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В статье описывается методы получения информации о деятельности биологических объектов. Наиболее универсальное отражение состояния биологического объекта показывает температура, так как является характеристикой мощности инфракрасного излучения. В работе отмечается, что при анализе результатов исследования используются методы визуального отображения информации, позволяющие не только отображать информацию о температуре в точках измерения, но и на основе данных измерений строить двумерные карты распределения температур. Также рассматривается возможность использования вычислительных систем в диагностических комплексах.

Analysis of bioinformatics data is an actual problem in modern computational biology and applied mathematics. With the development of biotechnology and tools for obtaining and processing such information, unresolved issues of the development and application of new algorithms and software have emerged.Authors propose practical algorithms and methods for processing transcriptomic data for efficient results of annotation, visualization and interpretation of bioinformatics data.

Popularisation of the key scientific problems occupied a significant place in D. I. Trubetskov’s work. In memory of this fact, the problem of electromagnetic field affecting biological objects is discussed in a popular manner in this article. This problem has more than a century in it’s history, but still being far from the final solution. Objectives. Analyze the problem of the interaction of electromagnetic fields with biological objects and social structures as complex multielement systems, and assess the possibility of identifying new effects in their behavior. Methods. As a result of many studies in different countries, by the mid-60s of the twentieth century, an idea was formed about the complex and systemic nature of the influence of electromagnetic fields on biological objects. Therefore, the interaction of electromagnetic fields with biological objects and social environments is considered in the work as a problem of external influence on complex multielement interconnected systems, using conceptual approaches of nonlinear dynamics. Results. It is shown that along with the effects of EMF on individual biological objects, there are effects of the influence of the information component of EMF on social systems, the elements of which are people considering as biological objects. The threshold power flux density where the influence effects on the social systems begin to manifest is significantly lower than the one for biological objects. Conclusion. Effective approaches aimed to reduce the negative impact of microwave radiation on humans can be implemented using personal means for monitoring the level and the received dose of radiation – electromagnetic radiation dosimeters, which are actually analogous to thermometers for measuring body temperature.

The article is devoted to optical microlens microscopy, which, in combination with scanning probe microscopy, can significantly improve the process of measuring biological objects in a natural environment.

Non-pollen palynomorphs (NPPs) form a large group of biological objects found in palynological slides besides pollen grains. This includes various remains of algae and fungi, shells, resting stages and eggs of invertebrates, among others. Publications of NPP-types started in the 1970s with studies of BvG and colleagues, and large numbers of new types continue to be published every year. For an overview of this diverse world of “extra fossils”, we created the Non-Pollen Palynomorph Image Database (NPP-ID) to gather NPP knowledge, structured by acronyms and known taxonomy to assist identification and palaeoecological interpretation (https://nonpollenpalynomorphs.tsu.ru/). An integral part is a database of illustrations, descriptions and ecological background of NPPs. While numerical data are routinely stored in open access repositories, the NPP-ID enables the definitions, identification and interpretation of the NPP taxa to be shared. The NPP-ID operates as an open research project aiming to provide open access to descriptions and illustrations of NPPs. However, due to publication rights, access to some original images is restricted and registration by users is required. We encourage palynologists to contribute to the further growth of the database by uploading their own microphotographs or drawings under an open access license. Contributors will be acknowledged by co-authorship in publications on updates of the NPP-ID., Российский Фонд Фундаментальных Исследований (РФФИ) http://dx.doi.org/10.13039/501100002261, Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659, Georg-August-Universität Göttingen (1018), http://nonpollenpalynomorphs.tsu.ru/

The work is devoted to the development of medical systems for monitoring biomedical indicators. The problem of developing a universal hardware software-controlled control system for the diagnosis of biological objects is solved. The main requirements for such a system are a wide range of functionality for combining different methods of measurement transformation and compliance with modern trends in the development of microelectronic sensors. Given the requirements for modern microcircuitry, in particular for sensing devices of the Internet of Things, the signal path of the sensors is implemented on the basis of PSoC family 5LP Family Cypress. Approbation of the developed system is carried out in the course of research of the character of optical radiation in the course of measurement of biomedical indicators.

