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Toward a unified information framework for cell atlas assembly

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National Science Review 2022年第3期9卷 7-10页

作者： Sijie Chen yanting luo Haoxiang Gao Fanhong Li Jiaqi Li Yixin Chen Renke You Hairong Lv Kui Hua Rui Jiang Xuegong Zhang Bioinformatics Division of BNRIST and Department of Automation MOE Key Lab of BioinformaticsTsinghua University Fuzhou Institute of Data Technology School of Medicine Tsinghua University School of Life Sciences Center for Synthetic and Systems Biology Tsinghua University

Cells are the basic structural and functional unit of the human body. Virtually all cells of a human body possess the same genome, but they exhibit colorful heterogeneities in phenotypes and *** heterogeneities includ...

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Large language model and domain-specific model collaboration for smart education

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Frontiers of Information Technology & Electronic Engineering 2024年第3期25卷 333-341页

作者： Yawei luo Yi YANG School of Software Technology Zhejiang UniversityNingbo 315048China College of Computer Science and Technology Zhejiang UniversityHangzhou 310027China

In this paper,we introduce the large language model and domain-specific model collaboration(LDMC)framework designed to enhance smart *** LDMC framework leverages the comprehensive and versatile knowledge of large domain-general models,combines it with the specialized and disciplinary knowledge from small domainspecific models(DSMs),and incorporates pedagogy knowledge from learning theory *** integration yields multiple knowledge representations,fostering personalized and adaptive educational *** explore various applications of the LDMC framework in the context of smart education.

关键词： smart language knowledge

Multi-omics Analysis of Primary Cell Culture Models Reveals Genetic and Epigenetic Basis of Intratumoral Phenotypic Diversity

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Genomics, Proteomics & Bioinformatics 2019年第6期17卷 576-589页

作者： Sixue Liu Zuyu Yang Guanghao Li Chunyan Li yanting luo Qiang Gong Xin Wu Tao Li Zhiqian Zhang Baocai Xing Xiaolan Xu Xuemei Lu CAS Key Laboratory of Genomics and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Invasive Pathogens Laboratory Institute of Environmental Science and ResearchPorirua 5022WellingtonNew Zealand Department of Cell Biology Key Laboratory of Carcinogenesis and Translational ResearchCenter for Molecular and Translational MedicinePeking University Cancer Hospital and InstituteBeijing 100142China Department of Hepatobiliary Surgery I Peking University Cancer Hospital and InstituteBeijing 100142China National Key Laboratory of Biomacromolecules Institute of BiophysicsChinese Academy of SciencesBeijing 100101China CAS Center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China

Uncovering the functionally essential variations related to tumorigenesis and tumor progression from cancer genomics data is still challenging due to the genetic diversity among patients,and extensive inter-and intra-tumoral heterogeneity at different levels of gene expression regulation,including but not limited to the genomic, epigenomic, and transcriptional levels. To minimize the impact of germline genetic heterogeneities, in this study, we establish multiple primary cultures from the primary and recurrent tumors of a single patient with hepatocellular carcinoma(HCC). Multiomics sequencing was performed for these cultures that encompass the diversity of tumor cells from the same patient. Variations in the genome sequence, epigenetic modification, and gene expression are used to infer the phylogenetic relationships of these cell cultures. We find the discrepancy among the relationships revealed by single nucleotide variations(SNVs) and transcriptional/epigenomic profiles from the cell cultures. We fail to find overlap between sample-specific mutated genes and differentially expressed genes(DEGs), suggesting that most of the heterogeneous SNVs among tumor stages or lineages of the patient are functionally insignificant. Moreover, copy number alterations(CNAs) and DNA methylation variation within gene bodies, rather than promoters, are significantly correlated with gene expression variability among these cell cultures. Pathway analysis of CNA/DNA methylation-related genes indicates that a single cell clone from the recurrent tumor exhibits distinct cellular characteristics and tumorigenicity, and such an observation is further confirmed by cellular experiments both in vitro and in vivo. Our systematic analysis reveals that CNAs and epigenomic changes, rather than SNVs, are more likely to contribute to the phenotypic diversity among subpopulations in the tumor. These findings suggest that new therapeutic strategies targeting gene dosage and epigenetic modification s

