This paper proposes a novel method for estimating the sparse inverse covariance matrixfor longitudinal data with informative dropouts. Based on the modified Cholesky decomposition,the sparse inverse covariance matrix ...This paper proposes a novel method for estimating the sparse inverse covariance matrixfor longitudinal data with informative dropouts. Based on the modified Cholesky decomposition,the sparse inverse covariance matrix is modelled by the autoregressive regression model,which guarantees the positive definiteness of the covariance matrix. To account for the informativedropouts, we then propose a penalized estimating equation method using the inverse probabilityweighting approach. The informative dropout propensity parameters are estimated by the generalizedmethod of moments. The asymptotic properties are investigated for the resulting estimators.Finally, we illustrate the effectiveness and feasibility of the proposed method through Monte Carlosimulations and a practical application.展开更多
In the paper, related research and progress of molecular clock hypothesis were summarized, including definition of molecular clock, supporting proofs, contro- versy, significance and perfection, application and accomp...In the paper, related research and progress of molecular clock hypothesis were summarized, including definition of molecular clock, supporting proofs, contro- versy, significance and perfection, application and accompanying challenges.展开更多
[Objective] The aim of this study was to perform genome-wide analysis of glucose-6-phosphate dehydrogenase(G6PDH) and reveal its evolution in Eucalyptus grandsis.[Method] The gene character,protein sequence and phyl...[Objective] The aim of this study was to perform genome-wide analysis of glucose-6-phosphate dehydrogenase(G6PDH) and reveal its evolution in Eucalyptus grandsis.[Method] The gene character,protein sequence and phylogenetic tree of G6PDH gene were analyzed by BLAST and other bioinformatics software within Eucalyptus grandsis whole genome database.[Result] Six G6PDH genes,including one cytomic type and five plastids,were detected in the E.grandsis genome.All the G6PDHs have conserved motifs of motif 1,motif 2,motif 3,motif 7,motif 9 and motif 11.Furthermore,promoter sequences of all E.grandsis G6PDH contain TATA box,enhancer,light-responsive,hormone-responsive and stress-responsive regulatory elements.[Conclusion] This study provided reference for the further revealing molecular function of E.grandsis G6PDH gene family展开更多
The molecular composition and evolution of the chalcone synthase (CHS) gene family from five species in Camellia (Theaceae) are explored in this study. Sixteen CHS exon 2 from four Camellia species were amplified from...The molecular composition and evolution of the chalcone synthase (CHS) gene family from five species in Camellia (Theaceae) are explored in this study. Sixteen CHS exon 2 from four Camellia species were amplified from total DNA by PCR method. Three sequences of the fifth species in Camellia and two sequences of Glycine max as the designated outgroups were obtained from GenBank. Our results indicated that CHS gene family in Camellia was differentiated to three subfamilies (A, B, C) during the evolutionary history with six groups (A1, A2, A3, BI, B2, C). Among them, only group A2 was possessed by all five species in this study. However, the other five groups were detected only in some species of the plants studied. All members of CHS gene family in this study had high sequence similarity, more than 90% among the members in the same subfamily and more than 78% among different subfamilies at nucleotide level., According to the estimated components of amino acids, the function of CHS genes in Camellia had been diverged. The nucleotide substitutions of the different groups were not identical. Based on phylogenetic analyse inferred from sequences of CHS genes and their deduced amino acid sequences, we concluded that the CHS genes with new function in this genus were evolved either by mutations on several important sites or by accumulation of the mutations after the gene duplication. A further analysis showed that the diversification of CHS genes in Camellia still occurred recently, and the evolutionary models were different to some extant among different species. So we assumed that the different evolutionary models resulted from the impacts of variable environmental elements after the events of speciation.展开更多
Two biological nitrogen removal processes are compared in the aspect of nitrogen removal, process operation and energy saving. Results show that when the returned sludge ratio is 50% of the inflow rate, the step-feedi...Two biological nitrogen removal processes are compared in the aspect of nitrogen removal, process operation and energy saving. Results show that when the returned sludge ratio is 50% of the inflow rate, the step-feeding process achieves over 80% total nitrogen (TN) removal efficiency, but the TN removal efficiency of the A/O process is only 40%. Moreover, filamentous sludge bulking can be well restrained in the step-feeding process. Given the conditions of a returned sludge ratio of 100% and a nitrifying liquor recycle ratio of 200%, the TN removal efficiency is 78.32% in the A/O process, but the sludge volume index (SVI) value increases to 143 mL/g. In the step-feeding process, the SVI is only 94.4 mL/g when the TN removal efficiency reaches 81. 1%. The step-feeding process has distinct advantages over the A/O process in the aspects of practicability, nitrogen removal and operating stability.展开更多
