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Discovering peptides and computational investigations of a multiepitope vaccine target Mycobacterium tuberculosis

Synthetic and Systems Biotechnology 2024年第3期9卷 391-405页

作者： Truc ly Nguyen Heebal Kim Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences Seoul National UniversitySeoul08826Republic of Korea Interdisciplinary Program in Bioinformatics Seoul National UniversitySeoul08826Republic of Korea eGnome Inc.Seoul05836Republic of Korea

Mycobacterium tuberculosis(MTB)is the causative agent of tuberculosis(TB),a prevalent airborne infectious *** the availability of the Bacille Calmette-Guerin vaccine,its global efficacy remains modest,and tuberculosis persists as a significant global public health *** this challenge and advancing towards the End MTB Strategy,we developed a multiepitope vaccine(MEV)based on immunoinformatics and compu-tational *** screening of MBT protein identified immune-dominant epitopes based on Major Histocompatibility Complex(MHC)allele binding,immunogenicity,antigenicity,allergenicity,toxicity,and cytokine *** epitopes were integrated into an MEV construct with adjuvant and linkers,forming a fully immunogenic vaccine *** analyses encompassed the evaluation of immunological and physicochemical properties,determination of tertiary structure,molecular docking with Toll-Like Receptors(TLR),molecular dynamics(MD)simulations for all atoms,and immune *** MEV comprises 534 amino acids,featuring 6 cytotoxic T lymphocyte,8 helper T lymphocyte,and 7 linear B lymphocyte epitopes,demonstrating high antigenicity and ***,molecular docking studies and triplicate MD simulations revealed enhanced interactions and stability of MEV with the TLR4 complex compared to *** addition,the immune simulation indicated the capacity to effectively induce elevated levels of an-tibodies and cytokines,emphasizing the vaccine’s robust immunogenic *** study presents a promising MEV against TB,exhibiting favorable immunological and physicochemical *** findings provide theoretical support for TB vaccine *** study aligns with the global initiative of the End MTB Strategy,emphasizing its potential impact on addressing persistent challenges in TB control.

关键词： Mycobacterium tuberculosis Tuberculosis Multiepitope vaccine Docking molecular Molecular dynamics simulation Immune simulation

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Restimate:Recovery Estimation Tool for Resilience Planning

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Journal of Safety Science and Resilience 2024年第1期5卷 47-63页

作者： Scott Miles Megan ly Nick Terry Youngjun Choe Department of Human Centered Design&Engineering Campus Box 352315University of WashingtonSeattleWA 98195United States of America Department of Industrial&Systems Engineering Box 352650University of WashingtonSeattleWA 98195United States of America

The *** Institute of Standards and Technology(NIST)published the Community Resilience Planning Guide in *** NIST Guide advocates for a participatory process for developing a performance measurement framework for the jurisdiction’s resilience against a scenario *** framework centers around tables of expected and desired recovery times for selected community assets,such as electricity,water,and natural gas *** NIST Guide does not provide a method for estimating the expected recovery ***,building high-fidelity computer models for such estimations requires substantial resources that even larger ju-risdictions cannot *** most promising approach to recovery time estimation is to systematically use data elicited from people to tap into the wisdom of the(knowledgeable)*** paper describes a novel research-through-design project to enable the computer-supported elicitation of recovery time series *** work is the first in the literature to examine people’s ability to estimate recovery curves and how design in-fluences such *** main contribution to resilience planning is three-fold:development of a new elicitation tool called Restimate,understanding its potential user base,and providing insights into how it can facilitate resilience *** is the first tool to enable evidence-based expert elicitation in any community with limited resources for resilience *** resilience planning,those who facilitate high-stakes planning activities under large uncertainties(e.g.,mission-critical system design and planning)will benefit from a similar research-through-design process.

关键词： expert elicitation disaster natural hazard infrastructure community resilience restoration user-centered design computer-supported cooperative work

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Integrating immunoinformatics and computational epitope prediction for a vaccine candidate against respiratory syncytial virus

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Infectious Disease Modelling 2024年第3期9卷 763-774页

Respiratory syncytial virus(RSV)poses a significant global health threat,especially affecting infants and the *** this,the present study proposes an innovative approach to vaccine design,utilizing immunoinformatics and computational *** analyzed RSV's structural proteins across both subtypes A and B,identifying potential helper T lymphocyte,cytotoxic T lymphocyte,and linear B lymphocyte *** such as antigenicity,allergenicity,toxicity,and cytokine-inducing potential were rigorously ***,we evaluated the conservancy of these epitopes and their population coverage across various RSV *** comprehensive analysis identified six major histocompatibility complex class I(MHC-I)binding,five MHC-II binding,and three B-cell *** were integrated with suitable linkers and adjuvants to form the ***,molecular docking and molecular dynamics simulations demonstrated stable interactions between the vaccine candidate and human Toll-like receptors(TLR4 and TLR5),with a notable preference for *** simulation analysis underscored the vaccine's potential to elicit a strong immune *** study presents a promising RSV vaccine candidate and offers theoretical support,marking a significant advancement in vaccine development ***,the promising in silico findings need to be further validated through additional in vivo studies.

