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Microsnoop: A generalist tool for microscopy image representation

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The Innovation 2024年第1期5卷 109-117页

作者： Dejin Xun rui wang Xingcai zhang Yi wang Pharmaceutical Informatics Institute College of Pharmaceutical SciencesZhejiang UniversityHangzhou 310058China State Key Lab of Computer-Aided Design&Computer Graphics Zhejiang UniversityHangzhou 310058China John A.Paulson School of Engineering and Applied Sciences Harvard UniversityCambridgeMA 02138USA Innovation Institute for Artificial Intelligence in Medicine of Zhejiang University Hangzhou 310018China National Key Laboratory of Chinese Medicine Modernization Innovation Center of Yangtze River DeltaZhejiang UniversityJiaxing 314100China

Accurate profiling of microscopy images from small scale to high throughput is an essential procedure in basic and applied biological research.Here,we present Microsnoop,a novel deep learning–based representation tool trained on large-scale microscopy images using masked self-supervised learning.Microsnoop can process various complex and heterogeneous images,and we classified images into three categories:single-cell,full-field,and batch-experiment images.Our benchmark study on 10 high-quality evaluation datasets,containing over 2,230,000 images,demonstrated Microsnoop’s robust and state-ofthe-art microscopy image representation ability,surpassing existing generalist and even several custom algorithms.Microsnoop can be integrated with other pipelines to perform tasks such as superresolution histopathology image and multimodal analysis.Furthermore,Microsnoop can be adapted to various hardware and can be easily deployed on local or cloud computing platforms.We will regularly retrain and reevaluate the model using communitycontributed data to consistently improve Microsnoop.

关键词： hardware image representation

Fully distributed dynamic event-triggered formation-containment tracking for multiagent systems with multiple types of disturbances

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Science China(Information Sciences) 2024年第1期67卷 168-186页

作者： Weihua LI Huaguang zhang Juan zhang rui wang College of Information Science and Engineering Northeastern University State Key Laboratory of Synthetical Automation for Process Industries Northeastern University

This paper is dedicated to addressing the time-varying output formation-containment tracking(TVOFCT) problem for heterogeneous linear multiagent systems(MASs) with multiple types of disturbances under directed communication topology.The agents are divided into tracking leaders,formation leaders,and followers.In the output space,the formation leaders are required to form an expected geometric formation while tracking the tracking leader,and the followers are required to enter the convex hull spanned by formation leaders.First,a disturbance observer is designed to observe the disturbance with deterministic dynamics.Then,by combining adaptive technology with event-triggered technology,an independent fully distributed dynamic event-triggered(FDDET) compensator is designed to estimate the state of the tracking leader.The main advantages of this compensator lie in the following three aspects:(1) the adaptive weight does not increase unboundedly;(2) the interval time between events is expanded;(3) the design does not rely on any global information.Similar to the design of this compensator,an independent FDDET convex hull observer is further designed to observe the convex hull spanned by formation leaders.Subsequently,based on the designed disturbance observer,compensator,and convex hull observer,the adaptive disturbance rejection control input which can make the MASs achieve TVOFCT is formulated.Finally,a numerical simulation is provided to clearly verify the validity of the theoretical results.

关键词： formation-containment tracking disturbance rejection multiagent systems fully distributed control dynamic event-triggered control

Ecological impacts of the expansion of offshore wind farms on trophic level species of marine food chain

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Journal of Environmental Sciences 2024年第5期139卷 226-244页

作者： Lijing wang Bangguo wang Wenxi Cen rui Xu Yuwei Huang Xin zhang Yinghui Han Yuanxun zhang College of Resources and Environment University of Chinese Academy of SciencesBeijing 101408China Yanshan Earth Critical Zone and Surface Fluxes Research Station University of Chinese Academy of SciencesBeijing 101408China Chinese Research Academy of Environmental Sciences Beijing 100012China National Joint Research Center for Yangtze River Conservation Beijing 100012China College of Environmental Engineering Beijing University of TechnologyBeijing 100124China Institute of Eco-Environmental Forensics Shandong UniversityQingdao 266237China

