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Big data technology in infectious diseases modeling,simulation,and prediction after the COVID-19 outbreak

智慧医学(英文) 2023年第2期3卷 85-96页

作者： Honghao Shi jingyuan Wang jiawei Cheng Xiaopeng Qi Hanran ji claudio j struchiner Daniel AM Villela Eduard V Karamov Ali S Turgiev School of Computer Science and Engineering Beihang UniversityBeijing 100191China Center for Global Public Health Chinese Center for Disease Control and PreventionBeijing 102211China Fundação Getúlio Vargas Rio de JaneiroBrazil Instituto de Medicina Social Hesio Cordeiro Universidade do Estado do Rio de JaneiroRio de JaneiroBrazil Programa de Computação Científica Fundação Oswaldo CruzRio de JaneiroBrazil Gamaleya National Research Center for Epidemiology and Microbiology of the Russian Ministry of Health Russia National Medical Research Center of Phthisiopulmonology and Infectious Diseases of the Russian Ministry of Health Russia

After the outbreak of COVID-19,the interaction of infectious disease systems and social systems has challenged traditional infectious disease modeling *** from the research purpose and data,researchers im-proved the structure and data of the compartment model or used agents and artificial intelligence based models to solve epidemiological *** terms of modeling methods,the researchers use compartment subdivi-sion,dynamic parameters,agent-based model methods,and artificial intelligence related *** terms of factors studied,the researchers studied 6 categories:human mobility,nonpharmaceutical interventions(NPIs),ages,medical resources,human response,and *** researchers completed the study of factors through modeling methods to quantitatively analyze the impact of social systems and put forward their suggestions for the future transmission status of infectious diseases and prevention and control *** review started with a research structure of research purpose,factor,data,model,and *** on the post-COVID-19 infectious disease prediction simulation research,this study summarized various improvement methods and analyzes matching improvements for various specific research purposes.

关键词： Infectious disease model Data embedding Social system Dynamic Modeling the social systems

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Hepatitis B virus genotypes in precision medicine of hepatitis Brelated hepatocellular carcinoma:Where we are now

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World journal of Gastrointestinal Oncology 2024年第4期16卷 1097-1103页

作者： Caecilia H C Sukowati Sri jayanti Turyadi Turyadi David H Muljono claudio Tiribelli Eijkman Research Center for Molecular Biology Research Organization for HealthNational Research and Innovation Agency of IndonesiaJakarta 10340Indonesia Liver Cancer Unit Fondazione Italiana Fegato ONLUSTrieste 34149Italy Faculty of Medicine Hasanuddin UniversityMakassar 90245South SulawesiIndonesia Faculty of Medicine and Health University of SydneySydney 2050Australia

Hepatitis B virus(HBV)infection is a major player in chronic hepatitis B that may lead to the development of hepatocellular carcinoma(HCC).HBV genetics are diverse where it is classified into at least 9 genotypes(A to I)and 1 putative genotype(j),each with specific geographical distribution and possible different clinical outcomes in the *** diversity may be associated with the precision medicine for HBV-related HCC and the success of therapeutical approaches against HCC,related to different pathogenicity of the virus and host *** Editorial discusses recent updates on whether the classification of HBV genetic diversity is still valid in terms of viral oncogenicity to the HCC and its precision medicine,in addition to the recent advances in cellular and molecular biology technologies.

关键词： Hepatitis B virus Hepatocellular carcinoma Genotypes Pathogenesis Precision medicine

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Association between Helicobacter pylori infection,mismatch repair,HER2 and tumor-infiltrating lymphocytes in gastric cancer

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World journal of Gastrointestinal Oncology 2024年第6期16卷 2487-2503页