关键词： Respiratory syncytial virus Multiepitope vaccine Immunoinformatics Docking molecular Molecular dynamics simulation Immune simulation

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Nearest Neighbor Sampling of Point Sets Using Rays

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Communications on Applied Mathematics and Computation 2024年第2期6卷 1131-1174页

作者： Liangchen Liu Louis ly Colin B.Macdonald Richard Tsai Department of Mathematics The University of Texas at Austin2515 SpeedwayAustinTX 78712USA oden Institute for Computational Engineering and Sciences The University of Texas at Austin201 E24th StAustinTX 78712USA Department of Mathematics University of British Columbia1984 Mathematics RdVancouverBCV6T1Z2Canada

We propose a new framework for the sampling,compression,and analysis of distributions of point sets and other geometric objects embedded in Euclidean *** approach involves constructing a tensor called the RaySense sketch,which captures nearest neighbors from the underlying geometry of points along a set of *** explore various operations that can be performed on the RaySense sketch,leading to different properties and potential *** information about the data set can be extracted from the sketch,independent of the ray *** integrals on point sets can be efficiently computed using the *** also present several examples illustrating applications of the proposed strategy in practical scenarios.

关键词： Point clouds Sampling Classification Registration Deep learning Voronoi cell analysis

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Application of extreme gradient boosting in predicting the viscoelastic characteristics of graphene oxide modified asphalt at medium and high temperatures

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Frontiers of Structural and Civil Engineering 2024年第6期18卷 899-917页

作者： Huong-Giang Thi HoANG Hai-Van Thi MAI Hoang Long NGUYEN Hai-Bang ly University of Transport Technology Hanoi 100000Vietnam

Complex modulus(G^(*))is one of the important criteria for asphalt classification according to AASHTo M320-10,and is often used to predict the linear viscoelastic behavior of asphalt *** addition,phase angle(φ)characterizes the deformation resilience of asphalt and is used to assess the ratio between the viscous and elastic *** is thus important to quickly and accurately estimate these two *** purpose of this investigation is to construct an extreme gradient boosting(XGB)model to predict G^(*)andφof graphene oxide(Go)modified asphaltat medium and high *** data sets are gathered from previously published experiments,consisting of 357 samples for G^(*)and 339 samples forφ,and the se are used to develop the XGB model using nine inputs representing theasphalt binder *** findings show that XGB is an excellent predictor of G^(*)andφof Go-modified asphalt,evaluated by the coefficient of determination R^(2)(R^(2)=0.990 and 0.9903 for G^(*)andφ,respectively)and root mean square error(RMSE=31.499 and 1.08 for G^(*)andφ,respectively).In addition,the model’s performance is compared with experimental results and five other machine learning(ML)models to highlight its *** the final step,the Shapley additive explanations(SHAP)value analysis is conducted to assess the impact of each input and the correlation between pairs of important features on asphalt’s two physical properties.

关键词： complex modulus phase angle graphene oxide asphalt extreme gradient boosting machine learning

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A deep neural network based surrogate model for damage identification in full-scale structures with incomplete noisy measurements

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Frontiers of Structural and Civil Engineering 2024年第3期18卷 393-410页

作者： Tram BUI-NGoC Duy-Khuong ly Tam T TRUoNG Chanachai THoNGCHoM T.NGUYEN-THoI Laboratory for Computational Mechanics Institute for Computational Science and Artificial IntelligenceVan Lang UniversityHo Chi Minh City 70000Vietnam Faculty of Mechanical-Electrical and Computer Engineering School of TechnologyVan Lang UniversityHo Chi Minh City 70000Vietnam Faculty of Civil Engineering School of TechnologyVan Lang UniversityHo Chi Minh City 70000Vietnam Department of Computer Science Aarhus UniversityAarhus 8000Denmark Thammasat University research unit in structural and foundation engineering Department of Civil EngineeringThammasat UniversityPathumthani 12120Thailand Laboratory for Applied and Industrial Mathematics Institute for Computational Science and Artificial IntelligenceVan Lang UniversityHo Chi Minh City 70000Vietnam Thammasat School of Engineering Thammasat UniversityPathumthani 12120Thailand

The paper introduces a novel approach for detecting structural damage in full-scale structures using surrogate models generated from incomplete modal data and deep neural networks(DNNs).A significant challenge in this field is the limited availability of measurement data for full-scale structures,which is addressed in this paper by generating data sets using a reduced finite element(FE)model constructed by SAP2000 software and the MATLAB programming *** surrogate models are trained using response data obtained from the monitored structure through a limited number of measurement *** proposed approach involves training a single surrogate model that can quickly predict the location and severity of damage for all potential *** achieve the most generalized surrogate model,the study explores different types of layers and hyperparameters of the training algorithm and employs state-of-the-art techniques to avoid overfitting and to accelerate the training *** approach’s effectiveness,efficiency,and applicability are demonstrated by two numerical *** study also verifies the robustness of the proposed approach on data sets with sparse and noisy measured ***,the proposed approach is a promising alternative to traditional approaches that rely on FE model updating and optimization algorithms,which can be computationally *** approach also shows potential for broader applications in structural damage detection.

