Rhizobia, crucial for nitrogen fixation in leguminous plants, play a vital role in soybean cultivation. This study, conducted in Mexico, a major soybean importer, aimed to identify bacteria from nodules of five soybea...Rhizobia, crucial for nitrogen fixation in leguminous plants, play a vital role in soybean cultivation. This study, conducted in Mexico, a major soybean importer, aimed to identify bacteria from nodules of five soybean varieties in high-production regions. Multilocus sequence analysis (MLSA) was employed for enhanced species resolution. The study identified six Bradyrhizobium species: Bradyrhizobium japonicum USDA 110, Bradyrhizobium japonicum USDA 6, Bradyrhizobium elkanii USDA 76, Bradyrhizobium neotropicale, Bradyrhizobium lablabi, and Bradyrhizobium icense. Bradyrhizobium japonicum USDA 110 predominated in the soils, displaying symbiotic preference for the Huasteca 400 variety. However, phylogenetic analysis didn't reveal a clear association between strains, soil, and soybean variety. This research sheds light on the diversity of rhizobia in Mexican soybean cultivation, contributing to the understanding of symbiotic relationships in soybean production systems.展开更多
Objective Human Lyme Borreliosis （LB）, which is caused by Borrefia burgdorferi sensu lato （B. burgdorferi）, has been identified as a major arthropod-borne infectious disease in China. We aimed to develop a multipl...Objective Human Lyme Borreliosis （LB）, which is caused by Borrefia burgdorferi sensu lato （B. burgdorferi）, has been identified as a major arthropod-borne infectious disease in China. We aimed to develop a multiple locus variable-number tandem repeat （VNTR） analysis （MLVA） assay for the genotyping of Borrelia burgdorJ：eri strains detected in China. Methods B. garinii PBi complete 904.246 kb chromosome and two plasmids （cp26 and Ip54） were screened by using Tandem Repeats Finder program for getting potential VNTR loci, the potential VNTR loci were analyzed and identified with PCR and the VNTR loci data were analyzed and MLVA clustering tree were constrcted by using the categorical coefficient and the unweighted pair-group method with arithmetic means （UPGMA）. Results We identified 5 new VNTR loci through analyzing 47 potential VNTR loci. We used the MLVA protocol to analyse 101 B. burgdorferi strains detected in China and finally identified 51 unique genotypes in 4 major clusters including B. burgdorferi sensu stricto （B.b.s.s）, B. garinii, B. a[zelii, and B. valaisiana, consistent with the current MLSA phylogeny studies. The allele numbers of VNTR-1, VNTR-2, VNTR-3, VNTR-4, and VNTR-5 were 7, 3, 9, 7, and 6. The Hunter-Gaston index （HGI） of five VNTR loci were 0.79, 0.22, 0.77, 0.71, and 0.67, respectively. The combined HGI of five VNTR loci was 0.96. Clustering of the strains of Xinjiang, Inner Mongolia and Heilongjiang was confirmed, and this situation was consistent with the close geographical distribution of those provinces. Conclusion The MLVA protocol esytablished in this study is easy and can show strains＇ phylogenetic relationships to distinguish the strains of Borrelia species. It is useful for further phylogenetic and epidemiological analyses of Borrelia strains.展开更多
The goal of this study is to solve the neutron diffusion equation by using a meshless method and evaluate its performance compared to traditional methods. This paper proposes a novel method based on coupling the meshl...The goal of this study is to solve the neutron diffusion equation by using a meshless method and evaluate its performance compared to traditional methods. This paper proposes a novel method based on coupling the meshless local Petrov–Galerkin approach and the moving least squares approximation. This computational procedure consists of two main steps. The first involved applying the moving least squares approximation to construct the shape function based on the problem domain. Then, the obtained shape function was used in the meshless local Petrov–Galerkin method to solve the neutron diffusion equation.Because the meshless method is based on eliminating the mesh-based topologies, the problem domain was represented by a set of arbitrarily distributed nodes. There is no need to use meshes or elements for field variable interpolation. The process of node generation is simply and fully automated, which can save time. As this method is a local weak form, it does not require any background integration cells and all integrations are performed locally over small quadrature domains. To evaluate the proposed method,several problems were considered. The results were compared with those obtained from the analytical solution and a Galerkin finite element method. In addition, the proposed method was used to solve neutronic calculations in thesmall modular reactor. The results were compared with those of the citation code and reference values. The accuracy and precision of the proposed method were acceptable. Additionally, adding the number of nodes and selecting an appropriate weight function improved the performance of the meshless local Petrov–Galerkin method. Therefore, the proposed method represents an accurate and alternative method for calculating core neutronic parameters.展开更多