作者： Carlos A Castaneda Miluska Castillo Luis A Bernabe joselyn Sanchez Matteo Fassan Katherine Tello Ignacio Ivan Wistuba Ivan Chavez Passiuri Eloy Ruiz juvenal Sanchez Fernando Barreda Daniel Valdivia Yaqueline Bazan Milagros Abad-Licham claudio Mengoa Hugo Fuentes Paola Montenegro Ebert Poquioma Raul Alatrista claudio j Flores Luis Taxa Faculty of Health Sciences Universidad Cientifica del SurLima 15038Peru GECO PERU Grupo de Estudios Clinicos Oncologicos del PeruLima 15038Peru Department of Research Instituto Nacional de Enfermedades NeoplasicasLima 15038Peru Faculty of Human Medicine Universidad Ricardo PalmaLima 15039Peru Department of Medicine Surgical Pathology&Cytopathology UnitUniversity of PaduaPadua 35121Italy Department of Translational Molecular Pathology The University of Texas MD Anderson Cancer CenterHoustonTX 77030United States Department of Abdominal Surgery Instituto Nacional de Enfermedades NeoplasicasLima 15038Peru Department of Pathology Instituto Nacional de Enfermedades NeoplasicasLima 15038Peru Department of Medical Specialties Instituto Nacional de Enfermedades NeoplasicasLima 15038Peru Department of Pathology Instituto Regional de Enfermedades Neoplasicas del NorteTrujillo 13001Peru Faculty of Human Medicine Universidad Privada Antenor OrregoTrujillo 13008Peru Department of Surgery Instituto Regional de Enfermedades Neoplasicas del SurArequipa 04002Peru Department of Medical Oncology Instituto Nacional de Enfermedades NeoplasicasLima 15038Peru Department of Epidemiology Instituto Nacional de Enfermedades NeoplasicasLima 15038Peru Unidad de Investigación Básica y Traslacional Oncosalud-AUNALima 15038Peru Faculty of Medicine Universidad San Martin de PorresLima 15008Peru

BACKGROUND The influence of Helicobacter-pylori(***)infection and the characteristics of gastric cancer(GC)on tumor-infiltrating lymphocyte(TIL)levels has not been extensively *** of infiltrating-immune-cell subtypes as well as survival is necessary to obtain comprehensive *** To determine the rates of deficient mismatch-repair(dMMR),HER2-status and *** infection and their association with TIL levels in *** Samples from 503 resected GC tumors were included and TIL levels were evaluated following the international-TILs-working-group recommendations with assessment of the intratumoral(IT),stromal(ST)and invasive-border(IB)*** density of CD3,CD8 and CD163 immune cells,and dMMR and HER2-status were determined by immunohistochemistry(IHC).*** infection was evaluated by routine histology and quantitative PCR(qPCR)in a subset of *** dMMR was found in 34.4%,HER2+in 5%and ***-positive in 55.7%of *** IT-TIL was associated with grade-3(P=0.038),while ST-TIL with grade-1(P<0.001),intestinal-histology(P<0.001)and no-recurrence(P=0.003).dMMR was associated with high TIL levels in the ST(P=0.019)and IB(P=0.01)compartments,and STCD3(P=0.049)and ST-CD8(P=0.05)***2-was associated with high IT-CD8(P=0.009).*** was associated with high IT-TIL levels(P=0.009)when assessed by routine-histology,and with high TIL levels in the 3 compartments(P=0.002-0.047)and CD8 density in the IT and ST compartments(P=0.001)when assessed by qPCR.A longer overall survival was associated with low IT-CD163(P=0.003)and CD8/CD3(P=0.001 in IT and P=0.002 in ST)and high IT-CD3(P=0.021),ST-CD3(P=0.003)and CD3/CD163(P=0.002).CONCLUSION TIL levels were related to dMMR and *** CD8/CD3 and high CD163/CD3 were associated with lower recurrence and longer survival.

关键词： Lymphocytes Macrophages Gastric cancer Helicobacter pylori HER2 Mismatch repair

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Resampling approaches for the quantitative analysis of spatially distributed cells

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Data Intelligence 2024年第1期6卷 104-119页

作者： Giorgio Bertolazzi Michele Tumminello Gaia Morello Beatrice Belmonte claudio Tripodo Department of Economics Business and StatisticsUniversity of PalermoPalermoItaly Tumor Immunology Unit Department of Health SciencesUniversity of PalermoPalermoItaly Histopathology Unit Institute of Molecular Oncology Foundation(IFOM)ETS-The AIRC Institute of Molecular OncologyMilanItaly

