In order to improve the detection accuracy of Doppler asymmetric spatial heterodyne(DASH)interferometer in harsh temperatures,an opto-mechanical-thermal integration analysis is carried out.Firstly,the correlation betw...In order to improve the detection accuracy of Doppler asymmetric spatial heterodyne(DASH)interferometer in harsh temperatures,an opto-mechanical-thermal integration analysis is carried out.Firstly,the correlation between the interference phase and temperature is established according to the working principle and the phase algorithm of the interferometer.Secondly,the optical mechanical thermal analysis model and thermal deformation data acquisition model are designed.The deformation data of the interference module and the imaging optical system at different temperatures are given by temperature load simulation analysis,and the phase error caused by thermal deformation is obtained by fitting.Finally,based on the wind speed error caused by thermal deformation of each component,a reasonable temperature control scheme is proposed.The results show that the interference module occupies the main cause,the temperature must be controlled within(20±0.05)℃,and the temperature control should be carried out for the temperature sensitive parts,and the wind speed error caused by the part is 3.8 m/s.The thermal drift between the magnification of the imaging optical system and the thermal drift of the relative position between the imaging optical system and the detector should occupy the secondary cause,which should be controlled within(20±2)℃,and the wind speed error caused by the part is 3.05 m/s.In summary,the wind measurement error caused by interference module,imaging optical system,and the relative position between the imaging optical system and the detector can be controlled within 6.85 m/s.The analysis and temperature control schemes presented in this paper can provide theoretical basis for DASH interferometer engineering applications.展开更多
Genomic studies of cancer cell alterations,such as mutations,copy number variations(CNVs),and translocations,greatly promote our understanding of the genesis and development of cancers.However,the 3D genome architectu...Genomic studies of cancer cell alterations,such as mutations,copy number variations(CNVs),and translocations,greatly promote our understanding of the genesis and development of cancers.However,the 3D genome architecture of cancers remains less studied due to the complexity of cancer genomes and technical difficulties.To explore the 3D genome structure in clinical lung cancer,we performed Hi-C experiments using paired normal and tumor cells harvested from patients with lung cancer,combining with RNA sequenceing analysis.We demonstrated the feasibility of studying 3D genome of clinical lung cancer samples with a small number of cells(1×10^(4)),compared the genome architecture between clinical samples and cell lines of lung cancer,and identified conserved and changed spatial chromatin structures between normal and cancer samples.We also showed that Hi-C data can be used to infer CNVs and point mutations in cancer.By integrating those different types of cancer alterations,we showed significant associations between CNVs,3D genome,and gene expression.We propose that 3D genome mediates the effects of cancer genomic alterations on gene expression through altering regulatory chromatin structures.Our study highlights the importance of analyzing 3D genomes of clinical cancer samples in addition to cancer cell lines and provides an integrative genomic analysis pipeline for future larger-scale studies in lung cancer and other cancers.展开更多
BACKGROUND Persistent left superior vena cava(PLSVC)is the most common venous system variant.The clinical characteristics and amniotic fluid cytogenetics of fetuses with PLSVC remain to be further explored.AIM To deve...BACKGROUND Persistent left superior vena cava(PLSVC)is the most common venous system variant.The clinical characteristics and amniotic fluid cytogenetics of fetuses with PLSVC remain to be further explored.AIM To develop reliable prenatal diagnostic recommendations through integrated analysis of the clinical characteristics of fetuses with PLSVC.METHODS Cases of PLSVC diagnosed using prenatal ultrasonography between September 2019 and November 2022 were retrospectively studied.The clinical characteristics of the pregnant women,ultrasonic imaging information,gestational age at diagnosis,pregnancy outcomes,and amniocentesis results were summarized and analyzed using categorical statistics and the chi-square test or Fisher’s exact test.RESULTS Of the 97 cases diagnosed by prenatal ultrasound,49(50.5%)had isolated PLSVC and 48(49.5%)had other structural abnormalities.The differences in pregnancy outcomes and amniocentesis conditions between the two groups were statistically significant(P<0.05).No significant differences were identified between the two groups in terms of advanced maternal age and gestational age(P>0.05).According to the results of the classification statistics,the most common intrac-ardiac abnormality was a ventricular septal defect and the most common extrac-ardiac abnormality was a single umbilical artery.In the subgroup analysis,the concurrent combination of intra-and extracardiac structural abnormalities was a risk factor for adverse pregnancy outcomes(odds ratio>1,P<0.05).Additional-ly,all abnormal cytogenetic findings on amniocentesis were observed in the comorbidity group.One case was diagnosed with 21-trisomy and six cases was diagnosed with chromosome segment duplication.CONCLUSION Examination for other structural abnormalities is strongly recommended when PLSVC is diagnosed.Poorer pregnancy outcomes and increased amniocentesis were observed in PLSVC cases with other structural abnor-malities.Amniotic fluid cytogenetics of fetuses is recommended for PLSVC with other structural abnormalities.展开更多
Non-alcoholic fatty liver disease(NAFLD)is associated with mutations in lipopolysaccharide-binding protein(LBP),but the underlying epigenetic mechanisms remain understudied.Herein,LBP^(-/-)rats with NAFLD were establi...Non-alcoholic fatty liver disease(NAFLD)is associated with mutations in lipopolysaccharide-binding protein(LBP),but the underlying epigenetic mechanisms remain understudied.Herein,LBP^(-/-)rats with NAFLD were established and used to conduct integrative targetingactive enhancer histone H3 lysine 27 acetylation(H3K27ac)chromatin immunoprecipitation coupled with high-throughput and transcriptomic sequencing analysis to explore the potential epigenetic pathomechanisms of active enhancers of NAFLD exacerbation upon LBP deficiency.Notably,LBP^(-/-)reduced the inflammatory response but markedly aggravated high-fat diet(HFD)-induced NAFLD in rats,with pronounced alterations in the histone acetylome and regulatory transcriptome.In total,1128 differential enhancer-target genes significantly enriched in cholesterol and fatty acid metabolism were identified between wild-type(WT)and LBP^(-/-)NAFLD rats.Based on integrative analysis,CCAAT/enhancer-binding proteinβ(C/EBPβ)was identified as a pivotal transcription factor(TF)and contributor to dysregulated histone acetylome H3K27ac,and the lipid metabolism gene SCD was identified as a downstream effector exacerbating NAFLD.This study not only broadens our understanding of the essential role of LBP in the pathogenesis of NAFLD from an epigenetics perspective but also identifies key TF C/EBPβand functional gene SCD as potential regulators and therapeutic targets.展开更多
