Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with Nan...Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with NanoTrans,we present an integrated computational framework that comprehensively covers all major DRS-based application scopes,including isoform clustering and quantification,poly(A)tail length estimation,RNA modification profiling,and fusion gene detection.In addition to its merit in providing such a streamlined one-stop solution,NanoTrans also shines in its workflow-orientated modular design,batch processing capability,all-in-one tabular and graphic report output,as well as automatic installation and configuration supports.Finally,by applying NanoTrans to real DRS datasets of yeast,Arabidopsis,as well as human embryonic kidney and cancer cell lines,we further demonstrate its utility,effectiveness,and efficacy across a wide range of DRS-based application settings.展开更多
Over the past decade,nanopore sequencing has experienced significant advancements and changes,transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing.However,...Over the past decade,nanopore sequencing has experienced significant advancements and changes,transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing.However,as advancements in next-generation sequencing technology persist,nanopore sequencing also improves.This paper reviews the developments,applications,and outlook on nanopore sequencing technology.Currently,nanopore sequencing supports both DNA and RNA sequencing,making it widely applicable in areas such as telomere-to-telomere(T2T)genome assembly,direct RNA sequencing(DRS),and metagenomics.The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams,signaling a transformative influence on life science research.As the nanopore sequencing technology advances,it provides a faster,more costeffective approach with extended read lengths,demonstrating the significant potential for complex genome assembly,pathogen detection,environmental monitoring,and human disease research,offering a fresh perspective in sequencing technologies.展开更多
According to the requirements of the high-sensitivity acquisition of Direct Sequence Spread Spectrum(DSSS) signals under ultrahigh dynamic environments in space communications, a three-dimensional joint search of the ...According to the requirements of the high-sensitivity acquisition of Direct Sequence Spread Spectrum(DSSS) signals under ultrahigh dynamic environments in space communications, a three-dimensional joint search of the phase of Pseudo-Noise-code(PN-code),Doppler frequency and its rate-of-change is presented to achieve high sensitivity in sensing high-frequency dynamics. By eliminating the correlation peak loss caused by ultrahigh Doppler frequency and its rate-of-change offset,the proposed method improves the acquisition sensitivity by increasing the non-coherent accumulation time. The validity of the algorithm is proved by theoretical analysis and simulation results. It is shown that signals with a carrier- to-noise ratio as low as 39 dBHz can be captured with high performance when the Doppler frequency is up to ±1 MHz and its rate-of-change is up to ±200 kHz/s.展开更多
Serveral methods for the pararrel acquisition of a PN sequence in a baseband direct sequence spread spectrum system are investigated. Four different kinds of schemes are considered: the optimal estimation scheme, the ...Serveral methods for the pararrel acquisition of a PN sequence in a baseband direct sequence spread spectrum system are investigated. Four different kinds of schemes are considered: the optimal estimation scheme, the locally optimal estimation scheme, the optimal testing searches and the locally optimal testing scheme. In the four kinds of parallel acquisition schemes, the expressions for the probability of error are given and compared with the actual error probabilities obtained via Monte Carlo simulation. We also outline a technique that can be suboptimal because of a large amount of hardware and computation when using the parallel acquisition schemes.展开更多
A novel direct sequence （DS） design method for suppressing the narrowband interference in DS spread spectrum ultra-wideband receivers is proposed. The method has low computational complexity and can be easily implem...A novel direct sequence （DS） design method for suppressing the narrowband interference in DS spread spectrum ultra-wideband receivers is proposed. The method has low computational complexity and can be easily implemented in practical systems. Simulation results prove that the proposed method is effective to suppress the narrowband interference. Therefore, the integrity of both the ultra-wide bandwidth and the narrowband systems can be highly enhanced.展开更多
Aiming at improving acquisition performance for direct sequence spread spectrum （DSSS） signals, a new acquisition algorithm based on fast Fourier transform （FFT） is proposed. The code phases are parallel searched ...Aiming at improving acquisition performance for direct sequence spread spectrum （DSSS） signals, a new acquisition algorithm based on fast Fourier transform （FFT） is proposed. The code phases are parallel searched throughout the Doppler frequency domain. Since the influence of Doppler frequency errors on peak-to- average ratios of correlation power shows a pattern similar to the sinc function, it is our belief that by judging on peak-to-average ratios for different Doppler frequency errors false alarm probabilities should be lowered. Analyses have supported the underlying principle of this new algorithm. Simulation results have also indicated that the new algorithm can effectively improve the acquisition performance for DSSS signals.展开更多
