Journal articles: 'Agriculture, Plant Pathology. Biology, Bioinformatics'

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Harborne, Jeffrey B. "Plant Pathology in Agriculture:." Phytochemistry 30, no. 4 (1991): 1355. http://dx.doi.org/10.1016/s0031-9422(00)95241-5.

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Yarden, O., D. J. Ebbole, S. Freeman, R. J. Rodriguez, and M. B. Dickman. "Fungal Biology and Agriculture: Revisiting the Field." Molecular Plant-Microbe Interactions® 16, no. 10 (October 2003): 859–66. http://dx.doi.org/10.1094/mpmi.2003.16.10.859.

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Plant pathology has made significant progress over the years, a process that involved overcoming a variety of conceptual and technological hurdles. Descriptive mycology and the advent of chemical plant-disease management have been followed by biochemical and physiological studies of fungi and their hosts. The later establishment of biochemical genetics along with the introduction of DNA-mediated transformation have set the stage for dissection of gene function and advances in our understanding of fungal cell biology and plant-fungus interactions. Currently, with the advent of high-throughput technologies, we have the capacity to acquire vast data sets that have direct relevance to the numerous subdisciplines within fungal biology and pathology. These data provide unique opportunities for basic research and for engineering solutions to important agricultural problems. However, we also are faced with the challenge of data organization and mining to analyze the relationships between fungal and plant genomes and to elucidate the physiological function of pertinent DNA sequences. We present our perspective of fungal biology and agriculture, including administrative and political challenges to plant protection research.

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Turner, R. Steven. "Potato Agriculture, Late Blight Science, and the Molecularization of Plant Pathology." Historical Studies in the Natural Sciences 38, no. 2 (2008): 223–57. http://dx.doi.org/10.1525/hsns.2008.38.2.223.

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By the mid-1980s nucleic-acid based methods were penetrating the farthest reaches of biological science, triggering rivalries among practitioners, altering relationships among subfields, and transforming the research front. This article delivers a "bottom up" analysis of that transformation at work in one important area of biological science, plant pathology, by tracing the "molecularization" of efforts to understand and control one notorious plant disease——the late blight of potatoes. It mobilizes the research literature of late blight science as a tool through which to trace the changing typography of the research front from 1983 to 2003. During these years molecularization intensified the traditional fragmentation of the late blight research community, even as it dramatically integrated study of the causal organism into broader areas of biology. In these decades the pathogen responsible for late blight, the oomycete Phytophthora infestans, was discovered to be undergoing massive, frightening, and still largely unexplained genetic diversification——a circumstance that lends the episode examined here an urgency that reinforces its historiographical significance as a casestudy in the molecularization of the biological sciences.

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Tello, Daniel, Juanita Gil, Cristian D. Loaiza, John J. Riascos, Nicolás Cardozo, and Jorge Duitama. "NGSEP3: accurate variant calling across species and sequencing protocols." Bioinformatics 35, no. 22 (April 25, 2019): 4716–23. http://dx.doi.org/10.1093/bioinformatics/btz275.

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Abstract Motivation Accurate detection, genotyping and downstream analysis of genomic variants from high-throughput sequencing data are fundamental features in modern production pipelines for genetic-based diagnosis in medicine or genomic selection in plant and animal breeding. Our research group maintains the Next-Generation Sequencing Experience Platform (NGSEP) as a precise, efficient and easy-to-use software solution for these features. Results Understanding that incorrect alignments around short tandem repeats are an important source of genotyping errors, we implemented in NGSEP new algorithms for realignment and haplotype clustering of reads spanning indels and short tandem repeats. We performed extensive benchmark experiments comparing NGSEP to state-of-the-art software using real data from three sequencing protocols and four species with different distributions of repetitive elements. NGSEP consistently shows comparative accuracy and better efficiency compared to the existing solutions. We expect that this work will contribute to the continuous improvement of quality in variant calling needed for modern applications in medicine and agriculture. Availability and implementation NGSEP is available as open source software at http://ngsep.sf.net. Supplementary information Supplementary data are available at Bioinformatics online.

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Jeyasri, Rajendran, Pandiyan Muthuramalingam, Lakkakula Satish, Shunmugiah Karutha Pandian, Jen-Tsung Chen, Sunny Ahmar, Xiukang Wang, Freddy Mora-Poblete, and Manikandan Ramesh. "An Overview of Abiotic Stress in Cereal Crops: Negative Impacts, Regulation, Biotechnology and Integrated Omics." Plants 10, no. 7 (July 19, 2021): 1472. http://dx.doi.org/10.3390/plants10071472.

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Abiotic stresses (AbS), such as drought, salinity, and thermal stresses, could highly affect the growth and development of plants. For decades, researchers have attempted to unravel the mechanisms of AbS for enhancing the corresponding tolerance of plants, especially for crop production in agriculture. In the present communication, we summarized the significant factors (atmosphere, soil and water) of AbS, their regulations, and integrated omics in the most important cereal crops in the world, especially rice, wheat, sorghum, and maize. It has been suggested that using systems biology and advanced sequencing approaches in genomics could help solve the AbS response in cereals. An emphasis was given to holistic approaches such as, bioinformatics and functional omics, gene mining and agronomic traits, genome-wide association studies (GWAS), and transcription factors (TFs) family with respect to AbS. In addition, the development of omics studies has improved to address the identification of AbS responsive genes and it enables the interaction between signaling pathways, molecular insights, novel traits and their significance in cereal crops. This review compares AbS mechanisms to omics and bioinformatics resources to provide a comprehensive view of the mechanisms. Moreover, further studies are needed to obtain the information from the integrated omics databases to understand the AbS mechanisms for the development of large spectrum AbS-tolerant crop production.

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Stewart, C. Neal, Patrick J. Tranel, David P. Horvath, James V. Anderson, Loren H. Rieseberg, James H. Westwood, Carol A. Mallory-Smith, Maria L. Zapiola, and Katrina M. Dlugosch. "Evolution of Weediness and Invasiveness: Charting the Course for Weed Genomics." Weed Science 57, no. 5 (October 2009): 451–62. http://dx.doi.org/10.1614/ws-09-011.1.

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The genetic basis of weedy and invasive traits and their evolution remain poorly understood, but genomic approaches offer tremendous promise for elucidating these important features of weed biology. However, the genomic tools and resources available for weed research are currently meager compared with those available for many crops. Because genomic methodologies are becoming increasingly accessible and less expensive, the time is ripe for weed scientists to incorporate these methods into their research programs. One example is next-generation sequencing technology, which has the advantage of enhancing the sequencing output from the transcriptome of a weedy plant at a reduced cost. Successful implementation of these approaches will require collaborative efforts that focus resources on common goals and bring together expertise in weed science, molecular biology, plant physiology, and bioinformatics. We outline how these large-scale genomic programs can aid both our understanding of the biology of weedy and invasive plants and our success at managing these species in agriculture. The judicious selection of species for developing weed genomics programs is needed, and we offer up choices, but noArabidopsis-like model species exists in the world of weeds. We outline the roadmap for creating a powerful synergy of weed science and genomics, given well-placed effort and resources.

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Derevnina, Lida, Benjamin Petre, Ronny Kellner, Yasin F. Dagdas, Mohammad Nasif Sarowar, Artemis Giannakopoulou, Juan Carlos De la Concepcion, et al. "Emerging oomycete threats to plants and animals." Philosophical Transactions of the Royal Society B: Biological Sciences 371, no. 1709 (December 5, 2016): 20150459. http://dx.doi.org/10.1098/rstb.2015.0459.

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Oomycetes, or water moulds, are fungal-like organisms phylogenetically related to algae. They cause devastating diseases in both plants and animals. Here, we describe seven oomycete species that are emerging or re-emerging threats to agriculture, horticulture, aquaculture and natural ecosystems. They include the plant pathogens Phytophthora infestans , Phytophthora palmivora , Phytophthora ramorum , Plasmopara obducens , and the animal pathogens Aphanomyces invadans , Saprolegnia parasitica and Halioticida noduliformans . For each species, we describe its pathology, importance and impact, discuss why it is an emerging threat and briefly review current research activities. This article is part of the themed issue ‘Tackling emerging fungal threats to animal health, food security and ecosystem resilience’.

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Kaufmane, Edīte, Māra Skrīvele, Edgars Rubauskis, Sarmīte Strautiņa, Laila Ikase, Gunārs Lācis, Dalija Segliņa, Inga Moročko-Bičevska, Silvija Ruisa, and Ilze Priekule. "Development of Fruit Science in Latvia." Proceedings of the Latvian Academy of Sciences. Section B. Natural, Exact, and Applied Sciences 67, no. 2 (August 1, 2013): 71–83. http://dx.doi.org/10.2478/prolas-2013-0013.

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Development of fruit growing and fruit science in Latvia has always been closely linked to the development of the whole country. After the founding of the independent Latvia state in 1918, fruit growing developed rapidly. Although in the Soviet times the situation was not favourable for quality fruit growing, research and breeding continued with good results. After Latvia regained independence, private land property rights were restored, and interest in intensive orchard establishment and growing technologies increased rapidly, which demanded change in the research focus. At present, the Latvia State Institute of Fruit-Growing is the leading institution in this field, working in cooperation with Pūre Horticultural Research Centre, Latvian Plant Protection Research Centre, Institute of Agrobiotechology, and Faculty of Food Technology, Latvia University of Agriculture, Laboratory of Plant Mineral Nutrition, Institute of Biology, University of Latvia. Research is carried out in the following directions: breeding and cultivar evaluation; genetics and molecular biology; plant pathology and entomology; orchard management; experimental processing and storage.

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Saad, Mohd Faiz Mat, Aziz Ramlee Sau, Muhamad Afiq Akbar, Syarul Nataqain Baharum, Ahmad Bazli Ramzi, Noraini Talip, and Hamidun Bunawan. "Construction of Infectious Clones of Begomoviruses: Strategies, Techniques and Applications." Biology 10, no. 7 (June 29, 2021): 604. http://dx.doi.org/10.3390/biology10070604.

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Begomovirus has become a potential threat to the agriculture sector. It causes significant losses to several economically important crops. Given this considerable loss, the development of tools to study viral genomes and function is needed. Infectious clones approaches and applications have allowed the direct exploitation of virus genomes. Infectious clones of DNA viruses are the critical instrument for functional characterization of the notable and newly discovered virus. Understanding of structure and composition of viruses has contributed to the evolution of molecular plant pathology. Therefore, this review provides extensive guidelines on the strategy to construct infectious clones of Begomovirus. Also, this technique’s impacts and benefits in controlling and understanding the Begomovirus infection will be discussed.

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Lee, Joan. "Reviewer Acknowledgements for Journal of Plant Studies, Vol. 6, No. 1." Journal of Plant Studies 6, no. 1 (February 26, 2017): 103. http://dx.doi.org/10.5539/jps.v6n1p103.

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Journal of Plant Studies wishes to acknowledge the following individuals for their assistance with peer review of manuscripts for this issue. Their help and contributions in maintaining the quality of the journal are greatly appreciated.Journal of Plant Studies is recruiting reviewers for the journal. If you are interested in becoming a reviewer, we welcome you to join us. Please find the application form and details at http://www.ccsenet.org/reviewer and e-mail the completed application form to jps@ccsenet.org.Reviewers for Volume 6, Number 1Adriana F. Sestras, University of Agricultural Sciences and Veterinary Medicine, RomaniaAna Simonovic, Institute for Biological Research "Sinisa Stankovic", SerbiaArthur T. O. Melo, College of Life Sciences and Agriculture, University of New Hampshire, United StatesBing Wang, Iowa State University, United StatesChrystian Iezid Maia e Almeida Feres, Tocantins Federal University, BrazilHoma Mahmoodzadeh, Department of Biology, Mashhad Branch, Islamic Azad University, Mashhad, IranKinga Kostrakiewicz-Gieralt, Institute of Botany, Jagiellonian University, PolandKirandeep Kaur Mani, California seed and Plant Labs, Pleasant Grove, CA, United States of AmericaMalgorzata Pietrowska-Borek, Poznan University of Life Sciences, PolandMartina Pollastrini, University of Florence, ItalyMassimo Zacchini, National Research Council of Italy (CNR), ItalyMelekber Sulusoglu, Arslanbey Vocational School Kocaeli University, TurkeyMontaser Fawzy Abdel-Monaim, Plant Pathology Res. Instatute, Agric. Res. Center, EgyptPanagiotis Madesis, Institiute of Applied Biosciences (CE.R.T.H.)/INAB, GreecePeter R. Greene, BGKT Consulting Ltd. Huntington, New York 11743, United StatesRosana Noemi Malpassi, Universidad Nacional de Rio Cuarto, ArgentinaSaid Laarabi, University Mohammed V/Ministry of National Education, MoroccoSlawomir Borek, Adam Mickiewicz University, PolandSuheb Mohammed, University of Virginia, United StatesVikas Mishra, Paher University, IndiaXiaomin Wu, Loyola University Chicago, United StatesYa-Yi Huang, Institution of Plant and Microbial Biology, Academia Sinica, Taiwan

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Ficke, Andrea, Christina Cowger, Gary Bergstrom, and Guro Brodal. "Understanding Yield Loss and Pathogen Biology to Improve Disease Management: Septoria Nodorum Blotch - A Case Study in Wheat." Plant Disease 102, no. 4 (April 2018): 696–707. http://dx.doi.org/10.1094/pdis-09-17-1375-fe.