Although many susceptibility loci for IgA nephropathy(IgAN)have been identified,they only account for 11.0%of the overall IgAN variance.We performed a large genome-wide meta-analysis of IgAN in Han Chinese with 3616 c...Although many susceptibility loci for IgA nephropathy(IgAN)have been identified,they only account for 11.0%of the overall IgAN variance.We performed a large genome-wide meta-analysis of IgAN in Han Chinese with 3616 cases and 10417 controls to identify additional genetic loci of IgAN.Considering that inflammatory bowel disease(IBD)and asthma might share an etiology of dysregulated mucosal immunity with IgAN,we performed cross-trait integrative analysis by leveraging functional annotations of relevant cell type and the pleiotropic information from IBD and asthma.Among 8669456 imputed variants,we identified a novel locus at 4p14 containing the long noncoding RNA LOC101060498.Cell type enrichment analysis based on annotations suggested that PMA-I-stimulated CD4+CD25–IL17+Th17 cell was the most relevant cell type for IgAN,which highlights the essential role of Th17 pathway in the pathogenesis of IgAN.Furthermore,we identified six more novel loci associated with IgAN,which included three loci showing pleiotropic effects with IBD or asthma(2q35/PNKD,6q25.2/SCAF8,and 22q11.21/UBE2L3)and three loci specific to IgAN(14q32.32/TRAF3,16q22.2/TXNL4B,and 21q21.3/LINC00113)in the pleiotropic analysis.Our findings support the involvement of mucosal immunity,especially T cell immune response and IL-17 signal pathway,in the development of IgAN and shed light on further investigation of IgAN.展开更多
Objective： Identification of colorectal cancer （CRC） metastasis genes is one of the most important issues in CRC research. For the purpose of mining CRC metastasis-associated genes, an integrated analysis of mJcroa...Objective： Identification of colorectal cancer （CRC） metastasis genes is one of the most important issues in CRC research. For the purpose of mining CRC metastasis-associated genes, an integrated analysis of mJcroarray data was presented, by combined with evidence acquired from comparative genornic hybridization （CGH） data. Methods： Gene expression profile data of CRC samples were obtained at Gene Expression Omnibus （GEO） website. The 15 important chromosomal aberration sites detected by using CGH technology were used for integrated genomic and transcriptomic analysis. Significant Analysis of Microarray （SAM） was used to detect significantly differentially expressed genes across the whole genome. The overlapping genes were selected in their corresponding chromosomal aberration regions, and analyzed by using the Database for Annotation, Visualization and Integrated Discovery （DAVID）. Finally, SVM-T-RFE gene selection algorithm was applied to identify ted genes in CRC. Results： A minimum gene set was obtained with the minimum number [14] of genes, and the highest classification accuracy （100%） in both PRI and META datasets. A fraction of selected genes are associated with CRC or its metastasis. Conclusions- Our results demonstrated that integration analysis is an effective strategy for mining cancer- associated genes.展开更多
In order to satisfy the requirement of SI-traceable on-orbit absolute radiation calibration transfer with high accuracy for satellite remote sensors,a transfer chain consisting of a fiber coupling monochromator（FBM）...In order to satisfy the requirement of SI-traceable on-orbit absolute radiation calibration transfer with high accuracy for satellite remote sensors,a transfer chain consisting of a fiber coupling monochromator（FBM） and an integrating sphere transfer radiometer（ISTR） was designed in this paper.Depending on the Sun,this chain based on detectors provides precise spectral radiometric calibration and measurement to spectrometers in the reflective solar band（RSB） covering 300–2500 nm with a spectral bandwidth of 0.5–6 nm.It shortens the traditional chain based on lamp source and reduces the calibration uncertainty from 5% to 0.5% by using the cryogenic radiometer in space as a radiometric benchmark and trap detectors as secondary standard.This paper also gives a detailed uncertainty budget with reasonable distribution of each impact factor,including the weak spectral signal measurement with uncertainty of 0.28%.According to the peculiar design and comprehensive uncertainty analysis,it illustrates that the spectral radiance measurement uncertainty of the ISTR system can reach to 0.48%.The result satisfies the requirements of SI-traceable on-orbit calibration and has wider significance for expanding the application of the remote sensing data with high-quality.展开更多
As the increase of the complexity of the information warfare,its intervention strategy needs to be designed in an integrated environment.However,the current research always breaks the internal relation between equipme...As the increase of the complexity of the information warfare,its intervention strategy needs to be designed in an integrated environment.However,the current research always breaks the internal relation between equipment and tactics,and it is difficult to meet the requirements of their integrated analysis.In this paper,the research status quo of the integrated analysis about equipment and tactics is discussed first,some shortages of the current methods are summarized then,and an evolvement mechanism of the integrated analysis for equipment and tactics is given finally.Based on these,a framework of integrated analysis is proposed.This method's effectiveness is validated by an example.展开更多
Process Capability Analysis (PCA) is a powerful too l to assess the ability of a process for manufacturing product that meets specific ations. The larger process capability index implies the higher process yield, a nd...Process Capability Analysis (PCA) is a powerful too l to assess the ability of a process for manufacturing product that meets specific ations. The larger process capability index implies the higher process yield, a nd the larger process capability index also indicates the lower process expected loss. Chen et al. (2001) has applied indices C pu, C pl, and C pk for evaluating the process capability for a multi-process product wi th smaller-the-better, larger-the-better, and nominal-the-best specificati ons respectively. However, C pk cannot reasonably reflect the process expected loss. In this paper, index C pn is selected to replace C pk. Indices C pu, C pl, and C pn are used to evalu ate the entire process capability for a multi-process product with smaller-the -better, larger-the-better, and nominal-the-best specifications respectivel y. An integrated process capability index for a multi-process product is propo sed. The relationship between process capability index and the process yield is introduced. A multi-process capability analysis chart (MPCAC), reasonably rev ealing the status of process capability for the entire product, is constructed f or practical application. An evaluating procedure of the process capability for the entire product is also provided.展开更多
