The reliability evaluation of a multistate network is primarily based on d-minimal paths/cuts(d-MPs/d-MCs).However,being a nondeterminism polynomial hard(NP-hard)problem,searching for all d-MPs is a rather challenging...The reliability evaluation of a multistate network is primarily based on d-minimal paths/cuts(d-MPs/d-MCs).However,being a nondeterminism polynomial hard(NP-hard)problem,searching for all d-MPs is a rather challenging task.In existing implicit enumeration algorithms based on minimal paths(MPs),duplicate d-MP candidates may be generated.An extra step is needed to locate and remove these duplicate d-MP candidates,which costs significant computational effort.This paper proposes an efficient method to prevent the generation of duplicate d-MP candidates for implicit enumeration algorithms for d-MPs.First,the mechanism of generating duplicate d-MP candidates in the implicit enumeration algorithms is discussed.Second,a direct and efficient avoiding-duplicates method is proposed.Third,an improved algorithm is developed,followed by complexity analysis and illustrative examples.Based on the computational experiments comparing with two existing algorithms,it is found that the proposed method can significantly improve the efficiency of generating d-MPs for a particular demand level d.展开更多
Background SRO(Similar to RCD1)genes family is largely recognized for their importance in the growth,develop-ment,and in responding to environmental stresses.However,genome-wide identification and functional character...Background SRO(Similar to RCD1)genes family is largely recognized for their importance in the growth,develop-ment,and in responding to environmental stresses.However,genome-wide identification and functional characteri-zation of SRO genes from cotton species have not been reported so far.Results A total of 36 SRO genes were identified from four cotton species.Phylogenetic analysis divided these genes into three groups with distinct structure.Syntenic and chromosomal distribution analysis indicated uneven distribu-tion of GaSRO,GrSRO,GhSRO,and GbSRO genes on A2,D5 genomes,Gh-At,Gh-Dt,Gb-At,and Gb-Dt subgenomes,respectively.Gene duplication analysis revealed the presence of six duplicated gene pairs among GhSRO genes.In promoter analysis,several elements responsive to the growth,development and hormones were found in GhSRO genes,implying gene induction during cotton growth and development.Several miRNAs responsive to plant growth and abiotic stress were predicted to target 12 GhSRO genes.Organ-specific expression profiling demonstrated the roles of GhSRO genes in one or more tissues.In addition,specific expression pattern of some GhSRO genes dur-ing ovule development depicted their involvement in these developmental processes.Conclusion The data presented in this report laid a foundation for understanding the classification and functions of SRO genes in cotton.展开更多
Heterogeneous computing is one effective method of high performance computing with many advantages. Task scheduling is a critical issue in heterogeneous environments as well as in homogeneous environments. A number of...Heterogeneous computing is one effective method of high performance computing with many advantages. Task scheduling is a critical issue in heterogeneous environments as well as in homogeneous environments. A number of task scheduling algorithms for homogeneous environments have been proposed, whereas, a few for heterogeneous environments can be found in the literature. A novel task scheduling algorithm for heterogeneous environments, called the heterogeneous critical task （HCT） scheduling algorithm is presented. By means of the directed acyclic graph and the gantt graph, the HCT algorithm defines the critical task and the idle time slot. After determining the critical tasks of a given task, the HCT algorithm tentatively duplicates the critical tasks onto the processor that has the given task in the idle time slot, to reduce the start time of the given task. To compare the performance of the HCT algorithm with several recently proposed algorithms, a large set of randomly generated applications and the Gaussian elimination application are randomly generated. The experimental result has shown that the HCT algorithm outperforms the other algorithm.展开更多
When the communication time is relatively shorter than the computation time for every task, the task duplication based scheduling (TDS) algorithm proposed by Darbha and Agrawal generates an optimal schedule. Park and ...When the communication time is relatively shorter than the computation time for every task, the task duplication based scheduling (TDS) algorithm proposed by Darbha and Agrawal generates an optimal schedule. Park and Choe also proposed an extended TDS algorithm whose optimality condition is less restricted than that of TDS algorithm, but the condition is very complex and is difficult to satisfy when the number of tasks is large. An efficient algorithm is proposed whose optimality condition is less restricted and simpler than both of the algorithms, and the schedule length is also shorter than both of the algorithms. The time complexity of the proposed algorithm is O(v2), where v represents the number of tasks.展开更多