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The estimated potential yield losses caused by plant pathogens is up to 16% globally and most research in plant pathology aims to reduce yield loss in our crops directly or indirectly. Yield losses caused by a certain disease depend not only on disease severity, but also on the weather factors, the pathogen’s aggressiveness, and the ability of the crop to compensate for reduced photosynthetic area. The yield loss-disease relationship in a certain host-pathogen system might therefore change from year to year, making predictions for yield loss very difficult at the regional or even at the farmer’s level. However, estimating yield losses is essential to determine disease management thresholds at which acute control measures such as fungicide applications, or strategic measures such as crop rotation or use of resistant cultivars are economically and environmentally sensible. Legislation in many countries enforces implementation of integrated pest management (IPM), based on economic thresholds at which the costs due to a disease justify the costs for its management. Without a better understanding of the relationship between disease epidemiology and yield loss, we remain insufficiently equipped to design adequate IPM strategies that will be widely adapted in agriculture. Crop loss studies are resource demanding and difficult to interpret for one particular disease, as crops are usually not invaded by only one pest or pathogen at a time. Combining our knowledge on disease epidemiology, crop physiology, yield development, damage mechanisms involved, and the effect of management practices can help us to increase our understanding of the disease-crop loss relationship. The main aim of this paper is to review and analyze the literature on a representative host-pathogen relationship in an important staple food crop to identify knowledge gaps and research areas to better assess yield loss and design management strategies based on economic thresholds.

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Nevame, Adedze Yawo Mawunyo, Lu Xia, Chofong Gilbert Nchongboh, Muhammad Mahmudul Hasan, Md Amirul Alam, Li Yongbo, Zhang Wenting, et al. "Development of a New Molecular Marker for the Resistance to Tomato Yellow Leaf Curl Virus." BioMed Research International 2018 (July 17, 2018): 1–10. http://dx.doi.org/10.1155/2018/8120281.

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Tomato yellow leaf curl virus(TYLCV) responsible for tomato yellow leaf curl disease (TYLCD) causes a substantial decrease in tomato (Solanum lycopersicumL.) yield worldwide. The use of resistant variety as a sustainable management strategy has been advocated. Tremendous progress has been made in genetically characterizing the resistance genes (Rgene) in tomato. Breeding tomato for TYLCV resistance has been based mostly onTy-3as a race-specific resistance gene by introgression originating from wild tomato species relatives. Improvement or development of a cultivar is achievable through the use of marker-assisted selection (MAS). Therefore, precise and easy use of gene-targeted markers would be of significant importance for selection in breeding programs. The present study was undertaken to develop a new marker based onTy-3gene sequence that can be used for MAS in TYLCV resistant tomato breeding program. The new developed marker was named ACY. The reliability and accuracy of ACY were evaluated against those ofTy-3linked marker P6-25 through screening of commercial resistant and susceptible tomato hybrids, and genetic segregation using F2 population derived from a commercial resistant hybrid AG208. With the use of bioinformatics and DNA sequencing analysis tools, deletion of 10 nucleotides was observed inTy-3gene sequence for susceptible tomato variety. ACY is a co-dominant indel-based marker that produced clear and strong polymorphic band patterns for resistant plant distinguishing it from its susceptible counterpart. The obtained result correlates with 3:1 segregation ratio of single resistant dominant gene inheritance, which depicted ACY as gene-tag functional marker. This marker is currently in use for screening 968 hybrids varieties and one thousand breeding lines of tomato varieties stocked in Jiangsu Green Port Modern Agriculture Development Company (Green Port). So far, ACY has been used to identify 56 hybrids and 51 breeding lines. These newly detected breeding lines were regarded as potential source of resistance for tomato breeding. This work exploited the sequence ofTy-3and subsequently contributed to the development of molecular marker ACY to aid phenotypic selection. We thus recommend this marker to breeders, which is suitable for marker-assisted selection in tomato.

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Huang, J. "First Report of Anthracnose Caused by Colletotrichum gloeosporioides on Schefflera actinophylla in China." Plant Disease 97, no. 7 (July 2013): 998. http://dx.doi.org/10.1094/pdis-12-12-1205-pdn.

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In China, in mild to warm climates, Schefflera actinophylla is commonly grown as a decorative tree in gardens. When mature, it has bright red flowers in inflorescences with up to 20 racemes that develop in summer or early autumn. From 2008 to 2011, lesions were observed on young and mature leaves in several locations in Guangzhou, China. The first symptoms were circular, necrotic areas that usually developed into irregular, dry, brown to reddish brown or black spots. Spots often first appeared at or near the margins of leaves. Reproductive bodies of the pathogen appeared as black specks in leaf spots. Under a 10× magnification, black, needle-like fungal structures (setae) were observed in the centers of spots on the upper leaf surface. A fungus was isolated from the lesion and was identified as Colletotrichum gloeosporioides (Penz.) Penz. & Sacc. based on cultural characteristics and conidial morphology (1). The voucher isolates were deposited in the Institute of Plant Pathology, Zhongkai University of Agriculture and Engineering. C. gloeosporioides is a species complex (2) and there is a degree of unresolved aspects of taxonomy in this species complex. Cultures on potato dextrose agar (PDA) had aerial white mycelium that turned gray to grayish black after 10 days at 25°C and a 12-h photoperiod and produced salmon to orange conidial masses. Brown, 80 to 120 μm long setae were observed in the acervulus. Conidia 14.1 to 18.0 × 4.0 to 6.1 μm in size were hyaline, thin-walled, aseptate, granular inside, clavate to slightly navicular in shape with an obtuse apex and a truncate base. To identify the fungus, a 588-bp segment of the ITS1-5.8S-ITS2 rDNA region was amplified by PCR and sequenced. The DNA sequence was submitted to GenBank as KC207404. A BLAST search of the DNA sequence showed 99% identity with accessions AY266389.1, EF423519.1, and HM575258.1 of C. gloeosporioides. Pathogenicity tests were conducted under greenhouse conditions at 25 ± 2°C. A total of 15 leaves from three 1-year-old S. actinophylla plants were inoculated with mycelial PDA plugs that were placed on 0.5-cm2 leaf wounds and then wrapped with Parafilm. Control leaves were treated similarly except that they were inoculated with PDA plugs without the fungus. No symptoms developed on control leaves after 10 days. Foliar lesions on inoculated leaves closely resembled those observed in the field. C. gloeosporioides was reisolated consistently from inoculated leaves. Pathogenicity was also tested by spraying leaves of potted S. actinophylla plants about 30 cm in height with 10 ml of a conidial suspension (1 × 105 conidia/ml) prepared from 7-day-old PDA cultures grown at 25°C. Leaves sprayed with distilled water were used as controls. Three plants were inoculated in each of two experiments and were incubated at 25°C and 90% relative humidity in a growth chamber. Tiny brown spots started to develop on all inoculated leaves 5 days after inoculation and the progression of symptom development was similar to that observed in the field. Control leaves remained asymptomatic. C. gloeosporioides was reisolated from inoculated leaves. To my knowledge, this is the first report of C. gloeosporioides causing anthracnose on S. actinophylla in China. References: (1) B. C. Sutton. The genus Glomerella and its anamorph Colletotrichum. In: Colletotrichum Biology, Pathology and Control. CAB International, Wallingford, UK, 1992. (2) B. S. Weir et al. The Colletotrichum gloeosporioides species complex. Stud. Mycol. 73:115, 2012.

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Alweera, Diluka, Nisha Sulari Kottearachchi, Dikkumburage Radhika Gimhani, and Kumudu Senarathna. "Single nucleotide polymorphisms in GBBSI and SSIIa genes in relation to starch physicochemical properties in selected rice (Oryza sativa L.) varieties." World Journal of Biology and Biotechnology 5, no. 2 (May 3, 2020): 23. http://dx.doi.org/10.33865/wjb.005.02.0305.

