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Large-scale genome-wide SNP analysis reveals the rugged(and ragged)landscape of global ancestry,phylogeny,and demographic history in chicken breeds

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第4期25卷 324-340页

作者： Natalia V.DeMeNTIeVA Yuri S.SHCHeRBAKOV Olga I.STANISHeVSKAYA Anatoly B.VAKHRAMeeV Tatiana A.LARKINA Artem P.DYSIN Olga A.NIKOLAeVA Anna e.RYABOVA Anastasiia I.AZOVTSeVA Olga V.MITROFANOVA Grigoriy K.PeGLIVANYAN Natalia R.ReINBACH Darren K.GRIFFIN michael N.ROMANOV Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K.ernst Federal Research Centre for Animal Husbandry.Pushkin St.Petersburg196601Russia School of Biosciences University of KentCanterburyCT27NJUK L.K.ernst Federal Research Center for Animal Husbandry DubrovitsyPodolskMoscow Oblast142132Russia

The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse *** study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 *** populations represent a significant sample of the world's chicken breeds from europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried *** included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population *** also included assessment of linkage disequilibrium and construction of phylogenetic *** multidimensional scaling,principal component analysis,and ADMIXTURe-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each *** overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous *** a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry *** general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

关键词： Chicken genome diversity Single nucleotide polymorphism(SNP)analysis Gene pool Global ancestry Phylogeny Demographic history

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Bacteria colonization and gene expression related to immune function in colon mucosa is associated with growth in neonatal calves regardless of live yeast supplementation

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Journal of Animal Science and Biotechnology 2024年第05期 1980-1995页

作者： Koki Nishihara Clothilde Villot Lautaro Cangiano Le Luo Guan michael Steele Department of Animal Biosciences Animal Science and Nutrition University of Guelph Department of Agricultural Food and Nutritional Science University of Alberta Lallemand SAS Department of Animal and Dairy Sciences University of Wisconsin-Madison Faculty of Land and Food Systems The University of British Columbia

Background As Holstein calves are susceptible to gastrointestinal disorders during the first week of life, understanding how intestinal immune function develops in neonatal calves is important to promote better intestinal health. Feeding probiotics in early life may contribute to host intestinal health by facilitating beneficial bacteria colonization and developing intestinal immune function. The objective of this study was to characterize the impact of early life yeast supplementation and growth on colon mucosa-attached bacteria and host immune *** Twenty Holstein bull calves received no supplementation(CON) or Saccharomyces cerevisiae boulardii(SCB) from birth to 5 d of life. Colon tissue biopsies were taken within 2 h of life(D0) before the first colostrum feeding and 3 h after the morning feeding at d 5 of age(D5) to analyze mucosa-attached bacteria and colon transcriptome. Metagenome sequencing showed that there was no difference in α and β diversity of mucosa-attached bacteria between day and treatment, but bacteria related to diarrhea were more abundant in the colon mucosa on D0 compared to D5. In addition, q PCR indicated that the absolute abundance of escherichia coli(e. coli) decreased in the colon mucosa on D5 compared to D0; however, that of Bifidobacterium, Lactobacillus, and Faecalibacterium prausnitzii, which could competitively exclude e. coli, increased in the colon mucosa on D5 compared to D0. RNA-sequencing showed that there were no differentially expressed genes between CON and SCB, but suggested that pathways related to viral infection such as “Interferon Signaling” were activated in the colon mucosa of D5 compared to *** Growth affected mucosa-attached bacteria and host immune function in the colon mucosa during the first 5 d of life in dairy calves independently of SCB supplementation. During early life, opportunistic pathogens may decrease due to intestinal environmental changes by beneficial bacteria and/or host immun

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Des racines et des ailes La culture du droit humain a la subsistance en Chine

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中国与非洲（法文版） 2024年第3期16卷 32-33页

作者： eHIZUeLeN michael MITCHeLL OMORUYI Centre d'etudes nigerianes Institut d'etudes africainesUniversite normale du Zhejiang

La Chine met en avant les droits a la subsistance et au développement commeétant les plus fondamentaux des droits *** peuple chinois s'est engage avec determination dans la protection des droits de I'homme,un idéal que I'humanite cherche a atteindre depuis de nombreuses *** son influence croissante sur la scene mondiale,la Chine aévolue d'une posture traditionnellement defensive vers un engagement plus actif dans la defense des droits de I'homme a I'eéchelle internationale,notamment au sein du Conseil des droits de I'homme des Nations unies.

