Background:Genotyping by sequencing(GBS)still has problems with missing genotypes.Imputation is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing genotypes.Mi...Background:Genotyping by sequencing(GBS)still has problems with missing genotypes.Imputation is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing genotypes.Minor allele frequency(MAF)is widely used as a marker data editing criteria for genomic predictions.In this study,three imputation methods(Beagle,IMPUTE2 and FImpute software)based on four MAF editing criteria were investigated with regard to imputation accuracy of missing genotypes and accuracy of genomic predictions,based on simulated data of livestock population.Results:Four MAFs(no MAF limit,MAF≥0.001,MAF≥0.01 and MAF≥0.03)were used for editing marker data before imputation.Beagle,IMPUTE2 and FImpute software were applied to impute the original GBS.Additionally,IMPUTE2 also imputed the expected genotype dosage after genotype correction(GcIM).The reliability of genomic predictions was calculated using GBS and imputed GBS data.The results showed that imputation accuracies were the same for the three imputation methods,except for the data of sequencing read depth(depth)=2,where FImpute had a slightly lower imputation accuracy than Beagle and IMPUTE2.GcIM was observed to be the best for all of the imputations at depth=4,5 and 10,but the worst for depth=2.For genomic prediction,retaining more SNPs with no MAF limit resulted in higher reliability.As the depth increased to 10,the prediction reliabilities approached those using true genotypes in the GBS loci.Beagle and IMPUTE2 had the largest increases in prediction reliability of 5 percentage points,and FImpute gained 3 percentage points at depth=2.The best prediction was observed at depth=4,5 and 10 using GcIM,but the worst prediction was also observed using GcIM at depth=2.Conclusions:The current study showed that imputation accuracies were relatively low for GBS with low depths and high for GBS with high depths.Imputation resulted in larger gains in the reliability of genomic predictions for GBS with lower depths.These results suggest that the application of IMPUTE2,based on a corrected GBS(GcIM)to improve genomic predictions for higher depths,and FImpute software could be a good alternative for routine imputation.展开更多
Background: MicroRNAs act as post-transcriptional regulators that repress translation or degrade mRNA transcripts.Each microRNA has many mRNA targets and each mRNA may be targeted by several microRNAs. Skeletal muscle...Background: MicroRNAs act as post-transcriptional regulators that repress translation or degrade mRNA transcripts.Each microRNA has many mRNA targets and each mRNA may be targeted by several microRNAs. Skeletal muscles express a plethora of microRNA genes that regulate muscle development and function by controlling the expression of protein-coding target genes. To expand our understanding of the role of microRNA, specifically btamiR-365-3 p, in muscle biology, we investigated its functions in regulating primary bovine myoblast proliferation and differentiation.Results: Firstly, we found that bta-miR-365-3 p was predominantly expressed in skeletal muscle and heart tissue in Chinese Qinchuan beef cattle. Quantitative PCR and western blotting results showed that overexpression of btamiR-365-3 p significantly reduced the expression levels of cyclin D1(CCND1), cyclin dependent kinase 2(CDK2) and proliferating cell nuclear antigen(PCNA) but stimulated the expression levels of muscle differentiation markers, i.e.,MYOD1, MYOG at both mRNA and protein level. Moreover, downregulation of bta-miR-365-3 p increased the expression of CCND1, CDK2 and PCNA but decreased the expression of MYOD1 and MYOG at both mRNA and protein levels. Furthermore, flow cytometry, EdU proliferation assays and immunostaining results showed that increased levels of bta-miR-365-3 p suppressed cell proliferation but promoted myotube formation, whereas decreased levels of bta-miR-365-3 p resulted in the opposite consequences. Finally, we identified that activin A receptor type I(ACVR1) could be a direct target of bta-miR-365-3 p. It was demonstrated that bta-miR-365-3 p can bind to the 3'UTR of ACVR1 gene to regulate its expression based on dual luciferase gene reporter assays.Consistently, knock-down of ACVR1 was associated with decreased expressions of CDK2, CCND1 and PCNA but increased expression of MYOG and MYOD1 both at mRNA and protein level.Conclusion: Collectively, these data suggested that bta-miR-365-3 p represses proliferation but promotes differentiation of bovine myoblasts through several biological mechanisms involving downregulation of ACVR1.展开更多