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Starch quality is one of the most important agronomic traits in rice (Oryza sativa L). In this study, we identified single nucleotide polymorphisms (SNPs) in the Waxy and Alk genes of eight rice varieties and their associations with starch physicochemical properties.vi.e.vamylose content (AC) and gelatinization temperature (GT). Seven Sri Lankan rice varieties, Pachchaperumal, Herathbanda, At 354, Bg 352, Balasuriya, H 6 and Bw 295-5 were detected as high amylose varieties while Nipponbare exhibited low amylose content. In silico analysis of the Waxy gene revealed that all tested Sri Lankan varieties possessed ‘G’ (Wxa allele) instead of ‘T’ in the first intron which could explain varieties with high and intermediate amylose content. All Sri Lankan varieties had ‘A’ instead of ‘C’ in exon 6 of the Waxy gene and this fact was tally with the varieties showing high amylose content. Therefore, possessing the Wxa allele in the first intron and ‘A’ in exon 6 could be used as a molecular marker for the selection of high amylose varieties as validated using several Sri Lankan varieties. All Sri Lankan varieties except, Bw 295-5 exhibited the intermediate type of GT which could not be explained using the so far reported allelic differences in the Alk gene. However, Bw 295-5 which is a low GT variety had two nucleotide polymorphisms in the last exon of the Alk gene, i.e. ‘G’ and ‘TT’ that represent low GT class. Therefore, it can be concluded that sequence variations of Waxy and Alk genes reported in this study are useful in breeding local rice varieties with preferential amylose content and GT class.Key word Alk gene, amylose content, single nucleotide polymorphism, Waxy gene.INTRODUCTIONRice (Oryza sativa L.) is one of the leading food crops of the world. More than half of the world’s population relies on rice as the major daily source of calories and protein (Sartaj and Suraweera, 2005). After grain yield, quality is the most important aspect of rice breeding. Grain size and shape largely determine the market acceptability of rice, while cooking quality is influenced by the properties of starch. In rice grains starch is the major component that primarily controls rice quality. Starch consists of two forms of glucose polymers, relatively unbranched amylose and a highly branched amylopectin. Starch-synthesizing genes may contribute to variation in starch physicochemical properties because they affect the amount and structure of amylose and amylopectin in rice grain (Kharabian-Masouleh et al., 2012). Amylose content (AC), gelatinization temperature (GT) and gel consistency (GC) is the three most important determinants of eating and cooking quality. Amylose content is the ratio of amylose amount present in endosperm to total starch content. Rice varieties are grouped based on their amylose content into waxy (0-2%), very low (3-9%), low (10-19%), intermediate (20-25%), and high (> 25%) (Kongseree and Juliano, 1972). The most widely used method for amylose determination is a colorimetric assay where iodine binds with amylose to produce a blue-purple color, which is measured spectrophotometrically at a single wavelength (620nm). Low amylose content is usually associated with tender, cohesive and glossy cooked rice; while, high amylose content is associated with firm, fluffy and separate grains of cooked rice. The Waxy (Wx) gene, which encodes granule-bound starch synthase I (GBSSI), is the major gene controlling AC in rice (Nakamura, 2002). The Waxy gene is located on chromosome six and various single nucleotide polymorphisms (SNPs) of Wx were found, including a ‘G’ to ‘T’ SNP of the first intron, ‘A’ to ‘C’ SNP of the sixth exon and ‘C’ to ‘T’ SNP of the tenth exon (Larkin and Park, 2003). The ‘AGGTATA’ sequence at the 5’splice-junction coincides with the presence of the Wxa allele, while the ‘AGTTATA’ sequence coincides with the presence of the Wxb allele. Therefore, all intermediate and high amylose cultivars had ‘G’ nucleotide while low amylose cultivars had ‘T’ nucleotide at the putative leader intron 5′ splice site. The cytosine and thymidine (CT) dinucleotide repeats in the 5’- untranslated region (UTR) of the Waxy gene were reported to be a factor associated with AC. However, the relationship between these polymorphisms and amylose contents is not clear. Amylopectin chain length distribution plays a very important role to determine GT in cooked rice. The time required for cooking is determined by the gelatinization temperature of starch. It is important because it affects the texture of cooked rice and it is related to the cooking time of rice. The gelatinization temperature is estimated by the alkali digestibility test. It is measured by the alkali spreading value (ASV). The degree of spreading value of individual milled rice kernels in a weak alkali solution (1.7% KOH) is very closely correlated with gelatinized temperature. According to the ASV, rice varieties may be classified as low (55 to 69°C), intermediate (70 to 74°C) and high (> 74°C) GT classes. In a breeding program ASV is extensively used to estimate the gelatinization temperature. The synthesis of amylopectin is more complex than that of amylose. Polymorphisms in the starch synthase IIa (SSIIa) gene which is recognized as the Alk gene are responsible for the differences in GT in rice (Umemoto and Aoki, 2005; Waters et al., 2006). Two single nucleotide polymorphisms (SNPs) in the last exon of the Alk gene are responsible for the differences in GT in rice. The biochemical analysis clearly showed that the function of the amino acids caused by these two SNPs is essential for SSIIa enzyme activity (Nakamura et al., 2005) and those are ‘G’/‘A’ SNP at 4424 bp position and ‘GC’/‘TT’ SNPs at 4533/4534 bp position with reference to Nipponbare rice genomic sequence. Based on the SNPs, Low SSIIa enzyme activity results in S-type amylopectin, which is enriched in short chains whereas high SSIIa enzyme activity produces L-type amylopectin (Umemoto et al., 2004). Therefore, the combination of ‘G’ at SNP3 and ‘GC’ at SNP4 is required to produce L-type rice starch and this has a higher GT relative to S-type starch. GC is a standard assay that is used in rice improvement programs to determine the texture of softness and firmness in high amylose rice cultivars. Intermediate and low amylose rice usually has soft gel consistency. Sequence variation in exon 10 of the Waxy gene associates with GC (Tran et al., 2011).OBJECTIVES The objectives of this study were to detect polymorphisms in major starch synthesizing genes among several rice cultivars as models and to determine the relationship between their SNP variations and starch physicochemical properties. Also, we analyzed major starch synthesizing gene sequences of several Sri Lankan rice varieties in silico aiming at utilizing this information in rice breeding programs.MATERIALS AND METHODSPlant materials: Seeds of eight Oryza sativa L. accessions were obtained from the Rice Research and Development Institute (RRDI), Bathalagoda, Sri Lanka and Gene Bank of Plant Genetic Resource Center (PGRC), Gannoruwa.Characterization of grain physical parameters: Grain length and width were determined using a vernier caliper. Ten grains from each sample were collected randomly and measured to obtain the average length and width of the milled rice. The average length and width were recorded as their length and width. Based on the length and width of the grains, the milled rice grains were classified into four classes (table 1) according to the method accepted by RRDI Bathalagoda, Sri Lanka.According to the scale L/S – Long Slender, L/M – Long Medium, I/B – Intermediate Bold and S/R –Short RoundAnalysis of amylose content: Initially, rice samples were dehusked and polished prior to milling. Ten whole – milled rice kernels of eight rice samples were ground separately by using mortar and pestle. Amylose content per 100 mg was determined by measuring the blue value of rice varieties as described by Juliano (1971). About 100mg rice sample was shifted into a 100 mL volumetric flask and 1mL of 95% ethanol was added. Then 9mL of 1N NaOH was added and the content was boiled for 20min. at boiling temperature to gelatinize the starch. After cooling the content, the volume was made up to 100mL and 5mL of starch solution was pipetted out into a 100mL volumetric flask. The blue color was developed by adding 1mL of 1N acetic acid and 2 mL of iodine solution (0.2g iodine and 2.0g potassium iodine in 10 mL aqueous solution). Then volume was made up to 100mL with distilled water and the solution was kept for 20min. after shaking. Finally, the absorbance of the solution was measured at 620nm using Spectrophotometer T80 (PG Instruments Limited) as described by Juliano (1971). The standard curve was prepared using 40mg of potato-amylose to calculate the amylose content of rice varieties through absorbance values. Forty mg of potato amylose was put into a 100 mL of volumetric flask and 1ml of 95% ethanol and 9mL of NaOH were added and content was heated for 20min at boiling temperature. After cooling the content volume of the solution was made up to 100mL using distilled water. Then 1mL, 2mL, 3mL, 4mL and 5mL of amylose solution were pipetted out into 100mL flasks. Then 0.2mL, 0.4mL, 0.6mL, 0.8mL and 1mL of 1N acetic acid were added to the flasks respectively. Finally, 2mL of iodine solution was added to each flask and volume was made up to 100mL with distilled water. Solutions were stood up for 20min. after shaking and absorbance values were measured at 620nm. Measured absorbance values were plotted at 620nm against the concentration of anhydrous amylose (mg).Analysis of gelatinization temperature: GT was indirectly measured on rice by the alkali spreading value. Husked and polished seeds per accession were used for the analysis. Selected duplicate sets of six milled grains without cracks of each sample were put into Petri dishes. About 10mL of 1.7% KOH was added and grains were spread in the petri dish to provide enough space. The constant temperature at 30°C was maintained to ensure better reproducibility. After 23hrs, the degree of disintegration was quantified by a standard protocol with a numerical scale of 1–7 (table 2) as reported by Cruz and Khush (2000). As reported by Juliano (2003), GT of rice was determined using the alkaline spreading scale, where 1.0-2.5: High (74-80 °C), 2.6-3.4: High-intermediate (70-74 °C), 3.5-5.4: Intermediate (70-74 °C) and 5.5-7.0 Low: (55-70 °C).Bioinformatics and statistical analysis: The available literature was used to identify the most likely candidate genes associated with rice starch quality and their SNPs of each gene (Hirose et al., 2006; Waters and Henry, 2007; Tran et al., 2011). In all the tested varieties except Bg 352 and At 354, the DNA sequence of each gene was retrieved from the Rice SNP Seek database (http://snp-seek.irri.org/). The gene sequences of At 354 and Bg 352 were obtained from the National Research Council 16-016 project, Wayamba University of Sri Lanka. Multiple sequence alignment was conducted for the DNA sequence using Clustal Omegavsoftware (https://www.ebi.ac.uk/Tools/msa/clustalo/). Starch physiochemical data obtained were subjected to a one-way analysis of variance (ANOVA) followed by Duncan’s New Multiple Range Test (DNMRT) to determine the statistical differences among varieties at the significance level of p ≤ 0.05. Statistical analysis was done using SAS version 9.1 (SAS, 2004).ESULTS AND DISCUSSION: Physical properties of rice grains: Physical properties such as length, width, size, shape and pericarp color of rice grains obtained from eight different rice varieties are given in table 3. Classification of rice grains was carried out, according to their sizes and shapes based on Juliano (1985). The size of the rice grains was determined as per grain length while grain shape was determined by means of length and width ratio of the rice kernel. In the local market, rice is classified as Samba (short grain), Nadu (intermediate grain) and Kora (long/medium) based on the size of the grain (Pathiraje et al., 2010). Lengths of rice kernels were varied from 5.58 to 6.725 mm for all varieties. The highest grain length and width were given by At 354 and Pachchaperumal respectively. The varieties, Bw 295-5 and H 6 showed a length: width ratio over 3 which is considered as slender in grain shape. Bw 295-5, H 6, At 354, Bg 352 and Nipponbare possessed white pericarp and others possessed red pericarp.Relationship between amylose content and SNPs variation of waxy loci in selected varieties: Amylose content was measured in seven Sri Lankan rice varieties and one exotic rice variety. Amylose content of the evaluated varieties varied significantly with p ≤ 0.05 with the lowest of 15.11% and highest of 28.63% which were found in Nipponbare and Bw 295-5, respectively (table 4). The majority of the evaluated varieties fell into the high AC category (between 25-28%). Only Nipponbare could be clearly categorized under the low amylose group (table 4). The amylose content of Bg 352, Pachchaperumal and Herathbanda have already been determined by early studies of Rebeira et al. (2014) and Fernando et al. (2015). Most of the data obtained in the present experiment has agreed with the results of previous studies. Major genes such as Waxy and their functional SNPs have a major influence on amylose in rice (Nakamura et al., 2005). Accordingly, single nucleotide polymorphism, ‘G’/‘T’, at the 5’ leader intron splice site of the GBSSI has explained the variation in amylose content of varieties. Accordingly, high and intermediate amylose varieties have ‘AGGTATA’ while low amylose varieties have the sequence ‘AGTTATA’, which might lead to a decrease in the splicing efficiency. Therefore, the GBSSI activity of Nipponbare might be considerably weak and resulted in starch with low amylose content. Hence, producing ‘G’/‘T’ polymorphism clearly differentiates low amylose rice varieties, as reported by Nakamura et al. (2005). In GBSSI, Larkin and Park (2003) identified an ‘A’/‘C’ polymorphism in exon 6 and a ‘C’/‘T’ polymorphism in exon 10 which resulted in non- synonymous amino acid change. Chen et al. (2008) reported that the non-synonymous ‘A’/‘C’ SNP at exon 6 had the highest possible impact on GBSSI. Accordingly, the ‘A’/‘C’ polymorphism in exon 6 causes a tyrosine/serine amino acid substitution while the ‘C’/‘T’ polymorphism in exon 10 causes a serine/proline amino acid substitution. In view of this information, there is a relationship between the polymorphism detected by in silico analysis and amylose content obtained from our experiment. Out of the eight tested rice varieties, only one variety, Nipponbare was categorized as low amylose variety (10-19%) and it exhibited ‘T’ nucleotide at the intron splice site (table 4; figure 1). Varieties such as Pachchaperumal, Balasuriya, Bw 295-5, H 6, Herathbanda, At 354 and Bg 352 which contained high amylose (> 25%), had ‘G’ and ‘A’ nucleotides at intron splice site and exon 6 respectively (table 4; figure 1). The predominant allelic pattern of intron splice site and exon 6 are different in varieties containing intermediate amylose content (20-25%) which showed ‘G’ and ‘C’ nucleotides respectively. Of these selected rice varieties, none of the intermediate type amylose variety was found.Relationship between gel consistency and SNPs variation in Waxy loci: In this study, GC data of Herathbanda, Hondarawalu, Kuruluthuda, Pachchaperumal and Bg 352 were obtained from Fernando et al. (2015). The results of Tran et al. (2011) showed that the exon 10 ‘C’/‘T’ SNP of Wx has mainly affected GC. Accordingly, rice with a ‘C’ at exon 10 had soft and viscous gels once cooked. However, a sample with a ‘T’ had short and firm gels. In this study, Herathbanda, Hondarawalu, Kuruluthuda and Pachchaperumal had ‘C’ nucleotide and Bg 352 had ‘T’ nucleotide in exon 10 (table 5; figure 2). However, ‘C’/‘T’ substitution analysis could not be used to explain the GC of tested varieties.Relationship between gelatinized temperature and SNPs variation of Alk loci in selected rice varieties: Although there were differences in the scores, the degree of disintegration of all samples was saturated at 23 hrs. Most of the selected rice varieties showed the intermediate disintegration score. Varieties, Pachchaperumal, Balasuriya, H 6, Herathbanda, At 354 and Bg 352 were categorized into intermediate GT class (70–74°C) as indicated by an alkali spreading (AS) value of 5 (table 6; figure 3). Nipponbare and Bw 295-5 showed the highest disintegration score indicating the dispersion of all grains. Hence these varieties were categorized into low GT class (55-69°C) as indicated by an AS value of 6 (table 6; figure 3). However, high GT class rice varieties (> 74°C) were not found in the tested samples. Chromosomal mutation within the Alk gene has led to a number of single nucleotide polymorphisms (SNPs). Umemoto et al. (2004) identified four SNPs in Alk gene. Thus, SNP3 and SNP4 may be important genetic polymorphisms that are associated with GT class. According to the SNP3 and SNP4, eight rice varieties could be classified into either high GT or low GT types. If there is ‘A’ instead of ‘G’ at 4424 bp position of Alk gene with reference to Nipponbare rice genomic sequence, it codes methionine instead of valine amino acid residue in SSIIa, whilst two adjacent SNPs at bases 4533 and 4534 code for either leucine (‘GC’) or phenylalanine (‘TT’). Rice varieties with high GT starch had a combination of valine and leucine at these residues. Rice varieties with low GT starch had a combination of either methionine and leucine or valine and phenylalanine at these same residues. Nipponbare carried the ‘A’ and ‘GC’ nucleotides, while Bw 295-5 carried the ‘G’ and ‘TT’ nucleotides. Hence these varieties were classified into low GT class. Varieties such as Pachchaperumal, Balasuriya, H 6, Herathbanda, At 354 and Bg 352 carried ‘G’ and ‘GC’ nucleotides and these varieties were classified into high GT rice varieties. However, intermediate GT status could not be determined by SNP3 and SNP4 mutation of Alk gene (table 6; figure 4).In silico analysis of the polymorphisms in GBSSI gene and Alk genes of rice varieties retrieved from Rice-SNP-database: In this study, GBSSI gene and Alk gene were compared with the sequences retrieved from the Rice-SNP-Seek database to validate the SNPs further. As previously reported by Ayres et al. (1997), all low amylose varieties had the sequence ‘AGTTATA’ in exon 1. In agreement with preliminary work done by Larkin and Park (2003), all of the intermediate amylose varieties have the allelic pattern of GCC. All of the high amylose varieties have either the GAC or GAT allele of GBSSI. Among 42 rice accessions with the Sri Lankan pedigree, four allelic patterns were found; TAC, GCC, GAC and GAT (table 7). In this allelic pattern, the first letter corresponds to the ‘G’/‘T’ polymorphism in 5’ leader intron splice-junction, the second letter corresponds to the ‘A’/‘C’ polymorphism in exon 6 and the third letter corresponds to the ‘C’/‘T’ polymorphism in exon10 of Waxy gene. Analysis of the ‘G’/‘T’ polymorphism in the Wx locus showed that 41 rice cultivars shared the same ‘AGGTATA’ sequence at the 5’ leader intron splice-junction. But only 1 rice cultivar, Puttu nellu was found with ‘T’ nucleotide in intron1/exon1 junction site, which could be categorized as a low amylose variety (table 7). As discussed above, varieties with an intermediate level of apparent amylose could be reliably distinguished from those with higher apparent amylose based on a SNP in exon 6. Hence, only three rice varieties Nalumoolai Karuppan, Pannithi and Godawel with ‘C’ nucleotide in exon 6 exhibited the possibility of containing intermediate amylose content (table 7). High activity of GBSSI produces high amylose content leading to a non-waxy, non-sticky or non-glutinous phenotype. Therefore, according to the in silico genotypic results, rest of the 38 rice varieties may produce high amylose content in the endosperm (table 7). Proving this phenomenon. Abeysekera et al. (2017) has reported that usually, most of Sri Lankan rice varieties contain high amylose content. Targeted sequence analysis of exon 8 of the Alk gene in 42 different rice cultivars were found with three SNP polymorphisms that resulted in a changed amino acid sequence and, of these three SNPs, two SNPs were reported to be correlated with possible GT differences. Accordingly, Puttu nellu and 3210 rice varieties carried the ‘G’ and ‘TT’ nucleotides in SNP3 and SNP4 respectively (table 7). Hence these varieties can be classified into low GT class and except these two; other rice varieties carried the ‘G’ and ‘GC’ nucleotides in SNP3 and SNP4 respectively. Therefore, those varieties can possibly be classified into high GT rice varieties (table 7). However, further experiments are necessary to check the phenotypic variations for grain amylose content and GT class of in silico analyzed rice varieties. CONCLUSION Present results revealed the relationship between SNPs variation at Waxy loci and the amylose content of selected rice varieties. Accordingly, Pachchaperumal, At 354, Bg 352, Herathbanda, H 6, Balasuriya and Bw 295-5 with high amylose content had ‘G’ instead of ‘T’ in the first intron exhibiting the presence of Wxa allele with reference to Nipponbare which had low amylose content. Also all tested varieties had ‘A’ in exon 6 of the Waxy gene. Thus present findings i.e. presence of Wxa allele and SNP ‘A’ in exon 6 could be used as a potential molecular marker for the selection of high amylose varieties. In addition, Bw 295-5 which is a low GT variety, had two SNPs variations in the last exon of the Alk gene i.e. ‘G’ and ‘TT’ which is likely to be used to represent low GT class. Accordingly, sequence variations identified in Waxy and Alk genes could be utilized in the future rice breeding programs for the development of varieties with preferential amylose content and GT class.ACKNOWLEDGMENTSDirector and staff of the Gene Bank, Plant Genetic Resources Center, Gannoruwa are acknowledged for giving rice accessions.CONFLICT OF INTERESTAuthors have no conflict of interest.REFERENCESAbeysekera, W., G. Premakumara, A. Bentota and D. S. Abeysiriwardena, 2017. Grain amylose content and its stability over seasons in a selected set of rice varieties grown in Sri Lanka. Journal of agricultural sciences Sri Lanka, 12(1): 43-50.Ayres, N., A. McClung, P. Larkin, H. Bligh, C. Jones and W. Park, 1997. Microsatellites and a single-nucleotide polymorphism differentiate apparentamylose classes in an extended pedigree of us rice germ plasm. Theoretical applied genetics, 94(6-7): 773-781.Chen, M.-H., C. Bergman, S. Pinson and R. Fjellstrom, 2008. Waxy gene haplotypes: Associations with apparent amylose content and the effect by the environment in an international rice germplasm collection. Journal of cereal science, 47(3): 536-545.Cruz, N. D. and G. Khush, 2000. Rice grain quality evaluation procedures. Aromatic rices, 3: 15-28.Fernando, H., T. Kajenthini, S. Rebeira, T. Bamunuarachchige and H. Wickramasinghe, 2015. Validation of molecular markers for the analysis of genetic diversity of amylase content and gel consistency among representative rice varieties in sri lanka. Tropical agricultural research, 26(2): 317-328.Hirose, T., T. Ohdan, Y. Nakamura and T. Terao, 2006. Expression profiling of genes related to starch synthesis in rice leaf sheaths during the heading period. Physiologia plantarum, 128(3): 425-435.Juliano, B., 1971. A simplified assay for milled rice amylose. Journal of cereal science today, 16: 334-360.Juliano, B. O., 1985. Rice: Chemistry and technology. The american association of cereal chemists. Inc. St. Paul, Minnesota, USA, 774.Juliano, B. O., 2003. Rice chemistry and quality. Island publishing house. Island publishing house, Manila: 1-7.Kharabian-Masouleh, A., D. L. Waters, R. F. Reinke, R. Ward and R. J. Henry, 2012. Snp in starch biosynthesis genes associated with nutritional and functional properties of rice. Scientific reports, 2(1): 1-9.Kongseree, N. and B. O. Juliano, 1972. Physicochemical properties of rice grain and starch from lines differing in amylose content and gelatinization temperature. Journal of agricultural food chemistry, 20(3): 714-718.Larkin, P. D. and W. D. Park, 2003. Association of waxy gene single nucleotide polymorphisms with starch characteristics in rice (Oryza sativa L.). Molecular Breeding, 12(4): 335-339.Nakamura, Y., 2002. Towards a better understanding of the metabolic system for amylopectin biosynthesis in plants: Rice endosperm as a model tissue. Plant cell physiology, 43(7): 718-725.Nakamura, Y., P. B. Francisco, Y. Hosaka, A. Sato, T. Sawada, A. Kubo and N. Fujita, 2005. Essential amino acids of starch synthase iia differentiate amylopectin structure and starch quality between Japonica and Indica rice varieties. Plant molecular biology, 58(2): 213-227.Pathiraje, P., W. Madhujith, A. Chandrasekara and S. Nissanka, 2010. The effect of rice variety and parboiling on in vivo glycemic response. Journal of tropical agricultural research, 22(1): 26-33.Rebeira, S., H. Wickramasinghe, W. Samarasinghe and B. Prashantha, 2014. Diversity of grain quality characteristics of traditional rice (Oryza sativa L.) varieties in sri lanka. Tropical agricultural research, 25(4): 470-478.Sartaj, I. Z. and S. A. E. R. Suraweera, 2005. Comparison of different parboiling methods on the quality characteristics of rice. Annals of the Sri Lankan Department of Agriculture, 7: 245-252.Tran, N., V. Daygon, A. Resurreccion, R. Cuevas, H. Corpuz and M. Fitzgerald, 2011. A single nucleotide polymorphism in the waxy gene explains a significant component of gel consistency. Theoretical applied genetics, 123(4): 519-525.Umemoto, T. and N. Aoki, 2005. Single-nucleotide polymorphisms in rice starch synthase iia that alter starch gelatinisation and starch association of the enzyme. Functional plant biology, 32(9): 763-768.Umemoto, T., N. Aoki, H. Lin, Y. Nakamura, N. Inouchi, Y. Sato, M. Yano, H. Hirabayashi and S. Maruyama, 2004. Natural variation in rice starch synthase iia affects enzyme and starch properties. Functional plant biology, 31(7): 671-684.Waters, D. L. and R. J. Henry, 2007. Genetic manipulation of starch properties in plants: Patents 2001-2006. Recent patents on biotechnology, 1(3): 252-259.Waters, D. L., R. J. Henry, R. F. Reinke and M. A. Fitzgerald, 2006. Gelatinization temperature of rice explained by polymorphisms in starch synthase. Plant biotechnology journal, 4(1): 115-122.

