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NeoHunter:Flexible software for systematically detecting neoantigens from sequencing data

Quantitative Biology 2024年第1期12卷 70-84页

作者： Tianxing ma Zetong Zhao Haochen Li lei Wei Xuegong Zhang MOE Key Lab of Bioinformatics Bioinformatics Division of BNRIST and Department of AutomationTsinghua UniversityBeijingChina School of Medicine Tsinghua UniversityBeijingChina School of Life Sciences Tsinghua UniversityBeijingChina

Complicated molecular alterations in tumors generate various mutant *** of these mutant peptides can be presented to the cell surface and then elicit immune responses,and such mutant peptides are called *** detection of neoantigens could help to design personalized cancer *** some computational frameworks for neoantigen detection have been proposed,most of them can only detect SNV-and indel-derived *** addition,current frameworks adopt oversimplified neoantigen prioritization *** factors hinder the comprehensive and effective detection of *** developed NeoHunter,flexible software to systematically detect and prioritize neoantigens from sequencing data in different *** can detect not only SNV-and indel-derived neoantigens but also gene fusion-and aberrant splicing-derived *** supports both direct and indirect immunogenicity evaluation strategies to prioritize candidate *** strategies utilize binding characteristics,existing biological big data,and T-cell receptor specificity to ensure accurate detection and *** applied NeoHunter to the TESLA dataset,cohorts of melanoma and non-small cell lung cancer *** achieved high performance across the TESLA cancer patients and detected 79%(27 out of 34)of validated neoantigens in ***-and indel-derived neoantigens accounted for 90%of the top 100 candidate neoantigens while neoantigens from aberrant splicing accounted for 9%.Gene fusion-derived neoantigens were detected in one *** is a powerful tool to‘catch all’neoantigens and is available for free academic use on Github(XuegongLab/NeoHunter).

关键词： cancer vaccine molecular alteration neoantigen neoantigen prioritization

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Simulation design of thin film lithium niobate electro-optic modulator with bimetallic layer electrodes

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Optoelectronics Letters 2024年第6期20卷 339-345页

作者： WU Qiulin FENG xinkai CHEN Jiaying ma lei CHEN Huaixi LIANG Wanguo Fujian Institute of Research on the Structure of matter Chinese Academy of SciencesFuzhou 350108China University of Chinese Academy of Sciences Beijing 100059China Fujian Science&Technology Innovation Laboratory for Optoelectronic Information of China Fuzhou 350108China1

Thin-film lithium niobate electro-optical modulator will become the key device in the future optical communication,which has the advantages of high modulation rate,low half-wave voltage,large bandwidth,and easy integration compared with conventional bulk lithium niobate ***,because the electrode gap of the lithium niobate film modulator is very narrow,when the microwave frequency gets higher,it leads to higher microwave loss,and the electro-optical performance of the modulator will be greatly ***,we propose a thin film lithium niobate electro-optic modulator with a bimetallic layer electrode structure to achieve microwave loss less than 8 dB/cm in the range of 200 GHz,exhibiting a voltage-length product of 1.1 V·cm and a 3 dB electro-optic bandwidth greater than 160 ***-speed data transmission test has been performed,showing good performance.

关键词： Simulation design of thin film lithium niobate electro-optic modulator with bimetallic layer electrodes

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Recent advances in Pt catalysts and membrane electrode assemblies fabrication for proton exchange membrane fuel cells

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Rare Metals 2024年第9期43卷 4198-4221页

作者： Miao ma Li-Xiao Shen Jing Liu Bin Xu Yun-Long Zhang lei Zhao Zhen-Bo Wang School of Chemistry and Chemical Engineering Harbin Institute of TechnologyHarbin 150001China College of Environmental and Chemical Engineering Yanshan UniversityQinhuangdao 066004China Unipower Hydrogen Technology(Jiangsu)Corporation Changzhou 213176China

Proton exchange membrane fuel cells(PEMFCs)have been identified as a highly promising means of achieving sustainable energy conversion.A crucial factor in enhancing the performance of PEMFCs for further potential energy applications is the advancement in the field of catalyst engineering that has led to remarkable performance enhancement in facilitating the oxygen reduction reaction(ORR).Subsequently,it is important to acknowledge that the techniques used in preparation of membrane electrode assemblies(MEAs),the vital constituents of PEMFCs,also possess direct and critical influence on exhibiting the full catalytic activity of meticulously crafted ***,a succinct summary of the most recent advancements in Pt catalysts for ORR was offered and their underly catalytic mechanism were ***,both laboratory-scale and industrial-scale MEA fabrication techniques of Pt catalysts were ***,a detailed analysis of the connections between materials,process,and performance in MEA fabrication was presented in order to facilitate the development of optimal catalyst layers.

