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Phenomics 2024年第1期4卷 81-89页

作者： Jialin Zhao Xuling Han Helian Li yali luo Yan Fang Yun Wang Jian Gao Yiran Zhao Jingxuan Han Feng Qian State Key Laboratory of Genetic Engineering ShanghaiPublic Health Clinical CenterHuman PhenomeInstituteZhangjiang Fudan International InnovationCenter and School of Life SciencesFudan UniversityShanghai 200438China Ministry of Education Key Laboratory of ContemporaryAnthropology School of Life SciencesFudan UniversityShanghai 200438China Institute of Immunophenome International Human PhenomeInstitutes(Shanghai)Shanghai 200433China

The immune system defends the body from infection and plays a vital role in a wide range of health conditions.Metabolism afects a series of physiological processes,including those linked to the function of human immune system.Cellular metabolism modulates immune cell activation and cytokine production.Understanding the relationship between metabolism and immune response has important implications for the development of immune-based therapeutics.However,the deployment of large-scale functional assays to investigate the metabolic regulation of immune response has been limited by the lack of standardized procedures.Here,we present a protocol for the analysis of immune response using standardized whole-blood stimulation with metabolism modulation.Diverse immune stimuli including pattern recognition receptor(PRR)ligands and microbial stimuli were incubated with fresh human whole blood.The metabolic inhibitors were used to modulate metabolic status in the immune cells.The variable immune responses after metabolic interventions were evaluated.We described in detail the main steps involved in the whole-blood stimulation and cytokines quantifcation,namely,collection and treatment of whole blood,preparation of samples and controls,cytokines detection,and stimulation with metabolic interventions.The metabolic inhibitors for anabolic pathways and catabolic pathways exert selective efects on the production of cytokines from immune cells.In addition to a robust and accurate assessment of immune response in cohort studies,the standardized whole-blood stimulation with metabolic regulation might provide new insights for modulating immunity.

关键词： Immune response Whole blood stimulation Cytokines Immunometabolism

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Identification and global characterization of eccDNA reveals hallmarks in iron nanoparticles-treated breast cancer cells

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Genes & Diseases 2024年第2期11卷 532-534页

作者： Wenxiang Lu Ying Wang Tao luo Fuyu Li yali Jiang Jinke Wang Weizhong Zhang Yunfei Bai State Key Lab of Bioelectronics School of Biological Science and Medical EngineeringSoutheast UniversityNanjingJiangsu 210096China The Friendship Hospital of Ili Kazakh Autonomous Prefecture Ili & Jiangsu Joint Institute of HealthYiningXinjiang 835000China Department of Ophthalmology First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsu 210029China

The biogenesis and functions of extrachromosomal circular DNA(eccDNA)have been studied for several decades.However,the heterogeneity of eccDNA is largely ignored.In this study,we purified and sequenced eccDNA and RNA using a method that simultaneously extracts DNA and RNA from cultured cells treated with iron nanoparticles.We discovered that the characteristics of eccDNA are altered by iron stress,particularly on genic and CpG islands regions,suggesting a biogenesis mechanism induced by transcription.

关键词： breast nanoparticles characterization

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Characteristics of Pre-summer Daytime Cloud Regimes over Coastal South China from the Himawari-8 Satellite

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Advances in Atmospheric Sciences 2022年第12期39卷 2008-2023,I0001-I0015页

作者： Mingxin LI yali luo Min MIN State Key Laboratory of Severe Weather Chinese Academy of Meteorological SciencesBeijing 100081China Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science and TechnologyNanjing 210044China School of Atmospheric Sciences and Guangdong Province Key Laboratory for Climate Change and Natural Disaster StudiesSun Yat-sen UniversityGuangzhou 519082China

