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Molecular dynamics simulation and purification of chimeric L1/L2 protein from human papillomavirus type 52 expressed in Escherichia coli BL21 (DE3)

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Journal of Immunoassay and Immunochemistry 2024年第5期45卷 395-414页

作者： Al Adawiah, Rabiyah Zaenal Mustopa, Apon Budiarti, Sri Nur Umami, Rifqiyah Hertati, Ai Irawan, Herman Ikramullah, Muh. Chaeril Arwansyah, Arwansyah Mamangkey, Jendri Kartikasari, Isti Salahudin Darusman, Huda Post Graduate Program of Microbiology IPB University Bogor Indonesia Research Center for Genetic Engineering National Research and Innovation Agency (BRIN) KST Soekarno Bogor Cibinong Indonesia Department of Biology IPB University Bogor Indonesia Biotechnology Study Program Postgraduate School of Universitas Gadjah Mada Yogyakarta Indonesia Department of Chemistry Education Tadulako University Palu Indonesia Department of Biology Education Faculty of Education and Teacher Training Universitas Kristen Indonesia Jakarta Indonesia Primate Animal Study Center IPB University Bogor Indonesia Department of Anatomy Physiology and Pharmacology School of Veterinary Medicine and Biomedical IPB University Bogor Indonesia Primate Animal Study Center Research Institution and Community Service (LPPM) IPB University Bogor Indonesia

The available prophylactic vaccines for human papillomavirus (HPV) in the market are only effective against specific types of HPV, rendering them ineffective for other types of HPV infections. The objective of this research is to investigate the stability of the recombinant protein constructed, namely chimeric L1/L2 protein from HPV type 52, with improved cross-neutralization ability. The 3D model, predicted using Alphafold, Robetta, I-Tasser, and refined with Galaxy Refinement, is validated using Ramachandran plot analysis. The stability is verified through molecular dynamics simulations, considering parameters such as RMSD, RMSF, Rg, and SASA, where stable conditions are observed. The chimeric L1/L2 protein from HPV type 52 is purified using affinity chromatography, and the His-tag is cleaved using SUMO protease to obtain pure chimeric protein with the size of ~ 55 kDa. Western blot analysis confirms binding to anti-L1 HPV type 52 polyclonal antibody. The obtained vaccine candidate can be utilized as an effective prophylactic vaccine against HPV. © 2024 Taylor & Francis.

关键词： HPV molecular dynamics purification vaccine

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Effect of Method and Duration of Curing on the Compressive Strength of the Lime-Fly Ash Geopolymer Concrete 1

Effect of Method and Duration of Curing on the Compressive S...

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1st Progress in Science and Technology Research Symposium, PSTRS 2019

作者： Adam, Andi Arham Akifa, Sri Nur Siregar, Atur P.N. Mustofa Department of Civil Engineering Tadulako University Indonesia Post-Graduate Program Tadulako University Indonesia Department of Mechanical Engineering Tadulako University Indonesia

The use of lime to produce ambient cured Geopolymer concrete is one of a practical solution to avoid heat curing in the production of geopolymer concrete. The addition of lime in the geopolymer system will add another hardened mechanism, i.e. hydration in addition to condensation-polymerisation. This research aims to determine the influence of air and water curing on the strength of geopolymer concrete which uses class F fly ash and lime as raw materials. The geopolymer concrete was produced by varying the activator (sodium silicate and sodium hydroxide) with the variation of the activator to binder ratio of 0.45, 0.50, 0.55, and 0.60. Five per cent of the fly ash was replaced by slaked lime and the water added to the mix to maintain the ratio of water to solid (activator + binder) to 0.32. The test specimens were 100 mm dia x 200 mm height cylinder. Water-immersion curing was performed for 7, 14, and 21 days and the compressive strength test was done at 28 days. The results show that there is a difference in the curing process between the geopolymer concrete and the normal concrete. In the geopolymer concrete, there is a decrease in compressive strength if soaked for seven days and recovered with the increase in the age of immersion. Whereas for normal concrete, the compressive strength continues to increase with increasing age of immersion. © Published under licence by IOP Publishing Ltd.

关键词： Compressive strength

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Investigation of Vorticity Fields During Two-Phase Flow in Flow Boiling 6th

Investigation of Vorticity Fields During Two-Phase Flow in F...