Background:INDETERMINATE DOMAIN(IDD)transcription factors form one of the largest and most conserved gene families in plant kingdom and play important roles in various processes of plant growth and development,such as...Background:INDETERMINATE DOMAIN(IDD)transcription factors form one of the largest and most conserved gene families in plant kingdom and play important roles in various processes of plant growth and development,such as flower induction in term of flowering control.Till date,systematic and functional analysis of IDD genes remained infancy in cotton.Results:In this study,we identified total of 162 IDD genes from eight different plant species including 65 IDD genes in Gossypium hirsutum.Phylogenetic analysis divided IDDs genes into seven well distinct groups.The gene structures and conserved motifs of GhIDD genes depicted highly conserved exon-intron and protein motif distribution patterns.Gene duplication analysis revealed that among 142 orthologous gene pairs,54 pairs have been derived by segmental duplication events and four pairs by tandem duplication events.Further,Ka/Ks values of most of orthologous/paralogous gene pairs were less than one suggested the purifying selection pressure during evolution.Spatiotemporal expression pattern by qRT-PCR revealed that most of the investigated GhIDD genes showed higher transcript levels in ovule of seven days post anthesis,and upregulated response under the treatments of multiple abiotic stresses.Conclusions:Evolutionary analysis revealed that IDD gene family was highly conserved in plant during the rapid phase of evolution.Whole genome duplication,segmental as well as tandem duplication significantly contributed to the expansion of IDD gene family in upland cotton.Some distinct genes evolved into special subfamily and indicated potential role in the allotetraploidy Gossypium hisutum evolution and development High transcript levels of GhIDD genes in ovules illustrated their potential roles in seed and fiber development Further,upregulated responses of GhIDD genes under the treatments of various abiotic stresses suggested them as important genetic regulators to improve stress resistance in cotton breeding.展开更多
Background： RING H2 finger E3 ligase （RH2FE3） genes encode cysteine rich proteins that mediate E3 ubiquitin ligase activity and degrade target substrates. The roles of these genes in plant responses to phytohormone...Background： RING H2 finger E3 ligase （RH2FE3） genes encode cysteine rich proteins that mediate E3 ubiquitin ligase activity and degrade target substrates. The roles of these genes in plant responses to phytohormones and abiotic stresses are well documented in various species, but their roles in cotton fiber development are poorly understood. To date, genome wide identification and expression analyses of Gossypium hirsutum RH2FE3 genes have not been reported. Methods： We performed computational identification, structural and phylogenetic analyses, chromosomal distribution analysis and estimated KJKs values of G hirsutum RH2FE3 genes. Orthologous and paralogous gene pairs were identified by all versus all BLASTP searches. We predicted cis regulatory elements and analyzed microarray data sets to generate heatmaps at different development stages. Tissue specific expression in cotton fiber, and hormonal and abiotic stress responses were determined by quantitative real time polymerase chain reaction （qRT PCR） analysis. Results： We investigated 140 G hirsutum, 80 G. orboreum, and evolutionary mechanisms and compared them with orthologs 89 G. roimondii putative RH2FB genes and their in Arobidopsis and rice. A domain based analysis of the G hirsutum RH2FE3 genes predicted conserved signature motifs and gene structures. Chromosomal localization showed the genes were distributed across all G hirsutum chromosomes, and 60 duplication events （4 tandem and 56 segmental duplications） and 98 orthologs were detected, cis elements were detected in the promoter regions of G hirsutum RH2FE3 genes. Microarray data and qRT PCR analyses showed that G hirsutum RH2FE3 genes were strongly correlated with cotton fiber development. Additionally, almost all the （brassinolide, gibberellic acid （GA）, indole 3-acetic acid drought, and salt）. dentified genes were up regulated in response to phytohormones （IAA）, and salicylic acid （SA）） and abiotic stresses （cold, heat, Conclusions： The genome wide identification, comprehensive analysis, and characterization of conserved domains and gene structures, as well as phylogenetic analysis, cis element prediction, and expression profile analysis of G hirsutum RH2FE3 genes and their roles in cotton fiber development and responses to plant hormones and abiotic stresses are reported here for the first time. Our findings will contribute to the genome wide analysis of putative RH2FE3 genes in other species and lay a foundation for future physiological and functional research on G hirsutum RH2FE3 genes.展开更多
