Управління якістю освітньої діяльності з підготовки спеціалістів у галузі охорони здоров’я: на прикладі українських медичних ВНЗ

The paper addresses the current background, shortcomings and improvement perspectives for the quality management system in training nurses, paramedics and midwives in HEIs of Ukraine. To reach the aim of the study, the authors analysed the legal and regulatory documents, website documentation and electronic resources of 23 medical HEIs. The methods of mathematical data processing and criterion analysis were used to analyze the effectiveness of the quality management system implementation medical HEIs. The survey of the managerial and administrative staff (n=398) was conducted. The aim of the survey was to gain insight into the internal quality management principles and procedures in medical higher educational institutions of Ukraine, to identify the main tools used for internal auditing of educational quality, the measures taken to assess the education quality at the institutional level. The research findings are discussed with due regard to the surveyed managerial staff needs and quality assurance guidelines in medical education. The results of the article have a few significant implications for practice of quality management system in medical colleges and its perspectives for enhancing Ukrainian higher education system. The conclusion was made that with introducing an effective quality management system in medical HEIs, continuous monitoring of quality assurance by HEI leaders, commitment to quality as an organizing factor in education management, future medical specialists will be competitive, demonstrating a sustainable growth in academic performance, developing relevant practical skills and professional mindset.У статті розглядаються сучасні передумови, недоліки та перспективи вдосконалення системи управління якістю підготовки медсестер, фельдшерів та акушерок у ВНЗ України. Для досягнення мети дослідження автори проаналізували нормативно-правові документи, документацію веб-сайтів та електронні ресурси 23 медичних ВНЗ. Методи математичної обробки даних та критеріального аналізу були використані для аналізу ефективності впровадження системи управління якістю медичних ВНЗ. Проведено опитування керівного та адміністративного персоналу (n = 398). Метою опитування було отримати уявлення про внутрішні принципи та процедури управління якістю у медичних вищих навчальних закладах України, визначити основні інструменти, що використовуються для внутрішнього аудиту якості освіти, заходи, вжиті для оцінки якості освіти на інституційному рівні. Результати дослідження обговорюються з урахуванням обстежених потреб управлінського персоналу та рекомендацій щодо забезпечення якості медичної освіти. Результати статті мають кілька суттєвих наслідків для практики системи управління якістю в медичних коледжах та її перспективи для вдосконалення української системи вищої освіти. Зроблено висновок, що із запровадженням ефективної системи управління якістю у медичних ВНЗ, постійним моніторингом забезпечення якості керівниками ВНЗ, прихильністю до якості як організуючий фактор управління освітою, майбутні медичні спеціалісти будуть конкурентоспроможними, демонструючи стійке зростання академічної успішності, розвиваючи відповідні практичні навички та професійне мислення

Селекционная оценка гибридной семьи смородины красной Белая Потапенко x ОС 1426-21-80