[Objective] The large-scale single-column fattening pig house with fermen- tation bed could hold 1 500 heads of fattening pigs. Since the number of pigs in piggery is too large, the management is difficult. The behavi...[Objective] The large-scale single-column fattening pig house with fermen- tation bed could hold 1 500 heads of fattening pigs. Since the number of pigs in piggery is too large, the management is difficult. The behavior of feeding, drinking, movement, sleeping, fighting of pigs is difficult to handle. The pigs cannot be man- aged well, resulting in the enhanced weakness of piglets, enhanced illness of weak pigs and missing treatment of ill pigs. The management for the pig populations is not satisfactory, and thus, it is needed to improve timely. [Method] The barriers for the fattening pigs in the large-scale pig house with fermentation bed were designed. The single management for single fattening pig was proposed. The large-scale fat- tening pig house was divided into 8 regions. Among them, 4 regions were located in both sides of the fermentation bed. Their main function was to separate ill, weak, small and bad pigs. In addition, the main column was divided into 4 gradual barri- ers. They were used to separate different-size fattening pigs. In view of manage- ment, the different-type pigs were managed dividedly with the gradual barriers. The equally-sized pigs were concentrated into one column. The ill, weak, small and bad pigs were isolated into barriers. Thus, the dynamic management was adopted. Until the fattening pigs grew up to 75 kg and their health was stable, the barriers among the columns were canceled to mix the pigs again and guarantee the pigs more gymnastic space. [Result] This design would improve the disease resistance of ill pigs, health status of weak pigs and management level of pig populations. This study would also provide a basis for the healthy running of large-scale fattening pig house with fermentation bed. [Conclusion] The pig-raising model with fermentation bed would improve the environment of pig house and the welfare of pigs. In addi- tion, the performance of pigs and quality of pork were also improved. The fermen- tation bed had an obvious advantage in safety and economics, and it had a broad application prospect.展开更多
The parallel-inlet holes with one-row, two-row and three-row film hole arrangements and different di- ameters are proposed to experimentally study their cooling characteristics. Detailed experimental processes and res...The parallel-inlet holes with one-row, two-row and three-row film hole arrangements and different di- ameters are proposed to experimentally study their cooling characteristics. Detailed experimental processes and results are described and carried out. Results indicate that heat transfer coefficient (HTC) is increased with the increase of blowing ratio. When the blowing ratio is lower, the distribution of HTC along the heated wall can be divided into three regions. For larger blowing ratio or diameter, the cooling characteristics oi parallel-inlet film holes are similar to those of convective heat transfer around flat. Furthermore, when hole diameter is deter- mined, the arrangement patterns of film hole and the blowing ratio take a great influence on HTC.展开更多
To investigate chromosome differentiation of genome A and B between common wheat and wild emmer wheat (Triticum turgidum var. dicoccoides (Koern.) Bowden), the authors conducted a RFLP analysis of the two species usin...To investigate chromosome differentiation of genome A and B between common wheat and wild emmer wheat (Triticum turgidum var. dicoccoides (Koern.) Bowden), the authors conducted a RFLP analysis of the two species using 153 genomic, cDNA and chromosome_specific probes. 75.8% of the probes had detected hybridization polymorphism in at least one of the five restriction enzymes. However, the polymorphic probes were unevenly distributed among different homoeologous groups, between different genomes and in different regions of a single chromosome. Homoeologous group 1 possessed the highest level of polymorphism (96.2%), followed by group 6 and 2 (84.6% and 82.1% respectively). In contrast, only 60%-67% of probes of the other four groups was polymorphic. In most groups the number of probes capable of detecting B chromosome polymorphism was slightly higher than that revealing A chromosome difference (totally 51.8% vs 43.1%). In a single chromosome, RFLP was predominant in the distal region (65.1%) and showed a decreasing trend from the proximal (46.2%) to the pericentric (42.4%) regions. The results suggest that there exists a substantial amount of DNA polymorphism between the A and B chromosomes of common wheat and those of wild emmer wheat, indicating that a considerable degree of genetic differentiation has taken place in the A and B genoms of two species during evolution from wild emmer to common wheat. The extent of the genetic differentiation may vary among different homoeologous groups, between A and B chromosomes and in different regions of individual chromosome.展开更多
