A modified DBSCAN algorithm is presented for deinterleaving of radar pulses in modern EW environments.A main characteristic of the proposed method is that using only time of arrival of pulses,the method can sort the p...A modified DBSCAN algorithm is presented for deinterleaving of radar pulses in modern EW environments.A main characteristic of the proposed method is that using only time of arrival of pulses,the method can sort the pulses efficiently.Other PDW information such as rise time,carrier frequency,pulse width,modulation on pulse,fall time and direction of arrival are not required.To identify the valid PRIs in a set of interleaved pulses,an innovative modification of the DBSCAN algorithm is introduced which is accurate and easy to implement.The proposed method determines valid PRIs more accurately and neglects the spurious ones more efficiently as compared to the classical histogram based algorithms such as SDIF.Furthermore,without specifying any input parameter,the proposed method can deinterleave radar pulses while up to 30%jitter is present in the associated PRI.The accuracy and efficiency of the proposed method are verified by computer simulations and real data results.Experimental simulations are based on different real and operational scenarios where the presence of missing and spurious pulses are also considered.So,the simulation results can be of practical significance.展开更多
The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes...The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes. Based on the appearance frequency of the key sequences of the genome, any DNA sequences on the genome could be expressed as a sequence spectrum with the adjoining base sequences, which could be used to study the corresponding biological phenomena. In this paper, we used 64 successive three- base sequences (triplets) as the key sequences, and determined and compared the spectra of specific genes to the chromosome, or specific genes to tRNA genes in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Escherichia coli. Based on these analyses, a gene and its corresponding position on the chromosome showed highly similar spectra with the same fold enlargement (approximately 400-fold) in the S. cerevisiae, S. pombe and E. coli genomes. In addition, the homologous structure of genes that encode proteins was also observed with appropriate tRNA gene(s) in the genome. This analytical method might faithfully reflect the encoded biological information, that is, the conservation of the base sequences was to make sense the conservation of the translated amino acids sequence in the coding region, and might be universally applicable to other genomes, even those that consisted of multiple chromosomes.展开更多
A novel diagrammtic method is proposed to show the angular distribution of bases of human protein sequences. Using this method, the distribution sphere[1-4] is divided into four regions with same volume. The picture i...A novel diagrammtic method is proposed to show the angular distribution of bases of human protein sequences. Using this method, the distribution sphere[1-4] is divided into four regions with same volume. The picture is clearer and more intuitive than that in [1] .A rule on the angular distribution of the representative points of bases of protein sequences is given. Besides, in 300 representative pointS of human protein sequence samples we find that there are three (not only one) points outside the sphere.展开更多
In this paper, we study the invertibility of sequences consisting of finitely many bounded linear operators from a Hilbert space to others. We show that a sequence of operators is left invertible if and only if it is ...In this paper, we study the invertibility of sequences consisting of finitely many bounded linear operators from a Hilbert space to others. We show that a sequence of operators is left invertible if and only if it is a g-frame. Therefore, our result connects the invertibility of operator sequences with frame theory.展开更多
The satellite-based automatic identification system (AIS) receiver has to encounter the frequency offset caused by the Doppler effect and the oscillator instability. This paper proposes a non-coherent sequence detecti...The satellite-based automatic identification system (AIS) receiver has to encounter the frequency offset caused by the Doppler effect and the oscillator instability. This paper proposes a non-coherent sequence detection scheme for the satellite-based AIS signal transmitted over the white Gaussian noise channel. Based on the maximum likelihood estimation and a Viterbi decoder, the proposed scheme is capable of tolerating a frequency offset up to 5% of the symbol rate. The complexity of the proposed scheme is reduced by the state-complexity reduction, which is based on per-survivor processing. Simulation results prove that the proposed non-coherent sequence detection scheme has high robustness to frequency offset compared to the relative scheme when messages collision exists.展开更多
