How to describe a cell: a path to automated versatile characterization of cells in imaging data

A cell is the basic functional unit of life. Most ulticellular organisms, including animals, are composed of a variety of different cell types that fulfil distinct roles. Within an organism, all cells share the same genome, however, their diverse genetic programs lead them to acquire different molecular and anatomical characteristics. Describing these characteristics is essential for understanding how cellular diversity emerged and how it contributes to the organism function. Probing cellular appearance by microscopy methods is the original way of describing cell types and the main approach to characterise cellular morphology and position in the organism. Present cutting-edge microscopy techniques generate immense amounts of data, requiring efficient automated unbiased methods of analysis. Not only can such methods accelerate the process of scientific discovery, they should also facilitate large-scale systematic reproducible analysis. The necessity of processing big datasets has led to development of intricate image analysis pipelines, however, they are mostly tailored to a particular dataset and a specific research question. In this thesis I aimed to address the problem of creating more general fully-automated ways of describing cells in different imaging modalities, with a specific focus on deep neural networks as a promising solution for extracting rich general-purpose features from the analysed data. I further target the problem of integrating multiple data modalities to generate a detailed description of cells on the whole-organism level. First, on two examples of cell analysis projects, I show how using automated image analysis pipelines and neural networks in particular, can assist characterising cells in microscopy data. In the first project I analyse a movie of drosophila embryo development to elucidate the difference in myosin patterns between two populations of cells with different shape fate. In the second project I develop a pipeline for automatic cell classification in a new imaging modality to show that the quality of the data is sufficient to tell apart cell types in a volume of mouse brain cortex. Next, I present an extensive collaborative effort aimed at generating a whole-body multimodal cell atlas of a three-segmented Platynereis dumerilii worm, combining high resolution morphology and gene expression. To generate a multi-sided description of cells in the atlas I create a pipeline for assigning coherent denoised gene expression profiles, obtained from spatial gene expression maps, to cells segmented in the EM volume. Finally, as the main project of this thesis, I focus on extracting comprehensive unbiased cell morphology features from an EM volume of Platynereis dumerilii. I design a fully unsupervised neural network pipeline for extracting rich morphological representations that enable grouping cells into morphological cell classes with characteristic gene expression. I further show how such descriptors could be used to explore the morphological diversity of cells, tissues and organs in the dataset

Moderating the Neuropsychological Impact of Online Learning on Psychology Students

The purpose of the study was to identify what neuropsychological effect online learning had on psychology students and how it could be moderated. The study was descriptive and combined qualitative and quantitative methods to address the research questions. The study relied on three phases such as baseline study, experiment, and reporting. The experiment utilised neuropsychology tests adopted from the NeurOn platform. It was found that the Psychology students’ perceptions of e-learning and their emotional reaction to them were found not to be appreciative. The practices in breathing exercises, meditation, or yoga were proved to be able to moderate the impact of online learning on the experimental group students’ attentional capacities, memory processes, and cognition abilities. The above findings were supported by the results obtained for the neuropsychology tests and the experimental group students’ self-reflections yielded from the use of the MovisensXS App. The students confirmed that breathing exercises, meditation, or yoga reduced study stress and burnout caused by e-learning and improved their academic performance. The focus group online discussion also showed that integration of breathing exercises, meditation, and yoga helped the experimental group students keep emotional balance, concentrate on their studies easier, remember more information, and meet deadlines in completing assignments. The education scientists are suggested to study how the e-learning curriculum could be reshaped so that it used relaxation practices on regular basis

Resolving discrepancies in forward and reverse ABO blood group typing

Background/Aim: There is a need of investigation of high frequency of the cases of ABO discrepancy revealed by forward and reverse typing. The aim of the study was to reveal optimal methods for detection of weak subgroups of group A and B antigens on erythrocytes. Methods: Sixteen persons with A blood group and anti-B antibody adsorbing ability (weak Bel, Bm and B3 antigens), 5 persons with B blood group and anti-A antibody adsorbing ability (weak Ax antigen) and 2 persons with O blood group and anti-B antibody adsorbing ability (weak Bel antigen) were investigated as the cases of type II-III of ABO discrepancy and weak B antigen. Liquid chromatography, agglutination, inhibition of agglutination and adsorption reactions at 4 °C and 37 °C with prolonged incubation (12 hours) were used in the study. Results: The persons with A blood group revealed by forward typing at 4 °C and O blood group detected by reverse typing at 37 °C showed the ability of the erythrocytes to adsorb anti-B antibody. The persons with B blood group revealed by forward typing with presence of anti-B antibodies reactive at 37 °C showed the ability of erythrocytes to adsorb anti-A antibody. Prolonged incubation at reverse typing, adsorption-elution tests, inhibition of haemagglutination and liquid chromatography were used to define blood group specificity. Conclusion: Prolonged incubation during reverse typing at 4 °C and 37 °C, adsorption at 4 °C, heat elution and liquid chromatography might help to detect blood group type in cases of type II-III of ABO discrepancy