The unmanned aerial vehicles( UAV) has been becoming more and more important in the aviation industry.Despite the superior performance and advanced technology,major accident of UAV happens frequently due to the impact...The unmanned aerial vehicles( UAV) has been becoming more and more important in the aviation industry.Despite the superior performance and advanced technology,major accident of UAV happens frequently due to the impact of their systems,long distance of remote control and skill of manipulator technology.According to the application of engineering application,failure mode effects and criticality analysis( FMECA),failure reporting analysis and corrective action comprehensive analysis systems( FRACAS)and fault tree analysis( FTA)( 3 F) were combined.And also a set of user-friendly,more time,more efficient and accurate reliability analysis system were explored.展开更多
Objective:This work aimed to illuminate the potential key genes and pathways in GC tumorigenesis based on bioinfOrmatics analysis.Methods:The differentially expressed genes(DEGs)between GPL tissue samples and GC tissu...Objective:This work aimed to illuminate the potential key genes and pathways in GC tumorigenesis based on bioinfOrmatics analysis.Methods:The differentially expressed genes(DEGs)between GPL tissue samples and GC tissue samples were investigated using the GSE55696 and GSE87666 microarray data from the Gene Expression Omnibus(GEO)database.DEGs were identified by an empirical Bayes method based on the Limma R package.Then,KEGG and GO enrichment analyses of DEGs were performed followed by protein-protein interaction(PPI)network construction.Finally,the overall survival(OS)analysis of key genes was performed by the Kaplan-Meier plotter online tool.Results:A total of 250 DEGs were obtained,of which 216 were up-regulated and 34 were down-regulated.KEGG pathways analysis showed that the up-regulated DEGs were enriched in cytokine-cytokine receptor interaction,chemokine signaling pathway,metabolic pathways,PI3K-Akt signaling pathway,NF-kappa B signaling pathway,and other signaling pathways about cancer,while no down-regulated pathways were enriched.A PPI network of DEGs was constructed with 117 nodes and 660 edges,and 20 genes were selected as hub genes owing to high degrees in the network.According to the Kaplan-Meier analysis,6 out of 20 hub genes including CCR7,FPR1,C3,CXCR5,GNB4,and PPBP with high mRNA expression were associated with poor OS for GC patients.Conclusion:The results of this study provide possible factors for the occurrence of GC,and the identification of the genes and pathways associated with the progression from GPL to GC provides valuable data for investigating the pathogenesis in future studies.展开更多
In this paper, sensitivity approaches are taken to analyze and design an integrated flight propulsion control system where the interaction between subsystems direitly affects the stability property and handling perfor...In this paper, sensitivity approaches are taken to analyze and design an integrated flight propulsion control system where the interaction between subsystems direitly affects the stability property and handling performances of the aircraft. The eigenvalue sen sitivity approach is employed to study the effect of coupling parameters on system stability and gain sensitivity approach is used to direct the reduced states feedback suboptimal control system design. Simulation results show that the integrated flight propulsion control system designed by sensitivity approaches is of good performance.展开更多
This article describes the significance of constructing integrated gateway office offices by telecom operators in the new era,as well as the change and improvement of the function requirements of in- tegrated gateway ...This article describes the significance of constructing integrated gateway office offices by telecom operators in the new era,as well as the change and improvement of the function requirements of in- tegrated gateway office offices with the continuous development of cross-network services.It puts forward ZTE's overall solution for the inter-network interworking with regard to the construction of in- tegrated gateway office offices.展开更多
Numerical climate models render data in a gridded format which is often problematic for integrated analysis with other kinds of data in jurisdictional formats. In this paper a joint analysis of municipal Gross Domesti...Numerical climate models render data in a gridded format which is often problematic for integrated analysis with other kinds of data in jurisdictional formats. In this paper a joint analysis of municipal Gross Domestic Product per capita (GDPc) and predicted temperature increase was undertaken in order to estimate different levels of human and economic exposure. This is based on a method of converting model outputs into a country municipal grid which enabled depicting climate predictions from the Eta-Hadgem2-ES Regional Climate Model (RCM) into the municipal level in Brazil. The conversion to country municipality grid was made using a combination of interpolation and buffering techniques in ArcGIS for two emission scenarios (RCP 4.5 and 8.5) and three timeframes (2011-2040, 2041-2070, 2071-2100) for mean temperature increase and number of heatwave days (WSDI). The results were used to support the Third National Communication (TCN) of Brazil to the United Nations Framework Convention on Climate Change (UNFCCC) and show a coherent matching of the gridded output from the original RCM. The joint climate and GDPc analysis show that in the beginning of the century the more severe warming is centred over regions where GDPc is generally higher (Centre-West and Southeast). At the end of the century, critical levels of warming spread north and northeastwards where municipalities have the lowest GDPc levels. In the high emission scenario (RCP 8.5), the strongest warming and the spreading over poorer regions are anticipated to the mid-century. These results are the key to further explore solutions for climate change adaptation based on current resources and prepare in different sectors, for long-term risk management and climate adaptation planning strategies.展开更多
Since China began implementing reform and opening-up policies, along with a fast development of the national economy and great changes of social life, an increasing number of peasan＇s have kept flowing into cities an...Since China began implementing reform and opening-up policies, along with a fast development of the national economy and great changes of social life, an increasing number of peasan＇s have kept flowing into cities and economically more developed regions. Aspiring to improve their life and yearning for a better urban life, they defy the restraint of the household registry system and, in the process of moving from one place to another, ignore economic and psychological costs. As early as in year 2000 China＇s migrant population reached 140 million, more than 10% of the total population. Since 2000 the migrant poptilation in Zhejiang Province, east China, has kept growing by 20% annually, the second fastest in the country for seven consecutive years.展开更多
