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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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The effects of local variations in conditions on carbon storage and release in the continental mantle

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National Science Review 2024年第6期11卷 22-36页

作者： Stephen f.foley Chunfei Chen Dorrit e.Jacob School of Natural Sciences Macquarie University Research School of earth Sciences Australian National University State Key Laboratory of Geological Processes and Mineral Resources School of Earth Sciences China University of Geosciences

Recent advances indicate that the amount of carbon released by gradual degassing from the mantle needs to be revised upwards, whereas the carbon supplied by plumes may have been overestimated in the *** in rock types and oxidation state may be very local and exert strong influences on carbon storage and release mechanisms. Deep subduction may be prevented by diapirism in thick sedimentary packages,whereas carbonates in thinner sequences may be subducted. Carbonates stored in the mantle transition zone will melt when they heat up, recognized by coupled stable isotope systems(e.g. Mg, Zn, Ca). There is no single ‘mantle oxygen fugacity’, particularly in the thermal boundary layer(TBL) and lowermost lithosphere, where very local mixtures of rock types coexist. Carbonate-rich melts from either subduction or melting of the uppermost asthenosphere trap carbon by redox freezing or as carbonate-rich dykes in this zone. Deeply derived, reduced melts may form further diamond reservoirs, recognized as polycrystalline diamonds associated with websteritic silicate minerals. Carbon is released by either edge-driven convection,which tears sections of the TBL and lower lithosphere down so that they melt by a mixture of heating and oxidation, or by lateral advection of solids beneath rifts. Both mechanisms operate at steps in lithosphere thickness and result in carbonate-rich melts, explaining the spatial association of craton edges and carbonate-rich magmatism. High-pressure experiments on individual rock types, and increasingly on reactions between rocks and melts, are fine-tuning our understanding of processes and turning up unexpected results that are not seen in studies of single rocks. future research should concentrate on elucidating local variations and integrating these with the interpretation of geophysical signals. Global concepts such as average sediment compositions and a uniform mantle oxidation state are not appropriate for small-scale processes; an increa

关键词： lithospheric mantle carbonate melts deep carbon cycle craton destruction continental rifts

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Converting TRex-RGB green-channel data to 557.7 nm auroral intensity:Methodology and initial results

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earth and Planetary Physics 2024年第1期8卷 258-274页

作者： Jun Liang D.M.Gillies e.Spanswick e.f.Donovan University of Calgary CalgaryT2N 1N4Canada

The recently deployed Transition Region explorer(TRex)-RGB(red-green-blue)all-sky imager(ASI)is designed to capture“true color”images of the aurora and *** the 557.7 nm green line is usually the brightest emission line in visible auroras,the green channel of a TRex-RGB camera is usually dominated by the 557.7 nm *** this rationale,the TRex mission does not include a specific 557.7 nm imager and is designed to use the RGB green-channel data as a proxy for the 557.7 nm *** this study,we present an initial effort to establish the conversion ratio or formula linking the RGB green-channel data to the absolute intensity of 557.7 nm auroras,which is crucial for quantitative uses of the RGB *** illustrate two approaches:(1)through a comparison with the collocated measurement of green-line auroras from the TRex spectrograph,and(2)through a comparison with the modeled green-line intensity according to realistic electron precipitation flux measurements from low-earth-orbit satellites,with the aid of an auroral transport *** demonstrate the procedures and provide initial results for the TRex-RGB ASIs at the Rabbit Lake and Lucky Lake *** RGB response is found to be *** conversion ratios or formulas between RGB green-channel data and the green-line auroral intensity are given and can be applied immediately by TRex-RGB data *** methodology established in this study will also be applicable to the upcoming SMILe ASI mission,which will adopt a similar RGB camera system in its deployment.

关键词： TRex RGB green-line aurora auroral transport model

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All-electron basis sets for H to Xe specific for ZORA calculations:Applications in atoms and molecules

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Chinese Physics B 2024年第8期33卷 238-246页

作者： C.S.Gomes f.e.Jorge A.Canal Neto Departamento de fisica Universidade Federal do Espirito Santo29075-910 VitoriaESBrazil Departamento de fisica Instituto de Ciencias Exatas e BiologicasUniversidade Federal de Ouro Preto Campus Universitario Morro do Cruzeiro35402-136 Ouro PretoMGBrazil

A segmented basis set of quadruple zeta valence quality plus polarization functions(QZP)for H through Xe was developed to be used in conjunction with the ZORA *** set was augmented with diffuse functions to describe electrons farther away from the nuclei *** the ZORA-CCSD(T)/QZP-ZORA theoretical model,atomic ionization energies and bond lengths,harmonic vibrational frequencies,and atomization energies of some molecules were *** addition of core-valence corrections has been shown to improve the agreement between theoretical and experimental results for molecular *** atomization energies,a similar observation emerges when considering spin-orbit *** the augmented QZP-ZORA set,static mean dipole polarizabilities of a set of atoms were calculated and compared with previously published recommended and experimental *** evaluations of the ZORA and Douglas–Kroll–Hess Hamiltonians were made for each property studied.

关键词： QZP-ZORA and AQZP-ZORA basis sets elements from H to Xe CCSD(T)method atomic and molecular properties

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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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