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Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion

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Protein & Cell 2024年第6期15卷 403-418页

作者： Song xue Yuru Han Fan Wu Qiao Wang Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS) Shanghai Institute of Infectious Disease and BiosecurityShanghai Frontiers Science Center of Pathogenic Microorganisms and InfectionSchool of Basic Medical SciencesShanghai Medical CollegeFudan UniversityShanghai 200032China

Intensive selection pressure constrains the evolutionary trajectory of SARS-CoV-2 genomes and results in various novel variants with distinct mutation profiles.Point mutations,particularly those within the receptor binding domain(RBD)of SARS-CoV-2 spike(S)protein,lead to the functional alteration in both receptor engagement and monoclonal antibody(mAb)recognition.Here,we review the data of the RBD point mutations possessed by major SARS-CoV-2 variants and discuss their individual effects on ACE2 affinity and immune evasion.Many single amino acid substitutions within RBD epitopes crucial for the antibody evasion capacity may conversely weaken ACE2 binding affinity.However,this weakened effect could be largely compensated by specific epistatic mutations,such as N501Y,thus maintaining the overall ACE2 affinity for the spike protein of all major variants.The predominant direction of SARS-CoV-2 evolution lies neither in promoting ACE2 affinity nor evading mAb neutralization but in maintaining a delicate balance between these two dimensions.Together,this review interprets how RBD mutations efficiently resist antibody neutralization and meanwhile how the affinity between ACE2 and spike protein is maintained,emphasizing the significance of comprehensive assessment of spike mutations.

关键词： ACE2 affinity maintained

Panoramic variation analysis of a family with neurodevelopmental disorders caused by biallelic loss-of-function variants in TMEM141,DDHD2,and LHFPL5

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Frontiers of Medicine 2024年第1期18卷 81-97页

作者： Liwei Sun xueting Yang Amjad Khan xue Yu Han Zhang Shirui Han Xiaerbati Habulieti Yang Sun Rongrong Wang xue Zhang McKusick-Zhang Center for Genetic Medicine State Key Laboratory for Complex Severe and Rare DiseasesInstitute of Basic Medical Sciences Chinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijing100005China Chongqing Key Laboratory of Human Embryo Engineering Center for Reproductive MedicineNational Key Clinical Speciality Construction Project(Obstetrics and Gynecology)Chongqing Health Center for Women and ChildrenChongqing400013China Chongqing Clinical Research Center for Reproductive Medicine Women and Children’s Hospital of Chongqing Medical UniversityChongqing400013China Faculty of Biological Sciences Department of ZoologyUniversity of Lakki MarwatKhyber Pakhtunkhwa28420Pakistan Institute for Medical Genetics and Applied Genomics University of TübingenTübingen72076Germany Alexander von Humboldt fellowship Foundation Berlin10117Germany Department of Pediatrics The First Affiliated Hospital of Guangxi Medical UniversityNanning530000China Department of Laboratory Medicine State Key Laboratory for Complex Severe and Rare DiseasesPeking Union Medical College HospitalChinese Academy of Medical Science and Peking Union Medical CollegeBeijing100730China

Highly clinical and genetic heterogeneity of neurodevelopmental disorders presents a major challenge in clinical genetics and medicine.Panoramic variation analysis is imperative to analyze the disease phenotypes resulting from multilocus genomic variation.Here,a Pakistani family with parental consanguinity was presented,characterized with severe intellectual disability(ID),spastic paraplegia,and deafness.Homozygosity mapping,integrated single nucleotide polymorphism(SNP)array,whole-exome sequencing,and whole-genome sequencing were performed,and homozygous variants in TMEM141(c.270G>A,p.Trp90^(*)),DDHD2(c.411+767_c.1249-327del),and LHFPL5(c.250delC,p.Leu84^(*))were identified.A Tmem141^(p.Trp90^(*)/p.Trp90^(*))mouse model was generated.Behavioral studies showed impairments in learning ability and motor coordination.Brain slice electrophysiology and Golgi staining demonstrated deficient synaptic plasticity in hippocampal neurons and abnormal dendritic branching in cerebellar Purkinje cells.Transmission electron microscopy showed abnormal mitochondrial morphology.Furthermore,studies on a human in vitro neuronal model(SH-SY5Y cells)with stable shRNA-mediated knockdown of TMEM141 showed deleterious effect on bioenergetic function,possibly explaining the pathogenesis of replicated phenotypes in the cross-species mouse model.Conclusively,panoramic variation analysis revealed that multilocus genomic variations of TMEM141,DDHD2,and LHFPL5 together caused variable phenotypes in patient.Notably,the biallelic loss-of-function variants of TMEM141 were responsible for syndromic ID.

