This paper proposes a new full Nesterov-Todd(NT) step infeasible interior-point algorithm for semidefinite programming. Our algorithm uses a specific kernel function, which is adopted by Liu and Sun, to deduce the fea...This paper proposes a new full Nesterov-Todd(NT) step infeasible interior-point algorithm for semidefinite programming. Our algorithm uses a specific kernel function, which is adopted by Liu and Sun, to deduce the feasibility step. By using the step, it is remarkable that in each iteration of the algorithm it needs only one full-NT step, and can obtain an iterate approximate to the central path. Moreover, it is proved that the iterative bound corresponds with the known optimal one for semidefinite optimization problems.展开更多
Two new versions of accelerated first-order methods for minimizing convex composite functions are proposed. In this paper, we first present an accelerated first-order method which chooses the step size 1/ Lk to be 1/ ...Two new versions of accelerated first-order methods for minimizing convex composite functions are proposed. In this paper, we first present an accelerated first-order method which chooses the step size 1/ Lk to be 1/ L0 at the beginning of each iteration and preserves the computational simplicity of the fast iterative shrinkage-thresholding algorithm. The first proposed algorithm is a non-monotone algorithm. To avoid this behavior, we present another accelerated monotone first-order method. The proposed two accelerated first-order methods are proved to have a better convergence rate for minimizing convex composite functions. Numerical results demonstrate the efficiency of the proposed two accelerated first-order methods.展开更多
Epstein-Barr virus(EBV)-associated gastric cancer(GC)manifests an intriguing immunotherapy response.However,the cellular basis for EBV-imprinted tumour immunity and on-treatment response remains undefined.This study a...Epstein-Barr virus(EBV)-associated gastric cancer(GC)manifests an intriguing immunotherapy response.However,the cellular basis for EBV-imprinted tumour immunity and on-treatment response remains undefined.This study aimed to finely characterize the dynamic tumour immune contexture of human EBV(+)GC treated with immunochemotherapy by longitudinal scRNA-seg and paired scTCR/BCR-seq.EBV(+)GC exhibits an inflamed-immune phenotype with increased T-cell and B-cell infiltration.展开更多
Ubiquitination,an essential post-transcriptional modification(PTM),plays a vital role in nearly every biological process,including development and growth.Despite its functions in plant reproductive development,its tar...Ubiquitination,an essential post-transcriptional modification(PTM),plays a vital role in nearly every biological process,including development and growth.Despite its functions in plant reproductive development,its targets in rice panicles remain unclear.In this study,we used proteome-wide profiling of lysine ubiquitination in rice(O.sativa ssp.indica)young panicles.We created the largest ubiquitinome dataset in rice to date,identifying 1638 lysine ubiquitination sites on916 unique proteins.We detected three conserved ubiquitination motifs,noting that acidic glutamic acid(E)and aspartic acid(D)were most frequently present around ubiquitinated lysine.Enrichment analysis of Gene Ontology(GO)annotations and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles.Interestingly,enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptorlike kinases and cytoplasmic tyrosine and serine-threonine kinases.Furthermore,we analyzed the crosstalk between ubiquitination,acetylation,and succinylation,and constructed a potential protein interaction network within our rice ubiquitinome.Moreover,we identified ubiquitinated proteins related to pollen and grain development,indicating that ubiquitination may play a critical role in the physiological functions in young panicles.Taken together,we reported the most comprehensive lysine ubiquitinome in rice so far,and used it to reveal the functional role of lysine ubiquitination in rice young panicles.展开更多
Autophagy is a lysosome-based degradation pathway,characterized by formation of a double-membrane vesicle named the autophagosome.During autophagy,various cargos are engulfed and delivered to lysosomes(or the vacuole ...Autophagy is a lysosome-based degradation pathway,characterized by formation of a double-membrane vesicle named the autophagosome.During autophagy,various cargos are engulfed and delivered to lysosomes(or the vacuole in yeast)for degradation.It is an evolutionarily conserved pathway and plays important roles in various physiological and pathological conditions such as develop-ment,immunity,cancer and neuronal degeneration(Jiang and Mizushima,2014;Martin et al.,2014).展开更多
