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Agent-based modeling of COVID-19 outbreaks for New york state and UK:Parameter identification algorithm

Infectious Disease Modelling 2022年第1期7卷 30-44页

作者： olga Krivorotko Mariia Sosnovskaia Ivan Vashchenko Cliff Kerr Daniel Lesnic Institute of Computational Mathematics and Mathematical Geophysics Siberian Branch of the Russian Academy of Sciences 6 Prospect Akademika Lavrentieva StreetNovosibirsk630090Russia Novosibirsk State University 2 Pirogova StreetNovosibirsk630090Russia Institute for Disease Modeling Bill&Melinda Gates FoundationSeattleUSA University of Leeds LS29JTUK

This paper uses Covasim,an agent-based model(ABM)of COVID-19,to evaluate and scenarios of epidemic spread in New york State(USA)and the *** parameters such as contagiousness(virus transmission rate),initial number of infected people,and probability of being tested depend on the region's demographic and geographical features,the containment measures introduced;they are calibrated to data about COVID-19 spread in the region of *** the first stage of our study,epidemiological data(numbers of people tested,diagnoses,critical cases,hospitalizations,and deaths)for each of the mentioned regions were *** data were characterized in terms of seasonality,stationarity,and dependency spaces,and were extrapolated using machine learning techniques to specify unknown epidemiological parameters of the *** the second stage,the Optuna optimizer based on the tree Parzen estimation method for objective function minimization was applied to determine the model's unknown *** model was validated with the historical data of *** modeled results of COVID-19 spread in New york State and the UK have demonstrated that if the level of testing and containment measures is preserved,the number of positive cases in New york State remain the same during March of 2021,while in the UK it will reduce.

关键词： Epidemiology Agent-based modeling COVID-19 Interventions analysis Coronavirus data analysis Forecasting scenarios Reproduction number Optimization Parameter identification

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Fungal infection dynamics in response to temperature in the lepidopteran insect Galleria mellonella

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Insect Science 2018年第3期25卷 454-466页

作者： Vadim y. Kryukov olga N. yaroslavtseva Miranda M. A. Whitten Maksim V. Tyurin Katherine J. Ficken Carolyn Greig Nadja R. Melo Viktor V. Glupov Ivan M. Dubovskiy Tariq M. Butt Institute of Systematics and Ecology of Animals Siberian Branch of Russian Academy of Science Novosibirsk Russia Institute of Life Science College of Medicine Swansea University Swansea Wales UK Department of Biosciences College of Science Swansea University Swansea Wales UK

This study examines how the dynamics of fungus-insect interactions can be modulated by temperature. The wax moth, Galleria mellonella, is a well-studied and important model insect whose larvae in the wild develop optimally at around 34 ℃ in beehives. However, surprisingly little research on wax moths has been conducted at relevant temperatures. In this study, the entomopathogenic fungus Metarhizium robertsii inflicted rapid and substantial mortality on wax moth larvae maintained at a constant temperature of 24 ℃, but at 34 ℃ a 10 fold higher dose was required to achieve an equivalent mortality. The cooler temperature favored fungal pathogenicity, with condial adhesion to the cuticle, germination and hemocoel invasion all significantly enhanced at 24 ℃, compared with 34 ℃. The wax moth larvae immune responses altered with the temperature, and with the infective dose of the fungus. Enzyme-based immune defenses （lysozyme and phenoloxidase） exhibited enhanced activity at the warmer temperature. A dramatic upregulation in the basal expression of galiomicin and gallerimycin was triggered by cooling, and this was augmented in the presence of the fungus. Profiling of the predominant insect epicuticular fatty acids revealed a 4-7 fold increase in palmetic, oleic and linoleic acids in larvae maintained at 24 ℃ compared with those at 34 ℃, but these failed to exert fungistatic effects on topically applied fungus. This study demonstrates the importance of choosing environmental conditions relevant to the habitat of the insect host when determining the dynamics and outcome of insect/fungus interactions, and has particular significance for the application of entomopathogens as biocontrol agents.