Deep learning has been increasingly popular in omics data analysis.Recent works incorporating variable selection into deep learning have greatly enhanced the model’s interpretability.However,because deep learning des...Deep learning has been increasingly popular in omics data analysis.Recent works incorporating variable selection into deep learning have greatly enhanced the model’s interpretability.However,because deep learning desires a large sample size,the existing methods may result in uncertain findings when the dataset has a small sample size,commonly seen in omics data analysis.With the explosion and availability of omics data from multiple populations/studies,the existing methods naively pool them into one dataset to enhance the sample size while ignoring that variable structures can differ across datasets,which might lead to inaccurate variable selection results.We propose a penalized integrative deep neural network(PIN)to simultaneously select important variables from multiple datasets.PIN directly aggregates multiple datasets as input and considers both homogeneity and heterogeneity situations among multiple datasets in an integrative analysis framework.Results from extensive simulation studies and applications of PIN to gene expression datasets from elders with different cognitive statuses or ovarian cancer patients at different stages demonstrate that PIN outperforms existing methods with considerably improved performance among multiple datasets.The source code is freely available on Github(rucliyang/PINFunc).We speculate that the proposed PIN method will promote the identification of disease-related important variables based on multiple studies/datasets from diverse origins.展开更多
Transfer RNA(t RNA)-derived small RNAs(ts RNAs) are a recently established family of regulatory small non-coding RNAs that modulate diverse biological processes. Growing evidence indicates that ts RNAs are involved in...Transfer RNA(t RNA)-derived small RNAs(ts RNAs) are a recently established family of regulatory small non-coding RNAs that modulate diverse biological processes. Growing evidence indicates that ts RNAs are involved in neurological disorders and play a role in the pathogenesis of neurodegenerative disease. However, whether ts RNAs are involved in traumatic brain injury-induced secondary injury remains poorly understood. In this study, a mouse controlled cortical impact model of traumatic brain injury was established, and integrated ts RNA and messenger RNA(m RNA) transcriptome sequencing were used. The results revealed that 103 ts RNAs were differentially expressed in the mouse model of traumatic brain injury at 72 hours, of which 56 ts RNAs were upregulated and 47 ts RNAs were downregulated. Based on micro RNA-like seed matching and Pearson correlation analysis, 57 differentially expressed ts RNA-m RNA interaction pairs were identified, including 29 ts RNAs and 26 m RNAs. Moreover, Gene Ontology annotation of target genes revealed that the significantly enriched terms were primarily associated with inflammation and synaptic function. Collectively, our findings suggest that ts RNAs may be associated with traumatic brain injury-induced secondary brain injury, and are thus a potential therapeutic target for traumatic brain injury. The study was approved by the Beijing Neurosurgical Institute Animal Care and Use Committee(approval No. 20190411) on April 11, 2019.展开更多
The Taoudeni Basin is a typical steady intracratonic basin. Based on the distribution of effective source rocks in the Taoudeni Basin, combined with the structure characteristics of the basin and the distribution char...The Taoudeni Basin is a typical steady intracratonic basin. Based on the distribution of effective source rocks in the Taoudeni Basin, combined with the structure characteristics of the basin and the distribution characteristics of reservoir beds, two petroleum systems are recognized in the basin： the infra-Cambrian petroleum system and the Silurian petroleum system. Structural uplift and timing of petroleum generation controlled the timing of petroleum charging and preservation of hydrocarbon accumulations. Maturity, evolution history, and distribution of effective source rocks controlled hydrocarbon richness. The geological key factors and geological processes controlled the type of hydrocarbon accumulations.展开更多
Soluble sugar content in seeds is an important quality trait of soybean. In this study, 57 quantitative trait loci(QTLs) related to soluble sugar contents in soybean seeds were collected from databases and published p...Soluble sugar content in seeds is an important quality trait of soybean. In this study, 57 quantitative trait loci(QTLs) related to soluble sugar contents in soybean seeds were collected from databases and published papers. After meta-overview-collinearity integrated analysis to refine QTL intervals, eight consensus QTLs were identified. To further verify the consensus QTLs, a population of chromosome segment substitution lines(CSSLs) was analyzed. Two lines containing fragments covering the regions of consensus QTLs and the recurrent parent were selected: one line showed high soluble sugar contents associated with a consensus QTL fragment, and the other line showed low soluble sugar contents. Transcriptome sequencing was conducted for these two lines at the early, middle, and late stages of seed development, which identified 158, 109 and 329 differentially expressed genes, respectively. Based on the analyses of re-sequencing data of the CSSLs and the consensus QTL region, three candidate genes(Glyma.19 G146800, Glyma.19 G122500, and Glyma.19 G128500) were identified in the genetic fragments introduced from wild soybean. Sequence comparisons between the two CSSL parents SN14 and ZYD00006 revealed a single nucleotide polymorphism(SNP) mutation in the coding sequence of Glyma.19 G122500, causing a nonsynonymous mutation in the amino acid sequence that affected the predicted protein structure. A Kompetitive allele-specific PCR(KASP) marker was developed based on this SNP and used to evaluate the CSSLs. These results lay the foundation for further research to identify genes related to soluble sugar contents in soybean seeds and for future soybean breeding.展开更多
文摘In order to improve the detection accuracy of Doppler asymmetric spatial heterodyne(DASH)interferometer in harsh temperatures,an opto-mechanical-thermal integration analysis is carried out.Firstly,the correlation between the interference phase and temperature is established according to the working principle and the phase algorithm of the interferometer.Secondly,the optical mechanical thermal analysis model and thermal deformation data acquisition model are designed.The deformation data of the interference module and the imaging optical system at different temperatures are given by temperature load simulation analysis,and the phase error caused by thermal deformation is obtained by fitting.Finally,based on the wind speed error caused by thermal deformation of each component,a reasonable temperature control scheme is proposed.The results show that the interference module occupies the main cause,the temperature must be controlled within(20±0.05)℃,and the temperature control should be carried out for the temperature sensitive parts,and the wind speed error caused by the part is 3.8 m/s.The thermal drift between the magnification of the imaging optical system and the thermal drift of the relative position between the imaging optical system and the detector should occupy the secondary cause,which should be controlled within(20±2)℃,and the wind speed error caused by the part is 3.05 m/s.In summary,the wind measurement error caused by interference module,imaging optical system,and the relative position between the imaging optical system and the detector can be controlled within 6.85 m/s.The analysis and temperature control schemes presented in this paper can provide theoretical basis for DASH interferometer engineering applications.