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Qing, Xue, Meng Wang, Gerrit Karssen, Patricia Bucki, Wim Bert, and Sigal Braun-Miyara. "PPNID: a reference database and molecular identification pipeline for plant-parasitic nematodes." Bioinformatics, September 14, 2019. http://dx.doi.org/10.1093/bioinformatics/btz707.

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Abstract Motivation The phylum Nematoda comprises the most cosmopolitan and abundant metazoans on Earth and plant-parasitic nematodes represent one of the most significant nematode groups, causing severe losses in agriculture. Practically, the demands for accurate nematode identification are high for ecological, agricultural, taxonomic and phylogenetic researches. Despite their importance, the morphological diagnosis is often a difficult task due to phenotypic plasticity and the absence of clear diagnostic characters while molecular identification is very difficult due to the problematic database and complex genetic background. Results The present study attempts to make up for currently available databases by creating a manually-curated database including all up-to-date authentic barcoding sequences. To facilitate the laborious process associated with the interpretation and identification of a given query sequence, we developed an automatic software pipeline for rapid species identification. The incorporated alignment function facilitates the examination of mutation distribution and therefore also reveals nucleotide autapomorphies, which are important in species delimitation. The implementation of genetic distance, plot and maximum likelihood phylogeny analysis provides more powerful optimality criteria than similarity searching and facilitates species delimitation using evolutionary or phylogeny species concepts. The pipeline streamlines several functions to facilitate more precise data analyses, and the subsequent interpretation is easy and straightforward. Availability and implementation The pipeline was written in vb.net, developed on Microsoft Visual Studio 2017 and designed to work in any Windows environment. The PPNID is distributed under the GNU General Public License (GPL). The executable file along with tutorials is available at https://github.com/xueqing4083/PPNID. Supplementary information Supplementary data are available at Bioinformatics online.

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PARIKESIT, Arli Aditya, Dito ANUROGO, and Riza A. PUTRANTO. "Pemanfaatan bioinformatika dalam bidang pertanian dan kesehatan (The utilization of bioinformatics in the field of agriculture and health)." E-Journal Menara Perkebunan 85, no. 2 (October 30, 2017). http://dx.doi.org/10.22302/iribb.jur.mp.v85i2.237.

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Bioinformatics can be used to manage the data storage resulted from in silico molecular biology experiments. Off-network (offline) applications require large computing resources, in which researchers in the bioinformatics field of agriculture and health sectors do not necessarily possess. This review paper addressed examples of affordable and applicable in silico analytical cases in both mentioned sectors. Genome sequence analysis and in silico drug design using (1) a computational method, pharmacokinetic parameter prediction, (2) Computer Aided Design and Drafting (CADD) technology, (3) potential protein action prediction, (4) OMICs application in stem cell biology, and (5) lncRNAs based database computing internet sites is one of examples. In agriculture, bioinformatics-based research has been used in (1) the development of molecular markers; (2) the design of primer for differential gene expression analysis; (3) the development of genetic maps; and (4) gene expression analysis. Further application of bioinformatics also targets the design of applicative products for pest control and the protection of plant varieties in the farm. Through this example, novice researchers in the bioinformatics field of agriculture and health sectors can conduct sophisticated research using standard computer tools, internet networks, and sufficient knowledge about bioinformatics. On the other hand, multidisciplinary collaboration between these scientists can be carried out through social networking. The synergy can be directed to improve computing capabilities and data analysis via procurement of computing resources and use of public information clusters. [Key words: genome sequences, in silico drug design, online, bioinformatics, health, agriculture.] AbstrakBioinformatika dapat digunakan dalam manajemen informasi di bidang penyimpanan data in silico dari eksperimen biologi molekuler. Aplikasi luar jaringan (luring) memerlukan sumber daya komputasi yang besar, yang belum tentu dimiliki oleh para peneliti dalam bidang bioinformatika kesehatan dan pertanian. Kajian ilmiah ini membahas contoh kasus analisis in silico yang terjangkau dan aplikatif dalam bidang kesehatan dan pertanian. Contoh kasus tersebut adalah analisis sekuen genom dan desain obat in silico, menggunakan pendekatan metode komputasional, prediksi parameter farmakokinetik, teknologi Computer Aided Design and Drafting (CADD), prediksi potensial aksi protein, aplikasi OMICs pada biologi sel punca, hingga komputasi basis data lncRNAs berbasis situs internet. Pada bidang pertanian, penelitian berbasis bioinformatika telah digunakan dalam (1) pengembangan penanda molekuler; (2) desain primer untuk analisis ekspresi gen diferensial; (3) pengembangan peta genetik; dan (4) analisis ekspresi gen. Pemanfaatan bio-informatika dalam ilmu terapan dibidang pertanian juga menyasar desain produk aplikatif untuk pengendalian hama dan perlindungan varietas tanaman. Melalui contoh tersebut, peneliti pemula dibidang bioinformatika kesehatan dan pertanian dapat melakukan penelitian canggih hanya dengan alat komputer standar, jaringan internet, dan pengetahuan mencukupi tentang bioinformatika. Disisi lain, sinergi dan kolaborasi antar peneliti multi-displiner dapat dilakukan melalui penggunaan jejaring sosial. Sinergi tersebut dapat diarahkan untuk meningkatkan kemampuan komputasi dan analisis data melalui pengadaan sumber daya komputasi dan penggunaan klaster informatika publik.[Kata kunci: sekuen genom, desain obat in silico, daring, bioinformatika, kesehatan, pertanian]

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Milazzo, Carla, Katherine G. Zulak, M. Jordi Muria-Gonzalez, Darcy Jones, Matthew Power, Kaylene Bransgrove, Michael Bunce, and Francisco J. Lopez-Ruiz. "High-Throughput Metabarcoding Characterizes Fungal Endophyte Diversity in the Phyllosphere of a Barley Crop." Phytobiomes Journal, August 31, 2021, PBIOMES—09–20–0. http://dx.doi.org/10.1094/pbiomes-09-20-0066-r.

