequency spectrum. We validate the MTF by comparing peak and mean wave periods retrieved from X-band marine radar image sequences with those measured by the buoy. It is shown that the retrieval accuracies of peak and mean wave periods of the new MTF are better than the conventional MTF. The results also show that the bias and root mean square errors of the peak and mean wave periods of the new MTF are 0.05 and 0.88 s, and 0.32 and 0.53 s, respectively, while those of the conventional MTF are 0.61 and 0.98 s, and 1.39 and 1.48 s, respectively. Moreover, it is also shown that the retrieval results are insensitive to the coefficients in the proposed MTF.
基金supported by the Main Direction Program of Knowledge Innovation of Chinese Academy of Sciences(Grant No.KGFZD-125-13-006)
摘要The atmospheric scattering optical transfer function (OTF) is solved by applying the multi-coupled single scattering (MCSS) method to the three-dimensional radiative transfer equation (RTE) under the periodic ground condition. This approach is a direct hit to the atmospheric scattering OTF using the same original context of modulation transfer function (MTF) measurement, i.e., images of sinusoidal grating at different spatial frequencies. Both the amplitude and phase shift of the OTF at various zenith and azimuth angles can be obtained at an arbitrary spatial frequency.
基金Project supported by the National Natural Science Foundation of China (Grant No. 60678043)the Research and Innovation Plan for Graduate Students of Jiangsu Higher Education Institutions,China (Grant No. CX09B 096Z)
摘要The resolution characteristic can be obtained by the modulation transfer function (MTF) of a GaAs/GaA1As photocathode. After establishing the theoretical model of GaAs(100)-oriented atomic configuration and the formula for the ionized impurity scattering of the non-equilibrium carriers, this paper calculates the trajectories of photoelectrons in a photocathode. Thus the distribution of photoelectron spots on the emit-face is obtained, which is namely the point spread function. The MTF is obtained by Fourier transfer of the line spread function obtained from the point spread function. The MTF obtained from these calculations is shown to depend heavily on the electron diffusion length, and enhanced considerably by decreasing the electron diffusion length and increasing the doping concentration. Furthermore, the resolution is enhanced considerably by increasing the active-layer thickness, especially at high spatial frequencies. The best spatial resolution is 860 lp/mm, for the GaAs photocathode of doping concentration 1 ×10^19 cm 3 electron diffusion length 3.6 μm and the active-layer thickness 2 μm, under the 633-nm light irradiated. This research will contribute to the future improvement of the cathode's resolution for preparing a high performance GaAs photocathode, and improve the resolution of a low light level image intensifier.
摘要The temporal characteristics of GaAs NEA and alkali metal photocathodes are studied using Monte Carlo simulation method. The electron transit time and its distribution functions in the photocathodes are calculated. Based on the results, the time modulation transfer functions and temporal resolutions of the photocathodes are obtained. The results show that the response time and temporal resolution of alkali metal photocathode is in femitosecond order and those of GaAs NEA photocathode are in picosecond order.