基金supported by the National Natural Science Foundation of China(Grant No.31871266)the National Key R&D Program of China(Grant No.2016YFA0100103)+1 种基金the National Natural Science Foundation of China Key Research Grant(Grant No.71532001)supported by funding from Shenzhen Municipal Government of China(Grant No.DRC-SZ[2016]884)。
文摘Genomic studies of cancer cell alterations,such as mutations,copy number variations(CNVs),and translocations,greatly promote our understanding of the genesis and development of cancers.However,the 3D genome architecture of cancers remains less studied due to the complexity of cancer genomes and technical difficulties.To explore the 3D genome structure in clinical lung cancer,we performed Hi-C experiments using paired normal and tumor cells harvested from patients with lung cancer,combining with RNA sequenceing analysis.We demonstrated the feasibility of studying 3D genome of clinical lung cancer samples with a small number of cells(1×10^(4)),compared the genome architecture between clinical samples and cell lines of lung cancer,and identified conserved and changed spatial chromatin structures between normal and cancer samples.We also showed that Hi-C data can be used to infer CNVs and point mutations in cancer.By integrating those different types of cancer alterations,we showed significant associations between CNVs,3D genome,and gene expression.We propose that 3D genome mediates the effects of cancer genomic alterations on gene expression through altering regulatory chromatin structures.Our study highlights the importance of analyzing 3D genomes of clinical cancer samples in addition to cancer cell lines and provides an integrative genomic analysis pipeline for future larger-scale studies in lung cancer and other cancers.
文摘BACKGROUND Persistent left superior vena cava(PLSVC)is the most common venous system variant.The clinical characteristics and amniotic fluid cytogenetics of fetuses with PLSVC remain to be further explored.AIM To develop reliable prenatal diagnostic recommendations through integrated analysis of the clinical characteristics of fetuses with PLSVC.METHODS Cases of PLSVC diagnosed using prenatal ultrasonography between September 2019 and November 2022 were retrospectively studied.The clinical characteristics of the pregnant women,ultrasonic imaging information,gestational age at diagnosis,pregnancy outcomes,and amniocentesis results were summarized and analyzed using categorical statistics and the chi-square test or Fisher’s exact test.RESULTS Of the 97 cases diagnosed by prenatal ultrasound,49(50.5%)had isolated PLSVC and 48(49.5%)had other structural abnormalities.The differences in pregnancy outcomes and amniocentesis conditions between the two groups were statistically significant(P<0.05).No significant differences were identified between the two groups in terms of advanced maternal age and gestational age(P>0.05).According to the results of the classification statistics,the most common intrac-ardiac abnormality was a ventricular septal defect and the most common extrac-ardiac abnormality was a single umbilical artery.In the subgroup analysis,the concurrent combination of intra-and extracardiac structural abnormalities was a risk factor for adverse pregnancy outcomes(odds ratio>1,P<0.05).Additional-ly,all abnormal cytogenetic findings on amniocentesis were observed in the comorbidity group.One case was diagnosed with 21-trisomy and six cases was diagnosed with chromosome segment duplication.CONCLUSION Examination for other structural abnormalities is strongly recommended when PLSVC is diagnosed.Poorer pregnancy outcomes and increased amniocentesis were observed in PLSVC cases with other structural abnor-malities.Amniotic fluid cytogenetics of fetuses is recommended for PLSVC with other structural abnormalities.
基金supported by the National Natural Science Foundation of China(81971875,82300661)Natural Science Foundation of Anhui province(2308085QH246)+3 种基金Natural Science Foundation of the Anhui Higher Education Institutions(KJ2021A0205)Basic and Clinical Cooperative Research Program of Anhui Medical University(2019xkjT002,2019xkjT022,2022xkjT013)Talent Training Program,School of Basic Medical Sciences,Anhui Medical University(2022YPJH102)National College Students Innovation and Entrepreneurship Training Program of China(202210366024)。
文摘Non-alcoholic fatty liver disease(NAFLD)is associated with mutations in lipopolysaccharide-binding protein(LBP),but the underlying epigenetic mechanisms remain understudied.Herein,LBP^(-/-)rats with NAFLD were established and used to conduct integrative targetingactive enhancer histone H3 lysine 27 acetylation(H3K27ac)chromatin immunoprecipitation coupled with high-throughput and transcriptomic sequencing analysis to explore the potential epigenetic pathomechanisms of active enhancers of NAFLD exacerbation upon LBP deficiency.Notably,LBP^(-/-)reduced the inflammatory response but markedly aggravated high-fat diet(HFD)-induced NAFLD in rats,with pronounced alterations in the histone acetylome and regulatory transcriptome.In total,1128 differential enhancer-target genes significantly enriched in cholesterol and fatty acid metabolism were identified between wild-type(WT)and LBP^(-/-)NAFLD rats.Based on integrative analysis,CCAAT/enhancer-binding proteinβ(C/EBPβ)was identified as a pivotal transcription factor(TF)and contributor to dysregulated histone acetylome H3K27ac,and the lipid metabolism gene SCD was identified as a downstream effector exacerbating NAFLD.This study not only broadens our understanding of the essential role of LBP in the pathogenesis of NAFLD from an epigenetics perspective but also identifies key TF C/EBPβand functional gene SCD as potential regulators and therapeutic targets.