A nucleic acid sequence-based amplification（NASBA）assay was established for the detection of Macrobrachium rosenbergii Nodavirus（MrNV）.The specific primers were designed according to the high conserved region of R...A nucleic acid sequence-based amplification（NASBA）assay was established for the detection of Macrobrachium rosenbergii Nodavirus（MrNV）.The specific primers were designed according to the high conserved region of RNA2 sequence of MrNV.The 224 bp specific amplification product was obtained in positive sample determined with 3%agarose gel electrophoresis,while no product was generated from shrimp infected with other viruses including DNA viruses（IHHNV,WSSV）and RNA viruses（TSV,IMNV,YHV）.The detecting limit of the assay was 8pg nucleic acid,which is more sensitive than that of PCR method.展开更多
In the present paper, we discuss some properties of piecewise linear spectral sequences introduced by Liu and Xu. We have a study on the pointwise and almost everywhere convergence of its corresponding series. Also, i...In the present paper, we discuss some properties of piecewise linear spectral sequences introduced by Liu and Xu. We have a study on the pointwise and almost everywhere convergence of its corresponding series. Also, it is shown that the set G constructed from piecewise linear spectral sequences are bases, but not unconditional bases, for LP（0, 1） where 1 〈 p 〈 ∞, p ≠2.展开更多
Base-level is a kind of surface which controls sedimentation and erosion. So, it can be concluded that it is base-level change that controls the formation and internal structure of a sequence. A single cycle of base-l...Base-level is a kind of surface which controls sedimentation and erosion. So, it can be concluded that it is base-level change that controls the formation and internal structure of a sequence. A single cycle of base-level change can generate four sets of different stacking patterns. They are two sets of aggradation, one progradation and one retrogradation, which affects the features of the internal structure of a sequence. Lishu fault subsidence of Songliao basin is a typical half-graben lacustrine basin. Comprehensive base-level change analysis indicates that six base-level cycles and their related six sequences can be recognized between T 4 and T 5 seismic reflection surface. The contemporaneous fault is the main controlling factor of the fault lacustrine basin. There are obvious differences exist in the composition of sedimentary systems and all systems tracts between its steep slope (the side that basin control fault existed) and flat slope. Except highstand systems tract is composed of fan delta-lacustrine system, lowstand systems tract, transgressive systems tract and regressive systems tract are all made up of fan delta-underwater fan-lacustrine sedimentary systems in the side of steep slope.展开更多
To understand the gene-based biological processes in-depth,the single-molecule real-time sequencing has drawn increasing attention with promoted by the Human Genome Project.Herein,a set of newly designed canonical flu...To understand the gene-based biological processes in-depth,the single-molecule real-time sequencing has drawn increasing attention with promoted by the Human Genome Project.Herein,a set of newly designed canonical fluorescent bases(A_(y),tC,G_(b),T_(p))are proposed for four-color DNA sequencing.These quasi-intrinsic probes are derived from the fluorophore replacement and ring expansion on natural bases,which still keep the pyrimidine or purine underlying skeleton and Watson–Crick hydrogen bonding face to allow minimal perturbation to the native DNA duplex.More importantly,these nucleobase analogues possess red-shifted absorption and efficient photoluminescence due to the enhancedπ-conjugation in character.Meanwhile,the four analogues could generate distinct emission wavelength(Δλ~50 nm)for real-time sequencing.To assess the biological employment of the proposed biosensors,the effects of base pairing and linking deoxyribose are also considered.展开更多
BACKGROUND Esophageal squamous cell carcinoma(ESCC)is a cancer with a poor prognosis,characterized by distinct geographical distribution and family clustering.AIM To investigate if ethnic differences(Han vs Kazakh)cau...BACKGROUND Esophageal squamous cell carcinoma(ESCC)is a cancer with a poor prognosis,characterized by distinct geographical distribution and family clustering.AIM To investigate if ethnic differences(Han vs Kazakh)cause molecular variations in ESCC patients via genomic sequencing 299 samples.METHODS Here,we sequenced samples from 299 ESCC patients collected from Henan Key Laboratory for Esophageal Cancer Research and National Key Laboratory of Metabolic Dysregulation and Esophageal Cancer Prevention and Treatment,The First Affiliated Hospital of Zhengzhou University,including Han and Kazakh ethnic groups,and performed a genomic comparative analysis of these two ethnic cohorts.RESULTS ESCC patients of Kazakh ethnicity present with a later age of onset compared to Han.Kazakh patients exhibit a slightly higher tumor mutation burden compared to their Han counterparts.Three genes GIGYF1,CACNA1D,and ACOT11 exhibited mutation frequencies threefold higher in Kazakh patients than in Han.This enrichment may be associated with Kazakhs’adaptation to cold climates and consumption of high-calorie diets.Among Han patients,the apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide(APOBEC)-associated single base substitutions(SBS)13 mutational signature is more prevalent,whereas SBS6,indicative of DNA mismatch repair deficiency,is more common in Kazakh patients.Additionally,Han Chinese patients with APOBEC-enriched tumors exhibit a significantly higher mutation load than those without.Moreover,patients lacking the APOBEC signature demonstrate superior survival probability compared to the APOBEC-enriched group.CONCLUSION Living environment and diet are major factors in the development of ESCC.Genomic difference may provide guidance for the formulation of clinical treatment plans for ESCC from different ethnics regions.展开更多
