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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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Growth of Micropropagated solanum tuberosum *** under Artificial solar spectrum and Different Mono-and Polychromatic LED Lights

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Horticultural Plant Journal 2022年第2期8卷 205-214页

作者： olga V.Grishchenko Eugeny P.subbotin Irina V.Gafitskaya Yulia V.Vereshchagina Elena V.Burkovskaya Yulia A.Khrolenko Valeria P.Grigorchuk olga V.Nakonechnaya Victor P.Bulgakov Yuri N.Kulchin Federal scientific Center of the East Asia Terrestrial Biodiversity Far Eastern Branch of the Russian Academy of SciencesVladivostok 690022Russia Institute of Automation and Control Processes Far Eastern Branch of the Russian Academy of SciencesVladivostok 690041Russia

In agriculture,LED light sources have increasingly replaced the standard luminescent lamps and have acquired an important role in plant *** studied the effect of different light sources such as narrow-band LEDs(bright blue,blue,green,yellow,deep red,and red)and wide-band LEDs(cold white,white,warm white,full spectrum,and an artificial solar spectrum sun box constructed by us)on development of potato plantlets in *** luminescent lamps were used as a *** light intensity of 49μmol·m^(-2)·s^(-1)was provided in all light *** showed that the long-wave narrow-band light treatments were inapplicable for potato micropropagation,because plantlets were weak with small leaves,inhibited roots,and significantly elongated *** lights provided growth of shortened plantlets with large leaves,well-growing roots,and abundant green *** chlorophyll content was lower under blue and bright blue light and was at the same level in the remained *** differences in the stomatal apparatus development were observed depending on the light *** differences were not always reflected in the plantlet phenotype:e.g.,plantlets under blue and bright blue lights showed no differences in any characteristics except stomatal density and size of stomatal guard *** found no significant effect of blue light portion in the white lights and full spectrum on plantlet *** artificial solar spectrum sun box was the most suitable for potato micropropagation,because it supported the development of plantlets with good fitness,uniform internodes length,abundant roots and green mass accumulation.

关键词： solanum tuberosum LED Artificial solar light Growth Micropropagation

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Perioperative coagulation activation after permanent pacemaker placement

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World Journal of Cardiology 2023年第4期15卷 174-183页

作者： Roman Kalinin Igor suchkov Vladislav Povarov Nina Mzhavanadze olga Zhurina Department of Cardiovascular Endovascular Surgery and Diagnostic RadiologyRyazan State Medical UniversityRyazan 390026Russia Department of surgical Treatment of Cardiac Arrhythmias and Cardiac Pacing Ryazan State"Regional Clinical Cardiology Dispensary"Ryazan 390026Russia scientific and Clinical Center for Hematology Oncology and ImmunologyRyazan State Medical UniversityRyazan 390026Russia

BACKGROUND Bradyarrhythmias are typically treated with permanent pacemakers(PM). The elimination of bradyarrhythmia by PM implantation improves the patient’s quality of life and prognosis, but it can also result in a number of sequalae. It is still unclear how PM implantation affects the hemostasis system’s parameters and how such parameters relate to different consequences after PM *** To assess the blood coagulation factor activity in PM patients throughout the perioperative *** Patients treated in the Department of surgical Therapy of Cardiac Arrhythmias and Pacing at the Ryazan state "Regional Clinical Cardiology Dispensary" from April 2020 to December 2021 were included in the study. Before surgery, 7 and 30 d after PM placement, peripheral venous blood samples were withdrawn to measure the level of blood coagulation factor Ⅰ(FⅠ) and the activity of blood coagulation factors Ⅱ(FⅡ), Ⅴ(FⅤ), Ⅶ(FⅦ), Ⅷ(FⅧ), ⅸ(Fⅸ), ⅹ(Fⅹ), Ⅺ(FⅪ), Ⅻ(FⅫ). We used an automatic coagulometer sysmex CA 660(sysmex Europe, Germany) and reagents from siemens(siemens Healthcare Diagnostics Products GmbH, Germany).REsULTs The study included 146 patients. The activity of factors FⅤ [147.7(102.1-247.55)% vs 103.85(60-161.6)% vs 81.8(67.15-130.65)%, P = 0.002], FⅧ [80.4(60.15-106.25)% vs 70.3(48.5-89.1)% vs 63.7(41.6-88.25)%, P = 0.039], Fⅸ [86.2(70.75-102.95)% vs 75.4(59.2-88.3)% vs 73.9(56.45-93.05)%, P = 0.014], Fⅹ [188.9(99.3-308.18)% vs 158.9(83.3-230)% vs 127.2(95.25-209.35)%, P = 0.022], FⅪ [82.6(63.9-103.6)% vs 69.75(53.8-97.6)% vs 67.3(54.25-98.05)%, P = 0.002], FⅫ [87.6(67.15-102.3)% vs 78.9(63.4-97.05)% vs 81.2(62.15-97.4)%, P sed at 7 and 30 d after surgery;FⅡ activity [157.9(109.7-245.25)% vs 130(86.8-192.5)% vs 144.8(103.31-185.6)%, P = 0.021] decreased at 7 d and increased at 30 d postoperatively. There were no statistically significant changes in the FVII activity within 30 d after PM placement [182.2(85.1-344.8)% vs 157.2(99.1-259)% vs 108.9(74.9