Relevance. One of the priority trends in berry crop breeding is to create highly adaptive and resistant to biotic and abiotic environmental factors varieties with high commodity and consumer quality of berries, not inferior to the best Western European varieties.Material and methods. The research was conducted in 2017-2018 at VNIISPK (Orel) on the selection plot of red currants, planted in 2012, with a planting scheme 2.8 x 0.8 m. The research object was the selection red currant family 2466 (♀Belaya Potapenko x ♂SS 1426-21-80) of VNIISPK breeding in the amount of 66 hybrid seedlings. The parent forms of this family were selected as sources of valuable economical and breeding characters. The variety Belaya Potapenko has a dessert taste of berries, and the selected seedling 1426-21-80 was taken due to its productivity and long racemes. The economical and biological characters of the hybrid seedlings were studied according to the “Program and methods of fruit, berry and nut crops variety investigation”, section “Currants, gooseberry and their hybrids” (1999).Results. The progeny of the crossing combination Belaya Potapenko x SS 1426-21-80 is characterized by high adaptability to soil and climatic conditions of cultivation that provides good development of the seedlings and their high productivity. When crossing white-fruit Belaya Potapenko with redfruit SS 1426-21-80, seedlings with white berries are absent in the offspring, which indicates that the paternal original form is homozygous for the dominant gene that controls the red color of the berries. Hybridological analysis showed that with medium weight of berries of parental forms, the manifestation of this trait in the offspring increased, the share of large-fruited seedlings was 18-37%, depending on the year of the study. The taste estimation of the off-spring of this family showed that a great amount of the seedlings had an intermediate sweet and sour taste, part of hybrids inherited sour taste from the paternal original parent. The hybrid family is valuable for the output of highly productive large-fruited seedlings with long racemes. Re-hybridization of the best seedlings with sources of high taste of berries is necessary to improve the taste.Актуальность. Одним из приоритетных направлений селекции ягодных культур является создание устойчивых к биотическим и абиотическим факторам среды сортов с высокими товарно-потребительскими качествами ягод, не уступающими лучшим западно-европейским сортам.Материал и методика. Исследования проводили в 2017-2018 годах на селекционном участке смородины красной ФГБНУ ВНИИСПК (г. Орёл) 2012 года посадки, схема посадки 2,8 x 0,8 м. Объекты исследования – селекционная семья смородины красной 2466 (♀Белая Потапенко x ♂ОС 1426-21-80) селекции ВНИИСПК, включающая 66 гибридных сеянцев. Родительские формы данной семьи отобраны в качестве источников важных хозяйственно-селекционных признаков. Сорт Белая Потапенко – десертный вкус ягод, отборный сеянец 1426-21-80 – продуктивности и длиннокистности. Изучение гибридных сеянцев по хозяйственно-биологическим признакам осуществляли согласно «Программе и методике сортоизучения плодовых, ягодных и орехоплодных культур», раздел "Смородина, крыжовник и их гибриды" (1999).Результаты. Потомство комбинации скрещивания Белая Потапенко x ОС 1426-21-80 обладает высокой адаптивностью к почвенно-климатическим условиям выращивания, обеспечивающей хорошее развитие сеянцев и их высокую продуктивность. При скрещивании белоплодного сорта Белая Потапенко с красноплодным ОС 1426-21-80 в потомстве отсутствуют сеянцы с белыми ягодами, что свидетельствует о том, что отцовская исходная форма является гомозиготной по доминантному гену, контролирующему красную окраску ягод. Гибридологический анализ показал, что при средней массе ягод родительских форм проявление этого признака в потомстве усилилось, доля крупноплодных сеянцев составила 18-37% в зависимости от года исследований. Оценка вкуса потомства данной семьи показала, что большая масса сеянцев имела промежуточный между родителями сладко-кислый вкус, часть гибридов уклонилась в сторону отцовской исходной формы с кислыми ягодами. Гибридная семья представляет селекционную ценность по выходу высокопродуктивных, крупноплодных и длиннокистных сеянцев, для улучшения вкуса необходима повторная гибридизация лучших сеянцев с источниками высоких вкусовых качеств ягод

BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms

Background: High-throughput genetic testing is increasingly applied in clinics. Next-Generation Sequencing (NGS) data analysis however still remains a great challenge. The interpretation of pathogenicity of single variants or combinations of variants is crucial to provide accurate diagnostic information or guide therapies. Methods: To facilitate the interpretation of variants and the selection of candidate non-synonymous polymorphisms (nsSNPs) for further clinical studies, we developed BALL-SNP. Starting from genetic variants in variant call format (VCF) files or tabular input, our tool, first, visualizes the three-dimensional (3D) structure of the respective proteins from the Protein Data Bank (PDB) and highlights mutated residues, automatically. Second, a hierarchical bottom up clustering on the nsSNPs within the 3D structure is performed to identify nsSNPs, which are close to each other. The modular and flexible implementation allows for straightforward integration of different databases for pathogenic and benign variants, but also enables the integration of pathogenicity prediction tools. The collected background information of all variants is presented below the 3D structure in an easily interpretable table format. Results: First, we integrated different data resources into BALL-SNP, including databases containing information on genetic variants such as ClinVar or HUMSAVAR; third party tools that predict stability or pathogenicity in silico such as I-Mutant2.0; and additional information derived from the 3D structure such as a prediction of binding pockets. We then explored the applicability of BALL-SNP on the example of patients suffering from cardiomyopathies. Here, the analysis highlighted accumulation of variations in the genes JUP, VCL, and SMYD2. Conclusion: Software solutions for analyzing high-throughput genomics data are important to support diagnosis and therapy selection. Our tool BALL-SNP, which is freely available at http://www.ccb.uni-saarland.de/BALL-SNP , combines genetic information with an easily interpretable and interactive, graphical representation of amino acid changes in proteins. Thereby relevant information from databases and computational tools is presented. Beyond this, proximity to functional sites or accumulations of mutations with a potential collective effect can be discovered

