Synchrotron microscopic data commonly suffer from poor image quality with degraded resolution incurred by instrumentation defects or experimental conditions.Image restoration methods are often applied to recover the r...Synchrotron microscopic data commonly suffer from poor image quality with degraded resolution incurred by instrumentation defects or experimental conditions.Image restoration methods are often applied to recover the reduced resolution,providing improved image details that can greatly facilitate scientific discovery.Among these methods,deconvolution techniques are straightforward,yet either require known prior information or struggle to tackle large experimental data.Deep learning(DL)-based super-resolution(SR)methods handle large data well,however data scarcity and model generalizability are problematic.In addition,current image restoration methods are mostly offline and inefficient for many beamlines where high data volumes and data complexity issues are encountered.To overcome these limitations,an online image-restoration pipeline that adaptably selects suitable algorithms and models from a method repertoire is promising.In this study,using both deconvolution and pretrained DL-based SR models,we show that different restoration efficacies can be achieved on different types of synchrotron experimental data.We describe the necessity,feasibility,and significance of constructing such an image-restoration pipeline for future synchrotron experiments.展开更多
BACKGROUND Oxidative stress is closely associated with hypertensive outcomes.The oxidative balance score(OBS)measures oxidative stress exposure from dietary and lifestyle elements.The objective of this study was to in...BACKGROUND Oxidative stress is closely associated with hypertensive outcomes.The oxidative balance score(OBS)measures oxidative stress exposure from dietary and lifestyle elements.The objective of this study was to investigate the association between OBS and mortality in hypertensive patients.METHODS This study included 7823 hypertensive patients from the National Health and Nutrition Examination Survey(NHA-NES)1999-2014.Several models,including Cox regression,restricted cubic splines(RCS),Kaplan-Meier survival analysis,subgroup,and sensitivity analyses,were exploited to investigate the relationship between OBS and the risk of mortality.RESULTS Controlling for all potential confounders,a significantly inverse association was observed between elevated OBS and all-cause[hazard ratio(HR)=0.90,95%CI:0.85-0.95]and cardiovascular mortality(HR=0.85,95%CI:0.75-0.95).With adjustment for covariates,significant associations between lifestyle OBS and mortality risks diminished,whereas associations between dietary OBS and these mortality risks remained robust(all-cause mortality:HR=0.91,95%CI:0.86-0.96;cardiovascular mortality:HR=0.85,95%CI:0.76-0.96).RCS demonstrated a linear relationship between OBS and all-cause and cardiovascular mortality risk(P_(nonlinear)=0.088 and P_(nonlinear)=0.447,respectively).Kaplan-Meier curves demonstrated that the mortality rate was lower with a high OBS(P<0.001).The consistency of the association was demonstrated in subgroup and sensitivity analyses.RCS after stratification showed that among current drinkers,those with higher OBS had a lower risk of mortality compared with former or never drinkers.CONCLUSIONS In hypertensive individuals,there was a negative association between OBS and all-cause and cardiovascular mortality.Encouraging hypertensive individuals,especially those currently drinking,to maintain high levels of OBS may be beneficial in improving their prognosis.展开更多
BACKGROUND： The integrative analysis of microRNA and mRNA expression profiles can elucidate microRNA-targeted gene function. We used this technique to elucidate insights into the immunological pathology of non-alcoho...BACKGROUND： The integrative analysis of microRNA and mRNA expression profiles can elucidate microRNA-targeted gene function. We used this technique to elucidate insights into the immunological pathology of non-alcoholic fatty liver disease （NAFLD）. METHODS： We analyzed differentially expressed microRNA and mRNA expression profiles of CD4＋ T lymphocytes from the liver and mesenteric lymph nodes （MLNs） of mice with NAFLD using microarrays and RNA sequencing. Normal mice were used as controls. The target genes of microRNAs were predicted by TargetScan. Integrative analysis showed that the mRNAs were overlapped with microRNAs. Furthermore, the Gene Ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） analyses were performed to predict the key genes and pathways. Then, 16 microRNAs and 10 mRNAs were validated by qRT-PCR. RESULTS： Microarray analysis suggested that 170 microRNAs were significantly de-regulated in CD4＋ T lymphocytes from the liver between the two groups. Eighty