Труды сотрудников ИЛ им. В.Н. Сукачева СО РАН

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Найдено документов в текущей БД: 9

    On influencing of a space geometry on dynamics of some CA pedestrian movement model
/ E. Kirik, T. Yurgel'Yan, D. Krouglov // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2010. - Vol. 6350 LNCS: 9th International Conference on Cellular Automata for Research and Industry, ACRI 2010 (21 September 2010 through 24 September 2010, Ascoli Piceno. - P474-479, DOI 10.1007/978-3-642-15979-4_50 . -
Аннотация: In this paper we show an effect that a shape of way contributes to dynamics of one Cellular Automata pedestrian movement model. The fundamental diagrams for a closed and strait pathes are presented and discussed. В© 2010 Springer-Verlag.

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Держатели документа:
Institute of Computational Modelling SB RAS, Krasnoyarsk, Akademgorodok, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation
V.N. Sukachev Institute of Forest SB RAS, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Kirik, E.; Yurgel'Yan, T.; Krouglov, D.

    Artificial intelligence of virtual people in CA FF pedestrian dynamics model
/ E. Kirik, T. Yurgel'Yan, D. Krouglov // Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). - 2010. - Vol. 6068 LNCS: 8th International Conference on Parallel Processing and Applied Mathematics, PPAM 2009 (13 September 2009 through 16 September 2009, Wroclaw, Is. PART 2. - P513-520, DOI 10.1007/978-3-642-14403-5_54 . -
Аннотация: This paper deals with mathematical model of pedestrian flows. We focus here on an "intelligence" of virtual people. From macroscopic viewpoint pedestrian dynamics is already well simulated but from microscopic point of view typical features of people movement need to be implemented to models. At least such features are "keeping in mind" two strategies - the shortest path and the shortest time and keeping a certain distance from other people and obstacles if it is possible. In this paper we implement mathematical formalization of these features to stochastic cellular automata (CA) Floor Field (FF) model. В© 2010 Springer-Verlag Berlin Heidelberg.

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Держатели документа:
Institute of Computational Modelling, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Akademgorodok 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, Russian Federation
V.N. Sukachev Institute of Forest, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, Russian Federation

Доп.точки доступа:
Kirik, E.; Yurgel'Yan, T.; Krouglov, D.

    SoilChip-XPS integrated technique to study formation of soil biogeochemical interfaces
/ X. Huang [et al.] // Soil Biol. Biochem. - 2017. - Vol. 113. - P71-79, DOI 10.1016/j.soilbio.2017.05.021 . - ISSN 0038-0717
Аннотация: Many soil functions are modulated by processes at soil biogeochemical interfaces (BGIs). However, characterizing the elemental dynamics at BGIs is hampered by the heterogeneity of soil microenvironments. In order to investigate the processes of BGI formation in an upland soil (Mollisol) and a paddy soil (Oxisol), we developed a SoilChip method by assembling dispersed soil particles onto homogeneous 800-?m-diameter microarray chips and then submerging them in a solution that contained dissolved organic matter (OM) extracted from one of the two soils. The chips with Mollisol particles were incubated at 95–100% humidity, whereas the chips with Oxisol particles were incubated at 100% humidity. Dynamics of individual elements at the soils’ BGIs were quantitatively determined using X-ray photoelectron spectroscopy (XPS). Distinct differences in the soil-microbe complexes and elemental dynamics between the Mollisol and Oxisol BGIs suggested that the formation of specific BGIs resulted from the complex interaction of physical, chemical, and microbial processes. By integrating the SoilChip and XPS, it was possible to elucidate the dynamic formation of the two different soil BGIs under standardized conditions. Therefore, the SoilChip method is a promising tool for investigating micro-ecological processes in soil. © 2017

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Держатели документа:
Key Laboratory of Agro-ecological Processes in the Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, China
University of Chinese Academy of Sciences, Beijing, China
Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics – Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
Institute of Soil Science, Leibniz Universitat Hannover, Hannover, Germany
VN Sukachev Institute of Forest, Russian Academy of Sciences - Siberian Branch, Akademgorodok, Krasnoyarsk, Russian Federation
Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture, College of Resources and Environment, Huazhong Agricultural University, Wuhan, China

Доп.точки доступа:
Huang, X.; Li, Y.; Liu, B.; Guggenberger, G.; Shibistova, O.; Zhu, Z.; Ge, T.; Tan, W.; Wu, J.

