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NeoHunter:Flexible software for systematically detecting neoantigens from sequencing data

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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

Interplant communication:an emerging battlefield in plant-aphid-virus interactions

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Science China(Life Sciences) 2024年第5期67卷 1069-1071页

作者： Yunjing Wang Qian Gong Yule Liu moe key laboratory of bioinformatics and Center for Plant Biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China

Plants constantly face threats from various organisms,including pathogens and *** the pathogens,plant viruses are obligate intracellular parasites that infect plants and cause serious crop yield losses.

关键词： plant Plants communication

Winter-spring minimum temperature variations inferred from tree-ring δ13C in southeastern China

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JOURNAL OF FORESTRY RESEARCH 2024年第1期35卷 1-9页

作者： Li, Wenli Zhou, Feifei Zhang, Heng Fang, keyan Fujian Normal Univ Coll Geog Sci Key Lab Humid Subtrop Ecogeog Proc MOE Fuzhou 350007 Peoples R China

Long-term temperature variations inferred from high-resolution proxies provide an important context to evaluate the intensity of current warming. However, temperature reconstructions in humid southeastern China are scarce and particularly lack long-term data, limiting us to obtain a complete picture of regional temperature evolution. In this study, we present a well-verified reconstruction of winter-spring (January-April) minimum temperatures over southeastern China based on stable carbon isotopic (delta C-13) records of tree rings from Taxus wallichiana var. mairei from 1860 to 2014. This reconstruction accounted for 56.4% of the total observed variance. Cold periods occurred during the 1860s-1910s and 1960s-1970s. Although temperatures have had an upward trend since the 1920s, most of the cold extremes were in recent decades. The El Ni & ntilde;o-Southern Oscillation (ENSO) variance acted as a key modulator of regional winter-spring minimum temperature variability. However, teleconnections between them were a nonlinear process, i.e., a reduced or enhanced ENSO variance may result in a weakened or intensified temperature-ENSO relationship.

关键词： Tree rings Carbon isotope Southeastern China Extreme coldness El nino-southern oscillation NORTHERN-HEMISPHERE TEMPERATURES 2 CENTURIES RECONSTRUCTION PRECIPITATION MILLENNIUM CELLULOSE IMPACT VARIABILITY DIFFERENCE CHRONOLOGY

Injection molding of highly filled microcrystalline cellulose/polycaprolactone composites with the aid of reversible Diels-Alder reaction

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Journal of Materials Science & Technology 2024年第3期170卷 246-254页

作者： Ze Pu Wang WenHong Ruan MinZhi Rong MingQiu Zhang key laboratory for Polymeric Composite and Functional Materials of moe GD HPPC LabIGCMESchool of ChemistrySun Yat-Sen UniversityGuangzhou 510275China

To tackle the challenge of producing highly filled polymer composites using the traditional injection molding technique,which is characterized by the fairly high melt viscosity that makes mold filling difficult,the authors propose a solution based on dynamic covalent *** demonstrated by the proof-of-concept experiments,the 4-arm starshaped polycaprolactone(PCL)oligomers and microcrystalline cel-lulose(MCC)are crosslinked by the reversible Diels-Alder(DA)*** flowability of the compounds greatly decreases due to the dissociation of the intercomponent DA bonds at the retro-reaction tempera-ture,and the networked architecture is reconstructed during cooling as a result of the forward DA ***,the high-loading MCC fillers are well distributed in the matrix and covalently bonded to the nearby PCL,forming a striking contrast to the control in which linear PCL acts as the *** DA bonds crosslinked biodegradable PCL composites exhibit decent mechanical strength(20.7 MPa)even at the MCC fraction of 65 wt%,which is superior to those(5-12.2 MPa)of the highly filled PCL composites(with filler contents of 50-63.8 wt%)reported so *** proposed approach has sufficient expansibility for the fabrication of the highly filled polymer composites constructed by other types of matrix and fillers.