An automated stochastic approach to the identification of the protein specificity determinants and functional subfamilies

<p>Abstract</p> <p>Background</p> <p>Recent progress in sequencing and 3 D structure determination techniques stimulated development of approaches aimed at more precise annotation of proteins, that is, prediction of exact specificity to a ligand or, more broadly, to a binding partner of any kind.</p> <p>Results</p> <p>We present a method, SDPclust, for identification of protein functional subfamilies coupled with prediction of specificity-determining positions (SDPs). SDPclust predicts specificity in a phylogeny-independent stochastic manner, which allows for the correct identification of the specificity for proteins that are separated on a phylogenetic tree, but still bind the same ligand. SDPclust is implemented as a Web-server <url>http://bioinf.fbb.msu.ru/SDPfoxWeb/</url> and a stand-alone Java application available from the website.</p> <p>Conclusions</p> <p>SDPclust performs a simultaneous identification of specificity determinants and specificity groups in a statistically robust and phylogeny-independent manner.</p

Systematic discovery of linear binding motifs targeting an ancient protein interaction surface on MAP kinases

Mitogen-activated protein kinases (MAPK) are broadly used regulators of cellular signaling. However, how these enzymes can be involved in such a broad spectrum of physiological functions is not understood. Systematic discovery of MAPK networks both experimentally and in silico has been hindered because MAPKs bind to other proteins with low affinity and mostly in less-characterized disordered regions. We used a structurally consistent model on kinase-docking motif interactions to facilitate the discovery of short functional sites in the structurally flexible and functionally under-explored part of the human proteome and applied experimental tools specifically tailored to detect low-affinity protein-protein interactions for their validation in vitro and in cell-based assays. The combined computational and experimental approach enabled the identification of many novel MAPK-docking motifs that were elusive for other large-scale protein-protein interaction screens. The analysis produced an extensive list of independently evolved linear binding motifs from a functionally diverse set of proteins. These all target, with characteristic binding specificity, an ancient protein interaction surface on evolutionarily related but physiologically clearly distinct three MAPKs (JNK, ERK, and p38). This inventory of human protein kinase binding sites was compared with that of other organisms to examine how kinase-mediated partnerships evolved over time. The analysis suggests that most human MAPK-binding motifs are surprisingly new evolutionarily inventions and newly found links highlight (previously hidden) roles of MAPKs. We propose that short MAPK-binding stretches are created in disordered protein segments through a variety of ways and they represent a major resource for ancient signaling enzymes to acquire new regulatory roles

The fungal literature-based occurrence database for southern West Siberia (Russia)

