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APIR:Aggregating Universal Proteomics Database Search Algorithms for Peptide Identification with FDR Control

Genomics, Proteomics & Bioinformatics 2024年第2期22卷 171-187页

作者： Yiling Elaine Chen Xinzhou Ge Kyla Woyshner MeiLu McDermott Antigoni Manousopoulou Scott B.Ficarro Jarrod A.Marto Kexin Li leo david wang Jingyi Jessica Li Department of Statistics and Data Science University of CaliforniaLos AngelesCA 90095USA Department of Immuno-Oncology Beckman Research InstituteCity of Hope National Medical CenterDuarteCA 91010USA Department of Quantitative and Computational Biology University of Southern CaliforniaLos AngelesCA 90089USA Department of Cancer Biology and Blais Proteomics Center Dana-Farber Cancer InstituteDepartment of PathologyBrigham and Women’s Hospital and Harvard Medical SchoolBostonMA 02215USA Department of Pediatrics City of Hope National Medical CenterDuarteCA 91010USA Bioinformatics Interdepartmental Program University of CaliforniaLos AngelesCA 90095USA Department of Human Genetics University of CaliforniaLos AngelesCA 90095USA Department of Computational Medicine University of CaliforniaLos AngelesCA 90095USA Department of Biostatistics University of CaliforniaLos AngelesCA 90095USA

Advances in mass spectrometry(MS)have enabled high-throughput analysis of proteomes in biological *** state-of-the-art MS data analysis relies on database search algorithms to quantify proteins by identifying peptide–spectrum matches(PSMs),which convert mass spectra to peptide *** database search algorithms use distinct search strategies and thus may identify unique ***,no existing approaches can aggregate all user-specified database search algorithms with a guaranteed increase in the number of identified peptides and a control on the false discovery rate(FDR).To fill in this gap,we proposed a statistical framework,Aggregation of Peptide Identification Results(APIR),that is universally compatible with all database search ***,under an FDR threshold,APIR is guaranteed to identify at least as many,if not more,peptides as individual database search algorithms *** of APIR on a complex proteomics standard dataset showed that APIR outpowers individual database search algorithms and empirically controls the *** data studies showed that APIR can identify disease-related proteins and post-translational modifications missed by some individual database search *** APIR framework is easily extendable to aggregating discoveries made by multiple algorithms in other high-throughput biomedical data analysis,e.g.,differential gene expression analysis on RNA sequencing *** APIR R package is available at https://***/yiling0210/APIR.

关键词： Shotgun proteomics Peptide–spectrum match Peptide identification Aggregation of lists FDR control

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Crystalline cyclic(alkyl)(amino)stannylene via transient stannyne

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Science China Chemistry 2024年

作者： Xinfeng wang Chaopeng Hu Zhihao Lu Liu leo Liu Department of Chemistry and Research Center for Chemical Biology and Omics Analysis College of Science Southern University of Science and Technology

We demonstrate that a bulky cyclic amino ligand, specifically 1,1,3,3-tetraphenylisoindolinyl, can facilitate the formation of a transient stannyne, endowed with adjacent ambiphilic carbon and tin centers. This stannyne, manifesting carbene-like behavior,engages in an unprecedented sequence of reactions, including Buchner ring expansion, [1,3]sigmatropic, and [1,5]-sigmatropic shifts, culminating in the synthesis of a stable cyclic(alkyl)(amino)stannylene. This compound represents the first tin analogue of the well-known cyclic(alkyl)(amino)carbenes. Both the bonding configuration and the formation process of this stannylene are thoroughly analyzed through quantum chemical computations. Our findings pave the way for further synthesis of unusual main group species using bulky isoindolinyl substituents, emphasizing their potential as a versatile tool in synthetic chemistry.