关键词： vibration-based damage detection deep neural network full-scale structures finite element model updating noisy incomplete modal data

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Self-assembly of tau fragments as a key pathologic event in tauopathies

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Neural Regeneration Research 2024年第12期19卷 2565-2566页

作者： ly Thi Huong Luu Le Jung Hoon Lee Min Jae Lee Department of Biochemistry and Molecular Biology Seoul National University College of MedicineSeoulKorea

Tau protein is encoded by the microtubuleassociated protein tau(MAPT)gene and stabilizes microtubules in the *** has unique biophysical properties that make it both highly water-soluble and positively *** tau is an intrinsically disordered protein lacking defined secondary structures,it can acquire highly organized-sheet structures and stack into a filamentous inclusion such as a paired helical filament(PHF).

关键词： tau pathologic assembly

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Photocatalytic degradation of antibiotic sulfamethizole by visible light activated perovskite LaZno_(3)

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Journal of Environmental Sciences 2024年第10期144卷 212-224页

作者： Bui The Huy XCuong Nguyen Vu Khac Hoang Bui Nguyen Ngoc Tri Iqra Rabani Nhu Hoa Thi Tran Quang Viet ly Hai Bang Truong Major of Biomedical Engineering Division of Smart HealthcareCollege of Information Technology and ConvergencePukyong National UniversityBusan 48513Korea Center for Advanced Chemistry Institute of Research and DevelopmentDuy Tan UniversityDa Nang 550000Viet Nam Faculty of Environmental and Chemical Engineering Duy Tan UniversityDa Nang 550000Viet Nam Department of Environment and Energy Sejong UniversitySeoul 05006Korea Lab of Computational Chemistry and Modelling Department of ChemistryFaculty of Natural SciencesQuy Nhon UniversityQuy NhonViet Nam Department of Nanotechnology and Advanced Materials Engineering Sejong UniversitySeoul 05006Korea Faculty of Materials Science and Technology University of ScienceHo Chi Minh City 700000Viet Nam Vietnam National University Ho Chi Minh City 700000Viet Nam Department of Environmental Engineering Seoul National University of Science and TechnologySeoul 01811Korea optical Materials Research Group Science and Technology Advanced InstituteVan Lang UniversityHo Chi Minh CityViet Nam Faculty of Applied Technology School of TechnologyVan Lang UniversityHo Chi Minh CityViet Nam

In thiswork,the perovskite LaZno_(3) was synthesized via sol-gel method and applied for photocatalytic treatment of sulfamethizole(SMZ)antibiotics under visible light *** was almost completely degraded(99.2%±0.3%)within 4 hr by photocatalyst LaZno3 at the optimal dosage of 1.1 g/L,with amineralization proportion of 58.7%±0.4%.The efficient performance of LaZno_(3) can be attributed to itswide-range light absorption and the appropriate energy band edge levels,which facilitate the formation of active agents such as·o_(2)^(−),h^(+),and·*** integration of RP-HPLC/Q-ToF-MS and DFT-based computational techniques revealed three degradation pathways of SMZ,which were initiated by the deamination reaction at the aniline ring,the breakdown of the sulfonamidemoieties,and a process known as Smile-type rearrangement and So2 *** toxicity of SMZ and the intermediateswere analyzed by quantitative structure activity relationship(QSAR),indicating the effectiveness of LaZno_(3)-based photocatalysis in preventing secondary pollution of the intermediates to the ecosystem during the degradation *** visible-light-activated photocatalyst LaZno_(3) exhibited efficient performance in the occurrence of inorganic anions and maintained high durability across multiple recycling tests,making it a promising candidate for practical antibiotic treatment.