For direct sequence spread spectrum (DSSS) communication systems suffering interference, it is known that code-aided interference suppression technique outperforms all of the previous linear or nonlinear methods. In t...For direct sequence spread spectrum (DSSS) communication systems suffering interference, it is known that code-aided interference suppression technique outperforms all of the previous linear or nonlinear methods. In this paper, we proposed an improved code-aided technique which can improve the system performance greatly by using the eigenvector sign (EVS) spreading sequence which depends on the statistical characteristics of the interference and the thermal noise.展开更多
Performances of BPSK, balanced quaternary modulation, dual quaternary modulation and complex quaternary modulation in direct sequence spectrum spread (DS SS) system are discussed in this paper. Based on the crit...Performances of BPSK, balanced quaternary modulation, dual quaternary modulation and complex quaternary modulation in direct sequence spectrum spread (DS SS) system are discussed in this paper. Based on the criterion the power of original signal is the same, it is shown that complex quaternary modulation has the best performance, and dual quaternary modulation degrades 2dB. Moreover, the frequency efficient of the two modulations is 2bit/Hz. Balanced quaternary has the same performance as BPSK with frequency efficient 1bit/Hz.展开更多
The transcriptome serves as a bridge that links genomic variation to phenotypic diversity.A vast number of studies using next-generation RNA sequencing(RNA-seq)over the last 2 decades have emphasized the essential rol...The transcriptome serves as a bridge that links genomic variation to phenotypic diversity.A vast number of studies using next-generation RNA sequencing(RNA-seq)over the last 2 decades have emphasized the essential roles of the plant transcriptome in response to developmental and environmental conditions,providing numerous insights into the dynamic changes,evolutionary traces,and elaborate regulation of the plant transcriptome.With substantial improvement in accuracy and throughput,direct RNA sequencing(DRS)has emerged as a new and powerful sequencing platform for precise detection of native and full-length transcripts,overcoming many limitations such as read length and PCR bias that are inherent to short-read RNA-seq.Here,we review recent advances in dissecting the complexity and diversity of plant transcriptomes using DRS as the main technological approach,covering many aspects of RNA metabolism,including novel isoforms,poly(A)tails,and RNA modification,and we propose a comprehensive workflow for processing of plant DRS data.Many challenges to the application of DRS in plants,such as the need for machine learning tools tailored to plant transcriptomes,remain to be overcome,and together we outline future biological questions that can be addressed by DRS,such as allele-specific RNA modification.This technology provides convenient support on which the connection of distinct RNA features is tightly built,sustainably refining our understanding of the biological functions of the plant transcriptome.展开更多
The performance of multi-user code to direct spreading bi-phase shift keying （DS-BPSK） direct impulse ultra wideband （UWB） systems under indoor multi-user and multi-path environment is analyzed and simulated. The ...The performance of multi-user code to direct spreading bi-phase shift keying （DS-BPSK） direct impulse ultra wideband （UWB） systems under indoor multi-user and multi-path environment is analyzed and simulated. The system output signals with Rake receiver are derived, then a simple and practical code selection scheme is given; i. e., with a large occupation to empty ratio of the repeating pulses, directly choosing those random or pseudo-random user codes with enough length and good co-relative orthogonal features will make the performance of DS-BPSK approximate the optimum and, so there is no need to carefully design the code or its type. The system multi-access performances are simulated using Gold sequence and PN codes as multi-user codes under CMI-CM4 multi-path channels. Simulation results prove that the proposed scheme is feasible.展开更多
In this paper, direct sequence spread spectrum multiple access (DS/SSMA) communication system employing serially concatenated trellis coded modulation (TCM) and continuous phase modulation (CPM) over flat Rayleigh fa...In this paper, direct sequence spread spectrum multiple access (DS/SSMA) communication system employing serially concatenated trellis coded modulation (TCM) and continuous phase modulation (CPM) over flat Rayleigh fading channel are presented. The performance of this concatenated TCM/CPM DS/SSMA system is exploited by the theoretical analysis and numerical simulations. The results demonstrate that significant improvements in error probability of this DS/SSMA system over the system with single TCM or CPM of different modulation indices can be achieved under the same conditions.展开更多
