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

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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

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

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

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

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

transient responses of double-curved sandwich two-layer shells resting on Kerr's foundations with laminated three-phase polymer/GNP/fiber surface and auxetic honeycomb core subjected to the blast load

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Defence Technology（防务技术） 2024年第5期35卷 222-247页

作者： nguyen Thi Hai Van Thi Hong nguyen Researcher&Lecturer Faculty of Industrial EducationThe University of Danang-University of Technology and Education48 Cao ThangDanang550000Viet Nam Researcher&Lecturer Faculty of Mechanical EngineeringThuyloi University175 Tay SonDong DaHanoi100000Viet Nam

This work uses refined first-order shear theory to analyze the free vibration and transient responses of double-curved sandwich two-layer shells made of auxetic honeycomb core and laminated three-phase polymer/GNP/fiber surface subjected to the blast *** of the two layers that make up the double-curved shell structure is made up of an auxetic honeycomb core and two laminated sheets of three-phase polymer/GNP/*** exterior is supported by a Kerr elastic foundation with three *** key innovation of the proposed theory is that the transverse shear stresses are zero at two free surfaces of each *** contrast to previous first-order shear deformation theories,no shear correction factor is ***'s exact solution was used to treat the double-curved shell problem with a single title boundary,while the finite element technique and an eight-node quadrilateral were used to address the other boundary *** ensure the accuracy of these results,a thorough comparison technique is employed in conjunction with credible *** problem model's edge cases allow for this kind of *** study's findings may be used in the post-construction evaluation of military and civil works structures for their ability to sustain explosive *** addition,this is also an important basis for the calculation and design of shell structures made of smart materials when subjected to shock waves or explosive loads.

关键词： Blast load Two-layer shell Polymer/GNP/Fiber surface Auxetic honeycomb Shear connectors

Chebyshev polynomial-based Ritz method for thermal buckling and free vibration behaviors of metal foam beams

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Applied Mathematics and Mechanics(English Edition) 2024年第5期45卷 891-910页

作者： N.D.nguyen T.N.nguyen Faculty of Civil Engineering Ho Chi Minh City University of Technology and EducationHo Chi Minh City 71309Viet Nam Faculty of Engineering and Technology Kien Giang UniversityChau Thanh 92000Viet Nam

This study presents the Chebyshev polynomials-based Ritz method to examine the thermal buckling and free vibration characteristics of metal foam *** analyses include three models for porosity distribution and two scenarios for thermal *** material properties are assessed under two conditions,i.e.,temperature dependence and temperature *** theoretical framework for the beams is based on the higher-order shear deformation theory,which incorporates shear deformations with higher-order *** governing equations are established from the Lagrange equations,and the beam displacement fields are approximated by the Chebyshev *** simulations are performed to evaluate the effects of thermal load,slenderness,boundary condition(BC),and porosity distribution on the buckling and vibration behaviors of metal foam *** findings highlight the significant influence of temperature-dependent(TD)material properties on metal foam beams'buckling and vibration responses.

关键词： Ritz method Chebyshev function buckling vibration metal foam beam higher-order beam theory(HOBT)

transient response of doubly-curved bio-inspired composite shells resting on viscoelastic foundation subject to blast load using improved first-order shear theory and isogeometric approach

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Defence Technology（防务技术） 2024年第8期38卷 171-193页

作者： Thuy tran Thi Thu Tu nguyen Anh Hue nguyen Thi Hong nguyen Thi School of Mechanical and Automotive Engineering Hanoi University of IndustryHanoiViet Nam Faculty of Technical Fundamental University of Transport TechnologyHanoiViet Nam Faculty of Mechanical Engineering Thuyloi University175 Tay SonDong DaHanoiViet Nam

Investigating natural-inspired applications is a perennially appealing subject for scientists. The current increase in the speed of natural-origin structure growth may be linked to their superior mechanical properties and environmental resilience. Biological composite structures with helicoidal schemes and designs have remarkable capacities to absorb impact energy and withstand damage. However, there is a dearth of extensive study on the influence of fiber redirection and reorientation inside the matrix of a helicoid structure on its mechanical performance and reactivity. The present study aimed to explore the static and transient responses of a bio-inspired helicoid laminated composite(B-iHLC) shell under the influence of an explosive load using an isomorphic method. The structural integrity of the shell is maintained by a viscoelastic basis known as the Pasternak foundation, which encompasses two coefficients of stiffness and one coefficient of damping. The equilibrium equations governing shell dynamics are obtained by using Hamilton's principle and including the modified first-order shear theory,therefore obviating the need to employ a shear correction factor. The paper's model and approach are validated by doing numerical comparisons with respected publications. The findings of this study may be used in the construction of military and civilian infrastructure in situations when the structure is subjected to severe stresses that might potentially result in catastrophic collapse. The findings of this paper serve as the foundation for several other issues, including geometric optimization and the dynamic response of similar mechanical structures.

关键词： Blast load Modified first-order shear theory Biological composite structures

Push forward LC-MS-based therapeutic drug monitoring and pharmacometabolomics for anti-tuberculosis precision dosing and comprehensive clinical management

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Journal of Pharmaceutical Analysis 2024年第1期14卷 16-38页

作者： nguyen Quang Thu nguyen tran Nam Tien nguyen Thi Hai Yen Thuc-Huy Duong nguyen Phuoc Long Huy Truong nguyen Department of Pharmacology and PharmacoGenomics Research Center Inje University College of MedicineBusan47392Republic of Korea Department of Chemistry University of EducationHo Chi Minh City700000Viet Nam Faculty of Pharmacy Ton Duc Thang UniversityHo Chi Minh City700000Viet Nam

The spread of tuberculosis(TB),especially multidrug-resistant TB and extensively drug-resistant TB,has strongly motivated the research and development of new anti-TB *** strategies to facilitate drug combinations,including pharmacokinetics-guided dose optimization and toxicology studies of first-and second-line anti-TB drugs have also been introduced and *** chromatography-mass spectrometry(LC-MS)has arguably become the gold standard in the analysis of both endo-and exo-genous *** technique has been applied successfully not only for therapeutic drug monitoring(TDM)but also for pharmacometabolomics *** improves the effectiveness of treatment,reduces adverse drug reactions,and the likelihood of drug resistance development in TB patients by determining dosage regimens that produce concentrations within the therapeutic target *** on TDM,the dose would be optimized individually to achieve favorable *** is essential in generating and validating hypotheses regarding the metabolism of anti-TB drugs,aiding in the discovery of potential biomarkers for TB diagnostics,treatment monitoring,and outcome *** article highlighted the current progresses in TDM of anti-TB drugs based on LC-MS bioassay in the last two ***,we discussed the advantages and disadvantages of this technique in practical *** pressing need for non-invasive sampling approaches and stability studies of anti-TB drugs was ***,we provided perspectives on the prospects of combining LC-MS-based TDM and pharmacometabolomics with other advanced strategies(pharmacometrics,drug and vaccine developments,machine learning/artificial intelligence,among others)to encapsulate in an all-inclusive approach to improve treatment outcomes of TB patients.

关键词： Tuberculosis Therapeutic drug monitoring LC-MS MIPD Pharmacometabolomics Precision medicine