The coronavirus disease 2019(COVID-19)pandemic has greatly damaged human society,but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)pathogen remain unclea...The coronavirus disease 2019(COVID-19)pandemic has greatly damaged human society,but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)pathogen remain unclear.Here,we reconstructed the transmission networks of SARS-CoV-2 during the first three and six months since its first report based on ancestor-offspring relationships using BANAL-52-referenced mutations.We explored the position(i.e.,root,middle,or tip)of early detected samples in the evolutionary tree of SARS-CoV-2.In total,6799 transmission chains and 1766 transmission networks were reconstructed,with chain lengths ranging from 1-9 nodes.The root node samples of the 1766 transmission networks were from 58 countries or regions and showed no common ancestor,indicating the occurrence of many independent or parallel transmissions of SARS-CoV-2 when first detected(i.e.,all samples were located at the tip position of the evolutionary tree).No root node sample was found in any sample(n=31,all from the Chinese mainland)collected in the first 15 days from 24 December 2019.Results using six-month data or RaTG13-referenced mutation data were similar.The reconstruction method was verified using a simulation approach.Our results suggest that SARS-CoV-2 may have already been spreading independently worldwide before the outbreak of COVID-19 in Wuhan,China.Thus,a comprehensive global survey of human and animal samples is essential to explore the origins of SARS-CoV-2 and its natural reservoirs and hosts.展开更多
Mutation breeding has been widely used in crop improvement, and prominent pro-gress has been achieved. However, little is known about the genomic changes duringthe processes of mutation and selection in later generati...Mutation breeding has been widely used in crop improvement, and prominent pro-gress has been achieved. However, little is known about the genomic changes duringthe processes of mutation and selection in later generations. In general, some ofthese changes can be identified only by phenotypic alterations and this, to some ex-展开更多
A local minimum is frequently encountered in the training of back propagation neural networks (BPNN), which sharply slows the training process. In this paper, an analysis of the formation of local minima is presented,...A local minimum is frequently encountered in the training of back propagation neural networks (BPNN), which sharply slows the training process. In this paper, an analysis of the formation of local minima is presented, and an improved genetic algorithm (GA) is introduced to overcome local minima. The Sigmoid function is generally used as the activation function of BPNN nodes. It is the flat characteristic of the Sigmoid function that results in the formation of local minima. In the improved GA, pertinent modifications are made to the evaluation function and the mutation model. The evaluation of the solution is associated with both the training error and gradient. The sensitivity of the error function to network parameters is used to form a self adapting mutation model. An example of industrial application shows the advantage of the improved GA to overcome local minima. 展开更多
基金supported by the Ministry of Science and Technology of the People’s Republic of China(2021YFC0863400)Institute of Zoology,Chinese Academy of Sciences(E0517111,E122G611)。
文摘The coronavirus disease 2019(COVID-19)pandemic has greatly damaged human society,but the origins and early transmission patterns of the severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)pathogen remain unclear.Here,we reconstructed the transmission networks of SARS-CoV-2 during the first three and six months since its first report based on ancestor-offspring relationships using BANAL-52-referenced mutations.We explored the position(i.e.,root,middle,or tip)of early detected samples in the evolutionary tree of SARS-CoV-2.In total,6799 transmission chains and 1766 transmission networks were reconstructed,with chain lengths ranging from 1-9 nodes.The root node samples of the 1766 transmission networks were from 58 countries or regions and showed no common ancestor,indicating the occurrence of many independent or parallel transmissions of SARS-CoV-2 when first detected(i.e.,all samples were located at the tip position of the evolutionary tree).No root node sample was found in any sample(n=31,all from the Chinese mainland)collected in the first 15 days from 24 December 2019.Results using six-month data or RaTG13-referenced mutation data were similar.The reconstruction method was verified using a simulation approach.Our results suggest that SARS-CoV-2 may have already been spreading independently worldwide before the outbreak of COVID-19 in Wuhan,China.Thus,a comprehensive global survey of human and animal samples is essential to explore the origins of SARS-CoV-2 and its natural reservoirs and hosts.
基金Project supported by the International Atomic Energy Agency (IAEA)the Rockefeller Foundation.
文摘Mutation breeding has been widely used in crop improvement, and prominent pro-gress has been achieved. However, little is known about the genomic changes duringthe processes of mutation and selection in later generations. In general, some ofthese changes can be identified only by phenotypic alterations and this, to some ex-
文摘A local minimum is frequently encountered in the training of back propagation neural networks (BPNN), which sharply slows the training process. In this paper, an analysis of the formation of local minima is presented, and an improved genetic algorithm (GA) is introduced to overcome local minima. The Sigmoid function is generally used as the activation function of BPNN nodes. It is the flat characteristic of the Sigmoid function that results in the formation of local minima. In the improved GA, pertinent modifications are made to the evaluation function and the mutation model. The evaluation of the solution is associated with both the training error and gradient. The sensitivity of the error function to network parameters is used to form a self adapting mutation model. An example of industrial application shows the advantage of the improved GA to overcome local minima.