Pea ( Pisum sativum Linn.) actin gene family contains at least three isoforms (PEAcⅠ, PEAcⅡand PEAcⅢ), and the DNA sequence of these isoforms show high similarity in the coding regions and significant divergence...Pea ( Pisum sativum Linn.) actin gene family contains at least three isoforms (PEAcⅠ, PEAcⅡand PEAcⅢ), and the DNA sequence of these isoforms show high similarity in the coding regions and significant divergence in the untranslated regions. RT_PCR and Southern blotting using 3′_untranslated region (3′_UTR) as specific probe revealed that pea isoactin genes were expressed in roots, stems, leaves, tendrils, pollen and juvenile siliques, but displayed different patterns of transcript accumulation. Two_fold serial dilution electrophoresis showed PEAcⅠ mRNA preferentially accumulated in rapidly developing tissues: it peaked in seven days' stem; remained at a rather high level in leaves within a month but decreased significantly later; varied a little in tendrils and reached a median and a very low level respectively in juvenile siliques and in pollen. PEAcⅡ displayed somewhat similar expression pattern to PEAcⅠ. The observed differences in sequences and transcript accumulation patterns suggest that the individual pea actin genes may differ in their transcriptional regulation and cellular function. Phylogenetic tree of actins showed that pea actin isoforms are as diverged from each other as they are from other plant actins, and pea actins might have originated from a common ancestor before the divergence of the dicot and monocot plants.展开更多
China's economic growth is heavily influenced by exports, while reconciling environmental regulation and economic growth requires handling the relationship between environmental regulation and industrial competitiven...China's economic growth is heavily influenced by exports, while reconciling environmental regulation and economic growth requires handling the relationship between environmental regulation and industrial competitiveness well. The effects of environmental regulation on industrial competitiveness are largely subject to the institutional design of environmental regulation. Despite numerous studies on the relationship between environmental regulation and industrial competitiveness, a consensus has yet to be reached. Aside from differences in research methodology, these studies failed to give sufficient consideration to the impact of environmental regulation on industrial competitiveness. Such effects can be negative or positive depending on the design of environmental regulatory policy. This paper has investigated the relationship between environmental regulation and the competitiveness of China's iron and steel industry and discovered that tighter environmental regulation does not diminish the competitiveness of the iron and steel industry since the policy design of environmental regulation accommodates the tolerance of advanced production capacity and includes a reasonable cost sharing mechanism. This discovery is of important reference for China to develop rational policy design to balance the relationship between environmental regulation and industrial competitiveness.展开更多
[Objective] The aim of this study was to analyze the sequence characteristics and molecular evolution of ubiquitins encoded by baculoviruses.[Methods]Clustal W software was used for multiple sequence alignment analysi...[Objective] The aim of this study was to analyze the sequence characteristics and molecular evolution of ubiquitins encoded by baculoviruses.[Methods]Clustal W software was used for multiple sequence alignment analysis,and neighbor-joining method(NJ)and maximum parsimony method(MP)were used for the construction of phylogenetic tree.[Results]The baculoviral ubiquitins showed 73%-86% sequence identity to eukaryotic ubiquitin.Two heterogeneous regions of baculoviral ubiquitins were observed:one was the residues from 15-32,the other was located from residues 53 to 60.The else parts were conserved,where many functional amino acids were also observed.Phylogenetic analysis indicated that baculoviral ubiquitins could be divided into three sub-families,including sub-family GV,sub-family I and sub-family II.The molecular evolution of baculoviral ubiquitins might be under negative selection to maintain their functional and structural stability.[Conclusion]The analysis had provided reference for the researches on functional characterization of baculoviral ubiquitins.展开更多
基金supported by the National Natural Science Foundation of China(Grant No.12171450).