Purpose:As scientific resources are widely distributed,researchers often have difficulties in acquiring information from different individual sources.This paper intends to present a new approach to construct a subject...Purpose:As scientific resources are widely distributed,researchers often have difficulties in acquiring information from different individual sources.This paper intends to present a new approach to construct a subject-knowledge-based integration platform which was carried out by the Institute of Software,Chinese Academy of Sciences(ISCAS).Our aim is to use technique tools to strengthen the library service by combining a variety of information service resources with knowledge tools.Design/methodology/approach:Based on the analysis of users' needs,we established a collaborative team across ISCAS Library,National Science Library of CAS(NSL CAS),and ISCAS' research groups or research labs.With the service tools developed by ISCAS Library,we embedded other multipurpose utility tools of knowledge integration into the platform as to make full use of software tools in knowledge integration,knowledge fusion,and intelligent push of library services to end users.Findings:With a hard effort of the construction team,the ISCAS subject group platform(hereinafter as ISCAS Platform) has integrated such information resources as institutional repository(IR) of ISCAS,open resources from websites and subject resources of computer sciences.Up to date,ISCAS platform can provide integrated information services including data collection for computer science and intelligent generation of citation reports,by means of embedding self-developed discovering tools for domain experts and subject content,and generation tools for scientific citation reports.Research limitations:Knowledge organization need be further improved in the ISCAS subject group platform.In addition,functions for academic exchanges need be maximized as to meet the individual demands of researchers for library services at the Platform.Practical implications:Since we Platform has been put into use through the Library website of the ISCAS in June 2012,many academic libraries from both domestic universities and CAS institutes have showed their strong interest for our self-developed tools,among which more than 10 cooperation partnerships have been formed.Originality/value:Through self-developed service tools and the integration of multiple-type resources,our Platform has solved such key problems as timely access and update of the trusted resources from a third party,and the rapid fusion and extension of library resources while establishing subject knowledge environment.So the ISCAS library can provide a flexible customization of library services according to the need of different users.展开更多
Vermicomposting is a feasible method for disposing of lignocellulosic waste while generating a useful product.The current study assessed the potential of vermicomposting green waste mixed with sugarcane bagasse in pro...Vermicomposting is a feasible method for disposing of lignocellulosic waste while generating a useful product.The current study assessed the potential of vermicomposting green waste mixed with sugarcane bagasse in proportions of 25%,50%,and 75%(v:v,based on dry weight).The suitability was evaluated based on the agrochemical properties,earthworm biomass,and phytotoxicity.The final vermicomposts exhibited near-neutral pH values(7.1-7.6),and lower EC values(0.43-0.72 mS/cm)and C:N ratios(14.1-19.9).The content of available nutrients and CEC for all the vermicomposts exceeded those of the control compost(without earthworms).For vermicomposts,the average values of NO3-N,AP,AK,and CEC were 53,517,1362 mg/kg,and 158 cmol/kg,respectively.The total contents of heavy metals increased in all vermicompost treatments compared to control composts with the following average final percentages:Zn(2.0%),Cr(15.5%),Pb(23.4%),and Cu(44.3%),but these amounts were safe for application in agroforestry.The addition of sugarcane bagasse to green waste significantly increased the content of total humic substance,humic acid and urease activity,acid and alkaline phosphatase activity,and Eisenia fetida reproduction.The addition of 25%sugarcane bagasse to green waste decreased the toxicity to germinating seeds.These results revealed that vermicomposting is a feasible way to degrade green waste into a value-added chemical product.展开更多
Frostbite in Southwestern China has been overlooked due to its low incidence,relatively mild temperature and lack of literature published before.However,it needs to be further studied for religious diversity and disti...Frostbite in Southwestern China has been overlooked due to its low incidence,relatively mild temperature and lack of literature published before.However,it needs to be further studied for religious diversity and distinct geomorphology.In this article,we reported an 18-year-old Tibetan girl who suffered from blizzard attack during pilgrimage.Her feet and several fingers showed mummified gangrene upon physical examination with poor movement.She was diagnosed with 3rd to 4th degree of frostbite.The girl was given oral ibuprofen,debridement and other regular treatment daily,but she was eventually amputated due to insufficient thrombolytic management in primary hospital,delayed informing consent in the referral hospital and ethnic conflict between religion and guidelines.This case enriched the experience of managing complex frostbite in Tibetan population and alarms that efforts should be integrated to protect pilgrims and mountaineers in the Tibetan region.展开更多