The complexity of biological objects makes the development of computerized medical systems a difficult algorithmic decision due to the natural uncertainty inherent in these objects. Human thinking is based on vague and approximate data that can be analyzed to form clear decisions. An exact mathematical model of biological objects may not exist in practice, or such a model may be too complex to implement. In this case, fuzzy logic is a suitable tool for solving the specified problem. The problem of medical diagnosis can be viewed as a classification problem. The article presents a literature review of the use of fuzzy classifiers in diagnostics of cardiovascular diseases. The main advantage of fuzzy classifiers in comparison with other artificial intelligence methods is the ability to interpret the resulting classification result. The review aims to expand the knowledge of various researchers working in the field of medical diagnostics.

The huge space of experimental data on biological and chemical objects and their interactions contributes to the rapid growth of scientific publications containing their analysis. Such data may include characteristics of low-molecular-weight compounds, results of their biological activity evaluation, and their interaction with human and animal proteins, methods of synthesis of organic compounds, and their classification. The past decades saw the development of methods for automated extraction of data from texts of scientific publications, including those for retrieval of names of organic compounds. These data can be used for the automatic identification of the names of organic compounds, including all possible synonyms. Since the topics of scientific publications are diverse, the extracted data can be applied to obtain information about (1) classification of organic compounds (2) methods of synthesis of a given organic compound; (3) physicochemical properties of this compound; (4) its interaction with high-molecular-weight compounds (including proteins, mRNA of animals and humans); and (5) the therapeutic properties of organic compounds, the active substance of the drug, and data on clinical trials. This review considers the methods aimed at searching and extracting data on names of low-molecular-weight compounds and interactions between them and animal and human proteins (biological objects), as well as data on experimentally confirmed biological activity and the effects of organic compounds (including drugs) on pathological processes. Here, we discuss the methods developed and the results of their application published over the past 10 years.

Stereology is the method of choice for the quantitative assessment of biological objects in microscopy. It takes into account the fact that, in traditional microscopy such as conventional light and transmission electron microscopy, although one has to rely on measurements on nearly two-dimensional sections from fixed and embedded tissue samples, the quantitative data obtained by these measurements should characterize the real three-dimensional properties of the biological objects and not just their “flatland” appearance on the sections. Thus, three-dimensionality is a built-in property of stereological sampling and measurement tools. Stereology is, therefore, perfectly suited to be combined with 3D imaging techniques which cover a wide range of complementary sample sizes and resolutions, e.g. micro-computed tomography, confocal microscopy and volume electron microscopy. Here, we review those stereological principles that are of particular relevance for 3D imaging and provide an overview of applications of 3D imaging-based stereology to the lung in health and disease. The symbiosis of stereology and 3D imaging thus provides the unique opportunity for unbiased and comprehensive quantitative characterization of the three-dimensional architecture of the lung from macro to nano scale.

Harnessing the power of graphics processing units (GPUs) to accelerate molecular dynamics (MD) simulations in the context of free-energy calculations has been a longstanding effort towards the development of versatile, high-performance MD engines. We report a new GPU-based implementation in NAMD of free-energy perturbation (FEP), one of the oldest, most popular importance-sampling approaches for the determination of free-energy differences that underlie alchemical transformations. Compared to the CPU implementation available since 2001 in NAMD, our benchmarks indicate that the new implementation of FEP in traditional GPU code is about four times faster, without any noticeable loss of accuracy, thereby paving the way towards more affordable free-energy calculations on large biological objects. Moreover, we have extended this new FEP implementation to a code path highly optimized for a single-GPU node, which proves to be up to nearly 30 times faster than the CPU implementation. Through optimized GPU performance, the present developments provide the community with a cost-effective solution for conducting FEP calculations. The new FEP-enabled code has been released with NAMD 3.0.

