New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, wh...New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, which enables the sequencing of several samples in a single run. It implies in cost reduction and simplifies the analysis of related samples. Meanwhile, this sequencing type requires an additional filtering step to ensure the reliability of the results. Thus, we propose in this paper a probabilistic model which considers the intrinsic characteristics of each sequencing to characterize multiplex runs and filter low-quality data, increasing the data analysis reliability of multiplex sequencing performed on SOLiD. The results show that the proposed model proves to be satisfactory due to: 1) identification of faults in the sequencing process;2) adaptation and development of new protocols for sample preparation;3) the assignment of a degree of confidence to the data generated;and 4) guiding a filtering process, without discarding useful sequences in an arbitrary manner.展开更多
The occurrence of Pseudomonas aeruginosa(P.aeruginosa)contamination in packaged drinking water has become a significant public health concern.Accurate,specific and rapid detection of P.aeruginosa in drinking water is ...The occurrence of Pseudomonas aeruginosa(P.aeruginosa)contamination in packaged drinking water has become a significant public health concern.Accurate,specific and rapid detection of P.aeruginosa in drinking water is crucial to safeguard public health.In this study,we developed a multiplex PCR assisted real-time nanopore sequencing method for rapid and accurate identification of target P.aeruginosa.Three primer sets of long amplicons with non-overlapping sequences were designed.By combining real-time sequencing,the time-varying current signals captured by nanopore proteins were used for real-time identification of the sequence information of the measured strand using the portable nanopore gene sequencing device.Rapid and on-site identification of P.aeruginosa in packaged drinking water were achieved through real-time bioinformatics analysis.The total time of sequence-based identification could be completed in less than 220 min from sampling to the final results output.Interestingly,with our designed multiplex PCR assisted strategy,the core sequencing operations were completed in just 5 min,and the detection limit could be achieved as 10^(2) CFU/250 mL without pre-culture treatment.Of greater significance,this multiplex PCR assisted real-time sequencing strategy can be applied for the identification of other common bacteria by designing corresponding long amplicon primer sets,making it a potential universal method for rapid and accurate bacteria identification in food safety.展开更多
In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower...In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower (Helianthus annuus L.) inbred lines. Results indicated that factors for a successful multiplex PCR assay were related to the cycling touchdown annealing temperature, the balance of primer concentration at the various loci, the concentration of PCR buffer and the Taq DNA polymerase. Based on the optimization, a tailed primer strategy was outlined, and the effective ways were proposed to overcome the troubleshootings commonly encountered in the multiplex PCR and the multiplex gel electrophoresis.展开更多
In this paper, a new partial transmit sequence（PTS）scheme with low computational complexity is proposed for the problems of high computational complexity in the conventional PTS method. By analyzing the relationship...In this paper, a new partial transmit sequence（PTS）scheme with low computational complexity is proposed for the problems of high computational complexity in the conventional PTS method. By analyzing the relationship of candidate sequences in the PTS method under the interleaved partition method, it has been discovered that some candidate sequences generated by phase factor sequences have the same peak average power ratio（PAPR）. Hence, phase factor sequences can be optimized to reduce their searching times. Then, the computational process of generating candidate sequences can be simplified by improving the utilization of data and minimizing the calculations of complex multiplication. The performance analysis shows that, compared with the conventional PTS scheme, the proposed approach significantly decreases the computational complexity and has no loss of PAPR performance.展开更多
Efforts have been made to establish various human pluripotent stem cell lines.However,such methods have not yet been duplicated in non-human primate cells.Here,we introduce a multiplexed single-cell sequencing techniq...Efforts have been made to establish various human pluripotent stem cell lines.However,such methods have not yet been duplicated in non-human primate cells.Here,we introduce a multiplexed single-cell sequencing technique to profile the molecular features of monkey pluripotent stem cells in published culture conditions.The results demonstrate suboptimized maintenance of pluripotency and show that the selected signaling pathways for resetting human stem cells can also be interpreted for establishing monkey cell lines.Overall,this work legitimates the translation of novel human cell line culture conditions to monkey cells and provides guidance for exploring chemical cocktails for monkey stem cell line derivation.展开更多
