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Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution,lignin biosynthesis regulation,and stress tolerance

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Science China(Life Sciences) 2024年第6期67卷 1266-1279页

作者： Wanwan Li Xin Chen Jianing yu yuxian zhu College of Life Sciences Shaanxi Normal UniversityXi’an 710119China The State Key Laboratory of Protein and Gene Research College of Life SciencesPeking UniversityBeijing 100871China The Institute for Advanced Studies Wuhan UniversityWuhan 430072China

Durian(Durio zibethinus)is a tropical fruit that has a unique flavor and aroma.It occupies a significant phylogenetic position within the Malvaceae family.Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling,resulting in an abundant genomic diversity.However,the ancestral karyotypes of the Malvaceae family,as well as the evolution trajectory leading to the28 chromosomes in durian,remain poorly understood.Here,we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses.By analyzing the collinear blocks between cacao and durian,we inferred 11 Malvaceae ancestral karyotypes.These blocks were present in a single-copy form in cacao and mainly in triplicates in durian,possibly resulting from a recent whole genome triplication(WGT)event that led to hexaploidization of the durian genome around 20(17–24)million years ago.A large proportion of the duplicated genes in durian,such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis,are derived directly from whole genome duplication,which makes it an important force in reshaping its genomic architecture.Transcriptome studies have revealed that genes involved in feruloyl-Co A formations were highly preferentially expressed in fruit peels,indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins.Among all the analyzed transcription factors(TFs),members of the heat shock factor family(HSF)were the most significantly upregulated under heat stress.All subfamilies of genes encoding heat shock proteins(HSPs)in the durian genome appear to have undergone expansion.The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified.Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome.We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.

关键词： Durio zibethinus whole genome duplication whole genome triplication Malvaceae ancestral karyotypes chromosome reshuffling lignin biosynthesis heat stress

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Elastohydrodynamic Lubrication Interface Stiffness and Damping Considering Asperity Lateral Contact

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Acta Mechanica Solida Sinica 2024年第1期37卷 109-123页

作者： Zhiqiang Gao yu Zhang xian Wei Yanfang zhu Lixia Peng Weiping Fu Wen Wang School of Mechanical and Precision Instrument Engineering Xi'an University of TechnologyXi'an 710048China School of Intelligent Manufacturing Panzhihua UniversityPanzhihua 617000China Material Corrosion and Protection Key Laboratory of Sichuan Province Sichuan University of Light Chemical TechnologyYibin 644002China School of Mechanical Engineering Anyang Institute of TechnologyAnyang 455099China

Elastohydrodynamic lubrication(EHL)point contact occurs between two rough surfaces at the mesoscopic level,while the interaction of rough surfaces involves contact between asperities at the microscale level.In most cases,the contact between asperities within an interface takes the form of lateral contact rather than peak contact.Regions devoid of contact asperities are filled with lubricating oil.However,conventional models often oversimplify lateral contact forms as interactions between asperities and a smooth,rigid plane.These simplifications fail to accurately represent the true contact conditions and can lead to inaccuracies in the analysis of EHL’s contact performance.To address this issue,we have developed a novel EHL interface model comprising two rough surfaces.This model allows us to explore the influence of asperity height,contact angle,and contact azimuth angle on EHL interface performance.

关键词： EHL interface Asperity lateral contact Contact stiffness Damping

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Acute suppurative terminal cholangitis:Clinical characteristics of a new subtype of acute cholangitis

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Hepatobiliary & Pancreatic Diseases International 2024年第3期23卷 293-299页

作者： Rong-Tao zhu Ye Li Chi-xian Zhang Wei-Jie Wang Ruo-Peng Liang Jian Li Kai Bai yu-Ling Sun Department of Hepatobiliary and Pancreatic Surgery the First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China Zhengzhou Key Laboratory of Hepatobiliary and Pancreatic Diseases Zhengzhou 450052China Institute of Hepatobiliary and Pancreatic Diseases Zhengzhou UniversityZhengzhou 450052China Department of Pathology the First Affiliated Hospital of Zhengzhou UniversityZhengzhou 450052China

Background:Acute suppurative terminal cholangitis(ASTC)is rarer than acute obstructive cholangitis and is not well studied.To explore this subtype of acute cholangitis,we described our clinical experience with ASTC.Methods:We performed a retrospective review of patients with ASTC admitted to our center from September 2014 to August 2020.We analyzed their clinical characteristics,including etiology,clinical manifestations,imaging features,treatment and prognosis.Results:A total of 32 ASTC patients were included in the analysis.The majority of the patients had a history of biliary operations,and clinical manifestations were occult and atypical.The positive rate of bacterial culture was 46.9%.All the patients had typical imaging features on computed tomography and magnetic resonance imaging.Treatment with effective antibiotics was provided as soon as diagnosis was established.After treatment,most patients had a good outcome.Elevated levels of total bilirubin,aspartate aminotransferase,procalcitonin and gamma-glutamyltransferase were the characteristics of critically ill patients and were associated with relatively poor prognosis.Conclusions:Our results demonstrated that ASTC should be recognized as a new subtype of acute cholangitis,and that earlier diagnosis and more personalized treatments are needed.