The importance of genomic information has now increased due to the possibility of its practical use. Meanwhile, the understanding of the term “genomic information” is specified based on different criteria. Genomic information is proposed to be classified depending on the following criteria: 1) the origin of a biological sample, 2) the place of fixation and storage of genomic information, 3) the purpose of use, 4) the completeness of examination, 5) the relation of a person to the acquisition of his or her genomic information, 6) the scope of content. Genomic information can be presented as a generic concept referring to all biological objects, as a special concept (species) referring only to humans, and as subspecies reflecting specificity of such information in a particular area of activity. Genomic information of a living being (human, animal, plant, microorganism) is understood as data on certain fragments of deoxyribonucleic acid (sometimes ribonucleic acid) on the basis of which the living being is identified or other permitted activity is carried out.Human genomic information is defined as biometric personal data extracted from certain fragments of deoxyribonucleic acid (sometimes ribonucleic acid) of a living individual or corpse, on the basis of which it is possible to identify, determine genetic predispositions or extract patterns of the development of the human being obtained voluntarily, and, in cases provided for by the law, forced to be fixed in a biological sample and/or stored in an information map or database.It is proved that the existing laws on information or a new law dedicated to regulation of the application of genomic technologies should be amended instead of adopting a special law “On Genetic Information”.

An important task in the development of sources of electromagnetic vibrations used in the design of dielkometrical systems for biological objects is to reduce the level of interference of the electromagnetic vibrations source in the output spectrum. Methods for suppressing side components in the output spectrum conflict with the dynamic characteristics of the electromagnetic vibrations source, in particular, they do not meet the requirements for the tuning speed in the specified wave ranges. (Research purpose) The research purpose is in developing the basic structure of the exciter of the dielkometric system for the study of biological objects, allowing obtaining previously unacceptable values of suppression of the comparison frequency and its harmonics. (Materials and methods) Authors applied the compensation method to obtain the required spectral and dynamic characteristics of the electromagnetic vibrations source. The article sets the problem of adaptive noise compensation, which was solved using a quasi-optimal method, the method of the minimum of the average square error. (Results and discussion) The article proposes the basic structure of the exciter of the dielkometric system for the study of biological objects. It was shown that the adaptive method results in suppression of side components in the spectrum of the output signal source while maintaining the required speed. The spectral components of the output signal of the electromagnetic source were studied using a functional method. It was found that there is an effective convergence of the transfer functions of adaptive filters of the adaptive compensator of side components to the nonlinear transfer function of the corresponding orders of the dynamic system. (Conclusions) The article presents the developed structure of the exciter of the dielkometrical system using an adaptive compensator of side components, which allows to obtain previously unacceptable values of suppression of the comparison frequency and its harmonics. It was found that the use of this structure of the exciter will improve the dynamic characteristics of the dielkometrical system as a whole. It was found that the use of adaptive filters increases the speed of the exciter by 5-10 times.

The system of Jones matrix mapping of blood plasma films for medical diagnosis of pathologies of biological objects was considered in this paper. The system of decision support on the basis of a neural network for differentiation of nosologies was constructed and analyzed.Keywords: Jones matrix, polarimetry, blood plasma, neural network.

Обсуждается возможность применения бортовых платформ с целью поддержки наземных сетей для использования ресурсов автономных транспортных средств как части критичных к задержкам приложений. Бортовые платформы могут повысить безопасность поездок транспортных средств, доставляя на них своевременную информацию об окружающей обстановке даже в отдаленных районах земного шара. Обсуждаются требования и потенциальные решения для поддержки инфраструктуры автономных транспортных средств как части интеллектуальной транспортной системы. Предлагается использовать вдоль дороги энергоэффективные сенсоры, которые могут объединяться друг с другом в Mesh-сети. Кроме того, предлагается новый подход к обнаружению активности биологических объектов на обочине дороги, основанный на технологиях искусственного интеллекта. The article discusses the possibility of using onboard platforms to support the terrestrial networks for autonomous vehicles resources as a part of delay-critical applications. Onboard platforms can improve the safety of vehicle rides by delivering time-critical information about the environment to the vehicles, even in remote areas of the world. In this paper, we discuss requirements and potential solutions for supporting the autonomous vehicle infrastructure, as a part of an intelligent transportation system. It is proposed to use energy-efficient sensors along the road, which can connect with each other in a Mesh network. In addition, a new approach for the detection of biological objects activity on the roadside, based on artificial intelligence technologies is suggested.