关键词： Hemostasis Blood coagulation Cardiac pacemaker Anticoagulants Postoperative complications

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The state of gold in phases of the Cu-Fe-s system:In situ X-ray absorption spectroscopy study

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Geoscience Frontiers 2023年第3期14卷 103-116页

作者： Boris R.Tagirov olga N.Filimonova Alexander L.Trigub Ilya V.Vikentyev Elena V.Kovalchuk Maximilian s.Nickolsky Andrey A.shiryaev Vladimir L.Reukov Dmitry A.Chareev Institute of Geology of Ore Deposits(IGEM RAs) 35Staromonetnyi per119017 MoscowRussia National Research Centre‘Kurchatov Institute’ 1Akademika Kurchatova pl123182 MoscowRussia Institute of Physical Chemistry and Electrochemistry(IPCE RAs) 31Leninsky Prospect119071 MoscowRussia Institute of Experimental Mineralogy(IEM RAs) 142432 ChernogolovkaMoscow RegionRussia

Chalcopyrite and bornite are the main Au-bearing minerals at Cu porphyry deposits,volcanogenic massive sulfide(VMs)deposits,Cu-Ni deposits of the mafic magmatic complexes,and ores of submarine sulfide *** and intermediate solid solutions with wide compositional variations(bnss and iss–high-temperature chalcopyrite,correspondingly),which can scavenge economic concentrations of Au,appear in the Cu-Fe-s system at ore-forming ***,the state of Au in bnss and iss is yet *** solve this conundrum,we synthesized samples with net chemical composition of bnss and iss,studied them by in situ X–ray absorption spectroscopy(XAs),and used the experimental data to explain the Au distribution among natural ore-forming *** sulfide samples were obtained at 495–700℃ in Au-saturated system by means of salt flux *** bnss contained1.2–1.6 log units more Au than iss:up to 18 wt.%Au in bnss vs 0.4 wt.%Au in iss at 700*** increase of temperature resulted in the sharp increase of Au concentration in both phases,1 log unit per 100℃ at f(s2)close to s_((l)) *** of Au L_(3)-edge spectra recorded at 25–675℃ revealed that at 25℃ Au exists mainly in the metallic *** t>500℃ the spectral features of Audisappear,and “chemically bound”Au *** Au form of occurrence in the iss field is interpreted as Au-bearing clusters with a stromeyerite-like(CuAgs)*** Cu_(2–x)s and bnss contain Au in a mixture of stromeyeritelike and petrovskaite-like(Au_(0.8)Ag_(1.2)s)*** chemical composition of both forms is close to CuAus,where the nearest Au neighbors are two s atoms at R_(Au-s)=2.34–2.36Å.Results of the present study allow to determine the state of Au and its concentration in the main Cu-bearing minerals of sulfide ores as a function of the T-f(s_(2))-compositional *** to the sharp increase of the CuAus clusters stability with increasing temperature,in high-temperature ores formed at t>350℃ A

关键词： “Invisible”gold Bornite solid solution Intermediate solid solution Digenite Chalcopyrite X-ray absorption spectroscopy

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RNA Polymerase V Functions in Arabidopsis Interphase Heterochromatin Organization Independently of the 24-nt siRNA-Directed DNA Methylation Pathway