This paper deals with optimal training design and placement over multiple orthogonal frequency division multiplexing(OFDM) symbols for the least squares(LS) channel estimation in multiple-input multipleoutput(MIMO) OF...This paper deals with optimal training design and placement over multiple orthogonal frequency division multiplexing(OFDM) symbols for the least squares(LS) channel estimation in multiple-input multipleoutput(MIMO) OFDM systems.First,the optimal pilot sequences over multiple OFDM symbols are derived by co-cyclic Jacket matrices based on the minimum mean square error(MSE) of the LS channel estimation.Then,an enhanced channel estimation method using sliding window is proposed to improve further the performance for the optimal pilot sequences in fast-varying channels.Simulation results show that the enhancedmethod can efficiently improve the performances for the optimal pilot sequences over two and four OFDM symbols,especially in fast-varying channels.展开更多
Partial transmit sequence (PTS) is a promising technique for peak-to-average power ratio (PAPR) re-duction in orthogonal frequency division multiplexing (OFDM). While in optimal PTS, an exhaustive search for all combi...Partial transmit sequence (PTS) is a promising technique for peak-to-average power ratio (PAPR) re-duction in orthogonal frequency division multiplexing (OFDM). While in optimal PTS, an exhaustive search for all combinations of phase factor sequences is required, this results in huge computation. In this paper, by introducing the orthogonal design, a phase factor sequences algorithm is proposed. The algorithm uses orthogonal table to gen-erate phase factor sequences, and the regular PAPR computation result is then followed by the parameter estima-tion. The simulation result shows that the proposed algorithm reduces the computation notably and obtains a good PAPR performance approaching the optimal PTS.展开更多
文摘New sequencing technologies such as Illumina/Solexa, SOLiD/ABI, and 454/Roche, revolutionized the biological researches. In this context, the SOLiD platform has a particular sequencing type, known as multiplex run, which enables the sequencing of several samples in a single run. It implies in cost reduction and simplifies the analysis of related samples. Meanwhile, this sequencing type requires an additional filtering step to ensure the reliability of the results. Thus, we propose in this paper a probabilistic model which considers the intrinsic characteristics of each sequencing to characterize multiplex runs and filter low-quality data, increasing the data analysis reliability of multiplex sequencing performed on SOLiD. The results show that the proposed model proves to be satisfactory due to: 1) identification of faults in the sequencing process;2) adaptation and development of new protocols for sample preparation;3) the assignment of a degree of confidence to the data generated;and 4) guiding a filtering process, without discarding useful sequences in an arbitrary manner.
基金supported by the grants of the National Key Research Program(2024YFF0618101)the National Key Research Program(2023YFF0611500)the Hainan Key Research Program(ZDYF2022XDNY248).
文摘The occurrence of Pseudomonas aeruginosa(P.aeruginosa)contamination in packaged drinking water has become a significant public health concern.Accurate,specific and rapid detection of P.aeruginosa in drinking water is crucial to safeguard public health.In this study,we developed a multiplex PCR assisted real-time nanopore sequencing method for rapid and accurate identification of target P.aeruginosa.Three primer sets of long amplicons with non-overlapping sequences were designed.By combining real-time sequencing,the time-varying current signals captured by nanopore proteins were used for real-time identification of the sequence information of the measured strand using the portable nanopore gene sequencing device.Rapid and on-site identification of P.aeruginosa in packaged drinking water were achieved through real-time bioinformatics analysis.The total time of sequence-based identification could be completed in less than 220 min from sampling to the final results output.Interestingly,with our designed multiplex PCR assisted strategy,the core sequencing operations were completed in just 5 min,and the detection limit could be achieved as 10^(2) CFU/250 mL without pre-culture treatment.Of greater significance,this multiplex PCR assisted real-time sequencing strategy can be applied for the identification of other common bacteria by designing corresponding long amplicon primer sets,making it a potential universal method for rapid and accurate bacteria identification in food safety.