Image segmentation is a crucial step in various image analysis pipelines and constitutes one of the cutting-edge areas of digital *** advent of quantitative analysis has enabled the evaluation of millions of individual cells in tissues,allowing for the combined assessment of morphological features,biomarker expression,and spatial *** recorded cells can be described as a point pattern ***,the classical statistical approaches to point pattern processes prove unreliable in this context due to the presence of multiple irregularly-shaped interstitial cell-devoid spaces in the domain,which correspond to anatomical features(***,lipid vacuoles,glandular lumina)or tissue artefacts(*** fractures),and whose coordinates are *** interstitial spaces impede the accurate calculation of the domain area,resulting in biased clustering ***,the mistaken inclusion of empty regions of the domain can directly impact the results of hypothesis *** literature currently lacks any introduced bias correction method to address interstitial cell-devoid *** address this gap,we propose novel resampling methods for testing spatial randomness and evaluating relationships among different cell *** methods obviate the need for domain area estimation and provide non-biased clustering *** created the SpaceR software(https://***/GBertolazzi/SpaceR)to enhance the accessibility of our methodologies.

关键词： Digital pathology spatial cytometry spatial clustering spatial randomness resampling

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Estimating the size of Aedes aegypti populations from dengue incidence data: Implications for the risk of yellow fever outbreaks

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Infectious Disease Modelling 2017年第4期2卷 441-454页

作者： Eduardo Massad Marcos Amaku Francisco Antonio Bezerra Coutinho claudio joséstruchiner Luis Fernandez Lopez Annelies Wilder-Smith Marcelo Nascimento Burattini School of Medicine University of Sao PauloBrazil London School of Hygiene and Tropical Medicine UK College of Life and Natural Sciences The University of DerbyUK Programme of Scientific Computation Fundação Oswaldo CruzRio de JaneiroBrazil Li Ka Shing Knowledge Institute St Michael's HospitalTorontoCanada Institute of Public Health University of HeidelbergGermany Department Public Health and Clinical Medicine Epidemiology and Global HealthUmeåUniversitySE-90185 UmeåSweden Lee Kong Chian School of Medicine Nanyang Technological UniversitySingapore Hospital São Paulo Escola Paulista de MedicinaUniversidade Federal de São PauloSão PauloSPBrazil

In this paper we present a model to estimate the density of aedes mosquitoes in a community affected by *** method consists in fitting a continuous function to the incidence of dengue infections,from which the density of infected mosquitoes is derived *** derivations allow the calculation of the latent and susceptible mosquitoes'densities,the sum of the three equals the total mosquitoes'*** method is illustrated with the case of the risk of urban yellow fever resurgence in dengue infested areas but the same procedures apply for other aedes-transmitted infections like Zika and chikungunya viruses.

关键词： Aedes aegypti Mosquitoes'densities Dengue Zika virus Yellow fever

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Modelling the test, trace and quarantine strategy to control the COVID-19 epidemic in the state of São Paulo, Brazil

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Infectious Disease Modelling 2021年第1期6卷 46-55页

作者： Marcos Amaku Dimas Tadeu Covas Francisco Antonio Bezerra Coutinho Raymundo Soares Azevedo Neto claudio struchiner Annelies Wilder-Smith Eduardo Massad School of Medicine University of Sao Paulo and LIM01-HCFMUSPSao PauloBrazil Instituto Butantan Sao PauloBrazil School of Applied Mathematics Fundacao Getulio VargasRio de JaneiroBrazil School of Veterinary Medicine University of Sao PauloSao PauloBrazil Department Public Health and Clinical Heidelberg Institute of Global HealthUniversity of HeidelbergGermany Medicine Epidemiology and Global HealthUmeåUniversitySE-90185UmeåSweden Department of Disease Control London School of Hygiene and TropicalMedicineUK

