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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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Understandings of Urban Sustainability in China:a Bibliometric Analysis Using Chinese literatures

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Journal of Geodesy and Geoinformation Science 2024年第1期7卷 105-122页

作者： WU Shuang YUE Yang li Xuesong Department of Urban Informatics School of Architecture and Urban PlanningShenzhen UniversityShenzhen 518060China Shenzhen Key Laboratory of Spatial Smart Sensing and Services Guangdong Key Laboratory for Urban InformaticsShenzhen UniversityShenzhen 518060China.

Cities hold a critical responsibility for achieving the Sustainable Development Goals(SDGs)due to their high population density,extensive resource consumption,and significant economic *** examine the present state of understandings regarding urban sustainability(SDG 11:Sustainable Cities and Communities)within Chinese research communities,this study collected 15950 papers from 1994 to 2022 on the 12 indicators of SDG 11,from the China National Knowledge Infrastructure(CNKI),a hub of Chinese academic papers,that directly relate to *** research topics on SDG 11 were identified for each indicator using bibliometrics analysis *** high-frequency keywords and clusters of keywords over the last three decades reveal that existing studies primarily concentrated on the physical aspects,such as transportation and environment,while there is a lack of consideration of societal *** indicates a limited and biased understanding of the urban sustainability within the Chinese academic ***,it is crucial to prioritize the societal aspects in order to develop a research agenda that further advances urban sustainability.

关键词： urban sustainability SDG 11 bibliometric Chinese research communities

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Non-Blind Image Deblurring via Shear Total Variation Norm

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Wuhan University Journal of Natural Sciences 2024年第3期29卷 219-227页

作者： li Weiyu ZHANG Tao GAO Qiuli School of Microelectronics and Data Science Anhui University of TechnologyMaanshan 243032AnhuiChina

In this paper, we propose a novel shear gradient operator by combining the shear and gradient operators. The shear gradient operator performs well to capture diverse directional information in the image gradient domain. Based on the shear gradient operator, we extend the total variation(TV) norm to the shear total variation(STV) norm by adding two shear gradient terms. Subsequently, we introduce a shear total variation deblurring model. Experimental results are provided to validate the ability of the STV norm to capture the detailed information. Leveraging the Block Circulant with Circulant Blocks(BCCB) structure of the shear gradient matrices, the alternating direction method of multipliers(ADMM) algorithm can be used to solve the proposed model efficiently. Numerous experiments are presented to verify the performance of our algorithm for non-blind image deblurring.

关键词： image deblurring shear total variation(STV)norm alternating direction method of multipliers(ADMM) Block Circulant with Circulant Blocks(BCCB)matrix

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Endoplasmic reticulum-targeted delivery of celastrol and PD-L1 siRNA for reinforcing immunogenic cell death and potentiating cancer immunotherapy

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Acta Pharmaceutica Sinica B 2024年第8期14卷 3643-3660页

作者： Jie Wang Zilong Zhang Yan Zhuo Zhuan Zhang Rongrong Chen li liang Xiaohe Jiang Di Nie Chang liu Zhiwen Zou Xiang li Jiaxin li Bingqi Wang Rui Wang Yong Gan Miaorong Yu School of Pharmacy Shanghai University of Traditional Chinese MedicineShanghai 201203China State Key Laboratory of Drug Research Shanghai Institute of Materia MedicaChinese Academy of SciencesShanghai 201203China Jiangxi Medical College Nanchang UniversityNanchang 330006China School of Pharmacy Nanjing University of Chinese MedicineNanjing 210023China University of Chinese Academy of Sciences Beijing 100049China NMPA Key Laboratory for Quality Research and Evaluation of Pharmaceutical Excipients National Institutes for Food and Drug ControlBeijing 100050China

The prospect of employing chemoimmunotherapy targeted towards the endoplasmic reticulum(ER)presents an opportunity to amplify the synergistic effects of chemotherapy and *** this study,we initially validated celastrol(CEL)as an inducer of immunogenic cell death(ICD)by promoting ER stress and autophagy in colorectal cancer(CRC)***,an ER-targeted strategy was posited,involving the codelivery of CEL with PD-L1 small interfering RNAs(siRNA)using KDEL peptide-modified exosomes derived from milk(KME),to enhance chemoimmunotherapy *** findings demonstrate the efficient transportation of KME to the ER via the Golgi-to-ER *** to their non-targeting counterparts,KME exhibited a significant augmentation of the CEL-induced ICD ***,it facilitated the release of danger signaling molecules(DAMPs),thereby stimulating the antigen-presenting function of dendritic cells and promoting the infiltration of T cells into the ***,the ER-targeted delivery of PD-L1 siRNA resulted in the downregulation of both intracellular and membrane PD-L1 protein expression,consequently fostering the proliferation and activity of CD8^(+)T ***,the ER-targeted formulation exhibited enhanced anti-tumor efficacy and provoked anti-tumor immune responses against orthotopic colorectal tumors in ***,a robust ER-targeted delivery strategy provides an encouraging approach for achieving potent cancer chemoimmunotherapy.