Objective:The current study aimed to profile the demographics,hematological index,and extrinsic factors of patients treated for frostbite in a single center in Southwest China.Methods:We collected the clinical data of...Objective:The current study aimed to profile the demographics,hematological index,and extrinsic factors of patients treated for frostbite in a single center in Southwest China.Methods:We collected the clinical data of patients with frostbite admitted to a regional hospital from January 1st,2009 to January 1st,2019.The baseline information was summarized,and the causes and hematological indexes of frostbite were analyzed.Results:The study cohort comprised 27 patients.The median patient age was 22 years(range 14-81 years).All frostbite injuries occurred between September 22nd and April 27th.Half of the patients were Tibetans.Cold injuries in Tibetan patients were associated with pilgrimage(70%,9/13)and grazing(15%,2/13),while the leading causes of frostbite in Han residents of the Southwest China basin were mandatory fieldwork without protection(36%,5/14)and loss of consciousness(36%,5/14).The hematological examination findings did not significantly differ between amputees and those who did not undergo amputation.Several hematological indexes significantly differed between patients with good outcomes versus those with poor outcomes.Conclusion:To avoid severe frostbite damage,routine mandatory activities like pilgrimage should be conducted under proper protection in extreme weather.Hematological indexes such as the red blood cell count,hematocrit,and hemoglobin level should be monitored closely by first-line medical personnel during hospitalization,as these indexes might indicate the outcome of frostbite.Further research is needed to improve the management of patients with frostbite in Southwest China.展开更多
基金This study was funded by the Genomic Selection in Animals and Plants(GenSAP)research project financed by the Danish Council of Strategic Research(Aarhus,Denmark).Xiao Wang received Ph.D.stipends from the Technical University of Denmark(DTU Bioinformatics and DTU Compute),Denmark,and the China Scholarship Council,China.
文摘Background:Genotyping by sequencing(GBS)still has problems with missing genotypes.Imputation is important for using GBS for genomic predictions,especially for low depths,due to the large number of missing genotypes.Minor allele frequency(MAF)is widely used as a marker data editing criteria for genomic predictions.In this study,three imputation methods(Beagle,IMPUTE2 and FImpute software)based on four MAF editing criteria were investigated with regard to imputation accuracy of missing genotypes and accuracy of genomic predictions,based on simulated data of livestock population.Results:Four MAFs(no MAF limit,MAF≥0.001,MAF≥0.01 and MAF≥0.03)were used for editing marker data before imputation.Beagle,IMPUTE2 and FImpute software were applied to impute the original GBS.Additionally,IMPUTE2 also imputed the expected genotype dosage after genotype correction(GcIM).The reliability of genomic predictions was calculated using GBS and imputed GBS data.The results showed that imputation accuracies were the same for the three imputation methods,except for the data of sequencing read depth(depth)=2,where FImpute had a slightly lower imputation accuracy than Beagle and IMPUTE2.GcIM was observed to be the best for all of the imputations at depth=4,5 and 10,but the worst for depth=2.For genomic prediction,retaining more SNPs with no MAF limit resulted in higher reliability.As the depth increased to 10,the prediction reliabilities approached those using true genotypes in the GBS loci.Beagle and IMPUTE2 had the largest increases in prediction reliability of 5 percentage points,and FImpute gained 3 percentage points at depth=2.The best prediction was observed at depth=4,5 and 10 using GcIM,but the worst prediction was also observed using GcIM at depth=2.Conclusions:The current study showed that imputation accuracies were relatively low for GBS with low depths and high for GBS with high depths.Imputation resulted in larger gains in the reliability of genomic predictions for GBS with lower depths.These results suggest that the application of IMPUTE2,based on a corrected GBS(GcIM)to improve genomic predictions for higher depths,and FImpute software could be a good alternative for routine imputation.
