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COSINE:A web server for clonal and subclonal structure inference and evolution in cancer genomics

Zoological Research 2022年第1期43卷 75-77页

作者： Xi-Guo Yuan Yuan Zhao Yang Guo Lin-Mei Ge Wei Liu Shi-Yu Wen Qi Li zhang-bo wan Pei-Na Zheng Tao Guo Zhi-Da Li Martin Peifer Yu-Peng Cun School of Computer Science and Technology Xidian UniversityXi'anShaanxi 710071China iFlora Bioinformatics Center Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of SciencesKunmingYunan 650201China Yuxi Rongjian Information Technology Co. Ltd.YuxiYunan 653100China Center for Molecular Medicine Cologne(CMMC) University of CologneCologne 50931Germany Pediatric Research Institute Ministry of Education Key Laboratory of Child Development and DisordersNational Clinical Research Center for Child Health and DisordersChina International Science and Technology Cooperation Base of Child Development and Critical DisordersChongqing Key Laboratory of Translational Medical Research in Cognitive Development and Learning and Memory DisordersChildren’s Hospital of Chongqing Medical UniversityChongqing 400014China

Cancer cell genomes originate from single-cell mutation with sequential clonal and subclonal expansion of somatic mutation acquisition during pathogenesis,thus exhibiting a Darwinian evolutionary process(Gerstung et al.,2020;Nik-Zainal et al.,2012).Through next-generation sequencing of tumor tissue,this evolutionary process can be characterized by statistical modelling,which can identify the clonal state,somatic mutation order,and evolutionary process(Gerstung et al.,2020;Mcgranahan&Swanton,2017).Inference of clonal and subclonal structure from bulk or single-cell tumor genomic sequencing data has a huge impact on studying cancer *** state and mutation order can provide detailed insight into tumor origin and future *** the past decade,various methods for subclonal reconstruction using bulk tumor sequencing data have been ***,these methods had different programming languages and data input formats,which limited their use and ***,we established a web server for Clonal and Subclonal Structure Inference and Evolution(COSINE)of cancer genomic data,which incorporated twelve popular subclonal reconstruction *** deconstructed each method to provide a detailed workflow of single processing steps with a user-friendly *** the best of our knowledge,this is the first web server providing online subclonal inference based on the integration of most popular subclonal reconstruction *** is freely accessible at ***.

关键词： .net server COSINE

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二氧化碳在环烷烃中的溶解度和体积膨胀

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化学工程 2018年第8期46卷 43-47,53页

作者：郭平张万博葛性波刘旭周小杰西南石油大学油气藏地质及开发工程国家重点实验室四川成都610500 西南石油大学化学化工学院四川成都610500

为研究环烷烃对注CO_2提高采收率效果的影响,利用PVT仪测量了在不同温度、压力条件下CO_2在环己烷(CH)和甲基环己烷(MCH)中的溶解度和在溶解了气体之后环烷烃的体积膨胀系数,并系统讨论了温度、压力、分子结构对溶解度、体积膨胀系数的... 详细信息

为研究环烷烃对注CO_2提高采收率效果的影响,利用PVT仪测量了在不同温度、压力条件下CO_2在环己烷(CH)和甲基环己烷(MCH)中的溶解度和在溶解了气体之后环烷烃的体积膨胀系数,并系统讨论了温度、压力、分子结构对溶解度、体积膨胀系数的影响,使用扩展的Chrastil模型关联了实验数据。研究表明:温度不利于CO_2在环烷烃中的溶解,压力增加溶解度增大。当环己烷上的氢原子被甲基取代后,溶解度略有降低。体积膨胀系数和溶解度随温度、压力、分子结构的变化趋势一致。膨胀系数受到CO_2在环烷烃中溶解度的影响。扩展的Chrastil模型的关联效果较好,最大平均相对误差为2.8%。

关键词：二氧化碳环己烷甲基环己烷溶解度体积膨胀

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SEISMOTECTONIC BACKGROUND AND RECURRENCE INTERVAL OF GREAT EARTHQUAKES IN 1679 SANHE- PINGGU M = 8 EARTHQUAKE AREA

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地震地质 1988年第1期 29-37页

作者： Xiang Hong-fa, Fang Zhong-jing, Xu Jie, Li Ru-cheng Jia San-fa, Hao Shu-jian, wang Jing-bo, and zhang wan-xia(Institute of Geology, State Seismological Bureau)