关键词： neurodevelopmental disorder autosomal recessive intellectual disability consanguinity spastic paraplegia hearing loss TMEM141

Comparison of a Spectral Bin and Two Multi-Moment Bulk Microphysics Schemes for Supercell Simulation:Investigation into Key Processes Responsible for Hydrometeor Distributions and Precipitation

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Advances in Atmospheric Sciences 2024年第5期41卷 784-800页

作者： Marcus JOHNSON Ming xue Youngsun JUNG Center for Analysis and Prediction of Storms University of OklahomaNormanOK 73072USA School of Meteorology University of OklahomaNormanOK 73072USA Office of Science and Technology Integration National Weather ServiceSilver SpringMD 20910USA

There are more uncertainties with ice hydrometeor representations and related processes than liquid hydrometeors within microphysics parameterization(MP)schemes because of their complicated geometries and physical properties.Idealized supercell simulations are produced using the WRF model coupled with“full”Hebrew University spectral bin MP(HU-SBM),and NSSL and Thompson bulk MP(BMP)schemes.HU-SBM downdrafts are typically weaker than those of the NSSL and Thompson simulations,accompanied by less rain evaporation.HU-SBM produces more cloud ice(plates),graupel,and hail than the BMPs,yet precipitates less at the surface.The limiting mass bins(and subsequently,particle size)of rimed ice in HU-SBM and slower rimed ice fall speeds lead to smaller melting-level net rimed ice fluxes than those of the BMPs.Aggregation from plates in HU-SBM,together with snow–graupel collisions,leads to a greater snow contribution to rain than those of the BMPs.Replacing HU-SBM’s fall speeds using the formulations of the BMPs after aggregating the discrete bin values to mass mixing ratios and total number concentrations increases net rain and rimed ice fluxes.Still,they are smaller in magnitude than bulk rain,NSSL hail,and Thompson graupel net fluxes near the surface.Conversely,the melting-layer net rimed ice fluxes are reduced when the fall speeds for the NSSL and Thompson simulations are calculated using HU-SBM fall speed formulations after discretizing the bulk particle size distributions(PSDs)into spectral bins.The results highlight precipitation sensitivity to storm dynamics,fall speed,hydrometeor evolution governed by process rates,and MP PSD design.

关键词： precipitation spectral bin microphysics bulk microphysics parameterization microphysics processes WRF model supercell storm

Testing Linearity in Functional Partially Linear Models

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Acta Mathematicae Applicatae Sinica 2024年第3期40卷 875-886页

作者： Fan-rong ZHAO Bao-xue ZHANG School of Mathematical Sciences Shanxi UniversityTaiyuan 030006China School of Statistics Capital University of Economics and BusinessBeijing 100070China

For the functional partially linear models including flexible nonparametric part and functional linear part,the estimators of the nonlinear function and the slope function have been studied in existing literature.How to test the correlation between response and explanatory variables,however,still seems to be missing.Therefore,a test procedure for testing the linearity in the functional partially linear models will be proposed in this paper.A test statistic is constructed based on the existing estimators of the nonlinear and the slope functions.Further,we prove that the approximately asymptotic distribution of the proposed statistic is a chi-squared distribution under some regularity conditions.Finally,some simulation studies and a real data application are presented to demonstrate the performance of the proposed test statistic.