The global demand for renewable energy has resulted in a rapid expansion of offshore wind farms(OWFs)and increased attention to the ecological impacts of OWFs on the marine ecosystem.Previous reviews mainly focused on the OWFs’impacts on individual species like birds,bats,or mammals.This review collected numerous field-measured data and simulated results to summarize the ecological impacts on phytoplankton,zooplankton,zoobenthos,fishes,and mammals from each trophic level and also analyze their interactions in the marine food chain.Phytoplankton and zooplankton are positively or adversely affected by the‘wave effect’,‘shading effect’,oxygen depletion and predation pressure,leading to a ±10% fluctuation of primary production.Although zoobenthos are threatened transiently by habitat destruction with a reduction of around 60% in biomass in the construction stage,their abundance exhibited an over 90% increase,dominated by sessile species,due to the‘reef effect’in the operation stage.Marine fishes and mammals are to endure the interferences of noise and electromagnetic,but they are also aggregated around OWFs by the‘reef effect’and‘reserve effect’.Furthermore,the complexity of marine ecosystem would increase with a promotion of the total system biomass by 40% through trophic cascade effects strengthen and resource partitioning alternation triggered by the proliferation of filter-feeders.The suitable site selection,long-term monitoring,and life-cycle-assessment of ecological impacts of OWFs that are lacking in current literature have been described in this review,as well as the carbon emission and deposition.

关键词： Offshore wind farms(OWFs) Ecological impacts Plankton Benthos Fish Mammal

Neurotoxicity of tetramethylammonium ion on larval and juvenile zebrafish:Effects on neurobehaviors and multiple biomarkers

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Journal of Environmental Sciences 2024年第9期143卷 138-147页

作者： ruixin zhang rui wang Jiajun Chang GDaniel Sheng Daqiang Yin Key Laboratory of Yangtze River Water Environment Ministry of EducationCollege of Environmental Science and EngineeringTongji UniversityShanghai 200092China Shanghai Institute of Pollution Control and Ecological Security Shanghai 200092China

Tetramethylammonium hydroxide(TMAH)is an important compound that utilized and released by the rapidly expanding semiconductor industry,which could hardly be removed by the conventional wastewater treatment techniques.As a cholinergic agonist,the tetramethylammonium ion(TMA^(+))has been reported to induce toxicity to muscular and respiratory systems of mammals and human,however the toxicity on aquatic biota remains poorly known.We investigated the neurotoxic effects of TMA^(+)exposure on zebrafish,based on neurobehavior tests and a series of biomarkers.Significant inhibitions on the swimming distance of zebrafish larvae were observed when the exposure level exceeded 50 mg/L,and significant alterations on swimming path angles(straight and deflective movements)occurred even at 10 mg/L.The tested neurobehavioral endpoints of zebrafish larvae were significantly positively correlated with reactive oxygen species(ROS)and malondialdehyde(MDA),significantly negatively related with the activities of antioxidant enzymes,but not significantly correlated with the level of acetylcholinesterase(AChE).Such relationship indicates that the observed neurotoxic effects on swimming behavior of zebrafish larvae is mainly driven by oxidative stress,rather than the alterations of neurotransmitter.At the highest exposure concentration(200 mg/L),TMA^(+)evoked more severe toxicity on zebrafish juveniles,showing significantly stronger elevation on the MDA activity,and greater inhibitions on the activities of antioxidant enzymes and ACh E,suggesting juveniles were more susceptible to TMA^(+)exposure than larval zebrafish.

关键词： Tetramethylammonium Zebrafish Oxidative stress Acetylcholinesterase Neurobehavior

Physiochemical and biological characteristics of fouling on landfill leachate treatment systems surface

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Journal of Environmental Sciences 2024年第1期135卷 59-71页

作者： Zhourui Gong Shu Yang rui zhang Yangqing wang Xiaoqing Wu Liyan Song School of resources and environmental engineering Anhui UniversityHefei 230601China Anhui Shengjin Lake Wetland Ecology National Long-term Scientific Research Base Dongzhi 247230China Key Laboratory of Three Gorges Reservoir Region’s Eco-Environment Ministry of EducationChongqing UniversityChongqing 400045China Chongqing Institute of Green and Intelligent Technology Chinese Academy of SciencesChongqing 400714China Xing Lu Huan Jing Co.LTD. Luzhou 646000China

