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DMF-scMT-seq linking methylome and transcriptome within single cells with digital microfluidics

Science China Chemistry 2024年第6期67卷 2070-2078页

作者： xing Xu xi Zeng xin Lin Shiyan Lin Shanshan Liang Tian Tian Rui Su Jia Song Chaoyong yang Collaborative Innovation Center of Chemistry for Energy Materials The MOE Key Laboratory of Spectrochemical Analysis and InstrumentationState Key Laboratory of Physical Chemistry of Solid SurfacesDepartment of Chemical BiologyCollege of Chemistry and Chemical EngineeringThe First Affiliated Hospital of Xiamen UniversityXiamen UniversityXiamen361005China Institute of Molecular Medicine Renji HospitalShanghai Jiao Tong University School of MedicineShanghai200127China Chemistry and Materials Science College Shanghai Normal UniversityShanghai200234China Chemistry and Biomedicine Innovation Center(ChemBIC) School of Chemistry and Chemical EngineeringNanjing UniversityNanjing210023China

Single-cell joint analysis of methylome and transcriptome reveals how the methylation regulates the transcriptional ***,traditional bench-top protocols for single-cell DNA methylation and RNA transcription co-detection are laborintensive,cost-ineffective and ***,we establish the DMF-sc MT-seq,a highly-efficient and cost-effective method to simultaneously analyze single-cell DNA methylation and transcriptional activity based on digital *** MT-seq automates the workflow of single-cell isolation,cellular hypotonic lysis,nucleic acid separation and methylome/transcriptome library construction in a contactless and addressable *** system ensures high accuracy(R>0.85),high gene detection ability(14,697 genes per cell at 4 million sequencing depth),and high CpG coverage(677,198 CpG sites per cell at 1million sequencing depth).By using DMF-sc MT-seq,the relationship of DNA methylation and RNA transcription under different genomic contexts is *** further apply DMF-sc MT-seq to study the dynamics of transcription regulation with methylation-inhibiting anti-tumor Decitabine,and identify the methylated promoter/gene body driven genes in response to Decitabine ***-sc MT-seq facilitates the construction of the correlation of DNA methylation and transcriptional activity at the single-cell level in a flexible,sensitive and accurate way,which is anticipated to be a powerful tool in studying single-cell biological systems.

关键词： single-cell analysis digital microfluidics methylome sequencing transcriptome sequencing

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A four-band index for both liquid and solid water and its applications in the Aral Sea Basin

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Science China Earth Sciences 2024年第3期67卷 769-788页

作者： Bing YUE xi CHEN Saibo LI Zhengping DU John WILSON Junhui yang Yimen JIAO Shuangyan HUANG Chenghu ZHOU xinjiang Institute of Ecology and Geography Chinese Academy of SciencesUrumqi 830011China College of Resources and Environment University of Chinese Academy of SciencesBeijing 100049China Institute of Geographical Sciences and Natural Resources Research Chinese Academy of SciencesBeijing 100101China Spatial Sciences Institute University of Southern CaliforniaLos AngelesCA 90089-0374USA

Various investigations have been conducted to analyze the water-coverage area of the Aral Sea and the Aral Sea Basin(ASB). However, the investigations incorporated considerable uncertainty and the used water indices had misclassification problem, which made different research groups present different results. Thus we first ascertain the boundaries of the ASB, the Syr and Amu river basins as well as their upper, middle and lower reaches. Then a four-band index for both liquid and solid water(ILSW) is proposed to address the misclassification problems of the classic water indices. ILSW is calculated by using the reflectance values of the green, red, near infrared, and thermal infrared bands, which combines the normalized difference water index(NDWI) and land surface temperature(LST) together. Validation results show that the ILSW water index has the highest accuracy by far in the Aral Sea Basin. Our results indicate that annual average decline of the water-coverage area was 963 km^(2) in the southern Aral Sea, whereas the northern Aral Sea has experienced little change. In the meanwhile, permanent ice and snow in upper reach of ASB has retreated considerably. Annual retreating rates of the permanent ice and snow were respectively 6233and 3841 km^(2) in upper reaches of Amu river basin(UARB) and Syr river basin(USRB). One of major reasons is that climate has become warmer in ASB. The climate change has caused serious water deficit problem. The water deficit had an increasing trend since the 1990s and its increasing rates was 3.778 billion m^(3) yearly on average. The total water deficit was 76.967 billion m^(3) on average in the whole area of ASB in the 2010s. However, up reaches of Syr river basin(USRB), a component area of ASB, had water surplus of 25.461 billion m^(3). These conclusions are useful for setting out a sustainable development strategy in ASB.