Automatically recognition and classification of biological objects under microscope methods are shown in paper. Problem of separated of white-black and color images is studied. Method of separation of different type of objects (visual diapason of specter) with compare results is shown in the paper. Quality of segmentation methods analyses is presented in the paper. Schemes and table results of segmentation are exist. Methods of pattern recognition applicability for Computer Vision Systems of analysis and pattern recognition scenes in the visual spectrum are studied in the paper. The methods and algorithms can be used in Real-time Sensing, white-black and color patterns, reasoning and adaptation for Computer Vision Systems too. Example of such systems is the glasses for people with visual impairments; when the camera mounted in glasses receives and transmits environment data, and the contact plate with electrical leads via e-pulse transmits data to the eye retina. Author analyzed several pattern recognition methods that will allow to process data of the environment for the brain. This will make the visually impaired persons with sub reality vision better orientation in environment. Theoretical basic, algorithms and their compared for apply is presented in paper.

In the context of environmental pollution, it is of prime importance to study the organism’s overall response to harmful environments. This could be carried out if there were suitable dynamic variables, describing the state of a living system. In this respect, a new approach to life phenomena is needed because in phenomenological aspect, the biological objects in their entirety could be not adequately described in the terms of other science fields.

Underwater images are susceptible to various distortions compared to images taken on land, due to the nature of the water environment. These images often suffer from diffraction, polarisation, absorption, scattering, colour loss and attenuation of light. Each part of the ocean will have its own sources of distortions, due to flickers caused by direct sunlight, marine snow, the fluorescence of biological objects, the presence of macroscopical organisms, loss of stability in divers, loss of light, artificial lighting and floating dust particles present in the water. There are numerous techniques and algorithms that may be used to restore these underwater images. This study reviews different algorithms and methods, developed in the past two decades, to give clearer ideas on the techniques present in the image restoration process, specifically for underwater images.