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6th Multiphase Flow Journey, JEM 2021

作者： de Oliveira, Jeferson D. Copetti, Jacqueline B. Cardoso, Elaine M. FSG-University Center Center of Innovation and Technology Department of Mechanical Engineering Os Dezoito do Forte 2366 RS Caxias do Sul95020-472 Brazil The University of Vale do Rio dos Sinos Mechanical Engineering Graduate Program LETEF Laboratory of Thermal and Fluid Dynamic Studies Unisinos Avenue 950 RS São Leopoldo93022-750 Brazil UNESP—São Paulo State University Post-Graduation Program in Mechanical Engineering Av. Brasil 56 SP Ilha Solteira15385-000 Brazil

ISBN: (纸本)9783030934552

Flow patterns are found in many processes involving multiphase flows in the industry. This experimental investigation focuses on the behavior of the vorticity fields found in the liquid-vapor interface during flow boiling of R-600a with heat flux varying from 5 to 20 kW/m 2 and fixed mass flux of 890 kg/(m 2 s) at a saturation temperature of 17 ∘ C. Tests were performed in a horizontal tube with 1.0 mm ID. Four different flow patterns were identified based on images, and the vorticity fields were investigated using an optical flow method. © 2022, The Author(s), under exclusive license to Springer Nature Switzerland AG.

关键词： Flow boiling Flow patterns Optical flow Vorticity

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Antioxidant system alterations and oxidative stress caused by polyfluoroalkyl substances (PFAS) in exposed biota: a review

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Science of the Total Environment 2025年 977卷 179395页

作者： Soares, Lorena Oliveira Souza de Araujo, Gabriel Farias Gomes, Thais Braga Júnior, Sidney Fernandes Sales Cuprys, Agnieszka Katarzyna Soares, Raquel Moraes Saggioro, Enrico Mendes Laboratory of Environmental Health Assessment and Promotion Oswaldo Cruz Institute Oswaldo Cruz Foundation Av. Brasil 4365 RJ Rio de Janeiro21045-900 Brazil Post-Graduate Program in Public Health and Environment Sergio Arouca National School of Public Health Oswaldo Cruz Foundation Av. Leopoldo Bulhões 1480 RJ Rio de Janeiro21041-210 Brazil Faculty of Science and Technology Norwegian University of Life Sciences P.O. Box 5003 Ås1432 Norway Post-Graduate Program in Environmental Technology and Water Resources Department of Civil and Environmental Engineering – FT University of Brasília Darcy Ribeiro Campus Via L3 Norte DF Brasília70910-900 Brazil

Contamination of aquatic and terrestrial organisms by Perfluoroalkyl substances (PFAS), emerging contaminants, is widespread, as these compounds are present in water, soil, air, and food, owing to their environmental persistence. PFAS exposure induces biochemical process alterations associated with the disruption of the antioxidant defense system in several species. This review aims to discuss how PFAS-induced antioxidant system alterations lead to changes in biochemical processes in different organisms exposed to these pollutants. This disruption, then leads to an imbalance in antioxidant defense systems, contributing to the formation of reactive oxidative species (ROS), which, in turn, can be exacerbate oxidative stress, induce cellular damage, enhance lipid peroxidation, destabilize lysosomal membranes, and cause genotoxic effects, ultimately compromising DNA integrity. In acute tests, PFAS have led to mortality, growth inhibition, diminished behavioral and locomotor abilities, and reproductive impairment. PFAS-induced effects differ with varying species or types of substances, and further bioaccumulation through food chains exacerbates environmental contamination, carrying considerable risks. These findings demonstrate the complex and enduring impact of PFAS on environmental health, emphasizing the importance of this review in corroborating studies on sub-lethal toxicity in exposed organisms and how these effects reflect on the environment. © 2025 Elsevier B.V.

关键词： Biotic

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Extremum Seeking Boundary Control for Euler-Bernoulli Beam PDEs

arXiv

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arXiv 2025年

作者： Biazetto, Paulo H.F. de Andrade, Gustavo A. Oliveira, Tiago Roux Krstic, Miroslav Post-graduate Program in Automation and Systems Engineering Federal University of Santa Catarina Florianópolis88040-370 Brazil Department of Automation and Systems Engineering Federal University of Santa Catarina Florianópolis88040-370 Brazil Department of Electronics and Telecommunication Engineering State University of Rio de Janeiro Rio de Janeiro20550-900 Brazil Department of Mechanical and Aerospace Engineering University of California San DiegoCA92093-0411 United States

This paper presents the design and analysis of an extremum seeking (ES) controller for scalar static maps in the context of infinite-dimensional dynamics governed by the 1D Euler-Bernoulli (EB) beam Partial Differential Equation (PDE). The beam is actuated at one end (using position and moment actuators). The map’s input is the displacement at the beam’s uncontrolled end, which is subject to a sliding boundary condition. Notably, ES for this class of PDEs remains unexplored in the existing literature. To compensate for PDE actuation dynamics, we employ a boundary control law via a backstepping transformation and averaging-based estimates for the gradient and Hessian of the static map to be optimized. This compensation controller leverages a Schrödinger equation representation of the EB beam and adapts existing backstepping designs to stabilize the beam. Using the semigroup and averaging theory in infinite dimensions, we prove local exponential convergence to a small neighborhood of the unknown optimal point. Finally, simulations illustrate the effectiveness of the design in optimizing the unknown static map. Copyright © 2025, The Authors. All rights reserved.