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Over the last decade, the microbiome has received increasing attention as a key factor in macroorganism fitness. Sustainable pest management requires an understanding of the complex microbial endophyte communities existing symbiotically within plants and the way synthetic pesticides interact with them. Fungal endophytes are known to benefit plant growth and fitness and may deter pests and diseases. Recent advances in high-throughput sequencing (HTS) have enabled integrative microbiome studies, especially in agricultural contexts. Here, we profile the fungal endophyte community in the phyllosphere of two barley (Hordeum vulgare) cultivars exposed to two systemic foliar fungicides using metabarcoding, an HTS tool that constructs community profiles from environmental DNA. We studied the fungal nuclear ribosomal large subunit D2 and internal transcribed spacer 2 (ITS2) DNA markers through a bioinformatics pipeline introduced here. We found 88 and 128 unique amplicon sequence variants (ASVs) using the D2 and ITS2 metabarcoding assays, respectively. With principal coordinate analysis and permutational analysis of variance, ASV diversity did not change in response to barley cultivar or fungicide treatment; however, the community structure of unsprayed plants did change between two collection times 8 days apart. The workflow described here can be applied to other microbiome studies in agriculture and we hope it encourages further research into crop microbiomes to improve agroecosystem management.

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Ayachit, Garima, Inayatullah Shaikh, Himanshu Pandya, and Jayashankar Das. "Salient Features, data and algorithms for microRNA screening from plants: A review on the gains and pitfalls of machine learning techniques." Current Bioinformatics 15 (June 1, 2020). http://dx.doi.org/10.2174/1574893615999200601121756.

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: The era of Big Data and high-throughput genomic technology has enabled scientists to have a clear view of plant genomic profiles. However, it has also led to a massive need of computational tools and strategies to interpret this data. In this scenario of huge data inflow, machine learning (ML) approaches are emerging to be the most promising for analysing heterogeneous and unstructured biological datasets. Extending its application to healthcare and agriculture, ML approaches are being useful for microRNA (miRNA) screening as well. Identification of miRNAs is a crucial step towards understanding post-transcriptional gene regulation and miRNA-related pathology. The use of ML tools is becoming indispensable in analysing such data and identifying species-specific, non-conserved miRNA. However, these techniques have their own benefits and lacunas. In this review, we discuss the current scenario and pitfalls of ML based tools for plant miRNA identification and provide some insights into the important features, the need for deep learning models and direction in which studies are needed.

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Brahmi, Pratibha, and Vandana Tyagi. "Intellectual Property Rights (IPR) issues related to access and use of genetic resources." Indian Journal of Genetics and Plant Breeding (The) 79, no. 01S (January 16, 2019). http://dx.doi.org/10.31742/ijgpb.79s.1.24.

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Genetic Resources (GR) refer to genetic material of actual or potential value. Use of GR refers to the process of researching their beneficial properties and using them to increase scientific knowledge and understanding, or to develop commercial products. There is continuous search for newer resources to meet the future demands that arise with the emergence of new diseases, abiotic stresses, climate change, and enhanced demand for food and nutritional security. GR are exchanged and searched continuously for specific traits to improve yields and nutritional value in crops and animal genetic resources. Every nation is concerned with acquisition of diverse and superior germplasm for conservation and utilization. The rapid advancements in the fields of molecular biology, biotechnology and bioinformatics, led to the emergence of new legal, political and technological regimes regulating access to GR. Three international negotiations impacted the access to GR, these are the Convention on Biological Diversity (CBD), the Agreement on Trade-Related Aspects of Intellectual Property Rights (TRIPS) as part of the Agreement establishing the World Trade Organization (WTO) and the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA). The regulation regarding access to GR, increasing application of IPRs and the vast potential of biological wealth yet to be tapped through bio-prospecting and genetic engineering, has placed greater demands on nations to adjust to the changing scenario of GR management. Currently access to GR is under the provisions of CBD and access to GR is based on mutually agreed terms (MAT), subject to prior informed consent (PIC). In response to CBD, India enacted the Biological Diversity Act (BDA), 2002 and established the National Biodiversity Authority (NBA) in 2003. Access to PGR from India is therefore regulated by BDA, 2002. The Nagoya Protocol which entered into force from October 2014 defines the international regime within the framework of CBD to promote and safeguard the fair and equitable sharing of benefits arising from the utilization of genetic resources. The paper discusses these agreements in detail with reference to access and use of GR.

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"The Phytochemical Society of Europe The Phytochemical Society of Europe (PSE) was founded in 1957. Its aim is to promote the understanding of plant constituents in respect of their chemistry, function, biosynthesis, and effects on the physiology and pathology of living organisms. A further objective is the application of such knowledge in agriculture and industry. Details of the PSE are given at:." Phytochemistry 65, no. 5 (March 2004): I—II. http://dx.doi.org/10.1016/s0031-9422(04)00053-6.