关键词： Aral Sea Basin Syr river basin Amu river basin Water indices Water-coverage area Water deficit Climate change

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Variational Analysis Based on Proximal Subdifferential on Smooth Banach Spaces

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Acta Mathematica Sinica,English Series 2024年第2期40卷 595-618页

作者： xi Yin ZHENG Department of Mathematics Yunnan UniversityKunming 650091P.R.China

This paper first shows that for any p∈(1,2)there exists a continuously differentiable function f on l^(p)(and L^(p))such that the proximal subdifferential of f is empty everywhere,and hence it is not suitable to develop theory on proximal subdifferential in the classical Banach spaces l^(P)and L^(P) with p∈(1,2).On the other hand,this paper establishes variational analysis based on the proximal subdifferential in the framework of smooth Banach spaces of power type 2,which conclude all Hilbert spaces and all the classical spaces l^(P)and L^(P)with p∈(2,+∞).In particular,in such a smooth space,we provide the proximal subdifferential rules for sum functions,product functions,composite functions and supremum functions,which extend the basic results on the proximal subdifferential established in the framework of Hilbert *** of our main results are new even in the Hilbert space *** applications,we provide KKT-like conditions for nonsmooth optimization problems in terms of proximal subdifferential.

关键词： Smooth Banach space proximal subdifferential proximal normal cone KKT condition

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Carbon emission reduction:Contribution of photovoltaic power and practice in China

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China Geology 2024年第2期7卷 371-376页

作者： Liang Wang Li-qiong Jia Geng xie xi-jie Chen yang Liu Natural Resources Integrated Survey Command Center China Geological SurveyMinistry of Natural ResourcesBeijing 100055China Development and Research Center China Geological SurveyMinistry of Natural ResourcesBeijing 100037China Center for Geophysical Survey China Geological SurveyLangfang 065000China

As a clean and renewable form of energy,photovoltaic(PV)power generation converts solar energy into electrical energy,reducing the consumption of fossil fuels and significantly lowering greenhouse gas *** the global t... 详细信息

关键词： convert power emissions

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Antibodies Targeting a Conserved Surface Polysaccharide Are Protective Against a Wide Range of Microbial Pathogens Producing b-1-6-Linked Poly-N-Acetylglucosamine(PNAG)

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Engineering 2024年第7期38卷 69-76页

作者： xi Lu Guoqing Li Jing Pang xinyi yang Colette Cywes-Bentley Xuefu You Gerald B.Pier Beijing Key Laboratory of Antimicrobial Agents Institute of Medicinal BiotechnologyChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100050China Division of Infectious Diseases Department of MedicineBrigham and Women’s HospitalHarvard Medical SchoolBostonMA 02115USA

The b-1-6-linked poly-N-acetylglucosamine(PNAG)polymer is a conserved surface polysaccharide produced by many bacteria,fungi,and protozoan(and even filarial)*** wide-ranging expression makes PNAG an attractive target for vaccine development,as it potentially encompasses a broad range of *** progress has been made in discovering important properties of the biology of PNAG expression in recent *** molecular characterization and regulation of operons for the production of PNAG biosynthetic proteins and enzymes have been studied in many *** addition,the physiological function of PNAG has been further ***-based vaccines and PNAG-targeting antibodies have shown great efficacy in preclinical ***,clinical tests for both vaccines and antibodies have been carried out in humans and economically important animals,and the results are *** it is not destined to be a smooth road,we are optimistic about new vaccines and immunotherapeutics targeting PNAG becoming validated and eventually licensed for clinical use against multiple infectious agents.