关键词： biocontrol entomopathogenic fungus immunity Metarhizium temperature

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Indicators of success for smart law enforcement in protected areas:A case study for Russian Amur tiger(Panthera tigris altaica)reserves

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Integrative Zoology 2016年第1期11卷 2-15页

作者： Michiel H.H.HÖTTE Igor A.KOLODIN Sergei L.BEREZNUK Jonathan C.SLAGHT Linda L.KERLEy Svetlana V.SOUTyRINA Galina P.SALKINA olga y.ZAUMySLOVA Emma J.STOKES Dale G.MIQUELLE Wildlife Conservation Society BronxNew YorkUSA Phoenix Fund VladivostokRussian Federation Zoological Society of London Regent’s ParkLondonEngland Sikhote-Alin Biosphere Zapovednik Primorskii KraiRussian Federation Lazovskii State Nature Zapovednik Primorskii KraiRussian Federation Department of Ecology Far Eastern Federal UniversityAyaksRusski Island

Although considerable conservation resources have been committed to develop and use law enforcement monitoring and management tools such as SMART,measures of success are ill-defined and,to date,few reports detail results ***,we present 4 case studies from protected areas with Amur tigers(Panthera tigris altaica)in Russia,in which indicators of success were defined and evaluated at *** ultimate goal was an increase in tiger numbers to 1 individual/100 km^(2)at each *** predicted that improvements in law enforcement effectiveness would be followed by increases in prey numbers and,subsequently,tiger *** used short-term and long-term indicators of success,including:(i)patrol team effort and effectiveness;(ii)catch per unit effort indicators(to measure reductions in threats);and(iii)changes in target species *** addition to implementing a monitoring system,we focused on improving law enforcement management using an adaptive management *** 4 years,we noted clear increases in patrol effort and a partial reduction in *** we did not detect clear trends in ungulate numbers,tiger populations remained stable or increased,suggesting that poaching of tigers may be more limiting than prey *** effectiveness is needed before a clear reduction in threats can be noted,and more time is needed before detecting responses in target ***,delineation of concrete goals and indicators of success provide a means of evaluating progress and *** monitoring should be a central component of law enforcement strategies for protected areas.

关键词： adaptive patrol management Amur tiger anti-poaching law enforcement monitoring SMART

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Nanostructured biohybrid material with wide-ranging antiviral action

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Nano Research 2023年第8期16卷 11455-11463页

作者： Noelia Losada-Garcia Angela Vazquez-Calvo David Ortega-Alarcon olga Abian Adrian Velazquez-Campoy Pilar Domingo-Calap Antonio Alcami Jose M.Palomo Instituto de Catálisis y Petroleoquímica(ICP) CSICC/Marie Curie 2.Madrid 28049Spain Centro de Biología Molecular Severo Ochoa Consejo Superior de Investigaciones Científicas(CSIC)-Universidad Autónoma de Madrid(UAM)Madrid 28049Spain Institute of Biocomputation and Physics of Complex Systems(BIFI) Joint Unit GBsC-CSIC-BIFIUniversity of ZaragozaZaragoza 50018Spain Fundación Instituto de Investigación Sanitaria de Aragón(IIS Aragón) Zaragoza 50009Spain CIBERehd Madrid 28029Spain Instituto de Biología Integrativa de Sistemas I2SyBioUniversitat de València-CSICValència E-46071Spain

Respiratory pathogens kill more people than any other infectious agent each year *** of novel,economically friendly,sustainable,and highly efficient materials against viruses is a major ***,we describe a nanostructured material composed of very small crystalline phosphate copper nanoparticles synthesized using a new biohybrid technology that employs a biological agent for its formation at room temperature in aqueous *** evaluation of different enzymes in the final preparation of the nanomaterial or even in synthetic methods was *** characterization revealed the formation of Cu species in the protein *** best biomaterial synthesized using a lipase called BioCuNPs showed excellent inhibition capacity against functional proteins of severe acute respiratory syndrome coronavirus 2(SARS-CoV-2);for example,assent 3-chymotrypsin like protease(3CLpro)complete inhibition was achieved by using 5µg/mL,or acetone(ACE)–spike protein interaction was inhibited by more than 80%in the presence of 400µg/mL of *** these in vitro results into account,an efficacy analysis against human coronavirus 229E(HCoV-E229)coronavirus was performed.A virus reduction of 99%was obtained in 5 ***,SARS-CoV-2 virus was tested to demonstrate high efficiency,with>99%inhibition in 15 min using 500 microgram of *** determine the wide applicability of this nanohybrid against viruses,an evaluation was carried out against a non-enveloped virus such as Human Rhinovirus(HRV-14),obtaining a virus reduction of 99.9%in 5 ***,the virucidal capacity against different bacteriophages was also evaluated,obtaining an excellent inhibition effect against PhageΦX174(99.999%reduction in 5 min).

