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Combining genome-wide association study and transcriptome analysis to identify molecular markers and genetic basis of population-asynchronous ovarian development in Coilia nasus

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Zoological research 2024年第3期45卷 491-505页

作者： Yue Yu Shi-Ming Wan Cheng-You Huang Shuang-Meng Zhang Ai-Li Sun Jun-Qi Liu Shun-Yao Li Yong-Fu Zhu Shu-Xin Gu Ze-Xia Gao College of Fisheries Hubei Hongshan Laboratory/Key Lab of Freshwater Animal BreedingMinistry of Agriculture and Rural Affairs/Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic BeltMinistry of EducationHuazhong Agricultural UniversityWuhanHubei 430070China Laboratory for Marine Biology and Biotechnology Qingdao Marine Science and Technology CenterQingdaoShandong 266237China Wuhan Hengyuxin Technology Breeding Professional Cooperative WuhanHubei 430117China hubei Provincial Aquatic Science research Institute WuhanHubei 430208China Zhenjiang Jiangzhiyuan Fishery Technology Co. Ltd.ZhenjiangJiangsu 212213China

Coilia nasus,a migratory fish species found in the middle and lower reaches of the Yangtze River and along offshore areas of China,possesses considerable aquacultural and economic potential.However,the species faces challenges due to significant variation in the gonadal development rate among females,resulting in inconsistent ovarian maturation times at the population level,an extended reproductive period,and limitations on fish growth rate due to ovarian prematurity.In the present study,we combined genome-wide association study(GWAS)and comparative transcriptome analysis to investigate the potential single nucleotide polymorphisms(SNPs)and candidate genes associated with population-asynchronous ovarian development in C.nasus.Genotyping of the female population based on whole-genome resequencing yielded 2120695 high-quality SNPs,39 of which were suggestively associated with ovarian development.Of note,a significant SNP peak on LG21 containing 30 suggestively associated SNPs was identified,with cpne5a determined as the causal gene of the peak.Therefore,single-marker and haplotype association analyses were performed on cpne5a,revealing four genetic markers(P0.9)significantly associated with the phenotype.Comparative transcriptome analysis of precociously and normally maturing individuals screened out 29 and 426 overlapping differentially expressed genes in the brain and ovary,respectively,between individuals of different body sizes.Integrating the GWAS and transcriptome analysis results,this study identified genes and pathways related to hypothalamic-pituitary-gonadal axis hormone secretion,extracellular matrix,angiogenesis,and gap junctions involved in population-asynchronous ovarian development.The insights gained from this study provide a basis for a deeper understanding of the molecular mechanisms underlying ovarian development in fish and may facilitate the genetic breeding of C.nasus strains exhibiting population-synchronous ovarian development in the future.

关键词： Coilia nasus GWAS Transcriptome Ovarian development SNP

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A data-driven method for feature assessment of historical settlements: A case study of Northeast hubei, China

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Frontiers of Architectural research 2024年第2期13卷 387-405页

作者： Gangyi Tan Zhanxiang Chen Jiangkun Zhu Kai Wang School of Architecture&Urban Planning Huazhong University of Science and TechnologyWuhan 430074China hubei Engineering and Technology research center of Urbanization Wuhan 430074China hubei rural Construction center Wuhan 430074China HUST Built Heritage research center Wuhan 430074China

Formulating criteria for the assessment system of historic settlements is challenging due to complex geographical conditions and evaluator knowledge limitations, leading to subjective bias in the assessment process. To address this issue, this study proposes a data-driven method for assessing the features of historical settlements to carry out scientific and refined assessment and result analysis. Focusing on Northeast hubei as the study area, this paper selects 3 historical settlements for validation and analysis. The results of the study show that (1) the data-driven method expands the methodological chain of assessing historical settlement features, and improves the assessment efficiency and scientificity of the assessment results by applying it to the new assessment process;(2) Through comparing the assessment results of the validation cases and data samples, the study establishes a comprehensive quantitative ranking of the assessment of historical settlement features and identifies the main influencing factors, thus enhancing the precision of result analysis;(3) By comparing the resulting assessment framework with the current assessment system, this study confirms the advantages of the proposed framework in identifying nuanced features and aligning with geographical conditions, thereby verifying the effectiveness of the data-driven method.

