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Accurate cell type annotation for single-cell chromatin accessibility data via contrastive learning and reference guidance

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Quantitative Biology 2024年第1期12卷 85-99页

作者： Siyu li Songming Tang Yunchang Wang sijie li Yuhang Jia Shengquan Chen School of Statistics and Data Science Nankai UniversityTianjinChina School of Mathematical Sciences and LPMC Nankai UniversityTianjinChina

Recent advances in single-cell chromatin accessibility sequencing(scCAS)technologies have resulted in new insights into the characterization of epigenomic heterogeneity and have increased the need for automatic cell type annotation.However,existing automatic annotation methods for scCAS data fail to incorporate the reference data and neglect novel cell types,which only exist in a test set.Here,we propose RAINBOW,a reference-guided automatic annotation method based on the contrastive learning framework,which is capable of effectively identifying novel cell types in a test set.By utilizing contrastive learning and incorporating reference data,RAINBOW can effectively characterize the heterogeneity of cell types,thereby facilitating more accurate annotation.With extensive experiments on multiple scCAS datasets,we show the advantages of RAINBOW over state-of-the-art methods in known and novel cell type annotation.We also verify the effectiveness of incorporating reference data during the training process.In addition,we demonstrate the robustness of RAINBOW to data sparsity and number of cell types.Furthermore,RAINBOW provides superior performance in newly sequenced data and can reveal biological implication in downstream analyses.All the results demonstrate the superior performance of RAINBOW in cell type annotation for scCAS data.We anticipate that RAINBOW will offer essential guidance and great assistance in scCAS data analysis.The source codes are available at the GitHub website(BioX-NKU/RAINBOW).

关键词： cell type annotation chromatin accessibility novel type reference-guided single-cell

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Brain-inspired multimodal approach for effluent quality prediction using wastewater surface images and water quality data

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Frontiers of Environmental Science & Engineering 2024年第3期18卷 69-82页

作者： Junchen li sijie lin liang Zhang Yuheng liu Yongzhen Peng Qing Hu School of Environment Harbin Institute of TechnologyHarbin 150090China School of Environmental Science and Engineering Southern University of Science and TechnologyShenzhen 518055China Engineering Innovation Center of SUSTech(Beijing) Southern University of Science and TechnologyBeijing 100083China Faculty of Environment and life Beijing University of TechnologyBeijing 100124China Engineering Research Center of Intelligence Perception and Autonomous Control Ministry of EducationBeijing 100124China

Efficiently predicting effluent quality through data-driven analysis presents a significant advancement for consistent wastewater treatment operations.In this study,we aimed to develop an integrated method for predicting effluent COD and NH3 levels.We employed a 200 L pilot-scale sequencing batch reactor(SBR)to gather multimodal data from urban sewage over 40 d.Then we collected data on critical parameters like COD,DO,pH,NH_(3),EC,ORP,SS,and water temperature,alongside wastewater surface images,resulting in a data set of approximately 40246 points.Then we proposed a brain-inspired image and temporal fusion model integrated with a CNN-LSTM network(BITF-CL)using this data.This innovative model synergized sewage imagery with water quality data,enhancing prediction accuracy.As a result,the BITF-CL model reduced prediction error by over 23%compared to traditional methods and still performed comparably to conventional techniques even without using DO and SS sensor data.Consequently,this research presents a cost-effective and precise prediction system for sewage treatment,demonstrating the potential of brain-inspired models.

关键词： Wastewater treatment system Water quality prediction Data driven analysis Brain-inspired model Multimodal data Attention mechanism

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miR-933 accelerates the growth of liver cancer cells by enhancing pyruvate kinase isoform M2

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Genes & Diseases 2024年第4期11卷 31-34页

作者： liyan Wang Shujie li Xinlei liu sijie Xie Shuting Song Xiaoxue Jiang Dongdong Lu Shanghai Putuo People's Hospital School of Life Science and TechnologyTongji UniversityShanghai 200092China

MicroRNAs(miRNAs)have been found to play an important role in human tumorigenesis.A study indicates that the plasma level of miR-933 was elevated in patients with dementia.1 Notably,miR-933(RS79402775)may contribute t... 详细信息