基金supported by the National Natural Science Foundation of China (No.31772574)the Program of National Beef Cattle and Yak Industrial Technology System (CARS-37)the scholarship from the China Scholarship Council (CSC),China。
文摘Background: MicroRNAs act as post-transcriptional regulators that repress translation or degrade mRNA transcripts.Each microRNA has many mRNA targets and each mRNA may be targeted by several microRNAs. Skeletal muscles express a plethora of microRNA genes that regulate muscle development and function by controlling the expression of protein-coding target genes. To expand our understanding of the role of microRNA, specifically btamiR-365-3 p, in muscle biology, we investigated its functions in regulating primary bovine myoblast proliferation and differentiation.Results: Firstly, we found that bta-miR-365-3 p was predominantly expressed in skeletal muscle and heart tissue in Chinese Qinchuan beef cattle. Quantitative PCR and western blotting results showed that overexpression of btamiR-365-3 p significantly reduced the expression levels of cyclin D1(CCND1), cyclin dependent kinase 2(CDK2) and proliferating cell nuclear antigen(PCNA) but stimulated the expression levels of muscle differentiation markers, i.e.,MYOD1, MYOG at both mRNA and protein level. Moreover, downregulation of bta-miR-365-3 p increased the expression of CCND1, CDK2 and PCNA but decreased the expression of MYOD1 and MYOG at both mRNA and protein levels. Furthermore, flow cytometry, EdU proliferation assays and immunostaining results showed that increased levels of bta-miR-365-3 p suppressed cell proliferation but promoted myotube formation, whereas decreased levels of bta-miR-365-3 p resulted in the opposite consequences. Finally, we identified that activin A receptor type I(ACVR1) could be a direct target of bta-miR-365-3 p. It was demonstrated that bta-miR-365-3 p can bind to the 3'UTR of ACVR1 gene to regulate its expression based on dual luciferase gene reporter assays.Consistently, knock-down of ACVR1 was associated with decreased expressions of CDK2, CCND1 and PCNA but increased expression of MYOG and MYOD1 both at mRNA and protein level.Conclusion: Collectively, these data suggested that bta-miR-365-3 p represses proliferation but promotes differentiation of bovine myoblasts through several biological mechanisms involving downregulation of ACVR1.
基金supported by the Chinese Academy of Sciences(Grant No.Y11006)
文摘Purpose:As scientific resources are widely distributed,researchers often have difficulties in acquiring information from different individual sources.This paper intends to present a new approach to construct a subject-knowledge-based integration platform which was carried out by the Institute of Software,Chinese Academy of Sciences(ISCAS).Our aim is to use technique tools to strengthen the library service by combining a variety of information service resources with knowledge tools.Design/methodology/approach:Based on the analysis of users' needs,we established a collaborative team across ISCAS Library,National Science Library of CAS(NSL CAS),and ISCAS' research groups or research labs.With the service tools developed by ISCAS Library,we embedded other multipurpose utility tools of knowledge integration into the platform as to make full use of software tools in knowledge integration,knowledge fusion,and intelligent push of library services to end users.Findings:With a hard effort of the construction team,the ISCAS subject group platform(hereinafter as ISCAS Platform) has integrated such information resources as institutional repository(IR) of ISCAS,open resources from websites and subject resources of computer sciences.Up to date,ISCAS platform can provide integrated information services including data collection for computer science and intelligent generation of citation reports,by means of embedding self-developed discovering tools for domain experts and subject content,and generation tools for scientific citation reports.Research limitations:Knowledge organization need be further improved in the ISCAS subject group platform.In addition,functions for academic exchanges need be maximized as to meet the individual demands of researchers for library services at the Platform.Practical implications:Since we Platform has been put into use through the Library website of the ISCAS in June 2012,many academic libraries from both domestic universities and CAS institutes have showed their strong interest for our self-developed tools,among which more than 10 cooperation partnerships have been formed.Originality/value:Through self-developed service tools and the integration of multiple-type resources,our Platform has solved such key problems as timely access and update of the trusted resources from a third party,and the rapid fusion and extension of library resources while establishing subject knowledge environment.So the ISCAS library can provide a flexible customization of library services according to the need of different users.
