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Inferring the Effects of Protein Variants on Protein-Protein Interactions with Interpretable Transformer Representations

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Research 2024年第2期2023卷 473-489页

作者： Zhe Liu Wei Qian Wenxiang Cai Weichen Song Weidi Wang Dhruba Tara Maharjan Wenhong Cheng Jue Chen Han Wang Dong Xu guan ning lin Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghaiChina Shanghai Key Laboratory of Psychotic Disorders ShanghaiChina School of Information Science and Technology Institute of Computational BiologyNortheast Normal UniversityChangchunChina Department of Electrical Engineering and Computer Science University of MissouriColumbiaMO 65211USA Christopher S.Bond Life Sciences Center University of MissouriColumbiaMO 65211USA

Identifying pathogenetic variants and inferring their impact on protein-protein interactions sheds light on their functional consequences on *** by the availability of experimental data on the consequences of protein interaction,most existing methods focus on building models to predict changes in protein binding ***,we introduced MIPPI,an end-to-end,interpretable transformer-based deep learning model that learns features directly from sequences by leveraging the interaction data from *** was specifically trained to determine the types of variant impact(increasing,decreasing,disrupting,and no effect)on protein-protein *** demonstrate the accuracy of MIPPI and provide interpretation through the analysis of learned attention weights,which exhibit correlations with the amino acids interacting with the ***,we showed the practicality of MIPPI in prioritizing de novo mutations associated with complex neurodevelopmental disorders and the potential to determine the pathogenic and driving ***,we experimentally validated the functional impact of several variants identified in patients with such ***,MIPPI emerges as a versatile,robust,and interpretable model,capable of effectively predicting mutation impacts on protein-protein interactions and facilitating the discovery of clinically actionable variants.

关键词： consequences weights versatile

PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders

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Genomics, Proteomics & Bioinformatics 2019年第4期17卷 453-464页

作者： guan ning lin Sijia Guo Xian Tan Weidi Wang Wei Qian Weichen Song Jingru Wang Shunying Yu Zhen Wang Donghong Cui Han Wang Shanghai Mental Health Center Shanghai Jiao Tong University School of MedicineSchool of Biomedical EngineeringShanghai Jiao Tong UniversityShanghai 200030China Shanghai Key Laboratory of Psychotic Disorders Shanghai 200030China Brain Science and Technology Research Center Shanghai Jiao Tong UniversityShanghai 200030China College of Information Science and Technology Northeast Normal UniversityChangchun 130117China Institution of Computational Biology Northeast Normal UniversityChangchun 130117China

De novo variants(DNVs)are one of the most significant contributors to severe earlyonset genetic disorders such as autism spectrum disorder,intellectual disability,and other developmental and neuropsychiatric(DNP)***,a plethora of DNVs have been identified using next-generation sequencing,and many efforts have been made to understand their impact at the gene ***,there has been little exploration of the effects at the isoform *** brain contains a high level of alternative splicing and regulation,and exhibits a more divergent splicing program than other ***,it is crucial to explore variants at the transcriptional regulation level to better interpret the mechanisms underlying DNP *** facilitate a better usage and improve the isoform-level interpretation of variants,we developed NeuroPsychiatric Mutation Knowledge Base(PsyMuKB).It contains a comprehensive,carefully curated list of DNVs with transcriptional and translational annotations to enable identification of isoformspecific *** allows a flexible search of genes or variants and provides both table-based descriptions and associated visualizations,such as expression,transcript genomic structures,protein interactions,and the mutation sites mapped on the protein *** also provides an easy-to-use web interface,allowing users to rapidly visualize the locations and characteristics of mutations and the expression patterns of the impacted genes and *** thus constitutes a valuable resource for identifying tissue-specific DNVs for further functional studies of related *** is freely accessible at http://***.

关键词： De novo mutation Developmental and neuropsychiatric disorders Database Isoforms Tissue specificity

1.42-fold enhancement of formate selectivity by linker conversion on the Zn-based metal organic framework catalyst

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Journal of Energy Chemistry 2024年第3期90卷 183-190,I0006页

作者： Yayu guan Yuyu Liu Fanghua ning Jin Yi Jiujun Zhang Institute for Sustainable Energy College of SciencesShanghai UniversityShanghai 200444China

Electro-reduction of carbon dioxide(ERCO_(2)) is considered an effective method to alleviate the greenhouse effect and produce value-added *** the dominant selectivity of Zn-based catalysts for formate remains a *** this article,the ZnIn-E_(12) catalyst is successfully prepared by solvent assisted ligand exchange(SALE) method to convert organic ligands,achieving a Faradaic efficiency of 72.28% for formate at-1.26 V ***(V_(RHE)),which is 1.42 times higher than the original *** shows that the successful conversion of organic ligands can transform the catalyst from the original large size polyhedron to cross-linked network of particles with a diameter of about 30 *** increased specific surface area can expose more active sites and facilitate the electrocatalytic conversion of CO_(2) to *** work is expected to provide inspiration for the regulation of formate selectivity and catalyst size in Zn-based catalysts.

