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NCAD v1.0: a database for non-coding variant annotation and interpretation

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Journal of Genetics and Genomics 2024年第2期51卷 230-242页

作者： Xiaoshu Feng Sihan liu ke li Fengxiao Bu Huijun Yuan Institute of Rare Diseases West China HospitalSichuan UniversityChengduSichuan 610044China

The application of whole genome sequencing is expanding in clinical diagnostics across various genetic disorders, and the significance of non-coding variants in penetrant diseases is increasingly being demonstrated. Therefore, it is urgent to improve the diagnostic yield by exploring the pathogenic mechanisms of variants in non-coding regions. However, the interpretation of non-coding variants remains a significant challenge, due to the complex functional regulatory mechanisms of non-coding regions and the current limitations of available databases and tools. Hence, we develop the non-coding variant annotation database (NCAD, http://***/), encompassing comprehensive insights into 665,679,194 variants, regulatory elements, and element interaction details. Integrating data from 96 sources, spanning both GRCh37 and GRCh38 versions, NCAD v1.0 provides vital information to support the genetic diagnosis of non-coding variants, including allele frequencies of 12 diverse populations, with a particular focus on the population frequency information for 230,235,698 variants in 20,964 Chinese individuals. Moreover, it offers prediction scores for variant functionality, five categories of regulatory elements, and four types of non-coding RNAs. With its rich data and comprehensive coverage, NCAD serves as a valuable platform, empowering researchers and clinicians with profound insights into non-coding regulatory mechanisms while facilitating the interpretation of non-coding variants.

关键词： Non-coding variants Annotation Variant interpretation Database

Sustainable management of campus fallen leaves through low-temperature pyrolysis and application in Pb immobilization

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Journal of Environmental Sciences 2024年第5期139卷 281-292页

作者： Rongli Tan ke li Yue Sun Xiaoliang Fan Zhengtao Shen lingyi Tang School of Environment Nanjing UniversityNanjing 210023China School of Chemistry and Chemical Engineering Nanjing UniversityNanjing 210023China School of Earth and Engineering Sciences Nanjing UniversityNanjing 210023China Department of Earth and Atmospheric Sciences University of AlbertaEdmonton T6G 2E3Canada

Realizing campus sustainability requires the environmental-friendly and economical treatment of tremendous fallen leaves.Producing fallen leaf biochar at a low temperature is a candidate approach.In this study,six common types of fallen leaves on the campus were pyrolyzed at 300℃.The obtained biochars were characterized and the adsorption mechanisms of lead(Pb)by the fallen leaf biochars were investigated.The adsorption capacity of leaf biochar for Pb was relatively high,up to 209 mg/g(Yulania denudata leaf biochar).Adsorption of Pb onto active sites was the rate-limiting step for most leaf biochars.But for Platanus leaf biochar,intraparticle diffusion of Pb^(2+)dominated owing to the lowest adsorption capacity.However,the highest exchangeable Pb fraction(27%)indicated its potential for removing aqueous Pb^(2+).Ginkgo and Prunus cerasifera leaf biochar immobilized Pb by surface complexation and precipitation as lead oxalate.Hence,they were suitable for soil heavy metal remediation.This study shed the light on the sustainable utilization of campus fallen leaves and the application of fallen leaf biochars in heavy metal remediation.

关键词： Fallen leaves Waste management Biochar Lead removal Sorption Circular campus

Protein post-translational modifications in auxin signaling

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Journal of Genetics and Genomics 2024年第3期51卷 279-291页

作者： Xiankui Cui Junxia Wang ke li Bingsheng Lv Bingkai Hou Zhaojun Ding The key Laboratory of Plant Development and Environmental Adaptation Biology Ministry of EducationSchool of Life SciencesShandong UniversityQingdaoShandong 266237China Shandong Academy of Grape JinanShandong 250100China College of Horticulture Qingdao Agricultural UniversityQingdaoShandong 266109China

Protein post-translational modifications(PTMs),such as ubiquitination,phosphorylation,and small ubiquitin-like modifier(SUMO)ylation,are crucial for regulating protein stability,activity,subcellular localization,and binding with cofactors.Such modifications remarkably increase the variety and complexity of proteomes,which are essential for regulating numerous cellular and physiological processes.The regulation of auxin signaling is finely tuned in time and space to guide various plant growth and development.Accumulating evidence indicates that PTMs play critical roles in auxin signaling regulations.Thus,a thorough and systematic review of the functions of PTMs in auxin signal transduction will improve our profound comprehension of the regulation mechanism of auxin signaling and auxin-mediated various processes.This review discusses the progress of protein ubiquitination,phosphorylation,histone acetylation and methylation,SUMOylation,and S-nitrosylation in the regulation of auxin signaling.