In view of the high accuracy and predictability, high-resolution sequence stratigraphy had been extensively applied to oil exploration and gotten prominent practicable results. This article takes the first layer, uppe...In view of the high accuracy and predictability, high-resolution sequence stratigraphy had been extensively applied to oil exploration and gotten prominent practicable results. This article takes the first layer, upper second submember, Shahejie （沙河街） Formation from Pucheng （濮城） oilfield as an example to analyze the application of high-resolution sequence stratigraphy in reservoir study on the basis of a comprehensive study of core log data. Firstly, facies analysis of this area reveals the corresponding terminal fan system occurring where sediment-laden streams decrease in size and vanish as a result of evaporation and transmission losses. The model includes a tripartite zonation of terminal fan into feeder, distributary, and basinal zones. Secondly, electrofacies were made by well-log analysis and then matched with sedimentary facies defined by core analysis. Four electrofacies characterizing the main sedimentary facies association and depositional environments within target area are defined （channel, lag deposit, lake or flood-plain, and overflow deposits）. Thirdly, related correlations based on high-resolution sequence stratigraphy were established. By observing the stacking arrangement of genetic sequences, different scales of stratigraphic cycle can be identified. Within scale and duration, the stratigraphic cycles are termed as genetic sequences, genetic sequence sets, and minor cycles.展开更多
The reservoirs within the Chang 8 Member of Yanchang （延长） Formation in the south- western Ordos basin are characterized by low permeability. It is significant to build a high-resolution sequence stratigraphic fram...The reservoirs within the Chang 8 Member of Yanchang （延长） Formation in the south- western Ordos basin are characterized by low permeability. It is significant to build a high-resolution sequence stratigraphic framework for the exploration and development of these reservoirs. Based on an integrated investigation of well logs, seismic data, cores and outcrops, the Chang 8 Member is interpreted as a 3rd-order transgressive-regressive （T-R） sequence, which consists of six 4th-order T-R se- quences, namely, K1, K2, K3, K4, K5 and K6, respectively, from base to top. Each 4th-order sequence comprises a transgressive systems tract overlain by a regressive systems tract. From K1 to transgressive systems tract of K4, it is characterized by the landward shifts of facies and overall retrogradational sequence stacking pattern due to accommodation increase more than sediment supply during the 3rd-order base-level rise. The distributary channels are mainly deposited in the transgressive systems tracts, and the interdistributary bays, sheet sands, and small-scale mouth bars are primarily developed in the regressive systems tracts in response to the 4th-order base-level fluctuations. From the regressivesystems tracts of K4 to K6, it is characterized by the basinward shifts of facies and overall progradational sequence stacking pattern because of accommodation increase less than sediment sup- ply during a fall in 3rd-order base level. The distributary channels are mainly accumulated in the transgressive systems tracts, and distributary channels and mouth bars are deposited in the regressive systems tracts as a result of the 4th-order base-level changes. Detailed stratigraphic and sedimentoiogical analyses indicate that sequences K1, K2, K5 and K6, as well as the basin edge of K3 and K4, remain potential for exploration and development due to their high reservoir quality in response to the low accommodation and more sediment supply.展开更多
Viruses are a cause of significant health problem world-wide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of whic...Viruses are a cause of significant health problem world-wide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of nextgeneration sequencers(NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequenceindependent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.展开更多
Based on non-homogeneous model, a modified model is proposed. The new model deals with codon preference in protein-coding regions, reflects more accurately the key biological features of the regions. In addition, it i...Based on non-homogeneous model, a modified model is proposed. The new model deals with codon preference in protein-coding regions, reflects more accurately the key biological features of the regions. In addition, it is demonstrated, via an example, the modified model offers better solutions than previous model does.展开更多