Fouling of landfill leachate,a biofilm formation process on the surface of the collection system,migration pipeline and treatment system causes low efficiency of leachate transportation and treatment and increases cost for maintenance of those facilities.In addition,landfill leachate fouling might accumulate pathogens and antibiotic resistance genes(ARGs),posing threats to the environment.Characterization of the landfill leachate fouling and its associated environmental behavior is essential for the management of fouling.In this study,physicochemical and biological properties of landfill leachate fouling and the possible accumulation capacity of pathogens and ARGs were investigated in nitrification(aerobic condition)and denitrification(anaerobic condition)process during landfill leachate biological treatment,respectively.Results show that microbial(bacterial,archaeal,eukaryotic,and viral)community structure and function(carbon fixation,methanogenesis,nitrification and denitrification)differed in fouling under aerobic and anaerobic conditions,driven by the supplemental leachate water quality.Aerobic fouling had a higher abundance of nitrification and denitrification functional genes,while anaerobic fouling harbored a higher abundance of carbon fixation and methanogenesis genes.Both forms of leachate fouling had a higher abundance of pathogens and ARGs than the associated leachate,suggesting the accumulation capacity of fouling on biotic pollutants.Specifically,aerobic fouling harbored three orders of magnitude higher multidrug resistance genes mex D than its associated leachate.This finding provides fundamental knowledge on the biological properties of leachate fouling and suggests that leachate fouling might harbor significant pathogens and ARGs.

关键词： Landfill leachate fouling Biofilm Microbiome Carbon and nitrogen cycle Pathogens Antibiotic resistance genes

MdbHLH162 connects the gibberellin and jasmonic acid signals to regulate anthocyanin biosynthesis in apple

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Journal of Integrative Plant Biology 2024年第2期66卷 265-284页

作者： Jian-Ping An rui-rui Xu Xiao-Na wang Xiao-Wei zhang Chun-Xiang You Yuepeng Han Apple technology innovation center of Shandong Province College of Horticulture Science and EngineeringShandong Agricultural UniversityTai-An 271018China CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture Wuhan Botanical GardenHubei Hongshan LaboratoryThe Innovative Academy of Seed Design of Chinese Academy of SciencesWuhan 430074China College of Biology and Oceanography Weifang UniversityWeifang 261061China

Anthocyanins are secondary metabolites induced by environmental stimuli and developmental signals.The positive regulators of anthocyanin biosynthesis have been reported,whereas the anthocyanin repressors have been neglected.Although the signal transduction pathways of gibberellin(GA)and jasmonic acid(JA)and their regulation of anthocyanin biosynthesis have been investigated,the cross-talk between GA and JA and the antagonistic mechanism of regulating anthocyanin biosynthesis remain to be investigated.In this study,we identified the anthocyanin repressor MdbHLH162 in apple and revealed its molecular mechanism of regulating anthocyanin biosynthesis by integrating the GA and JA signals.MdbHLH162 exerted passive repression by interacting with MdbHLH3 and MdbHLH33,which are two recognized positive regulators of anthocyanin biosynthesis.MdbHLH162 negatively regulated anthocyanin biosynthesis by disrupting the formation of the anthocyanin-activated MdMYB1-MdbHLH3/33complexes and weakening transcriptional activation of the anthocyanin biosynthetic genes MdDFR and MdUF3GT by MdbHLH3 and MdbHLH33.The GA repressor MdRGL2a antagonized MdbHLH162-mediated inhibition of anthocyanins by sequestering MdbHLH162 from the MdbHLH162-MdbHLH3/33 complex.The JA repressors MdJAZ1 and MdJAZ2 interfered with the antagonistic regulation of MdbHLH162 by MdRGL2a by titrating the formation of the MdRGL2a-MdbHLH162 complex.Our findings reveal that MdbHLH162 integrates the GA and JA signals to negatively regulate anthocyanin biosynthesis.This study provides new information for discovering more anthocyanin biosynthesis repressors and explores the cross-talk between hormone signals.

关键词： anthocyanin biosynthesis bHLH transcription factor gibberellin jasmonic acid regulatory network transcriptional regulation

A Two-Layer Encoding Learning Swarm Optimizer Based on Frequent Itemsets for Sparse Large-Scale Multi-Objective Optimization

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IEEE/CAA Journal of Automatica Sinica 2024年第6期11卷 1342-1357页

作者： Sheng Qi rui wang Tao zhang Xu Yang ruiqing Sun Ling wang College of Systems Engineering National University of Defense TechnologyChangsha 410073China Xiangjiang Laboratory Changsha 410205China College of Computer National University of Defense TechnologyChangsha 410073China Department of Automation Tsinghua UniversityBeijing 100084China IEEE

Traditional large-scale multi-objective optimization algorithms(LSMOEAs)encounter difficulties when dealing with sparse large-scale multi-objective optimization problems(SLM-OPs)where most decision variables are zero.As a result,many algorithms use a two-layer encoding approach to optimize binary variable Mask and real variable Dec separately.Nevertheless,existing optimizers often focus on locating non-zero variable posi-tions to optimize the binary variables Mask.However,approxi-mating the sparse distribution of real Pareto optimal solutions does not necessarily mean that the objective function is optimized.In data mining,it is common to mine frequent itemsets appear-ing together in a dataset to reveal the correlation between data.Inspired by this,we propose a novel two-layer encoding learning swarm optimizer based on frequent itemsets(TELSO)to address these SLMOPs.TELSO mined the frequent terms of multiple particles with better target values to find mask combinations that can obtain better objective values for fast convergence.Experi-mental results on five real-world problems and eight benchmark sets demonstrate that TELSO outperforms existing state-of-the-art sparse large-scale multi-objective evolutionary algorithms(SLMOEAs)in terms of performance and convergence speed.