    Siberian larch (Larix sibirica Ledeb.) chloroplast genome and development of polymorphic chloroplast markers
/ E. I. Bondar [et al.] // BMC Bioinformatics. - 2019. - Vol. 20: 11th International Multiconference on Bioinformatics of Genome (AUG 20-25, 2018, Novosibirsk, RUSSIA). - Ст. 38, DOI 10.1186/s12859-018-2571-x. - Cited References:25. - The presented study was a part of the project "Genomic studies of major boreal coniferous forest tree species and their most dangerous pathogens in the Russian Federation" funded by the Government of the Russian Federation (grant No 14.Y26.31.0004). Publication costs are funded by the BioMed Central Membership of the University of Gottingen. . - ISSN 1471-2105
РУБ Biochemical Research Methods + Biotechnology & Applied Microbiology

Аннотация: BackgroundThe main objectives of this study were sequencing, assembling, and annotation of chloroplast genome of one of the main Siberian boreal forest tree conifer species Siberian larch (Larix sibirica Ledeb.) and detection of polymorphic genetic markers - microsatellite loci or simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs).ResultsWe used thedata of the whole genome sequencing of three Siberian larch trees from different regions - theUrals, Krasnoyarsk, and Khakassia, respectively. Sequence reads were obtained using the Illumina HiSeq2000 in the Laboratory of Forest Genomics at the Genome Research and Education Center ofthe Siberian Federal University. The assembling was done using the Bowtie2 mapping program and the SPAdes genomic assembler. The genome annotation was performed using the RAST service. We used the GMATo program for the SSRs search, and the Bowtie2 and UGENE programs for the SNPs detection. Length of the assembled chloroplast genome was 122,561bp, which is similar to 122,474bp in the closely related European larch (Larix decidua Mill.). As a result of annotation and comparison of the data with theexisting data available only for three larch species - L. decidua, L. potaninii var. chinensis (complete genome 122,492bp), and L. occidentalis (partial genome of 119,680bp), we identified 110 genes, 34 of which represented tRNA, 4 rRNA, and 72 protein-coding genes. In total, 13 SNPs were detected; two of them were in the tRNA-Arg and Cell division protein FtsH genes, respectively. In addition, 23 SSR loci were identified.ConclusionsThe complete chloroplast genome sequence was obtained for Siberian larch for the first time. The reference complete chloroplast genomes, such as one described here, would greatly help in the chloroplast resequencing and search for additional genetic markers using population samples. The results of this research will be useful for further phylogenetic and gene flow studies in conifers.

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Держатели документа:
Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia.
Russian Acad Sci, VN Sukachev Inst Forest, Lab Forest Genet & Select, Siberian Branch, Krasnoyarsk 660036, Russia.
Georg August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, Busgenweg 2, D-37077 Gottingen, Germany.
Russian Acad Sci, Vavilov Inst Gen Genet, Lab Populat Genet, Moscow 119333, Russia.
Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA.

