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

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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

A synthesis of the Cretaceous wildfire record related to atmospheric oxygen levels?

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Journal of Palaeogeography 2024年第1期13卷 149-164页

作者： Da-Wei Lü Wen-xu Du Zhi-Hui Zhang Yuan Gao tian-tian Wang Jin-Cheng xu Ao-Cong Zhang Cheng-Shan Wang Shandong Provincial Key Laboratory of Depositional Mineralization and Sedimentary Minerals College of Earth Sciences and EngineeringShandong University of Science and TechnologyQingdao 266590Shandong ProvinceChina School of Earth Sciences and Resources China University of GeosciencesBejing 100083China Institute of Earth Sciences China University of Geosciences(Bejing)Beijing 100083China

The Cretaceous was a significant greenhouse period in Earth's history with higher atmospheric CO_(2) levels and temperatures than today. Although evidence of combustion has been widely described from the Cretaceous deposits, our understanding of the spatiotemporal diversification pattern and process of the Cretaceous wildfires is still limited. In this study, we comprehensively synthesize a total of 271 published Cretaceous wildfire occurrences based on the by-products of burning, including fossil charcoal, pyrogenic inertinite(fossil charcoal in coal), and pyrogenic polycyclic aromatic hydrocarbons(PAHs). Spatially, the dataset shows a distinctive distribution of reported wildfire evidence characterized by high concentration in the middle latitudinal areas of the Northern Hemisphere(30°N-60°N) over the Cretaceous. Temporally, an overall increasing trend of the reported wildfire data from the Early Cretaceous to the Late Cretaceous is coincident with higher atmospheric O_(2) levels. However, the spatial and temporal patterns may result from many types of factors, such as taphonomy, preservation, and researcher biases, instead of a real picture of the Cretaceous wildfire evolution. To better understand the spatiotemporal diversification of the Cretaceous wildfire, more investigations on the record of wildfire occurrences during this period would be necessary in the future.

关键词： Wildfire Cretaceous Atmospheric oxygen Taphonomy Charcoal

Modeling method for SSC prediction in pomelo using Vis-NIRS with wavelength selection and latent variable updating

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International Journal of Agricultural and Biological Engineering 2024年第1期17卷 251-260页

作者： Hao tian Shuai Wang Huirong xu Yibin Ying College of Biosystems Engineering and Food Science Zhejiang UniversityHangzhou 310058China Key Laboratory of On-Site Processing Equipment for Agricultural Products Ministry of Agriculture and Rural AffairsHangzhou 310058China College of Food Science Shihezi UniversityShihezi 832003XinjiangChina

The aim of this study was in-line,rapid,and non-destructive detection for soluble solid content(SSC)in pomelos using visible and near-infrared spectroscopy(Vis-NIRS).However,the large size and thick rind of pomelo affect the stability of spectral acquisition and the biological variabilities affect the robustness of *** these issues,in this study,an efficient prototype in-line detection system in transmittance mode was designed and evaluated in comparison with an off-line detection *** from the years 2019 and 2020 were used for modeling and the external validation data were obtained by the inline detection system in *** wavelength selection methods of changeable size moving window(CSMW),random frog(RF),and competitive adaptive reweighted sampling(CARS)were used to improve the prediction accuracy of partial least squares regression(PLSR)*** best performance of internal prediction was obtained by CARS-PLSR and the determination coefficient of prediction(),root mean square error of prediction(RMSEP),and residual predictive deviation(RPD)were 0.958,0.204%,and 4.821,***,all models obtained large prediction biases in external *** latent variable updating(LVU)method was proposed to update models and improve the performance in external *** samples from the external validation set were randomly selected to update the *** with the recalibration method,LVU could effectively modify the original models which matched the SSC range of the external validation *** CSMW-PLSR models were more robust in external *** off-line model with LVU performed best with a root mean square error of validation(RMSEV)of 0.599%and the in-line model with recalibration obtained RMSEV of 0.864%.These results demonstrated the application potential of the transmittance Vis-NIRS for in-line rapid prediction of SSC in pomelos and the modeling and updating methods could be applied to samples with biological variabi

关键词： Vis-NIRS in-line detection external validation wavelength selection model updating pomelo SSC

Gut-targeted therapies for type 2 diabetes mellitus: A review

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World Journal of Clinical Cases 2024年第1期12卷 1-8页