关键词： des les culture

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BDS-3 B1C/B2a长基线相对定位研究

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测绘通报 2024年第8期 31-36,53页

作者：方卓王立诗云 michael Floyd 南京数维测绘有限公司江苏南京211808 中铁四院集团南宁勘察设计院有限公司广西南宁430007 麻省理工学院地球、大气与行星科学系马萨诸塞州剑桥02139

为了验证北斗三号卫星导航系统(BDS-3)B1C/B2a长基线相对定位的精度,本文首先对2023年DOY(304~313)澳大利亚地区8个MGeX测站连续10 d观测数据进行质量分析;然后使用改进的GAMIT10.76软件对观测数据进行长基线相对定位解算;最后评估BDS-3... 详细信息

为了验证北斗三号卫星导航系统(BDS-3)B1C/B2a长基线相对定位的精度,本文首先对2023年DOY(304~313)澳大利亚地区8个MGeX测站连续10 d观测数据进行质量分析;然后使用改进的GAMIT10.76软件对观测数据进行长基线相对定位解算;最后评估BDS-3和GPS不同频点信号组合数据质量和双频无电离层线性组合基线解算,以及网平差的精度。试验结果表明,B1C/B2a、B1C/B2b和B1C/B3I频点信号组合数据质量、载噪比和伪距多路径误差基本相当,优于L1/L2;B1C/B2a的标准化均方根(NRMS)略优于B1C/B2b和L1/L2,显著优于B1C/B3I;B1C/B2a和B1C/B2b模糊度固定率基本相当,显著优于B1C/B3I,差于L1/L2。试验结果进一步表明,B1C/B2a相对于B1C/B3I的基线分量东(e)、北(N)和天顶(U)3方向标准差(STD)均值和三维点位误差均值分别降低了29.4%、27.0%、30.0%和41.0%。

关键词：北斗三号卫星导航系统频点信号数据质量相对定位

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Long-term impact of artificial intelligence on colorectal adenoma detection in high-risk colonoscopy

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World Journal of Gastrointestinal endoscopy 2024年第6期16卷 335-342页

作者： Kenneth W Chow Matthew T Bell Nicholas Cumpian Maryanne Amour Ryan H Hsu Viktor e eysselein Neetika Srivastava michael W Fleischman Sofiya Reicher Department of Medicine Harbor-UCLA Medical CenterTorranceCA 90502United States Department of Bioengineering Jacobs School of EngineeringUniversity of CaliforniaSan DiegoLa JollaCA 92093United States Department of Gastroenterology Harbor-UCLA Medical CenterTorranceCA 90502United States

BACKGROUND Improved adenoma detection rate(ADR)has been demonstrated with artificial intelligence(AI)-assisted ***,data on the real-world appli-cation of AI and its effect on colorectal cancer(CRC)screening outcomes is *** To analyze the long-term impact of AI on a diverse at-risk patient population undergoing diagnostic colonoscopy for positive CRC screening tests or *** AI software(GI Genius,Medtronic)was implemented into the standard proced-ure protocol in November *** was collected on patient demographics,procedure indication,polyp size,location,and *** screening outcomes were evaluated before and at different intervals after AI introduction with one year of *** We evaluated 1008 colonoscopies(278 pre-AI,255 early post-AI,285 established post-AI,and 190 late post-AI).The ADR was 38.1%pre-AI,42.0%early post-AI(P=0.77),40.0%established post-AI(P=0.44),and 39.5%late post-AI(P=0.77).There were no significant differences in polyp detection rate(PDR,baseline 59.7%),advanced ADR(baseline 16.2%),and non-neoplastic PDR(baseline 30.0%)before and after AI *** In patients with an increased pre-test probability of having an abnormal colonoscopy,the current generation of AI did not yield enhanced CRC screening metrics over high-quality *** the potential of AI in colonoscopy is undisputed,current AI technology may not universally elevate screening metrics across all situations and patient *** studies that analyze different AI systems across various patient populations are needed to determine the most effective role of AI in optimizing CRC screening in clinical practice.