文摘This paper proposes a novel method for estimating the sparse inverse covariance matrixfor longitudinal data with informative dropouts. Based on the modified Cholesky decomposition,the sparse inverse covariance matrix is modelled by the autoregressive regression model,which guarantees the positive definiteness of the covariance matrix. To account for the informativedropouts, we then propose a penalized estimating equation method using the inverse probabilityweighting approach. The informative dropout propensity parameters are estimated by the generalizedmethod of moments. The asymptotic properties are investigated for the resulting estimators.Finally, we illustrate the effectiveness and feasibility of the proposed method through Monte Carlosimulations and a practical application.
基金Supported by Hunan Education Reform ProjectEducation Reform Project of Hunan University of Humanities,Science and Technology(RKJGY1101)~~
文摘In the paper, related research and progress of molecular clock hypothesis were summarized, including definition of molecular clock, supporting proofs, contro- versy, significance and perfection, application and accompanying challenges.
基金Supported by Seeding Raising Project from Guangdong Provincial Department(LYM10040)Open Research Project of Key Laboratory for Genetics and Breeding in Forest Trees and Ornamental Plants,MOE,Beijing Forestry University(FOP2010-4)~~
文摘[Objective] The aim of this study was to perform genome-wide analysis of glucose-6-phosphate dehydrogenase(G6PDH) and reveal its evolution in Eucalyptus grandsis.[Method] The gene character,protein sequence and phylogenetic tree of G6PDH gene were analyzed by BLAST and other bioinformatics software within Eucalyptus grandsis whole genome database.[Result] Six G6PDH genes,including one cytomic type and five plastids,were detected in the E.grandsis genome.All the G6PDHs have conserved motifs of motif 1,motif 2,motif 3,motif 7,motif 9 and motif 11.Furthermore,promoter sequences of all E.grandsis G6PDH contain TATA box,enhancer,light-responsive,hormone-responsive and stress-responsive regulatory elements.[Conclusion] This study provided reference for the further revealing molecular function of E.grandsis G6PDH gene family
文摘The molecular composition and evolution of the chalcone synthase (CHS) gene family from five species in Camellia (Theaceae) are explored in this study. Sixteen CHS exon 2 from four Camellia species were amplified from total DNA by PCR method. Three sequences of the fifth species in Camellia and two sequences of Glycine max as the designated outgroups were obtained from GenBank. Our results indicated that CHS gene family in Camellia was differentiated to three subfamilies (A, B, C) during the evolutionary history with six groups (A1, A2, A3, BI, B2, C). Among them, only group A2 was possessed by all five species in this study. However, the other five groups were detected only in some species of the plants studied. All members of CHS gene family in this study had high sequence similarity, more than 90% among the members in the same subfamily and more than 78% among different subfamilies at nucleotide level., According to the estimated components of amino acids, the function of CHS genes in Camellia had been diverged. The nucleotide substitutions of the different groups were not identical. Based on phylogenetic analyse inferred from sequences of CHS genes and their deduced amino acid sequences, we concluded that the CHS genes with new function in this genus were evolved either by mutations on several important sites or by accumulation of the mutations after the gene duplication. A further analysis showed that the diversification of CHS genes in Camellia still occurred recently, and the evolutionary models were different to some extant among different species. So we assumed that the different evolutionary models resulted from the impacts of variable environmental elements after the events of speciation.
基金The Project of Scientific Research Base and Scientific Innovation Platform of Beijing Municipal Education Commission (No.PXM2008-014204-050843)the Project of Beijing Science and Technology Committee (No.D07050601500000)+1 种基金the Knowledge Innovation Program of the Chinese Academy of Sciences (No.RCEES-QN-200706)the Special Funds for Young Scholars of RCEES,CAS.
