Heterogeneity of biological samples is usually considered a major obstacle for three-dimensional (3D) structure determination of macromolecular complexes. Heterogeneity may occur at the level of composition or conform...Heterogeneity of biological samples is usually considered a major obstacle for three-dimensional (3D) structure determination of macromolecular complexes. Heterogeneity may occur at the level of composition or conformational variability of complexes and affects most 3D structure determination methods that rely on signal averaging. Here, an approach is described that allows sorting structural states based on a 3D statistical approach, the 3D sampling and classification (3D-SC) of 3D structures derived from single particles imaged by cryo electron microscopy (cryo-EM). The method is based on jackknifing & bootstrapping of 3D sub-ensembles and 3D multivariate statistical analysis followed by 3D classification. The robustness of the statistical sorting procedure is corroborated using model data from an RNA polymerase structure and experimental data from a ribosome complex. It allows resolving multiple states within heterogeneous complexes that thus become amendable for a structural analysis despite of their highly flexible nature. The method has important implications for high-resolution structural studies and allows describing structure ensembles to provide insights into the dynamics of multi-component macromolecular assemblies.展开更多
Cryo-electron microscopy makes use of transmission electron microscopy to image vitrified biological samples and reconstruct their three-dimensional structures from two-dimensional projections via computational approa...Cryo-electron microscopy makes use of transmission electron microscopy to image vitrified biological samples and reconstruct their three-dimensional structures from two-dimensional projections via computational approaches. After over40 years of development, this technique is now reaching its zenith and reforming the research paradigm of modern structural biology. It has been gradually taking over X-ray crystallography as the mainstream method. In this review, we briefly introduce the history of cryo-EM, recent technical development and its potential power to reveal dynamic structures. The technical barriers and possible approaches to tackle the upcoming challenges are discussed.展开更多
Realizing ultra-wideband absorption,desirable attenuation capability at high temperature and mechanical requirements for real-life applications remains a great challenge for microwave absorbing materials.Herein,we hav...Realizing ultra-wideband absorption,desirable attenuation capability at high temperature and mechanical requirements for real-life applications remains a great challenge for microwave absorbing materials.Herein,we have constructed a porous carbon fiber/polymethacrylimide(CP)structure for acquiring promising microwave absorption performance and withstanding both elevated temperature and high strength in a low density.Given the ability of porous structure to induce desirable impedance matching and multiple reflection,the absorption bandwidth of CP composite can reach ultra-wideband absorption of 14 GHz at room temperature and even cover the whole X-band at 473 K.Additionally,the presence of imide ring group in polymethacrylimide and hard bubble wall endows the composite with excellent heat and compressive behaviors.Besides,the lightweight of the CP composite with a density of only 110 mg cm^(−3) coupled with high compressive strength of 1.05 MPa even at 453 K also satisfies the requirements in engineering applica-tions.Compared with soft and compressible aerogel materials,we envision that the rigid porous foam absorbing material is particularly suitable for environmental extremes.展开更多
It is of both the theoretical and practical importance to reduce the storage andCPU time of moment methods by utilizing the geometrical and physical features of the scatterer.An unified approach based on the group the...It is of both the theoretical and practical importance to reduce the storage andCPU time of moment methods by utilizing the geometrical and physical features of the scatterer.An unified approach based on the group theory is presented to deal with the EM scattering fromsymmetric and anti-symmetric structures.展开更多
Classical survival analysis assumes all subjects will experience the event of interest, but in some cases, a portion of the population may never encounter the event. These survival methods further assume independent s...Classical survival analysis assumes all subjects will experience the event of interest, but in some cases, a portion of the population may never encounter the event. These survival methods further assume independent survival times, which is not valid for honey bees, which live in nests. The study introduces a semi-parametric marginal proportional hazards mixture cure (PHMC) model with exchangeable correlation structure, using generalized estimating equations for survival data analysis. The model was tested on clustered right-censored bees survival data with a cured fraction, where two bee species were subjected to different entomopathogens to test the effect of the entomopathogens on the survival of the bee species. The Expectation-Solution algorithm is used to estimate the parameters. The study notes a weak positive association between cure statuses (ρ1=0.0007) and survival times for uncured bees (ρ2=0.0890), emphasizing their importance. The odds of being uncured for A. mellifera is higher than the odds for species M. ferruginea. The bee species, A. mellifera are more susceptible to entomopathogens icipe 7, icipe 20, and icipe 69. The Cox-Snell residuals show that the proposed semiparametric PH model generally fits the data well as compared to model that assume independent correlation structure. Thus, the semi parametric marginal proportional hazards mixture cure is parsimonious model for correlated bees survival data.展开更多