关键词： elevated cancer liver

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Cadaverine and putrescine exposure influence carbon and nitrogen cycling genes in water and sediment of the Yellow River

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Journal of Environmental Sciences 2024年第8期142卷 236-247页

作者： Wanghong Su Qiaoling Yu Jiawei Yang Qian Han sijie Wang Petr Hedenec Xiaochen Wang Ruijun Wan-Yan Huan li School of Public Health Lanzhou UniversityLanzhou 730000China 2 Institute for Tropical Biodiversity and Sustainable DevelopmentUniversity Malaysia Terengganu21030Kuala NerusTerengganuMalaysia State Key Laboratory of Grassland Agro-ecosystems Center for Grassland MicrobiomeCollege of pastoral agriculture science and technology Lanzhou UniversityLanzhou 730000China

The response patterns of microbial functional genes involved in biogeochemical cycles to cadaver decay is a central topic of recent environmental sciences.However,the response mechanisms and pathways of the functional genes associated with the carbon(C)and nitrogen(N)cycling to cadaveric substances such as cadaverine and putrescine remain unclear.This study explored the variation of functional genes associated with C fixation,C degradation and N cycling and their influencing factors under cadaverine,putrescine and mixed treatments.Our results showed only putrescine significantly increased the alpha diversity of C fixation genes,while reducing the alpha diversity of N cycling genes in sediment.For the C cycling,the mixed treatment significantly decreased the total abundance of reductive acetyl-CoA pathway genes(i.e.,acsB and acsE)and lig gene linked to lignin degradation in water,while only significantly increasing the hydroxypropionate-hydroxybutylate cycle(i.e.,accA)gene abundance in sediment.For the N cycling,mixed treatment significantly decreased the abundance of the nitrification(i.e.,amoB),denitrification(i.e.,nirS3)genes in water and the assimilation pathway gene(i.e.,gdhA)in sediment.Environmental factors(i.e.,total carbon and total nitrogen)were all negatively associated with the genes of C and N cycling.Therefore,cadaverine and putrescine exposure may inhibit the pathway in C fixation and N cycling,while promoting C degradation.These findings can offer some new insight for the management of amine pollution caused by animal cadavers.

关键词： Carbon cycling Nitrogen cycling Cadaverine Putrescine Pollution management

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High strength mullite-bond SiC porous ceramics fabricated by digital light processing

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Journal of Advanced Ceramics 2024年第1期13卷 53-62页

作者： Jian Sun Jingde Zhang Xu Zhang Zihe li Jianzhang li sijie Wei Weibin Zhang Weili Wang Guifang Han Key Laboratory for liquid-Solid Structural Evolution and Processing of Materials(Ministry of Education) School of Materials Science and EngineeringShandong UniversityJinan 250061China Key Laboratory of Special Functional Aggregated Materials Ministry of EducationShandong UniversityJinan 250100China Materials and Structures Research Centre Department of Mechanical EngineeringUniversity of BathBath BA27AYUK National Engineering Research Centre of Ceramic Matrix Composite Manufacture Technology Xi’an Golden Mountain Ceramic Composites Co.Ltd.Xi’an 710118China School of Physics and Materials Science Changji UniversityChangji 831100China

Fabricating SiC ceramics via the digital light processing(DLP)technology is of great challenge due to strong light absorption and high refractive index of deep-colored SiC powders,which highly differ from those of resin,and thus significantly affect the curing performance of the photosensitive SiC slurry.In this paper,a thin silicon oxide(SiO_(2))layer was in-situ formed on the surface of SiC powders by pre-oxidation treatment.This method was proven to effectively improve the curing ability of SiC slurry.The SiC photosensitive slurry was fabricated with solid content of 55 vol%and viscosity of 7.77 Pa·s(shear rate of 30 s^(−1)).The curing thickness was 50μm with exposure time of only 5 s.Then,a well-designed sintering additive was added to completely convert low-strength SiO_(2) into mullite reinforcement during sintering.Complexshaped mullite-bond SiC ceramics were successfully fabricated.The flexural strength of SiC ceramics sintered at 1550℃in air reached 97.6 MPa with porosity of 39.2 vol%,as high as those prepared by spark plasma sintering(SPS)techniques.