Geminiviruses, in particular the members of the genus Begomovirus , are considered to be a major phytosanitary problem for tomato crops production in the world. They are responsible for yield losses of up to 20% to 10...Geminiviruses, in particular the members of the genus Begomovirus , are considered to be a major phytosanitary problem for tomato crops production in the world. They are responsible for yield losses of up to 20% to 100%. Regrettably, Togo is not spared from this situation. This work aims to show the genetic diversity of the begomoviruses affecting tomato crops production in Togo and their relationship with other begomoviruses. To achieve these objectives, 307 samples of tomato leaves and wild plant species with typical virus symptoms were collected in the Maritime, Plateaus, Central, Kara and Savannah regions and submitted to PCR analysis. The results revealed the presence of begomovirus in 25.40% of the analyzed samples. The PCR products obtained were submitted to direct sequencing. Phylogenetic analysis of sequences of DNA-A different regions of begomovirus identified in this work with that of other begomoviruses showed a nucleotide identity of 96% respectively for Tomato leaf curl Togo virus-Fontem, Tomato Leaf Curl Togo Virus , Ageratum leaf curl Cameroon Alphasatellite;98% respectively to Tomato leaf curl Nigeria virus , Ageratum leaf curl Cameroon virus , Tomato leaf curl Cameroon virus-Fontem, Ageratum leaf curl Cameroon virus and 99% respectively to Tomato leaf curl Kumasi virus , Pepper yellow vein Mali virus Bazegahot and Pepper yellow vein Mali virus-Ouaga. These results suggest a high degree of genetic diversity of tomato begomoviruses identified in Togo.展开更多
It is a necessary step to estimate the spreading sequence of direct sequence spread spectrum （DSSS） signal for blind despreading and demodulation in non-cooperative communications. Two innovative and effective detec...It is a necessary step to estimate the spreading sequence of direct sequence spread spectrum （DSSS） signal for blind despreading and demodulation in non-cooperative communications. Two innovative and effective detection statistics are proposed to implement the synchronization and spreading sequence estimation procedure. The proposed algorithm also has a low computational complexity with only linear additions and modifications. Theoretical analysis and simulation results show that the algorithm performs quite well in low SNR environment, and is much better than all the existing typical algorithms with a comprehensive consideration both in performance and computational complexity.展开更多
To estimate the spreading sequence of the direct sequence spread spectrum (DSSS) signal, a fast algorithm based on maximum likelihood function is proposed, and the theoretical derivation of the algorithm is provided. ...To estimate the spreading sequence of the direct sequence spread spectrum (DSSS) signal, a fast algorithm based on maximum likelihood function is proposed, and the theoretical derivation of the algorithm is provided. By simplifying the objective function of maximum likelihood estimation, the algorithm can realize sequence synchronization and sequence estimation via adaptive iteration and sliding window. Since it avoids the correlation matrix computation, the algorithm significantly reduces the storage requirement and the computation complexity. Simulations show that it is a fast convergent algorithm, and can perform well in low signal to noise ratio (SNR).展开更多
This paper presents an approach of singular value de- composition plus digital phase lock loop to solve the difficult problem of blind pseudo-noise （PN） sequence estimation in low signal to noise ratios （SNR） dire...This paper presents an approach of singular value de- composition plus digital phase lock loop to solve the difficult problem of blind pseudo-noise （PN） sequence estimation in low signal to noise ratios （SNR） direct sequence spread spectrum （DS-SS） signals with residual carrier. This approach needs some given parameters, such as the period and code rate of PN sequence. The received signal is firstly sampled and divided into non-overlapping signal vectors according to a temporal window, whose duration is two periods of PN sequence. An autocorrelation matrix is then computed and accumulated by those signal vectors one by one. The PN sequence with residual carrier can be estimated by the principal eigenvector of the autocorrelation matrix. Further more, a digital phase lock loop is used to process the estimated PN sequence, it estimates and tracks the residual carrier and removes the residual carrier in the end. Theory analysis and computer simulation results show that this approach can effectively realize the PN sequence blind estimation from the input DS-SS signals with residual carrier in lower SNR.展开更多
In hybrid Direct Sequence/Frequency Hopping Spread Spectrum （DS/FH SS） system, the fast acquisition is a key technique. A combined fast scanning and waiting method for FH acquisition is introduced, and a neural netw...In hybrid Direct Sequence/Frequency Hopping Spread Spectrum （DS/FH SS） system, the fast acquisition is a key technique. A combined fast scanning and waiting method for FH acquisition is introduced, and a neural network for DS acquisition is presented also. Using these two methods, the fast acquisition of the hybrid DS/FH SS system can be realized.展开更多
An approach based on discrete Karhunen-Loeve transformation of the DS/SS signals is proposed to estimate PN sequence in lower S/N ratio DS/SS signals. Characteristics of self-organization and principle components extr...An approach based on discrete Karhunen-Loeve transformation of the DS/SS signals is proposed to estimate PN sequence in lower S/N ratio DS/SS signals. Characteristics of self-organization and principle components extraction of unsupervised neural networks are exploited adequately. Theoretical analysis and experimental results are provided to show that this approach can work well on the lower S/N ratio input signals.展开更多
Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,the cDNA dependence of most RNA sequencing techniques constrains their ability...Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA,which is an important element for the post-transcriptional regulation of gene expression.To comprehensively profile the N^(6)-methyladenosine(m^(6)A)and N^(5)-methylcytosine(m5 C)modifications on RNA,direct RNA sequencing(DRS)using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice.Approximately 94 million reads were generated,with an average length ranging from 619 nt to 1013 nt,and a total of 45,707 transcripts across 34,763 genes were detected.Expression profiles of transcripts at the isoform level were quantified among tissues.Transcriptome-wide mapping of m^(6)A and m5 C demonstrated that both modifications exhibited tissue-specific characteristics.The transcripts with m^(6)A modifications tended to be modified by m5 C,and the transcripts with modifications presented higher expression levels along with shorter poly(A)tails than transcripts without modifications,suggesting the complexity of gene expression regulation.Gene Ontology analysis demonstrated that m^(6)A-and m5 C-modified transcripts were involved in central metabolic pathways related to the life cycle,with modifications on the target genes selected in a tissue-specific manner.Furthermore,most modified sites were located within quantitative trait loci that control important agronomic traits,highlighting the value of cloning functional loci.The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome,improving our understanding of the rice genome.展开更多
Tomato fruit are sensitive to chilling injury(CI)during cold storage.Several factors have been discovered to be involved in chilling injury of tomato fruit.Plant hormones play an important regulatory role,however,the ...Tomato fruit are sensitive to chilling injury(CI)during cold storage.Several factors have been discovered to be involved in chilling injury of tomato fruit.Plant hormones play an important regulatory role,however,the relationship between chilling injury and N6-methyladenosine(m^(6)A)methylation of transcripts in plant hormone pathways has not been reported yet.In order to clarify the complex regulatory mechanism of m^(6)A methylation on chilling injury in tomato fruit,Nanopore direct RNA sequencing was employed.A large number of enzymes and transcription factors were found to be involved in the regulation process of fruit chilling injury,which were associated with plant hormone,such as 1-aminocyclopropane 1-carboxylate synthase(ACS),aspartate aminotransferase(AST),auxin response factor(ARF2),ethylene response factor 2(ERF2),gibberellin 20-oxidase-3(GA20ox)and jasmonic acid(JA).By conjoint analysis of the differential expression transcripts related to chilling injury andm^(6)Amethylation differential expression transcripts 41 differential expression transcripts were identified involved in chilling injury including 1-aminocyclopropane-1-carboxylate oxidase(ACO)and pectinesterase(PE)were down-regulated and heat shock cognate 70 kD protein 2(cpHSC70),HSP70-binding protein(HspBP)and salicylic acid-binding protein 2(SABP2)were up-regulated.Our results will provide a deeper understanding for chilling injury regulatory mechanism and post-harvest cold storage of tomato fruit.展开更多
For direct sequence spread spectrum （DSSS） receivers, the capability of rejecting narrow-band interference can be significantly improved by a process of frequency-domain interference suppression （FDIS）. The key is...For direct sequence spread spectrum （DSSS） receivers, the capability of rejecting narrow-band interference can be significantly improved by a process of frequency-domain interference suppression （FDIS）. The key issue of this process is how to determine a threshold to eliminate interference in the frequency domain, which has been extensively studied. However, these previous methods are tedious or very complex. A simple and ef- ficient algorithm based on medians is proposed. The elimination threshold is only related to the median by a scale factor, which can be obtained by the numerical analysis. Simulation results show that the algorithm provides excellent narrow-band interfer- ence suppression while only slightly degrading the signal-to-noise ratio （SNR）. A one-pass algorithm using logarithmic segmentation is further derived to estimate medians with low computational complexity. Finally, the FDIS is implemented in a field programmable gate array （FPGA） of Xilinx. Experiments are carried out by connecting the FDIS FPGA to a DSSS receiver, and the results show that the receiver has an effective countermeasure for a 60 dB interference-to-signal ratio （ISR）.展开更多
基金facility support from the Single-Molecule Sequencing Platform at Sun Yat-sen University Cancer Center.This work is supported by the National Natural Science Foundation of China(32070592 to JXY,32000395 to JL,82272789 to LZ)Guangdong Basic and Applied Basic Research Foundation(2022A1515010717 and 2019A1515110762 to JXY and 2022A1515011873 to JL)+2 种基金Guangdong Pearl River Talents Program(2019QN01Y183 to JXY,2021QN02Y168 to JL)Guangzhou Municipal Science and Technology Bureau(202102020938 to JL)Young Talents Program of Sun Yat-sen University Cancer Center(YTP-SYSUCC-0042 to JXY and YTP-SYSUCC-0040 to JL)。
文摘Nanopore direct RNA sequencing(DRS)provides the direct access to native RNA strands with full-length information,shedding light on rich qualitative and quantitative properties of gene expression profiles.Here with NanoTrans,we present an integrated computational framework that comprehensively covers all major DRS-based application scopes,including isoform clustering and quantification,poly(A)tail length estimation,RNA modification profiling,and fusion gene detection.In addition to its merit in providing such a streamlined one-stop solution,NanoTrans also shines in its workflow-orientated modular design,batch processing capability,all-in-one tabular and graphic report output,as well as automatic installation and configuration supports.Finally,by applying NanoTrans to real DRS datasets of yeast,Arabidopsis,as well as human embryonic kidney and cancer cell lines,we further demonstrate its utility,effectiveness,and efficacy across a wide range of DRS-based application settings.