Доп.точки доступа:
Bondar, Eugeniya I.; Putintseva, Yuliya A.; Oreshkova, Nataliya V.; Krutovsky, Konstantin V.; Krutovsky, Konstantin; Government of the Russian Federation [14.Y26.31.0004]; University of Gottingen

    Stepwise large genome assembly approach: a case of Siberian larch (Larix sibirica Ledeb)
/ D. A. Kuzmin [et al.] // BMC Bioinformatics. - 2019. - Vol. 20: 11th International Multiconference on Bioinformatics of Genome (AUG 20-25, 2018, Novosibirsk, RUSSIA). - Ст. 37, DOI 10.1186/s12859-018-2570-y. - Cited References:32. - This study was funded by a research grant No. 14.Y26.31.0004 from the Government of the Russian Federation. No funding agency played any role in the design or conclusion of this study. Publication costs are funded by the BioMed Central Membership of the University of Gottingen. . - ISSN 1471-2105
РУБ Biochemical Research Methods + Biotechnology & Applied Microbiology
Рубрики:
SEQUENCE
   ARABIDOPSIS

   FEATURES

   SIZE

Кл.слова (ненормированные):
de novo genome assembly -- Siberian larch -- Larix sibirica

Аннотация: BackgroundDe novo assembling of large genomes, such as in conifers (similar to 12-30 Gbp), which also consist of similar to 80% of repetitive DNA, is a very complex and computationally intense endeavor. One of the main problems in assembling such genomes lays in computing limitations of nucleotide sequence assembly programs (DNA assemblers). As a rule, modern assemblers are usually designed to assemble genomes with a length not exceeding the length of the human genome (3.24 Gbp). Most assemblers cannot handle the amount of input sequence data required to provide sufficient coverage needed for a high-quality assembly.ResultsAn original stepwise method of de novo assembly by parts (sets), which allows to bypass the limitations of modern assemblers associated with a huge amount of data being processed, is presented in this paper. The results of numerical assembling experiments conducted using the model plant Arabidopsis thaliana, Prunus persica (peach) and four most popular assemblers, ABySS, SOAPdenovo, SPAdes, and CLC Assembly Cell, showed the validity and effectiveness of the proposed stepwise assembling method.ConclusionUsing the new stepwise de novo assembling method presented in the paper, the genome of Siberian larch, Larix sibirica Ledeb. (12.34 Gbp) was completely assembled de novo by the CLC Assembly Cell assembler. It is the first genome assembly for larch species in addition to only five other conifer genomes sequenced and assembled for Picea abies, Picea glauca, Pinus taeda, Pinus lambertiana, and Pseudotsuga menziesii var. menziesii.

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Держатели документа:
Siberian Fed Univ, Genome Res & Educ Ctr, Lab Forest Genom, Krasnoyarsk 660036, Russia.
Siberian Fed Univ, Inst Space & Informat Technol, Dept High Performance Comp, Krasnoyarsk 660074, Russia.
Natl Res Tech Univ, Dept Informat, Irkutsk 664074, Russia.
Russian Acad Sci, Limnol Inst, Siberian Branch, Irkutsk 664033, Russia.
Russian Acad Sci, VN Sukachev Inst Forest, Lab Forest Genet & Select, Siberian Branch, Krasnoyarsk 660036, Russia.
Georg August Univ Gottingen, Dept Forest Genet & Forest Tree Breeding, D-37077 Gottingen, Germany.
Russian Acad Sci, NI Vavilov Inst Gen Genet, Lab Populat Genet, Moscow 119333, Russia.
Texas A&M Univ, Dept Ecosyst Sci & Management, College Stn, TX 77843 USA.

Доп.точки доступа:
Kuzmin, Dmitry A.; Feranchuk, Sergey I.; Sharov, Vadim V.; Cybin, Alexander N.; Makolov, Stepan V.; Putintseva, Yuliya A.; Oreshkova, Natalya V.; Krutovsky, Konstantin V.; Krutovsky, Konstantin; Government of the Russian Federation - BioMed Central Membership of the University of Gottingen [14, Y26.31.0004]

    Nitrogen fertilization modifies organic transformations and coatings on soil biogeochemical interfaces through microbial polysaccharides synthesis
/ X. Huang [et al.] // Sci. Rep. - 2019. - Vol. 9, Is. 1. - Ст. 18684, DOI 10.1038/s41598-019-55174-y . - ISSN 2045-2322

