为建立中国(未包括香港、澳门特别行政区和台湾地区)水痘减毒活疫苗(Varicella Attenuated Live Vaccine,VarY)预防接种的流行病数学模型,对中国接种VarV效果进行预测,对数学模型所需要的水痘流行病学的主要参数(包括水痘病例的传染力...为建立中国(未包括香港、澳门特别行政区和台湾地区)水痘减毒活疫苗(Varicella Attenuated Live Vaccine,VarY)预防接种的流行病数学模型,对中国接种VarV效果进行预测,对数学模型所需要的水痘流行病学的主要参数(包括水痘病例的传染力、传染周期、免疫水平的阈值、母传抗体、新生儿水痘等)和VarV的免疫学参数(包括保护效果、免疫持久性、突破病例、成人病例、易感人群的积累和强化免疫活动等)进行了综述。展开更多
The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-...The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-1 genome sequences. By applying the rule inference algorithm RIPPER (Repeated Incremental Pruning to Produce Error Reduction) to multiple sequence alignments of Env sequences from four classes of compiled datasets, we generated four sets of signature patterns. We found that these patterns were able to distinguish southeastern Asian from non- southeastern Asian sequences with 97.5% accuracy, Chinese from non-Chinese sequences with 98.3% accuracy, African from non-African sequences with 88.4% accuracy, and southern African from non-southern African sequences with 91.2% accuracy. These patterns showed different associations with subtypes and with amino acid positions. In addition, some signature patterns were characteristic of the geographic area from which the sample was taken. Amino acid features corresponding to the phylogenetic clustering of HIV-1 sequences were consistent with some of the deduced patterns. Using a combination of patterns inferred from subtypes B, C, and all subtypes chimeric with CRF01_AE worldwide, we found that signature patterns of subtype C were extremely common in some sampled countries (for example, Zambia in southern Africa), which may hint at the origin of this HIV-1 subtype and the need to pay special attention to this area of Africa. Signature patterns of subtype B sequences were associated with different countries. Even more, there are distinct patterns at single position 21 with glycine, leucine and isoleucine corresponding to subtype C, B and all possible recombination forms chimeric with CRF01_AE, which also indicate distinct geographic features. Our method widens the scope of inference of signature from geographic, genetic, and genomic viewpoints. These findings may provide a valuable reference for epidemiological research or vaccine design.展开更多
Network epidemiology has become a core framework for investigating the role of human contact patterns in the spreadingof infectious diseases.In network epidemiology,one represents the contact structure as a network of...Network epidemiology has become a core framework for investigating the role of human contact patterns in the spreadingof infectious diseases.In network epidemiology,one represents the contact structure as a network of nodes(individuals)connected bylinks(sometimes as a temporal network where the links are not continuously active)and the disease as a compartmental model(whereindividuals are assigned states with respect to the disease and follow certain transition rules between the states).In this paper,we discussfast algorithms for such simulations and also compare two commonly used versions,one where there is a constant recovery rate(the numberof individuals that stop being infectious per time is proportional to the number of such people);the other where the duration of the diseaseis constant.The results show that,for most practical purposes,these versions are qualitatively the same.展开更多
文摘为建立中国(未包括香港、澳门特别行政区和台湾地区)水痘减毒活疫苗(Varicella Attenuated Live Vaccine,VarY)预防接种的流行病数学模型,对中国接种VarV效果进行预测,对数学模型所需要的水痘流行病学的主要参数(包括水痘病例的传染力、传染周期、免疫水平的阈值、母传抗体、新生儿水痘等)和VarV的免疫学参数(包括保护效果、免疫持久性、突破病例、成人病例、易感人群的积累和强化免疫活动等)进行了综述。
基金the funding by the Chinese Key National Science and Technology Program in the 12th Five-Year Period, grant 2012ZX10001006-002
文摘The epidemiology of HIV-1 varies in different areas of the world, and it is possible that this complexity may leave unique footprints in the viral genome. Thus, we attempted to find significant patterns in global HIV-1 genome sequences. By applying the rule inference algorithm RIPPER (Repeated Incremental Pruning to Produce Error Reduction) to multiple sequence alignments of Env sequences from four classes of compiled datasets, we generated four sets of signature patterns. We found that these patterns were able to distinguish southeastern Asian from non- southeastern Asian sequences with 97.5% accuracy, Chinese from non-Chinese sequences with 98.3% accuracy, African from non-African sequences with 88.4% accuracy, and southern African from non-southern African sequences with 91.2% accuracy. These patterns showed different associations with subtypes and with amino acid positions. In addition, some signature patterns were characteristic of the geographic area from which the sample was taken. Amino acid features corresponding to the phylogenetic clustering of HIV-1 sequences were consistent with some of the deduced patterns. Using a combination of patterns inferred from subtypes B, C, and all subtypes chimeric with CRF01_AE worldwide, we found that signature patterns of subtype C were extremely common in some sampled countries (for example, Zambia in southern Africa), which may hint at the origin of this HIV-1 subtype and the need to pay special attention to this area of Africa. Signature patterns of subtype B sequences were associated with different countries. Even more, there are distinct patterns at single position 21 with glycine, leucine and isoleucine corresponding to subtype C, B and all possible recombination forms chimeric with CRF01_AE, which also indicate distinct geographic features. Our method widens the scope of inference of signature from geographic, genetic, and genomic viewpoints. These findings may provide a valuable reference for epidemiological research or vaccine design.
基金Basic science research program through the national research foundation of Korea(NRF)funded by the ministry of education(2013R1A1A2011947)
文摘Network epidemiology has become a core framework for investigating the role of human contact patterns in the spreadingof infectious diseases.In network epidemiology,one represents the contact structure as a network of nodes(individuals)connected bylinks(sometimes as a temporal network where the links are not continuously active)and the disease as a compartmental model(whereindividuals are assigned states with respect to the disease and follow certain transition rules between the states).In this paper,we discussfast algorithms for such simulations and also compare two commonly used versions,one where there is a constant recovery rate(the numberof individuals that stop being infectious per time is proportional to the number of such people);the other where the duration of the diseaseis constant.The results show that,for most practical purposes,these versions are qualitatively the same.