This paper presented a speaker adaptable very low bit rate speech coder based on HMM (Hidden Markov Model) which includes the dynamic features, i.e., delta and delta delta parameters of speech. The performance of this...This paper presented a speaker adaptable very low bit rate speech coder based on HMM (Hidden Markov Model) which includes the dynamic features, i.e., delta and delta delta parameters of speech. The performance of this speech coder has been improved by using the dynamic features generated by an algorithm for speech parameter generation from HMM because the generated speech parameter vectors reflect not only the means of static and dynamic feature vectors but also the covariance of those. The encoder part is equivalent to an HMM based phoneme recognizer and transmits phoneme indexes, state durations, pitch information and speaker characteristics adaptation vectors to the decoder. The decoder receives those messages and concatenates phoneme HMM sequence according to the phoneme indexes. Then the decoder generates a sequence of mel cepstral coefficient vectors using HMM based speech parameter generation technique. Finally the decoder synthesizes speech by directly exciting the MLSA(Mel Log Spectrum Approximation) filter with the generated mel cepstral coefficient vectors, according to the pitch information.展开更多
Traditionally Nocardia asteroids was considered the predominant species of causing no-cardiosis. The improved identification of isolates using molecular techniques have shown that the genus exhibits considerable taxon...Traditionally Nocardia asteroids was considered the predominant species of causing no-cardiosis. The improved identification of isolates using molecular techniques have shown that the genus exhibits considerable taxonomic complexity and phenotypic base identification can be ambiguous. The aim of this study was to assess the species distribution of Nocardia strains mostly recovered from patients suspected of having tuberculosis, during three years period (2009-2012). The clinical isolates were identified to species level using conventional tests and genotypic methods using single and multi locus sequence analysis (MLSA) of 16S rRNA, gyrB and secA1 genes. Nocardiosis was diagnosed in 46 patients. The most frequent underlying condition were organ transplantation (6 patients;13%), cancer (6 patients;13%), human immunodeficiency virus (HIV) (6 patients;13%), non-infectious chronic lung disease (5 patients;10.8%) and tuberculosis (4 patients;8.7%). Nocardia species was recovered from 46 different clinical specimens, the most common of which was bronchoalveolar lavage (BAL) (43.5%). Eleven different Nocardia species were identified: N. asteroides (n = 12), N. cyriacigeorgica (n = 9), N. farcinica (n = 7), N. wallacei (n = 6), N. carnea (n = 3), N. otitidiscaviarum (n = 3), N. abscessus (n = 1), N. arthritidis (n = 1), N. kruczakiae (n = 1), N. nova (n = 2) and N. veterana (n = 1). In conclusion, infection caused by Nocardia species appears to be more common than generally appreciated. The current study provides further evidence that Nocardia species are capable of causing a wide range of human diseases in healthy and immunocompromised patients. MLSA is a reliable method for accurate species identification of Nocardia isolates and would be more feasible for routine use in clinical laboratories.展开更多
Goal of this study was to analyse the clinical course of cystic fibrosis (CF) patients with nontuberculous mycobacteria (NTM) in their respiratory secretions and to investigate the molecular epidemiology of the most p...Goal of this study was to analyse the clinical course of cystic fibrosis (CF) patients with nontuberculous mycobacteria (NTM) in their respiratory secretions and to investigate the molecular epidemiology of the most prevalent NTM species by multilocus sequence analysis (MLSA). The respiratory specimen and the clinical parameters forced expiratory volume in one second (FEV1), body-mass-index (BMI), erythrocyte sedimentation rate (ESR) 1 h and immunoglobulin G (IgG) of 357 CF patients, 0 - 52.4 years, mean FEV1 2009 81.5% pred were analysed between 1998 and 2010. In 13 patients NTM were detected. 12 of 13 patients carried M. abscessus, for one patient the NTM species was not characterized. 4 patients carried a second NTM species (M. avium, M. chelonae (2x), M. intracellulare). 6 patients exhibited a significant decline in FEV1, however changes in BMI, IgG and ESR were discordant. Molecular genotyping of M. abscessus isolates revealed a unique MLSA pattern in 6 patients. 2 patients harboured identical strains, and one patient a closely related strain. Whether the presence of identical strains is attributed to the acquisition of NTM clones from common environmental sources or to patient-to-patient transmission cannot be definitely clarified. Although cross-in- fection of the three patients with identical/closely related strains in the present cohort is highly unlikely, we recommend strict hygiene measures for all CF patients harbouring NTM.展开更多
文摘Rhizobia, crucial for nitrogen fixation in leguminous plants, play a vital role in soybean cultivation. This study, conducted in Mexico, a major soybean importer, aimed to identify bacteria from nodules of five soybean varieties in high-production regions. Multilocus sequence analysis (MLSA) was employed for enhanced species resolution. The study identified six Bradyrhizobium species: Bradyrhizobium japonicum USDA 110, Bradyrhizobium japonicum USDA 6, Bradyrhizobium elkanii USDA 76, Bradyrhizobium neotropicale, Bradyrhizobium lablabi, and Bradyrhizobium icense. Bradyrhizobium japonicum USDA 110 predominated in the soils, displaying symbiotic preference for the Huasteca 400 variety. However, phylogenetic analysis didn't reveal a clear association between strains, soil, and soybean variety. This research sheds light on the diversity of rhizobia in Mexican soybean cultivation, contributing to the understanding of symbiotic relationships in soybean production systems.