关键词： Arabidopsis thaliana Auxin Auxin signaling Post-translational modifications Protein regulation

Nano-sized stationary phase packings retained by single-particle frit for microchip liquid chromatography

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Chinese Chemical Letters 2024年第4期35卷 486-489页

作者： Wangyan Hu ke li Xiangnan Dou Ning li Xiayan Wang Center Excellence for Environmental Safety and Biological Effects Beijing Key Laboratory for Green Catalysis and SeparationDepartment of ChemistryBeijing University of TechnologyBeijing 100124China Center for Environmental Metrology National Institute of MetrologyBeijing 100029China

Modern chromatography is increasingly focused on miniaturization and integration. Compared to conventional liquid chromatography, microfluidic chip liquid chromatography(microchip-LC) has the potential due to its zero-dead volume connection and ease of integration. Nano-sized packings have the potential to significantly enhance separation performance in microchip-LC. However, their application has been hindered by packing difficulties. This study presents a method for packing nano-sized silica particles into a microchannel as the stationary phase. The microchip-LC packed column was prepared by combining the weir and the porous silica single-particle as frit to retain the packing particles. A surface tensionbased single-particle picking technique was established to insert porous single-particle frit into glass microchannels. Additionally, we developed a slurry packing method that utilizes air pressure to inject nano-sized packing into the microchannel. Pressure-driven chromatographic separation was performed using this nano-packed column integrated into a glass microchip. The mixture of four PAHs was successfully separated within just 8 min using a 5 mm separation channel length, achieving high theoretical plates(10~6plates/m). Overall, these findings demonstrate the potential of utilizing nano-sized packings for enhancing chromatographic performance in microchip systems.

关键词： Nano-size packing Single-particle frit Packed column Microchip LC Chromatographic separation

Fewer is more:efficient object detection in large aerial images

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Science China(Information Sciences) 2024年第1期67卷 105-123页

作者： Xingxing XIE Gong CHENG Qingyang li Shicheng MIAO ke li Junwei HAN School of Automation Northwestern Polytechnical University Zhengzhou Institute of Surveying and Mapping

Current mainstream object detection methods for large aerial images usually divide large images into patches and then exhaustively detect the objects of interest on all patches,no matter whether there exist objects or not.This paradigm,although effective,is inefficient because the detectors have to go through all patches,severely hindering the inference speed.This paper presents an objectness activation network(OAN) to help detectors focus on fewer patches but achieve more efficient inference and more accurate results,enabling a simple and effective solution to object detection in large images.In brief,OAN is a light fully-convolutional network for judging whether each patch contains objects or not,which can be easily integrated into many object detectors and jointly trained with them end-to-end.We extensively evaluate our OAN with five advanced detectors.Using OAN,all five detectors acquire more than 30.0% speed-up on three large-scale aerial image datasets,meanwhile with consistent accuracy improvements.On extremely large Gaofen-2 images(29200 × 27620 pixels),our OAN improves the detection speed by 70.5%.Moreover,we extend our OAN to driving-scene object detection and 4K video object detection,boosting the detection speed by 112.1% and 75.0%,respectively,without sacrificing the accuracy.

关键词： efficient object detection large aerial images objectness activation network

Exploring formation mechanism and source attribution of ozone during the 2019 Wuhan Military World Games:Implications for ozone control strategies

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Journal of Environmental Sciences 2024年第2期136卷 400-411页