基金supported by Guangdong-Hong Kong Joint Laboratory on Immunological and Genetic Kidney Diseases(No.2019B121205005)National Natural Science Foundation of China(Nos.81920108008,81770661,82170714,and 82003561)+2 种基金Guangzhou Municipal Science and Technology Project of China(No.202201011246)Basic and Applied Basic Research Foundation of Guangdong Province(No.2021A1515111054)Fundamental Research Funds for the Central Universities(No.2019kfyXJJS036).
文摘Although many susceptibility loci for IgA nephropathy(IgAN)have been identified,they only account for 11.0%of the overall IgAN variance.We performed a large genome-wide meta-analysis of IgAN in Han Chinese with 3616 cases and 10417 controls to identify additional genetic loci of IgAN.Considering that inflammatory bowel disease(IBD)and asthma might share an etiology of dysregulated mucosal immunity with IgAN,we performed cross-trait integrative analysis by leveraging functional annotations of relevant cell type and the pleiotropic information from IBD and asthma.Among 8669456 imputed variants,we identified a novel locus at 4p14 containing the long noncoding RNA LOC101060498.Cell type enrichment analysis based on annotations suggested that PMA-I-stimulated CD4+CD25–IL17+Th17 cell was the most relevant cell type for IgAN,which highlights the essential role of Th17 pathway in the pathogenesis of IgAN.Furthermore,we identified six more novel loci associated with IgAN,which included three loci showing pleiotropic effects with IBD or asthma(2q35/PNKD,6q25.2/SCAF8,and 22q11.21/UBE2L3)and three loci specific to IgAN(14q32.32/TRAF3,16q22.2/TXNL4B,and 21q21.3/LINC00113)in the pleiotropic analysis.Our findings support the involvement of mucosal immunity,especially T cell immune response and IL-17 signal pathway,in the development of IgAN and shed light on further investigation of IgAN.
基金supported by a grant from the National Natural Science Foundation of China(Grant No.61373057)a grant from the Zhejiang Provincial Natural Science Foundation of China(Grant No.Y1110763)
文摘Objective： Identification of colorectal cancer （CRC） metastasis genes is one of the most important issues in CRC research. For the purpose of mining CRC metastasis-associated genes, an integrated analysis of mJcroarray data was presented, by combined with evidence acquired from comparative genornic hybridization （CGH） data. Methods： Gene expression profile data of CRC samples were obtained at Gene Expression Omnibus （GEO） website. The 15 important chromosomal aberration sites detected by using CGH technology were used for integrated genomic and transcriptomic analysis. Significant Analysis of Microarray （SAM） was used to detect significantly differentially expressed genes across the whole genome. The overlapping genes were selected in their corresponding chromosomal aberration regions, and analyzed by using the Database for Annotation, Visualization and Integrated Discovery （DAVID）. Finally, SVM-T-RFE gene selection algorithm was applied to identify ted genes in CRC. Results： A minimum gene set was obtained with the minimum number [14] of genes, and the highest classification accuracy （100%） in both PRI and META datasets. A fraction of selected genes are associated with CRC or its metastasis. Conclusions- Our results demonstrated that integration analysis is an effective strategy for mining cancer- associated genes.
基金Project supported by the National Natural Science Foundation of China(Grant No.41474161)the National High-Technology Program of China(Grant No.2015AA123703)
文摘In order to satisfy the requirement of SI-traceable on-orbit absolute radiation calibration transfer with high accuracy for satellite remote sensors,a transfer chain consisting of a fiber coupling monochromator（FBM） and an integrating sphere transfer radiometer（ISTR） was designed in this paper.Depending on the Sun,this chain based on detectors provides precise spectral radiometric calibration and measurement to spectrometers in the reflective solar band（RSB） covering 300–2500 nm with a spectral bandwidth of 0.5–6 nm.It shortens the traditional chain based on lamp source and reduces the calibration uncertainty from 5% to 0.5% by using the cryogenic radiometer in space as a radiometric benchmark and trap detectors as secondary standard.This paper also gives a detailed uncertainty budget with reasonable distribution of each impact factor,including the weak spectral signal measurement with uncertainty of 0.28%.According to the peculiar design and comprehensive uncertainty analysis,it illustrates that the spectral radiance measurement uncertainty of the ISTR system can reach to 0.48%.The result satisfies the requirements of SI-traceable on-orbit calibration and has wider significance for expanding the application of the remote sensing data with high-quality.
基金Sponsored by the National Natural Science Foundation(71101149,71071160,91024006)Natural Science Foundation of Hunan Province(11JJ4065)Ph.D.Programs Foundation of Ministry of Education of China(20104307120020)
文摘As the increase of the complexity of the information warfare,its intervention strategy needs to be designed in an integrated environment.However,the current research always breaks the internal relation between equipment and tactics,and it is difficult to meet the requirements of their integrated analysis.In this paper,the research status quo of the integrated analysis about equipment and tactics is discussed first,some shortages of the current methods are summarized then,and an evolvement mechanism of the integrated analysis for equipment and tactics is given finally.Based on these,a framework of integrated analysis is proposed.This method's effectiveness is validated by an example.