关键词： Electrocatalyst Carbon dioxide Formate linker conversion

Flocking Effects of the Stochastic Cucker-Smale System with Noise

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Journal of Systems Science & Complexity 2024年第5期37卷 1978-1994页

作者： HAN ning GE Bin LI lin School of Mathematical Sciences Harbin Engineering University

In this paper, the flocking behavior of a Cucker-Smale model with a leader and noise is studied in a finite time. The authors present a Cucker-Smale system with two nonlinear controls for a complex network with stochastic synchronization in probability. Based on the finite-time stability theory of stochastic differential equations, the sufficient conditions for the flocking of stochastic systems in a finite time are obtained by using the Lyapunov function method. Finally, the numerical simulation of the particle system is carried out for the leader and noise, and the correctness of the results is verified.

关键词： Cucker-Smale model flocking behavior leader noise

Improving access to urban parks through public transit optimization

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Frontiers of Architectural Research 2024年第3期13卷 575-592页

作者： ning Xu Kaidan guan Pu Wang School of Architecture Southeast UniversityNanjing 210096China Jiangsu Provincial Urban and Rural Digital Technology Engineering Center Nanjing 210096China

This study establishes an evaluation and optimization framework for the public transit network based on social network analysis and a greedy algorithm,aiming to explore a quantitative approach to improving access to urban parks through public transit *** network analysis and the ArcGIS platform are used to build a public transit network model within Nanjing Old City and analyze its overall network structure *** study also focuses on a method to improve the convenience of reaching regional and citylevel parks by public transit by increasing access and connecting points accordingly.A greedy algorithm is introduced to generate an optimized solution for improving public transit accessibility to regional and city-level parks,consequently enhancing their *** major findings include:(1)The greedy algorithm effectively enhances the performance of the public transit network,but its benefits gradually diminish as more stations are added.(2)Strategically adding stations enhances the performance of most public transit access points,creating efficient pathways for other stations to directly reach these access points and enter regional and city-level parks.(3)The optimized public transit network model offers guidance for the planning and layout of regional and city-level *** site selection for new parks should prioritize establishing connections with the“hubs”in the public transit *** proposed optimization of the public transit network in this study is specific to a single type of urban park,but subsequent research could be conducted to extend the optimization of public transit accessibility around more urban public resources.

关键词： Urban parks Social network analysis Accessibility optimization Public transit network Greedy algorithm

Microbiome-driven anticancer therapy:A step forward from natural products

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mLife 2024年第2期3卷 219-230页

作者： Yunxuan guan Di Wu Hui Wang ning-ning Liu State Key Laboratory of Systems Medicine for Cancer Center for Single‐Cell OmicsSchool of Public HealthShanghai Jiao Tong University School of MedicineShanghaiChina

Human microbiomes,considered as a new emerging and enabling cancer hallmark,are increasingly recognized as critical effectors in cancer development and *** of microbiome revitalizing anticancer therapy from natural products shows promise toward improving cancer ***,we summarize our current understanding of the human microbiome‐driven molecular mechanisms impacting cancer progression and anticancer *** highlight the potential translational and clinical implications of natural products for cancer prevention and treatment by developing targeted therapeutic strategies as adjuvants for chemotherapy and immunotherapy against *** challenges and opportunities for future investigations using modulation of the microbiome for cancer treatment are further discussed in this review.

关键词： anticancer cancer chemotherapy immunotherapy microbiota

Design of Protograph LDPC-Coded MIMO-VLC Systems with Generalized Spatial Modulation

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China Communications 2024年第3期21卷 118-136页

作者： Dai lin Fang Yi guan Yongliang Mohsen Guizani School of Information Engineering Guangdong University of TechnologyGuangzhou 51006China The State Key Laboratory of Integrated Services Networks Xidian UniversityXi’an 710126China School of Electrical and Electronic Engineering Nanyang Technological UniversitySingapore Department of Machine Learning Mohamed Bin Zayed University of Artificial Intelligence(MBZUAI)Abu DhabiUnited Arab Emirates

