Human respiratory system is harbored by a vast array of transient and normal microbial flora.A number of pathogenic viruses were diagnosed from samples in different occasions from mild to severe infections of respirat...Human respiratory system is harbored by a vast array of transient and normal microbial flora.A number of pathogenic viruses were diagnosed from samples in different occasions from mild to severe infections of respiratory tract.Molecular methods were developed for detection of these viruses during last two decades.Nucleic acid amplification methods were introduced for rapid and accurate diagnosis of pathogenic viruses.Multiplex detection systems were employed to identify a panel of pathogenic viruses,which requires specialized kits and instruments in some cases.This review summarizes different types of molecular approaches which were developed with time and applied for the detection of pathogenic viruses associated with infections of the respiratory system.展开更多
[Objectives]The paper was to establish a molecular biological method for identification of bacterial strains.[Methods]The thalli of standard bacterial strains existing in the laboratory were collected and genomic DNA ...[Objectives]The paper was to establish a molecular biological method for identification of bacterial strains.[Methods]The thalli of standard bacterial strains existing in the laboratory were collected and genomic DNA was extracted for amplification of 16S rDNA and gyrB gene.The 16S rDNA and gyrB gene sequences were obtained after sequencing.Sequences were aligned and analyzed via EzBioCloud and NCBI database,and phylogenetic trees were constructed to determine the species relationship of strains.Meantime,they were compared with known strains.[Results]This method could identify 5 standard strains accurately to the species level.The 16S rDNA and gyrB gene sequences were aligned and analyzed in EzBioCloud database and NCBI database.The strain with the max score was consistent with the known strain.And the query cover and ident were both above 99%.[Conclusions]The established molecular biological method for identification of bacterial strains by 16S rDNA and gyrB gene has good accuracy,which effectively solves the problem that the laboratory identification of bacteria relies on traditional methods and the accuracy can not be guaranteed,and further improves the identification ability of laboratory bacterial strains.展开更多
The structure and properties of molten salt solution o J Li,K|F,Cl system have been investiged by computerized simulation of molecular dynamic method.The partial RDF,the partial molar energy of mixing and the diffusio...The structure and properties of molten salt solution o J Li,K|F,Cl system have been investiged by computerized simulation of molecular dynamic method.The partial RDF,the partial molar energy of mixing and the diffusion coeffients of Li^+,K^+,F^- and Cl^- have been calculated. The results are in agreement with the experimental values.The regularities of the distribution of ions and mieroscopic holes are discussed based on the results of computerized simulation.展开更多
A modified molecular structural mechanics method, based on molecular mechanics and similar to the finite element method, was developed. The energy of a system was expressed by the force field functions of the molecula...A modified molecular structural mechanics method, based on molecular mechanics and similar to the finite element method, was developed. The energy of a system was expressed by the force field functions of the molecular mechanics. Under the small deformation assumption and by the principle of minimum potential energy, the system function was established. The properties of tension and bending of single-walled carbon nanotubes were analyzed. The Young＇s modulus is about 0.36 TPa nm, which agrees perfectly with the results of previous analysis by other researchers. It is found, for the first time, that the Young＇s moduli, for Zigzag nanotubes, are different from each other when the system energy was expressed as the sum of two or three individual energy terms in molecular mechanics. Whereas, the Young＇s moduli were the same for the Armchair nanotubes. It is found, when simulating the bending, that the deflections are closer to the theoretical ones, of the classical elasticity, when the diameter of the carbon nanotube increases.展开更多
Objective: To study the treatment of B-Thalas-semia (ThE) with Chinese herbal medicine for Bushen Yisui (BSYS), its theoretical base and molecular mechanism. Methods: Seventy-eight patients with ThE were treated with ...Objective: To study the treatment of B-Thalas-semia (ThE) with Chinese herbal medicine for Bushen Yisui (BSYS), its theoretical base and molecular mechanism. Methods: Seventy-eight patients with ThE were treated with BSYS recipe (consisted of 11 Chinese herbal drugs as Dogwood fruit, Fleeceflower root, prepared Rehmannia root and turtle shell, etc.) orally taken, 3 times per day, 10 g/time, 3 months as one therapeutic course. Hemoglobin (Hb), red blood cell (RBC), reticulocyte (Ret) and hemoglobin F (HbF) were checked every month. At the same time, PAGE, PVR, PCR-SSCP, RT-PCR, DNA series analysis, mRNA gene expression analysis techniques were used to conduct the systematic gene analysis in patients to study the molecular mechanism of TCM treatment from aspects of gene mutation, gene expression and control-regulation. Results: All the blood criteria in patients after BSYS treatment were improved significantly with clinical symptoms展开更多