Testing for detecting the infection by SARS-CoV-2 is the bridge between the lockdown and the opening of *** this paper we modelled and simulated a test-trace-andquarantine strategy to control the COVID-19 outbreak in the State of São Paulo,*** State of São Paulo failed to adopt an effective social distancing strategy,reaching at most 59%in late March and started to relax the measures in late june,dropping to 41%in 08 ***,São Paulo relies heavily on a massive testing strategy in the attempt to control the *** alternative strategies combined with economic evaluations were *** strategy included indiscriminately testing the entire population of the State,reaching more than 40 million people at a maximum cost of 2.25 billion USD,that would reduce the total number of cases by the end of 2020 by 90%.The second strategy investigated testing only symptomatic cases and their immediate contacts e this strategy reached a maximum cost of 150 million USD but also reduced the number of cases by 90%.The conclusion is that if the State of São Paulo had decided to adopt the simulated strategy on April the 1st,it would have been possible to reduce the total number of cases by 90%at a cost of 2.25 billion US dollars for the indiscriminate strategy but at a much smaller cost of 125 million US dollars for the selective testing of symptomatic cases and their contacts.

关键词： COVID-19 SARS-CoV-2 Testing Cost-analysis Modelling

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Economic and Environmental Performance of Biowaste-to-energy Technologies for Small-scale Electricity Generation

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journal of Modern Power Systems and Clean Energy 2022年第1期10卷 12-18页

作者： Max j.A.Romero Rivas Davide Capuano claudio Miranda Graded S.p.A. NapoliNA 80141Italy

Electricity is predicted to be the energy vector that will undergo major changes in the future,and a transition would be observed in the resources such as waste and residual biomass that we use to satisfy the energy ***,this study aims to highlight the main economic and environmental performances of different biowaste-to-energy technologies for small-scale electricity generation by comparing the direct combustion of refined vegetable oil obtained from waste cooking oils(thermal pathway),anaerobic digestion of biowaste(biochemical pathway),and gasification of wood residues(thermochemical pathway).The economic analysis is mainly based on personal experiences in the energy sector and shows an overview of the performance in investment of combined heat and power(CHP)systems,ranging from 100 to 500 kW for a period of 20 *** environmental assessment is conducted considering the life-cycle thinking approach using support from the openLCA software,product environmental footprint(PEF)database,and previous studies that have reported environmental inventory data from real industrial cases.

关键词： Biowaste-to-energy small-scale generation economic assessment environmental assessment

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Finite Size Effects in the Dynamics of Opinion Formation

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Communications in Computational Physics 2007年第2期2卷 177-195页

作者： Raul Toral claudio j.Tessone Instituto Mediterr´aneo de Estudios Avanzados(IMEDEA) CSIC-UIBEd.Mateu OrfilaCampus UIBE-07122 Palma de MallorcaSpain.

For some models of relevance in the social sciences we review some exam-ples in which system size plays an important role in the final outcome of the *** discuss the conditions under which changes of behavior can appear only when the number of agents in the model takes a finite *** changes of behavior can be related to the apparent phase transitions that appear in some physical *** show examples in the Galam's model of opinion transmission and the Axelrod's model of culture formation stressing the role that the network of interactions has on the main results of both ***,we present the phenomenon of system-size stochastic resonance by which a forcing signal(identified as an advertising agent)is optimally amplified by a population of the right(intermediate)*** work stresses the role that the system size has in the dynamics of social systems and the inappropriateness of taking the thermodynamic limit for these systems.

关键词： Dynamics of social systems finite size effects scaling laws.

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Petrology and geochemistry of mafic and ultramafic cumulate rocks from the eastern part of the Sabzevar ophiolite(NE Iran): Implications for their petrogenesis and tectonic setting

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Geoscience Frontiers 2020年第6期11卷 2347-2364页

作者： Fatemeh Rahmani Mohamad Ali Mackizadeh Moussa Noghreyan claudio Marchesi Carlos j.Garrido Department of Geology Faculty of SciencesUniversity of IsfahanP.O.Box:81746-73441IsfahanIran Instituto Andaluz de Ciencias de La Tierra(IACT) CSIC-Universidad de GranadaAvenida de Las Palmeras 418100ArmillaGranadaSpain Departamento de Mineralogía y Petrología Facultad de CienciasUniversidad de GranadaAvenida Fuentenueva s/n18002GranadaSpain