基金This work was funded by the National Forestry Public Welfare Project of China(Grant No.201504205).
文摘Vermicomposting is a feasible method for disposing of lignocellulosic waste while generating a useful product.The current study assessed the potential of vermicomposting green waste mixed with sugarcane bagasse in proportions of 25%,50%,and 75%(v:v,based on dry weight).The suitability was evaluated based on the agrochemical properties,earthworm biomass,and phytotoxicity.The final vermicomposts exhibited near-neutral pH values(7.1-7.6),and lower EC values(0.43-0.72 mS/cm)and C:N ratios(14.1-19.9).The content of available nutrients and CEC for all the vermicomposts exceeded those of the control compost(without earthworms).For vermicomposts,the average values of NO3-N,AP,AK,and CEC were 53,517,1362 mg/kg,and 158 cmol/kg,respectively.The total contents of heavy metals increased in all vermicompost treatments compared to control composts with the following average final percentages:Zn(2.0%),Cr(15.5%),Pb(23.4%),and Cu(44.3%),but these amounts were safe for application in agroforestry.The addition of sugarcane bagasse to green waste significantly increased the content of total humic substance,humic acid and urease activity,acid and alkaline phosphatase activity,and Eisenia fetida reproduction.The addition of 25%sugarcane bagasse to green waste decreased the toxicity to germinating seeds.These results revealed that vermicomposting is a feasible way to degrade green waste into a value-added chemical product.
基金National Natural Science Foundation of China,No.81872535Sichuan Province Pharmaceutical Administration,No.2018HJZX022.
文摘Frostbite in Southwestern China has been overlooked due to its low incidence,relatively mild temperature and lack of literature published before.However,it needs to be further studied for religious diversity and distinct geomorphology.In this article,we reported an 18-year-old Tibetan girl who suffered from blizzard attack during pilgrimage.Her feet and several fingers showed mummified gangrene upon physical examination with poor movement.She was diagnosed with 3rd to 4th degree of frostbite.The girl was given oral ibuprofen,debridement and other regular treatment daily,but she was eventually amputated due to insufficient thrombolytic management in primary hospital,delayed informing consent in the referral hospital and ethnic conflict between religion and guidelines.This case enriched the experience of managing complex frostbite in Tibetan population and alarms that efforts should be integrated to protect pilgrims and mountaineers in the Tibetan region.
基金The study was supported by the 1.3.5 project for disciplines of excellence,West China Hospital,Sichuan University(No.ZYJC21036)National Natural Science Foundation of China(No.82003373).
文摘Objective:The current study aimed to profile the demographics,hematological index,and extrinsic factors of patients treated for frostbite in a single center in Southwest China.Methods:We collected the clinical data of patients with frostbite admitted to a regional hospital from January 1st,2009 to January 1st,2019.The baseline information was summarized,and the causes and hematological indexes of frostbite were analyzed.Results:The study cohort comprised 27 patients.The median patient age was 22 years(range 14-81 years).All frostbite injuries occurred between September 22nd and April 27th.Half of the patients were Tibetans.Cold injuries in Tibetan patients were associated with pilgrimage(70%,9/13)and grazing(15%,2/13),while the leading causes of frostbite in Han residents of the Southwest China basin were mandatory fieldwork without protection(36%,5/14)and loss of consciousness(36%,5/14).The hematological examination findings did not significantly differ between amputees and those who did not undergo amputation.Several hematological indexes significantly differed between patients with good outcomes versus those with poor outcomes.Conclusion:To avoid severe frostbite damage,routine mandatory activities like pilgrimage should be conducted under proper protection in extreme weather.Hematological indexes such as the red blood cell count,hematocrit,and hemoglobin level should be monitored closely by first-line medical personnel during hospitalization,as these indexes might indicate the outcome of frostbite.Further research is needed to improve the management of patients with frostbite in Southwest China.