文摘Process Capability Analysis (PCA) is a powerful too l to assess the ability of a process for manufacturing product that meets specific ations. The larger process capability index implies the higher process yield, a nd the larger process capability index also indicates the lower process expected loss. Chen et al. (2001) has applied indices C pu, C pl, and C pk for evaluating the process capability for a multi-process product wi th smaller-the-better, larger-the-better, and nominal-the-best specificati ons respectively. However, C pk cannot reasonably reflect the process expected loss. In this paper, index C pn is selected to replace C pk. Indices C pu, C pl, and C pn are used to evalu ate the entire process capability for a multi-process product with smaller-the -better, larger-the-better, and nominal-the-best specifications respectivel y. An integrated process capability index for a multi-process product is propo sed. The relationship between process capability index and the process yield is introduced. A multi-process capability analysis chart (MPCAC), reasonably rev ealing the status of process capability for the entire product, is constructed f or practical application. An evaluating procedure of the process capability for the entire product is also provided.
基金Naional Natural Science Foundntion of China(No.71761030)
文摘The unmanned aerial vehicles( UAV) has been becoming more and more important in the aviation industry.Despite the superior performance and advanced technology,major accident of UAV happens frequently due to the impact of their systems,long distance of remote control and skill of manipulator technology.According to the application of engineering application,failure mode effects and criticality analysis( FMECA),failure reporting analysis and corrective action comprehensive analysis systems( FRACAS)and fault tree analysis( FTA)( 3 F) were combined.And also a set of user-friendly,more time,more efficient and accurate reliability analysis system were explored.
文摘Objective:This work aimed to illuminate the potential key genes and pathways in GC tumorigenesis based on bioinfOrmatics analysis.Methods:The differentially expressed genes(DEGs)between GPL tissue samples and GC tissue samples were investigated using the GSE55696 and GSE87666 microarray data from the Gene Expression Omnibus(GEO)database.DEGs were identified by an empirical Bayes method based on the Limma R package.Then,KEGG and GO enrichment analyses of DEGs were performed followed by protein-protein interaction(PPI)network construction.Finally,the overall survival(OS)analysis of key genes was performed by the Kaplan-Meier plotter online tool.Results:A total of 250 DEGs were obtained,of which 216 were up-regulated and 34 were down-regulated.KEGG pathways analysis showed that the up-regulated DEGs were enriched in cytokine-cytokine receptor interaction,chemokine signaling pathway,metabolic pathways,PI3K-Akt signaling pathway,NF-kappa B signaling pathway,and other signaling pathways about cancer,while no down-regulated pathways were enriched.A PPI network of DEGs was constructed with 117 nodes and 660 edges,and 20 genes were selected as hub genes owing to high degrees in the network.According to the Kaplan-Meier analysis,6 out of 20 hub genes including CCR7,FPR1,C3,CXCR5,GNB4,and PPBP with high mRNA expression were associated with poor OS for GC patients.Conclusion:The results of this study provide possible factors for the occurrence of GC,and the identification of the genes and pathways associated with the progression from GPL to GC provides valuable data for investigating the pathogenesis in future studies.
文摘In this paper, sensitivity approaches are taken to analyze and design an integrated flight propulsion control system where the interaction between subsystems direitly affects the stability property and handling performances of the aircraft. The eigenvalue sen sitivity approach is employed to study the effect of coupling parameters on system stability and gain sensitivity approach is used to direct the reduced states feedback suboptimal control system design. Simulation results show that the integrated flight propulsion control system designed by sensitivity approaches is of good performance.
文摘This article describes the significance of constructing integrated gateway office offices by telecom operators in the new era,as well as the change and improvement of the function requirements of in- tegrated gateway office offices with the continuous development of cross-network services.It puts forward ZTE's overall solution for the inter-network interworking with regard to the construction of in- tegrated gateway office offices.
基金the United Nations Programme for Development(UNDP),Rede Clima(FINEP 01.13.0353.00)the Brazilian Ministry for Science and Technology for their financial support
文摘Numerical climate models render data in a gridded format which is often problematic for integrated analysis with other kinds of data in jurisdictional formats. In this paper a joint analysis of municipal Gross Domestic Product per capita (GDPc) and predicted temperature increase was undertaken in order to estimate different levels of human and economic exposure. This is based on a method of converting model outputs into a country municipal grid which enabled depicting climate predictions from the Eta-Hadgem2-ES Regional Climate Model (RCM) into the municipal level in Brazil. The conversion to country municipality grid was made using a combination of interpolation and buffering techniques in ArcGIS for two emission scenarios (RCP 4.5 and 8.5) and three timeframes (2011-2040, 2041-2070, 2071-2100) for mean temperature increase and number of heatwave days (WSDI). The results were used to support the Third National Communication (TCN) of Brazil to the United Nations Framework Convention on Climate Change (UNFCCC) and show a coherent matching of the gridded output from the original RCM. The joint climate and GDPc analysis show that in the beginning of the century the more severe warming is centred over regions where GDPc is generally higher (Centre-West and Southeast). At the end of the century, critical levels of warming spread north and northeastwards where municipalities have the lowest GDPc levels. In the high emission scenario (RCP 8.5), the strongest warming and the spreading over poorer regions are anticipated to the mid-century. These results are the key to further explore solutions for climate change adaptation based on current resources and prepare in different sectors, for long-term risk management and climate adaptation planning strategies.
文摘Since China began implementing reform and opening-up policies, along with a fast development of the national economy and great changes of social life, an increasing number of peasan＇s have kept flowing into cities and economically more developed regions. Aspiring to improve their life and yearning for a better urban life, they defy the restraint of the household registry system and, in the process of moving from one place to another, ignore economic and psychological costs. As early as in year 2000 China＇s migrant population reached 140 million, more than 10% of the total population. Since 2000 the migrant poptilation in Zhejiang Province, east China, has kept growing by 20% annually, the second fastest in the country for seven consecutive years.