关键词： Historical settlement Feature assessment Data-driven method Northeast hubei

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Design of Resilient Sensor Networks Balancing Resilience and Efficiency

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International Journal of Disaster Risk Science 2024年第1期15卷 107-115页

作者： Sergey N.Vecherin Kiril D.Ratmanski Luke Hogewood Igor Linkov Cold Regions research and Engineering Laboratory Engineering Research and Development CenterHanoverNH 03755USA Environmental Laboratory Engineering Research and Development CenterVicksburgMS 39180USA

In recent years,the notion of resilience has been developed and applied in many technical areas,becoming exceptionally pertinent to disaster risk science.During a disaster situation,accurate sensing information is the key to efficient recovery efforts.In general,resilience aims to minimize the impact of disruptions to systems through the fast recovery of critical functionality,but resilient design may require redundancy and could increase costs.In this article,we describe a method based on binary linear programming for sensor network design balancing efficiency with resilience.The application of the developed framework is demonstrated for the case of interior building surveillance utilizing infrared sensors in both twoand three-dimensional spaces.The method provides optimal sensor placement,taking into account critical functionality and a desired level of resilience and considering sensor type and availability.The problem formulation,resilience requirements,and application of the optimization algorithm are described in detail.Analysis of sensor locations with and without resilience requirements shows that resilient configuration requires redundancy in number of sensors and their intelligent placement.Both tasks are successfully solved by the described method,which can be applied to strengthen the resilience of sensor networks by design.The proposed methodology is suitable for large-scale optimization problems with many sensors and extensive coverage areas.

关键词： Binary linear programming Optimal sensor placement Redundant networks Resilience and efciency Resilient sensor networks

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Single transmembrane GPCR modulating proteins:neither single nor simple

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Protein & Cell 2024年第6期15卷 395-402页

作者： Meng Wang Jianjun Lyu Chao Zhang Department of Plastic and Reconstructive Surgery Shanghai Ninth People’s HospitalShanghai Jiao Tong University School of MedicineShanghai 200011China hubei Topgene research Institute of hubei Topgene Biotechnology Co. LtdEast Lake High-Tech Development ZoneWuhan 430205China Fundamental research center Shanghai Yangzhi Rehabilitation Hospital (Shanghai Sunshine Rehabilitation Center)Tongji UniversityShanghai 200092China

The discovery of G-protein coupled receptor(GPCR)accessory proteins has fundamentally redefined the pharmacological concept of GPCR signaling,demonstrating a more complex molecular basis for receptor specificity on the plasma membrane and impressionable downstream intracellular cascades.GPCR accessory proteins not only contribute to the proper folding and trafficking of receptors but also exhibit selectable receptor preferences.

关键词： specificity GPCR neither

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Prevalence of prolonged grief disorder and its symptoms among bereaved individuals in China:a systematic review and meta-analysis

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General Psychiatry 2024年第2期37卷 177-188页

作者： Meng-Di Yuan Jun-Fa Liu Bao-Liang Zhong research center for Psychological and Health Sciences China University of Geosciences(Wuhan)WuhanHubeiChina Department of Psychiatry Wuhan Mental Health CentreWuhanHubeiChina