The solidification microstructure has an important effect on the mechanical properties of castings. Therefore, an FE （Finite Element） - CA （Cellular Automaton） coupling model was developed for the simulation of so...The solidification microstructure has an important effect on the mechanical properties of castings. Therefore, an FE （Finite Element） - CA （Cellular Automaton） coupling model was developed for the simulation of solidification structure during the continuous casting process of 72A tire cord steel. In the model, the effect of phase transformation （λ→γ→α） during solidification was considered based on a thermodynamic database. The effect of electromagnetic stirring （EMS） was determined by increasing both the thermal conductivity and crystal formation rate in the liquid phase. The results show that the cooling curves and solidification structure calculated by this model agree well with the experimental results. The optimum pouring temperature range for tire cord steel casting was also discussed based on the present model. By comprehensive consideration of billet quality and smooth production, the pouring temperature should be controlled at about 1,495 ℃ under the casting conditions of the local plant in this study.展开更多
A breaking wave can exert a great influence on the electromagnetic（EM） scattering result from sea surfaces. In this paper, the process of small-scale wave breaking is simulated by the commercial computational fluid ...A breaking wave can exert a great influence on the electromagnetic（EM） scattering result from sea surfaces. In this paper, the process of small-scale wave breaking is simulated by the commercial computational fluid dynamics（CFD）software FLUENT, and the backscattering radar cross section（RCS） of the turbulence structure after breaking is calculated with the method of moments. The scattering results can reflect the turbulent intensities of the wave profiles and can indicate high polarization ratios at moderate incident angles, which should be attributed to the incoherent backscatter from surface disturbance of turbulence structure. Compared with the wave profile before breaking, the turbulence structure has no obvious geometrical characteristic of a plunging breaker, and no sea spikes are present at large incident angles either.In summary, the study of EM scattering from turbulence structure can provide a basis to explain the anomalies of EM scattering from sea surfaces and help us understand the scattering mechanism about the breaking wave more completely.展开更多
The CryoEM single particle structure determination method has recently received broad attention in the field of structural biology. The structures can be resolved to near-atomic resolutions after model reconstructions...The CryoEM single particle structure determination method has recently received broad attention in the field of structural biology. The structures can be resolved to near-atomic resolutions after model reconstructions from a large number of CryoEM images measuring molecules in different orientations. However, the determining factors for reconstructed map resolution need to be further explored. Here, we provide a theoretical framework in conjunction with numerical simulations to gauge the influence of several key factors to CryoEM map resolutions. If the projection image quality allows orientation assignment, then the number of measured projection images and the quality of each measurement(quantified using average signal-to-noise ratio) can be combined to a single factor, which is dominant to the resolution of reconstructed maps. Furthermore, the intrinsic thermal motion of molecules has significant effects on the resolution. These effects can be quantitatively summarized with an analytical formula that provides a theoretical guideline on structure resolutions for given experimental measurements.展开更多
Recent technical breakthroughs in cryo-electron microscopy（cryo-EM） revolutionized structural biology, which led to the 2017 Nobel Prize in chemistry being awarded to three scientists, Jacques Dubochet, Joachim Fran...Recent technical breakthroughs in cryo-electron microscopy（cryo-EM） revolutionized structural biology, which led to the 2017 Nobel Prize in chemistry being awarded to three scientists, Jacques Dubochet, Joachim Frank, and Richard Henderson, who made groundbreaking contributions to the development of cryo-EM. In this review, I will give a comprehensive review of the developmental history of cryo-EM, the technical aspects of the breakthrough in cryo-EM leading to the structural biology revolution, including electron microscopy, image recording devices and image processing algorithms,and the major scientific achievements by Chinese researchers employing cryo-EM, covering protein complexes involved in or related to gene expression and regulation, protein synthesis and degradation, membrane proteins, immunity, and viruses.Finally, I will give a perspective outlook on the development of cryo-EM in the future.展开更多