The Late Cretaceous Sabzevar ophiolite represents one of the largest and most complete fragments of Tethyan oceanic lithosphere in the NE *** is mainly composed of serpentinized mantle peridotites slices;nonetheless,minor tectonic slices of all crustal sequence constituents are observed in this *** crustal sequence contains a well-developed ultramafic and mafic cumulates section,comprising plagioclase-bearing wehrlite,olivine clinopyroxenite,olivine gabbronorite,gabbronorite,amphibole gabbronorite and quartz gabbronorite with adcumulate,mesocumulate,heteradcumulate and orthocumulate *** crystallization order for these rocks is olivine±chromian spinel→clinopyroxene→plagioclase→orthopyroxene→*** presence of primary magmatic amphiboles in the cumulate rocks shows that the parent magma evolved under hydrous ***,the studied rock units are characterized by low TiO2(0.18-0.57 wt.%),P2 O5(jacent *** REE plots of these rocks display increasing trend from La to Sm,positive Eu anomaly(Eu/Eu*=1.06-1.54)and an almost flat pattern from medium REE(MREE)to heavy REE(HREE)region[(Gd/Yb)N=1-1.17].Moreover,clinopyroxenes from the cumulate rocks have low REE contents and show marked depletion in light REE(LREE)compared to MREE and HREE[(La/Sm)N=0.10-0.27 and(La/Yb)N=0.08-0.22].The composition of calculated melts in equilibrium with the clinopyroxenes from less evolved cumulate samples are closely similar to island arc tholeiitic(IAT)*** mineralogy,geochemical features

关键词： Petrology Geochemistry Cumulate rocks Sabzevar ophiolite Supra-subduction zone Iran

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Antimicrobial Activity, Structural, Crystallographic and Thermal Characteristics of Alpha-Titanium Phosphate Promoted by Silver Ions

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Materials Sciences and Applications 2024年第8期15卷 253-269页

作者： Enzo Erbisti Garcia Agnes Maria Cupertino Fernandes Araujo Gerson Alberto Valencia Albitres Daniela de França da Silva Freitas Danielle Mattos Mariano Carlos Magno Fialho Soares Sibele Piedade Cestari Marco Antônio Lemos Miguel Luis claudio Mendes Institute of Macromolecules Professora Eloisa Mano Federal University of Rio de Janeiro Avenida Horacio Macedo 2030 Centro de Tecnologia Bloco J Ilha do Fundo Rio de Janeiro Brazil Institute of Microbiology Paulo de Ges Federal University of Rio de Janeiro Centro de Ciencias da Saude Bloco I Ilha do Fundo Rio de Janeiro Brazil Innovation in Polymer Engineering (PIEP) University of Minho Guimares Portugal

The recent global spread of the pandemic underscores the necessity of seeking new materials effective against microorganisms. Nanotechnology offers avenues for developing multifunctional materials. In this study, alpha-titanium phosphate (α-TiP) nanoparticles were synthesized and treated with silver salt to enhance their antimicrobial properties. The physicochemical characteristics and antimicrobial activity were evaluated. It was revealed by X-ray diffraction analysis that the structural integrity of α-TiP was influenced by ethylenediamine and silver ions. Distinct degradation profiles for each chemical modification were shown by thermogravimetric analysis. Infrared spectroscopy detected shifts and new absorption peaks in the spectra depending on the type of modification. Energy dispersive spectroscopy confirmed the disaggregation of α-TiP galleries following the addition of silver salt, which increased their effectiveness against microorganisms. Notably, only the sample treated with silver ions exhibited antimicrobial action. Antimicrobial activity was tested against the bacteria of medical importance Escherichia coli, Salmonella Enteritidis, Pseudomonas aeruginosa, Staphylococcus aureus, Bacillus cereus, Listeria momocytogenes and the yeast Candida albicans. All microorganisms were inhibited by sample containing silver. Minor inhibition was observed against the Gram-positive bacteria L. monocytogenes and Bacillus cereus, while the greatest inhibition occurred against the fungus (yeast) C. albicans. The results revealed a potential application of the nanoparticles for control of microorganisms in public health.

关键词： Titanium Phosphate Silver Nitrate Antimicrobial Action

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