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Dissecting the cell microenvironment of ovarian endometrioma through single-cell RNA sequencing

Science China Life Sciences 2025年第1期 116-129页

作者： Jiangpeng Wu Siyu Xia Wenting Ye Yan Sun Jing Cai Fubing Yu Haiping Wen Xiuwei Yi Taikang Li Mingwei Chen Jiayun Chen ge song Chuanbin Yang Yali song Jigang Wang Department of Reproductive Medicine Dongguan Maternal and Child Health Care Hospital Department of Urology and Shenzhen Clinical Research Centre for GeriatricsShenzhen People's HospitalSouthern University of Science and Technology State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs Artemisinin Research Centerand Institute of Chinese Materia MedicaChina Academy of Chinese Medical Sciences Reproductive Medicine Center Foshan Women and Children Hospital State Key Laboratory of Antiviral Drugs School of PharmacyHenan University

Ovarian endometrioma（OE）, also known as “chocolate cysts,” is a cystic mass that develops in the ovaries due to endometriosis and is a common gynecological condition characterized by the growth of endometrial tissue outside the uterus, leading to symptoms such as dysmenorrhea, pelvic pain, and infertility. However, the precise molecular and cellular mechanisms driving this pathophysiology remain largely unknown, posing challenges for diagnosis and treatment. Here, we employed integrated single-cell transcriptomic profiling of over 52,000 individual cells from endometrial tissues of OE patients and healthy donors and identified twelve major cell populations. We identified notable alterations in cell type-specific proportions and molecular signatures associated with OE. Notably, the activation of IGFBP5+macrophages with pro-inflammatory properties, NK cell exhaustion, and aberrant proliferation of IQCG+and KLF2+epithelium are key features and may be the potential mechanisms underlying the pathogenesis of OE. Collectively, our data contribute to a better understanding of OE at the single cell level and may pave the way for the development of novel therapeutic strategies.

关键词： ovary high-throughput sequencing transcriptomics gene expression analysis ligand-receptor analysis

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Hierarchical deep hashing for image retrieval

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Frontiers of Computer Science 2017年第2期11卷 253-265页

作者： ge song Xiaoyang TAN College of Computer Science and Technology Nanjing University of Aeronautics and Astronautics Nanjing 211106 China Collaborative Innovation Center of Novel Software Technology and Industrialization Nanjing 211106 China

We present a new method to generate efficient multi-level hashing codes for image retrieval based on the deep siamese conv01utional neural network （DSCNN）. Con- ventional deep hashing methods trade off the capability of capturing highly complex and nonlinear semantic informa- tion of images against very compact hash codes, usually lead- ing to high retrieval efficiency but with deteriorated accuracy. We alleviate the restrictive compactness requirement of hash codes by extending them to a two-level hierarchical coding scheme, in which the first level aims to capture the high-level semantic information extracted by the deep network using a rich encoding strategy, while the subsequent level squeezes them to more global and compact codes. At running time, we adopt an attention-based mechanism to select some of its most essential bits specific to each query image for retrieval instead of using the full hash codes of the first level. The attention-based mechanism is based on the guides of hash codes generated by the second level, taking advantage of both local and global properties of deep features. Experimental re- suits on various popular datasets demonstrate the advantages of the proposed method compared to several state-of-the-art methods.

关键词： image retrieval deep hashing hierarchical deep hashing

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The Subsurface and Surface Indian Ocean Dipoles and Their Association with ENSO in CMIP6 models

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Advances in Atmospheric Sciences 2023年第6期40卷 975-987页

作者： ge song Rongcai REN State Key Laboratory of Numerical Modeling for Atmospheric Sciences and geophysical Fluid Dynamics(LASG) Institute of Atmospheric PhysicsChinese Academy of SciencesBeijing 100029China Collaborative Innovation Center on Forecast and Evaluation of Meteorological Disasters(CIC-FEMD) Nanjing University of Information Science&TechnologyNanjing 210044China University of Chinese Academy of Sciences Beijing 100049China

This study assesses the reproducibility of 31 historical simulations from 1850 to 2014 in the Coupled Model Intercomparison Project phase 6(CMIP6) for the subsurface(Sub-IOD) and surface Indian Ocean Dipole(IOD) and their association with El Ni?o-Southern Oscillation(ENSO). Most CMIP6 models can reproduce the leading east-west dipole oscillation mode of heat content anomalies in the tropical Indian Ocean(TIO) but largely overestimate the amplitude and the dominant period of the Sub-IOD. Associated with the much steeper west-to-east thermocline tilt of the TIO, the vertical coupling between the Sub-IOD and IOD is overly strong in most CMIP6 models compared to that in the Ocean Reanalysis System 4(ORAS4). Related to this, most models also show a much tighter association of Sub-IOD and IOD events with the canonical ENSO than observations. This explains the more(less) regular Sub-IOD and IOD events in autumn in those models with stronger(weaker) surface-subsurface coupling in TIO. Though all model simulations feature a consistently low bias regarding the percentage of the winter–spring Sub-IOD events co-occurring with a Central Pacific(CP) ENSO, the linkage between a westward-centered CP-ENSO and the Sub-IOD that occurs in winter–spring, independent of the IOD, is well reproduced.