关键词： Polymer composites Microcrystalline cellulose Polycaprolactone Injection molding Dynamic reversible chemistry

A novel and promising engineering application of carbon dots:Enhancing the chloride binding performance of cement

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Chinese Chemical Letters 2024年第6期35卷 409-416页

作者： Wu-Jian Long Yang Yu Chuang He Guangdong Provincial key laboratory of Durability for Marine Civil Engineering Key Lab of Coastal Urban Resilient InfrastructureMOECollege of Civil and Transportation EngineeringShenzhen UniversityShenzhen 518060China

Corrosion of reinforcement induced by chloride invasion is extensively considered as the dominating deterioration mechanism of reinforced concrete(RC)structures,leading to serious safety hazards and tremendous economic ***,it still lacks well dispersive and cost-efficient nanomaterials to improve the anti-chloride-corrosion ability of RC ***,specific carbon dots(CDs)with high dispersity and low cost are deliberately designed,successfully prepared by hydrothermal processing,and then firstly applied to immensely enhance chloride binding performance of cement,thereby contributing to suppressing the corrosion of ***,the tailored CDs are composed of the carbon core with highly crystalline sp^(2)C structures and oxygen-containing groups connecting on the carbon core;The typical equilibrium test confirms that with respect to that of the blank cement paste,the chloride binding capacity of cement paste involving 0.2 wt%(by weight of cement)CDs is increased by 109% after 14-day exposure to 3 mol/L Na Cl solution;according to comprehensive analyses of phase compositions,the chloride binding mechanism of CDs-modified cement is rationally attributed to the fact that the incorporation of CDs advances the formation of calcium silicate hydrate(C-S-H)gels and Friedel's salt(Fs),thus enormously enhancing the physically adsorbed and chemically bound chloride ions of cement *** work not only firstly provides a novel high-dispersity and low-cost nanomaterial toward the durability enhancement of RC structures,but also broadens the application of CDs in the field of engineering,conducing to stimulating their industrialization development.

关键词： Carbon dots Chloride binding Cement Chloride binding mechanism Friedel’s salt

Perspective on new cell-free DNA technologies for early cancer detection

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Cancer Biology & Medicine 2024年第2期21卷 139-143页

作者： Jie Li Xun Lan Department of Basic Medical Sciences School of MedicineTsinghua UniversityBeijing 100084China moe key laboratory of bioinformatics Tsinghua UniversityBeijing 100084China Tsinghua-Peking Joint Center for Life Sciences Tsinghua UniversityBeijing 100084China

High cancer heterogeneity and aggressiveness are major factors contributing to the poor prognosis of patients with advanced cancer~(1-5).Early detection of cancer can significantly improve the prognosis of patients with early-stage cancer after standard *** traditional cancer detection technologies,such as endoscopy for gastrointestinal cancer,mammography for breast cancer。

关键词： prognosis cancer patients

Rearranged 19-nor-7,8-seco-labdane diterpenoids and Diels-Alder cycloadducts from the Chinese liverwort Pallavicinia ambigua:Structural elucidation,photoinduced rearrangement,and cytotoxic activity

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Chinese Chemical Letters 2024年第3期35卷 415-418页

作者： Chunyang Zhang Yuelan Li Zhaojun Chu Shuangzhi Yuan Yanan Qiao Jiaozhen Zhang Lin Li Yueqing Zhang Ruifeng Tian Yajie Tang Hongxiang Lou Department of Natural Products Chemistry Key Lab of Chemical Biology(MOE)School of Pharmaceutical SciencesShandong UniversityJi'nan 250012China State key laboratory of Microbial Technology Shandong UniversityQingdao 266237China

Two distinctive rearranged 19-nor-7,8-seco-labdane diterpenoids(1 and 2)with a novel tetracyclo[5.***.1.0^(2,5.)0^(4,10)]decane skeleton,a derivative of the open tetrahydrofuran ring(7),three dimeric compounds(8-10),and four revised homologs(3-6)were obtained from Chinese liverwort Pallavicinia *** structures were identified via combined analysis of their spectroscopic data,single-crystal X-ray diffraction patterns,and ECD *** light-driven conversion of compound 5 to compounds 1-4 demonstrated that photochemically induced postmodification involved in biosynthesis is an important way to diversify natural structures.A preliminary cytotoxicity assay revealed that compound 5 showed significant inhibition in the human prostate cancer(PC-3)cell line via an apoptotic pathway.