作者： tian-Cheng xu Yun Liu Zhi Yu Bin xu Key Laboratory of Acupuncture and Medicine Research of Ministry of Education Nanjing University of Chinese MedicineNanjing 210023Jiangsu ProvinceChina

Type 2 diabetes mellitus(T2DM)is a chronic metabolic disorder characterized by hyperglycemia and insulin *** global prevalence of T2DM has reached epidemic proportions,affecting approximately 463 million adults worldwide in *** treatments for T2DM include lifestyle modifications,oral antidiabetic agents,and insulin ***,these therapies may carry side effects and fail to achieve optimal glycemic control in some ***,there is a growing interest in the role of gut microbiota and more gut-targeted therapies in the management of *** gut microbiota,which refers to the community of microorganisms that inhabit the human gut,has been shown to play a crucial role in the regulation of glucose metabolism and insulin *** in gut microbiota composition and diversity have been observed in T2DM patients,with a reduction in beneficial bacteria and an increase in pathogenic *** dysbiosis may contribute to the pathogenesis of the disease by promoting inflammation and impairing gut barrier *** gut-targeted therapies have been developed to modulate the gut microbiota and improve glycemic control in *** potential approach is the use of probio-tics,which are live microorganisms that confer health benefits to the host when administered in adequate *** randomized controlled trials have demonstrated that certain probiotics,such as Lactobacillus and Bifidobacterium species,can improve glycemic control and insulin sensitivity in T2DM *** may include the production of short-chain fatty acids,the improvement of gut barrier function,and the reduction of *** gut-targeted therapy is fecal microbiota transplantation(FMT),which involves the transfer of fecal material from a healthy donor to a *** has been used successfully in the treatment of Clostridioides difficile infection and is now being investigated as a potential therapy for T2DM.A recent rand

关键词： Type 2 diabetes mellitus Gastroenterology Bacteria Implanted device

Super-high bed sintering for iron ores:behaviors,causes and solutions of horizontal segregation on strand

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Journal of Iron and Steel Research International 2024年第7期31卷 1590-1596页

作者： Liang-ping xu Hui-bo Liu zhong-lin Dong Qiang zhong Yu-chao Zhao Guang-hui Li School of Minerals Processing and Bioengineering Central South UniversityChangsha 410083HunanChina

Horizontal segregation has been a constraint to the development and application of super-high bed *** eliminate the horizontal segregation of super-high bed sintering,several typical sintering machines were sampled and analyzed,and theoretical calculation was made to compare the bed depth and their differences in different areas within the mixture ***,solutions were proposed and applied to a 265 m^(2) sintering *** results showed that the horizontal seg-regation of the 265 m^(2) sintering machine was dominated by particles larger than 8 mm with horizontal segregation degree of 0.48,while 360 and 550 m^(2) sintering machines were affected by 5-8 mm and 1-3 mm particles with horizontal segregation degree of 0.27 and 0.31,*** analysis indicated the different segregation distribution results from the matching of the bed depth of each area within the mixture ***,the horizontal segregation degree not larger than 0.06 was achieved by optimizing the time parameters and the division of three zones on the 265 m^(2) sintering machine.

关键词： Super-high bed sintering Horizontal segregation Feeder Particle distribution Agglomeration

Transition-metal-catalyzed remote meta-C-H alkylation and alkynylation of aryl sulfonic acids enabled by an indolyl template

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Chinese Chemical Letters 2024年第8期35卷 254-259页

作者： Pengfei Zhang Qingxue Ma Zhiwei Jiang Xiaohua xu zhong Jin College of Chemistry State Key Laboratory of Elemento-organic ChemistryNankai UniversityTianjin 300071China Key Laboratory of Xinjiang Native Medicinal and Edible Plant Resource Chemistry College of Chemistry and Environmental SciencesKashi UniversityKashgar 844007China

Transition-metal-catalyzed remote sp^(2)C-H functionalization of aryl sulfonic acids was hardly ever real-ized owing to competitive ortho-C-H functionalization of aryl sulfonates and electron-deficient nature of phenyl ***,with the assistance of a practical biaryl indolyl directing template,palladium-catalyzed remote sp^(2)C-H alkylation of aryl sulfonic acids have been achieved in moderate to good yields with exclusive meta ***,remote meta-selective C-H alkynylation of aryl sulfonic acids was also accomplished with a rhodium *** meta-C-H functionalized products proved to be the superior synthetic precursors,which are difficult to access using the conventional strategy.