Basined on comprehensive prospecting and investigation, the authors have ascertained that the 1679 San-he-Pinggu M = 8 earthquake occurred in the intersection region of active faults having deep-seated structural background. The NE-trending New Xiadian Fault, which was characterized by dextrall tensile-shear dislocation, was the seismogenic fault of the 1679 M = 8 earthquake. It is suggested that the macroscopic epicenter of the earthquake should be located in Pangezhuang area, where the vertical displacement of seismic faul’ was up to 3.16m. According to the average seismic slip rate in this area, and the displacement value of earthequake with a certain magnitude, the recurrence interval of M = 7.5, M=7.0 and M = 8.5 earthquakes in the magistoseismic area of 1679 M = 8 earthquake on Xiadian Fault Zone have been estimated to be 3800,1750, and 800 years (the lower limit), respectively.

关键词： Hebei Sanhe-Pinggu earthquake area. Shallow prospecting Seismogenic structure Recurrence intervals of great earthquakes

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黔滇公路二十四道拐的修筑及其历史价值研究

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重庆交通大学学报（自然科学版） 2016年第A1期35卷 79-85页

作者：张勃万宇刘玚邹人倜重庆交通大学马蒂亚斯国际设计学院重庆400074 重庆交通大学交通文化产业研究院重庆400074 重庆交通大学土木工程学院重庆400074 西安市文史馆陕西西安710007

黔滇公路是京滇公路的重要组成部分,它的通车使得中国的东部和西南首次有现代公路相连通。抗日战争期间,黔滇公路是昆明到重庆抗战生命线的重要组成部分,向西连接了滇缅公路、滇越铁路、驼峰航线等国际交通线,向东连接了陪都重庆和前线... 详细信息

黔滇公路是京滇公路的重要组成部分,它的通车使得中国的东部和西南首次有现代公路相连通。抗日战争期间,黔滇公路是昆明到重庆抗战生命线的重要组成部分,向西连接了滇缅公路、滇越铁路、驼峰航线等国际交通线,向东连接了陪都重庆和前线战场。由邹岳生主持设计的二十四道拐是黔滇公路的经典工程,向世界传达了中国人民抗战到底的决心。

关键词：黔滇公路京滇公路二十四道拐抗战生命线

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Gamma-glutamyl transferase 5 overexpression in cerebrovascular endothelial cells improves brain pathology,cognition,and behavior in APP/PS1 mice

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Neural Regeneration Research 2025年第2期20卷 533-547页

作者： Yanli zhang Tian Li Jie Miao Zhina zhang Mingxuan Yang Zhuoran wang bo Yang Jiawei zhang Haiting Li Qiang Su Junhong Guo Department of Neurology First Hospital of Shanxi Medical UniversityTaiyuanShanxi ProvinceChina Department of Neurology Sixth Hospital of Shanxi Medical University(General Hospital of Tisco)TaiyuanShanxi ProvinceChina Department of Physiology Key Laboratory of Cellular PhysiologyMinistry of EducationShanxi Medical UniversityTaiyuanShanxi ProvinceChina Department of Hernia and Abdominal Wall Surgery Shanxi Bethune HospitalShanxi Academy of Medical SciencesTongji Shanxi HospitalThird Hospital of Shanxi Medical UniversityTaiyuanShanxi ProvinceChina Department of Laboratory Medicine of Fenyang College Shanxi Medical UniversityFenyangShanxi ProvinceChina

In patients with Alzheimer’s disease,gamma-glutamyl transferase 5(GGT5)expression has been observed to be downregulated in cerebrovascular endothelial ***,the functional role of GGT5 in the development of Alzheimer’s disease remains *** study aimed to explore the effect of GGT5 on cognitive function and brain pathology in an APP/PS1 mouse model of Alzheimer’s disease,as well as the underlying *** observed a significant reduction in GGT5 expression in two in vitro models of Alzheimer’s disease(Aβ_(1-42)-treated hCMEC/D3 and bEnd.3 cells),as well as in the APP/PS1 mouse ***,injection of APP/PS1 mice with an adeno-associated virus encoding GGT5 enhanced hippocampal synaptic plasticity and mitigated cognitive ***,increasing GGT5 expression in cerebrovascular endothelial cells reduced levels of both soluble and insoluble amyloid-βin the brains of APP/PS1 *** effect may be attributable to inhibition of the expression ofβ-site APP cleaving enzyme 1,which is mediated by nuclear factor-kappa *** findings demonstrate that GGT5 expression in cerebrovascular endothelial cells is inversely associated with Alzheimer’s disease pathogenesis,and that GGT5 upregulation mitigates cognitive deficits in APP/PS1 *** findings suggest that GGT5 expression in cerebrovascular endothelial cells is a potential therapeutic target and biomarker for Alzheimer’s disease.

