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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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Lipocoacervate,a tunable vesicle for protein delivery

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Nano Research 2024年第10期17卷 9135-9140页

作者： Chia-Wei Yeh Nathaniel Wright chelsea Loh Nabeen Chu Yadong Wang Nancy E.and Peter C.Meinig School of Biomedical Engineering Cornell UniversityKimball Hall 290Ithaca 14853USA Human Biology Healthand Society.College of Human EcologyCornell UniversityIthaca 14853USA

Controlled delivery of proteins and other biologics is a growing medium of therapy for diseases previously *** we report a self-assembling,tunable vesicle for the controlled delivery of growth factors and *** made of heparin and a biocompatible polycation,PEAD,forms the core of the vesicle;lipids form the membrane of the *** call this vesicle lipocoacervate(LipCo),which has a high affinity for growth factors and cytokines due to *** is a tunable protein delivery *** vesicle size is controlled through polymer and salt *** functionalization enables potential for targeting capabilities with long-term storage through ***,the controlled delivery of therapeutics also avoids high toxicity to treated cells in *** we report on these key principles of LipCo assembly and design.

关键词： complex coacervate drug delivery protein delivery heparin lipid particle

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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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Jellyfish-inspired alginate composite hydrogel filter prepared by macro-micro double bionic strategy for efficient water purification

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Frontiers of Environmental Science & Engineering 2024年第4期18卷 141-157页

作者： Huiting Peng Yan Chen Jiaopan Lin chelsea.bena.ly Mohamed Gamal El-Din Junkai Gao School of Naval Architecture and Marinetime Zhejiang Ocean UniversityZhoushan 316022China Department of Civil and Environmental Engineering University of AlbertaEdmontonAB T6G 1H9Canada

Recently,research on hydrogel materials with a porous structure and superior water absorption capabilities significantly ***,the hydrogel under gravity-driven separation conditions often exhibit an unstable pore structure,poor mechanical properties,and limited *** this end,this work presents a novel approach that combines a macro-micro double bionic strategy with a triple crosslinking method to develop a multifunctional alginate composite hydrogel filter(2%-SA-κCG-PVA-Ca^(2+),2%-SKP-Ca^(2+)for short)with a stable pore structure and superior mechanical properties,which possessed an umbrella-shaped structure resembling that of *** 2%-SKPCa^(2+)filter was synthesized using polyvinyl alcohol(PVA)as a stable structure-directing agent,and sodium alginate(SA)andκ-carrageenan(κ-CG)as polymer *** distinctive umbrellashaped hydrogel of 2%-SKP-Ca^(2+)filter,formed through the triple crosslinking method,overcomes the limitations of unstable pore structure and poor durability seen in hydrogels prepared by traditional crosslinking ***,the utilization of the 2%-SKP-Ca^(2+)filter in water treatment demonstrates its good selective permeability,excellent resistance to fouling,and extended longevity,which enables it to simultaneously achieve the multifunctional water purification and the coating of multi-substrate anti-fouling ***,not only does this research provide an efficient,multifunctional,highly pollution-resistant preparation method for designing a new filter,but it also confirms the application prospect of the macro-micro dual bionic strategy developed in this study in complex water treatment.

关键词： Triple crosslinking method Alginate Umbrella-shaped Jellyfish Water purification

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Radiofrequency ablation versus microwave ablation for colorectal liver metastases:long-term results of a retrospective cohort surgical experience

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Hepatobiliary Surgery and Nutrition 2024年第5期13卷 759-770,I0001页

作者： Ali Gunduz Sarioglu Chase J.Wehrle Ege Akgun Arturan Ibrahimli James F.bena Eren Berber Department of Endocrine Surgery Cleveland ClinicClevelandOHUSA Department of General Surgery Cleveland ClinicClevelandOHUSA Department of Quantitative Health Sciences Cleveland ClinicClevelandOHUSA

Background:Ablation is an alternative treatment modality for selected patients with colorectal liver metastases(CRLMs).Although initially widely performed via radiofrequency ablation(RFA),more recently,microwave ablation(MWA)is being preferred due to its perceived superiority in creating the ablation *** aim of this study is to compare the long-term efficacy of these two modalities performed ***:Patients undergoing surgical liver ablation from 2005-2023 at a tertiary center by a single surgeon for CRLM were included in a retrospective institutional review board-approved *** were compared using Wilcoxon,Chi-square,Kaplan-Meier,and Cox multivariate regression *** data are presented as median(interquartile range).Results:There were a total of 242 *** RFA was done in 121 patients with 303 lesions and laparoscopic MWA in 121 patients with 300 *** was no difference between the groups regarding operative time(161 vs.147 minutes,respectively,P=0.4),perioperative morbidity(3%vs.8%,respectively,P=0.2)or hospital stay(1 vs.1 day,P=0.05).Local recurrence(LR)per lesion with at least 1 year of imaging follow-up was 29%in the RFA and 13%in the MWA group(Plysis,tumor size,blood vessel proximity,ablation margin,and ablation modality were independent predictors of *** control these variables,direct matching was *** cohort included 189 ***-Meier analysis of these cohorts showed increased LR-free survival in the MWA group *** RFA group(P=0.005).Conclusions:This large study confirms our initial observation that local tumor control rate is better after MWA ***.

关键词： Colorectal cancer liver metastasis liver ablation radiofrequency ablation(RFA) microwave ablation(MWA) local recurrence(LR)

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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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Hydromechanical characterization of gas transport amidst uncertainty for underground nuclear explosion detection

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Journal of Rock Mechanics and Geotechnical Engineering 2024年第6期16卷 2019-2032页

作者： Wenfeng Li chelsea W.Neil J William Carey Meng Meng Luke P.Frash Philip H.Stauffer Earth and Environmental Sciences Los Alamos National LaboratoryLos AlamosNM87544USA Department of Mineral Engineering New Mexico TechSocorroNM87801USA

Given the challenge of definitively discriminating between chemical and nuclear explosions using seismic methods alone,surface detection of signature noble gas radioisotopes is considered a positive identification of underground nuclear explosions(UNEs).However,the migration of signature radionuclide gases between the nuclear cavity and surface is not well understood because complex processes are involved,including the generation of complex fracture networks,reactivation of natural fractures and faults,and thermo-hydro-mechanical-chemical(THMC)coupling of radionuclide gas transport in the *** this study,we provide an experimental investigation of hydro-mechanical(HM)coupling among gas flow,stress states,rock deformation,and rock damage using a unique multi-physics triaxial direct shear rock testing *** testing system also features redundant gas pressure and flow rate measurements,well suited for parameter uncertainty *** porous tuff and tight granite samples that are relevant to historic UNE tests,we measured the Biot effective stress coefficient,rock matrix gas permeability,and fracture gas permeability at a range of pore pressure and stress *** Biot effective stress coefficient varies from 0.69 to 1 for the tuff,whose porosity averages 35.3%±0.7%,while this coefficient varies from 0.51 to 0.78 for the tight granite(porosityly correlated to effective stress for the granite,but not for the porous *** experiments reveal the following key engineering implications on transport of radionuclide gases post a UNE event:(1)The porous tuff shows apparent fracture dilation or compression upon stress changes,which does not necessarily change the gas permeability;(2)The granite fracture permeability shows strong stress sensitivity and is positively related to shear displacement;and(3)Hydromechanical coupling among stress states,rock damage,and gas flow appears to be

关键词： Underground nuclear explosion uncertainty quantification Radionuclide transport Biot effective stress coefficient Fracture permeability Matrix permeability

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