文摘Heterogeneity of biological samples is usually considered a major obstacle for three-dimensional (3D) structure determination of macromolecular complexes. Heterogeneity may occur at the level of composition or conformational variability of complexes and affects most 3D structure determination methods that rely on signal averaging. Here, an approach is described that allows sorting structural states based on a 3D statistical approach, the 3D sampling and classification (3D-SC) of 3D structures derived from single particles imaged by cryo electron microscopy (cryo-EM). The method is based on jackknifing & bootstrapping of 3D sub-ensembles and 3D multivariate statistical analysis followed by 3D classification. The robustness of the statistical sorting procedure is corroborated using model data from an RNA polymerase structure and experimental data from a ribosome complex. It allows resolving multiple states within heterogeneous complexes that thus become amendable for a structural analysis despite of their highly flexible nature. The method has important implications for high-resolution structural studies and allows describing structure ensembles to provide insights into the dynamics of multi-component macromolecular assemblies.
文摘Cryo-electron microscopy makes use of transmission electron microscopy to image vitrified biological samples and reconstruct their three-dimensional structures from two-dimensional projections via computational approaches. After over40 years of development, this technique is now reaching its zenith and reforming the research paradigm of modern structural biology. It has been gradually taking over X-ray crystallography as the mainstream method. In this review, we briefly introduce the history of cryo-EM, recent technical development and its potential power to reveal dynamic structures. The technical barriers and possible approaches to tackle the upcoming challenges are discussed.
基金supported by the National Natural Science Foundation of China(52172091 and 52172295)the Interdisciplinary Innovation Foundation for Graduates(Nanjing University of Aeronautics and Astronautics,No.KXKCXJJ202009).
文摘Realizing ultra-wideband absorption,desirable attenuation capability at high temperature and mechanical requirements for real-life applications remains a great challenge for microwave absorbing materials.Herein,we have constructed a porous carbon fiber/polymethacrylimide(CP)structure for acquiring promising microwave absorption performance and withstanding both elevated temperature and high strength in a low density.Given the ability of porous structure to induce desirable impedance matching and multiple reflection,the absorption bandwidth of CP composite can reach ultra-wideband absorption of 14 GHz at room temperature and even cover the whole X-band at 473 K.Additionally,the presence of imide ring group in polymethacrylimide and hard bubble wall endows the composite with excellent heat and compressive behaviors.Besides,the lightweight of the CP composite with a density of only 110 mg cm^(−3) coupled with high compressive strength of 1.05 MPa even at 453 K also satisfies the requirements in engineering applica-tions.Compared with soft and compressible aerogel materials,we envision that the rigid porous foam absorbing material is particularly suitable for environmental extremes.
文摘It is of both the theoretical and practical importance to reduce the storage andCPU time of moment methods by utilizing the geometrical and physical features of the scatterer.An unified approach based on the group theory is presented to deal with the EM scattering fromsymmetric and anti-symmetric structures.
文摘Classical survival analysis assumes all subjects will experience the event of interest, but in some cases, a portion of the population may never encounter the event. These survival methods further assume independent survival times, which is not valid for honey bees, which live in nests. The study introduces a semi-parametric marginal proportional hazards mixture cure (PHMC) model with exchangeable correlation structure, using generalized estimating equations for survival data analysis. The model was tested on clustered right-censored bees survival data with a cured fraction, where two bee species were subjected to different entomopathogens to test the effect of the entomopathogens on the survival of the bee species. The Expectation-Solution algorithm is used to estimate the parameters. The study notes a weak positive association between cure statuses (ρ1=0.0007) and survival times for uncured bees (ρ2=0.0890), emphasizing their importance. The odds of being uncured for A. mellifera is higher than the odds for species M. ferruginea. The bee species, A. mellifera are more susceptible to entomopathogens icipe 7, icipe 20, and icipe 69. The Cox-Snell residuals show that the proposed semiparametric PH model generally fits the data well as compared to model that assume independent correlation structure. Thus, the semi parametric marginal proportional hazards mixture cure is parsimonious model for correlated bees survival data.