mRNAs corresponded with microRNA targeted genes. KEGG analysis indicated that the MAPK pathway was consistently augmented in the liver of NAFLD mice. miR-23b, let-7e, miR-128 and miR-130b possibly played significant parts in the MAPK pathways. Furthermore, between the two groups, 237 microRNAs were significantly deregulated in CD4＋ T lymphocytes from MLNs. 38 mRNAs coincided with microRNA target genes. The metabolic pathway was consistently enriched in the MLNs of NAFLD mice. miR- 206-3p, miR-181a-Sp, miR-29c-3p and miR-30d-5p likely play important roles in the regulation of metabolic pathways. CONCLUSION： The results of this study presented a new perspective on the application of integrative analysis to identify complex regulation means involved in the immunological pathogenesis of NAFLD.展开更多
The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement.However,little is known about the factors t...The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement.However,little is known about the factors that shape and maintain genetic diversity.Here,we assembled a high-quality chromosome-level reference of the Chinese common apricot‘Yinxiangbai’,and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries.We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries.We also detected seven migration events among different apricot groups,where 27%of the genome was identified as being introgressed.Remarkably,we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups.Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.展开更多
The ASTER (Advanced Space-borne Thermal Emission and Reflection radiometer) data, including all the 3 parts: VNIR (Visible and Near-Infrared), SWIR (Short Wave Infrared), TIR (Thermal Infrared), were applied for extra...The ASTER (Advanced Space-borne Thermal Emission and Reflection radiometer) data, including all the 3 parts: VNIR (Visible and Near-Infrared), SWIR (Short Wave Infrared), TIR (Thermal Infrared), were applied for extraction of mineral deposits, such as the Ni-Cu deposit in eastern Tianshan, the gypsum in western Tianshan, and the borax in Tibetan. This paper discusses the extraction methodology using the ASTER remote sensing data and reveals the good extraction results. This paper bravely represents the summary of the main achievement for this field by the scientists in other countries and gives a comparison with the works by others. The new achievements, described in this paper, comprise the extraction of anomalies for Ni-Cu deposit, gypsum, and borax.展开更多
Purpose Fly scans are indispensable in many experiments at the High Energy Photon Source(HEPS).PandABox,the main platform to implement fly scans at HEPS,needs to be integrated into Mamba,the experiment control system ...Purpose Fly scans are indispensable in many experiments at the High Energy Photon Source(HEPS).PandABox,the main platform to implement fly scans at HEPS,needs to be integrated into Mamba,the experiment control system developed at HEPS based on Bluesky.Methods In less than 600 lines of easily customisable and extensible backend code,provided are full control of PandABox’s TCP server in native ophyd,automated configuration(also including wiring)of“PandA blocks”for constant-speed mapping experiments of various dimensions,as well as generation of scans deliberately fragmented to deal with hardware limits in numbers of exposure frames or sequencer table entries.Results The upper-level control system for PandABox has been ported to Bluesky,enabling the combination of both components’flexibility in fly-scan applications.Based on this backend,a user-friendly Mamba frontend is developed for X-ray fluorescence(XRF)mapping experiments,which provides fully online visual feedback.展开更多
Background： Survivin is an oncoprotein silenced in normal mature tissues but reactivated in serous ovarian cancer （SOC）. Although transcriptional activation is assumed for its overexpression, the long 3＇-untransla...Background： Survivin is an oncoprotein silenced in normal mature tissues but reactivated in serous ovarian cancer （SOC）. Although transcriptional activation is assumed for its overexpression, the long 3＇-untranslated region （3＇-UTR） in survivin gene, which contains many alternate polyadenylation （APA） sites, implies a propensity for posttranscriptional control and therefore was the aim of our study. Methods： The abundance of the coding region, the proximal and the distal region of survivin mRNA 3＇-UTR, was evaluated by real-time polymerase chain reaction （PCR） in SOC samples, cell lines, and normal fallopian tube （NFT） tissues. The APA sites were confirmed by rapid amplification ofcDNA 3＇ ends and DNA sequencing. Real-time PCR were used to screen survivin-targeting microRNAs （miRNAs） that were inversely correlated with survivin. The expression of an inversely correlated miRNA