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Chavdarov, Anatoliy V. "Special Issue No. – 10, June, 2020 Journal > Special Issue > Special Issue No. – 10, June, 2020 > Page 5 “Quantative Methods in Modern Science” organized by Academic Paper Ltd, Russia MORPHOLOGICAL AND ANATOMICAL FEATURES OF THE GENUS GAGEA SALISB., GROWING IN THE EAST KAZAKHSTAN REGION Authors: Zhamal T. Igissinova,Almash A. Kitapbayeva,Anargul S. Sharipkhanova,Alexander L. Vorobyev,Svetlana F. Kolosova,Zhanat K. Idrisheva, DOI: https://doi.org/10.26782/jmcms.spl.10/2020.06.00041 Abstract: Due to ecological preferences among species of the genus GageaSalisb, many plants are qualified as rare and/or endangered. Therefore, the problem of rational use of natural resources, in particular protection of early spring plant species is very important. However, literary sources analysis only reveals data on the biology of species of this genus. The present research,conducted in the spring of 2017-2019, focuses on anatomical and morphological features of two Altai species: Gagealutea and Gagea minima; these features were studied, clarified and confirmed by drawings and photographs. The anatomical structure of the stem and leaf blade was studied in detail. The obtained research results will prove useful for studies of medicinal raw materials and honey plants. The aforementioned species are similar in morphological features, yet G. minima issmaller in size, and its shoots appear earlier than those of other species Keywords: Flora,gageas,Altai species,vegetative organs., Refference: I. Atlas of areas and resources of medicinal plants of Kazakhstan.Almaty, 2008. II. Baitenov M.S. Flora of Kazakhstan.Almaty: Ġylym, 2001. III. DanilevichV. G. ThegenusGageaSalisb. of WesternTienShan. PhD Thesis, St. Petersburg,1996. IV. EgeubaevaR.A., GemedzhievaN.G. The current state of stocks of medicinal plants in some mountain ecosystems of Kazakhstan.Proceedings of the international scientific conference ‘”Results and prospects for the development of botanical science in Kazakhstan’, 2002. V. Kotukhov Yu.A. New species of the genus Gagea (Liliaceae) from Southern Altai. Bot. Journal.1989;74(11). VI. KotukhovYu.A. ListofvascularplantsofKazakhstanAltai. Botan. Researches ofSiberiaandKazakhstan.2005;11. VII. KotukhovYu. The current state of populations of rare and endangered plants in Eastern Kazakhstan. Almaty: AST, 2009. VIII. Kotukhov Yu.A., DanilovaA.N., AnufrievaO.A. Synopsisoftheonions (AlliumL.) oftheKazakhstanAltai, Sauro-ManrakandtheZaisandepression. BotanicalstudiesofSiberiaandKazakhstan. 2011;17: 3-33. IX. Kotukhov, Yu.A., Baytulin, I.O. Rareandendangered, endemicandrelictelementsofthefloraofKazakhstanAltai. MaterialsoftheIntern. scientific-practical. conf. ‘Sustainablemanagementofprotectedareas’.Almaty: Ridder, 2010. X. Krasnoborov I.M. et al. The determinant of plants of the Republic of Altai. Novosibirsk: SB RAS, 2012. XI. Levichev I.G. On the species status of Gagea Rubicunda. Botanical Journal.1997;6:71-76. XII. Levichev I.G. A new species of the genus Gagea (Liliaceae). Botanical Journal. 2000;7: 186-189. XIII. Levichev I.G., Jangb Chang-gee, Seung Hwan Ohc, Lazkovd G.A.A new species of genus GageaSalisb.(Liliaceae) from Kyrgyz Republic (Western Tian Shan, Chatkal Range, Sary-Chelek Nature Reserve). Journal of Asia-Pacific Biodiversity.2019; 12: 341-343. XIV. Peterson A., Levichev I.G., Peterson J. Systematics of Gagea and Lloydia (Liliaceae) and infrageneric classification of Gagea based on molecular and morphological data. Molecular Phylogenetics and Evolution.2008; 46. XV. Peruzzi L., Peterson A., Tison J.-M., Peterson J. Phylogenetic relationships of GageaSalisb.(Liliaceae) in Italy, inferred from molecular and morphological data matrices. Plant Systematics and Evolution; 2008: 276. XVI. Rib R.D. Honey plants of Kazakhstan. Advertising Digest, 2013. XVII. Scherbakova L.I., Shirshikova N.A. Flora of medicinal plants in the vicinity of Ust-Kamenogorsk. Collection of materials of the scientific-practical conference ‘Unity of Education, Science and Innovation’. Ust-Kamenogorsk: EKSU, 2011. XVIII. syganovA.P. PrimrosesofEastKazakhstan. Ust-Kamenogorsk: EKSU, 2001. XIX. Tsyganov A.P. Flora and vegetation of the South Altai Tarbagatay. Berlin: LAP LAMBERT,2014. XX. Utyasheva, T.R., Berezovikov, N.N., Zinchenko, Yu.K. ProceedingsoftheMarkakolskStateNatureReserve. Ust-Kamenogorsk, 2009. XXI. Xinqi C, Turland NJ. Gagea. Flora of China.2000;24: 117-121. XXII. Zarrei M., Zarre S., Wilkin P., Rix E.M. Systematic revision of the genus GageaSalisb. (Liliaceae) in Iran.BotJourn Linn Soc.2007;154. XXIII. Zarrei M., Wilkin P., Ingroille M.J., Chase M.W. A revised infrageneric classification for GageaSalisb. (Tulipeae; Liliaceae): insights from DNA sequence and morphological data.Phytotaxa.2011:5. View | Download INFLUENCE OF SUCCESSION CROPPING ON ECONOMIC EFFICIENCY OF NO-TILL CROP ROTATIONS Authors: Victor K. Dridiger,Roman S. Stukalov,Rasul G. Gadzhiumarov,Anastasiya A. Voropaeva,Viktoriay A. Kolomytseva, DOI: https://doi.org/10.26782/jmcms.spl.10/2020.06.00042 Abstract: This study was aimed at examining the influence of succession cropping on the economic efficiency of no-till field crop rotations on the black earth in the zone of unstable moistening of the Stavropol krai. A long-term stationary experiment was conducted to examine for the purpose nine field crop rotation patterns different in the number of fields (four to six), set of crops, and their succession in crop rotation. The respective shares of legumes, oilseeds, and cereals in the cropping pattern were 17 to 33, 17 to 40, and 50 to 67 %. It has been established that in case of no-till field crop cultivation the economic efficiency of plant production depends on the set of crops and their succession in rotation. The most economically efficient type of crop rotation is the soya-winter wheat-peas-winter wheat-sunflower-corn six-field rotation with two fields of legumes: in this rotation 1 ha of crop rotation area yields 3 850 grain units per ha at a grain unit prime cost of 5.46 roubles; the plant production output return and profitability were 20,888 roubles per ha and 113 %, respectively. The high production profitabilities provided by the soya-winter wheat-sunflower four-field and the soya-winter-wheat-sunflower-corn-winter wheat five-field crop rotation are 108.7 and 106.2 %, respectively. The inclusion of winter wheat in crop rotation for two years in a row reduces the second winter wheat crop yield by 80 to 100 %, which means a certain reduction in the grain unit harvesting rate to 3.48-3.57 thousands per ha of rotation area and cuts the production profitability down to 84.4-92.3 %. This is why, no-till cropping should not include winter wheat for a second time Keywords: No-till technology,crop rotation,predecessor,yield,return,profitability, Refference: I Badakhova G. Kh. and Knutas A. V., Stavropol Krai: Modern Climate Conditions [Stavropol’skiykray: sovremennyyeklimaticheskiyeusloviya]. Stavropol: SUE Krai Communication Networks, 2007. II Cherkasov G. N. and Akimenko A. S. Scientific Basis of Modernization of Crop Rotations and Formation of Their Systems according to the Specializations of Farms in the Central Chernozem Region [Osnovy moderniz atsiisevooborotoviformirovaniyaikh sistem v sootvetstvii so spetsi-alizatsiyeykhozyaystvTsentral’nogoChernozem’ya]. Zemledelie. 2017; 4: 3-5. III Decree 330 of July 6, 2017 the Ministry of Agriculture of Russia “On Approving Coefficients of Converting to Agricultural Crops to Grain Units [Ob utverzhdeniikoeffitsiyentovperevoda v zernovyyee dinitsysel’s kokhozyaystvennykhkul’tur]. IV Dridiger V. K., About Methods of Research of No-Till Technology [O metodikeissledovaniytekhnologii No-till]//Achievements of Science and Technology of AIC (Dostizheniyanaukiitekhniki APK). 2016; 30 (4): 30-32. V Dridiger V. K. and Gadzhiumarov R. G. Growth, Development, and Productivity of Soya Beans Cultivated On No-Till Technology in the Zone of Unstable Moistening of Stavropol Region [Rost, razvitiyeiproduktivnost’ soiprivozdelyvaniipotekhnologii No-till v zone ne-ustoychivog ouvlazhneniyaStavropol’skogokraya]//Oil Crops RTBVNIIMK (Maslichnyyekul’turyNTBVNIIMK). 2018; 3 (175): 52–57. VI Dridiger V. K., Godunova E. I., Eroshenko F. V., Stukalov R. S., Gadzhiumarov, R. G., Effekt of No-till Technology on erosion resistance, the population of earthworms and humus content in soil (Vliyaniyetekhnologii No-till naprotivoerozionnuyuustoychivost’, populyatsiyudozhdevykhcherveyisoderzhaniyegumusa v pochve)//Research Journal of Pharmaceutical, Biological and Chemical Sciences. 2018; 9 (2): 766-770. VII Karabutov A. P., Solovichenko V. D., Nikitin V. V. et al., Reproduction of Soil Fertility, Productivity and Energy Efficiency of Crop Rotations [Vosproizvodstvoplodorodiyapochv, produktivnost’ ienergeticheskayaeffektivnost’ sevooborotov]. Zemledelie. 2019; 2: 3-7. VIII Kulintsev V. V., Dridiger V. K., Godunova E. I., Kovtun V. I., Zhukova M. P., Effekt of No-till Technology on The Available Moisture Content and Soil Density in The Crop Rotation [Vliyaniyetekhnologii No-till nasoderzhaniyedostupnoyvlagiiplotnost’ pochvy v sevoob-orote]// Research Journal of Pharmaceutical, Biological and Chemical Sciences. 2017; 8 (6): 795-99. IX Kulintsev V. V., Godunova E. I., Zhelnakova L. I. et al., Next-Gen Agriculture System for Stavropol Krai: Monograph [SistemazemledeliyanovogopokoleniyaStavropol’skogokraya: Monogtafiya]. Stavropol: AGRUS Publishers, Stavropol State Agrarian University, 2013. X Lessiter Frank, 29 reasons why many growers are harvesting higher no-till yields in their fields than some university scientists find in research plots//No-till Farmer. 2015; 44 (2): 8. XI Rodionova O. A. Reproduction and Exchange-Distributive Relations in Farming Entities [Vosproizvodstvoiobmenno-raspredelitel’nyyeotnosheniya v sel’skokhozyaystvennykhorganizatsiyakh]//Economy, Labour, and Control in Agriculture (Ekonomika, trud, upravleniye v sel’skomkhozyaystve). 2010; 1 (2): 24-27. XII Sandu I. S., Svobodin V. A., Nechaev V. I., Kosolapova M. V., and Fedorenko V. F., Agricultural Production Efficiency: Recommended Practices [Effektivnost’ sel’skokhozyaystvennogoproizvodstva (metodicheskiyerekomendatsii)]. Moscow: Rosinforagrotech, 2013. XIII Sotchenko V. S. Modern Corn Cultivation Technologies [Sovremennayatekhnologiyavozdelyvaniya]. Moscow: Rosagrokhim, 2009. View | Download DEVELOPMENT AND TESTING OF AUTONOMOUS PORTABLE SEISMOMETER DESIGNED FOR USE AT ULTRALOW TEMPERATURES IN ARCTIC ENVIRONMENT Authors: Mikhail A. Abaturov,Yuriy V. Sirotinskiy, DOI: https://doi.org/10.26782/jmcms.spl.10/2020.06.00043 Abstract: This paper is concerned with solving one of the issues of the general problem of designing geophysical equipment for the natural climatic environment of the Arctic. The relevance of the topic has to do with an increased global interest in this region. The paper is aimed at considering the basic principles of developing and the procedure of testing seismic instruments for use at ultralow climatic temperatures. In this paper the indicated issue is considered through the example of a seismic module designed for petroleum and gas exploration by passive seismoacoustic methods. The seismic module is a direct-burial portable unit of around 5 kg in weight, designed to continuously measure and record microseismic triaxial orthogonal (ZNE) noise in a range from 0.1 to 45 Hz during several days in autonomous mode. The functional chart of designing the seismic module was considered, and concrete conclusions were made for choosing the necessary components to meet the ultralow-temperature operational requirements. The conclusions made served for developing appropriate seismic module. In this case, the components and tools used included a SAFT MP 176065 xc low-temperature lithium cell, industrial-spec electronic component parts, a Zhaofeng Geophysical ZF-4.5 Chinese primary electrodynamic seismic sensor, housing seal parts made of frost-resistant silicone materials, and finely dispersed silica gel used as water-retaining sorbent to avoid condensation in the housing. The paper also describes a procedure of low-temperature collation tests at the lab using a New Brunswick Scientific freezing plant. The test results proved the operability of the developed equipment at ultralow temperatures down to -55°C. In addition, tests were conducted at low microseismic noises in the actual Arctic environment. The possibility to detect signals in a range from 1 to 10 Hz at the level close to the NLNM limit (the Peterson model) has been confirmed, which allows monitoring and exploring petroleum and gas deposits by passive methods. As revealed by this study, the suggested approaches are efficient in developing high-precision mobile seismic instruments for use at ultralow climatic temperatures. The solution of the considered instrumentation and methodical issues is of great practical significance as a constituent of the generic problem of Arctic exploration. Keywords: Seismic instrumentation,microseismic monitoring,Peterson model,geological exploration,temperature ratings,cooling test, Refference: I. AD797: Ultralow Distortion, Ultralow Noise Op Amp, Analog Devices, Inc., Data Sheet (Rev. K). Analog Devices, Inc. URL: https://www.analog.com/media/en/technical-documentation/data-sheets/AD797.pdf(Date of access September 2, 2019). II. Agafonov, V. M., Egorov, I. V., and Shabalina, A. S. Operating Principles and Technical Characteristics of a Small-Sized Molecular–Electronic Seismic Sensor with Negative Feedback [Printsipyraboty I tekhnicheskiyekharakteristikimalogabaritnogomolekulyarno-elektronnogoseysmodatchika s otritsatel’noyobratnoysvyaz’yu]. SeysmicheskiyePribory (Seismic Instruments). 2014; 50 (1): 1–8. DOI: 10.3103/S0747923914010022. III. Antonovskaya, G., Konechnaya, Ya.,Kremenetskaya, E., Asming, V., Kvaema, T., Schweitzer, J., Ringdal, F. Enhanced Earthquake Monitoring in the European Arctic. Polar Science. 2015; 1 (9): 158-167. 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Chao Xu, Junbo Wang, Deyong Chen, Jian Chen, Bowen Liu, Wenjie Qi, XichenZheng, Hua Wei, Guoqing Zhang. The Electrochemical Seismometer Based on a Novel Designed.Sensing Electrode for Undersea Exploration. 