关键词： asymptotic theory functional partially linear model Nadaraya-Watson estimate test statistic

UNCONDITIONAL CONVERGENCE AND ERROR ESTIMATES OF A FULLY DISCRETE FINITE ELEMENT METHOD FOR THE MICROPOLAR NAVIER-STOKES EQUATIONS

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Journal of Computational Mathematics 2024年第1期42卷 71-110页

作者： Shipeng Mao Jiaao Sun Wendong xue NCMIS LSECInstitute of Computational Mathematics and Scientific/Enginnering ComputingAcademy of Mathematics and Systems ScienceChinese Academy of SciencesBeijing 100190China School of Mathematical Sciences University of Chinese Academy of SciencesBeijing 100049China

In this paper,we consider the initial-boundary value problem(IBVP)for the micropolar Naviers-Stokes equations(MNSE)and analyze a first order fully discrete mixed finite element scheme.We first establish some regularity results for the solution of MNSE,which seem to be not available in the literature.Next,we study a semi-implicit time-discrete scheme for the MNSE and prove L2-H1 error estimates for the time discrete solution.Furthermore,certain regularity results for the time discrete solution are establishes rigorously.Based on these regularity results,we prove the unconditional L2-H1 error estimates for the finite element solution of MNSE.Finally,some numerical examples are carried out to demonstrate both accuracy and efficiency of the fully discrete finite element scheme.

关键词： Micropolar fluids Regularity estimates Euler semi-implicit scheme Mixed finite element methods Unconditional convergence

Channel Estimation for Reconfigurable Intelligent Surface Aided Multiuser Millimeter-Wave/THz Systems

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China Communications 2024年第3期21卷 91-103页

作者： Chu Hongyun Pan xue Li Baijiang School of Communications and Information Engineering Xi’an University of Posts and TelecommunicationsXi’an 710121China

It is assumed that reconfigurable intelligent surface(RIS)is a key technology to enable the potential of mmWave communications.The passivity of the RIS makes channel estimation difficult because the channel can only be measured at the transceiver and not at the RIS.In this paper,we propose a novel separate channel estimator via exploiting the cascaded sparsity in the continuously valued angular domain of the cascaded channel for the RIS-enabled millimeter-wave/Tera-Hz systems,i.e.,the two-stage estimation method where the cascaded channel is separated into the base station(BS)-RIS and the RIS-user(UE)ones.Specifically,we first reveal the cascaded sparsity,i.e.,the sparsity exists in the hybrid angular domains of BS-RIS and the RIS-UEs separated channels,to construct the specific sparsity structure for RIS enabled multi-user systems.Then,we formulate the channel estimation problem using atomic norm minimization(ANM)to enhance the proposed sparsity structure in the continuous angular domains,where a low-complexity channel estimator via Alternating Direction Method of Multipliers(ADMM)is proposed.Simulation findings demonstrate that the proposed channel estimator outperforms the current state-of-the-arts in terms of performance.

关键词： atomic norm minimization cascaded channel estimation convex optimization mmWave/THz reconfigurable intelligent surface(RIS) sparsity

Fast Cross-Platform Binary Code Similarity Detection Framework Based on CFGs Taking Advantage of NLP and Inductive GNN

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Chinese Journal of Electronics 2024年第1期33卷 128-138页

作者： Jinxue PENG Yong WANG Jingfeng xue Zhenyan LIU School of Computer Science and Technology Beijing Institute of Technology

Cross-platform binary code similarity detection aims at detecting whether two or more pieces of binary code are similar or not. Existing approaches that combine control flow graphs(CFGs)-based function representation and graph convolutional network(GCN)-based similarity analysis are the best-performing ones. Due to a large amount of convolutional computation and the loss of structural information, the use of convolution networks will inevitably bring problems such as high overhead and sometimes inaccuracy. To address these issues, we propose a fast cross-platform binary code similarity detection framework that takes advantage of natural language processing(NLP)and inductive graph neural network(GNN) for basic blocks embedding and function representation respectively by simulating extracting structural features and temporal features. GNN’s node-centric and small batch is a suitable training way for large CFGs, it can greatly reduce computational overhead. Various NLP basic block embedding models and GNNs are evaluated. Experimental results show that the scheme with long short term memory(LSTM)for basic blocks embedding and inductive learning-based Graph SAGE(GAE) for function representation outperforms the state-of-the-art works. In our framework, we can take only 45% overhead. Improve efficiency significantly with a small performance trade-off.