Background The prevalence of prolonged grief disorder(PGD)and its symptoms among the bereaved population in China vary considerably.Aims This meta-analysis aims to estimate the prevalence of PGD and its symptoms among bereaved individuals in China.Methods We conducted a literature search in major Chinese and English databases from their inception to 4 October 2023,for cross-sectional studies on the prevalence of PGD or its symptoms in bereaved Chinese individuals.The risk of bias of the included studies and certainty of the evidence were assessed using the Joanna Briggs Institute Critical Appraisal Checklist for Studies Reporting Prevalence Data(‘JBI checklist’)and the Grading of Recommendations,Assessment,development and Evaluations(GRADE),respectively.The‘metaprop’package in R V.4.1.2 was used to synthesise the prevalence.Results A total of 28 studies involving 10994 bereaved individuals were included in the analysis,with JBI checklist scores between 3 and 7.The combined prevalence(95%confidence interval)of PGD and its symptoms was 8.9%(4.2%to 17.6%)and 32.4%(18.2%to 50.8%),respectively.PGD and its symptoms were most prevalent among those who had lost their only child(22.7%)and those bereaved by earthquakes(80.4%),respectively.The GRADE system assigned a very low certainty level to the evidence for the pooled prevalence of PGD and its symptoms.Conclusions The pooled prevalence of PGD and its symptoms indicate a potential high need for grief counselling services among bereaved individuals in China.This need is particularly pronounced in those who have lost their only child and those bereaved due to earthquakes.Further methodologically rigorous studies are needed to provide more accurate prevalence estimates.PROSPERO registration number CRD42023432553.

关键词： symptoms prevalence analysis

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Examining the Spatiotemporal Dynamics and Determinants of Land Urbanization in Prefecture-level Cities,China

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Chinese Geographical Science 2024年第1期34卷 19-33页

作者： YANG Zhen ZHU Huxiao ZHANG Xinlin OU Xiangjun School of Geography Geomatics and Planning&Urban-rural Integration Development Research InstituteJiangsu Normal UniversityXuzhou221116China

Examining the spatiotemporal dynamics and determinants of land urbanization is critical for promoting healthy urban development and the rational use of land resources.Based on the dataset consisting of land use change data and selected factors in 2010 and2020,this study used visual analysis to reveal the spatiotemporal dynamics of land urbanization across prefecture-level cities in China.Meanwhile,the driving forces underlying land urbanization were examined by using geographical detector technique.Following are the findings:1)we find that there exist notable spatial variances in land urbanization across prefecture-level cities.Currently,the differentiation in land urbanization between the northern and southern cities is more pronounced than that between the coastal and inland cities,or between the eastern and western cities.Prefecture-level cities located in central and western China have experienced the most rapid growth in land urbanization.Conversely,the growth rate in northeastern China is the lowest,while the velocity in eastern China remains relatively stable.By using spatial autocorrelation analysis,this study reveals that the land urbanization level in prefecture-level cities has significant spatial agglomeration.2)We further find that land urbanization in China is influenced by factors related to urban land supply and demand,and urban population growth,economic growth,land financial and political incentive have greater impact on land urbanization than other factors.3)We also find that the impacts of determinants on China’s land urbanization vary over time,the explanatory power of economic development increased,while the explanatory power of state forces declined.We argue that integrating the supply and demand factors of land urbanization can provide a more comprehensive understanding of the driving mechanisms underlying land urbanization in China and other transitional countries,and help decision-makers in these countries formulate more detailed and specific land urbanization policies.

关键词： land urbanization spatial pattern influencing factor geographical detector China

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Di-and tri-methylation of histone H3K36 play distinct roles in DNA double-strand break repair

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Science China(Life Sciences) 2024年第6期67卷 1089-1105页

作者： Runfa Chen Meng-Jie Zhao Yu-Min Li Ao-Hui Liu Ru-Xin Wang Yu-Chao Mei Xuefeng Chen Hai-Ning Du hubei Key Laboratory of Cell Homeostasis College of Life SciencesTaiKang Center for Life and Medical SciencesFrontier Science Center for Immunology and MetabolismHubei Clinical Research Center of Emergency and ResuscitationEmergency Center of Zhongnan HospitalWuhan UniversityWuhan 430072China hubei Key Laboratory of Cell Homeostasis College of Life SciencesTaiKang Center for Life and Medical SciencesFrontier Science Center for Immunology and MetabolismWuhan UniversityWuhan 430072China