关键词： Alzheimer’s disease amyloid-β APP/PS1 mice cerebrovascular endothelial cells cognitive deficits gamma-glutamyl transferase 5 neurovascular unit nuclear factor‐kappa B synaptic plasticity β-site APP cleaving enzyme 1

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boosting charge extraction and efficiency of inverted perovskite solar cells through coordinating group modification at the buffer layer/cathode interface

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Nano Research 2025年第1期18卷 415-423页

作者： Zhiqing Liang Ziqiu Ren Ziyu wang Nan Yan Ling Li bo zhang Yanlin Song College of Chemistry Zhengzhou UniversityZhengzhou 450052China Key Laboratory of Applied Surface and Colloid Chemistry Ministry of Education Shaanxi Key Laboratory for Advanced Energy DevicesShaanxi Engineering Lab for Advanced Energy Technology School of Materials Science and EngineeringShaanxi Normal UniversityXi’an 710119China Key Laboratory of Green Printing Institute of ChemistryChinese Academy of Sciences(ICCAS)Beijing Engineering Research Center of Nanomaterials for Green Printing TechnologyNational Laboratory for Molecular Sciences(BNLMS)Beijing 100190China

In inverted perovskite solar cells (PSCs),effective modification of the interface between the metalcathode and electron transport layer (ETL) is crucial forachieving high performance and stability. Herein, sulfonatedbathocuproine, commonly known as disodium bathocuproinedisulfonate (BCDS), was employed as a cathode buffer layerto address the interfacial issues at the [6,6]-phenyl-C61-butyricacid methyl ester (PCBM)/Ag interface. BCDS possesses theability to form coordinate bonds with Ag electrodes. Theutilization of the BCDS buffer layer enhanced the chargeextraction capability at the cathode interface whilesimultaneously achieving interfacial defect passivation,improving interfacial contact and increasing the built-in electricfield. Consequently, a power conversion efficiency (PCE) of25.06% was achieved. Furthermore, owing to the excellent filmforminguniformity of BCDS on PCBM, the stability of thedevice was also improved. After storage in dry air for morethan 2000 h, the device maintained 96% of its initial efficiency. This work underscores the remarkable potential of tailoringcoordination groups to enhance charge extraction efficiency at the ETL-cathode interface, unveiling a promising newfrontier in buffer layer development and performance optimization strategies for PSCs.

关键词： perovskite solar cells buffer layer bathocuproine disulfonate coordination group modification electron transport layer(ETL)-cathode interface

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Loss-of-function mutations of microRNA-142-3p promote ASH1L expression to induce immune evasion and hepatocellular carcinoma progression

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World Journal of Gastroenterology 2025年第1期31卷 126-145页

作者： Xing-Hui Yu Yan Xie Jian Yu Kun-Ning zhang Zhou-bo Guo Di wang Zhao-Xian Li Wei-Qi zhang Yu-Ying Tan Li zhang Wen-Tao Jiang School of Medicine Nankai UniversityTianjin 300192China Tianjin Key Laboratory of Molecular Diagnosis and Treatment of Liver Cancer Tianjin First Center HospitalTianjin 300192China Department of Liver Transplantation Tianjin First Center HospitalTianjin 300192China First Central Clinical School Tianjin Medical UniversityTianjin 300192China