关键词： Acute suppurative terminal cholangitis Acute cholangitis Gram-negative bacterial infections Diagnosis Treatment

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PROTEIN S-ACYL TRANSFERASE 13/16 modulate disease resistance by S-acylation of the nucleotide binding,leucine-rich repeat protein R5L1 in Arabidopsis

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Journal of Integrative Plant Biology 2022年第9期64卷 1789-1802页

作者： Jin Gao Gai Huang Xin Chen yu-xian zhu State Key Laboratory of Protein and Plant Gene Research College of Life SciencesPeking UniversityBeijing100871 China Institute for Advanced Studies Wuhan UniversityWuhan430072 China

Nucleotide binding,leucine-rich repeat(NB-LRR)proteins are critical for disease resistance in plants,while we do not know whether S-acylation of these proteins plays a role during bacterial infection.We identified 30 Arabidopsis mutants with mutations in NB-LRR encoding genes from the Nottingham Arabidopsis Stock Center and characterized their contribution to the plant immune response after inoculation with Pseudomonas syringae pv tomato DC3000(Pst DC3000).Of the five mutants that were hyper-susceptible to the pathogen,three(R5L1,R5L2 and RPS5)proteins contain the conserved S-acylation site in the N-terminal coiled-coil(CC)domain.In wild-type(WT)Arabidopsis plants,R5L1 was transcriptionally activated upon pathogen infection,and R5L1 overexpression lines had enhanced resistance.Independent experiments indicated that R5L1 localized at the plasma membrane(PM)via S-acylation of its N-terminal CC domain,which was mediated by PROTEIN S-ACYL TRANSFERASE 13/16(PAT13,PAT16).Modification of the S-acylation site reduced its affinity for binding the PM,with a consequent significant reduction in bacterial resistance.PM localization of R5L1 was significantly reduced in pat13 and pat16 mutants,similar to what was found for WT plants treated with 2-bromopalmitate,an S-acylationblocking agent.Transgenic plants expressing R5L1 in the pat13 pat16 double mutant showed no enhanced disease resistance.Overexpression of R5L1 in WT Arabidopsis resulted in substantial accumulation of reactive oxygen species after inoculation with Pst DC3000;this effect was not observed with a mutant R5L1 carrying a mutated Sacylation site.Our data suggest that PAT13-and PAT16-mediated S-acylation of R5L1 is crucial for its membrane localization to activate the plant defense response.

关键词： NB-LRR protein S-acyl transferases(PATs) Pst DC3000 S-acylation

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A Feature Transformation and Selection Method to Acquire an Interpretable Model Incorporating Nonlinear Effects

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Acta Mathematica Sinica,English Series 2024年

作者： yu ZHENG Jin zhu Jun xian zhu Xue Qin WANG International Institute of Finance School of Management University of Science and Technology of China Saw Swee Hock School of Public Health National University of Singapore Department of Statistical Science School of Mathematics Sun Yat-Sen University

Finding a highly interpretable nonlinear model has been an important yet challenging problem, and related research is relatively scarce in the current literature. To tackle this issue, we propose a new algorithm called Feat-ABESS based on a framework that utilizes feature transformation and selection for re-interpreting many machine learning algorithms. The core idea behind Feat-ABESS is to parameterize interpretable feature transformation within this framework and construct an objective function based on these parameters. This approach enables us to identify a proper interpretable feature transformation from the optimization perspective. By leveraging a recently advanced optimization technique, Feat-ABESS can obtain a concise and interpretable model. Moreover, Feat-ABESS can perform nonlinear variable selection. Our extensive experiments on 205 benchmark datasets and case studies on two datasets have demonstrated that Feat-ABESS can achieve powerful prediction accuracy while maintaining a high level of interpretability. The comparison with existing nonlinear variable selection methods exhibits Feat-ABESS has a higher true positive rate and a lower false discovery rate.