The 12C+12C fusion reaction is famous because of its complication of molecular resonances,and it plays an important role in both nuclear structural research and astrophysics. It is extremely difficult to measure the c...The 12C+12C fusion reaction is famous because of its complication of molecular resonances,and it plays an important role in both nuclear structural research and astrophysics. It is extremely difficult to measure the cross sections of 12C+12C fusions at energies of astrophysical relevance because of the very low reaction yields. To measure the complicated resonant structure that exists in this important reaction, an efficient thick target method has been developed and applied for the first time at energies Ec.m.<5.3 MeV. A scan of the cross sections over a relatively wide range of energies can be carried out using only a single beam energy. The result of measurement at Ec.m.=4.1 MeV is compared with results from previous work.This method will be useful for searching for potentially existing resonances of 12C+12C in the energy range 1 MeV<Ec.m.<3 MeV.展开更多
Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including...Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.展开更多
In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artem...In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artemisinin in the region of the endoperoxide ring compared to crystallographic data. We also classify these methods using statistical analysis. The results of PCA were based on three main components, explaining 98.0539% of the total variance, for the geometrical parameters C3O13, O1O2C3, O13C12C12a, and O2C3O13C12. The DFT method (B3LYP) corresponded well with the experimental data in the hierarchical cluster analysis (HCA). The experimental and theoretical angles were analyzed by simple linear regression, and statistical parameters (correlation coefficients, significance, and predictability) were evaluated to determine the accuracy of the calculations. The statistical analysis exhibited a good correlation and high predictive power for the DFT (B3LYP) method in the 6-31G** basis set.展开更多
In this paper, the numerical approximation by Galerkin method for completely compressible miscible displacement with molecular diffusion and dispersion in porous media is considered. Continuous time procedure is intro...In this paper, the numerical approximation by Galerkin method for completely compressible miscible displacement with molecular diffusion and dispersion in porous media is considered. Continuous time procedure is introduced and analysed. Some new techniques are applied to the analysis. Optimal error estimates in L ∞(J;H 1(Ω)) are proved, which implies an essential improvement to existed results. MR Subject Classification: 65N15,65N30.展开更多
Abstract A system of quasilinear coupled equations which arise from simulation of contamination of geologic nulear waste in porous media is studied. We’ll discuss Galerkin method for the model of compressible flow wi...Abstract A system of quasilinear coupled equations which arise from simulation of contamination of geologic nulear waste in porous media is studied. We’ll discuss Galerkin method for the model of compressible flow with molecular diffusion and dispersion. Some new techniques are introcued to error analysis. Only one dimensional case is considered. The optimal error estimate in both L^2 and H^1 is proved. A contribution of this paper is how the dispersion term can be handled,展开更多
AIM To compare(1) demographics in urea breath test(UBT) vs endoscopy patients; and(2) the molecular detection of antibiotic resistance in stool vs biopsy samples.METHODS Six hundred and sixteen adult patients undergoi...AIM To compare(1) demographics in urea breath test(UBT) vs endoscopy patients; and(2) the molecular detection of antibiotic resistance in stool vs biopsy samples.METHODS Six hundred and sixteen adult patients undergoing endoscopy or a UBT were prospectively recruited to the study. The Geno Type Helico DR assay was used to detect Helicobacter pylori(H. pylori) and antibiotic resistance using biopsy and/or stool samples from CLOpositive endoscopy patients and stool samples from UBT-positive patients. RESULTS Infection rates were significantly higher in patients referred for a UBT than endoscopy(overall rates: 33% vs 19%; treatment-na?ve patients: 33% vs 14.7%, respectively). H. pylori-infected UBT patients were younger than H. pylori-infected endoscopy patients(41.4 vs 48.4 years, respectively, P < 0.005), with a higher percentage of H. pylori-infected males in the endoscopy-compared to the UBT-cohort(52.6% vs 33.3%, P = 0.03). The Geno Type Helico DR assay was more accurate at detecting H. pylori infection using biopsy samples than stool samples [98.2%(n = 54/55) vs 80.3%(n =53/66), P < 0.005]. Subset analysis using stool and biopsy samples from CLO-positive endoscopy patients revealed a higher detection rate ofresistance-associated mutations using stool samples compared to biopsies. The concordance rates between stool and biopsy samples for the detection of H. pylori DNA, clarithromycin and fluoroquinolone resistance were just 85%, 53% and 35%, respectively. CONCLUSION Differences between endoscopy and UBT patients provide a rationale for non-invasive detection of H. pylori antibiotic resistance. However, the Geno Type Helico DR assay is an unsuitable approach.展开更多
文摘Human respiratory system is harbored by a vast array of transient and normal microbial flora.A number of pathogenic viruses were diagnosed from samples in different occasions from mild to severe infections of respiratory tract.Molecular methods were developed for detection of these viruses during last two decades.Nucleic acid amplification methods were introduced for rapid and accurate diagnosis of pathogenic viruses.Multiplex detection systems were employed to identify a panel of pathogenic viruses,which requires specialized kits and instruments in some cases.This review summarizes different types of molecular approaches which were developed with time and applied for the detection of pathogenic viruses associated with infections of the respiratory system.