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Antithetical impacts of deleterious LRP1B mutations in non-squamous and squamous NSCLCs on predicting benefits from immune checkpoint inhibitor alone or with chemotherapy over chemotherapy alone: retrospective analyses of the POPLAR/OAK and CHOICE-01 trial

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Science China Life Sciences 2024年

作者： Jinliang wang Wenyong Zhou Yu Xu Jianchun Duan Qiaoxia Zhou Guoqiang wang leo Li Chunwei Xu Wenxian wang Shangli Cai Zhijie wang Jie wang Department of Oncology The Fifth Medical Center of Chinese PLA General Hospital Department of Thoracic Surgery Shanghai Chest Hospital School of Medicine Shanghai Jiao Tong University Burning Rock Biotech CAMS Key Laboratory of Translational Research on Lung Cancer State Key Laboratory of Molecular Oncology Department of Medical Oncology National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital Chinese Academy of Medical Sciences and Peking Union Medical College Institute of Basic Medicine and Cancer (IBMC) Chinese Academy of Sciences Department of Clinical Trial The Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital)

In non-small cell lung cancers, the non-squamous and squamous subtypes （nsqNSCLC and sqNSCLC） exhibit disparities in pathophysiology,tumor immunology, and potential genomic correlates affecting responses to immune checkpoint inhibitor （ICI）-based treatments. In our inhouse training cohort （n=85）, the presence of the LRP1B deleterious mutation （LRP1B-del） was associated with longer and shorter progression-free survival （PFS） on ICIs alone in nsqNSCLCs and sqNSCLCs, respectively (Pinteraction=0.008). These results were validated using a larger public ICI cohort (n=208, Pinteraction<0.001). Multiplex immunofluorescence staining revealed an association between LRP1B-del and increased and decreased numbers of tumor-infiltrating CD8+T cells in nsqNSCLCs （P=0.040） and sqNSCLCs （P=0.014）, respectively. In the POPLAR/OAK cohort, nsqNSCLCs with LRP1B-del demonstrated improved PFS benefits from atezolizumab over docetaxel (hazard ratio （HR）=0.70, P=0.046), whereas this benefit was negligible in those without LRP1B-del （HR=1.05, P=0.64）. Conversely, sqNSCLCs without LRP1Bdel benefited more from atezolizumab （HR=0.60, P=0.002） than those with LRP1B-del （HR=1.30, P=0.31）. Consistent results were observed in the in-house CHOICE-01 cohort, in which nsqNSCLCs with LRP1B-del and sqNSCLCs without LRP1B-del benefited more from toripalimab plus chemotherapy than from chemotherapy alone (Pinteraction=0.008). This multi-cohort study delineates the antithetical impacts of LRP1Bdel in nsqNSCLCs and sqNSCLCs on predicting the benefits from ICI alone or with chemotherapy over chemotherapy alone. Our findings highlight the distinct clinical utility of LRP1B-del in guiding treatment choices for nsqNSCLCs and sqNSCLCs, emphasizing the necessity for a detailed analysis based on pathological subtypes when investigating biomarkers for cancer therapeutics.

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Joint Beam Scheduling and Power Optimization for Beam Hopping leo Satellite Systems

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China Communications 2024年第10期21卷 226-239页

作者： Zheng Shuang Zhang Xing wang Peng wang Wenbo Key Laboratory of Universal Wireless Communication Ministry of EducationSchool of Information and Communication EngineeringBeijing University of Posts and TelecommunicationsBeijing 100876China

Low earth orbit(leo) satellite communications can provide ubiquitous and reliable services,making it an essential part of the Internet of Everything network. Beam hopping(BH) is an emerging technology for effectively addressing the issue of low resource utilization caused by the non-uniform spatio-temporal distribution of traffic demands. However, how to allocate multi-dimensional resources in a timely and efficient way for the highly dynamic leo satellite systems remains a challenge. This paper proposes a joint beam scheduling and power optimization beam hopping(JBSPO-BH) algorithm considering the differences in the geographic distribution of sink nodes. The JBSPO-BH algorithm decouples the original problem into two sub-problems. The beam scheduling problem is modelled as a potential game,and the Nash equilibrium(NE) point is obtained as the beam scheduling strategy. Moreover, the penalty function interior point method is applied to optimize the power allocation. Simulation results show that the JBSPO-BH algorithm has low time complexity and fast convergence and achieves better performance both in throughput and fairness. Compared with greedybased BH, greedy-based BH with the power optimization, round-robin BH, Max-SINR BH and satellite resource allocation algorithm, the throughput of the proposed algorithm is improved by 44.99%, 20.79%,156.06%, 15.39% and 8.17%, respectively.