Histone H3 Lys36(H3K36)methylation and its associated modifiers are crucial for DNA double-strand break(DSB)repair,but the mechanism governing whether and how different H3K36 methylation forms impact repair pathways is unclear.Here,we unveil the distinct roles of H3K36 dimethylation(H3K36me2)and H3K36 trimethylation(H3K36me3)in DSB repair via non-homologous end joining(NHEJ)or homologous recombination(HR).Yeast cells lacking H3K36me2 or H3K36me3 exhibit reduced NHEJ or HR efficiency.y Ku70 and Rfa1 bind H3K36me2-or H3K36me3-modified peptides and chromatin,respectively.Disrupting these interactions impairs y Ku70 and Rfa1 recruitment to damaged H3K36me2-or H3K36me3-rich loci,increasing DNA damage sensitivity and decreasing repair efficiency.Conversely,H3K36me2-enriched intergenic regions and H3K36me3-enriched gene bodies independently recruit y Ku70 or Rfa1 under DSB stress.Importantly,human KU70 and RPA1,the homologs of y Ku70 and Rfa1,exclusively associate with H3K36me2 and H3K36me3 in a conserved manner.These findings provide valuable insights into how H3K36me2 and H3K36me3 regulate distinct DSB repair pathways,highlighting H3K36 methylation as a critical element in the choice of DSB repair pathway.

关键词： histone H3K36 methylation Ku70 RPA non-homologous end joining homologous recombination

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MiR-142-3p Regulates ILC1s by Targeting HMGB1 via the NF-κB Pathway in a Mouse Model of Early Pregnancy Loss

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Current Medical Science 2024年第1期44卷 195-211页

作者： Xiang-li PANG Jie LI Jing WANG Si-si YAN Jing YANG Department of Obstetrics and Gynecology Renmin Hospital of Wuhan UniversityWuhan 430060China Reproductive Medical center Renmin Hospital of Wuhan UniversityWuhan 430060China Clinic research center for Assisted Reproductive Technology and Embryonic development in hubei Province Wuhan 430060China

Objective Innate lymphoid cells(ILCs)are a class of newly discovered immunocytes.Group 1 ILCs(ILC1s)are identified in the decidua of humans and mice.High mobility group box 1(HMGB1)is predicted to be one of the target genes of miR-142-3p,which is closely related to pregnancy-related diseases.Furthermore,miR-142-3p and HMGB1 are involved in regulating the NF-κB signaling pathway.This study aimed to examine the regulatory effect of miR-142-3p on ILC1s and the underlying mechanism involving HMGB1 and the NF-κB signaling pathway.Methods Mouse models of normal pregnancy and abortion were constructed,and the alterations of ILC1s,miR-142-3p,ILC1 transcription factor(T-bet),and pro-inflammatory cytokines of ILC1s(TNF-α,IFN-γand IL-2)were detected in mice from different groups.The targeting regulation of HMGB1 by miR-142-3p in ILC1s,and the expression of HMGB1 in normal pregnant mice and abortive mice were investigated.In addition,the regulatory effects of miR-142-3p and HMGB1 on ILC1s were detected in vitro by CCK-8,Annexin-V/PI,ELISA,and RT-PCR,respectively.Furthermore,changes of the NF-κB signaling pathway in ILC1s were examined in the different groups.For the in vivo studies,miR-142-3p-Agomir was injected in the uterus of abortive mice to evaluate the abortion rate and alterations of ILC1s at the maternal-fetal interface,and further detect the expression of HMGB1,pro-inflammatory cytokines,and the NF-κB signaling pathway.Results The number of ILC1s was significantly increased,the level of HMGB1 was significantly upregulated,and that of miR-142-3p was considerably downregulated in the abortive mice as compared with the normal pregnant mice(all P<0.05).In addition,miR-142-3p was found to drastically inhibit the activation of the NF-κB signaling pathway(P<0.05).The number of ILC1s and the levels of pro-inflammatory cytokines were significantly downregulated and the activation of the NF-κB signaling pathway was inhibited in the miR-142-3p Agomir group(all P<0.05).Conclusion miR-142-3p can regulate ILC1s by targeting HMGB1

关键词： maternal-fetal interface group 1 innate lymphoid cells(ILCis) high mobility group box 1(HMGB1) miR-142-3p abortion

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The evolution and functional divergence of 10 Apolipoprotein D-like genes in Nilaparvata lugens

