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Widespread and active piezotolerant microorganisms mediate phenolic compound degradation under high hydrostatic pressure in hadal trenches

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Marine Life Science & Technology 2024年第2期6卷 331-348页

作者： hao ling Yongxin Lv Yu Zhang Ning‑Yi Zhou Ying Xu State Key Laboratory of Microbial Metabolism Joint International Research Laboratory of Metabolic and Developmental Sciences and School of Life Sciences and BiotechnologyShanghai Jiao Tong UniversityShanghai 200240China School of Oceanography Shanghai Jiao Tong UniversityShanghai 200240China State Key of Laboratory of Ocean Engineering Shanghai Jiao Tong UniversityShanghai 200240China

Phenolic compounds,as well as other aromatic compounds,have been reported to be abundant in hadal trenches.Although high-throughput sequencing studies have hinted at the potential of hadal microbes to degrade these compounds,direct microbiological,genetic and biochemical evidence under in situ pressures remain absent.Here,a microbial consortium and a pure culture of Pseudomonas,newly isolated from Mariana Trench sediments,efficiently degraded phenol under pressures up to 70 and 60 MPa,respectively,with concomitant increase in biomass.By analyzing a high-pressure(70 MPa)culture metatranscriptome,not only was the entire range of metabolic processes under high pressure generated,but also genes encod-ing complete phenol degradation via ortho-and meta-cleavage pathways were revealed.The isolate of Pseudomonas also contained genes encoding the complete degradation pathway.Six transcribed genes(dmpKLMNOP_(sed))were functionally identified to encode a multicomponent hydroxylase catalyzing the hydroxylation of phenol and its methylated derivatives by heterogeneous expression.In addition,key catabolic genes identified in the metatranscriptome of the high-pressure cultures and genomes of bacterial isolates were found to be all widely distributed in 22 published hadal microbial metagenomes.At microbiological,genetic,bioinformatics,and biochemical levels,this study found that microorganisms widely found in hadal trenches were able to effectively drive phenolic compound degradation under high hydrostatic pressures.This information will bridge a knowledge gap concerning the microbial aromatics degradation within hadal trenches.

关键词： Hadal trench High hydrostatic pressure Phenolic compounds degradation Piezotolerant microorganisms Widespread distribution

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Safe Motion Planning and Control Framework for Automated Vehicles with Zonotopic TRMPC

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Engineering 2024年第2期33卷 146-159页

作者： hao Zheng Yinong Li ling Zheng Ehsan Hashemi State Key Laboratory of Mechanical Transmissions College of Mechanical and Vehicle EngineeringChongqing UniversityChongqing 400044China Department of Mechanical Engineering University of AlbertaEdmontonAB T6G 2H5Canada

Model mismatches can cause multi-dimensional uncertainties for the receding horizon control strategies of automated vehicles(AVs).The uncertainties may lead to potentially hazardous behaviors when the AV tracks ideal trajectories that are individually optimized by the AV's planning layer.To address this issue,this study proposes a safe motion planning and control(SMPAC)framework for AVs.For the control layer,a dynamic model including multi-dimensional uncertainties is established.A zonotopic tube-based robust model predictive control scheme is proposed to constrain the uncertain system in a bounded minimum robust positive invariant set.A flexible tube with varying cross-sections is constructed to reduce the controller conservatism.For the planning layer,a concept of safety sets,representing the geometric boundaries of the ego vehicle and obstacles under uncertainties,is proposed.The safety sets provide the basis for the subsequent evaluation and ranking of the generated trajectories.An efficient collision avoidance algorithm decides the desired trajectory through the intersection detection of the safety sets between the ego vehicle and obstacles.A numerical simulation and hardware-in-the-loop experiment validate the effectiveness and real-time performance of the SMPAC.The result of two driving scenarios indicates that the SMPAC can guarantee the safety of automated driving under multi-dimensional uncertainties.

关键词： Automated vehicles Automated driving Motion planning Motion control Tube MPC Zonotope

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Reinforcement Learning-Based Dynamic Order Recommendation for On-Demand Food Delivery

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Tsinghua Science and Technology 2024年第2期29卷 356-367页

作者： Xing Wang ling Wang Chenxin Dong hao Ren Ke Xing Department of Automation Tsinghua UniversityBeijing 100080China School of Mechanical and Automotive Engineering Qingdao Hengxing University of Science and TechnologyQingdao 266100China Meituan Beijing 100015China

On-demand food delivery(OFD)is gaining more and more popularity in modern society.As a kernel order assignment manner in OFD scenario,order recommendation directly influences the delivery efficiency of the platform and the delivery experience of riders.This paper addresses the dynamism of the order recommendation problem and proposes a reinforcement learning solution method.An actor-critic network based on long short term memory(LSTM)unit is designed to deal with the order-grabbing conflict between different riders.Besides,three rider sequencing rules are accordingly proposed to match different time steps of the LSTM unit with different riders.To test the performance of the proposed method,extensive experiments are conducted based on real data from Meituan delivery platform.The results demonstrate that the proposed reinforcement learning based order recommendation method can significantly increase the number of grabbed orders and reduce the number of order-grabbing conflicts,resulting in better delivery efficiency and experience for the platform and riders.