基金supported by the National Basic Research Program of China (grant No.2010CB630806)
文摘The solidification microstructure has an important effect on the mechanical properties of castings. Therefore, an FE （Finite Element） - CA （Cellular Automaton） coupling model was developed for the simulation of solidification structure during the continuous casting process of 72A tire cord steel. In the model, the effect of phase transformation （λ→γ→α） during solidification was considered based on a thermodynamic database. The effect of electromagnetic stirring （EMS） was determined by increasing both the thermal conductivity and crystal formation rate in the liquid phase. The results show that the cooling curves and solidification structure calculated by this model agree well with the experimental results. The optimum pouring temperature range for tire cord steel casting was also discussed based on the present model. By comprehensive consideration of billet quality and smooth production, the pouring temperature should be controlled at about 1,495 ℃ under the casting conditions of the local plant in this study.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.61372004 and 41306188)the Fundamental Research Funds for the Central Universities,China(Grant No.K 5051207015)the Foundation of the Science and Technology on Electromagnetic Scattering Laboratory,China(Grant No.HX0113071414)
文摘A breaking wave can exert a great influence on the electromagnetic（EM） scattering result from sea surfaces. In this paper, the process of small-scale wave breaking is simulated by the commercial computational fluid dynamics（CFD）software FLUENT, and the backscattering radar cross section（RCS） of the turbulence structure after breaking is calculated with the method of moments. The scattering results can reflect the turbulent intensities of the wave profiles and can indicate high polarization ratios at moderate incident angles, which should be attributed to the incoherent backscatter from surface disturbance of turbulence structure. Compared with the wave profile before breaking, the turbulence structure has no obvious geometrical characteristic of a plunging breaker, and no sea spikes are present at large incident angles either.In summary, the study of EM scattering from turbulence structure can provide a basis to explain the anomalies of EM scattering from sea surfaces and help us understand the scattering mechanism about the breaking wave more completely.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11774011,11434001,U1530401,and U1430237)
文摘The CryoEM single particle structure determination method has recently received broad attention in the field of structural biology. The structures can be resolved to near-atomic resolutions after model reconstructions from a large number of CryoEM images measuring molecules in different orientations. However, the determining factors for reconstructed map resolution need to be further explored. Here, we provide a theoretical framework in conjunction with numerical simulations to gauge the influence of several key factors to CryoEM map resolutions. If the projection image quality allows orientation assignment, then the number of measured projection images and the quality of each measurement(quantified using average signal-to-noise ratio) can be combined to a single factor, which is dominant to the resolution of reconstructed maps. Furthermore, the intrinsic thermal motion of molecules has significant effects on the resolution. These effects can be quantitatively summarized with an analytical formula that provides a theoretical guideline on structure resolutions for given experimental measurements.
基金Project supported by the National Key Research and Development Program of China(Grant No.2017YFA0504700)the National Natural Science Foundation of China(Grant Nos.31570732 and 31770785)
文摘Recent technical breakthroughs in cryo-electron microscopy（cryo-EM） revolutionized structural biology, which led to the 2017 Nobel Prize in chemistry being awarded to three scientists, Jacques Dubochet, Joachim Frank, and Richard Henderson, who made groundbreaking contributions to the development of cryo-EM. In this review, I will give a comprehensive review of the developmental history of cryo-EM, the technical aspects of the breakthrough in cryo-EM leading to the structural biology revolution, including electron microscopy, image recording devices and image processing algorithms,and the major scientific achievements by Chinese researchers employing cryo-EM, covering protein complexes involved in or related to gene expression and regulation, protein synthesis and degradation, membrane proteins, immunity, and viruses.Finally, I will give a perspective outlook on the development of cryo-EM in the future.
