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Large-scale genome-wide SNP analysis reveals the rugged(and ragged)landscape of global ancestry,phylogeny,and demographic history in chicken breeds

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第4期25卷 324-340页

作者： natalia v.DEMENTIEvA Yuri S.SHCHERBAKOv Olga I.STANISHEvSKAYA Anatoly B.vAKHRAMEEv Tatiana A.LARKINA Artem P.DYSIN Olga A.NIKOLAEvA Anna E.RYABOvA Anastasiia I.AZOvTSEvA Olga v.MITROFANOvA Grigoriy K.PEGLIvANYAN natalia R.REINBACH Darren K.GRIFFIN Michael N.ROMANOv Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K.Ernst Federal Research Centre for Animal Husbandry.Pushkin St.Petersburg196601Russia School of Biosciences University of KentCanterburyCT27NJUK L.K.Ernst Federal Research Center for Animal Husbandry DubrovitsyPodolskMoscow Oblast142132Russia

The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse *** study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 *** populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried *** included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population *** also included assessment of linkage disequilibrium and construction of phylogenetic *** multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each *** overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous *** a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry *** general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

关键词： Chicken genome diversity Single nucleotide polymorphism(SNP)analysis Gene pool Global ancestry Phylogeny Demographic history

Core needle biopsy for thyroid nodules assessment-a new horizon?

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World Journal of Clinical Oncology 2024年第5期15卷 580-586页

作者： David D Dolidze Serghei Covantsev Grigorii M Chechenin natalia v Pichugina Anastasia v Bedina Anna Bumbu Department of Clinical Research and Development Botkin HospitalMoscow 125284Russia Department of Surgery Russian Medical Academy of Continuous Professional EducationMoscow 125445Russia Emergency Surgery No.76 Botkin HospitalMoscow 125284Russia Department of Surgery Botkin HospitalMoscow 125284Russia Department of Medical Ultrasonography Botkin HospitalMoscow 125284Russia Medicine Moscow State Medical University I.M.SechenovMoscow 119048Russia Department of Oncology Botkin HospitalMoscow 125284Russia

Ultrasound-guided fine-needle aspiration is the standard for evaluating thyroid nodules with a high safety profile and a relatively low number of non-diagnostic cytological ***,this diagnostic method traditionally has its weak *** diagnostic categories such as BethesdaⅠ,ⅢandⅣare not reliable for thyroid carcinoma risk *** advancements in a core needle biopsy made it possible to use this tool as a new method for thyroid nodules *** main feature of this method is the use of thin needles(18-21G)and guns with an automatic trigger *** histological material collected with the use of a core needle biopsy is usually superior to ***,the core needle biopsy can be used as a complementary technique to a standard fine needle aspiration in difficult and dubious cases of thyroid neoplasia with uncertain malignant potential.

关键词： Core-needle biopsy Thyroid Follicular tumor Fine-needle aspiration Thyroid cancer

Device-based neuromodulation for cardiovascular diseases and patient’s age

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Journal of Geriatric Cardiology 2022年第11期19卷 876-893页

作者： Evgeny N Mikhaylov Nigar Z Gasimova natalia N Belyaeva Heber Ivan Condori Leandro Aleksandr D vakhrushev Evgeny v Shlyakhto Almazov National Medical Research Centre Saint-PetersburgRussia