Bicoid is one of the important Drosophila maternal genes involved in the control of embryo polarity and larvae segmentation. To clone and characterize the rice bicoid-related genes, one cDNA clone, Rb24 (EMBL accessio...Bicoid is one of the important Drosophila maternal genes involved in the control of embryo polarity and larvae segmentation. To clone and characterize the rice bicoid-related genes, one cDNA clone, Rb24 (EMBL accession number: AJ2771380), was isolated by screening of rice unmature seed cDNA library. Sequence analysis indicates that Rb24 contains a putative amino acid sequence, which is homologous to unique 8 amino acids sequence within Drosophila bicoid homeodomain (50% identity, 75% similarity) and involves a lys-9 in putative helix 3. Northern blot analysis of rice RNA has shown that this sequence is expressed in a tissue-specific manner. The transcript was detected strongly in young panicles, but less in young leaves and roots. This results are further confirmed with paraffin section in situ hybridization. The signal is intensive in rice globular embryo and located at the apical tip of the embryo, then, along with the development of embryo, the signal is getting reduced and transfers into both sides of embryo. The existence of bicoid-related sequence in rice embryo and the similarity of polar distribution of bicoid and Rb24 mRNA in early embryo development may implicates a conserved maternal regulation mechanism of body axis presents in Drosophila and in rice.展开更多
Evolutionary algorithm is applied for distillation separation sequence optimization synthesis problems with combination explosion. The binary tree data structure is used to describe the distillation separation sequenc...Evolutionary algorithm is applied for distillation separation sequence optimization synthesis problems with combination explosion. The binary tree data structure is used to describe the distillation separation sequence, and it is directly applied as the coding method. Genetic operators, which ensure to prohibit illegal filial generations completely, are designed by using the method of graph theory. The crossover operator based on a single parent or two parents is designed successfully. The example shows that the average ratio of search space from evolutionary algorithm with two-parent genetic operation is lower, whereas the rate of successful minimizations from evolutionary algorithm with single parent genetic operation is higher.展开更多
Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis o...Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis on known native structures of proteins. Many knowledge-based potentials for proteins have been proposed. Contrary to most existing review articles which mainly describe technical details and applications of various potential models, the main foci for the discussion here are ideas and concepts involving the construction of potentials, including the relation between free energy and energy, the additivity of potentials of mean force and some key issues in potential construction. Sequence analysis is briefly viewed from an energetic viewpoint.展开更多
文摘A modified DBSCAN algorithm is presented for deinterleaving of radar pulses in modern EW environments.A main characteristic of the proposed method is that using only time of arrival of pulses,the method can sort the pulses efficiently.Other PDW information such as rise time,carrier frequency,pulse width,modulation on pulse,fall time and direction of arrival are not required.To identify the valid PRIs in a set of interleaved pulses,an innovative modification of the DBSCAN algorithm is introduced which is accurate and easy to implement.The proposed method determines valid PRIs more accurately and neglects the spurious ones more efficiently as compared to the classical histogram based algorithms such as SDIF.Furthermore,without specifying any input parameter,the proposed method can deinterleave radar pulses while up to 30%jitter is present in the associated PRI.The accuracy and efficiency of the proposed method are verified by computer simulations and real data results.Experimental simulations are based on different real and operational scenarios where the presence of missing and spurious pulses are also considered.So,the simulation results can be of practical significance.
文摘The nucleotide (base) sequence of the genome might reflect biological information beyond the coding sequences. The appearance frequencies of successive base sequences (key sequences) were calculated for entire genomes. Based on the appearance frequency of the key sequences of the genome, any DNA sequences on the genome could be expressed as a sequence spectrum with the adjoining base sequences, which could be used to study the corresponding biological phenomena. In this paper, we used 64 successive three- base sequences (triplets) as the key sequences, and determined and compared the spectra of specific genes to the chromosome, or specific genes to tRNA genes in Saccharomyces cerevisiae, Schizosaccharomyces pombe and Escherichia coli. Based on these analyses, a gene and its corresponding position on the chromosome showed highly similar spectra with the same fold enlargement (approximately 400-fold) in the S. cerevisiae, S. pombe and E. coli genomes. In addition, the homologous structure of genes that encode proteins was also observed with appropriate tRNA gene(s) in the genome. This analytical method might faithfully reflect the encoded biological information, that is, the conservation of the base sequences was to make sense the conservation of the translated amino acids sequence in the coding region, and might be universally applicable to other genomes, even those that consisted of multiple chromosomes.