BACKGROUND Hepatocellular carcinoma(HCC)has been a pervasive malignancy throughout the world with elevated *** therapeutic targets are beneficial to treat and predict the ***,the exact molecular mechanisms leading to the progression of HCC are still *** has shown that the microRNA-142-3p level decreases in HCC,whereas bioinformatics analysis of the cancer genome atlas database shows the ASH1L expression increased among liver tumor *** this paper,we will explore the effects and mechanisms of microRNA-142-3p and ASH1L affect the prognosis of HCC patients and HCC cell bioactivity,and the association between *** To investigate the effects and mechanisms of microRNA-142-3p and ASH1L on the HCC cell bioactivity and prognosis of HCC *** In this study,we grouped HCC patients according to their immunohistochemistry results of ASH1L with pathological tissues,and retrospectively analyzed the prognosis of HCC ***,explored the roles and mechanisms of microRNA-142-3p and ASH1L by cellular and animal experiments,which involved the following experimental methods:Immunohistochemical staining,western blot,quantitative real-time-polymerase chain reaction,flow cytometric analysis,tumor xenografts in nude mice,*** statistical methods involved in this study contained t-test,one-way analysis of variance,theχ^(2)test,the Kaplan-Meier approach and the log-rank *** In this study,we found that HCC patients with high expression of ASH1L possess a more recurrence rate as well as a decreased overall survival ***1L promotes the tumorigenicity of HCC and microRNA-142-3p exhibits reduced expression in HCC tissues and interacts with ASH1L through targeting the ASH1L 3′untranslated ***,microRNA-142-3p promotes apoptosis and inhibits proliferation,invasion,and migration of HCC cell lines in vitro via *** the exploration mechanism,we found ASH1L may promote an immunosuppressive mi

关键词： Hepatocellular carcinoma MicroRNA-142-3p ASH1L Immune evasion Tumor immune microenvironment Apoptosis

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Postnatal development of rat retina:a continuous observation and comparison between the organotypic retinal explant model and in vivo development

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Neural Regeneration Research 2025年第3期20卷 900-912页

作者： Baoqi Hu Rui wang Hanyue zhang Xiou wang Sijia Zhou bo Ma Yan Luan Xin wang Xinlin Chen Zhichao zhang Qianyan Kang Department of Ophthalmology The First Affiliated Hospital of Xi’an Jiaotong UniversityXi’anShaanxi ProvinceChina Department of Ophthalmology The First Affiliated Hospital of Northwest UniversityXi’anShaanxi ProvinceChina Institute of Neurobiology Xi’an Jiaotong University Health Science CenterXi’anShaanxi ProvinceChina

The organotypic retinal explant culture has been established for more than a decade and offers a range of unique advantages compared with in vivo experiments and cell ***,the lack of systematic and continuous comparison between in vivo retinal development and the organotypic retinal explant culture makes this model controversial in postnatal retinal development ***,we aimed to verify the feasibility of using this model for postnatal retinal development studies by comparing it with the in vivo *** this study,we showed that postnatal retinal explants undergo normal development,and exhibit a consistent structure and timeline with retinas in ***,we used SOX2 and PAX6 immunostaining to identify retinal progenitor *** then examined cell proliferation and migration by immunostaining with Ki-67 and doublecortin,***-67-and doublecortin-positive cells decreased in both in vivo and explants during postnatal retinogenesis,and exhibited a high degree of similarity in abundance and distribution between ***,we used Ceh-10 homeodomain-containing homolog,glutamate-ammonia ligase(glutamine synthetase),neuronal nuclei,and ionized calcium-binding adapter molecule 1 immunostaining to examine the emergence of bipolar cells,Müller glia,mature neurons,and microglia,*** timing and spatial patterns of the emergence of these cell types were remarkably consistent between in vivo and explant *** study showed that the organotypic retinal explant culture model had a high degree of consistency with the progression of in vivo early postnatal retina *** findings confirm the accuracy and credibility of this model and support its use for long-term,systematic,and continuous observation.

关键词： bipolar cells differentiation in vivo microglia Müller glia organotypic retinal explant culture postnatal retina development proliferation retinal progenitor cells

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Mutual regulation of microglia and astrocytes after Gas6 inhibits spinal cord injury

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Neural Regeneration Research 2025年第2期20卷 557-573页

作者： Jiewen Chen Xiaolin Zeng Le wang Wenwu zhang Gang Li Xing Cheng Peiqiang Su Yong wan Xiang Li Department of Spine Surgery The First Affiliated HospitalSun Yat-sen UniversityGuangzhouGuangdong ProvinceChina Guangdong Province Key Laboratory of Orthopedics and Traumatology GuangzhouGuangdong ProvinceChina