关键词： Pt catalysts Oxygen reduction reaction Membrane electrode assemblies MEA fabrication techniques

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Single-nucleus transcriptomics uncovers a geroprotective role of YAP in primate gingival aging

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Protein & Cell 2024年第8期15卷 612-632页

作者： Qinchao Hu Bin Zhang Yaobin Jing Shuai ma lei Hu jingyi Li Yandong Zheng Zijuan xin Jianmin Peng Si Wang Bin Cheng Jing Qu Weiqi zhang Guang-Hui Liu Songlin Wang State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Hospital of Stomatology Guanghua School of StomatologyGuangdong Provincial Key Laboratory of StomatologySun Yat-sen UniversityGuangzhou 510060China Salivary Gland Disease Center and Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction Beijing Laboratory of Oral Health and Beijing Stomatological HospitalCapital Medical UniversityBeijing 100050China Department of Biochemistry and Molecular Biology School of Basic Medical SciencesCapital Medical UniversityBeijing 100069China CAS Key Laboratory of Genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Organ Regeneration and Reconstruction Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders Xuanwu Hospital Capital Medical UniversityBeijing 100053China Aging Translational Medicine Center Intermational Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuan Wu HospitalCapital Medical UniversityBeijing 100053China Intemational Center for Aging and Cancer Hainan Medical UniversityHaikou 571199China Aging Biomarker Consortium Beijing 100101China

Aging has a profound impact on the gingiva and significantly increases its susceptibility to periodontitis,a worldwide prevalent inflammatory ***,a systematic characterization and comprehensive understanding of the regulatory mechanism underlying gingival aging is still ***,we systematically dissected the phenotypic characteristics of gingiva during aging in primates and constructed the first single-nucleus transcriptomic landscape of gingival aging,by which a panel of cell type-specific signatures were *** cells were identified as the most affected cell types by aging in the *** analyses pinpointed the crucial role of YAP in epithelial self-renew and homeostasis,which declined during aging in epithelial cells,especially in basal *** decline of YAP activity during aging was confrmed in the human gingival tissues,and downregulation of YAP in human primary gingival keratinocytes recapitulated the major phenotypic defects observed in the aged primate gingiva while overexpression of YAP showed rejuvenation *** work provides an in-depth understanding of gingival aging and serves as a rich resource for developing novel strategies to combat aging-associated gingival diseases,with the ultimate goal of advancing periodontal health and promoting healthy aging.

关键词： single-nucleus RNA-sequencing primate gingiva aging YAP

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Changes of the peripapillary vascular parameters inpremature infants without retinopathy of prematurityusing U-net segmentation

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International Journal of Ophthalmology(English edition) 2024年第8期17卷 1453-1461页

作者： Shuai Liu lei Liu Cui-Xia ma Liu-Hui Huang Bin Li School of Information Science and Technology University of Science and Technology of ChinaHefei 230022Anhui ProvinceChina Zhejiang Lab Hangzhou 311121Zhejiang ProvinceChina Eye Institute Affiliated Hospital of Nantong UniversityMedical School of Nantong UniversityNantong 226006Jiangsu ProvinceChina Anhui Province maternity and Child Health Hospital Maternity and Child Health Hospital Affiliated to Anhui Medical UniversityHefei 230001Anhui ProvinceChina Department of Ophthalmology Tenth People’s Hospital Affiliated with Shanghai Tongji University School of MedicineShanghai 200072China

AIM:To quantitatively assess the changes in mean vascular tortuosity(mVT)and mean vascular width(mVW)around the optic disc and their correlation with gestational age(GA)and birth weight(BW)in premature infants without retinopathy of prematurity(ROP).METHODS:A single-center retrospective study included a total of 133(133 eyes)premature infants[mean corrected gestational age(CGA)43.6wk]without ROP as the premature group and 130(130 eyes)CGA-matched fullterm infants as the control *** peripapillary mVT and mVW were quantitatively measured using computerassisted ***:Premature infants had significantly higher mVT(P=0.0032)and lower mVW(P=0.0086)by 2.68(10^(4) cm^(-3))and 1.85μm,*** analysis with GA showed significant differences(P=0.0244)in mVT between the early preterm and middle to late preterm groups,but the differences between mVW were not significant(P=0.6652).The results of the multiple linear regression model showed a significant negative correlation between GA and BW with mVT after adjusting sex and CGA(P=0.0211 and P=0.0006,respectively).For each day increase in GA at birth,mVT decreased by 0.1281(10^(4) cm^(-3))and for each 1 g increase in BW,mVT decreased by 0.006(10^(4) cm^(-3)).However,GA(P=0.9402)and BW(P=0.7275)were not significantly correlated with ***:Preterm birth significantly affects the peripapillary vascular parameters that indicate higher mVT and narrower mVW in premature infants without *** in these parameters may provide new insights into the pathogenesis of ocular vascular disease.