文摘In an effort to simplify the procedure and to reduce the cost of fluorescence SSR analysis, the conditions of the multiplex PCR and the multiplex gel electrophoresis were optimized in the genetic analysis of sunflower (Helianthus annuus L.) inbred lines. Results indicated that factors for a successful multiplex PCR assay were related to the cycling touchdown annealing temperature, the balance of primer concentration at the various loci, the concentration of PCR buffer and the Taq DNA polymerase. Based on the optimization, a tailed primer strategy was outlined, and the effective ways were proposed to overcome the troubleshootings commonly encountered in the multiplex PCR and the multiplex gel electrophoresis.
基金supported by the National Natural Science Foundation of China(6167309361370152)the Science and Technology Project of Shenyang(F16-205-1-01)
文摘In this paper, a new partial transmit sequence（PTS）scheme with low computational complexity is proposed for the problems of high computational complexity in the conventional PTS method. By analyzing the relationship of candidate sequences in the PTS method under the interleaved partition method, it has been discovered that some candidate sequences generated by phase factor sequences have the same peak average power ratio（PAPR）. Hence, phase factor sequences can be optimized to reduce their searching times. Then, the computational process of generating candidate sequences can be simplified by improving the utilization of data and minimizing the calculations of complex multiplication. The performance analysis shows that, compared with the conventional PTS scheme, the proposed approach significantly decreases the computational complexity and has no loss of PAPR performance.
基金supported by the National Key R&D Program of China(Nos.2021YFA0805700 and 2021YFA1102000)the National Natural Science Foundation of China(No.U2102204)the Natural Science Foundation of Yunnan Province,China(Nos.202001BC070001 and 202102AA100053)。
文摘Efforts have been made to establish various human pluripotent stem cell lines.However,such methods have not yet been duplicated in non-human primate cells.Here,we introduce a multiplexed single-cell sequencing technique to profile the molecular features of monkey pluripotent stem cells in published culture conditions.The results demonstrate suboptimized maintenance of pluripotency and show that the selected signaling pathways for resetting human stem cells can also be interpreted for establishing monkey cell lines.Overall,this work legitimates the translation of novel human cell line culture conditions to monkey cells and provides guidance for exploring chemical cocktails for monkey stem cell line derivation.
基金the National Natural Science Foundation of China (Nos. 60332030 and 60625103)the Science and Technology Commission of Shanghai Municipality (STCSM) (No. 05DZ22102)the National High Technology Research and Development Program(863) of China (No. 2007AA01Z237)
文摘This paper deals with optimal training design and placement over multiple orthogonal frequency division multiplexing(OFDM) symbols for the least squares(LS) channel estimation in multiple-input multipleoutput(MIMO) OFDM systems.First,the optimal pilot sequences over multiple OFDM symbols are derived by co-cyclic Jacket matrices based on the minimum mean square error(MSE) of the LS channel estimation.Then,an enhanced channel estimation method using sliding window is proposed to improve further the performance for the optimal pilot sequences in fast-varying channels.Simulation results show that the enhancedmethod can efficiently improve the performances for the optimal pilot sequences over two and four OFDM symbols,especially in fast-varying channels.
基金Supported by Tianjin Natural Science Foundation (No. 043600611)Key Scientific and Technological Training Program of Tianjin (No. 043102911).
文摘Partial transmit sequence (PTS) is a promising technique for peak-to-average power ratio (PAPR) re-duction in orthogonal frequency division multiplexing (OFDM). While in optimal PTS, an exhaustive search for all combinations of phase factor sequences is required, this results in huge computation. In this paper, by introducing the orthogonal design, a phase factor sequences algorithm is proposed. The algorithm uses orthogonal table to gen-erate phase factor sequences, and the regular PAPR computation result is then followed by the parameter estima-tion. The simulation result shows that the proposed algorithm reduces the computation notably and obtains a good PAPR performance approaching the optimal PTS.