was restored by pre-miRNA transfection or induction with a genotoxic agent to test its inhibitory effect on survivin overexpression. Results： Varying degrees of APA were observed in SOC by comparing the abundance of the proximal and the distal region of survivin 3＇-UTR, and changes of 3＇-UTR correlated significantly with survivin expression （r = 0.708, P 〈 0.01）. The main APA sites are proved at 1197 and 1673 of survivin 3＇-UTR by DNA sequencing. Higher level of 3＇-UTR proximal region than coding region was observed in NFT, as well as in SOC and cell lines. Among the survivin-targeting miRNAs, only a few highly expressed miRNAs were inversely correlated with survivin levels, and they mainly targeted the distal part of the 3＇-UTR. However, in ovarian cancer cells, restoration of an inversely correlated miRNA （miR-34c） showed little effect on survivin expression. Conclusions： In NFT tissues, survivin is not transcriptionally silenced but regulate posttranscriptionally. In SOC, aberrant APA leads to the shortening of survivin 3＇-UTR which enables it to escape the negative regulation of miRNAs and is responsible for survivin up-regulation.展开更多
基金supported by the Beijing Natural Science Foundation(No.1234042)the National Key Research and Development Program for Young Scientists(No.2023YFA1609900)+1 种基金the Strategic Priority Research Program of Chinese Academy of Sciences(No.XDB37000000)the National Natural Science Foundation of China(No.12305371)。
文摘Synchrotron microscopic data commonly suffer from poor image quality with degraded resolution incurred by instrumentation defects or experimental conditions.Image restoration methods are often applied to recover the reduced resolution,providing improved image details that can greatly facilitate scientific discovery.Among these methods,deconvolution techniques are straightforward,yet either require known prior information or struggle to tackle large experimental data.Deep learning(DL)-based super-resolution(SR)methods handle large data well,however data scarcity and model generalizability are problematic.In addition,current image restoration methods are mostly offline and inefficient for many beamlines where high data volumes and data complexity issues are encountered.To overcome these limitations,an online image-restoration pipeline that adaptably selects suitable algorithms and models from a method repertoire is promising.In this study,using both deconvolution and pretrained DL-based SR models,we show that different restoration efficacies can be achieved on different types of synchrotron experimental data.We describe the necessity,feasibility,and significance of constructing such an image-restoration pipeline for future synchrotron experiments.
基金supported by the National Natural Science Foundation of China(No.81960074)the Natural Science Foundation-Outstanding Youth Fund Project of Jiangxi Province(No.20232ACB216006)。
文摘BACKGROUND Oxidative stress is closely associated with hypertensive outcomes.The oxidative balance score(OBS)measures oxidative stress exposure from dietary and lifestyle elements.The objective of this study was to investigate the association between OBS and mortality in hypertensive patients.METHODS This study included 7823 hypertensive patients from the National Health and Nutrition Examination Survey(NHA-NES)1999-2014.Several models,including Cox regression,restricted cubic splines(RCS),Kaplan-Meier survival analysis,subgroup,and sensitivity analyses,were exploited to investigate the relationship between OBS and the risk of mortality.RESULTS Controlling for all potential confounders,a significantly inverse association was observed between elevated OBS and all-cause[hazard ratio(HR)=0.90,95%CI:0.85-0.95]and cardiovascular mortality(HR=0.85,95%CI:0.75-0.95).With adjustment for covariates,significant associations between lifestyle OBS and mortality risks diminished,whereas associations between dietary OBS and these mortality risks remained robust(all-cause mortality:HR=0.91,95%CI:0.86-0.96;cardiovascular mortality:HR=0.85,95%CI:0.76-0.96).RCS demonstrated a linear relationship between OBS and all-cause and cardiovascular mortality risk(P_(nonlinear)=0.088 and P_(nonlinear)=0.447,respectively).Kaplan-Meier curves demonstrated that the mortality rate was lower with a high OBS(P<0.001).The consistency of the association was demonstrated in subgroup and sensitivity analyses.RCS after stratification showed that among current drinkers,those with higher OBS had a lower risk of mortality compared with former or never drinkers.CONCLUSIONS In hypertensive individuals,there was a negative association between OBS and all-cause and cardiovascular mortality.Encouraging hypertensive individuals,especially those currently drinking,to maintain high levels of OBS may be beneficial in improving their prognosis.