The autonomic nervous system plays an important role in the pathogenesis of cardiovascular *** aging,autonomic activity changes,and this impacts the physiological reactions to internal and external *** sympathetic and parasympathetic responses seem to decline,reflecting functional and structural changes in nervous *** some investigators suggested that both the sympathetic and parasympathetic activities were suppressed,others found that only the parasympathetic activity was suppressed while the sympathetic activity *** addition,cardiac innervation progressively diminishes with ***,one may suggest that neuromodulation interventions may have different effects,and older age groups can express an attenuated *** article aims to discuss the effect of device-based neuromodulation in different cardiovascular diseases,depending on the patient’s ***,we cover renal denervation,pulmonary artery denervation,baroreceptor activation therapy,vagus nerve stimulation,spinal cord stimulation,ganglionated plexi ablation for the management of arterial and pulmonary hypertension,heart failure,angina and *** results of many clinical studies appeared to be *** view of the low rate of positive findings in clinical studies incorporating neuromodulation approaches,we suggest the underestimation of advanced age as a potential contributing factor to poorer *** of outcomes between different age groups in clinical trials may shed more light on the true effects of neuromodulation when neutral/ambiguous results are obtained.

关键词： stimulation cardiovascular diseases

Identifying,exploring,and interpreting time series shapes in multivariate time intervals

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visual Informatics 2023年第1期7卷 77-91页

作者： Gota Shirato natalia Andrienko Gennady Andrienko Fraunhofer IAIS Sankt Augustin53757Germany University of Bonn Regina-Pacis-Weg 3Bonn53113Germany City University of LondonNorthampton SquareLondonEC1V 0HBUK

We introduce a concept of episode referring to a time interval in the development of a dynamic phenomenon that is characterized by multiple time-variant attributes.A data structure representing a single episode is a multivariate time *** analyse collections of episodes,we propose an approach that is based on recognition of particular patterns in the temporal variation of the variables within *** episode is thus represented by a combination of *** this representation,we apply visual analytics techniques to fulfil a set of analysis tasks,such as investigation of the temporal distribution of the patterns,frequencies of transitions between the patterns in episode sequences,and co-occurrences of patterns of different variables within same *** demonstrate our approach on two examples using real-world data,namely,dynamics of human mobility indicators during the COvID-19 pandemic and characteristics of football team movements during episodes of ball turnover.

关键词： Temporal patterns Multivariate time series Time intervals

Electrolyte materials for protonic ceramic electrochemical cells:Main limitations and potential solutions

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Materials Reports(Energy) 2022年第4期2卷 19-35页

作者： Anna v.Kasyanova Inna A.Zvonareva natalia A.Tarasova Lei Bi Dmitry A.Medvedev Zongping Shao Laboratory of Electrochemical Devices Based on Solid Oxide Proton Electrolytes Institute of High Temperature Electrochemistry620990YekaterinburgRussia Hydrogen Energy Laboratory Ural Federal University620002YekaterinburgRussia School of Resource and Environment and Safety Engineering University of South ChinaHengyangHunan421001China State Key Laboratory of Materials-Oriented Chemical Engineering College of Chemical EngineeringNanjing Tech UniversityNanjing210009China WA School of Mines:Minerals Energy and Chemical Engineering(WASM-MECE)Curtin UniversityPerthWA6845Australia

Solid oxide fuel cells(SOFCs)and electrolysis cells(SOECs)are promising energy conversion devices,on whose basis green hydrogen energy technologies can be developed to support the transition to a carbon-free *** compared with oxygen-conducting cells,the operational temperatures of protonic ceramic fuel cells(PCFCs)and electrolysis cells(PCECs)can be reduced by several hundreds of degrees(down to low-and intermediatetemperature ranges of 400–700C)while maintaining high performance and *** is due to the distinctive characteristics of charge carriers for proton-conducting ***,despite achieving outstanding lab-scale performance,the prospects for industrial scaling of PCFCs and PCECs remain hazy,at least in the near future,in contrast to commercially available SOFCs and *** this review,we reveal the reasons for the delayed technological development,which need to be addressed in order to transfer fundamental findings into industrial *** solutions to the identified problems are also highlighted.