作者： Lei Zhang lili Wang Runyu Wang Nan Chen Yuan Yang ke li Jie Sun Dan Yao Yuesi Wang Minghui Tao Yang Sun Institute of Atmospheric Physics Chinese Academy of SciencesBeijing 100029China University of the Chinese Academy of Sciences Beijing 100049China Hubei Ecological Environment Monitoring Center Station Wuhan 430072China Guizhou Research and Designing Institute of Environmental Sciences Guizhou Academy of Environmental Science and DesignGuiyang 550081China Jiangsu key Laboratory of Atmospheric Environment Monitoring and Pollution Control Jiangsu Collaborative Innovation Center of Atmospheric Environment and Equipment TechnologySchool of Environmental Science and EngineeringNanjing University of Information Science and TechnologyNanjing 210044China School of Environment Key Laboratory for Yellow River and Huai River Water Environment and Pollution ControlMinistry of EducationHenan Normal UniversityXinxiang 453007China key Laboratory of Regional Ecology and Environmental Change School of Geography and Information EngineeringChina University of GeosciencesWuhan 430074China

A series of emission reduction measures were conducted in Wuhan,Central China,to ensure good air quality during the 7th Military World Games(MWG)in October 2019.To better understand the implications for ozone(O_(3))pollution control strategies,we applied integrated analysis approaches based on the de-weathered statistical model,parameterization methods,chemical box model,and positive matrix factorization model.During the MWG,concentrations of O_(3),NO_x,and volatile organic compound(VOCs),OFP(O_(3)formation potential),L_(OH)(OH radical loss rate)were 83μg/m^(3),43μg/m^(3),26 ppbv,188μg/m^(3),and 3.9 s^(-1),respectively,which were 26%,18%,3%,15%,and 13%lower than pre-MWG values and 6%,39%,30%,33%,and 50%lower than post-MWG values,respectively.After removing meteorological influence,O_(3)and its precursors during the MWG decreased largely compared with post-MWG values,and only O_(3),NO_(2),and oxygenated VOCs(OVOCs)declined compared with pre-MWG values,which revealed the emission reduction measures during the MWG played an important role for O_(3)decline.For six VOCs sources,the mass contributions of biomass burning and solvents usage during the MWG decreased largely compared with pre-MWG values.O_(3)production was sensitive to VOCs and the key species were aromatics,OVOCs,and alkenes,which originated mainly from solvents usage,biomass burning,industrial-related combustion,and vehicle exhaust.Decreasing O_(3)concentration during the strict control was mainly caused by OVOCs reduction due to biomass burning control.Generally,the O_(3)abatement strategies of Wuhan should be focused on the mitigation of high-reactivity VOCs.

关键词： VOCs Ozone Wuhan Military World Games Source apportionment Relative incremental reactivity Random forest

Oxygen‑Coordinated Single Mn Sites for Efficient Electrocatalytic Nitrate Reduction to Ammonia

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Nano-Micro Letters 2024年第1期16卷 147-159页

作者： Shengbo Zhang Yuankang Zha Yixing Ye ke li Yue lin lirong Zheng Guozhong Wang Yunxia Zhang Huajie Yin Tongfei Shi Haimin Zhang Laboratory of Materials Physics Centre for Environmental and Energy NanomaterialsAnhui Key Laboratory of Nanomaterials and NanotechnologyCAS Center for Excellence in NanoscienceInstitute of Solid State PhysicsHFIPSChinese Academy of SciencesHefei 230031People’s Republic of China University of Science and Technology of China Hefei 230026People’s Republic of China key Laboratory of Agricultural Sensors Ministry of AgricultureSchool of Information and ComputerAnhui Agricultural UniversityHefei 230026People’s Republic of China Hefei National Research Center for Physical Sciences at the Microscale University of Science and Technology of ChinaHefei 230026People’s Republic of China Beijing Synchrotron Radiation Facility Institute of High Energy PhysicsChinese Academy of Sciences19B Yuquan RoadBeijing 100049People’s Republic of China

Electrocatalytic nitrate reduction reaction has attracted increasing attention due to its goal of low carbon emission and environmental protection.Here,we report an efficient NitRR catalyst composed of single Mn sites with atomically dispersed oxygen(O)coordination on bacterial cellulose-converted graphitic carbon(Mn-O-C).Evidence of the atomically dispersed Mn-(O-C_(2))_(4)moieties embedding in the exposed basal plane of carbon surface is confirmed by X-ray absorption spectroscopy.As a result,the as-synthesized Mn-O-C catalyst exhibits superior NitRR activity with an NH_(3)yield rate(RNH_(3))of 1476.9±62.6μg h^(−1)cm^(−2)at−0.7 V(vs.reversible hydrogen electrode,RHE)and a faradaic efficiency(FE)of 89.0±3.8%at−0.5 V(vs.RHE)under ambient conditions.Further,when evaluated with a practical flow cell,Mn-O-C shows a high RNH_(3)of 3706.7±552.0μg h^(−1)cm^(−2)at a current density of 100 mA cm−2,2.5 times of that in the H cell.The in situ FT-IR and Raman spectroscopic studies combined with theoretical calculations indicate that the Mn-(O-C_(2))_(4)sites not only effectively inhibit the competitive hydrogen evolution reaction,but also greatly promote the adsorption and activation of nitrate(NO_(3)^(−)),thus boosting both the FE and selectivity of NH_(3)over Mn-(O-C_(2))_(4)sites.