基金supported by a grant from the National Natural Science Foundation of China(81170375)
文摘BACKGROUND： The integrative analysis of microRNA and mRNA expression profiles can elucidate microRNA-targeted gene function. We used this technique to elucidate insights into the immunological pathology of non-alcoholic fatty liver disease （NAFLD）. METHODS： We analyzed differentially expressed microRNA and mRNA expression profiles of CD4＋ T lymphocytes from the liver and mesenteric lymph nodes （MLNs） of mice with NAFLD using microarrays and RNA sequencing. Normal mice were used as controls. The target genes of microRNAs were predicted by TargetScan. Integrative analysis showed that the mRNAs were overlapped with microRNAs. Furthermore, the Gene Ontology （GO） and Kyoto Encyclopedia of Genes and Genomes （KEGG） analyses were performed to predict the key genes and pathways. Then, 16 microRNAs and 10 mRNAs were validated by qRT-PCR. RESULTS： Microarray analysis suggested that 170 microRNAs were significantly de-regulated in CD4＋ T lymphocytes from the liver between the two groups. Eighty mRNAs corresponded with microRNA targeted genes. KEGG analysis indicated that the MAPK pathway was consistently augmented in the liver of NAFLD mice. miR-23b, let-7e, miR-128 and miR-130b possibly played significant parts in the MAPK pathways. Furthermore, between the two groups, 237 microRNAs were significantly deregulated in CD4＋ T lymphocytes from MLNs. 38 mRNAs coincided with microRNA target genes. The metabolic pathway was consistently enriched in the MLNs of NAFLD mice. miR- 206-3p, miR-181a-Sp, miR-29c-3p and miR-30d-5p likely play important roles in the regulation of metabolic pathways. CONCLUSION： The results of this study presented a new perspective on the application of integrative analysis to identify complex regulation means involved in the immunological pathogenesis of NAFLD.
基金This work was funded by the National Key Research and Development Program of China(2019YFD1000600)the National Natural Science Foundation of China(No.3197236)+2 种基金the National Natural Science Foundation of China(No.31870199)the Scientific Research Fund for Public Welfare in Liaoning(20180025)the Program of Conservation and Utilization of Crop Germplasm Resources and National Crop Germplasm Resources Platform of China,and the National Key R&D Program of China(Grant No.2019YFD1000400).
文摘The genetic diversity of germplasm is critical for exploring genetic and phenotypic resources and has important implications for crop-breeding sustainability and improvement.However,little is known about the factors that shape and maintain genetic diversity.Here,we assembled a high-quality chromosome-level reference of the Chinese common apricot‘Yinxiangbai’,and we resequenced 180 apricot accessions that cover four major ecogeographical groups in China and other accessions from occidental countries.We concluded that Chinese-cultivated common apricot germplasms possessed much higher genetic diversity than those cultivated in Western countries.We also detected seven migration events among different apricot groups,where 27%of the genome was identified as being introgressed.Remarkably,we demonstrated that these introgressed regions drove the current high level of germplasm diversity in Chinese-cultivated common apricots by introducing different genes related to distinct phenotypes from different cultivated groups.Our results highlight the consideration that introgressed regions may provide an important reservoir of genetic resources that can be used to sustain modern breeding programs.