关键词： Chemoimmunotherapy Targeted drug delivery Endoplasmic reticulum Endoplasmic reticulum stress Immunogenic cell death siRNA Chemoimmunotherapy Targeted drug delivery Endoplasmic reticulum Endoplasmic reticulum stress Immunogenic cell death siRNA

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Natural Disaster Risk Monitoring for Immovable Cultural Relics Based on Digital Twin

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Journal of Geodesy and Geoinformation Science 2024年第1期7卷 90-104页

作者： li Bolun DONG Youqiang QIAO Yunfei HOU Miaole WEN Caihuan The International Joint Laboratory of Safety and Energy Conservation for Ancient Buildings Beijing University of Civil Engineering and ArchitectureBeijing 102616China China Cultural Heritage Information and Consulting Center Beijing 100029China Hebei Institute of Geological Surveying and Mapping Langfang 065000China

Natural disaster risk monitoring is an important task for disaster prevention and *** the case of immovable cultural relics,however,the feedback mechanism,risk factors,monitoring logic,and monitoring indicators of natural disaster risk monitoring are *** to achieve intelligent perception and monitoring of natural disaster risk for immovable cultural relics has always been a focus and a challenge for *** on the analysis of the concepts and issues related to the natural disaster risk of immovable cultural relics,this paper proposes a framework for natural disaster risk monitoring for immovable cultural relics based on the digital *** framework focuses on risk monitoring,including the physical entities of natural disaster risk for immovable cultural relics,monitoring indicators,and virtual entity construction.A platform for monitoring the natural disaster risk of immovable cultural relics is *** the Puzhou Ancient City Site as a test bed,the proposed concept can be used for monitoring the natural disaster risk of immovable cultural relics at different scales.

关键词： immovable cultural relics natural disaster risk digital twin risk monitoring

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A Modified Tikhonov Regularization Method for a Cauchy Problem of the Biharmonic Equation

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Journal of Mathematical Research with Applications 2024年第3期44卷 359-386页

作者： Fan YANG Jianming XU Xiaoxiao li School of Science Lanzhou University of Technology

In this paper, the Cauchy problem of biharmonic equation is considered. This problem is ill-posed, i.e., the solution(if exists) does not depend on the measurable data. Firstly, we give the conditional stability result under the a priori bound assumption for the exact ***, a modified Tikhonov regularization method is used to solve this ill-posed *** the a priori and the a posteriori regularization parameter choice rule, the error estimates between the regularization solutions and the exact solution are obtained. Finally, some numerical examples are presented to verify that our method is effective.

关键词： Biharmonic equations inverse problem Cauchy problem Tikhonov regularization method

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Quantitative studies on charcoalification:Physical and chemical changes of charring wood

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Fundamental Research 2024年第1期4卷 113-122页

作者： Gang li linlin Gao Fengwen liu Menghan Qiu Guanghui Dong MOE Key Laboratory of Western China's Environmental Systems College of Earth&Environmental SciencesLanzhou UniversityLanzhou 730000China Institute for Ecological Research and Pollution Control of Plateau Lakes School of Ecology and Environment ScienceYunnan UniversityKunming 650504China

Charcoal is commonly preserved in both natural and artificial sediments,and is intensively used in paleontological,paleoenvironmental,and archaeological studies due to the abundant bio-information it *** biochemical properties of charcoal are also used for paleoclimatic reconstruction;however,the reliability of this approach has been challenged due to a lack of clarity on how physicochemical properties change during the charring process,as well as the temperatures required for *** address this lack,in this study,Qinghai spruce and Chinese pine wood samples from the northeastern Tibetan Plateau were heated at different temperatures and for different lengths of time under restricted oxygen *** reflectance;carbon,nitrogen,and oxygen content;and tracheid morphology were quantified before and after heating to assess changes related to the charring *** charcoal remains were then evaluated to determine the charcoalification temperatures by comparing with the experimental *** minimum temperature required for wood charcoalification was∼300℃,while temperatures recorded by archaeological charcoal were concentrated at 400-500℃.During the charring experiments,the tracheid cell walls gradually homogenized,and tracheid cell wall thickness and lumen area decreased by∼20%.On average,50%mass losses were observed;the carbon and oxygen content(%wt.)approximately changed from 47%to 60%and 48%to 35%respectively,while the nitrogen content(%wt.)fluctuated around 0.2%.The reflectance increased slightly from 0%to 0.5%.We propose that the charcoalification of wood tissue refers to charring(in restricted air)and carbonization(in the almost absence of air)when the wood is exposed to a heat source,which then finally transforms into a black,inert *** quantitative study provided valuable data and a thorough assessment of the process of wood charcoalification,as well as accurately estimated the feasibility of using charcoal phys

关键词： Charcoalification Quantitative study Charcoal formation Archaeological charcoal Tracheid cell wall thickness Reflectance