关键词： Atomically dispersed Oxygen coordination Nitrate reduction reaction In situ spectroscopic studies Hydrogen evolution reaction

High-yield and rapid isolation of extracellular vesicles by flocculation via orbital acoustic trapping:FLOAT

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Microsystems & Nanoengineering 2024年第1期10卷 313-323页

作者： Joseph Rufo Peiran Zhang Zeyu Wang Yuyang Gu Kaichun Yang Joseph Rich Chuyi Chen Ruoyu Zhong ke Jin Ye He Jianping Xia ke li Jiarong Wu Yingshi Ouyang Yoel Sadovsky Luke P.Lee Tony Jun Huang Department of Mechanical Engineering and Materials Science Duke UniversityDurhamNCUSA Department of Biomedical Engineering Duke UniversityDurhamNCUSA Department of Obstetrics Gynecologyand Reproductive SciencesMagee-Womens Research InstituteUniversity of PittsburghPittsburghPAUSA Department of Microbiology and Molecular Genetics School of MedicineUniversity of PittsburghPittsburghPAUSA Renal Division and Division of Engineering in Medicine Department of MedicineBrigham and Women’s HospitalHarvard Medical SchoolBostonMAUSA Department of Bioengineering Department of Electrical Engineering and Computer ScienceUniversity of CaliforniaBerkeleyBerkeleyCAUSA Department of Biophysics Institute of Quantum BiophysicsSungkyunkwan UniversitySuwonKorea

Extracellular vesicles(EVs)have been identified as promising biomarkers for the noninvasive diagnosis of various diseases.However,challenges in separating EVs from soluble proteins have resulted in variable EV recovery rates and low purities.Here,we report a high-yield(>90%)and rapid(lizes an acoustofluidic droplet centrifuge to rotate and controllably heat liquid droplets.By adding a thermoresponsive polymer flocculant,nanoparticles as small as 20 nm can be rapidly and selectively concentrated at the center of the droplet.We demonstrate the ability of FLOAT to separate urinary EVs from the highly abundant Tamm-Horsfall protein,addressing a significant obstacle in the development of EV-based liquid biopsies.Due to its high-yield nature,FLOAT reduces biofluid starting volume requirements by a factor of 100(from 20 mL to 200µL),demonstrating its promising potential in point-of-care diagnostics.

关键词： trapping utilize separating

Two sandwich-type uranyl-containing polytungstates catalyze aerobic synthesis of benzimidazoles

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Rare Metals 2024年第3期43卷 1316-1322页

作者： Yu-Feng liu Qi-Long Hu Xue-Jiao Chen ke li Pei Luo Guo-Ping Yang School of Chemistry and Material Science Jiangxi Province Key Laboratory of Synthetic ChemistryJiangxi Key Laboratory for Mass Spectrometry and InstrumentationEast China University of TechnologyNanchang330013China School of Environmental Science and Engineering Southern University of Science and TechnologyShenzhen518055China

Diversified synthetic strategies are extremely important for the structural diversity of uranium-containing polyoxometalates(U-POMs)and their functional expansion.Herein,two sandwich-type U-POMs were reported,which are Na_(5.6)K_(6.4)[(UO_(2))(H_(2)O)(TeW_(9)O_(33))]_(2)·21H_(2)O(UTeW_(9))and Na_(8.9)K_(2.7)H_(1.19)[K_(0.79)(UO_(2))_(2.21)(PW_(9)O_(34))_(2)]·12H_(2)O(UPW_9)using in-situ strategy and lacunary precursor strategy,respectively.UTeW_9 shows a typical keggin-typeopen or half-sandwich configuration.

关键词： configuration expansion sandwich