基金National Natural Science Foundation of China,Grant/Award Number:72271237Building World-class Universities of Renmin University of China,Grant/Award Number:21XNF037。
文摘Deep learning has been increasingly popular in omics data analysis.Recent works incorporating variable selection into deep learning have greatly enhanced the model’s interpretability.However,because deep learning desires a large sample size,the existing methods may result in uncertain findings when the dataset has a small sample size,commonly seen in omics data analysis.With the explosion and availability of omics data from multiple populations/studies,the existing methods naively pool them into one dataset to enhance the sample size while ignoring that variable structures can differ across datasets,which might lead to inaccurate variable selection results.We propose a penalized integrative deep neural network(PIN)to simultaneously select important variables from multiple datasets.PIN directly aggregates multiple datasets as input and considers both homogeneity and heterogeneity situations among multiple datasets in an integrative analysis framework.Results from extensive simulation studies and applications of PIN to gene expression datasets from elders with different cognitive statuses or ovarian cancer patients at different stages demonstrate that PIN outperforms existing methods with considerably improved performance among multiple datasets.The source code is freely available on Github(rucliyang/PINFunc).We speculate that the proposed PIN method will promote the identification of disease-related important variables based on multiple studies/datasets from diverse origins.
基金supported by grants from the National Natural Science Foundation of China,Nos.81471238,81771327Construction of Central Nervous System Injury Basic Science and Clinical Translational Research Platform,Budget of Beijing Municipal Health Commission 2020,No.PXM2020_026280_000002(all to BYL)。
文摘Transfer RNA(t RNA)-derived small RNAs(ts RNAs) are a recently established family of regulatory small non-coding RNAs that modulate diverse biological processes. Growing evidence indicates that ts RNAs are involved in neurological disorders and play a role in the pathogenesis of neurodegenerative disease. However, whether ts RNAs are involved in traumatic brain injury-induced secondary injury remains poorly understood. In this study, a mouse controlled cortical impact model of traumatic brain injury was established, and integrated ts RNA and messenger RNA(m RNA) transcriptome sequencing were used. The results revealed that 103 ts RNAs were differentially expressed in the mouse model of traumatic brain injury at 72 hours, of which 56 ts RNAs were upregulated and 47 ts RNAs were downregulated. Based on micro RNA-like seed matching and Pearson correlation analysis, 57 differentially expressed ts RNA-m RNA interaction pairs were identified, including 29 ts RNAs and 26 m RNAs. Moreover, Gene Ontology annotation of target genes revealed that the significantly enriched terms were primarily associated with inflammation and synaptic function. Collectively, our findings suggest that ts RNAs may be associated with traumatic brain injury-induced secondary brain injury, and are thus a potential therapeutic target for traumatic brain injury. The study was approved by the Beijing Neurosurgical Institute Animal Care and Use Committee(approval No. 20190411) on April 11, 2019.
文摘The Taoudeni Basin is a typical steady intracratonic basin. Based on the distribution of effective source rocks in the Taoudeni Basin, combined with the structure characteristics of the basin and the distribution characteristics of reservoir beds, two petroleum systems are recognized in the basin： the infra-Cambrian petroleum system and the Silurian petroleum system. Structural uplift and timing of petroleum generation controlled the timing of petroleum charging and preservation of hydrocarbon accumulations. Maturity, evolution history, and distribution of effective source rocks controlled hydrocarbon richness. The geological key factors and geological processes controlled the type of hydrocarbon accumulations.
基金financially supported by the National Natural Science Foundation of China(31701449,31971968,31971899,and 31501332)the Natural Science Foundation of Heilongjiang,China(QC2017013)+7 种基金the National Key R&D Program of China(2016YFD0100500,2016YFD0100300 and 2016YFD0100201-21)the Special Financial Aid to PostDoctor Research Fellow in Heilongjiang,China(LBHTZ1714)the International Postdoctoral Exchange Fellowship Program of China Postdoctoral Council(20180004)the China Post Doctoral Project,China(2015M581419)the Post-Doctoral Project of Northeast Agricultural University,China(NEAUBH-19002)the Heilongjiang Funds for Distinguished Young Scientists,China(JC2016004 and JC2017006)the Dongnongxuezhe Project,China(to Chen Qingshan)the the Backbone of Young Talent Scholar Project(to Qi Zhaoming,18XG01)of Northeast Agricultural University,China。
文摘Soluble sugar content in seeds is an important quality trait of soybean. In this study, 57 quantitative trait loci(QTLs) related to soluble sugar contents in soybean seeds were collected from databases and published papers. After meta-overview-collinearity integrated analysis to refine QTL intervals, eight consensus QTLs were identified. To further verify the consensus QTLs, a population of chromosome segment substitution lines(CSSLs) was analyzed. Two lines containing fragments covering the regions of consensus QTLs and the recurrent parent were selected: one line showed high soluble sugar contents associated with a consensus QTL fragment, and the other line showed low soluble sugar contents. Transcriptome sequencing was conducted for these two lines at the early, middle, and late stages of seed development, which identified 158, 109 and 329 differentially expressed genes, respectively. Based on the analyses of re-sequencing data of the CSSLs and the consensus QTL region, three candidate genes(Glyma.19 G146800, Glyma.19 G122500, and Glyma.19 G128500) were identified in the genetic fragments introduced from wild soybean. Sequence comparisons between the two CSSL parents SN14 and ZYD00006 revealed a single nucleotide polymorphism(SNP) mutation in the coding sequence of Glyma.19 G122500, causing a nonsynonymous mutation in the amino acid sequence that affected the predicted protein structure. A Kompetitive allele-specific PCR(KASP) marker was developed based on this SNP and used to evaluate the CSSLs. These results lay the foundation for further research to identify genes related to soluble sugar contents in soybean seeds and for future soybean breeding.