Аннотация: The soil-water interfaces (SWI) in soil pores are hotspots for organic matter (OM) transformation. However, due to the heterogeneous and opaque nature of soil microenvironment, direct and continuous tracing of interfacial reactions, such as OM transformations and formation of organo-mineral associations, are rare. To investigate these processes, a new soil microarray technology (SoilChips) was developed and used. Homogeneous 800-?m-diameter SoilChips were constructed by depositing a dispersed Oxisol A horizon suspension on a patterned glass. Dissolved organic matter from the original soil was added on the SoilChips to mimic SWI processes. The effects of ammonium fertilization (90 mg N kg?1 soil) on chemical composition of SWIs were evaluated via X-ray photoelectron spectroscopy. Over 21 days, ammonium addition increased OM coatings at SWIs and modified the OM chemical structure with more alcoholic- and carboxylic-C compared to the unfertilized control. Molecular modeling of OM composition at SWIs showed that N fertilization mainly facilitated the microbial production of glucans. We demonstrated that N availability modifies the specific OM molecular processing and its immobilization on SWIs, thereby providing a direct insight into biogeochemical transformation of OM at micro-scale. © 2019, The Author(s).

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Держатели документа:
Britton Chance Center for Biomedical Photonics at Wuhan National Laboratory for Optoelectronics - Hubei Bioinformatics & Molecular Imaging Key Laboratory, Systems Biology Theme, Department of Biomedical Engineering, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, China
Key Laboratory of Agro-ecological Processes in the Subtropical Region, Institute of Subtropical Agriculture, The Chinese Academy of Sciences, Changsha, 410125, China
Changsha Research Station for Agricultural and Environmental Monitoring, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Hunan, 410125, China
Institute of Soil Science, Leibniz Universitat Hannover, Hannover, 30419, Germany
VN Sukachev Institute of Forest, SB-RAS, Krasnoyarsk, 660036, Russian Federation
Department of Soil Science of Temperate Ecosystems, Department of Agricultural Soil Science, University of Goettingen, Gottingen, Germany
Institute of Environmental Sciences, Kazan Federal University, Kazan, 420049, Russian Federation
Agro-Technology Institute, RUDN University, Moscow, Russian Federation

Доп.точки доступа:
Huang, X.; Guggenberger, G.; Kuzyakov, Y.; Shibistova, O.; Ge, T.; Li, Y.; Liu, B.; Wu, J.

    Metagenomic analysis as a bioinformatics tool to reconstruct the geochemical methane-driving processes in bottom sediments of the Yenisei River
/ S. Evgrafova, A. Zverev, E. Abakumov [et al.] // BMC Bioinformatics. - 2020. - Vol. 21: 4th International Conference on Bioinformatics - From Algorithms to (JUL 27-28, 2020, ELECTR NETWORK), Is. SUPPL 20. - Cited References:0 . - ISSN 1471-2105
РУБ Biochemical Research Methods + Biotechnology & Applied Microbiology


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Держатели документа:
VN Sukachev Inst Forest FRC KSC SB RAS, Krasnoyarsk, Russia.
St Petersburg State Univ, Dept Appl Ecol, St Petersburg, Russia.
Siberian Fed Univ, Krasnoyarsk, Russia.
Доп.точки доступа:
Evgrafova, Svetlana; Zverev, Alexey; Abakumov, Evgeny; Detsura, Anna; Prokushkin, Anatoly

    Non-English languages enrich scientific knowledge: The example of economic costs of biological invasions
/ E. Angulo, C. Diagne, L. Ballesteros-Mejia [et al.] // Sci. Total Environ. - 2021. - Vol. 775. - Ст. 144441, DOI 10.1016/j.scitotenv.2020.144441. - Cited By :2 . - ISSN 0048-9697