关键词： premature infants retinopathy of prematurity retinal vessels parameter computer-assisted techniques

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Automatic Generation Control in a Distributed Power Grid Based on Multi-step Reinforcement Learning

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Protection and Control of Modern Power Systems 2024年第4期9卷 39-50页

作者： Wenmeng Zhao Tuo Zeng Zhihong Liu Lihui Xie lei Xi Hui ma the Electric Power Research Institute Southern Power GridGuangzhou 510663China the Heyuan Power Supply Bureau Guang-dong Power Grid Co.Ltd.Heyuan 517000China the College of Electrical Engineering&New Energy China Three Gorges UniversityYichang 443002China the College of Electrical Engineering&New Energy and Hubei Provincial Key Laboratory for Operation and Control of Cascaded Hydropower Station China Three Gorges UniversityYichang 443002China IEEE

The increasing use of renewable energy in the power system results in strong stochastic disturbances and degrades the control performance of the distributed power *** this paper,a novel multi-agent collaborative reinforcement learning algorithm is proposed with automatic optimization,namely,Dyna-DQL,to quickly achieve an optimal coordination solution for the multi-area distributed power *** proposed Dyna framework is combined with double Q-learning to collect and store the environmental *** can iteratively update the agents through buffer replay and real-time *** the environmental data can be fully used to enhance the learning speed of the *** mitigates the negative impact of heavy stochastic disturbances caused by the integration of renewable energy on the control *** are conducted on two different models to validate the effectiveness of the proposed *** results demonstrate that the proposed Dyna-DQL algorithm exhibits superior stability and robustness compared to other reinforcement learning algorithms.

关键词： Automatic generation control Dyna framework distributed power grid multi-agent mod-el-based reinforcement learning

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Achieving an ion-homogenizing and corrosion-resisting interface through nitro-coordination chemistry for stable zinc metal anodes

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Journal of Energy Chemistry 2024年第7期94卷 10-18页

作者： Jizhen Wang Long Jiao Qiaoyun Liu Wei xin Yechen lei Tian Zhang leixin Yang Dengkun Shu Shuo Yang Kaihua Li Chenyang Li Chao Yi Hongyuan Bai Yuchao ma Huan Li Wenjun Zhang Bowen'Cheng schoolof Light Industry Science and Engineering State Key Laboratory of Biobased Fiber Manufacturing TechnologyTianjin Key Laboratory of Pulp and PaperChina Light Industry Key Laboratory of Papermaking and BiorefineryTianjin University of Science&TechnologyTianjin 300457China Department of materials Science and Engineering &Center of Super-Diamond and Advanced FilmsCity University of Hong Kong83 Tat Chee AvenueHong Kong 999077China School of Chemical Engineering and Advanced materials The University of AdelaideAdelaideSA 5005Australia

Suppression of uncontrollable dendrite growth and water-induced side reactions of Zn metal anodes is crucial for achieving long-lasting cycling stability and facilitating the practical implementations of aqueous Zn-metal *** address these challenges,we report in this study a functional nitro-cellulose interfacial layer(NCIL)on the surface of Zn anodes enlightened by a nitro-coordination chemistry *** NCIL exhibits strong zincophilicity and superior coordination capability with Zn^(2+)due to the highly electronegative and highly nucleophilic nature of the nitro functional *** characteristic facilitates a rapid Zn-ion desolvation process and homogeneous Zn plating,effectively preventing H_(2) evolution and dendrite ***,the negatively charged surface of NCIL acts as a shield,repelling SO_(4)^(2-)anions and inhibiting corrosive reactions on the Zn ***,reversible and stable Zn plating/stripping is achieved for over 5100 h at a current density of 1 ma cm^(-2),which is nearly 30 times longer than that of bare Zn ***,the Zn/V_(2)O_(5) full cells with the functional interface layer deliver a high-capacity retention of 80.3%for over 10,000 cycles at 5 A g^(-1).This research offers valuable insights for the rational development of advanced protective interface layers in order to achieve ultra-long-lifeZnmetal batteries.