Using the high spatiotemporal resolution(2 km-and-10 min)data from the Advanced Himawari Imager onboard the Himawari-8 satellite,this study documents the fine-scale characteristics of daytime cloud regimes(CRs)over coastal South China during the pre-summer rainy season(April–June).Six CRs(CR1–CR6)are identified based on the joint frequency distribution of cloud top brightness temperature and cloud optical thickness,namely,the optically thin-to-moderate cloud mixture,optically thin warm clouds with cirrus,optically thick warm clouds,weak convective cloud mixture,strong convective clouds,and extreme,deep convective clouds.The optically thick warm clouds are the major CR during April and May,with higher frequencies over land,especially along the urban agglomeration,rather than the offshore which may be an indicator of the higher aerosol concentrations being a contributing factor over the cities.The CRs with weak convective cloud mixtures and strong convective clouds appear more frequently over the land,while the two CRs with optically thinner clouds occur mainly offshore.Synoptic flow patterns(SPs)are objectively identified and examined focusing on those favoring the two major rainproducing CRs(CR5 and CR6)and the highly reflective CR with optically thick warm clouds(CR3).The two SPs favoring CR5 and CR6 are characterized by abundant moisture with low-level jets after monsoon onset,and a northwest highsoutheast low pattern with strong dynamic convergence along the coastline,respectively.The non-convective CR3 with high reflectance is related to a SP that features the western North Pacific subtropical high extending more westward,leading to a moderate moisture supply and a wide range of convective available potential energy,but also,large convective inhibition.

关键词： cloud regime monsoon onset synoptic pattern satellite data spatiotemporal distribution

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Efficiently Improving Ensemble Forecasts of Warm-Sector Heavy Rainfall over Coastal Southern China: Targeted Assimilation to Reduce the Critical Initial Field Errors

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气象学报:英文版 2023年第4期37卷 486-507页

作者： Xinghua BAO Rudi XIA yali luo Jian YUE State Key Laboratory of Severe Weather Chinese Academy of Meteorological Sciences(CAMS)China Meteorological Administration(CMA)Beijing 100081 Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters(CIC-FEMD) Nanjing University of Information Science&TechnologyNanjing 210044 CMA Earth System Modeling and Prediction Centre China Meteorological AdministrationBeijing 100081

Warm-sector heavy rainfall events over southern China are difficult to accurately forecast, due in part to inaccurate initial fields in numerical weather prediction models. In order to determine an efficient way of reducing the critical initial field errors, this study conducts and compares two sets of 60-member ensemble forecast experiments of a warm-sector heavy rainfall event over coastal southern China without data assimilation(NODA) and with radar radial velocity data assimilation(RadarDA). Yangjiang radar data, which can provide offshore high-resolution wind field information, were assimilated by using a Weather Research and Forecasting(WRF)-based ensemble Kalman filter(EnKF) system. The results show that the speed and direction errors of the southeasterly airflow in the marine boundary layer over the northern South China Sea may primarily be responsible for the forecast errors in rainfall and convection evolution. Targeted assimilation of radial velocity data from the Yangjiang radar can reduce the critical initial field errors of most members, resulting in improvements to the ensemble forecast. Specifically, RadarDA simulations indicate that radial-velocity data assimilation(VrDA) can directly reduce the initial field errors in wind speed and direction, and indirectly and slightly adjust the initial moisture fields in most members, thereby improving the evolution features of moisture transport during the subsequent forecast period. Therefore, these RadarDA members can better capture the initiation and development of convection and have higher forecast skill for the convection evolution and rainfall. The improvement in the deterministic forecasts of most members results in an improved overall ensemble forecast performance. However, VrDA sometimes results in inappropriate adjustment of the initial wind field,so the forecast skill of a few members decreases rather than increases after VrDA. This suggests that a degree of uncertainty remains about the effect of the WRF-based EnKF system. Moreover, the results

关键词： ensemble forecast targeted assimilation warm-sector heavy rainfall

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Energy Paths that Sustain the Warm-Sector Torrential Rainfall over South China and Their Contrasts to the Frontal Rainfall: A Case Study

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Advances in Atmospheric Sciences 2022年第9期39卷 1519-1535页