关键词： Poly-N-acetylglucosamine Conjugate vaccine Monoclonal antibody

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Petrogenesis and tectonic implications of the Silurian adakitic granitoids in the eastern segment of the Qilian Orogenic Belt,Northwest China

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Acta Geochimica 2024年第1期43卷 72-86页

作者： Jiao-Long Zhao xiao-Jun Huang Pei-Qing Hu Zhen-xi yang Ying Fan Er-Teng Wang Fu-Bo yang Jing-Yu Zhang School of Earth Sciences Key Laboratory of Mineral Resources in Western China(Gansu Province)Lanzhou UniversityLanzhou 730000China Nuclear Industry 247 Brigade Tianjin North China Geological Survey BureauTianjin 301800China Fourth Institute of Geological and Mineral Exploration of Gansu Provincial Bureau of Geology and Mineral Resources Jiuquan 735000China

Geodynamic mechanism responsible for the generation of Silurian granitoids and the tectonic evolution of the Qilian orogenic belt remains controversial. In this study, we report the results of zircon U–Pb age, and systematic whole-rock geochemical data for the Haoquangou and Liujiaxia granitoids within the North Qilian orogenic belt and the Qilian Block, respectively, to constrain their petrogenesis, and the Silurian tectonic evolution of the Qilian orogenic belt. Zircon U–Pb ages indicate that the Haoquangou and Liujiaxia intrusions were emplaced at423 ± 3 Ma and 432 ± 4 Ma, respectively. The Haoquangou granodiorites are calc-alkaline, while the Liujiaxia granites belong to the high-K calc-alkaline *** are peraluminous in composition and have relatively depleted Nd isotopic [ε_(Nd)(t) =(-3.9 – + 0.6)] characteristics compared with regional basement rocks, implying their derivation from a juvenile lower crust. They show adakitic geochemical characteristics and were generated by partial melting of thickened lower continental crust. Postcollisional extensional regime related to lithospheric delamination was the most likely geodynamic mechanism for the generation of the Haoquangou granodiorite, while the Liujiaxia granites were generated in a compressive setting during continental collision between the Qaidam and Qilian blocks.

关键词： Silurian adakitic granitoids Petrogenesis Tectonic setting Qilian Orogenic Belt

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Comparing the effects of dual-task training and single-task training on walking,balance and cognitive functions in individuals with Parkinson’s disease:A systematic review

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Chinese Medical Journal 2024年第13期137卷 1535-1543页

作者： xiaoying Lin Yanming Zhang xiaowei Zhang xi Chen Jianhua Liu Lei yang Marco Yiu Chung Pang Department of Rehabilitation Medicine the First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anShaanxi 710061China Department of Rehabilitation Medicine The Second People’s Hospital of KunmingKunmingYunnan 650051China Department of Rehabilitation Medicine Xuanwu HospitalCapital Medical UniversityBeijing 100000China Department of Physical Therapy China Rehabilitation Research CenterBeijing 100000China Department of Rehabilitation Sciences The Hong Kong Polytechnic UniversityHong Kong 999077China