Invasive inflammation and excessive scar formation are the main reasons for the difficulty in repairing nervous tissue after spinal cord *** and astrocytes play key roles in the spinal cord injury micro-environment and share a close ***,the mechanisms involved remain *** this study,we found that after spinal cord injury,resting microglia(M0)were polarized into pro-inflammatory phenotypes(MG1 and MG3),while resting astrocytes were polarized into reactive and scar-forming *** expression of growth arrest-specific 6(Gas6)and its receptor Axl were significantly down-regulated in microglia and astrocytes after spinal cord *** vitro experiments showed that Gas6 had negative effects on the polarization of reactive astrocytes and pro-inflammatory microglia,and even inhibited the cross-regulation between *** further demonstrated that Gas6 can inhibit the polarization of reactive astrocytes by suppressing the activation of the Yes-associated protein signaling ***,in turn,inhibited the polarization of pro-inflammatory microglia by suppressing the activation of the nuclear factor-κB/p65 and Janus kinase/signal transducer and activator of transcription signaling *** vivo experiments showed that Gas6 inhibited the polarization of pro-inflammatory microglia and reactive astrocytes in the injured spinal cord,thereby promoting tissue repair and motor function ***,Gas6 may play a role in the treatment of spinal cord *** can inhibit the inflammatory pathway of microglia and polarization of astrocytes,attenuate the interaction between microglia and astrocytes in the inflammatory microenvironment,and thereby alleviate local inflammation and reduce scar formation in the spinal cord.

关键词： astrocytes Axl cell polarization Gas6 Hippo signal inflammatory micro-environment intercellular interaction microglia single-cell sequencing spinal cord injury

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AAV2-PDE6B restores retinal structure and function in the retinal degeneration 10 mouse model of retinitis pigmentosa by promoting phototransduction and inhibiting apoptosis

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Neural Regeneration Research 2025年第8期20卷 2408-2419页

作者： Ruiqi Qiu Mingzhu Yang Xiuxiu Jin Jingyang Liu Weiping wang Xiaoli zhang Jinfeng Han bo Lei Henan Eye Hospital Henan Provincial People’s HospitalPeople’s Hospital of Zhengzhou UniversityZhengzhouHenan ProvinceChina Eye Institute Henan Academy of Innovations in Medical ScienceZhengzhouHenan ProvinceChina Branch of National Clinical Research Center for Ocular Disease Henan Provincial People’s HospitalZhengzhouHenan ProvinceChina Academy of Medical Science Zhengzhou UniversityZhengzhouHenan ProvinceChina

Retinitis pigmentosa is a group of inherited diseases that lead to retinal degeneration and photoreceptor cell ***,there is no effective treatment for retinitis pigmentosa caused by PDE6B ***-associated virus(AAV)-mediated gene therapy is a promising strategy for treating retinitis *** aim of this study was to explore the molecular mechanisms by which AAV2-PDE6B rescues retinal *** do this,we injected retinal degeneration 10(rd10)mice subretinally with AAV2-PDE6B and assessed the therapeutic effects on retinal function and structure using dark-and light-adapted electroretinogram,optical coherence tomography,and ***-independent acquisition-mass spectrometry-based proteomic analysis was conducted to investigate protein expression levels and pathway enrichment,and the results from this analysis were verified by real-time polymerase chain reaction and western ***2-PDE6B injection significantly upregulated PDE6βexpression,preserved electroretinogram responses,and preserved outer nuclear layer thickness in rd10 *** expressed proteins between wild-type and rd10 mice were closely related to visual perception,and treating rd10 mice with AAV2-PDE6B restored differentially expressed protein expression to levels similar to those seen in wild-type *** Encyclopedia of Genes and Genome analysis showed that the differentially expressed proteins whose expression was most significantly altered by AAV2-PDE6B injection were enriched in phototransduction ***,the phototransductionrelated proteins Pde6α,Rom1,Rho,Aldh1a1,and Rbp1 exhibited opposite expression patterns in rd10 mice with or without AAV2-PDE6B ***,Bax/Bcl-2,p-ERK/ERK,and p-c-Fos/c-Fos expression levels decreased in rd10 mice following AAV2-PDE6B *** data suggest that AAV2-PDE6B-mediated gene therapy promotes phototransduction and inhibits apoptosis by inhibiting the ERK signaling pathway and upr

关键词： apoptosis AAV2-PDE6B ERK1/2 gene therapy phototransduction proteomics rd10 retinitis pigmentosa

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