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Insect Science 2024年第1期31卷 91-105页

作者： Jia-Bao Lu Peng-Peng Ren Qiao Li Fang He Zhong-Tian Xu Sai-Nan Wang Jian-Ping Chen Jun-Min Li Chuan-Xi Zhang Citrus research Institute Southwest University/Chinese Academy of Agricultural SciencesNational Engineering Research Center for CitrusChongqingChina Technology center of Wuhan Customs District HubeiChina Institute of Insect Science Zhejiang UniversityHangzhouChina

Apolipoprotein D(ApoD),a member of the lipocalin superfamily of proteins,is involved in lipid transport and stress resistance.Whereas only a single copy of the ApoD gene is found in humans and some other vertebrates,there are typically several ApoD-like genes in insects.To date,there have been relatively few studies that have examined the evolution and functional differentiation of ApoD-like genes in insects,particularly hemi-metabolous insects.In this study,we identified 10 ApoD-like genes(NlApoD1−10)with distinct spatiotemporal expression patterns in Nilaparvata lugens(BPH),which is an important pest of rice.NlApoD1−10 were found to be distributed on 3 chromosomes in a tandem array of NlApoD1/2,NlApoD3−5,and NlApoD7/8,and show sequence and gene structural divergence in the coding regions,indicating that multiple gene duplication events occurred during evolution.Phylogenetic analysis revealed that NlApoD1−10 can be clustered into 5 clades,with NlApoD3−5 and NlApoD7/8 potentially evolving exclusively in the Delphacidae family.Functional screening using an RNA interference approach revealed that only NlApoD2 was essential for BPH development and survival,whereas NlApoD4/5 are highly expressed in testes,and might play roles in reproduction.Moreover,stress response analysis revealed that NlApoD3−5/9,NlApoD3−5,and NlApoD9 were up-regulated after treatment with lipopolysaccharide,H2O2,and ultraviolet-C,respectively,indicating their potential roles in stress resistance.

关键词： Apolipoprotein D BPH evolution functional divergence gene duplication NIApoD

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Problem identification and revitalization strategies for the recovery and reconstruction of traditional villages in the Ms 6.8 Luding Earthquake

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Journal of Mountain Science 2024年第2期21卷 361-379页

作者： HUANG Chao QIU Jian LIU Chun JIANG Rui ZHAO Chuanrong ZHANG Yi School of Architecture and research center of Space Planning and Engineering Design Southwest Jiaotong UniversityChengdu 611756China Sichuan Provincial rural Construction and development center Chengdu 610041China Sichuan Institute of Urban and rural Construction Chengdu 610043China China Association for Promoting Democracy(CAPD)Sichuan Provincial Committee Chengdu 610016China Sichuan Provincial Architectural Design and research Institute(SADI) Chengdu 610095China

Post-disaster reconstruction is a topic of global concern,and traditional villages have special heritage attributes and need to face more requirements and obstacles in post-disaster reconstruction.This paper summarizes four concepts based on the research on post-disaster reconstruction both domestically and internationally,as well as the recovery and reconstruction of cultural heritage.Through a field survey of traditional villages in the Ms 6.8 Luding earthquake-stricken area,it is found that there are problems such as insufficient awareness of heritage value,misalignment of scientific reconstruction technology,and insufficient protection of reconstruction elements during the reconstruction process.Traditional villages face the risk of declining or even loss of heritage value.In order to effectively protect traditional villages and inherit the carrier of regional culture,four targeted reconstruction response strategies are proposed,i.e.,to"establish special planning for traditional village preservation","emphasize recovery of the authenticity of village heritage","ensure elements for village heritage recovery"and"promote the activation and utilization of village heritage",based on the problems discovered during the survey and the four concepts summarized in the research on post-disaster reconstruction of traditional villages.The research results hope to provide useful reference for ancient cultural areas affected by earthquakes on how to protect cultural heritage during the post-disaster reconstruction process.

关键词： Seismic hazard Decision making Traditional village Cultural heritage protection Post-earthquake recovery and reconstruction Revitalization strategy

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