文摘A novel diagrammtic method is proposed to show the angular distribution of bases of human protein sequences. Using this method, the distribution sphere[1-4] is divided into four regions with same volume. The picture is clearer and more intuitive than that in [1] .A rule on the angular distribution of the representative points of bases of protein sequences is given. Besides, in 300 representative pointS of human protein sequence samples we find that there are three (not only one) points outside the sphere.
基金supported partially by the National Natural Science Foundation of China (10971105 and 10990012)the Natural Science Foundation of Tianjin (09JCYBJC01000)
文摘In this paper, we study the invertibility of sequences consisting of finitely many bounded linear operators from a Hilbert space to others. We show that a sequence of operators is left invertible if and only if it is a g-frame. Therefore, our result connects the invertibility of operator sequences with frame theory.
文摘The satellite-based automatic identification system (AIS) receiver has to encounter the frequency offset caused by the Doppler effect and the oscillator instability. This paper proposes a non-coherent sequence detection scheme for the satellite-based AIS signal transmitted over the white Gaussian noise channel. Based on the maximum likelihood estimation and a Viterbi decoder, the proposed scheme is capable of tolerating a frequency offset up to 5% of the symbol rate. The complexity of the proposed scheme is reduced by the state-complexity reduction, which is based on per-survivor processing. Simulation results prove that the proposed non-coherent sequence detection scheme has high robustness to frequency offset compared to the relative scheme when messages collision exists.
基金Supported by Special Fund for Agro-scientific Research in the Public Interest(201103034)Huzhou Science and Technology Project(2012GN08,2011ZD2005)Science and Technology Innovation Team Project of Freshwater Aquaculture of Zhejiang Province(2012R10026-11)
文摘A nucleic acid sequence-based amplification（NASBA）assay was established for the detection of Macrobrachium rosenbergii Nodavirus（MrNV）.The specific primers were designed according to the high conserved region of RNA2 sequence of MrNV.The 224 bp specific amplification product was obtained in positive sample determined with 3%agarose gel electrophoresis,while no product was generated from shrimp infected with other viruses including DNA viruses（IHHNV,WSSV）and RNA viruses（TSV,IMNV,YHV）.The detecting limit of the assay was 8pg nucleic acid,which is more sensitive than that of PCR method.
基金Supported by Prof.Y.Xu under his grant in program of"One Hundred Distingulshed Chi-nese Scientists"of the Chinese Academy of Sciences,the NNSF(10371122)of China and Poetgraduate Innovation Fund of Chinese Academy of Sciences.
文摘In the present paper, we discuss some properties of piecewise linear spectral sequences introduced by Liu and Xu. We have a study on the pointwise and almost everywhere convergence of its corresponding series. Also, it is shown that the set G constructed from piecewise linear spectral sequences are bases, but not unconditional bases, for LP（0, 1） where 1 〈 p 〈 ∞, p ≠2.
文摘Base-level is a kind of surface which controls sedimentation and erosion. So, it can be concluded that it is base-level change that controls the formation and internal structure of a sequence. A single cycle of base-level change can generate four sets of different stacking patterns. They are two sets of aggradation, one progradation and one retrogradation, which affects the features of the internal structure of a sequence. Lishu fault subsidence of Songliao basin is a typical half-graben lacustrine basin. Comprehensive base-level change analysis indicates that six base-level cycles and their related six sequences can be recognized between T 4 and T 5 seismic reflection surface. The contemporaneous fault is the main controlling factor of the fault lacustrine basin. There are obvious differences exist in the composition of sedimentary systems and all systems tracts between its steep slope (the side that basin control fault existed) and flat slope. Except highstand systems tract is composed of fan delta-lacustrine system, lowstand systems tract, transgressive systems tract and regressive systems tract are all made up of fan delta-underwater fan-lacustrine sedimentary systems in the side of steep slope.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.11804195,11847224,11674198,and 12274265)the Natural Science Foundation of Shandong Province,China(Grant Nos.ZR2018BA034 and ZR2022MA006)。
文摘To understand the gene-based biological processes in-depth,the single-molecule real-time sequencing has drawn increasing attention with promoted by the Human Genome Project.Herein,a set of newly designed canonical fluorescent bases(A_(y),tC,G_(b),T_(p))are proposed for four-color DNA sequencing.These quasi-intrinsic probes are derived from the fluorophore replacement and ring expansion on natural bases,which still keep the pyrimidine or purine underlying skeleton and Watson–Crick hydrogen bonding face to allow minimal perturbation to the native DNA duplex.More importantly,these nucleobase analogues possess red-shifted absorption and efficient photoluminescence due to the enhancedπ-conjugation in character.Meanwhile,the four analogues could generate distinct emission wavelength(Δλ~50 nm)for real-time sequencing.To assess the biological employment of the proposed biosensors,the effects of base pairing and linking deoxyribose are also considered.