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Molecular Plant 2009年第4期2卷 700-710页

作者： olga Pontes Pedro Costa-Nunes Paul Vithayathil Craig s. Pikaard Biology Department Washington University 1 Brookings Drive St Louis MO 63130 USA

In Arabidopsis, pericentromeric repeats, retroelements, and silenced rRNA genes are assembled into heterochromatin within nuclear structures known as chromocenters. The mechanisms governing higher-order heterochromatin organization are poorly understood but 24-nt small interfering RNAs （siRNAs） are known to play key roles in heterochromatin formation. Nuclear RNA polymerase IV （Pol IV）, RNA-DEPENDENT RNA POLYMERAsE 2 （RDR2）, and DICER-LIKE 3 （DCL3） are required for biogenesis of 24-nt siRNAs that associate with ARGONAUTE 4 （AGO4）. Nuclear RNA polymerase V （Pol V） collaborates with DRD1 （DEFICIENT IN RNA-DEPENDENT DNA METHYLATION 1） to generate transcripts at heterochromatic loci that are hypothesized to bind to siRNA-AGO4 complexes and subsequently recruit the de-novo DNA methylation and/or histone modifying machinery. Here, we report that decondensation of the major pericentromeric repeats and depletion of the heterochromatic mark histone H3 lysine 9 dimethylation at chromocenters occurs specifically in pol V and drdl mutants. Disruption of pericentromeric repeats condensation is coincident with transcriptional reactivation of specific classes of pericentromeric 180-bp repeats. We further demonstrate that Pol V functions independently of Pol IV, RDR2, and DCL3-mediated siRNA production to affect interphase heterochromatin organization, possibly by involving RNAs that recruit structural or chromatin-modifying proteins.

关键词： RNA polymerase V RNA-directed DNA methylation heterochromatin centromere gene expression.

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Hidden stage of intracranial hemorrhage in newborn rats studied with laser speckle contrast imaging and wavelets

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Journal of Innovative Optical Health sciences 2015年第5期8卷 99-106页

作者： Alexey N.Pavlov Arkady s.Abdurashitov olga N.Pavlova Valery V.Tuchin olga s.sindeeva sergey s.sindeev Oxana V.semyachkina-Glushkovskaya Department of Physics Saratov State University 83 Astrakhanskaya Str.Saratov 410012Russia Department of Biology Saratov State University 83 Astrakhanskaya Str.Saratov 410012Russia

Using the laser speckle contrast imaging and wavelet-based analyses,we investigate a latent("hidden")stage of the development of intracranial hemorrhages(ICHs)in newborn *** apply two measures based on the continuous wavelet-transform of blood flow velocity in the sagittal sinus,namely,the spectral energy in distinct frequency ranges and a multiscality degree characterizing complexity of experimental *** show that the wavelet-based multifractal formalism reveals changes in the cerebrovascular blood flow at the development of ICH.

关键词： Cerebral blood flow laser speckle contrast imaging stress wavelet-analysis complexity

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Evaluating chromosomal segregation in a family where both spouses carry an autosomal translocation

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Reproductive and Developmental Medicine 2023年第3期7卷 189-192页

作者： Irina L.Puppo Ziravard N.Tonyan Alsu F.saifitdinova Julia A.Loginova Anna A.Kinunen Alisa N.Panina Julia R.Pastuhova olga A.Leonteva olga G.Chiryaeva olga V.Malysheva Oleg s.Glotov Irina V.Poliakova Andrey V.Tikhonove Tatyana V.Vavilova Irina L.Menshikova Elvira V.Isakova Andrey s.Glotov Natalya K.Bichevaya International Centre for Reproductive Medicine Saint-Petersburg 197350Russia Department of Laboratory Medicine and Genetics Almazov National Medical Research CentreSaint-Petersburg197341Russia Department of Genomic Medicine D.O.Ott's Institute of ObstetricsGynecologyand ReproductologySaint-Petersburg 199034Russia Department of Biology.Herzen state Pedagogical University of Russia Saint-Petersburg 191186Russia DiaCarta Inc.2600 Hilltop DriveRichmondCA 94806 st.Petersburg Centre for Medical Genetics Saint Petersburg194044Russia Department of ExperimentalMedical Virology MolecularGenetics and Biobankingof Pediatric Researchand Clinical Center for Infectious DiseasesSaint-Petersburg 197022Russia Medical institute of surgut state University Surgut 628403 Russia CerbaLab Ltd. Saint-Petersburg 199106Russia