Кл.слова (ненормированные):
Ecological bias -- InvaCost -- Knowledge gaps -- Management -- Native languages -- Stakeholders -- Cost benefit analysis -- Cost estimating -- Data transfer -- Biological invasion -- Ecological bias -- Economic costs -- Invacost -- Knowledge gaps -- Native language -- Non-English languages -- Scientific data -- Scientific knowledge -- Stakeholder -- Database systems -- academic performance -- communication -- cost analysis -- data acquisition -- data management -- data set -- database -- global perspective -- invasive species -- knowledge based system -- language -- performance assessment -- policy making -- stakeholder -- appendix -- article -- data completeness -- ecological fallacy -- Europe -- human -- human experiment -- introduced species -- invasive species -- language -- nonhuman -- physician -- species invasion

Аннотация: We contend that the exclusive focus on the English language in scientific research might hinder effective communication between scientists and practitioners or policy makers whose mother tongue is non-English. This barrier in scientific knowledge and data transfer likely leads to significant knowledge gaps and may create biases when providing global patterns in many fields of science. To demonstrate this, we compiled data on the global economic costs of invasive alien species reported in 15 non-English languages. We compared it with equivalent data from English documents (i.e., the InvaCost database, the most up-to-date repository of invasion costs globally). The comparison of both databases (~7500 entries in total) revealed that non-English sources: (i) capture a greater amount of data than English sources alone (2500 vs. 2396 cost entries respectively); (ii) add 249 invasive species and 15 countries to those reported by English literature, and (iii) increase the global cost estimate of invasions by 16.6% (i.e., US$ 214 billion added to 1.288 trillion estimated from the English database). Additionally, 2712 cost entries — not directly comparable to the English database — were directly obtained from practitioners, revealing the value of communication between scientists and practitioners. Moreover, we demonstrated how gaps caused by overlooking non-English data resulted in significant biases in the distribution of costs across space, taxonomic groups, types of cost, and impacted sectors. Specifically, costs from Europe, at the local scale, and particularly pertaining to management, were largely under-represented in the English database. Thus, combining scientific data from English and non-English sources proves fundamental and enhances data completeness. Considering non-English sources helps alleviate biases in understanding invasion costs at a global scale. Finally, it also holds strong potential for improving management performance, coordination among experts (scientists and practitioners), and collaborative actions across countries. Note: non-English versions of the abstract and figures are provided in Appendix S5 in 12 languages. © 2021 The Authors

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Держатели документа:
Universite Paris-Saclay, CNRS, AgroParisTech, Ecologie Systematique Evolution, Orsay, 91405, France
Institut de Recherche pour le Developpement, Centre de Biologie pour la Gestion des Populations, UMR IRD-INRAE-CIRAD-Institut Agro, Montferrier-sur-Lez, 34988, France
Centre for Applied Mathematics and Bioinformatics, Department of Mathematics and Natural Sciences, Gulf University for Science and Technology, Hawally, 32093, Kuwait
Russian Plant Quarantine Center, Krasnoyarsk Branch, Krasnoyarsk, 660075, Russian Federation
School of Life Sciences, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
Centro de Estudos Geograficos, Instituto de Geografia e Ordenamento do Territorio – IGOT, Universidade de Lisboa, Rua Branca Edmee Marques, Lisboa, 1600-276, Portugal
Department of Animal Biology, Sciences and Technics Faculty, Cheikh Anta DIOP University, B.P. Dakar, 5005, Senegal
Grupo de Ecologia de Invasiones, INIBIOMA, CONICET/Universidad Nacional del Comahue, Av. de los Pioneros 2350, Bariloche, 8400, Argentina
Department of Community Ecology, Helmholtz-Centre for Environmental Research – UFZ, Halle (Saale), 06120, Germany
Senckenberg Research Institute and Natural History Museum Frankfurt, Department of River Ecology and Conservation, Gelnhausen, 63571, Germany
University of South Bohemia in Ceske Budejovice, Faculty of Fisheries and Protection of Waters, South Bohemian Research Center of Aquaculture and Biodiversity of Hydrocenoses, Vodnany, 389 25, Czech Republic
Programa de Pos-Graduacao em Ecologia Aplicada, Departamento de Ecologia e Conservacao, Instituto de Ciencias Naturais, Universidade Federal de Lavras – UFLA, Lavras, Minas Gerais 37200-900, Brazil
Sukachev Institute of Forest, Siberian Branch of Russian Academy of Sciences, Federal Research Center «Krasnoyarsk Science Center SB RAS», Krasnoyarsk, 660036, Russian Federation
Siberian Federal University, Krasnoyarsk, 660041, Russian Federation
Woods Hole Oceanographic Institution, Marine Policy Center, Woods Hole, MA 02543, United States
University of Southern Denmark, Department of Sociology, Environmental and Business Economics, Esbjerg O, 6705, Denmark
Institute of Marine Biological Resources and Inland Waters, Hellenic Center for Marine Research, Athens, 16452, Greece
Institute of Biology, Freie Universitat Berlin, Berlin, 14195, Germany
Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Berlin, 12587, Germany
Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, 14195, Germany
Universite de Rennes, CNRS, EcoBio (Ecosystemes, biodiversite, evolution) - UMR 6553, Rennes, 35000, France
Institut Universitaire de France, Paris Cedex 05, 75231, France
MIVEGEC, IRD, CNRS, Universite Montpellier, Montpellier, 34394, France
Departement de Biologie, Faculte des Sciences, Universite Chouaib Doukkali, El Jadida, 24000, Morocco
University of Helsinki, Faculty of Agriculture and Forestry, Department of Forest Sciences, Helsinki, 00014, Finland
Aalto University, Department of Built Environment, Water & Development Research Group, Aalto, FI-00076, Finland
Forestry and Forest Products Research Institute, Tsukuba, Ibaraki 305-8687, Japan
College of Fisheries, Guangdong Ocean University, Zhanjiang, 524088, China