关键词： digital light processing(DLP) SiC ceramics pre-oxidation mullite-bond SiC mechanical properties

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Effect of TiB_(2)Addition on Microstructure and Mechanical Properties of AA8009 Alloy Fabricated by Laser Additive Manufacturing

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Acta Metallurgica Sinica(English Letters) 2024年第1期37卷 67-77页

作者： Xinxing Xiong sijie Yu Pei Wang Junfang Qi Haichao li Xulei Wang Michael Ryan Debajyoti Bhaduri Rossitza Setchi Additive Manufacturing Institute Shenzhen UniversityShenzhen518060China Henan Key Laboratory of High Performance Carbon Fiber Reinforced Composites Institute of Carbon Matrix CompositesHenan Academy of SciencesZhengzhou450046China School of Materials Science and Engineering Shanghai University of Engineering ScienceShanghai201620China School of Materials Science and Engineering Zhengzhou University of AeronauticsZhengzhou450046China High-Value Manufacturing Research Group School of EngineeringCardiff UniversityCardiffCF243AAUK

The research involves the addition of 5 vol.%TiB_(2)particles into AA8009 alloy powder to synthesize TiB_(2)/AA8009 composite parts produced via laser powder bed fusion(LPBF).The addition of the TiB_(2)particles causes the TiB_(2)/AA8009 composites with and without annealing have lower compressive strength than AA8009 alloy due to the change of the strengthening mechanism.The results further indicated that solid solution strengthening was the main strengthening mechanism of the LPBF AA8009 alloy at room temperature whereas Orowan strengthening became the primary strengthening factor after annealing at 673 K.In contrast,Orowan strengthening always remained the main strengthening mechanism for the TiB_(2)/AA8009 composite,irrespective of the annealing temperature.In addition,after annealing of the LPBF parts at 673 K,the compressive yield strength(CYS)of the unblended AA8009 alloy specimens had a~2.5 times greater reduction(from 705±16 to 459±30 MPa)compared to that of the composite TiB_(2)/AA8009 samples(from 466±23 to 368±3 MPa).Therefore,TiB_(2)particles can suppress the drop in yield strength of LPBF AA8009 alloy below 673 K,providing a theoretical and experimental basis for the applications of both LPBF AA8009 and TiB_(2)/AA8009 alloys at low and medium temperatures.

关键词： Laser powder bed fusion AA8009 alloy Microstructure Mechanical properties

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A nonradical oxidation process initiated by Ti-peroxo complex showed high specificity toward the degradation of tetracycline antibiotics

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Chinese Chemical Letters 2024年第5期35卷 366-370页

作者： Jian Peng Yue Jiang Shuangyu Wu Yanran Cheng Jingyu liang Yixin Wang Zhuo li sijie lin College of Environmental Science and Engineering Biomedical Multidisciplinary Innovation Research InstituteShanghai East HospitalTongji UniversityShanghai 200092China Key Laboratory of Yangtze River Water Environment Shanghai Institute of Pollution Control and Ecological SecurityTongji UniversityShanghai 200092China

Nonradical oxidation has received wide attention in advanced oxidation processes for environmental remediation.Understanding the relationship between material characteristics and their ability to initiate nonradical oxidation processes is the key to better material design and performance.Herein,a novel titanium-based metal-organic framework MIL-125-Ti/H_(2)O_(2) system was established to show a highly selective degradation efficacy toward tetracycline antibiotics.MIL-125-Ti with the abundance of TiO6 octahedra units was found to effectively activate H_(2)O_(2) under dark conditions by forming an oxidative Ti-peroxo complex.The presence of the Ti-peroxo complex,confirmed by UV-visible spectrophotometer,fourier transform infrared spectroscopy,and X-ray photoelectron spectroscopy characterizations,showed superior degradation(>95%removal rate)of oxytetracycline hydrochloride(OTC),doxycycline hydrochloride,chlortetracycline hydrochloride,and tetracycline.Density functional theory calculations were performed to assist the elucidation on the mechanism of H_(2)O_(2) activation and antibiotics degradation.The MIL-125-Ti/H_(2)O_(2) system was highly resistant to halogens and background organics,and could well maintain its original catalytic activity in actual water matrices.It retained the ability to degrade 75%of OTC within ten test cycles.This study provides new insight into the nonradical oxidation process initiated by the unique Ti-peroxo complex of Ti-based MOF.