基金Supported by Special Project of"Grassland Talents"in Inner Mongolia.
文摘[Objectives]The paper was to establish a molecular biological method for identification of bacterial strains.[Methods]The thalli of standard bacterial strains existing in the laboratory were collected and genomic DNA was extracted for amplification of 16S rDNA and gyrB gene.The 16S rDNA and gyrB gene sequences were obtained after sequencing.Sequences were aligned and analyzed via EzBioCloud and NCBI database,and phylogenetic trees were constructed to determine the species relationship of strains.Meantime,they were compared with known strains.[Results]This method could identify 5 standard strains accurately to the species level.The 16S rDNA and gyrB gene sequences were aligned and analyzed in EzBioCloud database and NCBI database.The strain with the max score was consistent with the known strain.And the query cover and ident were both above 99%.[Conclusions]The established molecular biological method for identification of bacterial strains by 16S rDNA and gyrB gene has good accuracy,which effectively solves the problem that the laboratory identification of bacteria relies on traditional methods and the accuracy can not be guaranteed,and further improves the identification ability of laboratory bacterial strains.
文摘The structure and properties of molten salt solution o J Li,K|F,Cl system have been investiged by computerized simulation of molecular dynamic method.The partial RDF,the partial molar energy of mixing and the diffusion coeffients of Li^+,K^+,F^- and Cl^- have been calculated. The results are in agreement with the experimental values.The regularities of the distribution of ions and mieroscopic holes are discussed based on the results of computerized simulation.
文摘A modified molecular structural mechanics method, based on molecular mechanics and similar to the finite element method, was developed. The energy of a system was expressed by the force field functions of the molecular mechanics. Under the small deformation assumption and by the principle of minimum potential energy, the system function was established. The properties of tension and bending of single-walled carbon nanotubes were analyzed. The Young＇s modulus is about 0.36 TPa nm, which agrees perfectly with the results of previous analysis by other researchers. It is found, for the first time, that the Young＇s moduli, for Zigzag nanotubes, are different from each other when the system energy was expressed as the sum of two or three individual energy terms in molecular mechanics. Whereas, the Young＇s moduli were the same for the Armchair nanotubes. It is found, when simulating the bending, that the deflections are closer to the theoretical ones, of the classical elasticity, when the diameter of the carbon nanotube increases.