关键词： Artificial intelligence Colonoscopy Adenoma detection rate Screening Colorectal adenoma

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Feeding ecology and interactions with mammal hosts in a symbiotic genus of birds(Buphagus spp.)in Namibia

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Avian Research 2024年第3期15卷 336-344页

作者： michael S.Lukubwe Daniel Velarde-Garcéz Fernando Sequeira Susana Lopes Adrian J.F.K.Craig Vanessa A.Mata Department of Zoology and entomology Rhodes UniversityMakhandaSouth Africa Department of Wildlife Management and Tourism Studies University of NamibiaKatima Mulilo CampusNamibia Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPortoPortugal CIBIO Centro de Investigação em Biodiversidade e Recursos GenéticosInBIO Laboratório AssociadoCampus de VairãoVairãoPortugal BIOPOLIS Program in Genomics Biodiversity and Land PlanningCIBIOCampus de VairãoVairãoPortugal

As the sole obligate symbiotic birds in Africa,oxpeckers offer a unique model for studying symbiotic *** to the multitrophic level they occupy and the context dependent foraging behavior they exhibit,the type of symbiotic relationship can be *** addition to providing a cleaning service to the host by removing ticks,oxpeckers frequently feed on blood,mucus,and saliva,inflicting potential damage on the ***,we used DNA metabarcoding on faecal samples to analyze the taxonomic composition of the trophic interactions of the Yellow-billed Oxpecker(Buphagus africanus)and Red-billed Oxpecker(***)in northeastern *** contrast to conventional methods,DNA metabarcoding allows for a detailed identification of dietary resources encompassing both mammal hosts and consumed arthropods within the same *** this information,we examined differences in the diet composition between oxpecker species and localities,as well as the co-occurrence between host and arthropod *** findings revealed that oxpeckers predominantly source their diet from mammals,ticks,and flies;however,ticks and flies rarely co-occur in the diet of an *** observed variability among individuals in their feeding ecology,which is strongly correlated with locality and,to a lesser extent,with the mammal *** noted a high degree of mobility between hosts within relatively short periods,with 32%of the samples showing traces of at least two mammal *** study illustrates the dynamic foraging behavior of these specialized symbiotic birds,shedding light on their potential role in pest control services and disease transmission.

关键词： Commensalism Diet DNA metabarcoding Oxpeckers Parasitism Trophic ecology

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Landscape of global urban environmental resistome and its association with local socioeconomic and medical status

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Science China(Life Sciences) 2024年第6期67卷 1292-1301页