Background:This systematic review aimed to examine whether dual-task(DT)training was superior to single-task(ST)training in improving DT walking,balance and cognitive functions for individuals with Parkinson’s disease(PD).Methods:Literature search was performed in the following electronic databases:PubMed,the Cochrane Library,Web of Science,and Metstr covering inception to May 10,*** in order to facilitate comparison across trials,we calculated the effect size(Hedges’g)of gait,balance,cognitive,and other parameters under both ST and DT conditions,using the mean change score and standard deviation(SD)of change score of the experimental and control *** controlled trials that examined the effects of DT motor and cognitive training in individuals with Parkinson’s disease were included for this systematic ***:A total of 214 participants recruited from six articles(actually five trials)were involved in this *** terms of walking ability,only double support time and stride time variability showed significant between-group difference(Hedges’g=0.34,0.18,respectively).Compared to ST training group,DT training group had a more improvement effect in laboratory balance measurement(Hedges’g=0.18,1.25),but no significant improvement in clinical balance *** significant between-group differences were observed,thus its training effect on cognitive function was ***:The DT training failed to achieve promising results better than ST training in improving DT walking and balance functions for individuals with *** firm conclusion cannot be drawn at present,due to the limited number of eligible *** sample size and high-quality studies are needed to investigate the effectiveness of DT training in individuals with PD.

关键词： Parkinson’s disease Dual-task training Mobility Cognition Systematic review

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Direct detection of C9orf72 hexanucleotide repeat expansions by nanopore biosensor

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Chinese Chemical Letters 2024年第5期35卷 351-354页

作者： xinqiong Li Guocheng Rao xi Peng Chan yang Yanjing Zhang Yan Tian xianghui Fu Jia Geng State Key Laboratory of Biotherapy and Cancer Center West China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengdu 610041China Division of Endocrinology and Metabolism West China School of Medicine/West China HospitalSichuan UniversityChengdu 610041China Department of Endocrinology and Metabolism Affiliated Hospital of North Sichuan Medical CollegeNorth Sichuan Medical CollegeNanchong 637000China Division of Endocrinology and Metabolism National Clinical Research Center for GeriatricsState Key Laboratory of Biotherapy and Cancer CenterWest China HospitalSichuan University and Collaborative Innovation Center of BiotherapyChengdu 610041China Department of Laboratory Medicine State Key Laboratory of BiotherapyMed-X Center for ManufacturingWest China HospitalSichuan University and Collaborative Innovation CenterChengdu 610041China Tianfu Jincheng Laboratory City of Future MedicineChengdu 641400China

Diagnostic C9orf72 hexanucleotide repeat expansions(C9-HRE)is essential for the early and accurate diagnosis of amyotrophic lateral sclerosis(ALS)and will provide support for the prognosis and gene therapy of *** the present study,by combining catalytic hairpin assembly(CHA)with Mycobacterium smegmatis porin A(MspA)nanopore,a new nanopore-based strategy for the detection of C9-HRE was *** than 30 repeats of C9-HRE could be detected via this method,and the results have the potential to help distinguish between patients and healthy ***,the method demonstrated its great specificity for C9-HRE by identifying other repeat *** the high selectivity,this approach had been successfully used to detect C9-HRE in cell and blood samples with high *** detection strategy is user-friendly and has a strong anti-interference ability,thus providing a powerful tool for clinical diagnosis.

关键词： MspA nanopore C9orf72 HRE Detection Biosensor Catalytic hairpin assembly

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CRABP2 regulates infiltration of cancer-associated fibroblasts and immune response in melanoma

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Oncology Research 2024年第2期32卷 261-272页

作者： SHUANGSHUANG ZENG xi CHEN QIAOLI YI ABHIMANYU THAKUR HUI yang YUANLIANG YAN SHAO LIU Department of Pharmacy Xiangya HospitalCentral South UniversityChangsha410008China National Clinical Research Center for Geriatric Disorders Xiangya HospitalCentral South UniversityChangsha410008China Pritzker School of Molecular Engineering Ben May Department for Cancer ResearchUniversity of ChicagoChicagoILUSA Department of Pathology The Second Affiliated Hospital of Shandong First Medical UniversityTaian271000China