关键词： on-demand food delivery order recommendation reinforcement learning actor-critic network long short term memory

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Digital signal acquisition system for complex nuclear reaction experiments

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Nuclear Science and Techniques 2024年第1期35卷 124-133页

作者： Wei-Liang Pu Yan-Lin Ye Jian-ling Lou Jia-hao Chen School of Physics and State Key Laboratory of Nuclear Physics and Technology Peking UniversityBeijing 100871China Institute of Applied Physics and Computational Mathematics Beijing 100094China

A digital data-acquisition system based on XIA LLC products was used in a complex nuclear reaction experiment using radioactive ion beams.A flexible trigger system based on a field-programmable gate array(FPGA)parametrization was developed to adapt to different experimental sizes.A user-friendly interface was implemented,which allows converting script language expressions into FPGA internal control parameters.The proposed digital system can be combined with a conventional analog data acquisition system to provide more flexibility.The performance of the combined system was veri-fied using experimental data.

关键词： Digital signal acquisition system Trigger Programmable logic Timestamp

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Intermittent Theta Burst Stimulation Attenuates Cognitive Deficits and Alzheimer’s Disease-Type Pathologies via ISCA1-Mediated Mitochondrial Modulation in APP/PS1 Mice

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Neuroscience Bulletin 2024年第2期40卷 182-200页

作者： Yang Zhu hao Huang Zhi Chen Yong Tao ling-Yi Liao Shi-hao Gao Yan-Jiang Wang Chang-Yue Gao Department of Rehabilitation Medicine Daping HospitalArmy Medical UniversityChongqing 400042China Department of Neurology and Center for Clinical Neuroscience Daping HospitalArmy Medical UniversityChongqing 400042China Department of Special Medicine Daping HospitalArmy Medical UniversityChongqing 400042China

Intermittent theta burst stimulation(iTBS),a time-saving and cost-effective repetitive transcranial magnetic stimulation regime,has been shown to improve cognition in patients with Alzheimer’s disease(AD).However,the specific mechanism underlying iTBS-induced cognitive enhancement remains unknown.Previous studies suggested that mitochondrial functions are modulated by magnetic stimulation.Here,we showed that iTBS upregulates the expression of iron-sulfur cluster assembly 1(ISCA1,an essential regulatory factor for mitochondrial respiration)in the brain of APP/PS1 mice.In vivo and in vitro studies revealed that iTBS modulates mitochondrial iron-sulfur cluster assembly to facilitate mitochondrial respiration and function,which is required for ISCA1.Moreover,iTBS rescues cognitive decline and attenuates AD-type pathologies in APP/PS1 mice.The present study uncovers a novel mechanism by which iTBS modulates mitochondrial respiration and function via ISCA1-mediated iron-sulfur cluster assembly to alleviate cognitive impairments and pathologies in AD.We provide the mechanistic target of iTBS that warrants its therapeutic potential for AD patients.

关键词： Intermittent theta burst stimulation Alzheimer’s disease Iron-sulfur cluster assembly 1 Mitochondrial dysfunction Neurodegeneration

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Transient self-assembly driven by chemical fuels

ChemPhysMater

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ChemPhysMater 2024年第1期3卷 1-23页

作者： ling Wang Jin Yuan Jingcheng hao Key Laboratory of Colloid and Interface Chemistry Shandong UniversityMinistry of EducationJinan 250100China School of Chemistry and Chemical Engineering Qilu Normal UniversityJinan 250200China

Self-assembly has been extensively studied in chemistry,physics,biology,and materials engineering and has become an important“bottom-up”approach in creating intriguing structures for different applications.Using dissipative self-assembly to construct fuel-dependent,energy-consuming,and dynamic nonequilibrium systems is important for developing intelligent life-like materials.Furthermore,dissipative self-assembly has become a research hotspot in materials chemistry,biomedical science,environmental chemistry,and physical chemistry.An in-depth understanding of the process and mechanism provides useful insights to the researchers for devel-oping materials using dissipative self-assembly and also helps guide future innovation in material fabrication.This critical review comprehensively analyzes various chemical fuel input and energy consumption mechanisms,supported by numerous illustrative examples.Versatile transient assemblies,including gels,vesicles,micelles,and nanoparticle aggregates,have been systematically studied in our and other laboratories.The relationship between the molecular structure of precursors and temporal assemblies in dissipative self-assemblies is discussed from the perspective of physical chemistry.Using dissipative self-assembly methods to construct functional assemblies provides important implications for constructing high-energy,nonequilibrium,and intelligent functional materials.

