In this paper, we focus on two-qubit pure state tomography. For an arbitrary unknown two-qubit pure state, separable or entangled, it has been found that the measurement probabilities of 16 projections onto the tensor...In this paper, we focus on two-qubit pure state tomography. For an arbitrary unknown two-qubit pure state, separable or entangled, it has been found that the measurement probabilities of 16 projections onto the tensor products of Pauli eigenstates are enough to uniquely determine the state. Moreover, these corresponding product states are arranged into five orthonormal bases. We design five quantum circuits, which are decomposed into the common gates in universal quantum computation, to simulate the five projective measurements onto these bases. At the end of each circuit, we measure each qubit with the projective measurement {｜0〉〈0 ｜,｜1〉,〈1｜ }. Then, we consider the open problem whether three orthonormal bases are enough to distinguish all two-qubit pure states. A necessary condition is given. Suppose that there are three orthonormal bases {B1,B2,B3}. Denote the unitary transition matrices from B1 to {B2,B3 } as U1 and U2. All 32 elements of matrices U1 and U2 should not be zero. If not, these three bases cannot distinguish all two-qubit pure states.展开更多
There have been studies on the structure and properties of segmented polyetherurethane (SPEU)based on polytetramethylene glycol (PTMG)/4, 4′-diphenylmethane diisoeyanate (MDI)/1,4-butandiol (BD). It was shown that on...There have been studies on the structure and properties of segmented polyetherurethane (SPEU)based on polytetramethylene glycol (PTMG)/4, 4′-diphenylmethane diisoeyanate (MDI)/1,4-butandiol (BD). It was shown that only sufficient long hard segment (MDI/BD) domains could crystallize under certain conditions, while the shorter hard domains (hard segment in the SPEU with 1000 n PTMG and mole展开更多
The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:rumi...The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:ruminants,camels and cetaceans,as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations.We identified genes with relatively high expression in the rumen,of which many appeared to be recruited from other tissues.These genes show functional enrichment in ketone body metabolism,regulation of microbial community,and epithelium absorption,which are the most prominent biological processes involved in rumen innovations.Several modes of genetic change underlying rumen functional innovations were uncovered,including coding mutations,genes newly evolved,and changes of regulatory elements.We validated that the key ketogenesis rate-limiting gene(HMGCS2)with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals.Two newly evolved genes(LYZ1 and DEFB1)are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium.Furthermore,we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment.These results greatly improve our understanding of rumen evolution and organ evo-devo in general.展开更多
Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and...Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and high carbon dioxide concentration.Methods:We provide an integrated resource,ZokorDB,for tissue specific regulatory network annotation for zokor.ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain,heart,liver,kidney,and lung.The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.Results:ZokorDB provides a general draft gene regulatory network(GRN),Le?potential transcription factor(TF)binds to non-coding regulatory elements and regulates the expression of target genes(TG).Furthermore,we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks.Conclusions:A web-based,open-access database is developed for easily searching,visualizing,and downloading the annotation and data.The pipeline of non-coding region annotation for zokor will be useful for other non-model species.ZokorDB is free available at the website(bigd.big.ac.cn/zokordb/).展开更多
Human genetic variants can influence the severity of symptoms infected with SARS-COV-2.Several genome-wide asso-ciation studies have identified human genomic risk single nucleotide polymorphisms(SNPs)associated with c...Human genetic variants can influence the severity of symptoms infected with SARS-COV-2.Several genome-wide asso-ciation studies have identified human genomic risk single nucleotide polymorphisms(SNPs)associated with coronavirus disease 2019(COVID-19)severity.However,the causal tissues or cell types underlying COVID-19 severity are uncertain.In addition,candidate genes associated with these risk SNPs were investigated based on genomic proximity instead of their functional cellular contexts.Here,we compiled regulatory networks of 77 human contexts and revealed those risk SNPs’enriched cellular contexts and associated risk SNPs with transcription factors,regulatory elements,and target genes.Twenty-one human contexts were identified and grouped into two categories:immune cells and epithelium cells.We further aggregated the regulatory networks of immune cells and epithelium cells.These two aggregated regulatory networks were investigated to reveal their association with risk SNPs’regulation.Two genomic clusters,the chemokine receptors cluster and the oligoadenylate synthetase(OAS)cluster,showed the strongest association with COVID-19 severity,and they had different regulatory programs in immune and epithelium contexts.Our findings were supported by analysis of both SNP array and whole genome sequencing-based genome wide association study(GWAS)summary statistics.展开更多
基金Project supported partially by the National Key Research and Development Program of China(Grant No.2016YFB1000902)the National Natural Science Foundation of China(Grant No.61472412)the Program for Creative Research Group of the National Natural Science Foundation of China(Grant No.61621003)
文摘In this paper, we focus on two-qubit pure state tomography. For an arbitrary unknown two-qubit pure state, separable or entangled, it has been found that the measurement probabilities of 16 projections onto the tensor products of Pauli eigenstates are enough to uniquely determine the state. Moreover, these corresponding product states are arranged into five orthonormal bases. We design five quantum circuits, which are decomposed into the common gates in universal quantum computation, to simulate the five projective measurements onto these bases. At the end of each circuit, we measure each qubit with the projective measurement {｜0〉〈0 ｜,｜1〉,〈1｜ }. Then, we consider the open problem whether three orthonormal bases are enough to distinguish all two-qubit pure states. A necessary condition is given. Suppose that there are three orthonormal bases {B1,B2,B3}. Denote the unitary transition matrices from B1 to {B2,B3 } as U1 and U2. All 32 elements of matrices U1 and U2 should not be zero. If not, these three bases cannot distinguish all two-qubit pure states.