作者： Jun Wu Yige Hu michael H Perlin David Danko Jun Lu Manuela Oliveira Johannes Werner Maria M Zambrano Maria A Sierra Olayinka O Osuolale Paweł Łabaj Nicolás Rascovan Nur Hazlin Hazrin-Chong Soojin Jang Haruo Suzuki Marina Nieto-Caballero Bharath Prithiviraj Patrick K H Lee Agnieszka Chmielarczyk Anna Różańska Yongxiang Zhao Lan Wang Christopher e Mason Tieliu Shi Center for Bioinformatics and Computational Biology and the Institute of Biomedical SciencesSchool of Life SciencesEast China Normal UniversityShanghai 200241China Department of Biology Program on Disease EvolutionUniversity of LouisvilleLouisville 40292USA Weill Cornell Medicine New York 10065USA The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine New York 10065USA Department of Pulmonary Medicine Shanghai Chest HospitalShanghai Jiao Tong UniversityShanghai 200025China i3S-Instituto de Investiga玢o e Inova玢o em Saúde Universidade do PortoPorto 4050-290Portugal Ipatimup-Instituto de Patologia e Imunologia Molecular da Universidade do Porto Porto 4200-465Portugal Departamento de Biologia Faculdade de CiênciasUniversidade do PortoPorto 4050-290Portugal High Performance and Cloud Computing Group Zentrum für Datenverarbeitung(ZDV)Eberhard Karls University of TübingenW鋍hterstra遝7672074TübingenGermany Corporación Corpogen Research Center Bogotá110311Colombia Applied environmental Metagenomics and Infectious Diseases Research(AeMIDR) Department of Biological SciencesElizade UniversityIlara-Mokin 340271Nigeria Maopolska Centre of Biotechnology Jagiellonian UniversityKraków 30-005Poland Aix-Marseille Université Mediterranean Institute of OceanologyUniversitéde ToulonCNRSIRDUM 110Marseille 83041France Department of Biological Sciences and Biotechnology Faculty of Science and TechnologyUniversiti Kebangsaan Malaysia43600 UKM BangiSelangor Institut Pasteur Korea Seoul 13488Republic of Korea Faculty of environment and Information Studies Keio UniversityFujisawaKanagawa 252-0882Japan University of Colorado at Boulder CivilEnvironmental and Architectural DepartmentBoulder 80303USA Brooklyn College of the City University of New York Brooklyn 11210USA School of energy and environment City University of Hong KongHong Kong 999077China Department of Microbiology Faculty of MedicineJagiellonian UniversityKraków 30-005Poland Biological Targeting Diagnosis and The

Antimicrobial resistance(AMR)poses a critical threat to global health and development,with environmental factors—particularly in urban areas—contributing significantly to the spread of antibiotic resistance genes(ARGs).However,most research to date has been conducted at a local level,leaving significant gaps in our understanding of the global status of antibiotic resistance in urban *** address this issue,we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples,which were collected by the Meta SUB International Consortium involving diverse urban environments in 60 cities of 27 countries,utilizing a deep-learning based *** findings demonstrated the strong geographical specificity of urban environmental resistome,and their correlation with various local socioeconomic and medical *** also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters(BGCs)across different countries,and discovered that the urban environment represents a rich source of novel *** study provides a comprehensive overview of the global urban environmental resistome,and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.

关键词： urban environment metagenome antibiotic resistance resistance diversity biosynthetic gene clusters

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Piezo1 expression in chondrocytes controls endochondral ossification and osteoarthritis development

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Bone Research 2024年第1期12卷 199-214页

作者： Laura J.Brylka Assil-Ramin Alimy Miriam e.A.Tschaffon-Müller Shan Jiang Tobias Malte Ballhause Anke Baranowsky Simon von Kroge Julian Delsmann eva Pawlus Kian eghbalian Klaus Püschel Astrid Schoppa Melanie Haffner-Luntzer David J.Beech Frank Timo Beil michael Amling Johannes Keller Anita Ignatius Timur A.Yorgan Tim Rolvien Thorsten Schinke Department of Osteology and Biomechanics University Medical Center Hamburg-Eppendorf20246 HamburgGermany Department of Trauma and Orthopedic Surgery University Medical Center Hamburg-Eppendorf20246 HamburgGermany Institute of Orthopedic Research and Biomechanics University Medical Center UlmBadenWürttemberg89081 UlmGermany Department Legal Medicine University Medical Center Hamburg-Eppendorf20246 HamburgGermany Leeds Institute of Cardiovascular and Metabolic Medicine School of MedicineUniversity of LeedsLS29JT LeedsUK