Autosomal reciprocal translocations represent exchanges of chromatin fragments between non-homologous *** are facilitated by the creation of quadrivalent structures during the first meiotic division,which are characterized by the length of the translocated and centric segments,asymmetry,and the presence of terminal breakpoints,all of which may impact segregation ***,we report a rare case of multiple reciprocal translocations within a single *** includes the evaluation of the translocations in each of the spouses and an analysis of their chromosome segregation patterns as determined by the constellation of universal characteristics in each of their *** obtained results will be of interest to fundamental biology,as they will expand the understanding of the factors affecting chromosome segregation during meiosis.

关键词： Embryo viability Genetic counseling Pre-implantation genetic testing Quadrivalent characteristics

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Regulatory role of sphingosine kinase and sphingosine-1-phosphate receptor signaling in progenitor/stem cells

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World Journal of stem Cells 2018年第9期10卷 119-133页

作者： Mei Li Ng Nagendra s Yarla Mario Menschikowski olga A sukocheva Centenary Institute of Cancer Medicine and Cell Biology Sydney NSW 2050Australia Department of Biochemistry and Bioinformatics Institute of ScienceGITAM UniversityRushikondaVisakhapatnam 530 045Andhra PradeshIndia Institute of Clinical Chemistry and Laboratory Medicine Carl Gustav Carus University HospitalTechnical University of DresdenDresden D-01307Germany College of Nursing and Health sciences Flinders University of South AustraliaBedford Park SA 5042Australia

Balanced sphingolipid signaling is important for the maintenance of homeostasis. sphingolipids were demonstrated to function as structural components, second messengers, and regulators of cell growth and survival in normal and disease-affected tissues. Particularly, sphingosine kinase 1 (sphK1) and its product sphingosine-1-phosphate (s1P) operate as mediators and facilitators of proliferation-linked signaling. Unlimited proliferation (selfrenewal) within the regulated environment is a hallmark of progenitor/stem cells that was recently associated with the s1P signaling network in vasculature, nervous,muscular, and immune systems. s1P was shown to regulate progenitor-related characteristics in normal and cancerstemcells(CsCs) viaG-protein coupled receptorss1Pn(n=1 to 5). The sphK/s1P axis is crucially involved in the regulation of embryonic development of vasculature and the nervous system, hematopoietic stem cell migration, regeneration of skeletal muscle, and development of multiple sclerosis. The ratio of the s1P receptor expression, localization, and specific s1P receptoractivated downstream effectors influenced the rate of selfrenewal and should be further explored as regeneration related targets. Considering malignant transformation,it is essential to control the level of self-renewal *** of the progenitor cell should be synchronized with differentiation to provide healthy lifelong function of blood, immune systems, and replacement of damaged ordead cells. The differentiation-related role of sphK/s1P remains poorly assessed. A few pioneering investigations exploredpharmacologicaltoolsthattargetsphingolipid signaling and can potentially confine and direct self-renewal towards normal differentiation. Further investigation is required to test the role of the sphK/s1P axis in regulation of self-renewal and differentiation.

关键词： sphingosine-1-phosphate sphingolipids Embryonic stem cells Mesenchymal stem cells Bone marrow hematopoietic stem cells sphingosine kinase Progenitor

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Risk modeling of femoral neck fracture based on geometric parameters of the proximal epiphysis

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World Journal of Orthopedics 2022年第8期13卷 733-743页

作者： Anna D shitova olga N Kovaleva Anna V Olsufieva Inchekhanum A Gadzhimuradova Dmitry D Zubkov Mikhail O Kniazev Tatyana s Zharikova Yury O Zharikov International school“Medicine of the Future” I.M.Sechenov First Moscow State Medical University(Sechenov University)Moscow 119991MoscowRussia Department of Human Anatomy I.M.Sechenov First Moscow State Medical University(Sechenov University)Moscow 125009MoscowRussia Department of Biomedical Disciplines of the Faculty of Medicine Nonstate Educational Private Institution of Higher Education"Moscow Financial and Industrial University“Synergy”Moscow 125190MoscowRussia Institute of Clinical Medicine I.M.Sechenov First Moscow State Medical University(Sechenov University)Moscow 119991MoscowRussia