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Angulo, E.; Diagne, C.; Ballesteros-Mejia, L.; Adamjy, T.; Ahmed, D. A.; Akulov, E.; Banerjee, A. K.; Capinha, C.; Dia, C. A.K.M.; Dobigny, G.; Duboscq-Carra, V. G.; Golivets, M.; Haubrock, P. J.; Heringer, G.; Kirichenko, N.; Kourantidou, M.; Liu, C.; Nunez, M. A.; Renault, D.; Roiz, D.; Taheri, A.; Verbrugge, L. N.H.; Watari, Y.; Xiong, W.; Courchamp, F.

    Mitochondrial DNA Confirms the American Origin of Modern Firs
/ V. L. Semerikov, S. A. Semerikova, Y. A. Putintseva // Russ. J. Gen. - 2021. - Vol. 57, Is. 11. - P1258-1262, DOI 10.1134/S1022795421100112 . - ISSN 1022-7954
Аннотация: Abstract: The results of phylogenetic analysis of 15 species, representing all the main evolutionary lineages of the genus Abies, and Keteleeria davidiana, used as an outgroup, are presented. The data include the nucleotide sequences of mitochondrial DNA about 28 kb in length obtained by partial resequencing of the assembly of the mitochondrial genome of the Siberian fir A. sibirica. The basal position of the mtDNA haplotypes of some American firs has been established, which confirms the American origin of modern Abies. The mitotypes of most Eurasian species form a daughter clade with respect to American firs, indicating its origin as a result of one migration from America to Eurasia. At the same time, previously obtained data on nuclear and chloroplast DNA indicate repeated migrations of firs from America to Eurasia. This conflict between mitochondrial and nuclear data can be explained by a hybrid capture of mitochondrial DNA of native Eurasian species by migrant species. © 2021, Pleiades Publishing, Inc.

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Держатели документа:
Institute of Plant and Animal Ecology, Ural Branch, Russian Academy of Sciences, Yekaterinburg, 620144, Russian Federation
Sukachev Institute of Forest, Siberian Branch, Russian Academy of Sciences, Krasnoyarsk, 660036, Russian Federation

Доп.точки доступа:
Semerikov, V. L.; Semerikova, S. A.; Putintseva, Y. A.