基金financially supported by the Natural Science Foundation of China(32470055 and U23A20148)the China Postdoctoral Science Foundation(2024M753580)the Agricultural Science and Technology Innovation Program(CAAS-ZDRW202308)。
文摘Over the past decade,nanopore sequencing has experienced significant advancements and changes,transitioning from an initially emerging technology to a significant instrument in the field of genomic sequencing.However,as advancements in next-generation sequencing technology persist,nanopore sequencing also improves.This paper reviews the developments,applications,and outlook on nanopore sequencing technology.Currently,nanopore sequencing supports both DNA and RNA sequencing,making it widely applicable in areas such as telomere-to-telomere(T2T)genome assembly,direct RNA sequencing(DRS),and metagenomics.The openness and versatility of nanopore sequencing have established it as a preferred option for an increasing number of research teams,signaling a transformative influence on life science research.As the nanopore sequencing technology advances,it provides a faster,more costeffective approach with extended read lengths,demonstrating the significant potential for complex genome assembly,pathogen detection,environmental monitoring,and human disease research,offering a fresh perspective in sequencing technologies.
基金supported by the Youth Science Fund,National Natural Science Foundation of China under Grant No.61102130
文摘According to the requirements of the high-sensitivity acquisition of Direct Sequence Spread Spectrum(DSSS) signals under ultrahigh dynamic environments in space communications, a three-dimensional joint search of the phase of Pseudo-Noise-code(PN-code),Doppler frequency and its rate-of-change is presented to achieve high sensitivity in sensing high-frequency dynamics. By eliminating the correlation peak loss caused by ultrahigh Doppler frequency and its rate-of-change offset,the proposed method improves the acquisition sensitivity by increasing the non-coherent accumulation time. The validity of the algorithm is proved by theoretical analysis and simulation results. It is shown that signals with a carrier- to-noise ratio as low as 39 dBHz can be captured with high performance when the Doppler frequency is up to ±1 MHz and its rate-of-change is up to ±200 kHz/s.
文摘Serveral methods for the pararrel acquisition of a PN sequence in a baseband direct sequence spread spectrum system are investigated. Four different kinds of schemes are considered: the optimal estimation scheme, the locally optimal estimation scheme, the optimal testing searches and the locally optimal testing scheme. In the four kinds of parallel acquisition schemes, the expressions for the probability of error are given and compared with the actual error probabilities obtained via Monte Carlo simulation. We also outline a technique that can be suboptimal because of a large amount of hardware and computation when using the parallel acquisition schemes.
文摘A novel direct sequence （DS） design method for suppressing the narrowband interference in DS spread spectrum ultra-wideband receivers is proposed. The method has low computational complexity and can be easily implemented in practical systems. Simulation results prove that the proposed method is effective to suppress the narrowband interference. Therefore, the integrity of both the ultra-wide bandwidth and the narrowband systems can be highly enhanced.