关键词： Self-Assembly Chemical Fuel Consumption mechanisms Functional assemblies

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Differential expression of miRNAs and mRNAs in the livers of largemouth bass Micropterus salmoides under heat stress

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Journal of Oceanology and Limnology 2024年第2期42卷 594-608页

作者： Xuqian Zhao Zijie LIN Caijuan LI hao ZHU lingling LI Wenjia MAO Qufei ling School of Biology and Basic Medical Sciences Suzhou Medical College of Soochow UniversitySuzhou 215000China

Global warming threatens freshwater ecosystems and compromises fish survival.To elucidate the role of miRNAs in the livers of heat stressed largemouth bass,juvenile fish was subject to heat stress under 37°C.Both mRNA-seq and miRNA-seq were conducted on the liver tissues under control and heat stress conditions.Differential gene expression analysis and enrichment analysis were performed on mRNA and miRNA expression profiles.A total of 406 differentially expressed genes(DEGs)were discovered,of which 212 were up-regulated and 194 were down-regulated.Most of the DEGs were significantly implicated in the regulation of“protein processing in endoplasmic reticulum”,“proteasome”,“steroid biosynthesis”,and“ornithine decarboxylase inhibitor activity”pathways.In addition,47 differentially expressed miRNAs(DEMs)were identified in largemouth bass livers under heat stress,including 21 up-regulated and 25 down-regulated miRNAs.A negatively regulated miRNA-mRNA network including 12 miRNAs and 19 mRNAs was constructed with DEMs involved in“protein degradation”,“calcium ion regulation”,“cell apoptosis”,and“lipid metabolism”.Moreover,this study indicated novel-miR-144 activated the IRE1 signaling pathway by targeting txndc5 to induce liver apoptosis in largemouth bass under heat stress.This study revealed the involvement of miRNA regulation in largemouth bass in response to heat stress.

关键词： heat stress largemouth bass miRNA-mRNA interaction

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Detection of Novel BEST1 Variations in Autosomal Recessive Bestrophinopathy Using Third-generation Sequencing

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Current Medical Science 2024年第2期44卷 419-425页

作者： Jia-xun LI ling-rui MENG Bao-ke HOU Xiao-lu hao Da-jiang WANG ling-hui QU Zhao-hui LI Lei ZHANG Xin JIN Department of Senior Ophthalmology the Third Medical Center of PLA General HospitalBeijing 100853China Department of Ophthalmology the 74th Army Group HospitalGuangzhou 510318China

Objective:Autosomal recessive bestrophinopathy(ARB),a retinal degenerative disease,is characterized by central visual loss,yellowish multifocal diffuse subretinal deposits,and a dramatic decrease in the light peak on electrooculogram.The potential pathogenic mechanism involves mutations in the BEST1 gene,which encodes Ca2+-activated Cl−channels in the retinal pigment epithelium(RPE),resulting in degeneration of RPE and photoreceptor.In this study,the complete clinical characteristics of two Chinese ARB families were summarized.Methods:Pacific Biosciences(PacBio)single-molecule real-time(SMRT)sequencing was performed on the probands to screen for disease-causing gene mutations,and Sanger sequencing was applied to validate variants in the patients and their family members.Results:Two novel mutations,c.202T>C(chr11:61722628,p.Y68H)and c.867+97G>A,in the BEST1 gene were identified in the two Chinese ARB families.The novel missense mutation BEST1 c.202T>C(p.Y68H)resulted in the substitution of tyrosine with histidine in the N-terminal region of transmembrane domain 2 of bestrophin-1.Another novel variant,BEST1 c.867+97G>A(chr11:61725867),located in intron 7,might be considered a regulatory variant that changes allele-specific binding affinity based on motifs of important transcriptional regulators.Conclusion:Our findings represent the first use of third-generation sequencing(TGS)to identify novel BEST1 mutations in patients with ARB,indicating that TGS can be a more accurate and efficient tool for identifying mutations in specific genes.The novel variants identified further broaden the mutation spectrum of BEST1 in the Chinese population.