关键词： antiviral compound coronaviruses copper nanoparticles nanobiotechnology viruses

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Relationship between Ethanol and 2-phenylethanol Stress Tolerance and Fatty Acid Compositions of Saccharomyces cerevisiae

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Journal of Food Science and Engineering 2013年第2期3卷 71-78页

作者： olga Mameeva Valentin Podgorsky Department of Physiology of Industrial Microorganisms Zabolotny Institute of Microbiology and Virology of National Academy ofSciences of Ukraine Kiev D03680 Ukraine

In the present study, we investigated of the ethanol （Eth）, 2-phenylethanol （2-PE） and ethanol/2-phenylethanol （Eth/2-PE） stress tolerance and established relationship between stress tolerance and fatty acid compositions of wine yeast strain S. cerevisiae UCM y-524 in relation to different cultivation factors. Changes in cell membrane fatty acid profiles studied under different temperature and media. The active oxygenation, semi-aerobic cultivation supplemented Tween 80 conditions were used in different combinations. The concentrations of 2-PE and Eth, the fatty acids methyl esters （FAMES） in the media were measured by GC-MS analyses. 2-PE, Eth, FAMES were identified by NIST02 MS database at the 2-PE and Eth standard solution （Merck, Germany）, bacterial FAMES standard （Supelco）. Palmitoleic and oleic acid were dominated for S. cerevisiae UCM y-524. The unsaturated/saturated fatty acid （UFA/SFA） ratio was higher than five for S. cerevisiae UCM y-524 at 14 ~C in simple medium and about more than three for other conditions. It has been found that yeast cells grown in the presence of the 2-PE, Eth and Eth/2-PE appear to increase the amount of unsaturated fatty acids, especially oleic acid, in cellular lipids especially under active oxygenation supplemented with Tween 80. S. cerevisiae UCM y-524 has a higher tolerance under 2-PE, Eth and Eth/2-PE stress at 28 ~C in a simple medium under aerobic conditions. A higher concentration of unsaturated fatty acids in the membrane S. cerevisiae UCM y-524 and a lower temperature under aerobic conditions, has been considered to have a positive influence on the excretion of 2-phenylethanol.

关键词： yeasts 2-phenylethanol ethanol stress tolerance fatty acids.

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Population dynamics of Amur tigers(Panthera tigris altaica)in Sikhote-Alin Biosphere Zapovednik:1966–2012

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Integrative Zoology 2015年第4期10卷 315-328页

作者： Dale G.MIQUELLE Evgeny N.SMIRNOV olga yu.ZAUMySLOVA Svetlana V.SOUTyRINA Douglas H.JOHNSON Wildlife Conservation Society BronxNew YorkUSA Sikhote-Alin Biosphere Zapovednik TerneiPrimorskii KraiRussia USGS Northern Prairie Wildlife Research Center Saint PaulMinnesotaUSA

In 2010,the world’s tiger(Panthera tigris)range countries agreed to the goal of doubling tiger numbers over 12 years,but whether such an increase is biologically feasible has not been ***-term monitoring of tigers in Sikhote-Alin Biosphere Zapovednik(SABZ),Russia provided an opportunity to determine growth rates of a recovering population.A 41-year growth phase was followed by a rapid decline in tiger *** growth rates during the growth phase averaged 4.6%,beginning near 10%in the earliest years but quickly dropping below 5%.Sex ratio(females per male)mirrored growth rates,declining as population size *** rapid decline from 2009 to 2012 appeared to be tied to multiple factors,including poaching,severe winters and *** indicators of this population are similar to those of Bengal tiger populations,suggesting that growth rates may be *** results suggest that,first,tiger populations likely in general grow slowly:3–5%yearly increases are realistic and larger growth rates are likely only when populations are highly depressed,mortality rates are low and prey populations are high relative to numbers of adult ***,while more research is needed,it should not be assumed that tiger populations with high prey densities will necessarily grow more quickly than populations with low prey ***,while growth is slow,decline can be ***,because declines can happen so quickly,there is a constant need to monitor populations and be ready to respond with appropriate and timely conservation interventions if tiger populations are to remain ***,an average annual growth rate across all tiger populations of 6%,required to reach the Global Tiger Initiative’s goal of doubling tiger numbers in 12 years,is a noble but unlikely scenario.