关键词： Liverwort Pallavicinia ambigua 19-nor-7 8-seco-labdan diterpenoid Photoinduced rearrangement Cytotoxic activity

A Review on the Mullins Effect in Tough Elastomers and Gels

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Acta Mechanica Solida Sinica 2024年第2期37卷 181-214页

作者： Lin Zhan Shaoxing Qu Rui Xiao moe key lab of Disaster Forecast and Control in Engineering College of Mechanics and Construction EngineeringJinan UniversityGuangzhou510632China State key laboratory of Fluid Power and Mechatronic System Key Laboratory of Soft Machines and Smart Devices of Zhejiang ProvinceDepartment of Engineering MechanicsZhejiang UniversityHangzhou310027China

Tough elastomers and gels have garnered broad research interest due to their wide-ranging potential ***,during the loading and unloading cycles,a clear stress softening behavior can be observed in many material systems,which is also named as the Mullins *** this work,we aim to provide a complete review of the Mullins effect in soft yet tough materials,specifically focusing on nanocomposite gels,double-network hydrogels,and multi-network *** first revisit the experimental observations for these soft *** then discuss the recent developments of constitutive models,emphasizing novel developments in the damage mechanisms or network *** phenomenological models will also be briefly *** attention is then placed on the anisotropic and multiaxial modeling *** is demonstrated that most of the existing models fail to accurately predict the multiaxial data,posing a significant challenge for developing future anisotropic models tailored for tough gels and elastomers.

关键词： Mullins effect Double-network hydrogels Nanocomposite gels Multi-network elastomers Anisotropic damage model Multiaxial model

A highly sensitive multiple-mode optical thermometer designed in Eu^(2+/3+)and Li^(+)co-doped polymorphism compound LaSc_(3)(BO_(3))_(4)

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Journal of Advanced Ceramics 2024年第6期13卷 821-833页

作者： Nan Yang Zhuo Li Tingxia Zhou Ziwang Zhang Wen Shi Yexiang Tong Jianxin Shi School of Chemistry IGCMESun Yat-sen UniversityGuangzhou 510006China moe of the key laboratory of Bioinorganic and Synthetic Chemistry IGCMEThe Key Lab of Low-Carbon Chemistry&Energy Conservation of Guangdong ProvinceSun Yat-sen UniversityGuangzhou 510006China

Noncontact optical thermometers have attracted widespread attention,but existing problems such as single-mode and low-sensitivity thermometers still urgently need to be ***,a novel multiple-mode thermometer was designed for the polymorphism LaSc_(3)(BO_(3))_(4):Eu^(2+/3+),Li^(+).X-ray diffraction(XRD)patterns revealed a slight transition betweenα-andβ-phases with the concentrations of the dopants,which is further proved by structure refinements and first-principles *** coexistence of Eu^(2+)and Eu^(3+)in the phosphors and their relative percentages were confirmed by X-ray absorption near-edge structure(XANES)*** from appropriate emissions from Eu^(2+)and Eu^(3+)without obvious energy transfer and their opposite changing trends with temperatures under 307 nm excitation,a triple-mode optical thermometer is obtained for this material within the temperature range of 150–450 *** highest sensitivities of 27.65,14.05,and 7.68%·K^(−1)are achieved based on two fluorescence intensity ratio(FIR)modes of Eu^(2+)and Eu^(3+)(5d–4f/^(5)D_(0)–^(7)F_(2,4))and the fluorescence lifetime(FL)mode of Eu^(2+),*** the best of our knowledge,the former is almost the highest in Eu^(2+)and Eu^(3+)co-doped *** results indicate that this material may be used as an excellent multiple-mode optical thermometer.

关键词： phase transition europium(Eu)ions multiple-mode optical thermometer thermal quenching properties fluorescence intensity ratio(FIR) fluorescence lifetime(FL)