作者： Shenming FU Jingping ZHANG yali luo Wenying YANG Jianhua SUN International Center for Climate and Environment Sciences Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China University of Chinese Academy of Sciences Beijing 100049China Laboratory of Cloud-Precipitation Physics and Severe Storms Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China State Key Laboratory of Severe Weather Chinese Academy of Meteorological SciencesBeijing 100081China Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science and TechnologyNanjing 210044China

Predicting warm-sector torrential rainfall over South China,which is famous for its destructive power,is one of the most challenging issues of the current numerical forecast field.Insufficient understanding of the key mechanisms underlying this type of event is the root cause.Since understanding the energetics is crucial to understanding the evolutions of various types of weather systems,a general methodology for investigating energetics of torrential rainfall is provided in this study.By applying this methodology to a persistent torrential rainfall event which had concurrent frontal and warm-sector precipitation,the first physical image on the energetics of the warm-sector torrential rainfall is established.This clarifies the energy sources for producing the warm-sector rainfall during this event.For the first time,fundamental similarities and differences between the warm-sector and frontal torrential rainfall are shown in terms of energetics.It is found that these two types of rainfall mainly differed from each other in the lower-tropospheric dynamical features,and their key differences lay in energy sources.Scale interactions(mainly through downscale energy cascade and transport)were a dominant factor for the warm-sector torrential rainfall during this event,whereas,for the frontal torrential rainfall,they were only of secondary importance.Three typical signals in the background environment are found to have supplied energy to the warm-sector torrential rainfall,with the quasi-biweekly oscillation having contributed the most.

关键词： torrential rainfall warm-sector rainfall frontal rainfall South China scale interactions baroclinic energy conversion

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Cause–Effect Relationship between Meso-γ-Scale Rotation and Extreme Short-Term Precipitation:Observational Analyses at Minute and Sub-Kilometer Scales

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Journal of Meteorological Research 2022年第4期36卷 539-552页

作者： Qiuyang ZHANG yali luo Ying TANG Xin XU Shuting YU Chong WU School of Atmospheric Sciences Chengdu University of Information TechnologyChengdu 610225 State Key Laboratory of Severe Weather Chinese Academy of Meteorological SciencesChina Meteorological AdministrationBeijing 100081 Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science&TechnologyNanjing 210044 Nanjing Marine Radar Institute Nanjing 211153 School of Atmospheric Sciences Nanjing UniversityNanjing 210023

The cause–effect relationship between meso-γ-scale rotation and extreme short-term precipitation events remains elusive in mesoscale meteorological research.We aimed to elucidate this relationship by analyzing a rainstorm over the Pearl River Delta during the nocturnal hours of 15 May 2017 based on 6-min radar observations and 1-min rain gauge data.This rainstorm had a maximum hourly rainfall of 100.1 mm,with 26 stations recording hourly rainfall>60 mm h^(−1) in 5 h.Extreme heavy precipitation was produced in association with a convergence zone along the southern side of a synoptic low-level shear line,where southwesterly warm,humid airflows with precipitable water of>60 mm,little convection inhibition(100 mm h^(−1)),reached its peak intensity after the peak of the collocated 6-min rainfall accumulation,and then weakened rapidly after the extreme rainfall region moved away.The radar-retrieved liquid water path was about five to seven times the ice water path and the specific differential phase(Kdp)below 0°C increased sharply downward during the lifetime of the vortex,suggesting the presence of active warm rain microphysical processes.These results indicate that the release of the latent heat of condensation induced by extreme rainfall could have contributed to the formation of the vortex in an environment with a weak 0–1-km vertical wind shear(about 4–5 m s^(−1))through enhanced lowlevel convergence,although the strengthening of low-level updrafts by rotational dynamic effects and short-term rainfall cannot be ruled out.