关键词： beam hopping interior point method potential game resource allocation

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Superior antibody and membrane protein‑specific T‑cell responses to CoronaVac by intradermal versus intramuscular routes in adolescents

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World Journal of Pediatrics 2024年第4期20卷 353-370页

作者： Jaime S.Rosa Duque Samuel M.S.Cheng Carolyn A.Cohen Daniel Leung Xiwei wang Xiaofeng Mu Yuet Chung Tsun Ming Lau Manni wang Wenyue Zhang Yanmei Zhang Howard H.W.Wong leo C.H.Tsang Sara Chaothai Tsz Chun Kwan John K.C.Li Karl C.K.Chan leo L.H.Luk Jenson C.H.Ho Wing Yan Li Amos M.T.Lee Jennifer H.Y.Lam Sau Man Chan Wilfred H.S.Wong Issan Y.S.Tam Masashi Mori Sophie A.Valkenburg Malik Peiris Wenwei Tu Yu Lung Lau Department of Paediatrics and Adolescent Medicine The University of Hong KongHong KongChina School of Public Health The University of Hong KongHong KongChina HKU‑Pasteur Research Pole School of Public HealthThe University of Hong KongHong KongChina Research Institute for Bioresources and Biotechnology Ishikawa Prefectural UniversityNonoichiJapan Department of Microbiology and Immunology Peter Doherty Institute for Infectionand ImmunityUniversity of MelbourneMelbourneVICAustralia Center for Immunology and Infection C2i Hong KongChina

Background Optimising the immunogenicity of COVID-19 vaccines to improve their protection against disease is *** dosing by intradermal(ID)administration has been shown to be equally immunogenic as intramuscular(IM)administration for several vaccines,but the immunogenicity of ID inactivated whole severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)at the full dose is *** study(NCT04800133)investigated the superiority of antibody and T-cell responses of full-dose CoronaVac by ID over IM administration in *** Participants aged 11–17 years received two doses of IM or ID vaccine,followed by the 3rd dose 13–42 days *** and cellular immunogenicity outcomes were measured post-dose 2(IM-CC versus ID-CC)and post-dose 3(IMCCC versus ID-CCC).Doses 2 and 3 were administered to 173 and 104 adolescents,*** Spike protein(S)immunoglobulin G(IgG),S-receptor-binding domain(RBD)IgG,S IgG Fcγreceptor IIIa(FcγRIIIa)-binding,SNM[sum of individual(S),nucleocapsid protein(N),and membrane protein(M)peptide pool]-specific interleukin-2(IL-2)+CD4^(+),SNM-specific IL-2^(+)CD8^(+),S-specific IL-2^(+)CD8^(+),N-specific IL-2^(+)CD4^(+),N-specific IL-2^(+)CD8^(+)and M-specific IL-2^(+)CD4^(+)responses fulfilled the superior and non-inferior criteria for ID-CC compared to IM-CC,whereas IgG avidity was *** ID-CCC,S-RBD IgG,surrogate virus neutralisation test,90%plaque reduction neutralisation titre(PRNT90),PRNT50,S IgG avidity,S IgG FcγRIIIa-binding,M-specific IL-2^(+)CD4^(+),interferon-γ+CD8^(+)and IL-2^(+)CD8^(+)responses were superior and non-inferior to *** estimated vaccine efficacies were 49%,52%,66%and 79%for IM-CC,ID-CC,IM-CCC and ID-CCC,*** ID groups reported more local,mild adverse *** This is the first study to demonstrate superior antibody and M-specific T-cell responses by ID inactivated SARSCoV-2 vaccination and serves as the basis for future research to improve the