关键词： Evolutionary algorithms learning swarm optimiza-tion sparse large-scale optimization sparse large-scale multi-objec-tive problems two-layer encoding.

PCK1 attenuates tumor stemness via activating the Hippo signaling pathway in hepatocellular carcinoma

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Genes & Diseases 2024年第4期11卷 340-352页

作者： rui Liu Yi Liu Wenlu zhang Guiji zhang Zhirong zhang Luyi Huang Ni Tang Kai wang Key Laboratory of Molecular Biology for Infectious Diseases(Ministry of Education) Institute for Viral HepatitisDepartment of Infectious DiseasesThe Second Affiliated HospitalChongqing Medical UniversityChongqing 400016China Department of Clinical Laboratory Sichuan Clinical Research Center for CancerSichuan Cancer Hospital&InstituteSichuan Cancer CenterAffiliated Cancer Hospital of University of Electronic Science and Technology of ChinaChengduSichuan 610041China

Liver cancer stem cells were found to rely on glycolysis as the preferred metabolic program.Phosphoenolpyruvate carboxylase 1(PCK1),a gluconeogenic metabolic enzyme,is down-regulated in hepatocellular carcinoma and is closely related to poor prognosis.The onco-genesis and progression of tumors are closely related to cancer stem cells.It is not completely clear whether the PCK1 deficiency increases the stemness of hepatoma cells and promotes the oncogenesis of hepatocellular carcinoma.Herein,the results showed that PCK1 inhibited the self-renewal property of hepatoma cells,reduced the mRNA level of cancer stem cell markers,and inhibited tumorigenesis.Moreover,PCK1 increased the sensitivity of hepatocellular carci-noma cells to sorafenib.Furthermore,we found that PCK1 activated the Hippo pathway by enhancing the phosphorylation of YAP and inhibiting its nuclear translocation.Verteporfin reduced the stemness of hepatoma cells and promoted the pro-apoptotic effect of sorafenib.Thus,combined treatment with verteporfin and sorafenib may be a potential anti-tumor strat-egy in hepatocellular carcinoma.

关键词： Cancer stem cells Chemoresistance Gluconeogenesis Hepatocellular carcinoma YAP

Numerical Analysis of Perforation during Hydraulic Fracture Initiation Based on Continuous-Discontinuous Element Method

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Computer Modeling in Engineering & Sciences 2024年第8期140卷 2103-2129页

作者： rui zhang Lixiang wang Jing Li Chun Feng Yiming zhang School of Civil and Transportation Engineering Hebei University of TechnologyTianjin300401China Key Laboratory for Mechanics in Fluid Solid Coupling Systems Institute of MechanicsChinese Academy of SciencesBeijing100190China School of Civil Engineering and Architecture Zhejiang Sci-Tech UniversityHangzhou310018China Jinyun Institute Zhejiang Sci-Tech UniversityLishui321400China

Perforation is a pivotal technique employed to establish main flow channels within the reservoir formation at the outset of hydraulic fracturing operations.Optimizing perforation designs is critical for augmenting the efficacy of hydraulic fracturing and boosting oil or gas production.In this study,we employ a hybrid finite-discrete element method,known as the continuous–discontinuous element method(CDEM),to simulate the initiation of post-perforation hydraulic fractures and to derive enhanced design parameters.The model incorporates the four most prevalent perforation geometries,as delineated in an engineering technical report.Real-world perforations deviate from the ideal cylindrical shape,exhibiting variable cross-sectional profiles that typically manifest as an initial constriction followed by an expansion,a feature consistent across all four perforation types.Our simulations take into account variations in perforation hole geometries,cross-sectional diameters,and perforation lengths.The findings show that perforations generated by the 39g DP3 HMX perforating bullet yield the lowest breakdown pressure,which inversely correlates with increases in sectional diameter and perforation length.Moreover,this study reveals the relationship between breakdown pressure and fracture degree,providing valuable insights for engineers and designers to refine perforation strategies.

关键词： Hydraulic fracturing real perforation shape breakdown pressure perforation layout design CDEM