文摘Objective: To study the treatment of B-Thalas-semia (ThE) with Chinese herbal medicine for Bushen Yisui (BSYS), its theoretical base and molecular mechanism. Methods: Seventy-eight patients with ThE were treated with BSYS recipe (consisted of 11 Chinese herbal drugs as Dogwood fruit, Fleeceflower root, prepared Rehmannia root and turtle shell, etc.) orally taken, 3 times per day, 10 g/time, 3 months as one therapeutic course. Hemoglobin (Hb), red blood cell (RBC), reticulocyte (Ret) and hemoglobin F (HbF) were checked every month. At the same time, PAGE, PVR, PCR-SSCP, RT-PCR, DNA series analysis, mRNA gene expression analysis techniques were used to conduct the systematic gene analysis in patients to study the molecular mechanism of TCM treatment from aspects of gene mutation, gene expression and control-regulation. Results: All the blood criteria in patients after BSYS treatment were improved significantly with clinical symptoms
基金supported by the National Key R&D Program of China(No.2016YFA0400500)the National Natural Science Foundation of China(Nos.11805291,11475228,11490560,11490564,11875329)+4 种基金the National Science Foundation of the US(Nos.PHY-1068192,PHY-1419765)the US Department of Energy(No.DE-AC07-05ID14517)the Key Program(No.XDPB09-2)the ‘‘Hundred Talents Program’’ of the Chinese Academy of Sciencesthe Fundamental Research Funds for the Central Universities(No.18lgpy84)
文摘The 12C+12C fusion reaction is famous because of its complication of molecular resonances,and it plays an important role in both nuclear structural research and astrophysics. It is extremely difficult to measure the cross sections of 12C+12C fusions at energies of astrophysical relevance because of the very low reaction yields. To measure the complicated resonant structure that exists in this important reaction, an efficient thick target method has been developed and applied for the first time at energies Ec.m.<5.3 MeV. A scan of the cross sections over a relatively wide range of energies can be carried out using only a single beam energy. The result of measurement at Ec.m.=4.1 MeV is compared with results from previous work.This method will be useful for searching for potentially existing resonances of 12C+12C in the energy range 1 MeV<Ec.m.<3 MeV.
文摘Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.
文摘In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artemisinin in the region of the endoperoxide ring compared to crystallographic data. We also classify these methods using statistical analysis. The results of PCA were based on three main components, explaining 98.0539% of the total variance, for the geometrical parameters C3O13, O1O2C3, O13C12C12a, and O2C3O13C12. The DFT method (B3LYP) corresponded well with the experimental data in the hierarchical cluster analysis (HCA). The experimental and theoretical angles were analyzed by simple linear regression, and statistical parameters (correlation coefficients, significance, and predictability) were evaluated to determine the accuracy of the calculations. The statistical analysis exhibited a good correlation and high predictive power for the DFT (B3LYP) method in the 6-31G** basis set.
文摘In this paper, the numerical approximation by Galerkin method for completely compressible miscible displacement with molecular diffusion and dispersion in porous media is considered. Continuous time procedure is introduced and analysed. Some new techniques are applied to the analysis. Optimal error estimates in L ∞(J;H 1(Ω)) are proved, which implies an essential improvement to existed results. MR Subject Classification: 65N15,65N30.
基金This work is suported by National Science Foundation
文摘Abstract A system of quasilinear coupled equations which arise from simulation of contamination of geologic nulear waste in porous media is studied. We’ll discuss Galerkin method for the model of compressible flow with molecular diffusion and dispersion. Some new techniques are introcued to error analysis. Only one dimensional case is considered. The optimal error estimate in both L^2 and H^1 is proved. A contribution of this paper is how the dispersion term can be handled,
文摘AIM To compare(1) demographics in urea breath test(UBT) vs endoscopy patients; and(2) the molecular detection of antibiotic resistance in stool vs biopsy samples.METHODS Six hundred and sixteen adult patients undergoing endoscopy or a UBT were prospectively recruited to the study. The Geno Type Helico DR assay was used to detect Helicobacter pylori(H. pylori) and antibiotic resistance using biopsy and/or stool samples from CLOpositive endoscopy patients and stool samples from UBT-positive patients. RESULTS Infection rates were significantly higher in patients referred for a UBT than endoscopy(overall rates: 33% vs 19%; treatment-na?ve patients: 33% vs 14.7%, respectively). H. pylori-infected UBT patients were younger than H. pylori-infected endoscopy patients(41.4 vs 48.4 years, respectively, P < 0.005), with a higher percentage of H. pylori-infected males in the endoscopy-compared to the UBT-cohort(52.6% vs 33.3%, P = 0.03). The Geno Type Helico DR assay was more accurate at detecting H. pylori infection using biopsy samples than stool samples [98.2%(n = 54/55) vs 80.3%(n =53/66), P < 0.005]. Subset analysis using stool and biopsy samples from CLO-positive endoscopy patients revealed a higher detection rate ofresistance-associated mutations using stool samples compared to biopsies. The concordance rates between stool and biopsy samples for the detection of H. pylori DNA, clarithromycin and fluoroquinolone resistance were just 85%, 53% and 35%, respectively. CONCLUSION Differences between endoscopy and UBT patients provide a rationale for non-invasive detection of H. pylori antibiotic resistance. However, the Geno Type Helico DR assay is an unsuitable approach.