关键词： Protonic ceramic fuel cells(PCFCs) Protonic ceramic electrolysis cells(PCECs) Proton transport Electrochemistry Hydrogen energy

Probiotics and autoprobiotics for treatment of Helicobacter pylori infection

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World Journal of Clinical Cases 2023年第20期11卷 4740-4751页

作者： natalia v Baryshnikova Anastasia S Ilina Elena I Ermolenko Yury P Uspenskiy Alexander N Suvorov Department of Molecular Microbiology Institute of Experimental MedicineSt.Petersburg 197376Russia Internal Diseases Department of Stomatological Faculty Pavlov First St-Petersburg State Medical UniversitySt.Petersburg 197022Russia Laboratory of Medical and Social Pediatric Problems St-Petersburg State Pediatric Medical UniversitySt.Petersburg 194100Russia Clinical Department Institute of Experimental MedicineSt.Petersburg 197376Russia Department of Faculty Therapy Named After v.A.valdman St-Petersburg State Pediatric Medical UniversitySt.Petersburg 194100Russia

The article discusses various approaches for probiotic treatment of Helicobacter pylori(***)infection:Probiotics as an adjuvant treatment in the standard eradication therapy;probiotic strains as a monotherapy;and autoprobiotics as a *** refer to indigenous bifidobacteria,lactobacilli,or enterococci isolated from a specific individual,intended to restore his/her microbiota and improve his/her *** potential mechanisms of probiotic action against *** include correction of the gut microbiota,immunological effects(enhancement of humoral and cellular immunity,and reduction of oxidative stress),direct antagonistic effects against ***(such as colonization resistance and bacteriocin synthesis),and stimulation of local immunological protection(strengthening of the mucous protective barrier and reduction of gastric mucosa inflammation).The incorporation of probiotics into comprehensive eradication therapy shows promise in optimizing the treatment of *** *** can enhance the eradication rates of ***,reduce the occurrence and severity of side effects,and improve patient *** or autoprobiotic monotherapy can be considered as an alternative treatment approach in cases of allergic reactions and insufficient effectiveness of *** recommend including probiotics as adjunctive medications in *** ***,further randomized multicenter studies are necessary to investigate the effects of probiotics and autoprobiotics against ***,in order to gain a better understanding of their mechanisms of action.

关键词： Helicobacter pylori Probiotic Autoprobiotic Eradication Microbiota Gut Immunity

Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

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Journal of Animal Science and Biotechnology 2023年第3期14卷 887-907页

作者： Michael N.Romanov Alexandra S.Abdelmanova vladimir I.Fisinin Elena A.Gladyr natalia A.volkova Olga A.Koshkina Andrey N.Rodionov Anastasia N.vetokh Igor v.Gusev Dmitry v.Anshakov Olga I.Stanishevskaya Arsen v.Dotsev Darren K.Griffin natalia A.Zinovieva L.K.Ernst Federal Research Centre for Animal Husbandry DubrovitsyPodolskMoscow RegionRussia School of Biosciences University of KentCanterburyUK Federal State Budget Scientific Institution Federal Research Centre“All-Russian Poultry Research and Technological Institute”of the Russian Academy of Sciences Sergiev PosadMoscow RegionRussia Breeding and Genetic Centre“Zagorsk Experimental Breeding Farm”–Branch of the Federal Research Centre“All-Russian Poultry Research and Technological Institute”of the Russian Academy of Sciences Sergiev PosadMoscow RegionRussia Russian Research Institute of Farm Animal Genetics and Breeding–Branch of the L.K.Ernst Federal Research Centre for Animal Husbandry St.PetersburgRussia

Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture *** to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed *** Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White *** of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation *** regions of true selection signatures were identified by two or more methods or in two or more *** these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other *** them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold *** factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken *** include genes representing the sine qua non for adaptation to harsh *** tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.