基金Sponsored by the National "863" Program Project (1010021310XXX)
文摘Aiming at improving acquisition performance for direct sequence spread spectrum （DSSS） signals, a new acquisition algorithm based on fast Fourier transform （FFT） is proposed. The code phases are parallel searched throughout the Doppler frequency domain. Since the influence of Doppler frequency errors on peak-to- average ratios of correlation power shows a pattern similar to the sinc function, it is our belief that by judging on peak-to-average ratios for different Doppler frequency errors false alarm probabilities should be lowered. Analyses have supported the underlying principle of this new algorithm. Simulation results have also indicated that the new algorithm can effectively improve the acquisition performance for DSSS signals.
基金the National Natural Science Foundation of China (No. 60772100)
文摘For direct sequence spread spectrum (DSSS) communication systems suffering interference, it is known that code-aided interference suppression technique outperforms all of the previous linear or nonlinear methods. In this paper, we proposed an improved code-aided technique which can improve the system performance greatly by using the eigenvector sign (EVS) spreading sequence which depends on the statistical characteristics of the interference and the thermal noise.
基金ThisprojectwassupportedbytheKeyProjectoftheNaturalScienceFoundationofChina (No .6 98310 30 )
文摘Performances of BPSK, balanced quaternary modulation, dual quaternary modulation and complex quaternary modulation in direct sequence spectrum spread (DS SS) system are discussed in this paper. Based on the criterion the power of original signal is the same, it is shown that complex quaternary modulation has the best performance, and dual quaternary modulation degrades 2dB. Moreover, the frequency efficient of the two modulations is 2bit/Hz. Balanced quaternary has the same performance as BPSK with frequency efficient 1bit/Hz.
基金Guangxi Natural Science Foundation(2024GXNSFGA010003)National Natural Science Foundation of China(32270712 and 31871269)Guangxi Science and Technology Major Program(AA23062085).
文摘The transcriptome serves as a bridge that links genomic variation to phenotypic diversity.A vast number of studies using next-generation RNA sequencing(RNA-seq)over the last 2 decades have emphasized the essential roles of the plant transcriptome in response to developmental and environmental conditions,providing numerous insights into the dynamic changes,evolutionary traces,and elaborate regulation of the plant transcriptome.With substantial improvement in accuracy and throughput,direct RNA sequencing(DRS)has emerged as a new and powerful sequencing platform for precise detection of native and full-length transcripts,overcoming many limitations such as read length and PCR bias that are inherent to short-read RNA-seq.Here,we review recent advances in dissecting the complexity and diversity of plant transcriptomes using DRS as the main technological approach,covering many aspects of RNA metabolism,including novel isoforms,poly(A)tails,and RNA modification,and we propose a comprehensive workflow for processing of plant DRS data.Many challenges to the application of DRS in plants,such as the need for machine learning tools tailored to plant transcriptomes,remain to be overcome,and together we outline future biological questions that can be addressed by DRS,such as allele-specific RNA modification.This technology provides convenient support on which the connection of distinct RNA features is tightly built,sustainably refining our understanding of the biological functions of the plant transcriptome.
文摘The performance of multi-user code to direct spreading bi-phase shift keying （DS-BPSK） direct impulse ultra wideband （UWB） systems under indoor multi-user and multi-path environment is analyzed and simulated. The system output signals with Rake receiver are derived, then a simple and practical code selection scheme is given; i. e., with a large occupation to empty ratio of the repeating pulses, directly choosing those random or pseudo-random user codes with enough length and good co-relative orthogonal features will make the performance of DS-BPSK approximate the optimum and, so there is no need to carefully design the code or its type. The system multi-access performances are simulated using Gold sequence and PN codes as multi-user codes under CMI-CM4 multi-path channels. Simulation results prove that the proposed scheme is feasible.
文摘In this paper, direct sequence spread spectrum multiple access (DS/SSMA) communication system employing serially concatenated trellis coded modulation (TCM) and continuous phase modulation (CPM) over flat Rayleigh fading channel are presented. The performance of this concatenated TCM/CPM DS/SSMA system is exploited by the theoretical analysis and numerical simulations. The results demonstrate that significant improvements in error probability of this DS/SSMA system over the system with single TCM or CPM of different modulation indices can be achieved under the same conditions.
基金the West African Agricultural Productivity Program(WAAPP/TOGO)and Bill and Melinda Gates Foundation(BMGF)for supporting this project.