文摘There have been studies on the structure and properties of segmented polyetherurethane (SPEU)based on polytetramethylene glycol (PTMG)/4, 4′-diphenylmethane diisoeyanate (MDI)/1,4-butandiol (BD). It was shown that only sufficient long hard segment (MDI/BD) domains could crystallize under certain conditions, while the shorter hard domains (hard segment in the SPEU with 1000 n PTMG and mole
基金supported by the National Natural Science Foundation of China(31822052,31572381)the National Thousand Youth Talents Plan to Y.J.+3 种基金National Natural Science Foundation of China(31660644)to S.H.National Natural Science Foundation of China(41422604)to S.L.The Villum Foundation(VKR 023447)the Independent Research Fund Denmark(8049-00098B)。
文摘The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers.We analyzed 897 transcriptomes from three Cetartiodactyla lineages:ruminants,camels and cetaceans,as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations.We identified genes with relatively high expression in the rumen,of which many appeared to be recruited from other tissues.These genes show functional enrichment in ketone body metabolism,regulation of microbial community,and epithelium absorption,which are the most prominent biological processes involved in rumen innovations.Several modes of genetic change underlying rumen functional innovations were uncovered,including coding mutations,genes newly evolved,and changes of regulatory elements.We validated that the key ketogenesis rate-limiting gene(HMGCS2)with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals.Two newly evolved genes(LYZ1 and DEFB1)are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium.Furthermore,we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment.These results greatly improve our understanding of rumen evolution and organ evo-devo in general.
基金ZokorDB is supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(No.XDB13000000)The authors are also supported by the National Natural Science Foundation of China(NSFC)(Nos.11871463,11871462,61671444 and 61621003)+1 种基金We thank all the lab members for discussions on data collection,genome alignment,annotation,GRN reconstructionWe thank Dr.Yilei Wu and his group for help on database design and management.
文摘Background:Plateau zokor inhabits in sealed burrows from 2,000 to 4,200 meters at Qinghai-Tibet Plateau.This extreme living env ironment makes it a great model to study animal adaptation to hypoxia,low temperature,and high carbon dioxide concentration.Methods:We provide an integrated resource,ZokorDB,for tissue specific regulatory network annotation for zokor.ZokorDB is based on a high-quality draft genome of a plateau zokor at 3,300 m and its transcriptional profiles in brain,heart,liver,kidney,and lung.The conserved non-coding elements of zokor are annotated by their nearest genes and upstream transcriptional factor motif binding sites.Results:ZokorDB provides a general draft gene regulatory network(GRN),Le?potential transcription factor(TF)binds to non-coding regulatory elements and regulates the expression of target genes(TG).Furthermore,we refined the GRN by incorporating matched RNA-seq and DNase-seq data from mouse ENCODE project and reconstructed five tissue-specific regulatory networks.Conclusions:A web-based,open-access database is developed for easily searching,visualizing,and downloading the annotation and data.The pipeline of non-coding region annotation for zokor will be useful for other non-model species.ZokorDB is free available at the website(bigd.big.ac.cn/zokordb/).
基金funding from the Strategic Priority Research Program of the Chinese Academy of Sciences(XDPB17)National Key Research and Development Program of China(2020YFA0712402)+2 种基金the National Natural Science Foundation of China(grants 12025107,11871463,61621003,11688101)The Genotype-Tissue Expression(GTEx)Project was supported by the Common Fund of the Office of the Director of the National Institutes of Health,and by NCI,NHGRI,NHLBI,NIDA,NIMH,and NINDSThe data used for the analyses described in this manuscript were obtained from the GTEx Portal under dbGaP accession number phs000424.v8.p2 on 12/09/2020.
文摘Human genetic variants can influence the severity of symptoms infected with SARS-COV-2.Several genome-wide asso-ciation studies have identified human genomic risk single nucleotide polymorphisms(SNPs)associated with coronavirus disease 2019(COVID-19)severity.However,the causal tissues or cell types underlying COVID-19 severity are uncertain.In addition,candidate genes associated with these risk SNPs were investigated based on genomic proximity instead of their functional cellular contexts.Here,we compiled regulatory networks of 77 human contexts and revealed those risk SNPs’enriched cellular contexts and associated risk SNPs with transcription factors,regulatory elements,and target genes.Twenty-one human contexts were identified and grouped into two categories:immune cells and epithelium cells.We further aggregated the regulatory networks of immune cells and epithelium cells.These two aggregated regulatory networks were investigated to reveal their association with risk SNPs’regulation.Two genomic clusters,the chemokine receptors cluster and the oligoadenylate synthetase(OAS)cluster,showed the strongest association with COVID-19 severity,and they had different regulatory programs in immune and epithelium contexts.Our findings were supported by analysis of both SNP array and whole genome sequencing-based genome wide association study(GWAS)summary statistics.