关键词： Control flow graph Natural language processing Inductive graph neural network Binary code similarity detection

Energy transfer, anticounterfeiting, white light emission and sensing in fine-regulating series of lanthanide metal-organic frameworks

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Journal of Rare Earths 2024年第3期42卷 446-454,I0001页

作者： Juanjuan xue Yao Wang Guoping Yang Yaoyu Wang Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of the Ministry of Education Shaanxi Key Laboratory of Physico-Inorganic ChemistryCollege of Chemistry&Materials ScienceNorthwest UniversityXi'an710127China

Three lanthanide ions and a rigid(1,1'-biphenyl)-2,4,6-tricarboxylic acid(H_(3)bptc) ligand led to the isostructural lanthanide metal-organic frameworks(Ln-MOFs) {[Ln(bptc)(H_(2)O)_(3)]·3H_(2)O}_n(Lnbptc, Ln = Eu,Tb, Gd, Eu_(x)Tb_(1—x), Eu_(x)Gd_(1-x), Tb_(x)Gd_(1-x), and Eu_(0.12)Tb_(0.52)Gd_(0.36)). The density functional theory(DFT) and time-dependent DFT calculation were expanded on H_3bptc, which point to the occurrence of “antenna effect”. The minor diameter samples of Eubptc, Tbbptc, and Gdbptc can also be attained via the microwave synthesis and employed for handwriting anticounterfeiting. Interestingly, the typical red emission of Eu^(3+) and green emission of Tb~(3+) could be fine-tuned by Gd^(3+) via chemical mixing to be full-color emissions bimetallic doped Eu_(x)Tb_(1-x)bptc, Eu_(x)Gd_(1-x)bptc, and Tb_(x)Gd_(1-x)bptc. The above synthetic bimetallic MOFs can be fixed in positioning boxes of quick response(QR) codes with diverse emission for anticounterfeiting. The message can be decoded under the irradiation of 365 nm ultraviolet lamp while invisible in the daylight. Notably, the trimetallic doped Eu_(0.12)Tb_(0.52)Gd_(0.36)bptc emits white light with the CIE color coordinate(0.34, 0.34). Furthermore, Tbbptc is demonstrated to be a sensitive probe toward nitrobenzene and acetone with multiple mechanisms.

关键词： Metal-organic frameworks Anticounterfeiting White light-emitting Sensing Rare earths

Joint Sample Position Based Noise Filtering and Mean Shift Clustering for Imbalanced Classification Learning

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Tsinghua Science and Technology 2024年第1期29卷 216-231页

作者： Lilong Duan Wei xue Jun Huang Xiao Zheng School of Computer Science and Technology Anhui University of TechnologyMaanshan 243032China Institute of Artificial Intelligence Hefei Comprehensive National Science CenterHefei 230088China

The problem of imbalanced data classification learning has received much attention.Conventional classification algorithms are susceptible to data skew to favor majority samples and ignore minority samples.Majority weighted minority oversampling technique(MWMOTE)is an effective approach to solve this problem,however,it may suffer from the shortcomings of inadequate noise filtering and synthesizing the same samples as the original minority data.To this end,we propose an improved MWMOTE method named joint sample position based noise filtering and mean shift clustering(SPMSC)to solve these problems.Firstly,in order to effectively eliminate the effect of noisy samples,SPMsC uses a new noise filtering mechanism to determine whether a minority sample is noisy or not based on its position and distribution relative to the majority sample.Note that MWMOTE may generate duplicate samples,we then employ the mean shift algorithm to cluster minority samples to reduce synthetic replicate samples.Finally,data cleaning is performed on the processed data to further eliminate class overlap.Experiments on extensive benchmark datasets demonstrate the effectiveness of SPMsC compared with other sampling methods.

关键词： imbalanced data classification oversampling noise filtering clustering