基金Supported by the National Natural Science Foundation of China,No.U1301227National Major Science and Technology Projects,No.2024ZD05209060Henan Province Jointly Built Science and Technology Key Projects,No.LHGJ20210337.
文摘BACKGROUND Esophageal squamous cell carcinoma(ESCC)is a cancer with a poor prognosis,characterized by distinct geographical distribution and family clustering.AIM To investigate if ethnic differences(Han vs Kazakh)cause molecular variations in ESCC patients via genomic sequencing 299 samples.METHODS Here,we sequenced samples from 299 ESCC patients collected from Henan Key Laboratory for Esophageal Cancer Research and National Key Laboratory of Metabolic Dysregulation and Esophageal Cancer Prevention and Treatment,The First Affiliated Hospital of Zhengzhou University,including Han and Kazakh ethnic groups,and performed a genomic comparative analysis of these two ethnic cohorts.RESULTS ESCC patients of Kazakh ethnicity present with a later age of onset compared to Han.Kazakh patients exhibit a slightly higher tumor mutation burden compared to their Han counterparts.Three genes GIGYF1,CACNA1D,and ACOT11 exhibited mutation frequencies threefold higher in Kazakh patients than in Han.This enrichment may be associated with Kazakhs’adaptation to cold climates and consumption of high-calorie diets.Among Han patients,the apolipoprotein B messenger RNA-editing enzyme catalytic polypeptide(APOBEC)-associated single base substitutions(SBS)13 mutational signature is more prevalent,whereas SBS6,indicative of DNA mismatch repair deficiency,is more common in Kazakh patients.Additionally,Han Chinese patients with APOBEC-enriched tumors exhibit a significantly higher mutation load than those without.Moreover,patients lacking the APOBEC signature demonstrate superior survival probability compared to the APOBEC-enriched group.CONCLUSION Living environment and diet are major factors in the development of ESCC.Genomic difference may provide guidance for the formulation of clinical treatment plans for ESCC from different ethnics regions.
基金supported by the National Key Technology R&D Program (No. 2006BAC18B05)
文摘In view of the high accuracy and predictability, high-resolution sequence stratigraphy had been extensively applied to oil exploration and gotten prominent practicable results. This article takes the first layer, upper second submember, Shahejie （沙河街） Formation from Pucheng （濮城） oilfield as an example to analyze the application of high-resolution sequence stratigraphy in reservoir study on the basis of a comprehensive study of core log data. Firstly, facies analysis of this area reveals the corresponding terminal fan system occurring where sediment-laden streams decrease in size and vanish as a result of evaporation and transmission losses. The model includes a tripartite zonation of terminal fan into feeder, distributary, and basinal zones. Secondly, electrofacies were made by well-log analysis and then matched with sedimentary facies defined by core analysis. Four electrofacies characterizing the main sedimentary facies association and depositional environments within target area are defined （channel, lag deposit, lake or flood-plain, and overflow deposits）. Thirdly, related correlations based on high-resolution sequence stratigraphy were established. By observing the stacking arrangement of genetic sequences, different scales of stratigraphic cycle can be identified. Within scale and duration, the stratigraphic cycles are termed as genetic sequences, genetic sequence sets, and minor cycles.