Large-scale sequencing has characterized an enormous number of genetic variations(GVs),and the functional analysis of GVs is fundamental to understanding differences in disease susceptibility and therapeutic response ...Large-scale sequencing has characterized an enormous number of genetic variations(GVs),and the functional analysis of GVs is fundamental to understanding differences in disease susceptibility and therapeutic response among and within populations.Using a combination of a sequence-based predictor with known phosphorylation and protein–protein interaction information,we computationally detected 9606 potential phosSNPs(phosphorylation-related single nucleotide polymorphisms),including 720 known,disease-associated SNPs that dramatically modify the human phosSNP-associated kinase–substrate network.Further analyses demonstrated that the proteins in the network are heavily associated in various signaling and cancer pathways,while cancer genes and drug targets are significantly enriched.We re-constructed four population-specific kinase–substrate networks and found that several inherited disease or cancer genes,such as IRS1,RAF1,and EGFR,were differentially regulated by phosSNPs.Thus,phosSNPs may influence disease susceptibility and be involved in cancer development by reconfiguring phosphorylation networks in different populations.Moreover,by systematically characterizing potential phosphorylation-related cancer mutations(phosCMs)in 12 types of cancers,we observed that both types of GVs preferentially occur in the known cancer genes,while a considerable number of phosphorylated proteins,especially those over-representing cancer genes,contain both phosSNPs and phosCMs.Furthermore,it was observed that phosSNPs were significantly enriched in amplification genes identified from breast cancers and tyrosine kinase circuits of lung cancers.Taken together,these results should prove helpful for further elucidation of the functional impacts of disease-associated SNPs.展开更多
A new adaptive subspace minimization three-term conjugate gradient algorithm with nonmonotone line search is introduced and analyzed in this paper.The search directions are computed by minimizing a quadratic approxima...A new adaptive subspace minimization three-term conjugate gradient algorithm with nonmonotone line search is introduced and analyzed in this paper.The search directions are computed by minimizing a quadratic approximation of the objective function on special subspaces,and we also proposed an adaptive rule for choosing different searching directions at each iteration.We obtain a significant conclusion that the each choice of the search directions satisfies the sufficient descent condition.With the used nonmonotone line search,we prove that the new algorithm is globally convergent for general nonlinear functions under some mild assumptions.Numerical experiments show that the proposed algorithm is promising for the given test problem set.展开更多
基金Sponsored by the National Natural Science Foundation of China(Grant No.11461021)the Natural Science Basic Research Plan in Shaanxi Province of China(Grant No.2017JM1014)Scientific Research Project of Hezhou University(Grant Nos.2014YBZK06 and 2016HZXYSX03)
文摘This paper proposes a new full Nesterov-Todd(NT) step infeasible interior-point algorithm for semidefinite programming. Our algorithm uses a specific kernel function, which is adopted by Liu and Sun, to deduce the feasibility step. By using the step, it is remarkable that in each iteration of the algorithm it needs only one full-NT step, and can obtain an iterate approximate to the central path. Moreover, it is proved that the iterative bound corresponds with the known optimal one for semidefinite optimization problems.
基金Sponsored by the National Natural Science Foundation of China(Grant No.11461021)the Natural Science Basic Research Plan in Shaanxi Province of China(Grant No.2017JM1014)
文摘Two new versions of accelerated first-order methods for minimizing convex composite functions are proposed. In this paper, we first present an accelerated first-order method which chooses the step size 1/ Lk to be 1/ L0 at the beginning of each iteration and preserves the computational simplicity of the fast iterative shrinkage-thresholding algorithm. The first proposed algorithm is a non-monotone algorithm. To avoid this behavior, we present another accelerated monotone first-order method. The proposed two accelerated first-order methods are proved to have a better convergence rate for minimizing convex composite functions. Numerical results demonstrate the efficiency of the proposed two accelerated first-order methods.
基金This work was supported by National Natural Science Foundation of China(81930065,82173128 to R-H.X.,82073377,81772587 to M.Z.Q.,82172861 to Q.Z.)CAMS Innovation Fund for Medical Sciences(CIFMS)(2019-12M-5-036,to R.-H.X.)+2 种基金Natural Science Foundation of Guangdong(2021A1515012439 to M.Z.Q.2021A1515011743 to Q.Z.)Opening Fund of Guangdong Provincial Key Laboratory of Biomedical Imaging(No.GPKLBI202108 of 2018B030322006 to H.Y.Z.)Ministry of Education Frontiers Science Centre for Precision Oncology,University of Macao(SP2023-00001-FSCPO to H.Y.Z.).
文摘Epstein-Barr virus(EBV)-associated gastric cancer(GC)manifests an intriguing immunotherapy response.However,the cellular basis for EBV-imprinted tumour immunity and on-treatment response remains undefined.This study aimed to finely characterize the dynamic tumour immune contexture of human EBV(+)GC treated with immunochemotherapy by longitudinal scRNA-seg and paired scTCR/BCR-seq.EBV(+)GC exhibits an inflamed-immune phenotype with increased T-cell and B-cell infiltration.