关键词： Perovskite Antibiotics Photocatalysis Density functional theory Toxicity

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中原传奇在中国的营销策略研究

中原传奇在中国的营销策略研究

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作者： ly THI HoNG LoAN 河北大学

学位级别：硕士

在全球化日益加深的市场背景下,各企业进军国际市场并在外国市场上取得成功显得尤为重要,但同时充满了诸多挑战。本文通过深入研究越南知名咖啡品牌——越南传奇(Trung Nguyen Legend)在具有复杂多变特性的中国市场上所采用的多元化营... 详细信息

在全球化日益加深的市场背景下,各企业进军国际市场并在外国市场上取得成功显得尤为重要,但同时充满了诸多挑战。本文通过深入研究越南知名咖啡品牌——越南传奇(Trung Nguyen Legend)在具有复杂多变特性的中国市场上所采用的多元化营销策略,旨在揭示这一品牌如何有效应对市场入侵和扩张的策略问题。特别地,研究聚焦于分析该品牌如何利用市场细分、目标定位和产品定位(STP)的策略来精准触达目标消费者群体,并对7P营销理论框架——包括产品、价格、推广、渠道、人员、流程和实物证据——进行了全面的审视和探讨。通过详尽的市场分析,本文揭示了越南传奇在中国市场上的策略选择背后的复杂性。研究表明,越南传奇在切入中国多元化的消费者市场时,不仅识别了具有高利润潜力的市场细分,而且在竞争激烈的市场环境中实施了有效的品牌定位策略。研究通过详细分析包括产品创新、价格策略、渠道管理、推广活动、服务人员的培训、业务流程优化以及强化实物证据在内的营销组合要素,进一步阐述了越南传奇为巩固及扩大其在中国咖啡市场中的地位所采取的具体行动和策略。此外,本研究采用创新的方法,通过实施调查问卷收集了一手数据,这些数据直接反映了中国消费者对于越南传奇产品的认知、偏好和购买行为。基于调查结果的数据分析不仅验证了研究的理论框架,还为越南传奇在中国市场上进一步优化其营销策略提供了实用的建议和深入的见解。综上所述,本文贡献于深化我们对国际营销策略复杂性的理解,特别是在研究越南传奇品牌进军中国市场的过程中。通过结合理论分析、实证研究和策略实施的实际成果,本研究不仅为学术界提供了新的研究视角,也为业界专业人士和政策制定者提供了宝贵的策略指导和决策支持,进而丰富了全球营销战略及跨文化消费行为研究的学术讨论。

关键词：中原传奇越南咖啡中国咖啡市场营销策略

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越南学生“常常”“往往”习得偏误及教学对策研究

越南学生“常常”“往往”习得偏误及教学对策研究

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作者： NGUYEN THI LUU ly（阮氏琉璃）河北大学

学位级别：硕士

“常常”“往往”是汉语中典型的频率副词,在语义、句法和语用特征方面较为复杂且不易区分。笔者作为越南留学生,在学习汉语过程中发现,越南学生受母语的影响在理解和应用“常常”“往往”时遇到了显著的障碍。为了探究越南学生在习得... 详细信息

“常常”“往往”是汉语中典型的频率副词,在语义、句法和语用特征方面较为复杂且不易区分。笔者作为越南留学生,在学习汉语过程中发现,越南学生受母语的影响在理解和应用“常常”“往往”时遇到了显著的障碍。为了探究越南学生在习得“常常”“往往”时出现的偏误情况,并据此提出适用于越南学生的教学与学习策略,文章从本体角度对“常常”“往往”进行了对比分析,从语义、句法及语用三个角度综合比较了“常常”与“往往”的共性与差异。研究显示,尽管这两个词在词性和功能方面有很大相似性,但在语义和使用上各有特点。在此基础上,文章将汉语的“常常”“往往”与越南语中相应的词语进行了对照分析,发现越南语中有“th(?)(?)ng”“th(?)(?)ng th(?)(?)ng”“th(?)(?)ng xuyên”“th(?)(?)ng hay”“lu(?)n lu(?)n”几个词语与汉语的“常常”“往往”在语义上非常相似,但在句法特征和语用情景方面,越南语中的相应表达表现出较强的灵活性和自由度。为更确切地了解越南学生习得“常常”“往往”的情况,本文以问卷调查的形式考察了越南学生在习得“常常”“往往”时的感受和可能存在的偏误。通过对问卷情况的分析,总结出越南学习者的偏误可分为语义偏误、句法偏误和语用偏误三种类型。文章从语义及句法复杂性、学习者母语及教学媒介语因素、教材因素等三个角度进行了原因分析,研究结果表明,母语影响是导致越南学生在汉语学习中出现偏误的重要因素之一,同时也指出了教材在处理这些频率副词时存在的不足。基于以上研究,本文有针对性地提出了面向越南学生习得“常常”“往往”的教学对策。在教材编写方面,建议提高翻译的精确度、注释的准确性,并增强练习的针对性。对于教师,本文倡导采用情境教学法、对比教学法以及强化实践练习。此外,给越南学生的语言习得提出了若干建议,包括通过汉语思维减少母语负迁移、善于对比以及敢于交际的学习策略。

关键词：越南学生常常往往问卷调查教学对策

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