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Topological Stability and Entropy for Certain Set-valued Maps

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Acta Mathematica Sinica,English Series 2024年第4期40卷 962-984页

作者： yu ZHANG yu Jun zhu School of Mathematical Sciences Xiamen UniversityXiamen 361005P.R.China

In this paper,the dynamics(including shadowing property,expansiveness,topological stability and entropy)of several types of upper semi-continuous set-valued maps are mainly considered from differentiable dynamical systems points of view.It is shown that(1)if f is a hyperbolic endomorphism then for eachε>0 there exists a C^(1)-neighborhood U of f such that the induced set-valued map F_(f,U)has theε-shadowing property,and moreover,if f is an expanding endomorphism then there exists a C^(1)-neighborhood U of f such that the induced set-valued map F_(f,U)has the Lipschitz shadowing property;(2)when a set-valued map F is generated by finite expanding endomorphisms,it has the shadowing property,and moreover,if the collection of the generators has no coincidence point then F is expansive and hence is topologically stable;(3)if f is an expanding endomorphism then for eachε>0 there exists a C^(1)-neighborhood U of f such that h(F_(f,U,ε))=h(f);(4)when F is generated by finite expanding endomorphisms with no coincidence point,the entropy formula of F is given.Furthermore,the dynamics of the set-valued maps based on discontinuous maps on the interval are also considered.

关键词： Set-valued map orbit space hyperbolic endomorphism perturbation shadowing expansiveness topological stability entropy

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Interfacial Electronic Modulation of Dual-Monodispersed Pt–Ni_(3)S_(2) as Efficacious Bi-Functional Electrocatalysts for Concurrent H_(2) Evolution and Methanol Selective Oxidation

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Nano-Micro Letters 2024年第4期16卷 415-431页

作者： Qianqian Zhao Bin Zhao Xin Long Renfei Feng Mohsen Shakouri Alisa Paterson Qunfeng Xiao yu Zhang xian‑zhu Fu Jing‑Li Luo Shenzhen Key Laboratory of Energy Electrocatalytic Materials Shenzhen Key Laboratory of Polymer Science and TechnologyGuangdong Research Center for Interfacial Engineering of Functional MaterialsCollege of Materials Science and EngineeringShenzhen UniversityShenzhen 518060People’s Republic of China Canadian Light Source Inc. SaskatoonSK S7N 0X4Canada Instrumental Analysis Center of Shenzhen University(Lihu Campus) Shenzhen UniversityShenzhen 518055People’s Republic of China

Constructing the efficacious and applicable bifunctional electrocatalysts and establishing out the mechanisms of organic electro-oxidation by replacing anodic oxygen evolution reaction(OER) are critical to the development of electrochemicallydriven technologies for efficient hydrogen production and avoid CO_(2) emission. Herein, the hetero-nanocrystals between monodispersed Pt(~ 2 nm) and Ni_(3)S_(2)(~ 9.6 nm) are constructed as active electrocatalysts through interfacial electronic modulation, which exhibit superior bi-functional activities for methanol selective oxidation and H_(2) generation. The experimental and theoretical studies reveal that the asymmetrical charge distribution at Pt–Ni_(3)S_(2) could be modulated by the electronic interaction at the interface of dual-monodispersed heterojunctions, which thus promote the adsorption/desorption of the chemical intermediates at the interface. As a result, the selective conversion from CH_(3)OH to formate is accomplished at very low potentials(1.45 V) to attain 100 m A cm^(-2) with high electronic utilization rate(~ 98%) and without CO_(2) emission. Meanwhile, the Pt–Ni_(3)S_(2) can simultaneously exhibit a broad potential window with outstanding stability and large current densities for hydrogen evolution reaction(HER) at the cathode. Further, the excellent bi-functional performance is also indicated in the coupled methanol oxidation reaction(MOR)//HER reactor by only requiring a cell voltage of 1.60 V to achieve a current density of 50 m A cm^(-2) with good reusability.

关键词： Dual-monodispersed heterostructure Electronic interactive modulation Reaction mechanism Methanol oxidation reaction Hydrogen generation

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Promotion effect of FOXCUT as a microRNA sponge for miR-24-3p on progression in triple-negative breast cancer through the p38 MAPK signaling pathway

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Chinese Medical Journal 2024年第1期137卷 105-114页

作者： Xiafei yu Fangze Qian Xiaoqiang Zhang Yanhui zhu Gao He Junzhe Yang xian Wu Yi Zhou Li Shen Xiaoyue Shi Hongfei Zhang Xiao’an Liu Department of Breast Surgery The First Affiliated Hospital of Nanjing Medical UniversityNanjingJiangsu 210029China