关键词： Amur tiger growth rates population dynamics

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Translating new data to the daily practice in second line treatment of renal cell carcinoma:The role of tumor growth rate

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World Journal of Clinical Oncology 2017年第2期8卷 100-105页

作者： Enrique Grande olga Martínez-Sáez Pablo Gajate-Borau Teresa Alonso-Gordoa Medical Oncology Department Ramón y Cajal University Hospital

The therapeutic options for patients with metastatic renal cell carcinoma(mRCC) have completely changed during the last ten years. With the sequential use of targeted therapies, median overall survival has increased in daily practice and now it is not uncommon to see patients surviving kidney cancer for more than four to five years. Once treatment fails with the first line targeted therapy, head to head comparisons have shown that cabozantinib, nivolumab and the combination of lenvatinib plus everolimus are more effective than everolimus alone and that axitinib is more active than sorafenib. Unfortunately, it is very unlikely that we will ever have prospective data comparing the activity of axitinib, cabozantinib, lenvatinib or nivolumab. It is frustrating to observe the lack of biomarkers that we have in this field, thus there is no firm recommendation about the optimal sequence of treatment in the second line. In the absence of reliable biomarkers, there are several clinical endpoints that can help physicians to make decisions for an individual patient, such as the tumor burden, the expected response rate and the time to achieve the response to each agent, the prior response to the agent administered, the toxicity profile of the different compounds and patient preference. Here, we propose the introduction of the tumor-growth rate(TGR) during first-line treatment as a new tool to be used to select the second line strategy in m RCC. The rapidness of TGR before the onset of the treatment reflects the variability between patients in terms of tumor growth kinetics and it could be a surrogate marker of tumor aggressiveness that may guide treatment decisions.

关键词： Axitinib Everolimus Cabozantinib Kidney cancer Nivolumab Renal cell Sequence Second line Sorafenib Tumor-growth rate

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Continuous cardiac output measured with a Swan-Ganz catheter reacts too slowly in animal experiments with sudden circulatory failure

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Animal Models and Experimental Medicine 2022年第3期5卷 258-265页

作者： Sigríður olga Magnúsdóttir Carsten Simonsen Bodil Steen Rasmussen Peter Enemark Lund Benedict Kjærgaard Biomedical Research Laboratory Aalborg University HospitalAalborgDenmark Department of Clinical Medicine Aalborg UniversityAalborgDenmark Department of Cardiothoracic Surgery Aalborg University HospitalAalborgDenmark Department of Anesthesia and Intensive Care Aalborg University HospitalAalborgDenmark Unit of Clinical Biostatistics Aalborg University HospitalAalborgDenmark

Background : In many animal experiments, it is vital to detect sudden changes in cardiac output(CO). This porcine study compared CO that was measured with a SwanGanz pulmonary catheter with the gold standard(which was a transit-time flow probe around the pulmonary artery) during interventions that caused hemodynamic *** : In one series, 7 pigs were exposed to sudden changes in CO. In another series, 9 pigs experienced more prolonged changes in CO. All the pigs had a Swan-Ganz catheter placed into the pulmonary artery and a flow probe around the pulmonary artery. Adrenaline infusion and controlled hemorrhage were used to increase and decrease CO, respectively. The measurements of CO before and after each intervention were compared for correlation, agreement, and the time delay that it took each method to detect at least a 30% change in CO. A Bland– Altman test was used to identify correlations and agreements between the *** : In the first series, there was a delay of 5– 7 min for the Swan Ganz catheter to register a 30% change in cardiac output, compared with the flow probe. However,during prolonged changes in CO in the second series, there was a good correlation between the 2 methods. Mixed venous oxygen saturation reacted faster to changes than did CO;both were measured via the Swan-Ganz *** : In many animal studies, the use of Swan-Ganz catheters is suitable;however, in experiments with sudden hemodynamic instability, the flow probe is the most advantageous method for measuring CO.