关键词： extreme short-term precipitation meso-γ-scale vortex observational analysis minute-and kilometerscale resolution

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On the Influences of Urbanization on the Extreme Rainfall over Zhengzhou on 20 July 2021: A Convection-Permitting Ensemble Modeling Study

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Advances in Atmospheric Sciences 2023年第3期40卷 393-409页

作者： yali luo Jiahua ZHANG Miao YU Xudong LIANG Rudi XIA Yanyu GAO Xiaoyu GAO Jinfang YIN State Key Laboratory of Severe Weather Chinese Academy of Meteorological SciencesBeijing 100081China Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science and TechnologyNanjing 210044China School of Atmospheric Sciences Chengdu University of Information TechnologyChengdu 610225China

This study investigates the influences of urban land cover on the extreme rainfall event over the Zhengzhou city in central China on 20 July 2021 using the Weather Research and Forecasting model at a convection-permitting scale[1-km resolution in the innermost domain(d3)].Two ensembles of simulation(CTRL,NURB),each consisting of 11 members with a multi-layer urban canopy model and various combinations of physics schemes,were conducted using different land cover scenarios:(i)the real urban land cover,(ii)all cities in d3 being replaced with natural land cover.The results suggest that CTRL reasonably reproduces the spatiotemporal evolution of rainstorms and the 24-h rainfall accumulation over the key region,although the maximum hourly rainfall is underestimated and displaced to the west or southwest by most members.The ensemble mean 24-h rainfall accumulation over the key region of heavy rainfall is reduced by 13%,and the maximum hourly rainfall simulated by each member is reduced by 15–70 mm in CTRL relative to NURB.The reduction in the simulated rainfall by urbanization is closely associated with numerous cities/towns to the south,southeast,and east of Zhengzhou.Their heating effects jointly lead to formation of anomalous upward motions in and above the planetary boundary layer(PBL),which exaggerates the PBL drying effect due to reduced evapotranspiration and also enhances the wind stilling effect due to increased surface friction in urban areas.As a result,the lateral inflows of moisture and high-θe(equivalent potential temperature)air from south and east to Zhengzhou are reduced.

关键词： urbanization extreme rainfall convection-permitting ensemble simulation land-atmosphere interaction boundary layer water vapor transport

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Deep Immunophenotyping of Human Whole Blood by Standardized Multi‑parametric Flow Cytometry Analyses

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Phenomics 2023年第3期3卷 309-328页

作者： Jian Gao yali luo Helian Li Yiran Zhao Jialin Zhao Xuling Han Jingxuan Han Huiqin Lin Feng Qian State Key Laboratory of Genetic Engineering Shanghai Public Health Clinical CenterHuman Phenome InstituteZhangjiang Fudan International Innovation Center and School of Life SciencesFudan UniversityShanghai 200438China Ministry of Education Key Laboratory of Contemporary Anthropology School of Life SciencesFudan UniversityShanghai 200438China Institute of Immunophenome International Human Phenome Institutes(Shanghai)Shanghai 200433China

Immunophenotyping is proving crucial to understanding the role of the immune system in health and disease.High-through-put flow cytometry has been used extensively to reveal changes in immune cell composition and function at the single-cell level.Here,we describe six optimized 11-color flow cytometry panels for deep immunophenotyping of human whole blood.A total of 51 surface antibodies,which are readily available and validated,were selected to identify the key immune cell populations and evaluate their functional state in a single assay.The gating strategies for effective flow cytometry data analysis are included in the protocol.To ensure data reproducibility,we provide detailed procedures in three parts,including(1)instrument characterization and detector gain optimization,(2)antibody titration and sample staining,and(3)data acquisition and quality checks.This standardized approach has been applied to a variety of donors for a better understanding of the complexity of the human immune system.

关键词： Deep immunophenotyping Multi-parametric flow cytometry Human whole blood Gating strategies Standardization

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Analysis of Paths and Sources of Moisture for the South China Rainfall during the Presummer Rainy Season of 1979–2014

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Journal of Meteorological Research 2018年第5期32卷 744-757页

作者： Yangruixue CHEN yali luo State Key Laboratory of Severe Weather Chinese Academy of Meteorological SciencesBeijing 100081 University of Chinese Academy of Sciences Beijing 100049 Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science&TechnologyNanjing 210044