Background:Triple-negative breast cancer(TNBC)is a type of highly invasive breast cancer with a poor prognosis.According to new research,long noncoding RNAs(lncRNAs)play a significant role in the progression of cancer.Although the role of lncRNAs in breast cancer has been well reported,few studies have focused on TNBC.This study aimed to explore the biological function and clinical significance of forkhead box C1 promoter upstream transcript(FOXCUT)in triple-negative breast cancer.Methods:Based on a bioinformatic analysis of the cancer genome atlas(TCGA)database,we detected that the lncRNA FOXCUT was overexpressed in TNBC tissues,which was further validated in an external cohort of tissues from the General Surgery Department of the First Affiliated Hospital of Nanjing Medical University.The functions of FOXCUT in proliferation,migration,and invasion were detected in vitro or in vivo.Luciferase assays and RNA immunoprecipitation(RIP)were performed to reveal that FOXCUT acted as a competitive endogenous RNA(ceRNA)for the microRNA miR-24-3p and consequently inhibited the degradation of p38.Results:lncRNA FOXCUT was markedly highly expressed in breast cancer,which was associated with poor prognosis in some cases.Knockdown of FOXCUT significantly inhibited cancer growth and metastasis in vitro or in vivo.Mechanistically,FOXCUT competitively bounded to miR-24-3p to prevent the degradation of p38,which might act as an oncogene in breast cancer.Conclusion:Collectively,this research revealed a novel FOXCUT/miR-24-3p/p38 axis that affected breast cancer progression and suggested that the lncRNA FOXCUT could be a diagnostic marker and therapeutic target for breast cancer.

关键词： Triple negative breast neoplasms RNA,long noncoding FOXCUT miR-24-3p p38 MAPK signaling pathway Disease progression

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Limit Theorems for Critical Galton-Watson Processes with Immigration Stopped at Zero

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Acta Mathematica Sinica,English Series 2024年第2期40卷 435-450页

作者： Dou Dou LI Mei ZHANG xian yu ZHANG College of Statistics and Data Science Faculty of ScienceBeijing University of TechnologyBeijing 100124P.R.China Laboratory of Mathematics and Complex Systems(Ministry of Education) School of Mathematical SciencesBeijing Normal UniversityBeijing 100875P.R.China

In this paper,we consider a critical Galton-Watson branching process with immigration stopped at zero W.Some precise estimation on the probability generating function of the n-th population are obtained,and the tail probability of the life period of W is studied.Based on above results,two conditional limit theorems for W are established.

关键词： Branching immigration critical life period limit theorems

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Spatial patterns of zooplankton abundance,biovolume,and size structure in response to environmental variables:a case study in the Yellow Sea and East China Sea

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Journal of Oceanology and Limnology 2024年第1期42卷 113-127页

作者： Song SUN Haochen xian Xiaoxia SUN Mingliang zhu Mengtan LIU Key Laboratory of Marine Ecology and Environmental Sciences Institute of OceanologyChinese Academy of SciencesQingdao 266071China Jiaozhou Bay National Marine Ecosystem Research Station Institute of OceanologyChinese Academy of SciencesQingdao 266071China University of Chinese Academy of Sciences Beijing 100049China Laboratory for Marine Ecology and Environmental Science Laoshan LaboratoryQingdao 266237China

The Yellow Sea(YS)and East China Sea(ECS)are highly dynamic marginal seas of the northwestern Pacific Ocean.To gain an in-depth understanding of zooplankton community structure,zooplankton abundance,biovolume,and size structure in summer 2017 in the YS and ECS were assessed using ZooScan imaging analysis.Zooplankton abundance and biovolume ranged 2.94–1187.14 inds./m^(3)and 3.13–3438.51 mm^(3)/m^(3),respectively.Based on the biovolume data of the categorized size classes of 26 identified taxonomic groups,the zooplankton community was classified into five groups,and each group was coupled with distinctive oceanographic features.Under the influence of the Yellow Sea Cold Water Mass,the Yellow Sea offshore group featured the lowest bottom temperature(10.84±3.42℃)and the most abundant Calanoids(mainly in the 2–3 mm size class).In the Yellow Sea inshore group,Hydrozoans showed the largest biovolume and dominated in the 3–4-mm and>5-mm size classes.The East China Sea offshore group,which was affected by the Kuroshio Branch Current,featured high temperature and salinity,and the lowest bottom dissolved oxygen(2.58±0.5 mg/L).The lowest values of zooplankton abundance and biovolume in the East China Sea offshore group might be attributed to the bottom dissolved oxygen contents.The East China Sea inshore group,which was mainly influenced by the Zhejiang-Fujian Coastal Current and Changjiang Diluted Water,was characterized by high chlorophyll a and the largest biovolume of carnivorous Siphonophores(280.82±303.37 mm^(3)/m^(3)).The Changjiang River estuary offshore group showed the most abundant Cyclopoids,which might be associated with the less turbid water mass in this region.Seawater temperature was considered the most important factor in shaping the size compositions of Calanoids in different groups.

关键词： zooplankton size structure ZooScan Yellow Sea East China Sea

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