Background:Calmodulin(CaM)is one of the most important Ca^(2+)signaling receptors because it regulates diverse physiological and biochemical reactions in plants.CaM functions by interacting with CaM-binding proteins(C...Background:Calmodulin(CaM)is one of the most important Ca^(2+)signaling receptors because it regulates diverse physiological and biochemical reactions in plants.CaM functions by interacting with CaM-binding proteins(CaMBPs)to modulate Ca^(2+)signaling.IQ domain(IQD)proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites.Results:In this study,we identified 102 GhIQD genes in the Gossypium hirsutum L.genome.The GhIQD gene family was classified into four clusters(Ⅰ,Ⅱ,Ⅲ,andⅣ),and we then mapped the GhIQD genes to the G.hirsutum L.chromosomes.Moreover,we found that 100 of the 102 GhIQD genes resulted from segmental duplication events,indicating that segmental duplication is the main force driving GhIQD gene expansion.Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells,suggesting that GhIQD genes may contribute to fiber cell development in cotton.In addition,we found that 20 selected GhIQD genes were highly expressed in various tissues.Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes.Conclusions:Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA.Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes,as well as clues to breed better cotton varieties in the future.展开更多
A scheduling scheme is proposed to reduce execution time by means of both checkpoint sharing and task duplication under a peer-to-peer(P2P) architecture. In the scheme, the checkpoint executed by each peer(i.e., a res...A scheduling scheme is proposed to reduce execution time by means of both checkpoint sharing and task duplication under a peer-to-peer(P2P) architecture. In the scheme, the checkpoint executed by each peer(i.e., a resource) is used as an intermediate result and executed in other peers via its duplication and transmission. As the checkpoint is close to a final result, the reduction of execution time for each task becomes higher, leading to reducing turnaround time. To evaluate the performance of our scheduling scheme in terms of transmission cost and execution time, an analytical model with an embedded Markov chain is presented. We also conduct simulations with a failure rate of tasks and compare the performance of our scheduling scheme with that of the existing scheme based on client-server architecture. Performance results show that our scheduling scheme is superior to the existing scheme with respect to the reduction of execution time and turnaround time.展开更多
2016年9月30日,应西南大学生物技术学院王茜龄副教授邀请,美国田纳西大学植物科学系程宗明教授来生物技术学院访问交流,并分别做了题为＂Duplication and post-duplication divergence in functions＂的学术报告和＂How to publish your...2016年9月30日,应西南大学生物技术学院王茜龄副教授邀请,美国田纳西大学植物科学系程宗明教授来生物技术学院访问交流,并分别做了题为＂Duplication and post-duplication divergence in functions＂的学术报告和＂How to publish your research work in high impact international journals＂的辅导报告。展开更多
基金supported by the National Natural Science Foundation of China(71701207)the Science and Technology on Reliability&Environmental Engineering Laboratory(6142004004-2)the Science and Technology Commission of the CMC(2019-JCJQ-JJ-180)。
文摘The reliability evaluation of a multistate network is primarily based on d-minimal paths/cuts(d-MPs/d-MCs).However,being a nondeterminism polynomial hard(NP-hard)problem,searching for all d-MPs is a rather challenging task.In existing implicit enumeration algorithms based on minimal paths(MPs),duplicate d-MP candidates may be generated.An extra step is needed to locate and remove these duplicate d-MP candidates,which costs significant computational effort.This paper proposes an efficient method to prevent the generation of duplicate d-MP candidates for implicit enumeration algorithms for d-MPs.First,the mechanism of generating duplicate d-MP candidates in the implicit enumeration algorithms is discussed.Second,a direct and efficient avoiding-duplicates method is proposed.Third,an improved algorithm is developed,followed by complexity analysis and illustrative examples.Based on the computational experiments comparing with two existing algorithms,it is found that the proposed method can significantly improve the efficiency of generating d-MPs for a particular demand level d.
文摘Background SRO(Similar to RCD1)genes family is largely recognized for their importance in the growth,develop-ment,and in responding to environmental stresses.However,genome-wide identification and functional characteri-zation of SRO genes from cotton species have not been reported so far.Results A total of 36 SRO genes were identified from four cotton species.Phylogenetic analysis divided these genes into three groups with distinct structure.Syntenic and chromosomal distribution analysis indicated uneven distribu-tion of GaSRO,GrSRO,GhSRO,and GbSRO genes on A2,D5 genomes,Gh-At,Gh-Dt,Gb-At,and Gb-Dt subgenomes,respectively.Gene duplication analysis revealed the presence of six duplicated gene pairs among GhSRO genes.In promoter analysis,several elements responsive to the growth,development and hormones were found in GhSRO genes,implying gene induction during cotton growth and development.Several miRNAs responsive to plant growth and abiotic stress were predicted to target 12 GhSRO genes.Organ-specific expression profiling demonstrated the roles of GhSRO genes in one or more tissues.In addition,specific expression pattern of some GhSRO genes dur-ing ovule development depicted their involvement in these developmental processes.Conclusion The data presented in this report laid a foundation for understanding the classification and functions of SRO genes in cotton.