关键词： Nonradical oxidation Metal-organic frameworks Advanced oxidation process Ti-peroxo complex Antibiotics degradation

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Research on Performance Optimization of liquid Cooling and Composite Phase Change Material Coupling Cooling Thermal Management System for Vehicle Power Battery

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Journal of Renewable Materials 2023年第2期11卷 707-730页

作者： Gang Wu Feng liu sijie li Na Luo Zhiqiang liu Yuqaing li Changsha University of Science&Technolog Changsha410114China Hunan Province Key Laboratory of Intelligent Manufacturing Technology for High-Performance Mechanical Equipment Changsha410114China Central South University Changsha410083China

The serpentine tube liquid cooling and composite PCM coupled cooling thermal management system is designed for 18650 cylindrical power batteries,with the maximum temperature and temperature difference of the power pack within the optimal temperature operating range as the target.The initial analysis of the battery pack at a 5C discharge rate,the influence of the single cell to cooling tube distance,the number of cooling tubes,inlet coolant temperature,the coolant flow rate,and other factors on the heat dissipation performance of the battery pack,initially determined a reasonable value for each design parameter.A control strategy is used to regulate the inlet flow rate and coolant temperature of the liquid cooling system in order to make full use of the latent heat of the composite PCM and reduce the pump’s energy consumption.The simulation results show that the maximum battery pack temperature of 309.8 K and the temperature difference of 4.6 K between individual cells with the control strategy are in the optimal temperature operating range of the power battery,and the utilization rate of the composite PCM is up to 90%.

关键词： Power battery thermal management phase change materials liquid cooling

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Low-temperature li-S batteries enabled by all amorphous con version process of organosulfur cathode

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Journal of Energy Chemistry 2022年第1期31卷 496-502,I0013页

作者： Zhenkang Wang Xiaowei Shen sijie li Yuxuan Wu Tingzhou Yang Jie liu Tao Qian Chenglin Yan College of Energy Key Laboratory of Advanced Carb on Materials and Wearable Energy Technologies of Jiangsu ProvinceSoochow UniversitySuzhou 215006JiangsuChina College of Chemistry and Chemical Engineering.Nantong University Seyuan 9Nantong 226000JiangsuChina

The high degree of crystallinity of discharging in termediates of li-S batteries(li_(2)S_(2)/li_(2)S)causes a severe capacity attenuation at low temperatures.Herein,a sulfur-rich polymer is fabricated,which enables all the discharging in termediates to exist in an amorphous state without long-range order,promoti ng the substantial conversion of discharging intermediates and enhancing li-S batteries'performance at low temperatures greatly.This cathode material exhibits excellent performance both at room and low temperatures.Even under an extremely low temperature(-40℃),the discharge capacity can remain 67% of that at room temperature.Besides,in-situ UV/Vis spectroscopy and density functional theory calculations reveal that this organosulfur cathode undergoes a new mechanism during discharge.li_(2)S_(6) and li_(2)S_(3) are the primary discharging intermediates that are quite different from conventional li-S batteries.These results provide a new directi on for a broader range of applications of li-S batteries.

关键词： Low temperature Organosulfur polymers li-S battery Crystallinity

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A quality status encoding scheme for PCB-based products in IoT-enabled remanufacturing

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Frontiers of Computer Science 2021年第5期15卷 173-186页

作者： sijie li You SHANG School of Economics and Management Southeast UniversityNanjing 211189China

In this paper,a binary-extensible quality status encoding scheme,named IQSCT(IoT quality status code table),is proposed for the PCB-based product with available recovery options in remanufacturing.IQSCT is achieved by code evolution based on binary logic,in which the product flow and the quality information flow are integrated,and three key features of PCB-based product(PCB-module association,assembly-disassembly logic,and disassembly risk)are involved in production costing.With IQSCT,the manufacturer can have better decisions to reduce remanufacturing cost and improve resource utilization,which is verified by a case study based on the real data from BOM cost and corresponding estimation of Apple iPhone 11 series.

关键词： Intemet-of-Things binary encoding scheme binary logic bit operations PCB-based products remanufacturing recovery option

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