关键词： Intra-individual tumor heterogeneity Parallel primary culture Multi-omics Functional phenotypic diversity

Catalyst design and structure control for photocatalytic refineries of cellulosic biomass to fuels and chemicals

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Journal of Energy Chemistry 2024年第7期94卷 102-127页

作者： Lulu Sun Nengchao luo State Key Laboratory of Catalysis Dalian National Laboratory for Clean EnergyDalian Institute of Chemical PhysicsChinese Academy of SciencesDalian 116023LiaoningChina

Lignocellulosic biomass is the largest renewable hydrocarbon resource on *** cellulose,one of the major components of lignocellulose,powered by solar energy is a promising way of providing lowcarbon-footprint energy chemicals such as H_(2),HCOOH,CO,and transportation ***-of-the-art biorefineries target the full use of biomass feedstocks as they have a maximum collection radius of 75-100 km,requesting efficient and selective photocatalysts that significantly influence the outcome of photocatalytic ***-performed photocatalysts can harvest a broad solar spectrum and are active in breaking the chemical bonds of cellulose,decreasing the capital investments of ***,photocatalysts should control the selectivity of cellulose conversion,originating target products to level down separation *** separation in photocatalysts and interfacial charge transfer between photocatalysts and cellulose affect the activity and selectivity of cellulose refineries to H2 and carbonaceous *** account for the challenges above,this review summarizes photocatalysts for the refineries of cellulose and downstream platform molecules based on the types of products,with the structure features of different types of photocatalysts discussed in relation to the targets of either improving the activity or product *** addition,this review also sheds light on the methods for designing and regulating photocatalyst structures to facilitate photocatalytic refineries of cellulose and platform molecules,meanwhile summarizing proposed future research challenges and opportunities for designing efficient photocatalysts.

关键词： Photocatalysts Biorefineries Cellulose Fuels Hydrogen

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浅析西宁市公共交通服务质量乘客满意度评价

青海交通科技 2022年第1期34卷 41-44,40页

作者：罗雁婷青海民族大学西宁810007

随着西宁市国家公交都市创建成功,西宁市公共交通从方方面面得到了提升。本文通过西宁市主城区公共交通现状,着重介绍西宁市公共交通服务质量乘客满意度调查方案,并通过相关数据的计算和分析,得到西宁市主城区的公共交通服务质量乘客满... 详细信息

随着西宁市国家公交都市创建成功,西宁市公共交通从方方面面得到了提升。本文通过西宁市主城区公共交通现状,着重介绍西宁市公共交通服务质量乘客满意度调查方案,并通过相关数据的计算和分析,得到西宁市主城区的公共交通服务质量乘客满意度结果分值,进而对西宁市公共交通服务质量提出建议。

关键词：公共交通服务质量满意度评价

Precision regulation of plant aromatic amino acid homeostasis

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Science China(Life Sciences) 2024年第6期67卷 1316-1317页

作者： Jie luo Yazhouwan National Laboratory(YNL) Sanya 572025China School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication) Hainan UniversitySanya 572025China

The aromatic amino acids(AAAs)phenylalanine(Phe),tyrosine(Tyr),and tryptophan(Trp)are not only building blocks of proteins,but also precursors of numerous primary and specialized metabolites(Schenck and Maeda,2018).For instance,Trp is a precursor of the phytohormone auxin and the plant defense compounds indole glucosinolates,while Phe serves as a precursor of lignin,coumarin and *** plant natural products such as morphine and vitamin E are derived from Tyr,and have been employed in human medicine and nutrition(Schenck and Maeda,2018;Wu et al.,2022;Yokoyama et al.,2021).