文摘Heterogeneous computing is one effective method of high performance computing with many advantages. Task scheduling is a critical issue in heterogeneous environments as well as in homogeneous environments. A number of task scheduling algorithms for homogeneous environments have been proposed, whereas, a few for heterogeneous environments can be found in the literature. A novel task scheduling algorithm for heterogeneous environments, called the heterogeneous critical task （HCT） scheduling algorithm is presented. By means of the directed acyclic graph and the gantt graph, the HCT algorithm defines the critical task and the idle time slot. After determining the critical tasks of a given task, the HCT algorithm tentatively duplicates the critical tasks onto the processor that has the given task in the idle time slot, to reduce the start time of the given task. To compare the performance of the HCT algorithm with several recently proposed algorithms, a large set of randomly generated applications and the Gaussian elimination application are randomly generated. The experimental result has shown that the HCT algorithm outperforms the other algorithm.
文摘When the communication time is relatively shorter than the computation time for every task, the task duplication based scheduling (TDS) algorithm proposed by Darbha and Agrawal generates an optimal schedule. Park and Choe also proposed an extended TDS algorithm whose optimality condition is less restricted than that of TDS algorithm, but the condition is very complex and is difficult to satisfy when the number of tasks is large. An efficient algorithm is proposed whose optimality condition is less restricted and simpler than both of the algorithms, and the schedule length is also shorter than both of the algorithms. The time complexity of the proposed algorithm is O(v2), where v represents the number of tasks.
基金supported by the Major Research Plan of National Natural Science Foundation of China(NO.31690093)Creative Research Groups of China(31621005)the Agricultural Science and Technology Innovation Program Cooperation and Innovation Mission(CAAS-XTCX2016)
文摘Background:INDETERMINATE DOMAIN(IDD)transcription factors form one of the largest and most conserved gene families in plant kingdom and play important roles in various processes of plant growth and development,such as flower induction in term of flowering control.Till date,systematic and functional analysis of IDD genes remained infancy in cotton.Results:In this study,we identified total of 162 IDD genes from eight different plant species including 65 IDD genes in Gossypium hirsutum.Phylogenetic analysis divided IDDs genes into seven well distinct groups.The gene structures and conserved motifs of GhIDD genes depicted highly conserved exon-intron and protein motif distribution patterns.Gene duplication analysis revealed that among 142 orthologous gene pairs,54 pairs have been derived by segmental duplication events and four pairs by tandem duplication events.Further,Ka/Ks values of most of orthologous/paralogous gene pairs were less than one suggested the purifying selection pressure during evolution.Spatiotemporal expression pattern by qRT-PCR revealed that most of the investigated GhIDD genes showed higher transcript levels in ovule of seven days post anthesis,and upregulated response under the treatments of multiple abiotic stresses.Conclusions:Evolutionary analysis revealed that IDD gene family was highly conserved in plant during the rapid phase of evolution.Whole genome duplication,segmental as well as tandem duplication significantly contributed to the expansion of IDD gene family in upland cotton.Some distinct genes evolved into special subfamily and indicated potential role in the allotetraploidy Gossypium hisutum evolution and development High transcript levels of GhIDD genes in ovules illustrated their potential roles in seed and fiber development Further,upregulated responses of GhIDD genes under the treatments of various abiotic stresses suggested them as important genetic regulators to improve stress resistance in cotton breeding.