关键词： Acclimation Adaptation Chicken breeds Cold tolerance Divergent selection Genetic diversity Genomewide scan Phenotypic traits Selective sweeps

Identification of genes involved in the formation of soluble dietary fiber in winter rye grain and their expression in cultivars with different viscosities of wholemeal water extract

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The Crop Journal 2022年第2期10卷 532-549页

作者： Liudmila v.Kozlova Alsu R.Nazipova Oleg v.Gorshkov Liliya F.Gilmullina Olga v.Sautkina natalia v.Petrova Oksana I.Trofimova Sergey N.Ponomarev Mira L Ponomareva Tatyana A.Gorshkova Kazan Institute of Biochemistry and Biophysics Federal Research CenterKazan Scientific Center of the Russian Academy of Sciences420111 KazanRussia Tatar Scientific Research Institute of Agriculture Federal Research CenterKazan Scientific Center of the Russian Academy of Sciences420059 KazanRussia

The grain of rye(Secale cereale L.) used for baking contains a large amount of non-starch polysaccharides,making it an excellent component of functional foods. But rye grain intended for alcohol production and forage use should have a reduced content of these polysaccharides. A comprehensive parameter that can predict the best field of application for winter rye grain is the viscosity of its wholemeal water ***, our understanding of the genetic background underlying this key trait and associated features of rye grain is poor. By analyzing six Russian winter rye cultivars, we identified the most contrasting forms and characterized the peculiarities of their water-soluble carbohydrates capable of influencing the viscosity of water extracts. Then, using phylogenetic and transcriptomic analyses, we identified in the rye genome many genes encoding putative glycosyltransferases and glycosylhydrolases responsible for the synthesis and degradation of arabinoxylans, mixed-linkage glucans, cellulose, and some other polysaccharides. We determined the dynamics of m RNA abundance for these genes at three stages of kernel development. Comparisons of gene expression levels in two contrasting cultivars revealed specific members of multigene families that may serve as promising targets for manipulating non-starch polysaccharide content in rye grain. High-viscosity cultivars were characterized by up-regulation of many glycosyltransferases involved in the biosynthesis of arabinoxylans and other cell-wall polysaccharides,whereas low-viscosity cultivars showed up-regulation of several genes encoding polysaccharidedegrading enzymes.

关键词： Rye(Secale cereale) Kernel development Arabinoxylan Mixed-linkage glucan viscosity

3,6-bis(2,2,2-trinitroethylnitramino)-1,2,4,*** and energy abilities as a component of solid composite propellants

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Defence Technology（防务技术） 2022年第7期18卷 1148-1155页

作者： Anatoly G.Korepin natalia M.Glushakova David B.Lempert Anatoly I.Kazakov Gennady v.Shilov Denis v.Korchagin vadim M.volokhov Elena S.Amosova Sergey M.Aldoshin Institute of Problems of Chemical Physics Ac.Semenov Avenue 1Chernogolovka142432Russian Federation

The work addresses to the study of the molecular and crystal structure and properties of a new energyintensive compound 3,6-bis(2,2,2-trinitroethylnitramino)-1,2,4,5-tetrazine(NBTAT),first obtained by the authors in *** compound crystallizes in the monoclinic system,space group P2(1)/n,density at room temperature 1.939 g/cm^(3).The energies of crystal packing and pairwise intermolecular interactions in NBTAT and its unnitrated analogue BTAT were calculated,and their comparative analysis was carried *** enthalpy of formation of NBTAT molecules was calculated by quantum-chemical methods using Gaussian 09,and the enthalpy of formation of NBTAT in the solid phase(618 kJ/mol)was *** energy capabilities of NBTAT as an oxidizer of solid composite propellants are *** is shown that in metal-free compositions NBTAT is significantly superior to ammonium perchlorate(AP),dinitramide ammonium salt(ADN),HMX,BTAT at all stages of rocket systems,and is comparable to the superdense CL-20 yielding to the latter at the lower stages and slightly winning at the upper stages.

关键词： Nitrogen heterocycles Quantum chemistry Enthalpy of formation 3,6-bis(2,2,2-trinitroethylnitramino)-1,2,4,5-tetrazine Crystal structure Energetic ability