BACKGROUND Fractures of the proximal femur epiphysis are problematic for state health care because they are associated with severe medical and social problems and high morbidity and mortality *** To model the potential risk of hip fracture via femur geometric *** seventy educational cadaveric femurs from people aged 14 to 80 years,10 X-ray images from the records of the Human Anatomy Department and 10 X-ray images from the Department of Traumatology,Orthopedics and Disaster surgery of sechenov University,were *** parameters of the fractured bone were measured using images captured with a Canon d60 *** projection values of the proximal epiphysis of the cadaveric femurs and geometric parameters of the bones shown in the X-ray images were measured with Autodesk software(AutoCAD 2018).Analysis of the video frames showing bone rotation reveal that the greater trochanter can be inscribed in a parallelepiped,where one of the faces is parallel to the plane of view in the frontal standard projection and is *** angle of bone rotation obtained by turning the cube corresponded to the angle measured with the second *** reliable method of calculating the rotation of the bone relative to the anterior projection was employed in subsequent *** geometric parameters of the femur were measured using X-ray images according to the proposed *** The geometric parameters of 70 femurs were analyzed,and correlation coefficients were *** measurement results were compared with those reported by other *** potential influence of femur geometry on force distribution in the proximal epiphysis of the femur was described,and a 2-dimensional model of the femur epiphysis associated with minimal neck fracture risk was *** assessment of the geometric parameters of the femoral epiphysis indicated the greatest risk of a varus fracture of the neck if the angle of the minimal resistance zone(AMRZ)

关键词： Fracture Proximal epiphysis of femur Risk Traumatology Hip neck Risk assessment scale

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Antitumor efficacy of multi-target in situ vaccinations with CpG oligodeoxynucleotides,anti-OX40,anti-PD1 antibodies,and aptamers

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The Journal of Biomedical Research 2023年第3期37卷 194-212页

作者： Anastasia s.Proskurina Vera s.Ruzanova Genrikh s.Ritter Yaroslav R.Efremov Zakhar s.Mustafin sergey A.Lashin Ekaterina A.Burakova Alesya A.Fokina Timofei s.Zatsepin Dmitry A.stetsenko olga Y.Leplina Alexandr A.Ostanin Elena R.Chernykh sergey s.Bogachev Institute of Cytology and Genetics Siberian Branch of the Russian Academy of SciencesNovosibirsk 630090Russia Department of Natural sciences Novosibirsk State UniversityNovosibirsk 630090Russia Department of Physics Novosibirsk State UniversityNovosibirsk 630090Russia Department of Chemistry Moscow State UniversityMoscow 119991Russia Research Institute of Fundamental and Clinical Immunology Novosibirsk630099Russia

To overcome immune tolerance to cancer,the immune system needs to be exposed to a multi-target action ***,we investigated the activating effect of CpG oligodeoxynucleotides(ODNs),mesyl phosphoramidate CpG ODNs,anti-OX40 antibodies,and OX40 RNA aptamers on major populations of immunocompetent cells ex *** analysis of the antitumor effects of in situ vaccination with CpG ODNs and anti-OX40 antibodies,as well as several other combinations,such as mesyl phosphoramidate CpG ODNs and OX40 RNA aptamers,was *** against programmed death 1(PD1)checkpoint inhibitors or their corresponding PD1 DNA aptamers were also added to vaccination regimens for analytical *** scenarios were considered:a weakly immunogenic Krebs-2 carcinoma grafted in CBA mice;a moderately immunogenic Lewis carcinoma grafted in C57Black/6 mice;and an immunogenic A20 B cell lymphoma or an Ehrlich carcinoma grafted in BALB/c *** anti-PD1 antibodies(CpG+αOX40+αPD1)to in situ vaccinations boosts the antitumor *** to be used instead of antibodies,aptamers also possess antitumor activity,although this effect was less *** strongest effect across all the tumors was observed in highly immunogenic A20 B cell lymphoma and Ehrlich carcinoma.

关键词： immunogenicity Krebs-2 carcinoma Lewis carcinoma Ehrlich carcinoma A20 B cell lymphoma mesyl phosphoramidate

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