文摘Geminiviruses, in particular the members of the genus Begomovirus , are considered to be a major phytosanitary problem for tomato crops production in the world. They are responsible for yield losses of up to 20% to 100%. Regrettably, Togo is not spared from this situation. This work aims to show the genetic diversity of the begomoviruses affecting tomato crops production in Togo and their relationship with other begomoviruses. To achieve these objectives, 307 samples of tomato leaves and wild plant species with typical virus symptoms were collected in the Maritime, Plateaus, Central, Kara and Savannah regions and submitted to PCR analysis. The results revealed the presence of begomovirus in 25.40% of the analyzed samples. The PCR products obtained were submitted to direct sequencing. Phylogenetic analysis of sequences of DNA-A different regions of begomovirus identified in this work with that of other begomoviruses showed a nucleotide identity of 96% respectively for Tomato leaf curl Togo virus-Fontem, Tomato Leaf Curl Togo Virus , Ageratum leaf curl Cameroon Alphasatellite;98% respectively to Tomato leaf curl Nigeria virus , Ageratum leaf curl Cameroon virus , Tomato leaf curl Cameroon virus-Fontem, Ageratum leaf curl Cameroon virus and 99% respectively to Tomato leaf curl Kumasi virus , Pepper yellow vein Mali virus Bazegahot and Pepper yellow vein Mali virus-Ouaga. These results suggest a high degree of genetic diversity of tomato begomoviruses identified in Togo.
基金supported by the Specialized Research Fund for the Doctoral Program of Higher Education (20060003032)
文摘It is a necessary step to estimate the spreading sequence of direct sequence spread spectrum （DSSS） signal for blind despreading and demodulation in non-cooperative communications. Two innovative and effective detection statistics are proposed to implement the synchronization and spreading sequence estimation procedure. The proposed algorithm also has a low computational complexity with only linear additions and modifications. Theoretical analysis and simulation results show that the algorithm performs quite well in low SNR environment, and is much better than all the existing typical algorithms with a comprehensive consideration both in performance and computational complexity.
基金supported by Joint Foundation of and China Academy of Engineering Physical (10676006)
文摘To estimate the spreading sequence of the direct sequence spread spectrum (DSSS) signal, a fast algorithm based on maximum likelihood function is proposed, and the theoretical derivation of the algorithm is provided. By simplifying the objective function of maximum likelihood estimation, the algorithm can realize sequence synchronization and sequence estimation via adaptive iteration and sliding window. Since it avoids the correlation matrix computation, the algorithm significantly reduces the storage requirement and the computation complexity. Simulations show that it is a fast convergent algorithm, and can perform well in low signal to noise ratio (SNR).
基金supported by the National Natural Science Foundation of China (10776040 60602057)+4 种基金Program for New Century Excellent Talents in University (NCET)the Project of Key Laboratory of Signal and Information Processing of Chongqing (CSTC2009CA2003)the Natural Science Foundation of Chongqing Science and Technology Commission (CSTC2009BB2287)the Natural Science Foundation of Chongqing Municipal Education Commission (KJ060509 KJ080517)
文摘This paper presents an approach of singular value de- composition plus digital phase lock loop to solve the difficult problem of blind pseudo-noise （PN） sequence estimation in low signal to noise ratios （SNR） direct sequence spread spectrum （DS-SS） signals with residual carrier. This approach needs some given parameters, such as the period and code rate of PN sequence. The received signal is firstly sampled and divided into non-overlapping signal vectors according to a temporal window, whose duration is two periods of PN sequence. An autocorrelation matrix is then computed and accumulated by those signal vectors one by one. The PN sequence with residual carrier can be estimated by the principal eigenvector of the autocorrelation matrix. Further more, a digital phase lock loop is used to process the estimated PN sequence, it estimates and tracks the residual carrier and removes the residual carrier in the end. Theory analysis and computer simulation results show that this approach can effectively realize the PN sequence blind estimation from the input DS-SS signals with residual carrier in lower SNR.
文摘In hybrid Direct Sequence/Frequency Hopping Spread Spectrum （DS/FH SS） system, the fast acquisition is a key technique. A combined fast scanning and waiting method for FH acquisition is introduced, and a neural network for DS acquisition is presented also. Using these two methods, the fast acquisition of the hybrid DS/FH SS system can be realized.
文摘An approach based on discrete Karhunen-Loeve transformation of the DS/SS signals is proposed to estimate PN sequence in lower S/N ratio DS/SS signals. Characteristics of self-organization and principle components extraction of unsupervised neural networks are exploited adequately. Theoretical analysis and experimental results are provided to show that this approach can work well on the lower S/N ratio input signals.
基金supported by the National Natural Science Foundation of China(Grant No.31671775).