20th International Conference on Solid-State Sensors, Actuators and Microsystems &Eurosensors XXXIII (TRANSDUCERS &EUROSENSORS XXXIII). IEEE, 2019. DOI: 10.1109/TRANSDUCERS.2019.8808450. VIII. Chebotareva, I. Ya. New algorithms of emission tomography for passive seismic monitoring of a producing hydrocarbon deposit: Part I. Algorithms of processing and numerical simulation [Novyye algoritmyemissionnoyto mografiidlyapassivnogoseysmicheskogomonitoringarazrabatyvayemykhmestorozhdeniyuglevodorodov. Chast’ I: Algoritmyobrabotki I chislennoyemodelirovaniye]. FizikaZemli. 2010; 46(3):187-98. DOI: 10.1134/S106935131003002X IX. Danilov, A. V. and Konechnaya, Ya. V. Analytical comparison of seismic instruments for stationary surveys in the Arctic [Sravnitel’nyyanalizseysmicheskoyapparaturydlyastatsionarnykhnablyudeniy v Arktike]. DSYS. URL: https://dsys.ru/upload/id254_docPDF_FranzJosefLand.pdf(Date of access September 2, 2019). X. Dew point temperature calculator. Maple Tech. International LLC. URL: https://www.calculator.net/dew-point-calculator.html?airtemperature=20&airtemperatureunit=celsius&humidity=0.34&dewpoint=&dewpointunit=celsius&x=51&y=14(Date of access September 2, 2019). XI. Frolov, A. S. Matching of wave fields recorded by different geophysical receivers [Soglasovaniyevolnovykhpoley, poluchennykh s primeneniyemrazlichnoyregistriruyushcheyapparatury]. Abstracts IX International scientific and technical conference competition of young specialists “Geophysics-2013”. Saint-Petersburg: Gubkin University, 2013. URL: https://www.gubkin.ru/faculty/geology_and_geophysics/chairs_and_departments/exploration_geophysics_and_computers_systems/files/2013_SPb_Frolov.pdf. (Date of access September 2, 2019). XII. Gibbons, S. J., Asming, V., Fedorov, A., Fyen, J., Kero, J., Kozlovskaya, E., Kværna, T., Liszka, L., Näsholm, S.P., Raita, T., Roth, M., Tiira, T., Vinogradov, Yu. The European Arctic: A laboratory for seismoacoustic studies. Seism. Res. Letters. 2015; 86 (3): 917–928. XIII. GOST 8.395-80. State system for ensuring the uniformity of measurements. Reference conditions of measurements while calibrating. General requirements [Gosudarstvennayasistemaobespecheniyaedinstvaizmereniy. Normal’nyyeusloviyaizmereniypripoverke. Obshchiyetrebovaniya]. Moscow: Standartinform, 2008. URL: http://gostrf.com/normadata/1/4294821/4294821960.pdf (Date of access September 2, 2019). XIV. Guralp 6TD. Operators’ Guide. Document Number: MAN-T60-0002, Issue J: April, 2017. Guralp Systems Limited. 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Passive seismic tomography: A passive concept actively evolving. First Break. 2012; 30 (7): 83-90. XXII. Matveev, I. V. and Matveeva, N. V. Portable seismic recorder “SEISAR-5” with very low energy consumption for autonomous work in harsh climatic conditions [Portativnyyseysmicheskiyregistrator «Seysar-5» s ochen’ nizkimenergopotrebleniyemdlyaavtonomnoyraboty v slozhnykhklimatic heskikhusloviyakh]. Nauka I tekhnologicheskierazrabotki (Science and Technological Developments). 2017; 96 (3): 33-40. [Special Issue “Applied Geophysics: New Developments and Results. Part 1. Seismology and Seismic Exploration]. DOI: 10.21455/std2017.3-3. XXIII. Mishra, R. The Temperature Ratings of Electronic Parts.Electronics Cooling magazine. URL: http://www.electronics-cooling.com/2004/02/the-temperature-ratings-of-electronic-parts(Date of access September 2, 2019). XXIV. Moore, Sue E.; Stabeno, Phyllis J.; Van Pelt, Thomas I. The Synthesis of Arctic Research (SOAR) project. 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View | Download COMPARATIVE ANALYSIS OF RESULTS OF TREATMENT OF PATIENTS WITH FOOT PATHOLOGY WHO UNDERWENT WEIL OPEN OSTEOTOMY BY CLASSICAL METHOD AND WITHOUT STEOSYNTHESIS Authors: Yuriy V. Lartsev,Dmitrii A. Rasputin,Sergey D. Zuev-Ratnikov,Pavel V.Ryzhov,Dmitry S. Kudashev,Anton A. Bogdanov, DOI: https://doi.org/10.26782/jmcms.spl.10/2020.06.00044 Abstract: The article considers the problem of surgical correction of the second metatarsal bone length. The article analyzes the results of treatment of patients with excess length of the second metatarsal bones that underwent osteotomy with and without osteosynthesis. The results of treatment of patients who underwent metatarsal shortening due to classical Weil-osteotomy with and without osteosynthesis were analyzed. The first group consisted of 34 patients. They underwent classical Weil osteotomy. The second group included 44 patients in whomosteotomy of the second metatarsal bone were not by the screw. When studying the results of the treatment in the immediate postoperative period, weeks 6, 12, slightly better results were observed in patients of the first group, while one year after surgical treatment the results in both groups were comparable. One year after surgical treatment, there were 2.9% (1 patient) of unsatisfactory results in the first group and 4.5% (2 patients) in the second group. Considering the comparability of the results of treatment in remote postoperative period, the choice of concrete method remains with the operating surgeon. Keywords: Flat feet,hallux valgus,corrective osteotomy,metatarsal bones, Refference: I. A novel modification of the Stainsby procedure: surgical technique and clinical outcome [Text] / E. Concannon, R. MacNiocaill, R. Flavin [et al.] // Foot Ankle Surg. – 2014. – Dec., Vol. 20(4). – P. 262–267. II. Accurate determination of relative metatarsal protrusion with a small intermetatarsal angle: a novel simplified method [Text] / L. Osher, M.M. Blazer, S. Buck [et al.] // J. Foot Ankle Surg. – 2014. – Sep.-Oct., Vol. 53(5). – P. 548–556. III. Argerakis, N.G. The radiographic effects of the scarf bunionectomy on rearfoot alignment [Text] / N.G. Argerakis, L.Jr. Weil, L.S. Sr. Weil // Foot Ankle Spec. – 2015. – Apr., Vol. 8(2). – P. 89–94. IV. Bauer, T. Percutaneous forefoot surgery [Text] / T. Bauer // Orthop. Traumatol. Surg. Res. – 2014. – Feb., Vol. 100(1 Suppl.). – P. S191–S204. V. Biomechanical Evaluation of Custom Foot Orthoses for Hallux Valgus Deformity [Text] // J. Foot Ankle Surg. – 2015. – Sep.-Oct., Vol.54(5). – P. 852–855. VI. Chopra, S. Characterization of gait in female patients with moderate to severe hallux valgus deformity [Text] / S. Chopra, K. Moerenhout, X. Crevoisier // Clin. Biomech. (Bristol, Avon). – 2015. – Jul., Vol. 30(6). – P. 629–635. VII. Computer assisted planning and custom-made surgical guide for malunited pronation deformity after first metatarsophalangeal joint arthrodesis in rheumatoid arthritis: a case report [Text] / M. Hirao, S. Ikemoto, H. Tsuboi [et al.] // Comput. Aided Surg. – 2014. – Vol. 19(1-3). – P. 13–19. VIII. Correlation between static radiographic measurements and intersegmental angular measurements during gait using a multisegment foot model [Text] / D.Y. Lee, S.G. Seo, E.J. Kim [et al.] // Foot Ankle Int. – 2015. – Jan., Vol.36(1). – P. 1–10. IX. Correlative study between length of first metatarsal and transfer metatarsalgia after osteotomy of first metatarsal [Text]: [Article in Chinese] / F.Q. Zhang, B.Y. Pei, S.T. Wei [et al.] // Zhonghua Yi XueZaZhi. – 2013. – Nov. 19, Vol. 93(43). – P. 3441–3444. X. Dave, M.H. Forefoot Deformity in Rheumatoid Arthritis: A Comparison of Shod and Unshod Populations [Text] / M.H. Dave, L.W. Mason, K. Hariharan // Foot Ankle Spec. – 2015. – Oct., Vol. 8(5). – P. 378–383. XI. Does arthrodesis of the first metatarsophalangeal joint correct the intermetatarsal M1M2 angle? Analysis of a continuous series of 208 arthrodeses fixed with plates [Text] / F. Dalat, F. Cottalorda, M.H. Fessy [et al.] // Orthop. Traumatol. Surg. Res. – 2015. – Oct., Vol. 101(6). – P. 709–714. XII. Dynamic plantar pressure distribution after percutaneous hallux valgus correction using the Reverdin-Isham osteotomy [Text]: [Article in Spanish] / G. Rodríguez-Reyes, E. López-Gavito, A.I. Pérez-Sanpablo [et al.] // Rev. Invest. Clin. – 2014. – Jul., Vol. 66, Suppl. 1. – P. S79-S84. XIII. Efficacy of Bilateral Simultaneous Hallux Valgus Correction Compared to Unilateral [Text] / A.V. Boychenko, L.N. Solomin, S.G. Parfeyev [et al.] // Foot Ankle Int. – 2015. – Nov., Vol. 36(11). – P. 1339–1343. XIV. Endolog technique for correction of hallux valgus: a prospective study of 30 patients with 4-year follow-up [Text] / C. Biz, M. Corradin, I. Petretta [et al.] // J. OrthopSurg Res. – 2015. – Jul. 2, № 10. – P. 102. XV. First metatarsal proximal opening wedge osteotomy for correction of hallux valgus deformity: comparison of straight versus oblique osteotomy [Text] / S.H. Han, E.H. Park, J. Jo [et al.] // Yonsei Med. J. – 2015. – May, Vol. 56(3). – P. 744–752. XVI. Long-term outcome of joint-preserving surgery by combination metatarsal osteotomies for shortening for forefoot deformity in patients with rheumatoid arthritis [Text] / H. Niki, T. Hirano, Y. Akiyama [et al.] // Mod. Rheumatol. – 2015. – Sep., Vol. 25(5). – P. 683–638. XVII. Maceira, E. Transfer metatarsalgia post hallux valgus surgery [Text] / E. Maceira, M. Monteagudo // Foot Ankle Clin. – 2014. – Jun., Vol. 19(2). – P.285–307. XVIII. Nielson, D.L. Absorbable fixation in forefoot surgery: a viable alternative to metallic hardware [Text] / D.L. Nielson, N.J. Young, C.M. Zelen // Clin. Podiatr. Med. Surg. – 2013. – Jul., Vol. 30(3). – P. 283–293 XIX. Patient’s satisfaction after outpatient forefoot surgery: Study of 619 cases [Text] / A. Mouton, V. Le Strat, D. Medevielle [et al.] // Orthop. Traumatol. Surg. Res. – 2015. – Oct., Vol. 101(6 Suppl.). – P. S217–S220. XX. Preference of surgical procedure for the forefoot deformity in the rheumatoid arthritis patients–A prospective, randomized, internal controlled study [Text] / M. Tada, T. Koike, T. Okano [et al.] // Mod. Rheumatol. – 2015. – May., Vol. 25(3). – P.362–366. XXI. Redfern, D. Percutaneous Surgery of the Forefoot [Text] / D. Redfern, J. Vernois, B.P. Legré // Clin. Podiatr. Med. Surg. – 2015. – Jul., Vol. 32(3). – P. 291–332. XXII. Singh, D. Bullous pemphigoid after bilateral forefoot surgery [Text] / D. Singh, A. Swann // Foot Ankle Spec. – 2015. – Feb., Vol. 8(1). – P. 68–72. XXIII. Treatment of moderate hallux valgus by percutaneous, extra-articular reverse-L Chevron (PERC) osteotomy [Text] / J. Lucas y Hernandez, P. Golanó, S. Roshan-Zamir [et al.] // Bone Joint J. – 2016. – Mar., Vol. 98-B(3). – P. 365–373. XXIV. Weil, L.Jr. Scarf osteotomy for correction of hallux abducto valgus deformity [Text] / L.Jr. Weil, M. Bowen // Clin. Podiatr. Med. Surg. – 2014. – Apr., Vol.31(2). – P. 233–246. View | Download QUANTITATIVE ULTRASONOGRAPHY OF THE STOMACH AND SMALL INTESTINE IN HEALTHYDOGS Authors: Roman A. Tcygansky,Irina I. Nekrasova,Angelina N. Shulunova,Alexander I.Sidelnikov, DOI: https://doi.org/10.26782/jmcms.spl.10/2020.06.00045 Abstract: Purpose.To determine the quantitative echogenicity indicators (and their ratio) of the layers of stomach and small intestine wall in healthy dogs. Methods. A prospective 3-year study of 86 healthy dogs (aged 1-7 yrs) of different breeds and of both sexes. Echo homogeneity and echogenicity of the stomach and intestines wall were determined by the method of Silina, T.L., et al. (2010) in absolute values of average brightness levels of ultrasound image pixels using the 8-bit scale with 256 shades of gray. Results. Quantitative echogenicity indicators of the stomach and the small intestine wall in dogs were determined. Based on the numerical values characterizing echogenicity distribution in each layer of a separate structure of the digestive system, the coefficient of gastric echogenicity is determined as 1:2.4:1.1 (mucosa/submucosa/muscle layers, respectively), the coefficient of duodenum and jejunum echogenicity is determined as 1:3.5:2 and that of ileum is 1:1.8:1. Clinical significance. The echogenicity coefficient of the wall of the digestive system allows an objective assessment of the stomach and intestines wall and can serve as the basis for a quantitative assessment of echogenicity changes for various pathologies of the digestive system Keywords: Ultrasound (US),echogenicity,echogenicity coefficient,digestive system,dogs,stomach,intestines, Refference: I. Agut, A. Ultrasound examination of the small intestine in small animals // Veterinary focus. 2009.Vol. 19. No. 1. P. 20-29. II. Bull. 4.RF patent 2398513, IPC51A61B8 / 00 A61B8 / 14 (2006.01) A method for determining the homoechogeneity and the degree of echogenicity of an ultrasound image / T. Silina, S. S. Golubkov. – No. 2008149311/14; declared 12/16/2008; publ. 09/10/2010 III. Choi, M., Seo, M., Jung, J., Lee, K., Yoon, J., Chang, D., Park, RD. Evaluation of canine gastric motility with ultrasonography // J. of Veterinary Medical Science. – 2002. Vol. 64. – № 1. – P. 17-21. IV. Delaney, F., O’Brien, R.T., Waller, K.Ultrasound evaluation of small bowel thickness compared to weight in normal dogs // Veterinary Radiology and Ultrasound. 2003 Vol. 44, № 5. Р 577-580. V. Diana, A., Specchi, S., Toaldo, M.B., Chiocchetti, R., Laghi, A., Cipone, M. Contrast-enhanced ultrasonography of the small bowel in healthy cats // Veterinary Radiology and Ultrasound. – 2011. – Vol. 52, № 5. – Р. 555-559. VI. Garcia, D.A.A., Froes, T.R. Errors in abdominal ultrasonography in dogs and cats // J. of Small Animal Practice. – 2012. Vol. 53. – № 9. – P. 514-519. VII. Garcia, D.A.A., Froes, T.R. Importance of fasting in preparing dogs for abdominal ultrasound examination of specific organs // J. of Small Animal Practice. – 2014. Vol. 55. – № 12. – P. 630-634. VIII. Gaschen, L., Granger, L.A., Oubre, O., Shannon, D., Kearney, M., Gaschen, F. The effects of food intake and its fat composition on intestinal echogenicity in healthy dogs // Veterinary Radiology and Ultrasound. 2016. Vol. 57. № 5. P. 546-550 IX. Gaschen, L., Kircher, P., Stussi, A., Allenspach, K., Gaschen, F., Doherr, M., Grone, A. Comparison of ultrasonographic findings with clinical activity index (CIBDAI) and diagnosis in dogs with chronic enteropathies // Veterinary radiology and ultrasound. – 2008. – Vol. 49. – № 1. – Р. 56-64. X. Gil, E.M.U. Garcia, D.A.A. Froes, T.R. In utero development of the fetal intestine: Sonographic evaluation and correlation with gestational age and fetal maturity in dogs // Theriogenology. 2015. Vol. 84, №5. Р. 681-686. XI. Gladwin, N.E. Penninck, D.G., Webster, C.R.L. Ultrasonographic evaluation of the thickness of the wall layers in the intestinal tract of dogs // American Journal of Veterinary Research. 2014. Vol. 75, №4. Р. 349-353. XII. Gory, G., Rault, D.N., Gatel, L, Dally, C., Belli, P., Couturier, L., Cauvin, E. Ultrasonographic characteristics of the abdominal esophagus and cardia in dogs // Veterinary Radiology and Ultrasound. 