关键词： CoronaVac Coronavirus disease 2019 Immunity Intradermal Vaccine

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Accurately tracking hypersonic gliding vehicles via an leo mega-constellation in relay tracking mode

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Journal of Systems Engineering and Electronics 2024年第1期35卷 211-221页

作者： LI Zhao wang Yidi ZHENG Wei College of Aerospace Science and Engineering National University of Defense TechnologyChangsha 410073China

In order to effectively defend against the threats of the hypersonic gliding vehicles(HGVs),HGVs should be tracked as early as possible,which is beyond the capability of the ground-based *** benefited by the developing megaconstellations in low-Earth orbit,this paper proposes a relay tracking mode to track HGVs to overcome the above *** whole tracking mission is composed of several tracking intervals with the same *** each tracking interval,several appropriate satellites are dispatched to track the *** that are planned to take part in the tracking mission are selected by a new derived observability *** tracking performances of the proposed tracking mode and the other two traditional tracking modes,including the stare and track-rate modes,are compared by *** results show that the relay tracking mode can track the whole trajectory of a HGV,while the stare mode can only provide a very short tracking ***,the relay tracking mode achieve higher tracking accuracy with fewer attitude controls than the track-rate mode.

关键词： target tracking mega-constellation hypersonic gliding vehicle(HGV) sensor selection observability analysis

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Precise orbit determination for low Earth orbit satellites using GNSS:Observations,models,and methods

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Astrodynamics 2024年第3期8卷 349-374页

作者： Xinyuan Mao Wenbing wang Yang Gao Technology and Engineering Center for Space Utilization Chinese Academy of SciencesBeijing100094China University of Chinese Academy of Sciences Beijing101408China

Spaceborne global navigation satellite system(GNSS)has significantly revolutionized the development of autonomous orbit determination techniques for low Earth orbit satellites for *** a state-of-the-art combination of GNSS observations and satellite dynamics,the absolute orbit determination for a single satellite reached a precision of 1 *** orbit determination(i.e.,precise baseline determination)for the dual satellites reached a precision of 1 *** paper reviews the recent advancements in GNSS products,observation processing,satellite gravitational and non-gravitational force modeling,and precise orbit determination *** key aspects have increased the precision of the orbit determination to fulfill the requirements of various scientific ***,recommendations are made to further investigate multi-GNSS combinations,satellite high-fidelity geometric models,geometric offset calibration,and comprehensive orbit determination strategies for satellite constellations.

关键词： low Earth orbit(leo) precise orbit determination(POD) precise baseline determination(PBD) global navigation satellite system(GNSS) multi-GNSS satellite constellation

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Channel Correlation Based User Grouping Algorithm for Nonlinear Precoding Satellite Communication System

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China Communications 2024年第1期21卷 200-214页

作者： Ke wang Baorui Feng Jingui Zhao Wenliang Lin Zhongliang Deng Dongdong wang Yi Cen Genan Wu School of Information and Communication Engineering Beijing University of Posts and TelecommunicationsBeijing 100876China School of Information Engineering Minzu University of ChinaBeijing 100081China Institute of Spacecraft Application System Engineering China Academy of Space TechnologyBeijing 100094China Academy for Network and Communications of CETC Science and Technology on Communication Networks LaboratoryShijiazhuang 050081China

Low Earth Orbit(leo)multibeam satellites will be widely used in the next generation of satellite communication systems,whose inter-beam interference will inevitably limit the performance of the whole *** precoding such as Tomlinson-Harashima precoding(THP)algorithm has been proved to be a promising technology to solve this problem,which has smaller noise amplification effect compared with linear ***,the similarity of different user channels(defined as channel correlation)will degrade the performance of THP *** this paper,we qualitatively analyze the inter-beam interference in the whole process of leo satellite over a specific coverage area,and the impact of channel correlation on Signal-to-Noise Ratio(SNR)of receivers when THP is *** user grouping algorithm is proposed based on the analysis of channel correlation,which could decrease the number of users with high channel correlation in each precoding group,thus improve the performance of ***,our algorithm is designed under the premise of co-frequency deployment and orthogonal frequency division multiplexing(OFDM),which leads to more users under severe inter-beam interference compared to the existing research on geostationary orbit satellites broadcasting *** results show that the proposed user grouping algorithm possesses higher channel capacity and better bit error rate(BER)performance in high SNR conditions relative to existing works.