关键词： autosomal recessive bestrophinopathy BEST1 gene third-generation sequencing mutation

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Genome-wide CRISPR screening reveals key genes and pathways associated with 20-hydroxyecdysone signal transduction in the silkworm(Bombyx mori)

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Insect Science 2024年第1期31卷 47-58页

作者： hao Sun Jingya Chen Ruolin Wang Dan Liu Na Zhang Tong Zhang ling Jia Sanyuan Ma Qingyou Xia State Key Laboratory of Silkworm Genome Biology Southwest UniversityChongqingChina Biological Science Research Center Southwest UniversityChongqingChina

Metamorphosis is a complex developmental process involving multiple pathways and a large number of genes that are regulated by juvenile hormone(JH)and 20-hydroxyecdysone(20E).Despite important progress in understanding various aspects of silkworm biology,the hormone signaling pathway in the silkworm remains poorly understood.Genome-wide screening using clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9)-based libraries has recently emerged as a novel method for analyzing genome function,enabling further research into essential genes,drug targets,and virus-host interaction.Previously,we constructed a genome-wide CRISPR/Cas9-based library of the silkworm(Bombyx mori)and successfully revealed the genes involved in biotic or abiotic stress factor responses.In this study,we used our silkworm CRISPR library and large-scale genome-wide screening to analyze the key genes in the silkworm 20E signaling pathway and their mechanisms of action.Functional annotation showed that 20E regulates key proteins in processes that mainly occur in the cytoplasm and nucleus.Pathway enrichment analysis showed that 20E can activate phosphorylation and may affect innate immunity,interfere with intracellular nutrition and energy metabolism,and eventually cause cell apoptosis.The screening results were experimentally validated by generating cells with knockout alleles of the relevant genes,which had increased tolerance to 20E.Our findings provide a panoramic overview of signaling in response to 20E in the silkworm,underscoring the utility of genome-wide CRISPR mutant libraries in deciphering hormone signaling pathways and the mechanisms that regulate metamorphosis in insects.

关键词： CRISPR/Cas9 CRISPR library screening ecdysone 20E signal transduction silkworm whole genome editing

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Multiple thermal events recorded in the Acasta Gneiss Complex:Evidence from in-situ dating of zircon, titanite, and apatite

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Science China Earth Sciences 2024年第3期67卷 673-686页

作者： Qingfeng MEI Jinhui YANG Jinfeng SUN Qiuli LI Shitou WU Xiaoxiao ling Peng PENG hao WANG State Key Laboratory of Lithospheric Evolution Institute of Geology and GeophysicsChinese Academy of SciencesBeijing 100029China College of Earth and Planetary Sciences University of Chinese Academy of SciencesBeijing 100049China Key Laboratory of Computational Geodynamics University of Chinese Academy of SciencesBeijing 100049China

In-situ dating of the zircons, titanites, and apatites in the rock fragments of approximately 1 cm2in size from the Acasta Gneiss Complex was performed using secondary ion mass spectrometry or laser ablation inductively coupled plasma mass spectrometry to provide constraints on the thermal history of the Acasta Gneiss Complex. The zircons in these rock fragments typically exhibit multiple age populations, reflecting the presence of inherited zircons or the post-crystallization process of zircon overgrowth. Combined with previous studies, our zircon dating results reveal multiple magmatic events that occurred in the Acasta Gneiss Complex, specifically at >3.96, ~3.72, and ~3.57 Ga, respectively. A titanite Pb-Pb isochron age of2911±22 Ma(95% confidence level, MSWD=1.5) for sample AY199 is identified, consistent with the timing of the latest Archean magmatism in the Acasta Gneiss Complex. The titanite U-Pb ages for samples AC478 and AY066 are 1932±270 Ma(95% confidence level, MSWD=2.3) and 1813±45 Ma(95% confidence level, MSWD=2.3), respectively. The apatites in sample P090803-C exhibit a Pb-Pb isochron age of 1833±26 Ma(95% confidence level, MSWD=1.4). The apatite U-Pb ages for samples AC478, AY199, and AY066 are 1850±20 Ma(95% confidence level, MSWD=1.3), 1827±100 Ma(95% confidence level, MSWD=6.3), and 1807±58 Ma(95% confidence level, MSWD=3.9), respectively. Titanites in samples AC478 and AY066, as well as the apatites in all four investigated samples, show a uniform age(Pb-Pb or U-Pb age) of ~1.9–1.8 Ga,indicating U-Pb system reset in these minerals due to the Wopmay orogeny and documenting that the peak temperature condition associated with the Wopmay orogeny exceeded the apatite U-Pb closure temperature and approached or exceeded that of titanite.

关键词： Zircon Titanite Apatite Acasta Gneiss Complex Wopmay Orogen

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