Електромагнітні поля (ЕМП) можуть виникати як природно, так і внаслідок людської діяльності. У сучасних умовах стрімкого поширення набувають нові джерела штучних ЕМП через інноваційні технології зв’язку. Тому виникає потреба у дослідженні техногенних ЕМП і механізмів їх впливу на біосистеми. У роботі розглядається питання впливу штучних ЕМП на здоров’я людини, дов­кілля та біологічні об’єкти. Проаналізовано експериментальні та теоретичні роботи стосовно дії ЕМП. Наведено опис принципів нормування рівнів неспецифічних ЕМП і захисту від впливу техногенних ЕМП. Обговорюються можливі механізми дії ЕМП та електромагнітних випромінювань (ЕМВ) на біологічні об’єкти, в тому числі через накопичення біогенних магнітних наночастинок в організмі. Метою дослідження є огляд сучасних способів виявлення біологічних ефектів нетеплових неіонізуючих ЕМП і ЕМВ та визначення перспектив використання біологічних тест-систем для оцінки ефектів ЕМП. Найбільшу увагу приділено сенсорам ЕМП на основі культур мікроорганізмів. Запропоновано класифікацію існуючих тест-систем за критеріями: 1) життєздатності клітин; 2) рухової активності клітин; 3) біолюмінесценції та змін кольору під впливом ЕМП. Аргументовано потребу в розробці простих і надійних біологічних індикаторів різних видів ЕМП, насамперед надвисокочастотного випромінювання, у зв’язку з впровадженням технології 5G-зв’язку. Наголошено на необхідності стандартизованих протоколів випробувань для порівняння результатів досліджень. Показано, що опис відповідних експериментів доцільно супроводжувати такими ознаками: 1) назва культури клітин; нативні клітини або модифіковані; 2) фізичні характеристики ЕМП або ЕМВ (частота, потужність, модуляція, вид джерела); 3) тривалість впливу; 4) перелік досліджуваних параметрів; 5) методи дослідження; 6) абсолютні виміри і результати та відносна величина ефекту; 7) від чого залежить вплив (температура, вік культури клітин, склад живильного середовища); 8) успадковування змін у клітинах; 9) час релаксації ефекту. Electromagnetic fields (EMF) can occur both naturally and due to human activity. Nowadays, through the innovative communication technologies, the new sources of artificial EMFs are widely disseminated. Therefore, one needs to study the artificial EMFs and mechanisms of their influence on biosystems. The paper deals with the issues of the influence of artificial EMFs on human health, environment and biological objects. The experimental and theoretical investigations concerning an action of EMF are analyzed. The description of principles of standardization of non-specific EMFs and protection from the influence of man-made fields is presented. Possible mechanisms of EMF and electromagnetic radiation (EMR) action on biological objects, including those due to the accumulation of biogenic magnetic nanoparticles in an organism, are discussed. The aim of the research is to review state-of-the-art methods for detecting the biological effects of non-thermal non-ionizing EMF and EMR and to determine the prospects of using biological test-systems for evaluation of effects of EMFs. Hereby, the main attention is drawn to EMF sensors based on the cultures of microorganisms. The classification of existing test-systems is proposed according to criteria: 1) vitality of cells; 2) motor activity of cells; 3) bioluminescence and color changes under the influence of EMF. The need to develop simple and reliable biological indicators for various types of EMFs, especially for ultrahigh-frequency radiation in connection with the introduction of 5G communications technology, is substantiated. The necessity of standardized test-protocols for comparison of research results is emphasized. It is shown that the description of corresponding experiments should be accompanied by the following features: 1) name of the cell culture; native or modified cells; 2) physical characteristics of EMF or EMR (frequency, power, modulation, source type); 3) exposure duration of; 4) list of parameters to be investigated; 5) research methods; 6) absolute measurements, results and the relative magnitude of an effect; 7) what does the influence depend on (temperature, age of cell culture, composition of the nutrient medium); 8) inheritance of changes in cells; 9) relaxation time of the effect. Электромагнитные поля (ЭМП) имеют как естественное происхождение, так и являются результатом человеческой деятельности. В современных условиях стремительное распространение получили новые источники искусственных ЭМП из-за появления инновационных технологий связи. Поэтому возникает потребность в исследовании техногенных ЭМП и механизмов их воздействия на биосистемы. В работе раскрыты вопросы влияния искусственных ЭМП на здоровье человека, окружающую среду и биологические объекты. Проанализированы экспериментальные и теоретические работы, касающиеся действия ЭМП. Приведено описание принципов нормирования уровней неспецифическихЭМП и защиты от влияния техногенных ЭМП. Обсуждаются возможные механизмы действия ЭМП и электромагнитных излучений (ЭМИ) на биологические объекты, в том числе в результате накопления биогенных магнитных наночастиц в организме. Целью исследования является обзор современных способов выявления биологических эффектов нетепловых неионизирующих ЭМП и ЭМИ и обозначение перспектив использования биологических тест-систем для оценки эффектов ЭМП. Наибольшее внимание уделено сенсорам ЭМП на основе культур микроорганизмов. Предложена классификация существующих тест-систем по критериям: 1) жизнеспособности клеток; 2) двигательной активности клеток; 3) биолюминесценции и изменения цвета под влиянием ЭМП. Аргументирована потребность в разработке простых и надежных биологических индикаторов разных видов ЭМП, прежде всего сверхвысокочастотного излучения, в связи с внедрением технологии 5G-связи. Подчеркнута необходимость стандартизованных протоколов испытаний для сравнения результатов исследований. Показано, что описание соответствующих экспериментов целесообразно сопровождать такими признаками: 1) название культуры клеток; нативные клетки или модифицированные; 2) физические характеристики ЭМП или ЭМИ (частота, мощность, модуляция, вид источника); 3) длительность влияния; 4) перечень исследуемых параметров; 5) методы исследований; 6) абсолютные значения, результаты и относительная величина эффекта; 7) от чего зависит влияние (температура, возраст культуры клеток, состав питательной среды); 8) наследование изменений в клетках; 9) время релак­сации эффекта.

The aim of the work was to develop electronic database of biological organisms (fishes, viruses) on the base of the methods that have been used before in mathematics, engineering, physics. The methods of object-oriented system analysis, construction of models of subject spaces (problem space, solution space), ER-diagrams, of constructing databases and others were applied. The examples of prototypes of modern databases with information about fishes developed over the past years in Western European and American countries were presented. An overview of applied methods, concepts and terminology from the areas of object-oriented system analysis, database designing was disclosed. In conclusions the description of constructed database and practical recommendations for the development of databases with the information about domestic biological organisms for electronic information systems are given.