关键词： channel correlation inter-beam interference multibeam satellite Tomlinson-Harashima precoding user grouping

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Numerical Simulation of the Parallel Gap Resistance Welding Process of a Solar Cell and Mo/Pt/Ag Interconnector

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Transactions of Tianjin University 2024年第5期30卷 419-427页

作者： Xingyu Chen Kai wang Zhicheng Wu Bin Su Xinyu Cui Yuan Huang Zumin wang Institute of Advanced Metallic Materials School of Materials Science and EngineeringTianjin UniversityTianjin 300350China No.18 Research Institute China Electronics Technology Group CorporationTianjin 300350China

Energy for space vehicles in low Earth orbit(leo) is mainly generated by solar arrays, and the service time of the vehicles is controlled by the lifetime of these arrays, which depends mainly on the lifetime of the interconnects. To increase the service life of leo satellites, molybdenum/platinum/silver(Mo/Pt/Ag) laminated metal matrix composite(LMMC) interconnectors are widely used in place of Mo/Ag LMMC and Ag interconnectors in solar arrays. A 2D thermal-electrical-mechanical coupled axisymmetric model was established to simulate the behavior of the parallel gap resistance welding(PGRW) process for solar cells and Mo/Pt/Ag composite interconnectors using the commercial software ANSYS. The direct multicoupled PLANE223 element and the contact pair elements TARGE169 and CONTA172 were employed. A transitional meshing method was applied to solve the meshing problem due to the ultrathin(1 μm) intermediate Pt layer. A comparison of the analysis results with the experimental results revealed that the best parameters were 60 W, 60 ms, and 0.0138 MPa. The voltage and current predicted by the finite element method agreed well with the experimental results. This study contributes to a further understanding of the mechanism of PGRW and provides guidance for finite element simulation of the process of welding with an ultrathin interlayer.

关键词： Solar arrays Parallel gap resistance welding Finite element method Heat transfer coefficient Ultrathin intermediate Pt layer

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The First Verification Test of Space-Ground Collaborative Intelligence via Cloud-Native Satellites

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China Communications 2024年第4期21卷 208-217页

作者： wang Shangguang Zhang Qiyang Xing Ruolin Qi Fei Xu Mengwei State Key Laboratory of Networking and Switching Beijing University of Posts and TelecommunicationsBeijing 100876China Star Network and Intelligent Computing Laboratory Beiyou Shenzhen InstituteShenzhen 518000China Huawei Technologies Co. LtdShenzhen 518129China

Recent advancements in satellite technologies and the declining cost of access to space have led to the emergence of large satellite constellations in Low Earth Orbit(leo).However,these constellations often rely on bent-pipe architecture,resulting in high communication *** onboard inference architectures suffer from limitations in terms of low accuracy and inflexibility in the deployment and management of in-orbit *** address these challenges,we propose a cloud-native-based satellite design specifically tailored for Earth Observation tasks,enabling diverse computing *** this work,we present a case study of a satellite-ground collaborative inference system deployed in the Tiansuan constellation,demonstrating a remarkable 50%accuracy improvement and a substantial 90%data *** work sheds light on in-orbit energy,where in-orbit computing accounts for 17%of the total onboard energy *** approach represents a significant advancement of cloud-native satellite,aiming to enhance the accuracy of in-orbit computing while simultaneously reducing communication cost.

关键词： cloud-native satellite orbital edge computing satellite inference verification test

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