关键词： Schrodinger equation

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The impact of copper oxide nanoparticles reinforced nanocellulose acetate membrane on antibacterial and dye removal Potency

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Results in engineering 2024年 23卷

作者： Yanuhar, Uun Suryanto, Heru Amin, Muhamad Maulana, Jibril Mohamad Lal, Mohammad Tamrin Caesar, Nico Rahman Study Program of Aquatic Resources Management Faculty of Fisheries and Marine Sciences Universitas Brawijaya East Java Indonesia Department of Mechanical and Industrial Engineering Faculty of Engineering Universitas Negeri Malang Jl. Semarang 5 Malang65145 Indonesia Department of Aquaculture Faculty of Fisheries and Marine Universitas Airlangga Jl. Dharmahusada Permai Surabaya60115 Indonesia Borneo Marine Research Institute Universiti Malaysia Sabah Jalan UMS Sabah Kota Kinabalu88400 Malaysia Doctoral Program of Environment Science Post Graduate Program Universitas Brawijaya Jalan Veteran East Java Malang65145 Indonesia

With the rapid growth of the textile, leather, cosmetics, and pharmaceutical industries, concerns about pollutants in these sectors, especially dye pollutants, are increasing. This research characterizes bacterial nanocellulose acetate membranes made from Sargassum extract reinforced with copper oxide nanoparticles and tests their antibacterial properties and dye removal in water. Sargassum sp. extract was fermented using Acetobacter xylinum for 10 days, producing bacterial nanocellulose, which was then esterified to create bacterial nanocellulose acetate. Copper oxide nanoparticles were added to the bacterial nanocellulose acetate solution in varying concentrations, cast, and oven-dried. The membrane was analyzed using Fourier-transform infrared spectroscopy, X-ray diffraction, scanning electron microscope, antibacterial activity, and dye removal. Results showed uniform copper oxide nanoparticles distribution on the membrane surface. Structure analysis revealed diffraction peaks at 35.44° and 38.57°, indicating a reduced crystalline index but improved membrane effectiveness. Antibacterial tests showed a zone of inhibition against bacterial growth, increasing with higher copper oxide nanoparticle content. The addition of copper oxide nanoparticles also influenced the dye removal capacity for Metanil Yellow, Congo Red, Eosin Yellow, Methylene Blue, and Malachite Green. The kinetic analysis showed that the adsorption process follows a pseudo-first-order model, with higher correlation coefficients (R2) compared to the pseudo-second-order model. © 2024 The Author(s)

关键词： Fourier transform infrared spectroscopy

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ADHD Diagnosis through Resting-State EEG Frequency Analysis with Random Forest

ADHD Diagnosis through Resting-State EEG Frequency Analysis ...

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Annual International Conference of the IEEE engineering in Medicine and Biology Society (EMBC)

作者： Guilherme R. Pedrollo Leia B. Bagesteiro Alexandre R. Franco Alexandre Balbinot Post-Graduate Program in Electrical Engineering Universidade Federal do Rio Grande do Sul Porto Alegre Brazil Department of Kinesiology San Francisco State University San Francisco USA Child Mind Institute The Nathan Kline Institute for Psychiatric Research NYU Grossman School of Medicine New York USA

ISBN: (数字)9798350371499

ISBN: (纸本)9798350371505

Attention-deficit hyperactivity disorder (ADHD) affects about 5% of the population. In order to minimize ADHD effects, it is important to identify its biomarkers. We analyzed electroencephalographic (EEG) signals using a random forest (RF) classifier optimized with a genetic algorithm (GA) to find differences between control and ADHD groups. Data from 856 participants were analyzed with a preprocessing procedure that included artifact subspace reconstruction (ASR) and independent component analysis (ICA). After preprocessing and GA optimization, the RF classifier achieved 88.6% total average accuracy considering the theta frequency band. This outcome suggests that this approach has great potential as a biomarker analyzer for ADHD diagnosis.

关键词： Filters Quality control Independent component analysis Forestry Biomarkers Feature extraction Electroencephalography Optimization Genetic algorithms Classification tree analysis

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Statistical trend characteristics of rainfall over Kerala, India evaluated through analysing modern era retrospective analysis for research and applications (MERRA-2) reanalysis data

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Bulletin of Atmospheric Science and Technology 2025年第1期6卷 1-38页