关键词： CMIP6 subsurface Indian Ocean Dipole surface Indian Ocean Dipole El Niño-Southern Oscillation

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The Puzzle of Rice Domestication

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Journal of Integrative Plant Biology 2007年第6期49卷 760-768页

作者： Tao Sang song ge Department of Plant Biology Michigan State University East Lansing MI 48824 USA State Key Laboratory of Systematic and Evolutionary Botany the Institute of Botany the Chinese Academy of Sciences Beijing 100093 China

The origin of cultivated rice has puzzled plant biologists for decades. This is due, at least in part, to the complex evolutionary dynamics in rice cultivars and wild progenitors, particularly rapid adaptive differentiation and continuous gene flow within and between cultivated and wild rice. The long-standing controversy over single versus multiple and annual versus perennial origins of cultivated rice has been brought into shaper focus with the rapid accumulation of genetic and phylogenetic data. Molecular phylogenetic analyses revealed ancient genomic differentiation between rice cultivars, suggesting that they were domesticated from divergent wild populations. However, the recently cloned domestication gene sh4, responsible for the reduction of grain shattering from wild to cultivated rice, seems to have originated only once. Herein, we propose two models to reconcile apparently conflicting evidence regarding rice domestication. The snowoballing model considers a single origin of cultivated rice. In this model, a core of critical domestication alleles was fixed in the founding cultivar and then acted to increase the genetic diversity of cultivars through hybridization with wild populations. The combination model considers multiple origins of cultivated rice. In this model, Initial cultivars were domesticated from divergent wild populations and fixed different sets of domestication alleles. Subsequent crosses among these semi-domesticated cultivars resulted in the fixation of a similar set of critical domestication alleles in the contemporary cultivars. In both models, introgression has played an important role in rice domestication. Recent and future introgression of beneficial genes from the wild gene pool through conventional and molecular breeding programs can be viewed as the continuation of domestication.

关键词： Oryza sativa Oryza rufipogon Oryza nivara phylogeny population genetics QTL shattering sh4.

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Evolution of genes and genomes in the genomics era

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Science China(Life Sciences) 2020年第4期63卷 602-605页

作者： song ge Ya-Long Guo State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of Sciences100093 BeijingChina University of Chinese Academy of Sciences 100049 BeijingChina

During recent decades,we have witnessed substantial technological advances and revolutions in DNA *** range and scope of DNA sequencing applications has expanded tremendously,which have impacted all the disciplines of life sciences and even beyond(Shendure et al.,2017).The low-cost,high-throughput sequencing has brought vast new molecular and genomic data from both model and non-model organisms,and enables us to study the patterns and processes of evolution and the mechanisms underlying in an unprecedented scale and *** particular,genomic data plus sophisticated computational techniques and molecular biology have been combined in the dimension of evolution.

关键词： expanded enable Evolution

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Evolutionary History and Complementary Selective Relaxation of the Duplicated PI genes in Grasses

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Journal of Integrative Plant Biology 2011年第8期53卷 682-693页

作者： Ruo-Xun Wei song ge State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany the Chinese Academy of Sciences Beijing 100093 China Graduate University of the Chinese Academy of Sciences Beijing 100049 China

gene duplication plays an important role in the evolution of organisms by allowing functional innovation and the divergence of duplicate genes. Previous studies found two PI-like genes in grass species, sug- gesting functional divergence between the paralogous copies. Here, we reconstructed the evolutionary history of two PI genes from major lineages of grasses and other monocot species, and demonstrated that two PI genes （PI1 and PI2） arose from a whole genome duplication that occurred in a common ancestor of extant grasses. Molecular evolutionary analyses at the family and tribal levels found strong purifying selection acting on two genes in grasses, consistent with the conserved class B function of the PI genes. Importantly, we detected different patterns of selective relaxation between the duplicated PI genes although no signature of positive selection was found. Likelihood ratio tests revealed that the ω ratio for M domain is significantly higher in PI1 than in PI2 but that for K domain is significantly higher in PI2 than in PI1. These findings imply that complementary selective relaxation occurs in two PI genes after duplication, and provide additional molecular evidence for the subfunctionalization of the duplicated PI genes in grasses.

关键词： evolution selective relaxation duplication PI genes grasses.