2014. Vol. 55, № 5. P. 552-560. XIII. Günther, C.S. Lautenschläger, I.E., Scholz, V.B. Assessment of the inter- and intraobserver variability for sonographical measurement of intestinal wall thickness in dogs without gastrointestinal diseases | [Inter-und Intraobserver-Variabilitätbei der sonographischenBestimmung der Darmwanddicke von HundenohnegastrointestinaleErkrankungen] // Tierarztliche Praxis Ausgabe K: Kleintiere – Heimtiere. 2014. Vol. 42 №2. Р. 71-78. XIV. Hanazono, K., Fukumoto, S., Hirayama, K., Takashima, K., Yamane, Y., Natsuhori, M., Kadosawa, T., Uchide, T. Predicting Metastatic Potential of gastrointestinal stromal tumors in dog by ultrasonography // J. of Veterinary Medical Science. – 2012. Vol. 74. – № 11. – P. 1477-1482. XV. Heng, H.G., Lim, Ch.K., Miller, M.A., Broman, M.M.Prevalence and significance of an ultrasonographic colonic muscularishyperechoic band paralleling the serosal layer in dogs // Veterinary Radiology and Ultrasound. 2015. Vol. 56 № 6. P. 666-669. XVI. Ivančić, M., Mai, W. Qualitative and quantitative comparison of renal vs. hepatic ultrasonographic intensity in healthy dogs // Veterinary Radiology and Ultrasound. 2008. Vol. 49. № 4. Р. 368-373. XVII. Lamb, C.R., Mantis, P. Ultrasonographic features of intestinal intussusception in 10 dogs // J. of Small Animal Practice. – 2008. Vol. 39. – № 9. – P. 437-441. XVIII. Le Roux, A. B., Granger, L.A., Wakamatsu, N, Kearney, M.T., Gaschen, L.Ex vivo correlation of ultrasonographic small intestinal wall layering with histology in dogs // Veterinary Radiology and Ultrasound.2016. Vol. 57. № 5. P. 534-545. XIX. Nielsen, T. High-frequency ultrasound of Peyer’s patches in the small intestine of young cats / T. Nielsen [et al.] // Journal of Feline Medicine and Surgery. – 2015. – Vol. 18, № 4. – Р. 303-309. XX. PenninckD.G. Gastrointestinal tract. In Nyland T.G., Mattoon J.S. (eds): Small Animal Diagnostic Ultrasound. Philadelphia: WB Saunders. 2002, 2nd ed. Р. 207-230. XXI. PenninckD.G. Gastrointestinal tract. In: PenninckD.G.,d´Anjou M.A. Atlas of Small Animal Ultrasonography. Blackwell Publishing, Iowa. 2008. Р. 281-318. XXII. Penninck, D.G., Nyland, T.G., Kerr, L.Y., Fisher, P.E. Ultrasonographic evaluation of gastrointestinal diseases in small animals // Veterinary Radiology. 1990. Vol. 31. №3. P. 134-141. XXIII. Penninck, D.G.,Webster, C.R.L.,Keating, J.H. The sonographic appearance of intestinal mucosal fibrosis in cats // Veterinary Radiology and Ultrasound. – 2010. – Vol. 51, № 4. – Р. 458-461. XXIV. Pollard, R.E.,Johnson, E.G., Pesavento, P.A., Baker, T.W., Cannon, A.B., Kass, P.H., Marks, S.L. Effects of corn oil administered orally on conspicuity of ultrasonographic small intestinal lesions in dogs with lymphangiectasia // Veterinary Radiology and Ultrasound. 2013. Vol. 54. № 4. P. 390-397. XXV. Rault, D.N., Besso, J.G., Boulouha, L., Begon, D., Ruel, Y. Significance of a common extended mucosal interface observed in transverse small intestine sonograms // Veterinary Radiology and Ultrasound. 2004. Vol. 45. №2. Р. 177-179. XXVI. Sutherland-Smith, J., Penninck, D.G., Keating, J.H., Webster, C.R.L. Ultrasonographic intestinal hyperechoic mucosal striations in dogs are associated with lacteal dilation // Veterinary Radiology and Ultrasound. – 2007. Vol. 48. – № 1. – P. 51-57. View | Download EVALUATION OF ADAPTIVE POTENTIAL IN MEDICAL STUDENTS IN THE CONTEXT OF SEASONAL DYNAMICS Authors: Larisa A. Merdenova,Elena A. Takoeva,Marina I. Nartikoeva,Victoria A. Belyayeva,Fatima S. Datieva,Larisa R. Datieva, DOI: https://doi.org/10.26782/jmcms.spl.10/2020.06.00046 Abstract: The aim of this work was to assess the functional reserves of the body to quantify individual health; adaptation, psychophysiological characteristics of the health quality of medical students in different seasons of the year. When studying the temporal organization of physiological functions, the rhythm parameters of physiological functions were determined, followed by processing the results using the Cosinor Analysis program, which reveals rhythms with an unknown period for unequal observations, evaluates 5 parameters of sinusoidal rhythms (mesor, amplitude, acrophase, period, reliability). The essence of desynchronization is the mismatch of circadian rhythms among themselves or destruction of the rhythms architectonics (instability of acrophases or their disappearance). Desynchronization with respect to the rhythmic structure of the body is of a disregulatory nature, most pronounced in pathological desynchronization. High neurotism, increased anxiety reinforces the tendency to internal desynchronization, which increases with stress. During examination stress, students experience a decrease in the stability of the temporary organization of the biosystem and the tension of adaptive mechanisms develops, which affects attention, mental performance and the quality of adaptation to the educational process. Time is shortened and the amplitude of the “initial minute” decreases, personal and situational anxiety develops, and the level of psychophysiological adaptation decreases. The results of the work are priority because they can be used in assessing quality and level of health. Keywords: Desynchronosis,biorhythms,psycho-emotional stress,mesor,acrophase,amplitude,individual minute, Refference: I. Arendt, J., Middleton, B. Human seasonal and circadian studies in Antarctica (Halley, 75_S) – General and Comparative Endocrinology. 2017: 250-259. (http://dx.doi.org/10.1016/j.ygcen.2017.05.010). II. BalandinYu.P. A brief methodological guide on the use of the agro-industrial complex “Health Sources” / Yu.P. Balandin, V.S. Generalov, V.F. Shishlov. Ryazan, 2007. III. Buslovskaya L.K. Adaptation reactions in students at exam stress/ L.K. Buslovskaya, Yu.P. Ryzhkova. Scientific bulletin of Belgorod State University. Series: Natural Sciences. 2011;17(21):46-52. IV. Chutko L. S. Sindromjemocionalnogovygoranija – Klinicheskie I psihologicheskieaspekty./ L.S Chutko. Moscow: MEDpress-inform, 2013. V. Eroshina K., Paul Wilkinson, Martin Mackey. The role of environmental and social factors in the occurrence of diseases of the respiratory tract in children of primary school age in Moscow. Medicine. 2013:57-71. VI. Fagrell B. “Microcirculation of the Skin”. The physiology and pharmacology of the microcirculation. 2013:423. VII. Gurova O.A. Change in blood microcirculation in students throughout the day. New research. 2013; 2 (35):66-71. VIII. Khetagurova L.G. – Stress/Ed. L.G. Khetagurov. Vladikavkaz: Project-Press Publishing House, 2010. IX. Khetagurova L.G., Urumova L.T. et al. Stress (chronomedical aspects). International Journal of Experimental Education 2010; 12: 30-31. X. Khetagurova L.G., Salbiev K.D., Belyaev S.D., Datieva F.S., Kataeva M.R., Tagaeva I.R. Chronopathology (experimental and clinical aspects/ Ed. L.G. Khetagurov, K.D. Salbiev, S.D.Belyaev, F.S. Datiev, M.R. Kataev, I.R. Tagaev. Moscow: Science, 2004. XI. KlassinaS.Ya. Self-regulatory reactions in the microvasculature of the nail bed of fingers in person with psycho-emotional stress. Bulletin of new medical technologies, 2013; 2 (XX):408-412. XII. Kovtun O.P., Anufrieva E.V., Polushina L.G. Gender-age characteristics of the component composition of the body in overweight and obese schoolchildren. Medical Science and Education of the Urals. 2019; 3:139-145. XIII. Kuchieva M.B., Chaplygina E.V., Vartanova O.T., Aksenova O.A., Evtushenko A.V., Nor-Arevyan K.A., Elizarova E.S., Efremova E.N. A comparative analysis of the constitutional features of various generations of healthy young men and women in the Rostov Region. Modern problems of science and education. 2017; 5:50-59. XIV. Mathias Adamsson1, ThorbjörnLaike, Takeshi Morita – Annual variation in daily light expo-sure and circadian change of melatonin and cortisol consent rations at a northern latitude with large seasonal differences in photoperiod length – Journal of Physiological Anthropology. 2017; 36: 6 – 15. XV. Merdenova L.A., Tagaeva I.R., Takoeva E.A. Features of the study of biological rhythms in children. The results of fundamental and applied research in the field of natural and technical sciences. Materials of the International Scientific and Practical Conference. Belgorod, 2017, pp. 119-123. XVI. Ogarysheva N.V. The dynamics of mental performance as a criterion for adapting to the teaching load. Bulletin of the Samara Scientific Center of the Russian Academy of Sciences. 2014;16:5 (1): S.636-638. XVII. Pekmezovi T. Gene-environment interaction: A genetic-epidemiological approach. Journal of Medical Biochemistry. 2010;29:131-134. XVIII. Rapoport S.I., Chibisov S.M. Chronobiology and chronomedicine: history and prospects/Ed. S.M. Chibisov, S.I. Rapoport ,, M.L. Blagonravova. Chronobiology and Chronomedicine: Peoples’ Friendship University of Russia (RUDN) Press. Moscow, 2018. XIX. Roustit M., Cracowski J.L. “Non-invasive assessment of skin microvascular function in humans: an insight into methods” – Microcirculation 2012; 19 (1): 47-64. XX. Rud V.O., FisunYu.O. – References of the circadian desinchronosis in students. Ukrainian Bulletin of Psychoneurology. 2010; 18(2) (63): 74-77. XXI. Takoeva Z. A., Medoeva N. O., Berezova D. T., Merdenova L. A. et al. Long-term analysis of the results of chronomonitoring of the health of the population of North Ossetia; Vladikavkaz Medical and Biological Bulletin. 2011; 12(12,19): 32-38. XXII. Urumova L.T., Tagaeva I.R., Takoeva E.A., Datieva L.R. – The study of some health indicators of medical students in different periods of the year. Health and education in the XXI century. 2016; 18(4): 94-97. XXIII. Westman J. – Complex diseases. In: Medical genetics for the modern clinician. USA: Lippincott Williams & Wilkins, 2006. XXIV. Yadrischenskaya T.V. Circadian biorhythms of students and their importance in educational activities. Problems of higher education. Pacific State University Press. 2016; 2:176-178. View | Download TRIADIC COMPARATIVE ANALYSIS Authors: Stanislav A.Kudzh,Victor Ya. Tsvetkov, DOI: https://doi.org/10.26782/jmcms.spl.10/2020.06.00047 Abstract: The present study of comparison methods based on the triadic model introduces the following concepts: the relation of comparability and the relation of comparison, and object comparison and attributive comparison. The difference between active and passive qualitative comparison is shown, two triadic models of passive and active comparison and models for comparing two and three objects are described. Triadic comparison models are proposed as an alternative to dyadic comparison models. Comparison allows finding the common and the different; this approach is proposed for the analysis of the nomothetic and ideographic method of obtaining knowledge. The nomothetic method identifies and evaluates the general, while the ideographic method searches for unique in parameters and in combinations of parameters. Triadic comparison is used in systems and methods of argumentation, as well as in the analysis of consistency/inconsistency. Keywords: Comparative analysis,dyad,triad,triadic model,comparability relation,object comparison,attributive comparison,nomothetic method,ideographic method, Refference: I. AltafS., Aslam.M.Paired comparison analysis of the van Baarenmodel using Bayesian approach with noninformativeprior.Pakistan Journal of Statistics and Operation Research 8(2) (2012) 259{270. II. AmooreJ. E., VenstromD Correlations between stereochemical assessments and organoleptic analysis of odorous compounds. Olfaction and Taste (2016) 3{17. III. BarnesJ., KlingerR. Embedding projection for targeted cross-lingual sentiment: model comparisons and a real-world study. Journal of Artificial Intelligence Research 66 (2019) 691{742. doi.org/10.1613/jair.1.11561 IV. Castro-SchiloL., FerrerE.Comparison of nomothetic versus idiographic-oriented methods for making predictions about distal outcomes from time series data. Multivariate Behavioral Research 48(2) (2013) 175{207. V. De BonaG.et al. Classifying inconsistency measures using graphs. Journal of Artificial Intelligence Research 66 (2019) 937{987. VI. FideliR. La comparazione. Milano: Angeli, 1998. VII. GordonT. F., PrakkenH., WaltonD. The Carneades model of argument and burden of proof. Artificial Intelligence 10(15) (2007) 875{896. VIII. GrenzS.J. The social god and the relational self: A Triad theology of the imago Dei. Westminster: John Knox Press, 2001. IX. HermansH.J. M.On the integration of nomothetic and idiographic research methods in the study of personal meaning.Journal of Personality 56(4) (1988) 785{812. X. JamiesonK. G., NowakR. Active ranking using pairwise comparisons.Advances in Neural Information Processing Systems (2011) 2240{2248. XI. JongsmaC.Poythress’s triad logic: a review essay. Pro Rege 42(4) (2014) 6{15. XII. KärkkäinenV.M. Trinity and Religious Pluralism: The Doctrine of the Trinity in Christian Theology of Religions. London: Routledge, 2017. XIII. KudzhS. A., TsvetkovV.Ya. Triadic systems. Russian Technology Magazine 7(6) (2019) 74{882. XIV. NelsonK.E.Some observations from the perspective of the rare event cognitive comparison theory of language acquisition.Children’s Language 6 (1987) 289{331. XV. NiskanenA., WallnerJ., JärvisaloM.Synthesizing argumentation frameworks from examples. Journal of Artificial Intelligence Research 66 (2019) 503{554. XVI. PührerJ.Realizability of three-valued semantics for abstract dialectical frameworks.Artificial Intelligence 278 (2020) 103{198. XVII. SwansonG.Frameworks for comparative research: structural anthropology and the theory of action. In: Vallier, Ivan (Ed.). Comparative methods in sociology: essays on trends and applications.Berkeley: University of California Press, 1971 141{202. XVIII. TsvetkovV.Ya.Worldview model as the result of education.World Applied Sciences Journal 31(2) (2014) 211{215. XIX. TsvetkovV. Ya. Logical analysis and variable scales. Slavic Forum 4(22) (2018) 103{109. XX. Wang S. et al. Transit traffic analysis zone delineating method based on Thiessen polygon. Sustainability 6(4) (2014) 1821{1832. View | Download DEVELOPING TECHNOLOGY OF CREATING WEAR-RESISTANT CERAMIC COATING FOR ICE CYLINDER." JOURNAL OF MECHANICS OF CONTINUA AND MATHEMATICAL SCIENCES spl10, no. 1 (June 28, 2020). http://dx.doi.org/10.26782/jmcms.spl.10/2020.06.00048.

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