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Wavelength injection locking actively Q-switched random fiber laser based on random phase-shifted fiber Bragg grating and electro-optic modulator

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Optoelectronics Letters 2024年第3期20卷 135-141页

作者： PAN Honggang ZHANG Bo SONG Dianyou CHEN Zhipan CHEN Chunqi li Rupeng School of Integrated Circuit Science and Engineering Tianjin University of TechnologyTianjin 300384China

In this paper, an actively Q-switched wavelength injection locking random fiber laser(RFL) based on random phase-shifted fiber Bragg grating(RPS-FBG) is proposed, and the performance of the laser is verified by experiments. Within the reflection bandwidth range of RPS-FBG, spanning from 1 549.2 nm to 1 549.9 nm, different laser modes with stable central wavelength and peak power can be selectively chosen by varying the injected light wavelength. The power fluctuation within 1 h is less than 0.1 d Bm, and the central wavelength drift is less than 0.02 nm. When the pump power increases from 90 mW to 300 mW, the pulse width decreases from 3.2 μs to 1.5 μs, and the pulse repetition frequency is 20 kHz. The RFL can reach a stable locking state at the lowest pump power of 100 mW and the lowest injection power of 3 d Bm. When the wavelength is locked, the output pulse is a single pulse. On the contrary, the unlocked output pulse is multi-pulse. The laser has the characteristics of high wavelength tunability in the reflection range of RPS-FBG and it can be an ideal light source in the fields of laser imaging and pulse coding.

关键词： fiber switched modulator

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Thermal decomposition mechanism and kinetics of bastnaesite in suspension roasting process:A comparative study in N2 and air atmospheres

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Journal of Rare Earths 2024年第9期42卷 1809-1816页

作者： Wenbo li Jijia Chen Shaokai Cheng Junyan Sun Xiaolong Zhang School of Resources and Civil Engineering Northeastern University National-Local Joint Engineering Research Center of High-Efficient Exploitation Technology for Refractory Iron Ore Resources

To investigate the thermal decomposition behavior and reaction kinetics of bastnaesite in suspension roasting,the gas and solid products of bastnaesite roasted in N2 and air atmospheres were examined using a gas analyzer,X-ray diffraction（XRD）,scanning electron microscopy（SEM）,and energy dispersive spectrometry（EDS）.Subsequently,the kinetic parameters of bastnaesite in the suspension roasting process were derived and calculated using the isothermal *** results show that the decomposition product of bastnaesite in N2is ***,once the roasting temperature exceeds 600℃,CO is generated in addition to CO2,and all the XRD diffraction peaks of CeOF are shifted to the right,indicating that CO2can oxidize CeOF and lead to the transformation of Ce（Ⅲ） into Ce（Ⅳ）.When roasted in air,the decomposition product CeOF can be completely converted to CeF3 and Ce7O12as it easily ***,the reaction rate of bastnaesite in air is higher than that of N2,and the starting reaction temperature is lower than that of N2.A large number of irregular cracks and holes appear on the surface of solid-phase products following suspension roasting,which are due to the thermal decomposition of bastnaesite that produces CO2as well as the reconstruction of the lattice of the solid-phase *** reaction kinetic model of bastnaesite roasted in N2（temperature range 600-750℃） and air（temperatu re range 500-575℃） confo rms to the A3/2model with the mechanism function G（α）=-ln（1-α）2/3,and the reaction activation energy is 59.78 kj/mol and lnA is 1.65 s-1in *** air,the reaction activation energy is 100.30 kj/mol and lnA is 9.63 s-1.

关键词： Rare earths Bastnaesite Suspension roasting Thermal decomposition mechanism Reaction kinetics

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Effects of nitrogen deposition on the carbon budget and water stress in Central Asia under climate change

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Journal of Arid Land 2024年第8期16卷 1118-1129页

作者： HAN Qifei XU Wei li Chaofan School of Geographical Sciences Nanjing University of Information Science&TechnologyNanjing 210044China

Atmospheric deposition of nitrogen(N)plays a significant role in shaping the structure and functioning of various terrestrial ecosystems ***,the magnitude of N deposition on grassland ecosystems in Central Asia still remains highly *** this study,a multi-data approach was adopted to analyze the distribution and amplitude of N deposition effects in Central Asia from 1979 to 2014 using a process-based denitrification decomposition(DNDC)*** showed that total vegetation carbon(C)in Central Asia was 0.35(±0.09)Pg C/a and the averaged water stress index(WSI)was 0.20(±0.02)for the whole *** N deposition led to an increase in the vegetation C of 65.56(±83.03)Tg C and slightly decreased water stress in Central *** of this study will expand both our understanding and predictive capacity of C characteristics under future increases in N deposition,and also serve as a valuable reference for decision-making regarding water resources management and climate change mitigation in arid and semi-arid areas globally.

关键词： carbon dynamics climate change grassland ecosystems nitrogen deposition water stress index

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