Piezo proteins are mechanically activated ion channels,which are required for mechanosensing functions in a variety of cell *** we and others have previously demonstrated that the expression of Piezo1 in osteoblast lineage cells is essential for boneanabolic processes,there was only suggestive evidence indicating a role of Piezo1 and/or Piezo2 in *** we addressed the question if and how chondrocyte expression of the mechanosensitive proteins Piezo1 or Piezo2 controls physiological endochondral ossification and pathological osteoarthritis(OA)*** with chondrocyte-specific inactivation of Piezo1(Piezo1^(Col2a1Cre)),but not of Piezo2,developed a near absence of trabecular bone below the chondrogenic growth plate ***,all Piezo1^(Col2a1Cre) animals displayed multiple fractures of rib bones at 7 days of age,which were located close to the growth *** skeletal growth was only mildly affected in these mice,OA pathologies were markedly less pronounced compared to littermate controls at 60 weeks of ***,when OA was induced by anterior cruciate ligament transection,only the chondrocyte inactivation of Piezo1,not of Piezo2,resulted in attenuated articular cartilage ***,osteophyte formation and maturation were also reduced in Piezo1^(Col2a1Cre) *** further observed increased Piezo1 protein abundance in cartilaginous zones of human ***,we identified Ptgs2 and Ccn2 as potentially relevant Piezo1 downstream genes in ***,our data do not only demonstrate that Piezo1 is a critical regulator of physiological and pathological endochondral ossification processes,but also suggest that Piezo1 antagonists may be established as a novel approach to limit osteophyte formation in OA.

关键词： Piezo1 markedly ossification

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evaluation of ruminal methane and ammonia formation and microbiota composition as affected by supplements based on mixtures of tannins and essential oils using Rusitec

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Journal of Animal Science and Biotechnology 2024年第4期15卷 1607-1622页

作者： Giulia Foggi Melissa Terranova Matteo Daghio Sergej L.Amelchanka Giuseppe Conte Simon Ineichen Monica Agnolucci Carlo Viti Alberto Mantino Arianna Buccioni michael Kreuzer Marcello Mele Department of Agriculture Food and Environment(DAFE)University of Pisa56124 PisaItaly AgroVet‑Strickhof ETH ZurichLindauSwitzerland Department of Agriculture FoodEnvironment and ForestryUniversity of FlorenceFlorence 50144Italy Centro Di Ricerche Agro‑Ambientali“e.Avanzi” University of PisaPisa 56122Italy School of Agricultural Forest and Food Sciences HAFLBern University of Applied SciencesZollikofenSwitzerland Institute of Agricultural Sciences ETH ZurichLindauSwitzerland

Background Dietary supplements based on tannin extracts or essential oil compounds(eOC)have been repeatedly reported as a promising feeding strategy to reduce the environmental impact of ruminant husbandry.A previous batch culture screening of various supplements identified selected mixtures with an enhanced potential to mitigate ruminal methane and ammonia *** these,Q-2(named after quebracho extract and eOC blend 2,composed of carvacrol,thymol,and eugenol)and C-10(chestnut extract and eOC blend 10,consisting of oregano and thyme essential oils and limonene)have been investigated in detail in the present study with the semi-continuous rumen simulation technique(Rusitec)in three independent *** this purpose,Q-2 and C-10,dosed according to the previous study,were compared with a non-supplemented diet(negative control,NC)and with one supplemented with the commercial eOC-based Agolin^(R) Ruminant(positive control,PC).Results From d 5 to 10 of fermentation incubation liquid was collected and analysed for pH,ammonia,protozoa count,and gas *** residues were collected for the determination of ruminal *** d 10,samples of incubation liquid were also characterised for bacterial,archaeal and fungal communities by high-throughput sequencing of 16S rRNA and 26S ribosomal large subunit gene *** of the duration of the fermentation period,Q-2 and C-10 were similarly efficient as PC in mitigating either ammonia(-37%by Q-2,-34%by PC)or methane formation(-12%by C-10,-12%by PC).The PC was also responsible for lower feed degradability and bacterial and fungal richness,whereas Q-2 and C-10 effects,particularly on microbiome diversities,were limited compared to *** All additives showed the potential to mitigate methane or ammonia formation,or both,in vitro over a period of 10 ***,several differences occurred between PC and Q-2/C-10,indicating different mechanisms of *** pronounced defaunation caused by PC a