The paths and sources of moisture supplied to South China during two periods of the presummer rainy season （April-June） of 1979-2014, i.e., before and after the onset of the summer monsoon over the South China Sea （SCS）, are investigated by using the Hybrid Single-Particle Lagrangian Integrated Trajectory （HYSPLIT） model. During the premonsoon-onset period, the moisture transport trajectories are clustered into 6 groups, with four ocean-originating paths providing 83.9% and two continent-originating paths （originating over Lake Baikal and the Persian Gulf） con- tributing the remaining 16.1% of the total moisture. The two Pacific-originating paths, from the western Pacific Ocean and the East China Sea, combined account for about 46%, the SCS-originating path contributes about 24.3%, while the Bay of Bengal-originating path accounts for 13.6% of the total moisture over South China. The trajectories during the postmonsoon-onset period are clustered into 4 groups, with three southwesterly paths （from the Arabian Sea, the central Indian Ocean, and the western Indian Ocean, respectively） accounting for more than 76% and the sole Pacific-originating path accounting for 23.8% of the total moisture. The formation of the moisture transport tra-jectories is substantially affected by the topography, especially the Tibetan Plateau and the Indian and Indo-China Peninsulas. The SCS region contributes the most moisture during both periods （35.3% and 31.1%）. The Pacific Ocean is ranked second during the former period （about 21.0%） but its contribution is reduced to 5.0% during the lat-ter period, while the contribution from the Bay of Bengal and the Indian Ocean combined increases from 17.1% to 43.2%.

关键词： presummer rainy season South China the Hybrid Single-Particle Lagrangian Integrated Trajectory （HYSPLIT） model water vapor path moisture source

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Classification and Diurnal Variations of Precipitation Echoes Observed by a C-band Vertically-Pointing Radar in Central Tibetan Plateau during TIPEX-Ⅲ 2014-IOP

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Journal of Meteorological Research 2018年第6期32卷 985-1001页

作者： Ruoyun MA yali luo Hui WANG State Key Laboratory of Severe Weather Chinese Academy of Meteorological Sciences Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters Nanjing University of Information Science & Technology Key Laboratory for Cloud Physics and Weather Modification of China Meteorological Administration Chinese Academy of Meteorological Sciences

This study investigates classification and diurnal variations of the precipitation echoes over the central Tibetan Plateau based on the observations collected from a C-band vertically-pointing frequency-modulated continuous-wave(C-FMCW)radar during the Third Tibetan Plateau Atmospheric Scientific Experiment(TIPEX-Ⅲ)2014-Intensive Observation Period(2014-IOP).The results show that 51.32%of the vertical profiles have valid echoes with reflectivity>–10 dBZ,and 35.06% of the valid echo profiles produce precipitation at the ground(precipitation profiles);stratiform precipitation with an evident bright-band signature,weak convective precipitation,and strong convective precipitation account for 52.03%,42.98%,and 4.99% of the precipitation profiles,respectively.About 59.84% of the precipitation occurs in the afternoon to midnight,while 40.16% of the precipitation with weaker intensity is observed in the nocturnal hours and in the morning.Diurnal variation of occurrence frequency of precipitation shows a major peak during 2100–2200 LST(local solar time)with 59.02%being the stratiform precipitation;the secondary peak appears during 1300–1400 LST with 59.71% being the weak convective precipitation;the strong convective precipitation occurs mostly(81.83%)in the afternoon and evening with two peaks over 1200–1300 and 1700–1800 LST,respectively.Starting from approximately 1100 LST,precipitation echoes develop with enhanced vertical air motion,elevated echo top,and increasing radar reflectivity.Intense upward air motion occurs most frequently in 1700–1800 LST with a secondary peak in 1100–1400 LST,while the tops of precipitation echoes and intense upward air motion reach their highest levels during 1600–1800 LST.The atmospheric conditions in the early morning are disadvantageous for convective initiation and development.Around noon,the convective available potential energy(CAPE)increases markedly,convective inhibition(CIN)is generally small,and a super-dry-adiabatic layer is present near the surface(0–400 m).In the early evenin

关键词： TIPEX-Ⅲ vertically-pointing radar precipitation echoes diurnal variation

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