基金the grants from the National Key Research and Development Program of China(Grant No.2016YFD0100400 to HZ)the National Natural Science Foundation of China(Grant Nos.31501069 to ZL,31601067 to HC,and 31571255 to HZ)+2 种基金the Guangdong Natural Science Funds for Distinguished Young Scholars,China(Grant No.2017A030306001 to HZ)the Pearl River S&T Nova Program of Guangzhou,China(Grant No.201710010106 to HZ)the Scientific Research Project of Guangzhou,China(Grant No.201504010004 to CZ)。
文摘Ubiquitination,an essential post-transcriptional modification(PTM),plays a vital role in nearly every biological process,including development and growth.Despite its functions in plant reproductive development,its targets in rice panicles remain unclear.In this study,we used proteome-wide profiling of lysine ubiquitination in rice(O.sativa ssp.indica)young panicles.We created the largest ubiquitinome dataset in rice to date,identifying 1638 lysine ubiquitination sites on916 unique proteins.We detected three conserved ubiquitination motifs,noting that acidic glutamic acid(E)and aspartic acid(D)were most frequently present around ubiquitinated lysine.Enrichment analysis of Gene Ontology(GO)annotations and Kyoto Encyclopedia of Genes and Genomes(KEGG)pathways of these ubiquitinated proteins revealed that ubiquitination plays an important role in fundamental cellular processes in rice young panicles.Interestingly,enrichment analysis of protein domains indicated that ubiquitination was enriched on a variety of receptorlike kinases and cytoplasmic tyrosine and serine-threonine kinases.Furthermore,we analyzed the crosstalk between ubiquitination,acetylation,and succinylation,and constructed a potential protein interaction network within our rice ubiquitinome.Moreover,we identified ubiquitinated proteins related to pollen and grain development,indicating that ubiquitination may play a critical role in the physiological functions in young panicles.Taken together,we reported the most comprehensive lysine ubiquitinome in rice so far,and used it to reveal the functional role of lysine ubiquitination in rice young panicles.
文摘Autophagy is a lysosome-based degradation pathway,characterized by formation of a double-membrane vesicle named the autophagosome.During autophagy,various cargos are engulfed and delivered to lysosomes(or the vacuole in yeast)for degradation.It is an evolutionarily conserved pathway and plays important roles in various physiological and pathological conditions such as develop-ment,immunity,cancer and neuronal degeneration(Jiang and Mizushima,2014;Martin et al.,2014).
基金This work was supported by grants from the National Basic Research Program(973 project)(2013CB933900,2012CB910101,and 2012CB911201)the National Natural Science Foundation of China(31171263,81272578,and 31071154)+1 种基金the International Science and Technology Cooperation Program of China(2014DFB30020)China Postdoctoral Science Foundation(2014M550392).
文摘Large-scale sequencing has characterized an enormous number of genetic variations(GVs),and the functional analysis of GVs is fundamental to understanding differences in disease susceptibility and therapeutic response among and within populations.Using a combination of a sequence-based predictor with known phosphorylation and protein–protein interaction information,we computationally detected 9606 potential phosSNPs(phosphorylation-related single nucleotide polymorphisms),including 720 known,disease-associated SNPs that dramatically modify the human phosSNP-associated kinase–substrate network.Further analyses demonstrated that the proteins in the network are heavily associated in various signaling and cancer pathways,while cancer genes and drug targets are significantly enriched.We re-constructed four population-specific kinase–substrate networks and found that several inherited disease or cancer genes,such as IRS1,RAF1,and EGFR,were differentially regulated by phosSNPs.Thus,phosSNPs may influence disease susceptibility and be involved in cancer development by reconfiguring phosphorylation networks in different populations.Moreover,by systematically characterizing potential phosphorylation-related cancer mutations(phosCMs)in 12 types of cancers,we observed that both types of GVs preferentially occur in the known cancer genes,while a considerable number of phosphorylated proteins,especially those over-representing cancer genes,contain both phosSNPs and phosCMs.Furthermore,it was observed that phosSNPs were significantly enriched in amplification genes identified from breast cancers and tyrosine kinase circuits of lung cancers.Taken together,these results should prove helpful for further elucidation of the functional impacts of disease-associated SNPs.
基金the editor and the anonymous referees for their valuable comments,which are helpful to improve the quality of this paper.We would like to thank Professor Dai Y.H.and Dr.Kou C.X.for their CGOPT code,and thank Professors Hager W.W.and Zhang H.C.for their CG_DESCENT(5.3)codeThis research is supported by National Science Foundation of China(No.11901561),China Postdoctoral Science Foundation(2019M660833)Guangxi Natural Science Foundation(No.2018GXNSFBA281180).
文摘A new adaptive subspace minimization three-term conjugate gradient algorithm with nonmonotone line search is introduced and analyzed in this paper.The search directions are computed by minimizing a quadratic approximation of the objective function on special subspaces,and we also proposed an adaptive rule for choosing different searching directions at each iteration.We obtain a significant conclusion that the each choice of the search directions satisfies the sufficient descent condition.With the used nonmonotone line search,we prove that the new algorithm is globally convergent for general nonlinear functions under some mild assumptions.Numerical experiments show that the proposed algorithm is promising for the given test problem set.