基金The National High Technology Research and Development Program of China(2012AA101501)National Infrastructure of Microbial Resources of China(NIMR2014-7)
文摘目的掌握江苏省2018年人感染布鲁氏菌主要流行株的种型和基因型。方法运用普通PCR及AMOS多重PCR确认分离株的生物种型;采用多位点序列分型(Multilocus sequence analysis,MLSA)和多位点串联重复序列分析(Multiple-locus variable number tandem repeat analysis,MLVA)鉴定基因型,并与国内外流行株进行聚类分析。结果2018年共分离到56株布鲁氏菌,MLSA分型显示一株菌为猪种布鲁氏菌ST(Sequence type)17型,其他均为羊种布鲁氏菌ST8型。MLVA将56株菌分为47个基因亚型(46个羊种,1个猪种),聚类显示羊种布鲁氏菌全部为“东地中海簇”。结论2018年江苏省人感染布病主要为“东地中海簇”的ST8型羊种布鲁氏菌,并首次发现一例人感染ST17型猪种布鲁氏菌。
基金supported by Natural Science foundation(Grant No.31100105)China Mega-Project for Infectious Disease(2012ZX10004-215 and 2013ZX10004221)
文摘Objective Human Lyme Borreliosis （LB）, which is caused by Borrefia burgdorferi sensu lato （B. burgdorferi）, has been identified as a major arthropod-borne infectious disease in China. We aimed to develop a multiple locus variable-number tandem repeat （VNTR） analysis （MLVA） assay for the genotyping of Borrelia burgdorJ：eri strains detected in China. Methods B. garinii PBi complete 904.246 kb chromosome and two plasmids （cp26 and Ip54） were screened by using Tandem Repeats Finder program for getting potential VNTR loci, the potential VNTR loci were analyzed and identified with PCR and the VNTR loci data were analyzed and MLVA clustering tree were constrcted by using the categorical coefficient and the unweighted pair-group method with arithmetic means （UPGMA）. Results We identified 5 new VNTR loci through analyzing 47 potential VNTR loci. We used the MLVA protocol to analyse 101 B. burgdorferi strains detected in China and finally identified 51 unique genotypes in 4 major clusters including B. burgdorferi sensu stricto （B.b.s.s）, B. garinii, B. a[zelii, and B. valaisiana, consistent with the current MLSA phylogeny studies. The allele numbers of VNTR-1, VNTR-2, VNTR-3, VNTR-4, and VNTR-5 were 7, 3, 9, 7, and 6. The Hunter-Gaston index （HGI） of five VNTR loci were 0.79, 0.22, 0.77, 0.71, and 0.67, respectively. The combined HGI of five VNTR loci was 0.96. Clustering of the strains of Xinjiang, Inner Mongolia and Heilongjiang was confirmed, and this situation was consistent with the close geographical distribution of those provinces. Conclusion The MLVA protocol esytablished in this study is easy and can show strains＇ phylogenetic relationships to distinguish the strains of Borrelia species. It is useful for further phylogenetic and epidemiological analyses of Borrelia strains.