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Guaranteeing Wireless Communication Reliability via an Extended Hybrid Carrier System

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China Communications 2023年第7期20卷 192-202页

作者： ge song Xiaojie Fang Xuejun Sha School of Electronics and Information Engineering Harbin Institute of TechnologyHarbin 150001China Engineering Research Center for Dedicated Communication System Ministry of EducationHarbin 150080China

In this paper,we propose an extended hybrid carrier system based on the weighted fractional Fourier transform to ensure the reliability of wireless *** proposed scheme improves the dispersion and compensation capabilities of the hybrid carrier system for channel fading through the design of the signal power distribution,which has greatly reduced the probability of high-power distortion of the signal and improved the bit error rate performance as a *** analysis has shown the superiority of the extended hybrid carrier *** a lower cost of computational complexity increment,the proposed scheme obtains a performance improvement without occupying additional time-frequency physical *** with the existing hybrid carrier scheme,numerical simulation results have shown that the proposed extended hybrid carrier scheme has better anti-fading performance under the doubly-selective channel and improves the reliability of the wireless communication system effectively.

关键词： extended hybrid carrier weighted frac-tional Fourier transform bit error rate doubly-selective channel

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genetic and geographic Patterns of Duplicate DPL genes Causing genetic Incompatibility Within Rice:Implications for Multiple Domestication Events in Rice

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Rice science 2021年第1期28卷 58-68页

作者： Xu Xun ge song Zhang Fumin State Key Laboratory of Systematic and Evolutionary Botany Institute of BotanyChinese Academy of SciencesBeijing 100093China University of Chinese Academy of Sciences Beijing 100049China

Strong genetic incompatibilities exist between two primary rice subspecies,indica and ***,the wild ancestors of rice,*** Sharma et Shastry and *** Griff.,are genetically *** this genetic incompatibility became established has not been clearly *** provide insights into the process,we analyzed a pair of hybrid sterility genes in rice,DOPPELGANgeR 1(DPL1)and DOPPELGANgeR 2(DPL2).Either of the two loci can have one defective allele(DPL1-and DPL2-).Hybrid pollen carrying both DPL1-and DPL2-alleles is *** explore the origination of DPL1-and DPL2-,we sequenced the DPL1 and DPL2 genes of 811 individual plants,including Oryza sativa(132),***(296)and ***(383).We then obtained 20 DPL1 and 34 DPL2 sequences of *** from online *** these sequences,we analyzed the genetic and geographic distribution patterns of DPL genes in modern rice and its wild *** with the ancestral populations,DPL1-and DPL2-showed reduced diversity but increased frequency in modern *** speculated that the diversity reduction was due to a historic genetic bottleneck,and the frequency had likely increased because the defective alleles were preferred following this artificial *** results indicated that standing variances in ancestral lines can lead to severe incompatibilities among *** analysis indicated that the DPL1-haplotype of rice emerged from an *** population in India,whereas the DPL2-haplotype emerged from *** in South ***,the evolutionary history of DPLs conforms to the presumed multiple domestication events of modern rice.

关键词： rice DPL gene domestication genetic incompatibility phylogeography

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The Extended Hybrid Carrier-Based Multiple Access Technology for High Mobility Scenarios

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China Communications 2024年第1期21卷 53-68页

作者： ge song Xiaojie Fang Xuejun Sha School of Electronics and Information Engineering Harbin Institute of TechnologyHarbin 150001China

The hybrid carrier(HC)system rooted in the carrier fusion concept is gradually garnering *** this paper,we study the extended hybrid carrier(EHC)multiple access scheme to ensure reliable wireless *** employing the EHC modulation,a power layered multiplexing framework is realized,which exhibits enhanced interference suppression capability owing to the more uniform energy distribution *** implementation method and advantage mechanism are explicated respectively for the uplink and downlink,and the performance analysis under varying channel conditions is *** addition,considering the connectivity demand,we explore the non-orthogonal multiple access(NOMA)method of the EHC system and develop the EHC sparse code multiple access *** proposed scheme melds the energy spread superiority of EHC with the access capacity of NOMA,facilitating superior support for massive connectivity in high mobility *** results have verified the feasibility and advantages of the proposed *** with existing HC multiple access schemes,the proposed scheme exhibits robust bit error rate performance and can better guarantee multiple access performance in complex scenarios of nextgeneration communications.

关键词： extended hybrid carrier system high mo-Received:Jun.09,2023 Revised:Nov.20,2023 Editor:Yuanwei Liu bility communications multiple access

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Updated thoughts on SARS-CoV-2 and coronavirus therapies,fighting and surviving

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BIOCELL 2020年第2期44卷 127-135页

作者： WENJUAN LI ge song Department of Immunology and Microbiology The Scripps Research InstituteLa JollaUSA

From late December 2019 a new human-adapted coronavirus,SARS-CoV-2,was observed and isolated in clustered patients in Wuhan,*** has been proved to be able to transmit human-to-human and cause pneumonia,leading to about 2%*** genome characteristics,immune responses and related potential treatments,such as chemical drugs,serum transfusion and vaccines including DNA vaccines,are discussed in this review for a brief summary.

关键词： SARS-CoV2 Cellular mechanism Therapies Antibody Vaccine

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