基金supported by the National Natural Science Foundation of China (No. 40702024)
文摘The reservoirs within the Chang 8 Member of Yanchang （延长） Formation in the south- western Ordos basin are characterized by low permeability. It is significant to build a high-resolution sequence stratigraphic framework for the exploration and development of these reservoirs. Based on an integrated investigation of well logs, seismic data, cores and outcrops, the Chang 8 Member is interpreted as a 3rd-order transgressive-regressive （T-R） sequence, which consists of six 4th-order T-R se- quences, namely, K1, K2, K3, K4, K5 and K6, respectively, from base to top. Each 4th-order sequence comprises a transgressive systems tract overlain by a regressive systems tract. From K1 to transgressive systems tract of K4, it is characterized by the landward shifts of facies and overall retrogradational sequence stacking pattern due to accommodation increase more than sediment supply during the 3rd-order base-level rise. The distributary channels are mainly deposited in the transgressive systems tracts, and the interdistributary bays, sheet sands, and small-scale mouth bars are primarily developed in the regressive systems tracts in response to the 4th-order base-level fluctuations. From the regressivesystems tracts of K4 to K6, it is characterized by the basinward shifts of facies and overall progradational sequence stacking pattern because of accommodation increase less than sediment sup- ply during a fall in 3rd-order base level. The distributary channels are mainly accumulated in the transgressive systems tracts, and distributary channels and mouth bars are deposited in the regressive systems tracts as a result of the 4th-order base-level changes. Detailed stratigraphic and sedimentoiogical analyses indicate that sequences K1, K2, K5 and K6, as well as the basin edge of K3 and K4, remain potential for exploration and development due to their high reservoir quality in response to the low accommodation and more sediment supply.
基金Supported by The author’s laboratory is supported by the Defence Research and Development Organization(DRDO),Ministry of Defence,Government of India
文摘Viruses are a cause of significant health problem world-wide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of nextgeneration sequencers(NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequenceindependent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.
文摘Based on non-homogeneous model, a modified model is proposed. The new model deals with codon preference in protein-coding regions, reflects more accurately the key biological features of the regions. In addition, it is demonstrated, via an example, the modified model offers better solutions than previous model does.
文摘Bicoid is one of the important Drosophila maternal genes involved in the control of embryo polarity and larvae segmentation. To clone and characterize the rice bicoid-related genes, one cDNA clone, Rb24 (EMBL accession number: AJ2771380), was isolated by screening of rice unmature seed cDNA library. Sequence analysis indicates that Rb24 contains a putative amino acid sequence, which is homologous to unique 8 amino acids sequence within Drosophila bicoid homeodomain (50% identity, 75% similarity) and involves a lys-9 in putative helix 3. Northern blot analysis of rice RNA has shown that this sequence is expressed in a tissue-specific manner. The transcript was detected strongly in young panicles, but less in young leaves and roots. This results are further confirmed with paraffin section in situ hybridization. The signal is intensive in rice globular embryo and located at the apical tip of the embryo, then, along with the development of embryo, the signal is getting reduced and transfers into both sides of embryo. The existence of bicoid-related sequence in rice embryo and the similarity of polar distribution of bicoid and Rb24 mRNA in early embryo development may implicates a conserved maternal regulation mechanism of body axis presents in Drosophila and in rice.
文摘Evolutionary algorithm is applied for distillation separation sequence optimization synthesis problems with combination explosion. The binary tree data structure is used to describe the distillation separation sequence, and it is directly applied as the coding method. Genetic operators, which ensure to prohibit illegal filial generations completely, are designed by using the method of graph theory. The crossover operator based on a single parent or two parents is designed successfully. The example shows that the average ratio of search space from evolutionary algorithm with two-parent genetic operation is lower, whereas the rate of successful minimizations from evolutionary algorithm with single parent genetic operation is higher.
基金Project supported in part by the National Natural Science Foundation of China(Grant Nos.11175224 and 11121403)
文摘Biological raw data are growing exponentially, providing a large amount of information on what life is. It is believed that potential functions and the rules governing protein behaviors can be revealed from analysis on known native structures of proteins. Many knowledge-based potentials for proteins have been proposed. Contrary to most existing review articles which mainly describe technical details and applications of various potential models, the main foci for the discussion here are ideas and concepts involving the construction of potentials, including the relation between free energy and energy, the additivity of potentials of mean force and some key issues in potential construction. Sequence analysis is briefly viewed from an energetic viewpoint.