文摘Two biological nitrogen removal processes are compared in the aspect of nitrogen removal, process operation and energy saving. Results show that when the returned sludge ratio is 50% of the inflow rate, the step-feeding process achieves over 80% total nitrogen (TN) removal efficiency, but the TN removal efficiency of the A/O process is only 40%. Moreover, filamentous sludge bulking can be well restrained in the step-feeding process. Given the conditions of a returned sludge ratio of 100% and a nitrifying liquor recycle ratio of 200%, the TN removal efficiency is 78.32% in the A/O process, but the sludge volume index (SVI) value increases to 143 mL/g. In the step-feeding process, the SVI is only 94.4 mL/g when the TN removal efficiency reaches 81. 1%. The step-feeding process has distinct advantages over the A/O process in the aspects of practicability, nitrogen removal and operating stability.
基金Supported by International Science and Technology Cooperation Project of China(2012DFA31120)Special Fund for Agro-scientific Research in the Public Interest(201303094)National Key Technology Research and Development Program(2012BAD14B15)~~
文摘[Objective] The large-scale single-column fattening pig house with fermen- tation bed could hold 1 500 heads of fattening pigs. Since the number of pigs in piggery is too large, the management is difficult. The behavior of feeding, drinking, movement, sleeping, fighting of pigs is difficult to handle. The pigs cannot be man- aged well, resulting in the enhanced weakness of piglets, enhanced illness of weak pigs and missing treatment of ill pigs. The management for the pig populations is not satisfactory, and thus, it is needed to improve timely. [Method] The barriers for the fattening pigs in the large-scale pig house with fermentation bed were designed. The single management for single fattening pig was proposed. The large-scale fat- tening pig house was divided into 8 regions. Among them, 4 regions were located in both sides of the fermentation bed. Their main function was to separate ill, weak, small and bad pigs. In addition, the main column was divided into 4 gradual barri- ers. They were used to separate different-size fattening pigs. In view of manage- ment, the different-type pigs were managed dividedly with the gradual barriers. The equally-sized pigs were concentrated into one column. The ill, weak, small and bad pigs were isolated into barriers. Thus, the dynamic management was adopted. Until the fattening pigs grew up to 75 kg and their health was stable, the barriers among the columns were canceled to mix the pigs again and guarantee the pigs more gymnastic space. [Result] This design would improve the disease resistance of ill pigs, health status of weak pigs and management level of pig populations. This study would also provide a basis for the healthy running of large-scale fattening pig house with fermentation bed. [Conclusion] The pig-raising model with fermentation bed would improve the environment of pig house and the welfare of pigs. In addi- tion, the performance of pigs and quality of pork were also improved. The fermen- tation bed had an obvious advantage in safety and economics, and it had a broad application prospect.
文摘The parallel-inlet holes with one-row, two-row and three-row film hole arrangements and different di- ameters are proposed to experimentally study their cooling characteristics. Detailed experimental processes and results are described and carried out. Results indicate that heat transfer coefficient (HTC) is increased with the increase of blowing ratio. When the blowing ratio is lower, the distribution of HTC along the heated wall can be divided into three regions. For larger blowing ratio or diameter, the cooling characteristics oi parallel-inlet film holes are similar to those of convective heat transfer around flat. Furthermore, when hole diameter is deter- mined, the arrangement patterns of film hole and the blowing ratio take a great influence on HTC.