关键词： aromatic instance coumarin

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Detecting APT-Exploited Processes through Semantic Fusion and Interaction Prediction

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Computers, Materials & Continua 2024年第2期78卷 1731-1754页

作者： Bin luo Liangguo Chen Shuhua Ruan Yonggang luo School of Cyber Science and Engineering Sichuan UniversityChengdu610065China Key Laboratory of Data Protection and Intelligent Management(Sichuan University) Ministry of EducationChengdu610065China Cyber Science Research Institute Sichuan UniversityChengdu610065China

Considering the stealthiness and persistence of Advanced Persistent Threats(APTs),system audit logs are leveraged in recent studies to construct system entity interaction provenance graphs to unveil threats in a ***-based provenance graph APT detection approaches require elaborate rules and cannot detect unknown attacks,and existing learning-based approaches are limited by the lack of available APT attack samples or generally only perform graph-level anomaly detection,which requires lots of manual efforts to locate attack *** paper proposes an APT-exploited process detection approach called ThreatSniffer,which constructs the benign provenance graph from attack-free audit logs,fits normal system entity interactions and then detects APT-exploited processes by predicting the rationality of entity ***,ThreatSniffer understands system entities in terms of their file paths,interaction sequences,and the number distribution of interaction types and uses the multi-head self-attention mechanism to fuse these ***,based on the insight that APT-exploited processes interact with system entities they should not invoke,ThreatSniffer performs negative sampling on the benign provenance graph to generate non-existent edges,thus characterizing irrational entity interactions without requiring APT attack *** last,it employs a heterogeneous graph neural network as the interaction prediction model to aggregate the contextual information of entity interactions,and locate processes exploited by attackers,thereby achieving fine-grained APT *** results demonstrate that anomaly-based detection enables ThreatSniffer to identify all attack *** to the node-level APT detection method APT-KGL,ThreatSniffer achieves a 6.1%precision improvement because of its comprehensive understanding of entity semantics.

关键词： Advanced persistent threat provenance graph multi-head self-attention graph neural network

THE GRADIENT ESTIMATE OF SUBELLIPTIC HARMONIC MAPS WITH A POTENTIAL

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Acta Mathematica Scientia 2024年第4期44卷 1189-1199页

作者： Han luo School of Mathematical Sciences Fudan UniversityShanghai 200433China

In this paper,we investigate subelliptic harmonic maps with a potential from noncompact complete sub-Riemannian manifolds corresponding to totally geodesic Riemannian *** some suitable conditions,we give the gradient ... 详细信息

关键词： sub-Riemannian manifolds subelliptic harmonic maps with potential gradient estimate Liouville Theorem

Single-cell RNA sequencing in juvenile idiopathic arthritis

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Genes & Diseases 2024年第2期11卷 633-644页

作者： Xiwen luo Xuemei Tang Department of Rheumatology and Immunology Children’s Hospital of Chongqing Medical UniversityChongqing 400014China Chongqing Key Laboratory of Child Infection and Immunity Ministry of Education Key Laboratory of Child Development and DisordersNational Clinical Research Center for Child Health and DisordersChina International Science and Technology Cooperation Base of Child Development and Critical DisordersChildren's Hospital of Chongqing Medical UniversityChongqing 400014China

Juvenile idiopathic arthritis (JIA) is one of the most common chronic inflammatory rheumatic diseases in children,with onset before age 16 and lasting for more than 6 *** is a highly heterogeneous condition with various consequences for health and quality of *** some JIA patients,early detection and intervention remain *** a result,further investigation of the complex and unknown mechanisms underlying JIA is *** in technology now allow us to describe the biological heterogeneity and function of individual cell populations in *** this review,we hope to provide novel ideas and potential targets for the diagnosis and treatment of JIA by summarizing the current findings of single-cell RNA sequencing studies and understanding how the major cell subsets drive JIA pathogenesis.

关键词： Juvenile idiopathic arthritis Macrophage Macrophage activation syndrome Monocyte Single-cell RNA sequencing Synoviocyte T cell