Проектне навчання у підготовці майбутніх філологів

The objective of the research is to determine the effectiveness and relevance of the implementation of project-based learning technology (PBL) and students' assessment of the prospects for learning linguistic theory, theory and practice of translation using the PBL method. Methodology. The use of project-based learning technologies within language courses increases understanding of native linguistic concepts, strengthens the link between translation theory and technology is the research hypothesis. To implement the research goals an innovative educational project was presented and implemented on the basis of Kharkiv National Pedagogical University named after Hryhoriy Skovoroda, Ukraine. Participants of the project attended the course “Fundamentals of Translation” during the academic year. The whole process of project creation was formed in three stages and contained 6 steps: initiation, definition, design, development, implementation, and summarizing. Results of the paper. The results of the study showed that the students have a very positive evaluation of the use of project technology in professional training of philological field,thusthis training is effective. Examination of practical cases on the implementation of the PBL method will allow identifying more prospects in such areas as collaboration and project design.Цель исследования - определить эффективность и актуальность использования технологии проектного обучения (ПТО) и оценка студентами перспектив для изучения лингвистической теории, теории и практики перевода методом ПТО. Методология. Использование проектных технологий обучения в рамках языковедческих курсов способствует пониманию отечественных лингвистических концепций, укрепляет связь между теорией и практикой перевода. Гипотеза исследования. Для реализации целей исследования было представлено инновационный образовательный проект и реализовано его на базе Харьковского национального педагогического университета имени Григория Сковороды, Украина. Учасники проекта пройшли курс «Основи перевода» в течение учебного года. Весь процесс создания проекта состоял из трех этапов и реализовывался в шесть шагов: инициация, определение, проектирование, разработка, реализация и обобщение. Результаты роботы. Результаты исследования показали, що студенти высоко оценивают использование проектной технологии в профессиональной подготовке в филологической специальности и считают ее эффективной. Изучение практических кейсов реализации метода ПТО позволит выявить больше перспектив в таких сферах как сотрудничество и проектирование.Метою дослідження є визначення ефективності та актуальності впровадження проектної технології навчання (ПТН) та оцінка студентами її перспектив у вивченні лінгвістичної теорії, теорії та практики перекладу з використанням ПТН. Методологія. Використання проектних технологій навчання в рамках мовних курсів покращує розуміння вітчизняних лінгвістичних концепцій, зміцнює зв'язок між теорією і практикою перекладу. Гіпотеза дослідження. Для реалізації цілей дослідження було представлено інноваційний освітній проект та реалізовано його на базі Харківського національного педагогічного університету імені Григорія Сковорода, Україна. Учасники проекту пройшли курс «Основи перекладу» протягом навчального року. Весь процес створення проекту складався в три етапи і містив 6 кроків: ініціювання, визначення, проектування, розробка, впровадження та підсумовування. Результати роботи. Результати дослідження показали, що студенти дуже позитивно оцінюють використання проектної технології у професійній підготовці у філологічній галузі, отже, ця підготовка є ефективною. Вивчення практичних кейсів щодо впровадження методу PBL дозволить виявити більше перспективи в таких сферах як співпраця та проектування

Whole-body integration of gene expression and single-cell morphology

Animal bodies are composed of cell types with unique expression programs that implement their distinct locations, shapes, structures, and functions. Based on these properties, cell types assemble into specific tissues and organs. To systematically explore the link between cell-type-specific gene expression and morphology, we registered an expression atlas to a whole-body electron microscopy volume of the nereid Platynereis dumerilii. Automated segmentation of cells and nuclei identifies major cell classes and establishes a link between gene activation, chromatin topography, and nuclear size. Clustering of segmented cells according to gene expression reveals spatially coherent tissues. In the brain, genetically defined groups of neurons match ganglionic nuclei with coherent projections. Besides interneurons, we uncover sensory-neurosecretory cells in the nereid mushroom bodies, which thus qualify as sensory organs. They furthermore resemble the vertebrate telencephalon by molecular anatomy. We provide an integrated browser as a Fiji plugin for remote exploration of all available multimodal datasets