This paper investigates the bit-interleaved coded generalized spatial modulation(BICGSM) with iterative decoding(BICGSM-ID) for multiple-input multiple-output(MIMO) visible light communications(VLC). In the BICGSM-ID scheme, the information bits conveyed by the signal-domain(SiD) symbols and the spatial-domain(SpD) light emitting diode(LED)-index patterns are coded by a protograph low-density parity-check(P-LDPC) code. Specifically, we propose a signal-domain symbol expanding and re-allocating(SSER) method for constructing a type of novel generalized spatial modulation(GSM) constellations, referred to as SSERGSM constellations, so as to boost the performance of the BICGSM-ID MIMO-VLC ***, by applying a modified PEXIT(MPEXIT) algorithm, we further design a family of rate-compatible P-LDPC codes, referred to as enhanced accumulate-repeat-accumulate(EARA) codes,which possess both excellent decoding thresholds and linear-minimum-distance-growth property. Both analysis and simulation results illustrate that the proposed SSERGSM constellations and P-LDPC codes can remarkably improve the convergence and decoding performance of MIMO-VLC systems. Therefore, the proposed P-LDPC-coded SSERGSM-mapped BICGSMID configuration is envisioned as a promising transmission solution to satisfy the high-throughput requirement of MIMO-VLC applications.

关键词： bit-interleaved coded modulation generalized spatial modulation multiple-input multipleoutput protograph LDPC codes visible light communication

Realizing the excellent oxidation resistance of an environmental barrier coating through aluminum surface modification

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Journal of Advanced Ceramics 2024年第7期13卷 976-986页

作者： lin Dong Wen-Qi Yang lin Chen guan-Jun Yang Chang-Jiu Li State Key Laboratory for Mechanical Behavior of Materials School of Materials Science and EngineeringXi’an Jiaotong UniversityXi’an 710049China Xi’an Aerospace Engine Company Limited in China Aerospace Science and Technology Corporation Xi’an 710065China

The lifetime of Si-based environmental barrier coatings(EBCs)is constrained by thermally grown SiO_(2)oxidelayer(SiO_(2)-TGO),which can cause premature cracking and *** address this issue,a new approach for surfacemodification using aluminum is *** oxidation performance was examined in a 50 vol%H_(2)O-50 vol%O_(2)environment at 1350℃for up to 300 *** results indicate that a dense ytterbium aluminum garnet(YbAG)layer wasformed after modification,decreasing the porosity by 80%.Due to the elimination of fast diffusion channels and the lowoxygen permeability of YbAG,aluminum modification significantly reduced the growth rate of SiO_(2)-TGO by nearly twoorders of ***,its thickness decreased by more than 70%after 300 h of exposure.A diffusioncontrolled oxidation mechanism indicates that the modified dense surface is equivalent to an initial SiO_(2)layer with a specificthickness,causing a shift in the oxidation time and increasing the oxidation *** research provides valuableinsights for designing Si-based EBC with improved lifetimes.

关键词： environmental barrier coating(EBC) oxidation modification diffusion cracking

High-current pulsed electron beam modification on microstructure and performance of Cu/CuW diffusion bonding joints

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Rare Metals 2024年第6期43卷 2819-2831页

作者： Na-Na Tian Cong-lin Zhang Peng Lyu Jin-Tong guan Jie Cai Qing-Feng guan Shun Guo School of Materials Science and Engineering Jiangsu UniversityZhenjiang 212013China School of Material Science and Engineering Yancheng Institute of TechnologyYancheng 221051China Engineering Institute of Advanced Manufacturing and Modern Equipment Technology Jiangsu UniversityZhenjiang 212013China

This study investigates the influence of high-current pulsed electron beam(HCPEB)modification on the microstructure and shear strength of Cu/CuW *** solid-state diffusion bonding of modified-Cu(MCu)and modified-CuW(M-CuW)was achieved by HCPEB modification pretreatment at a temperature of 800-900℃and a pressure of 5 MPa for 10-50 *** demonstrate that HCPEB modification facilitates the dissolution of W and Cu,resulting in the formation of a Cu_(0.4)W_(0.6)solid solution and thus enhancing the uniform distribution of ***,HCPEB-induced defects play a beneficial role in promoting the diffusion process by providing fast diffusion paths for *** optimal joints with the maximum shear strength of 213.7 MPa were obtained through bonding M-Cu and M-CuW at 900℃and 5 MPa for 30 min,which attributes to the combined effects of fine-grained strengthening and solid solution ***,the application of HCPEB modification showcases its effectiveness in promoting element diffusion and enhancing the mechanical performance of the joints.

关键词： HCPEB Element diffusion Shear strength Crystal defects Surface modification