基金supported by the Major Research Plan of National Natural Science Foundation of China(NO.31690093)Young Elite Scientist Sponsorship Program by CAST(China Association for Science and Technology)
文摘Background： RING H2 finger E3 ligase （RH2FE3） genes encode cysteine rich proteins that mediate E3 ubiquitin ligase activity and degrade target substrates. The roles of these genes in plant responses to phytohormones and abiotic stresses are well documented in various species, but their roles in cotton fiber development are poorly understood. To date, genome wide identification and expression analyses of Gossypium hirsutum RH2FE3 genes have not been reported. Methods： We performed computational identification, structural and phylogenetic analyses, chromosomal distribution analysis and estimated KJKs values of G hirsutum RH2FE3 genes. Orthologous and paralogous gene pairs were identified by all versus all BLASTP searches. We predicted cis regulatory elements and analyzed microarray data sets to generate heatmaps at different development stages. Tissue specific expression in cotton fiber, and hormonal and abiotic stress responses were determined by quantitative real time polymerase chain reaction （qRT PCR） analysis. Results： We investigated 140 G hirsutum, 80 G. orboreum, and evolutionary mechanisms and compared them with orthologs 89 G. roimondii putative RH2FB genes and their in Arobidopsis and rice. A domain based analysis of the G hirsutum RH2FE3 genes predicted conserved signature motifs and gene structures. Chromosomal localization showed the genes were distributed across all G hirsutum chromosomes, and 60 duplication events （4 tandem and 56 segmental duplications） and 98 orthologs were detected, cis elements were detected in the promoter regions of G hirsutum RH2FE3 genes. Microarray data and qRT PCR analyses showed that G hirsutum RH2FE3 genes were strongly correlated with cotton fiber development. Additionally, almost all the （brassinolide, gibberellic acid （GA）, indole 3-acetic acid drought, and salt）. dentified genes were up regulated in response to phytohormones （IAA）, and salicylic acid （SA）） and abiotic stresses （cold, heat, Conclusions： The genome wide identification, comprehensive analysis, and characterization of conserved domains and gene structures, as well as phylogenetic analysis, cis element prediction, and expression profile analysis of G hirsutum RH2FE3 genes and their roles in cotton fiber development and responses to plant hormones and abiotic stresses are reported here for the first time. Our findings will contribute to the genome wide analysis of putative RH2FE3 genes in other species and lay a foundation for future physiological and functional research on G hirsutum RH2FE3 genes.
基金the State Key Laboratory of Cotton Biology Open Fund(grant numbers CB2019A03 and CB2018A07)comprehensive Scientific research fund project of Xianyang Normal University(XSYK20002)+2 种基金the Innovation and Entrepreneurship Training Program for College Students in Shaanxi Province(S202010722071)the National Natural Science Foundation of China(grant number 31872175)Key Research and Development Program of Shaanxi Province(grant number 2019NY-103).
文摘Background:Calmodulin(CaM)is one of the most important Ca^(2+)signaling receptors because it regulates diverse physiological and biochemical reactions in plants.CaM functions by interacting with CaM-binding proteins(CaMBPs)to modulate Ca^(2+)signaling.IQ domain(IQD)proteins are plant-specific CaMBPs that bind to CaM by their specific CaM binding sites.Results:In this study,we identified 102 GhIQD genes in the Gossypium hirsutum L.genome.The GhIQD gene family was classified into four clusters(Ⅰ,Ⅱ,Ⅲ,andⅣ),and we then mapped the GhIQD genes to the G.hirsutum L.chromosomes.Moreover,we found that 100 of the 102 GhIQD genes resulted from segmental duplication events,indicating that segmental duplication is the main force driving GhIQD gene expansion.Gene expression pattern analysis showed that a total of 89 GhIQD genes expressed in the elongation stage and second cell wall biosynthesis stage of the fiber cells,suggesting that GhIQD genes may contribute to fiber cell development in cotton.In addition,we found that 20 selected GhIQD genes were highly expressed in various tissues.Exogenous application of MeJA significantly enhanced the expression levels of GhIQD genes.Conclusions:Our study shows that GhIQD genes are involved in fiber cell development in cotton and are also widely induced by MeJA.Thw results provide bases to systematically characterize the evolution and biological functions of GhIQD genes,as well as clues to breed better cotton varieties in the future.
基金supported by the Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education (2012R1A1A4A0105777)supported by the MSIP (Ministry of Science, ICT and Future Planning), Korea, under the ITRC (Information Technology Research Center) support program (NIPA-2013-H030113-4007) supervised by the NIPA (National IT Industry Promotion Agency)
文摘A scheduling scheme is proposed to reduce execution time by means of both checkpoint sharing and task duplication under a peer-to-peer(P2P) architecture. In the scheme, the checkpoint executed by each peer(i.e., a resource) is used as an intermediate result and executed in other peers via its duplication and transmission. As the checkpoint is close to a final result, the reduction of execution time for each task becomes higher, leading to reducing turnaround time. To evaluate the performance of our scheduling scheme in terms of transmission cost and execution time, an analytical model with an embedded Markov chain is presented. We also conduct simulations with a failure rate of tasks and compare the performance of our scheduling scheme with that of the existing scheme based on client-server architecture. Performance results show that our scheduling scheme is superior to the existing scheme with respect to the reduction of execution time and turnaround time.
文摘2016年9月30日,应西南大学生物技术学院王茜龄副教授邀请,美国田纳西大学植物科学系程宗明教授来生物技术学院访问交流,并分别做了题为＂Duplication and post-duplication divergence in functions＂的学术报告和＂How to publish your research work in high impact international journals＂的辅导报告。