关键词： cardiac output flow probe hemodynamics pigs Swan-Ganz catheter

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Celecoxib enhances the detoxification of diethylnitrosamine in rat liver cancer

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World Journal of Gastroenterology 2009年第19期15卷 2345-2350页

作者： Martha Estela Salcido-Neyoy Adolfo Sierra-Santoyo olga Beltrán-Ramírez José Roberto Macías-Pérez Saúl Villa-Trevio Department of Cell Biology Center of Research and Advanced Studies of the National Politechnic InstituteMexicoDFCP 07360México External Section of Toxicology Center of Research and Advanced Studies of the National Politechnic InstituteMexicoDFCP 07360México

AIM： To study the effect of celecoxib （CXB） on diethylnitrosamine activation through the regulation of cytochrome P450 in a hepatocarcinogenesis ***： Six-week-old male Sprague-Dawley rats were randomly divided into five groups, a non-treated group （NT）, a diethylnitrosamine-treated group （DEN）, a DEN＋CXB-treated group （DEN＋CXB）,and CXB 8 d-treated and CXB 32 d-treated groups. The effects of celecoxib on the enzymatic activities of CyP1A1, 2A, 2B1/2, and 2E1 were assessed in hepatic microsomes 24 h after DEN *** in CyPIA1 and CyP2B1/2 protein expression were also evaluated. The rate of DEN metabolism was measured by the production of the deethylation metabolite acetaldehyde, and the denitrosation metabolite ***： DEN＋CXB administration produced a significant increase in the enzymatic activities ofCyP2B1/2 and 1A1, whereas it did not change the activities of CyP2A and 2E1, compared to that of the DEN group. CXB treatment for eight days did not produce a significant effect on enzymatic activity when compared to the NT group; however, when it was administered for prolonged times （CXB 32 d group）,the enzymatic activities were increased in a similar pattern to those in the DEN＋CXB group. The observed increase in the enzymatic activities in the DEN＋CXB group was accompanied by an increase in the CyP2B1/2 protein levels; no changes were observed in the levels of CyPIA1. In vitro, CXB increased the denitrosation of DEN, a pathway of metabolic detoxification. The addition of SKF-525A, a preferential inhibitor of CyP2B, abrogated the denitrosation of ***： These results suggest that the mechanism of action of CXB involves enhancement of the detoxification of DEN by an increasing denitrosation via CyP2B1/2.

关键词： Hepatocarcinogenesis Chemoprevention Diebhylnitrosamine Denitrosation Celecoxib CytochromesP450

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Intestinal bile acid physiology and pathophysiology

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World Journal of Gastroenterology 2008年第37期14卷 5630-5640页

作者： olga Martínez-Augustin Fermín Sánchez de Medina Department of Biochemistry and Molecular Biology II School of Pharmacy University of Granada Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y DigestivasGranada 18071 Spain Department of Pharmacology School of Pharmacy University of Granada Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y DigestivasGranada 18071 Spain

Bile acids (BAs) have a long established role in fat digestion in the intestine by acting as tensioactives, due to their amphipatic characteristics. BAs are reabsorbed very efficiently by the intestinal epithelium and recycled back to the liver via transport mechanisms that have been largely elucidated. The transport and synthesis of BAs are tightly regulated in part by specific plasma membrane receptors and nuclear receptors. In addition to their primary effect, BAs have been claimed to play a role in gastrointestinal cancer, intestinal inflammation and intestinal ionic transport. BAs are not equivalent in any of these biological activities, and structural requirements have been generally identified. In particular, some BAs may be useful for cancer chemoprevention and perhaps in inflammatory bowel disease, although further research is necessary in this field. This review covers the most recent developments in these aspects of BA intestinal biology.

关键词： Colitis Bile acid absorption Colon cancer

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