关键词： Additive Bacteria Continuous culture Degradability Fermentation Fungi Greenhouse gas In vitro Microbiome Rumen

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New Record Ocean Temperatures and Related Climate Indicators in 2023

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Advances in Atmospheric Sciences 2024年第6期41卷 1068-1082页

作者： Lijing CHeNG John ABRAHAM Kevin e.TReNBeRTH Tim BOYeR michael eMANN Jiang ZHU Fan WANG Fujiang YU Ricardo LOCARNINI John FASULLO Fei ZHeNG Yuanlong LI Bin ZHANG Liying WAN Xingrong CHeN Dakui WANG Licheng FeNG Xiangzhou SONG Yulong LIU Franco ReSeGHeTTI Simona SIMONCeLLI Viktor GOUReTSKI Gengxin CHeN Alexey MISHONOV Jim ReAGAN Karina VON SCHUCKMANN Yuying PAN Zhetao TAN Yujing ZHU Wangxu WeI Guancheng LI Qiuping ReN Lijuan CAO Yayang LU International Center for Climate and environment Sciences Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China University of St.Thomas School of EngineeringMinnesota 55105USA NSF National Center for Atmospheric Research BoulderColorado 80307USA University of Auckland Auckland 1010New Zealand National Oceanic and Atmospheric Administration National Centers for Environmental InformationSilver SpringMaryland 20910USA Department of earth and environmental Science University of PennsylvaniaPhiladelphiaPennsylvania 19104USA Institute of Oceanology Chinese Academy of SciencesQingdao 266071China National Marine environmental Forecasting Center Ministry of Natural Resources of ChinaBeijing 100081China Oceanographic Data Center Chinese Academy of SciencesQingdao 266071China College of Oceanography Hohai UniversityNanjing 210098China National Marine Data and Information Service Tianjin 300171China Italian National Agency for New Technologies Energy and Sustainable Economic DevelopmentS.Teresa Research CenterLerici 19032Italy Istituto Nazionale di Geofisica e Vulcanologia Sede di BolognaBologna 40128Italy South China Sea Institute of Oceanology Chinese Academy of SciencesGuangzhou 510301China eSSIC/CISeSS-MD University of MarylandCollege ParkMD20740USA Mercator Ocean International Toulouse 31400France eco-environmental Monitoring and Research Center Pearl River Valley and South China Sea Ecology and Environment AdministrationMinistry of Ecology and EnvironmentPRCGuangzhou 510611China National Meteorological Information Center China Meteorological AdministrationBeijing 100081China International Research Center of Big Data for Sustainable Development Goals Beijing 100094China

The global physical and biogeochemical environment has been substantially altered in response to increased atmospheric greenhouse gases from human *** 2023,the sea surface temperature(SST)and upper 2000 m ocean heat content(OHC)reached record *** 0–2000 m OHC in 2023 exceeded that of 2022 by 15±10 ZJ(1 Zetta Joules=1021 Joules)(updated IAP/CAS data);9±5 ZJ(NCeI/NOAA data).The Tropical Atlantic Ocean,the Mediterranean Sea,and southern oceans recorded their highest OHC observed since the *** with the onset of a strong el Niño,the global SST reached its record high in 2023 with an annual mean of~0.23℃ higher than 2022 and an astounding>0.3℃ above 2022 values for the second half of *** density stratification and spatial temperature inhomogeneity indexes reached their highest values in 2023.

关键词： ocean heat content salinity stratification global warming climate

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