The paper presents the initiative on literature-based occurrence data mobilisation of fungi and fungi-related organisms (literature-based occurrences, Darwin Core MaterialCitation) to develop the Fungal literature-based occurrence database for the southern West Siberia (FuSWS). The initiative on mobilisation of literature-based occurrence data started in the northern part of West Siberia in 2016. The present project extends the initiative to the southern regions and includes ten administrative territories (Tyumen Region, Sverdlovsk Region, Chelyabinsk Region, Omsk Region, Kurgan Region, Tomsk Region, Novosibirsk Region, Kemerovo Region, Altai Territory and Republic of Altai). The area occupies the central to southern part of the West Siberian Plain and extends for about 1.5 K km from the west to the east from the eastern slopes of the Ural Mountains to Yenisey River and from north to south—about 1.3 K km. The total area equals about 1.4 million km . The initiative is actively growing in spatial, collaboration and data accumulation terms. The working group of about 30 mycologists from eight organisations dedicated to the data mobilisation was created as part of the Siberian Mycological Society (informal organisation since 2019). They have compiled the almost complete bibliographic list of mycology-related papers for the southern West Siberia, including over 900 publications for the last two centuries (the earliest dated 1800). All literature sources were digitised and an online library was created to integrate bibliography metadata and digitised papers using Zotero bibliography manager. The analysis of published sources showed that about two-thirds of works contain occurrences of fungi for the scope of mobilisation. At the time of the paper submission, the database had been populated with a total of about 8 K records from 93 sources. The dataset is uploaded to GBIF, where it is available for online search of species occurrences and/or download. The project's page with the introduction, templates, bibliography list, video-presentations and written instructions is available (in Russian) at the web site of the Siberian Mycological Society. The initiative will be continued in the following years to extract the records from all published sources. New information The paper presents the first project with the aim of literature-based occurrence data mobilisation of fungi and fungi-related organisms in the southern West Siberia. The full bibliography and a digital library of all regional mycological publications created for the first time includes about 900 published works. By the time of paper submission, nearly 8 K occurrence records were extracted from about 90 literature sources and integrated into the FuSWS database published in GBIF

The fungal literature-based occurrence database in southern West Siberia (Russia)

The abstract presents the initiative to develop the Fungal Literature-based Occurrence Database for Southern West Siberia (FuSWS), which mobilizes occurrences of fungi from published literature (literature-based occurrences, Darwin Core MaterialCitation). The FuSWS database includes 28 fields describing species name, publication source, herbarium number (if exists), date of sampling or observation, locality information, vegetation, substrate, and others. The initiative on digitization of literature-based occurrence data started in the northern part of Western Siberia two years ago (Filippova et al. 2021a). The present project extends the initiative to the south and includes eight administrative regions (Sverdlovsk, Omsk, Kurgan, Tomsk, Novosibirsk, Kemerovo, Altay, and Gorny Altay). The area occupies the central to southern part of the West Siberian Plain. It extends for about 1.5 thousand km from the west to the east from the eastern slopes of the Ural Mountains to Yenisey River, and from north to south—about 1.3 thousand km. The total area equals about 1.2 million km2.Currently, the project is actively growing in spatial, collaboration and data accumulation terms. The working group of about 30 mycologists from 16 organizations dedicated to the digitization initiative was created as part of the Siberian Mycological Society (informal organization since 2019). They have created the most complete bibliographic list of mycology-related papers for the Southern West Siberia, including over 800 publications for the last two centuries (the earliest dated 1800). At abstract submission, the database had been populated with a total of about 10K records from about 100 sources. The dataset is uploaded to GBIF, where it is available for online search of species occurrences and/or download (Filippova et al. 2021b) Fig. 1. The project's page with the introduction, templates, bibliography list, video-presentations and written instructions is available at the website of the Siberian Mycological Society (https://sibmyco.org/literaturedatabase).The following protocol describes the digitization workflow in detail:The bibliography of related publications is compiled using Zotero bibliographic manager. Only published works (peer-reviewed papers, conference proceedings, PhD theses, monographs or book chapters) are selected. If possible, the sources are digitized and added to the library as PDF files. The template of the FuSWS database is made with Google Sheets, which allows simultaneous use by several specialists, in a common data format provided. The simple Microsoft Excel template is also available for the offline databasing. The Darwin Core standard is applied to the database field structure to accommodate the relevant information extracted from the publications.From the available bibliography of publications related to the region, only works with species occurrences are selected for the databasing purpose. The main source of occurrences is annotated species lists with exact localities of the records. However, different sorts of other species citations are also extracted, provided that they had the connection to any geography. All occurrences are georeferenced, either from the coordinates provided in the paper, or from the verbatim description of the field work locality. The georeferencing of the verbatim descriptions is made using Yandex or Google map services. Depending on the quality of georeference provided in publications, the uncertainty is estimated as follows: 1) the coordinate of a fruiting structure or a plot provided in the publication gives the uncertainty about 3-30 meters; 2) the coordinate of the field work locality provided in publication gives the uncertainty about 500 m to 5 km; 3) the report of the species presence in a particular region gives the centroid of the area with the uncertainty radius to include its borders.The locality names reported in Russian are translated to English and written in the «locality» field. Russian descriptions are reserved in the field «verbatimLocality» for accuracy.When possible, the «eventDate» is extracted from the annotation data. Whenever this information is absent, the date of the publication is used instead with the remarks in the «verbatimEventDate» field.The ecological features, habitat and substrate preferences are written in the «habitat» field and reserved in Russian.The original scientific names reported in publications are filled in the «originalNameUsage» field. Correction of spelling errors is made using the GBIF Species Matching tool. This tool is also used to create the additional fields of taxonomic hierarchy from species to kingdom, to fill in the «taxonRank» field and to synonymize according to the GBIF Backbone Taxonomy.To track the digitization process, a worksheet is maintained. Each bibliographic record has a series of fields to describe the digitization process and its results: the total number of extracted occurrence records, general description of the occurrence quality, presence of the observation date, details of georeferencing and the name of a person responsible for the digitization