Formalized approach to the analysis of biomedical signals and images with locally concentrated features is developed on the basis of matched morphological filtering taking into account the useful signal models that allowed generalizing the existing methods of digital processing and analysis of biomedical signals and images with locally concentrated features. The proposed matched morphological filter has been adapted to solve such problems as localization of the searched structural elements on biomedical signals with locally concentrated features, estimation of the irregular background aimed at the visualization quality improving of biological objects on X-ray biomedical images, pathologic structures selection on mammogram. The efficiency of the proposed methods of matched morphological filtration of biomedical signals and images with locally concentrated features is proved by experiments.

We present a new optimization method for permanent magnet systems for magnetic targeted drug delivery. On the example of a human eye, special attention is paid to the challenging situation, where the placement of magnets in close vicinity of the targeted area is impossible. In this paper, we demonstrate how a system of magnets can be optimized to provide the maximal magnitude of the magnetic field gradient with a prescribed orientation in an extended area (vitreous body). The presented methodology is applicable for all tasks involving a magnetic targeted drug delivery to biological objects.

An instrument has been developed for measuring the force of affine interactions, in particular, in biological systems. The structure of the instrument is described. It includes a replaceable cartridge with a quartz resonator for analyzing various biosystems by measuring the signal of detachment of molecules from the resonator surface. The instrument is a sensor device with which it is possible to analyze various biological objects, including viruses and bacteria, as well as to carry out DNA identification. Software has been developed to automate the processing of results and the identification of objects. The instrument can be used to carry out express analysis in medical institutions and research laboratories.

Parametric curve models are convenient to describe and quantitatively characterize the contour of objects in bioimages. Unfortunately, designing algorithms to fit smoothly such models onto image data classically requires significant domain expertise. Here, we propose a convolutional neural network-based approach to predict a continuous parametric representation of the outline of biological objects. We successfully apply our method on the Kaggle 2018 Data Science Bowl dataset composed of a varied collection of images of cell nuclei. This work is a first step towards user-friendly bioimage analysis tools that extract continuously-defined representations of objects.

Back in the middle of the last century, information began to appear about the existence of a certain electromagnetic field, called a biofield, which is emitted by biological objects - animals and plants. A scientist from China, Jiang Kanzhen Yu. V., suggested that if you concentrate this radiation from several plants or animals, this field will affect other biological objects. Further research proved this phenomenon. Jian Kanzhen designed the device that concentrated radiation from many biological objects using spherical copper mirrors. He called this device a BIOTRON. Another Russian scientist, E. V. Komrakov, developed and patented a modified Biotron device, more powerful, in 58 countries of the world, and called it BIOTRON-EKOM. Plant seedlings are placed in front of mirrors, and the radiation from them is focused on biological objects. It was found that when irradiated in a Biotron with seedlings of cereal plants, the average life span of C57Bl mice increased to 24.5%, and the nematodes Caenorhabditis elegans increased to 30.1% (the maximum life span was up to 23.2 and 25%, respectively) compared to the control groups. The acceleration of the growth of animal cells in the culture, an increase in the saturating density, an increase in the "total" and "stationary" life span of culture by 23 and 22%, respectively, and an increase in the germination energy of barley seeds by 7.5% were revealed.

This paper describes the results of work on developing the mobile application for recognition of faces and other biological objects. The application is designed with a focus on loading external machine learning models over the Internet, which allows you to change the model without making any modifications to the application. With such realization, the application can be used in many cases. For example, at carrying out conferences: organizers just need to train a model and send out the link for its downloading to all participants of the conference without any changes in source code. Participants will be able to find out the information about other members they are interested in, as well as contact them directly from the application, both by phone and by e-mail. Instructions are given for teaching your own face recognition model using the Microsoft Custom Vision cloud service, which allows you to train regardless of the power of your local computer. As an example, a classification model was trained and the following assessments of recognition quality indicators were obtained precision: 97.8% and recall: 95.8%. In our future work we consider adding the functionality of emotion recognition based on the pattern recognition algorithm, described in this paper.