关键词： Zinc metal anode Nitro-cellulose interfacial layer Coordination capability Dendrite-free deposition Long-term cycling

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Simulation of magnetization process and Faraday effect of magnetic bilayer films

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Chinese Physics B 2024年第9期33卷 590-597页

作者： Sheng Gao An Du lei Zhang Tian-Guang Li Da-Cheng ma Department of Basic and General Studies Shenyang Institute of Science and TechnologyShenyang 110167China College of Science Northeastern UniversityShenyang 110819China National Frontiers Science Center for Industrial Intelligence and Systems Optimization Northeastern UniversityShenyang 110819China Office of Academic Research Shenyang Institute of Science and TechnologyShenyang 110167China State Key Laboratory of Robotics Shenyang Institute of AutomationChinese Academy ofSciencesShenyang 110016China Institutes for Robotics and Intelligent manufacturing Chinese Academy of SciencesShenyang110016China

We described ferromagnetic film and bilayer films composed of two ferromagnetic layers coupled through antiferromagnetic interfacial interaction by classical Heisenberg model and simulated their magnetization state,magnetic permeability,and Faraday effect at zero and finite temperature by using the Landau–Lifshitz–Gilbert(LLG)*** results indicate that in a microwave field with positive circular polarization,the ferromagnetic film has one resonance peak while the bilayer film has two resonance ***,the resonance peak disappears in ferromagnetic film,and only one resonance peak emerges in bilayer film in the negative circularly polarized microwave *** the microwave field’s frequency exceeds the film’s resonance frequency,the Faraday rotation angle of the ferromagnetic film is the greatest,and it decreases when the thickness of the two halves of the bilayer is *** the microwave field’s frequency remains constant,the Faraday rotation angle fluctuates with temperature in the same manner as spontaneous magnetization *** a DC magnetic field is applied in the direction of the anisotropic axis of the film,the Faraday rotation angle varies with the DC magnetic field and shows a similar shape of the hysteresis loop.

关键词： magnetic bilayer films magnetic permeability hysteresis loop Faraday effect Landau–Lifshitz– Gilbert (LLG) equation

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Trauma in The Lonely Soldier

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Journal of Literature and Art Studies 2024年第8期14卷 689-692页

作者： LI De-kun ma Xiao-lei LI xin-yue Undergraduate School National University of Defense TechnologyChangsha 410072China

Benedict is an award-winning novelist and non-fiction writer specializing in social *** non-fiction book The Lonely Soldier reflects the impact of war on violence against *** soldiers are always the victims of violence,before,during,and after serving in the Iraq *** thesis aims to explore their trauma and illuminate the book’s meaning.

关键词： Helen Benedict The Lonely Soldier female soldiers victims of violence meaning of writing

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Knocking down AR promotes osteoblasts to recruit prostate cancer cells by altering exosomal circ-DHPS/miR-214-3p/CCL5 pathway

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Asian Journal of Andrology 2024年第2期26卷 195-204页

作者： Zhao Yang Jia-Qi Chen Tian-Jie Liu Yu-Le Chen Zhen-Kun ma Yi-Zeng Fan Zi-Xi Wang Shan Xu Ke Wang xin-Yang Wang lei Li Hong-Jun Xie Department of Urology The First Affiliated Hospital of Xi'an Jiaotong UniversityXi'an 710061China

Tumor-derived exosomes have been shown to play a key role in organ-specific metastasis,and the androgen receptor regulates prostate cancer(PCa)*** is unclear whether the androgen receptor regulates the recruitment of prostate cancer cells to the bone microenvironment,even bone metastases,through ***,we found that exosomes isolated from PCa cells after knocking down androgen receptor(AR)or enzalutamide treatment can facilitate the migration of prostate cancer cells to *** addition,AR silencing or treatment with the AR antagonist enzalutamide may increase the expression of circular RNA-deoxyhypusine synthase(circ-DHPS)in PCa cells,which can be transported to osteoblasts by ***-DHPS acts as a competitive endogenous RNA(ceRNA)against endogenous miR-214-3p to promote C-C chemokine ligand 5(CCL5)levels in *** the level of CCL5 in osteoblasts could recruit more PCa cells into the bone ***,blocking the circ-DHPS/miR-214-3p/CCL5 signal may decrease exosome-mediated migration of prostate cancer cells to osteoblasts.

关键词： androgen receptor circRNA exosome prostate cancer

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