关键词： C-H functionalization Aryl sulfonic acid Site-selectivity Transition-metal catalysis Alkylation Alkynylation

Dopaminergic Remodeling During a Critical Developmental Window:Linking Drug Use to Adult Aggression

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Neuroscience Bulletin 2024年第6期40卷 845-848页

作者： Dadao An Lingyan Zheng Zhengyi xu Yanrong Zheng zhong Chen Key Laboratory of Neuropharmacology and Translational Medicine of Zhejiang Province Zhejiang Chinese Medical UniversityHangzhou310053China

Behaviors can be shaped and modulated by the dopamine system,which can be remodeled in adolescents due to environmental factors,including pharmacologic exposure,stress,and rewarding experiences,leading to various adolescentonset neuropsychiatric disorders[1-3].A deficiency of dopamine transporter(DAT),responsible for reuptaking extracellular DA.

关键词： Window shaped Dopamine

MPI/OpenMP-Based Parallel Solver for Imprint Forming Simulation

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Computer Modeling in Engineering & Sciences 2024年第7期140卷 461-483页

作者： Yang Li Jiangping xu Yun Liu Wen zhong Fei Wang School of Mechanical Engineering Jiangsu UniversityZhenjiang212016China School of Mechanical Engineering Wuhan Polytechnic UniversityWuhan430023China Shenyang Mint Company Limited Shenyang110092China

In this research,we present the pure open multi-processing(OpenMP),pure message passing interface(MPI),and hybrid MPI/OpenMP parallel solvers within the dynamic explicit central difference algorithm for the coining process to address the challenge of capturing fine relief features of approximately 50 *** such precision demands the utilization of at least 7 million tetrahedron elements,surpassing the capabilities of traditional serial programs previously *** mitigate data races when calculating internal forces,intermediate arrays are introduced within the OpenMP *** helps ensure proper synchronization and avoid conflicts during parallel ***,in the MPI implementation,the coins are partitioned into the desired number of *** division allows for efficient distribution of computational tasks across multiple *** simulation examples are conducted to compare the three solvers with serial programs,evaluating correctness,acceleration ratio,and parallel *** results reveal a relative error of approximately 0.3%in forming force among the parallel and serial solvers,while the predicted insufficient material zones align with experimental ***,speedup ratio and parallel efficiency are assessed for the coining process *** pureMPI parallel solver achieves a maximum acceleration of 9.5 on a single computer(utilizing 12 cores)and the hybrid solver exhibits a speedup ratio of 136 in a cluster(using 6 compute nodes and 12 cores per compute node),showing the strong scalability of the hybrid MPI/OpenMP programming *** approach effectively meets the simulation requirements for commemorative coins with intricate relief patterns.

关键词： Hybrid MPI/OpenMP parallel computing MPI OpenMP imprint forming

Super-high bed sintering for iron ores: inhomogeneous phenomena and its mechanism during mineralizing

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Journal of Iron and Steel Research International 2024年第8期31卷 1850-1860页

作者： Hui-bo Liu Liang-ping xu Xi-duan Yang zhong-lin Dong Qiang zhong Guang-hui Li School of Minerals Processing and Bioengineering Central South UniversityChangsha 410083HunanChina

The inhomogeneous sinter properties in super-high bed sintering have been reported in our previous *** inves-tigate the reasons for the inhomogeneous phenomena,detailed sampling and analysis of mixed material bed and sintered bed in super-high bed sintering plant were *** results indicated that the higher porosity and thinner dendrite of silico-ferrite of calcium and aluminum in the upper layer as well as dense structure and higher secondary hematite content in the lower layer led to the heterogeneities of mechanical strength and reduction properties exceeding 20%and 10%,*** the bed top downward,the basicity of mixed material decreased from 2.13 to 1.68 because the average particle size increased from 2.65 to 4.56 *** and fuels gathered in finer particles(-3 mm)of mixed material,and the-3 mm particles of mixed material generated more liquid phase than+3 mm *** heat input of super-high sintering bed was inhomogeneous due to the heat accumulation effect and unreasonable fuel *** inhomo-geneous sintering heat condition in sintering bed resulted in the different quantities and properties of liquid *** inhomogeneous quantities and properties of liquid phase that were influenced by inhomogeneous distribution of chemical composition,particle size,and heat input led to inhomogeneous mineralizing *** mineralizing condition is the key for homogeneous super-high bed sintering.

关键词： Iron ore Super-high bed sintering Mineralization Material segregation Heat accumulation