Finding biomarkers for immunotherapy is an urgent issue in cancer *** retinoic acid-binding protein 2(CRABP2)is a controversial factor in the occurrence and development of human ***,there is limited research on the relationship between CRABP2 and immunotherapy *** study found that negative correlations of CRABP2 and immune checkpoint markers(PD-1,PD-L1,and CTLA-4)were observed in breast invasive carcinoma(BRCA),skin cutaneous melanoma(SKCM),stomach adenocarcinoma(STAD)and testicular germ cell tumors(TGCT).In particular,in SKCM patients who were treated with PD-1 inhibitors,high levels of CRABP2 predicted poor ***,CRABP2 expression was elevated in cancer-associated fibroblasts(CAFs)at the single-cell *** expression of CRABP2 was positively correlated with markers of CAFs,such as MFAP5,PDPN,ITGA11,PDGFRα/βand THY1 in *** validate the tumor-promoting effect of CRABP2 in vivo,SKCM xenograft mice models with CRABP2 overexpression have been *** models showed an increase in tumor weight and *** analysis indicated that CRABP2 may be involved in immunerelated pathways of SKCM,such as extracellular matrix(ECM)receptor interaction and epithelial-mesenchymal transition(EMT).The study suggests that CRABP2 may regulate immunotherapy in SKCM patients by influencing infiltration of *** conclusion,this study provides new insights into the role of CRABP2 in immunotherapy *** findings suggest that CRABP2 may be a promising biomarker for PD-1 inhibitors in SKCM *** research is needed to confirm these findings and to explore the clinical implications of CRABP2 in immunotherapy.

关键词： CRABP2 Melanoma PD-1 Cancer-associated fibroblasts Immune infiltration

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Long-term thinning decreases the contribution of heterotrophic respiration to soil respiration in subalpine plantations

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Journal of Forestry Research 2024年第3期35卷 189-204页

作者： Longfei Chen Zhibin He Wenzhi Zhao xi Zhu Qin Shen Mingdan Song Zhengpeng Li Junqia Kong Shuping yang Yuan Gao Northwest Institute of Eco-Environment and Resources Chinese Academy of SciencesLanzhou 730000People's Republic of China State Forestry Administration Key Laboratory of Forest Resources and Environmental Management Beijing Forestry UniversityBeijing 100083People's Republic of China Academy of Agriculture and Forestry Sciences Qinghai UniversityXining 810000People's Republic of China College of Landscape Architecture Zhejiang A&F UniversityHangzhou 310000People's Republic of China

Interest in the dynamics of soil respiration(R_(S))in subalpine forest ecosystems is increasing due to their high soil carbon density and potential sensitivity to environmental ***,as a principal silvicultural practice,the long-term impacts of thinning on R_(S) and its heterotrophic and autotrophic respiration components(R_(h) and Ra,respectively)in subalpine plantations are poorly understood,espe-cially in winter.A 3-year field observation was carried out with consideration of winter CO_(2) efflux in middle-aged sub-alpine spruce plantations in northwestern China.A trench-ing method was used to explore the long-term impacts of thinning on Rs,Rn and R_(a).Seventeen years after thinning,mean annual Rs,Rn and R_(a) increased,while the contribu-tion of R_(h) to R_(s) decreased with thinning *** significantly decreased winter R,because of the reduction in R_(n) but had no significant effect on *** temperature sensitivity(Q_(10))of R_(h) and R_(a) also increased with thinning intensity,with lower Q_(10) values for R_(h)(2.1-2.6)than for Ra(2.4-2.8).The results revealed the explanatory variables and pathways related to R_(n) and R_(a) *** increased soil moisture and nitrate nitrogen(NO_(3)^(-)-N),and the enhanced nitrogen and water availability promoted R_(h) and R_(a) by improving fine root biomass and microbial *** results highlight the positive roles of NO_(3)^(-)-N in stimulating R_(s) components following long-term ***,applications of nitrogen fertilizer are not recommended while thinning subalpine spruce plantations from the perspective of reducing soil CO_(2) *** increased Q_(10) values of R_(s) components indicate that a large increase in soil CO_(2) emissions would be expected following thinning because of more pronounced climate warming in alpineregions.

关键词： Heterotrophic respiration Autotrophic respiration Long-term thinning impacts Cold seasons Subalpine plantations Temperature sensitivity

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