Dynamics of carbon pools in post-agrogenic sandy soils of southern taiga of Russia

<p>Abstract</p> <p>Background</p> <p>Until recently, a lot of arable lands were abandoned in many countries of the world and, especially, in Russia, where about half a million square kilometers of arable lands were abandoned in 1961-2007. The soils at these fallows undergo a process of natural restoration (or self-restoration) that changes the balance of soil organic matter (SOM) supply and mineralization.</p> <p>Results</p> <p>A soil chronosequence study, covering the ecosystems of 3, 20, 55, 100, and 170 years of self-restoration in southern taiga zone, shows that soil organic content of mineral horizons remains relatively stable during the self-restoration. This does not imply, however, that SOM pools remain steady. The C/N ratio of active SOM reached steady state after 55 years, and increased doubly (from 12.5 - 15.6 to 32.2-33.8). As to the C/N ratio of passive SOM, it has been continuously increasing (from 11.8-12.7 to 19.0-22.8) over the 170 years, and did not reach a steady condition.</p> <p>Conclusion</p> <p>The results of the study imply that soil recovery at the abandoned arable sandy lands of taiga is incredibly slow process. Not only soil morphological features of a former ploughing remained detectable but also the balance of soil organic matter input and mineralization remained unsteady after 170 years of self-restoration.</p

Combining specificity determining and conserved residues improves functional site prediction

<p>Abstract</p> <p>Background</p> <p>Predicting the location of functionally important sites from protein sequence and/or structure is a long-standing problem in computational biology. Most current approaches make use of sequence conservation, assuming that amino acid residues conserved within a protein family are most likely to be functionally important. Most often these approaches do not consider many residues that act to define specific sub-functions within a family, or they make no distinction between residues important for function and those more relevant for maintaining structure (e.g. in the hydrophobic core). Many protein families bind and/or act on a variety of ligands, meaning that conserved residues often only bind a common ligand sub-structure or perform general catalytic activities.</p> <p>Results</p> <p>Here we present a novel method for functional site prediction based on identification of conserved positions, as well as those responsible for determining ligand specificity. We define Specificity-Determining Positions (SDPs), as those occupied by conserved residues within sub-groups of proteins in a family having a common specificity, but differ between groups, and are thus likely to account for specific recognition events. We benchmark the approach on enzyme families of known 3D structure with bound substrates, and find that in nearly all families residues predicted by SDPsite are in contact with the bound substrate, and that the addition of SDPs significantly improves functional site prediction accuracy. We apply SDPsite to various families of proteins containing known three-dimensional structures, but lacking clear functional annotations, and discusse several illustrative examples.</p> <p>Conclusion</p> <p>The results suggest a better means to predict functional details for the thousands of protein structures determined prior to a clear understanding of molecular function.</p