The article describes the basics of microwave diagnostics from the point of view of creating a new method for obtaining data to detect pathologies in biological objects, as well as sensors and computational human phantoms for preliminary modeling of experimental equipment.

Light can be employed as a tool to alter and manipulate matter in many ways. An example has been the implementation of optical trapping, the so called optical tweezers, in which light can hold and move small objects with 3D control. Of interest for the Life Sciences and Biotechnology is the fact that biological objects in the size range from tens of nanometers to hundreds of microns can be precisely manipulated through this technology. In particular, it has been shown possible to optically trap and move genetic material (DNA and chromatin) using optical tweezers. Also, these biological entities can be severed, rearranged and reconstructed by the combined use of laser scissors and optical tweezers. In this review, the background, current state and future possibilities of optical tweezers and laser scissors to manipulate, rearrange and alter genetic material (DNA, chromatin and chromosomes) will be presented. Sources of undesirable effects by the optical procedure and measures to avoid them will be discussed. In addition, first tentative approaches at cellular-level genetic and organelle surgery, in which genetic material or DNA-carrying organelles are extracted out or introduced into cells, will be presented., Spanish Nuclear Security Council (CSN-UAM15112018).

From the start of digital video microscopy over 20 years ago, single particle tracking has been dominated by algorithmic approaches. These methods are successful at tracking well-defined particles in good imaging conditions but their performance degrades severely in more challenging conditions. To overcome the limitations of traditional algorithmic approaches, data-driven methods using deep learning have been introduced. They managed to successfully track colloidal particles as well as non-spherical biological objects, even in unsteady imaging conditions.

Research on the field of implantable electronic devices that can be directly applied in the body with various functionalities is increasingly intensifying due to its great potential for various therapeutic applications. While conventional implantable electronics generally include rigid and hard conductive materials, their surrounding biological objects are soft and dynamic. The mechanical mismatch between implanted devices and biological environments induces damages in the body especially for long-term applications. Stretchable electronics with outstanding mechanical compliance with biological objects effectively improve such limitations of existing rigid implantable electronics. In this article, the recent progress of implantable soft electronics based on various conductive nanocomposites is systematically described. In particular, representative fabrication approaches of conductive and stretchable nanocomposites for implantable soft electronics and various in vivo applications of implantable soft electronics are focused on. To conclude, challenges and perspectives of current implantable soft electronics that should be considered for further advances are discussed.

One of the essential tasks in connectomics is the morphology analysis of neurons and organelles like mitochondria to shed light on their biological properties. However, these biological objects often have tangled parts or complex branching patterns, which make it hard to abstract, categorize, and manipulate their morphology. In this paper, we develop a novel topological nomenclature system to name these objects like the appellation for chemical compounds to promote neuroscience analysis based on their skeletal structures. We first convert the volumetric representation into the topology-preserving reduced graph to untangle the objects. Next, we develop nomenclature rules for pyramidal neurons and mitochondria from the reduced graph and finally learn the feature embedding for shape manipulation. In ablation studies, we quantitatively show that graphs generated by our proposed method align with the perception of experts. On 3D shape retrieval and decomposition tasks, we qualitatively demonstrate that the encoded topological nomenclature features achieve better results than state-of-the-art shape descriptors. To advance neuroscience, we will release a 3D segmentation dataset of mitochondria and pyramidal neurons reconstructed from a 100um cube electron microscopy volume with their reduced graph and topological nomenclature annotations. Code is publicly available at https://github.com/donglaiw/ibexHelper., Technical report

Optical tweezers (OTs) are innovative instruments utilized for the manipulation of microscopic biological objects of interest. Rapid improvements in precision and degree of freedom of multichannel and multifunctional OTs have ushered in a new era of studies in basic physical and chemical properties of living tissues and unknown biomechanics in biological processes. Nowadays, OTs are used extensively for studying living cells and have initiated far-reaching influence in various fundamental studies in life sciences. There is also a high potential for using OTs in haemorheology, investigations of blood microcirculation and the mutual interplay of blood cells. In fact, in spite of their great promise in the application of OTs-based approaches for the study of blood, cell formation and maturation in erythropoiesis have not been fully explored. In this review, the background of OTs, their state-of-the-art applications in exploring single-cell level characteristics and bio-rheological properties of mature red blood cells (RBCs) as well as the OTs-assisted studies on erythropoiesis are summarized and presented. The advance developments and future perspectives of the OTs&rsquo, application in haemorheology both for fundamental and practical in-depth studies of RBCs formation, functional diagnostics and therapeutic needs are highlighted.