作者： Modon Valappil, Ninu Krishnan de Oliveira Júnior, José Francisco Mendes, David Jamjareegulgarn, Punyawi Hamza, Vijith Environmental Technology Division School of Industrial Technology Universiti Sains Malaysia Pulau Pinang 11800 Malaysia Laboratory of Applied Meteorology and Environment (LAMMA) Institute of Atmospheric Sciences (ICAT) Federal University of Alagoas (UFAL) LourivalMeloMota avenue S/N Alagoas Tabuleiro dos Martins Maceió CEP: 57072-970 Brazil Post-Graduate Program in Aerospace Engineering – PPGEA Federal University of Rio Grande do Norte – UFRN Campus Universitário Lagoa Nova RN Natal Brazil Prince of Chumphon Campus King Mongkut’s Institute of Technology Ladkrabang Chumphon 86160 Thailand Kerala State Disaster Management Authority Kerala Thiruvananthapuram 695033 India

Statistical trends of rainfall (annual and seasonal rainfalls) in Kerala, India were characterised using the 44-years (1980–2023) data of Modern-Era Retrospective Analysis for Research and Applications (MERRA) version 2. Monthly rainfall data were collected from the selected fifty locations which represent the state as a whole, and the collected data were then categorised into annual as well as seasonal (winter, summer, monsoon and post-monsoon) datasets based on the classification proposed by Indian Meteorological Organisation (IMD). Lag-1 autocorrelation, modified Mann Kendall (mMK), Pettitt test and Theil-Sen’s slope methods were used to determine the statistical characteristics of rainfalls in Kerala. Mean rainfalls were 3124 mm, 66 mm, 527 mm, 1667 mm and 862 mm, respectively, for annual, winter, summer, monsoon and post-monsoon periods. mMK based statistical trend analysis revealed an overall decreasing trend characteristics in annual (-0.54 mm.y⁻¹), monsoon (-1.20 mm.y⁻¹), and post-monsoon (-0.93 mm.y⁻¹) seasons whereas winter and summer rainfalls showed an increasing trend (0.67 mm.y⁻¹ and 3.40 mm.y⁻¹, respectively) for the state as a single unit. Pettitt test indicated four dominant periods of change in rainfall characteristics in the study area that spanned over the decades of 1980, 1990, 2000 and 2010, in which major changes in annual and seasonal rainfalls were occurred during 1990’s, 2000’s and 2010’s. Theil-Sen’s slope-based estimation of rate of change in rainfall showed an average variation of -4.33 mm.y⁻¹, 0.17 mm.y⁻¹, 6.27 mm.y⁻¹, -6.54 mm.y⁻¹ and − 3.28 mm.y⁻¹ for annual, winter, summer, monsoon and post-monsoon seasons, respectively. Though the winter and summer rainfalls showed an increase in its rate during the period of analysis, annual rainfall showed an overall reduction in the amount of rainfall received in the state. The study ulti

关键词： MERRA-2 Modified Mann Kendall Period of change Rainfall variation Spatial statistics

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A Novel Non-Linear Peridynamic Model for Quasi-Brittle Materials Under Cyclic Loading

SSRN

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SSRN 2024年

作者： Friedrich, Leandro F. Colpo, Angélica B. Iturrioz, Ignacio Zanichelli, Andrea Vantadori, Sabrina Departament of Mechanical Engineering Federal University of Pampa Av. Tiaraju 810 AlegreteCEP 97546-550 Brazil Mechanical Post-Graduate Program Federal University of Rio Grande do Sul Sarmento Leite 425 Porto AlegreCEP 90050-170 Brazil Department of Engineering & Architecture University of Parma Parco Area delle Scienze 181/A Parma43124 Italy

In the present paper, a novel non-linear peridynamic (PD) model is proposed to numerically simulate the fatigue behaviour of quasi-brittle materials. The model implements a non-linear degradation law for the bonds, function of the number of loading cycles. More precisely, a calibration function and a calibration parameter are included in such a law. The novel PD model is applied to simulate cyclic three-point bending experimental tests performed on concrete notched beams, and available in the literature. The results are presented in terms of fatigue lifetime, Paris law parameters and crack path. © 2024, The Authors. All rights reserved.

关键词： Bending tests

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Solid waste management in the paper industry 5

Solid waste management in the paper industry

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5th International Conference on Energy, Environmental and Information System, ICENIS 2020

作者： Devichi Wibowo, Isabella Purwanto, P. Suherman, S. Master Program of Environmental Science Post-Graduate Studies Universitas Diponegoro Semarang Indonesia Department of Chemical Engineering Faculty of Engineering Universitas Diponegoro Semarang Indonesia

The industry developed rapidly since the Industrial Revolution in the 18th century. The side effect of industrial development was a large amount of non-hazardous waste and hazardous waste. All of this waste must be managed properly so that environmental sustainability is maintained and does not cause harm or problems to the community. A review will be conducted from various research journals in various countries and the types of waste also vary, namely plastic, pulp and paper industry waste, and other solid waste. A comparison of solid waste management will be carried on to reduce the generation of waste in the environment. © The Authors, published by EDP Sciences, 2020.

关键词： Solid wastes

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