文摘The goal of this study is to solve the neutron diffusion equation by using a meshless method and evaluate its performance compared to traditional methods. This paper proposes a novel method based on coupling the meshless local Petrov–Galerkin approach and the moving least squares approximation. This computational procedure consists of two main steps. The first involved applying the moving least squares approximation to construct the shape function based on the problem domain. Then, the obtained shape function was used in the meshless local Petrov–Galerkin method to solve the neutron diffusion equation.Because the meshless method is based on eliminating the mesh-based topologies, the problem domain was represented by a set of arbitrarily distributed nodes. There is no need to use meshes or elements for field variable interpolation. The process of node generation is simply and fully automated, which can save time. As this method is a local weak form, it does not require any background integration cells and all integrations are performed locally over small quadrature domains. To evaluate the proposed method,several problems were considered. The results were compared with those obtained from the analytical solution and a Galerkin finite element method. In addition, the proposed method was used to solve neutronic calculations in thesmall modular reactor. The results were compared with those of the citation code and reference values. The accuracy and precision of the proposed method were acceptable. Additionally, adding the number of nodes and selecting an appropriate weight function improved the performance of the meshless local Petrov–Galerkin method. Therefore, the proposed method represents an accurate and alternative method for calculating core neutronic parameters.
文摘This paper presented a speaker adaptable very low bit rate speech coder based on HMM (Hidden Markov Model) which includes the dynamic features, i.e., delta and delta delta parameters of speech. The performance of this speech coder has been improved by using the dynamic features generated by an algorithm for speech parameter generation from HMM because the generated speech parameter vectors reflect not only the means of static and dynamic feature vectors but also the covariance of those. The encoder part is equivalent to an HMM based phoneme recognizer and transmits phoneme indexes, state durations, pitch information and speaker characteristics adaptation vectors to the decoder. The decoder receives those messages and concatenates phoneme HMM sequence according to the phoneme indexes. Then the decoder generates a sequence of mel cepstral coefficient vectors using HMM based speech parameter generation technique. Finally the decoder synthesizes speech by directly exciting the MLSA(Mel Log Spectrum Approximation) filter with the generated mel cepstral coefficient vectors, according to the pitch information.
文摘Traditionally Nocardia asteroids was considered the predominant species of causing no-cardiosis. The improved identification of isolates using molecular techniques have shown that the genus exhibits considerable taxonomic complexity and phenotypic base identification can be ambiguous. The aim of this study was to assess the species distribution of Nocardia strains mostly recovered from patients suspected of having tuberculosis, during three years period (2009-2012). The clinical isolates were identified to species level using conventional tests and genotypic methods using single and multi locus sequence analysis (MLSA) of 16S rRNA, gyrB and secA1 genes. Nocardiosis was diagnosed in 46 patients. The most frequent underlying condition were organ transplantation (6 patients;13%), cancer (6 patients;13%), human immunodeficiency virus (HIV) (6 patients;13%), non-infectious chronic lung disease (5 patients;10.8%) and tuberculosis (4 patients;8.7%). Nocardia species was recovered from 46 different clinical specimens, the most common of which was bronchoalveolar lavage (BAL) (43.5%). Eleven different Nocardia species were identified: N. asteroides (n = 12), N. cyriacigeorgica (n = 9), N. farcinica (n = 7), N. wallacei (n = 6), N. carnea (n = 3), N. otitidiscaviarum (n = 3), N. abscessus (n = 1), N. arthritidis (n = 1), N. kruczakiae (n = 1), N. nova (n = 2) and N. veterana (n = 1). In conclusion, infection caused by Nocardia species appears to be more common than generally appreciated. The current study provides further evidence that Nocardia species are capable of causing a wide range of human diseases in healthy and immunocompromised patients. MLSA is a reliable method for accurate species identification of Nocardia isolates and would be more feasible for routine use in clinical laboratories.
文摘Goal of this study was to analyse the clinical course of cystic fibrosis (CF) patients with nontuberculous mycobacteria (NTM) in their respiratory secretions and to investigate the molecular epidemiology of the most prevalent NTM species by multilocus sequence analysis (MLSA). The respiratory specimen and the clinical parameters forced expiratory volume in one second (FEV1), body-mass-index (BMI), erythrocyte sedimentation rate (ESR) 1 h and immunoglobulin G (IgG) of 357 CF patients, 0 - 52.4 years, mean FEV1 2009 81.5% pred were analysed between 1998 and 2010. In 13 patients NTM were detected. 12 of 13 patients carried M. abscessus, for one patient the NTM species was not characterized. 4 patients carried a second NTM species (M. avium, M. chelonae (2x), M. intracellulare). 6 patients exhibited a significant decline in FEV1, however changes in BMI, IgG and ESR were discordant. Molecular genotyping of M. abscessus isolates revealed a unique MLSA pattern in 6 patients. 2 patients harboured identical strains, and one patient a closely related strain. Whether the presence of identical strains is attributed to the acquisition of NTM clones from common environmental sources or to patient-to-patient transmission cannot be definitely clarified. Although cross-in- fection of the three patients with identical/closely related strains in the present cohort is highly unlikely, we recommend strict hygiene measures for all CF patients harbouring NTM.