文摘To investigate chromosome differentiation of genome A and B between common wheat and wild emmer wheat (Triticum turgidum var. dicoccoides (Koern.) Bowden), the authors conducted a RFLP analysis of the two species using 153 genomic, cDNA and chromosome_specific probes. 75.8% of the probes had detected hybridization polymorphism in at least one of the five restriction enzymes. However, the polymorphic probes were unevenly distributed among different homoeologous groups, between different genomes and in different regions of a single chromosome. Homoeologous group 1 possessed the highest level of polymorphism (96.2%), followed by group 6 and 2 (84.6% and 82.1% respectively). In contrast, only 60%-67% of probes of the other four groups was polymorphic. In most groups the number of probes capable of detecting B chromosome polymorphism was slightly higher than that revealing A chromosome difference (totally 51.8% vs 43.1%). In a single chromosome, RFLP was predominant in the distal region (65.1%) and showed a decreasing trend from the proximal (46.2%) to the pericentric (42.4%) regions. The results suggest that there exists a substantial amount of DNA polymorphism between the A and B chromosomes of common wheat and those of wild emmer wheat, indicating that a considerable degree of genetic differentiation has taken place in the A and B genoms of two species during evolution from wild emmer to common wheat. The extent of the genetic differentiation may vary among different homoeologous groups, between A and B chromosomes and in different regions of individual chromosome.
文摘Pea ( Pisum sativum Linn.) actin gene family contains at least three isoforms (PEAcⅠ, PEAcⅡand PEAcⅢ), and the DNA sequence of these isoforms show high similarity in the coding regions and significant divergence in the untranslated regions. RT_PCR and Southern blotting using 3′_untranslated region (3′_UTR) as specific probe revealed that pea isoactin genes were expressed in roots, stems, leaves, tendrils, pollen and juvenile siliques, but displayed different patterns of transcript accumulation. Two_fold serial dilution electrophoresis showed PEAcⅠ mRNA preferentially accumulated in rapidly developing tissues: it peaked in seven days' stem; remained at a rather high level in leaves within a month but decreased significantly later; varied a little in tendrils and reached a median and a very low level respectively in juvenile siliques and in pollen. PEAcⅡ displayed somewhat similar expression pattern to PEAcⅠ. The observed differences in sequences and transcript accumulation patterns suggest that the individual pea actin genes may differ in their transcriptional regulation and cellular function. Phylogenetic tree of actins showed that pea actin isoforms are as diverged from each other as they are from other plant actins, and pea actins might have originated from a common ancestor before the divergence of the dicot and monocot plants.
文摘China's economic growth is heavily influenced by exports, while reconciling environmental regulation and economic growth requires handling the relationship between environmental regulation and industrial competitiveness well. The effects of environmental regulation on industrial competitiveness are largely subject to the institutional design of environmental regulation. Despite numerous studies on the relationship between environmental regulation and industrial competitiveness, a consensus has yet to be reached. Aside from differences in research methodology, these studies failed to give sufficient consideration to the impact of environmental regulation on industrial competitiveness. Such effects can be negative or positive depending on the design of environmental regulatory policy. This paper has investigated the relationship between environmental regulation and the competitiveness of China's iron and steel industry and discovered that tighter environmental regulation does not diminish the competitiveness of the iron and steel industry since the policy design of environmental regulation accommodates the tolerance of advanced production capacity and includes a reasonable cost sharing mechanism. This discovery is of important reference for China to develop rational policy design to balance the relationship between environmental regulation and industrial competitiveness.
基金Supported by China Postdoctoral Scientific Foundation(201004713-87)Natural Science Foundation for Universities of Jiangsu Province(07KJB180013)Foundation for Talented Man in Jiangsu University(05JDG048)~~
文摘[Objective] The aim of this study was to analyze the sequence characteristics and molecular evolution of ubiquitins encoded by baculoviruses.[Methods]Clustal W software was used for multiple sequence alignment analysis,and neighbor-joining method(NJ)and maximum parsimony method(MP)were used for the construction of phylogenetic tree.[Results]The baculoviral ubiquitins showed 73%-86% sequence identity to eukaryotic ubiquitin.Two heterogeneous regions of baculoviral ubiquitins were observed:one was the residues from 15-32,the other was located from residues 53 to 60.The else parts were conserved,where many functional amino acids were also observed.Phylogenetic analysis indicated that baculoviral ubiquitins could be divided into three sub-families,including sub-family GV,sub-family I and sub-family II.The molecular evolution of baculoviral ubiquitins might be under negative selection to maintain their functional and structural stability.[Conclusion]The analysis had provided reference for the researches on functional characterization of baculoviral ubiquitins.