文摘The ASTER (Advanced Space-borne Thermal Emission and Reflection radiometer) data, including all the 3 parts: VNIR (Visible and Near-Infrared), SWIR (Short Wave Infrared), TIR (Thermal Infrared), were applied for extraction of mineral deposits, such as the Ni-Cu deposit in eastern Tianshan, the gypsum in western Tianshan, and the borax in Tibetan. This paper discusses the extraction methodology using the ASTER remote sensing data and reveals the good extraction results. This paper bravely represents the summary of the main achievement for this field by the scientists in other countries and gives a comparison with the works by others. The new achievements, described in this paper, comprise the extraction of anomalies for Ni-Cu deposit, gypsum, and borax.
基金supported by the National Science Foundation for Young Scientists of China(Grants No.12005253 and No.12205328)the Strategic Priority Research Program of Chinese Academy of Sciences(XDB37000000)the Technological Innovation Program of Institute of High Energy Physics of Chinese Academy of Sciences(E25455U210).
文摘Purpose Fly scans are indispensable in many experiments at the High Energy Photon Source(HEPS).PandABox,the main platform to implement fly scans at HEPS,needs to be integrated into Mamba,the experiment control system developed at HEPS based on Bluesky.Methods In less than 600 lines of easily customisable and extensible backend code,provided are full control of PandABox’s TCP server in native ophyd,automated configuration(also including wiring)of“PandA blocks”for constant-speed mapping experiments of various dimensions,as well as generation of scans deliberately fragmented to deal with hardware limits in numbers of exposure frames or sequencer table entries.Results The upper-level control system for PandABox has been ported to Bluesky,enabling the combination of both components’flexibility in fly-scan applications.Based on this backend,a user-friendly Mamba frontend is developed for X-ray fluorescence(XRF)mapping experiments,which provides fully online visual feedback.
文摘Background： Survivin is an oncoprotein silenced in normal mature tissues but reactivated in serous ovarian cancer （SOC）. Although transcriptional activation is assumed for its overexpression, the long 3＇-untranslated region （3＇-UTR） in survivin gene, which contains many alternate polyadenylation （APA） sites, implies a propensity for posttranscriptional control and therefore was the aim of our study. Methods： The abundance of the coding region, the proximal and the distal region of survivin mRNA 3＇-UTR, was evaluated by real-time polymerase chain reaction （PCR） in SOC samples, cell lines, and normal fallopian tube （NFT） tissues. The APA sites were confirmed by rapid amplification ofcDNA 3＇ ends and DNA sequencing. Real-time PCR were used to screen survivin-targeting microRNAs （miRNAs） that were inversely correlated with survivin. The expression of an inversely correlated miRNA was restored by pre-miRNA transfection or induction with a genotoxic agent to test its inhibitory effect on survivin overexpression. Results： Varying degrees of APA were observed in SOC by comparing the abundance of the proximal and the distal region of survivin 3＇-UTR, and changes of 3＇-UTR correlated significantly with survivin expression （r = 0.708, P 〈 0.01）. The main APA sites are proved at 1197 and 1673 of survivin 3＇-UTR by DNA sequencing. Higher level of 3＇-UTR proximal region than coding region was observed in NFT, as well as in SOC and cell lines. Among the survivin-targeting miRNAs, only a few highly expressed miRNAs were inversely correlated with survivin levels, and they mainly targeted the distal part of the 3＇-UTR. However, in ovarian cancer cells, restoration of an inversely correlated miRNA （miR-34c） showed little effect on survivin expression. Conclusions： In NFT tissues, survivin is not transcriptionally silenced but regulate posttranscriptionally. In SOC, aberrant APA leads to the shortening of survivin 3＇-UTR which enables it to escape the negative regulation of miRNAs and is responsible for survivin up-regulation.