文摘Transcriptome analysis based on high-throughput sequencing of a cDNA library has been widely applied to functional genomic studies.However,the cDNA dependence of most RNA sequencing techniques constrains their ability to detect base modifications on RNA,which is an important element for the post-transcriptional regulation of gene expression.To comprehensively profile the N^(6)-methyladenosine(m^(6)A)and N^(5)-methylcytosine(m5 C)modifications on RNA,direct RNA sequencing(DRS)using the latest Oxford Nanopore Technology was applied to analyze the transcriptome of six tissues in rice.Approximately 94 million reads were generated,with an average length ranging from 619 nt to 1013 nt,and a total of 45,707 transcripts across 34,763 genes were detected.Expression profiles of transcripts at the isoform level were quantified among tissues.Transcriptome-wide mapping of m^(6)A and m5 C demonstrated that both modifications exhibited tissue-specific characteristics.The transcripts with m^(6)A modifications tended to be modified by m5 C,and the transcripts with modifications presented higher expression levels along with shorter poly(A)tails than transcripts without modifications,suggesting the complexity of gene expression regulation.Gene Ontology analysis demonstrated that m^(6)A-and m5 C-modified transcripts were involved in central metabolic pathways related to the life cycle,with modifications on the target genes selected in a tissue-specific manner.Furthermore,most modified sites were located within quantitative trait loci that control important agronomic traits,highlighting the value of cloning functional loci.The results provide new insights into the expression regulation complexity and data resource of the transcriptome and epitranscriptome,improving our understanding of the rice genome.
基金supported by grants from the National Natural Science Foundation of China(Grant Nos.31772022,32072284 and 31501544)the Special Innovation Ability Construction Fund of Beijing Academy of Agricultural and Forestry Sciences(Grant Nos.20200427 and 20210437)+4 种基金Science and Technology Planning Project of Tianjin City(Grant No.19YFSLQY00100)the Beijing Municipal Science and Technology Commission(Grant Nos.Z191100008619004 and Z191100004019010)Supported by China Agriculture Research System of MOF and MARA,collaborative innovation center of Beijing Academy of Agricultural and Forestry Sciences(Grant No.201915)the Young Investigator Fund of Beijing Academy of Agricultural and Forestry Sciences(Grant No.202016)the key scientific research projects of colleges and universities in Henan Province(Grant No.20A550014)。
文摘Tomato fruit are sensitive to chilling injury(CI)during cold storage.Several factors have been discovered to be involved in chilling injury of tomato fruit.Plant hormones play an important regulatory role,however,the relationship between chilling injury and N6-methyladenosine(m^(6)A)methylation of transcripts in plant hormone pathways has not been reported yet.In order to clarify the complex regulatory mechanism of m^(6)A methylation on chilling injury in tomato fruit,Nanopore direct RNA sequencing was employed.A large number of enzymes and transcription factors were found to be involved in the regulation process of fruit chilling injury,which were associated with plant hormone,such as 1-aminocyclopropane 1-carboxylate synthase(ACS),aspartate aminotransferase(AST),auxin response factor(ARF2),ethylene response factor 2(ERF2),gibberellin 20-oxidase-3(GA20ox)and jasmonic acid(JA).By conjoint analysis of the differential expression transcripts related to chilling injury andm^(6)Amethylation differential expression transcripts 41 differential expression transcripts were identified involved in chilling injury including 1-aminocyclopropane-1-carboxylate oxidase(ACO)and pectinesterase(PE)were down-regulated and heat shock cognate 70 kD protein 2(cpHSC70),HSP70-binding protein(HspBP)and salicylic acid-binding protein 2(SABP2)were up-regulated.Our results will provide a deeper understanding for chilling injury regulatory mechanism and post-harvest cold storage of tomato fruit.
基金supported by the National Natural Science Foundation of China(60904090)
文摘For direct sequence spread spectrum （DSSS） receivers, the capability of rejecting narrow-band interference can be significantly improved by a process of frequency-domain interference suppression （FDIS）. The key issue of this process is how to determine a threshold to eliminate interference in the frequency domain, which has been extensively studied. However, these previous methods are tedious or very complex. A simple and ef- ficient algorithm based on medians is proposed. The elimination threshold is only related to the median by a scale factor, which can be obtained by the numerical analysis. Simulation results show that the algorithm provides excellent narrow-band interfer- ence suppression while only slightly degrading the signal-to-noise ratio （SNR）. A one-pass algorithm using logarithmic segmentation is further derived to estimate medians with low computational complexity. Finally, the FDIS is implemented in a field programmable gate array （FPGA） of Xilinx. Experiments are carried out by connecting the FDIS FPGA to a DSSS receiver, and the results show that the receiver has an effective countermeasure for a 60 dB interference-to-signal ratio （ISR）.