An ideal self-healing material is supposed to automatically, without any external action, recover its characteristics and integrity in a minimum amount of time necessary after the suffering damage and repeat this countless times. Inspired by nature, self-healing materials represent the forefront of recent developments in materials chemistry and engineering. Artificial self-healing materials that would be similar to biological objects in terms of restoring characteristics would offer huge opportunities, especially in the cases where it is necessary to provide the reliability of materials in not easily accessible zones as long as possible during their service life. Biocompatible self-healing composite may extend the service life of artificial bone, artificial teeth, and so on. Self-healing hydrogels are widely use as drug delivery, tissue engineering, wound dressing and 3D printing applications. Self-healing rubber could find applications in toy industry. Since it is a growing area, these materials find applications in various fields. But this chapter discusses the main applications of self-healing materials such as wound healing, tissue engineering, 3D printing, drug delivery, anticorrosion coatings, aerospace and electronics applications.

Advances in laser and optoelectronic technologies have brought the general concept of optomechanical manipulation to the level of standard biophysical tools, paving the way towards controlled experiments and measurements of tiny mechanical forces. Recent developments in direct laser writing (DLW) have enabled the realization of new types of micron-scale optomechanical tools, capable of performing designated functions. Here we further develop the concept of DLW-fabricated optomechanically-driven tools and demonstrate full-3D manipulation capabilities over biological objects. In particular, we resolved the long-standing problem of out-of-plane rotation in a pure liquid, which was demonstrated on a living cell, clamped between a pair of forks, designed for efficient manipulation with holographic optical tweezers. The demonstrated concept paves the way for the realization of flexible tools for performing on-demand functions over biological objects, such as cell tomography and surgery to name just few.

Bioinformatics is a multidisciplinary field of managing health information digitally, which can be used further for analyzing and justifying the biological behavior of the nature. In the advancement of different computational tools and algorithms, these biological data can be managed very efficiently, and by analyzing those data, it is very much possible to find and discover different unknown mysteries of nature like the cause of happening any disease, the evolution of biological objects like virus, bacteria or any kind of living species, customized drug management, prediction of protein structure, DNA sequencing, etc. In the era of digitization, there are huge amount of biological data that are now possible to store in digital platform, and these can be processed through various computational tools that can analyze those data and produce various statistical reports. Machine learning in the domain of artificial intelligence is now a common tool for different bioinformatics applications. The main advantages of machine learning techniques are to predict the optimized results based on the previous data record. In this paper, we will discuss about the different tools and its application on bioinformatics and the artificial intelligence approach to the bioinformatics application.

This paper reports a feedback-based manoeuvre planning approach for automated nonprehensile selective micromanipulation of large, microscopic biological objects ( ∼ 100 μ m ). We employ ferromagnetic micro-particles as microrobots actuated via a global magnetic field produced by electromagnetic coils placed in quadrupole configuration. The microrobot motion is programmed to push the target object to the goal location. We employ a three-step approach comprising: (a) generate a collision-free optimal path between the initial and the commanded goal location, (b) generate a manoeuvre planning algorithm that invokes one of the three motion manoeuvres, namely, ‘approach’, ‘push’, and ‘align’ depending upon the instantaneous locations of the microrobot, target object, and the desired waypoint, and (c) deploy a simple proportional controller that determines the currents required in the electromagnetic coils that can produce a suitable magnetic field for executing the manoeuvre invoked by the manoeuvre planner. This paper reports a number of validation experiments conducted on both zebrafish, i.e., Danio rerio embryos and silica beads as target objects. We envisage that the developed inexpensive approach can be useful in robotic manipulation of biological objects with sizes in hundreds of microns including large biological cells, polyploid giant cancer cells (PGCC), multicellular spheroids, Dictyostelium slug, human oocytes, and autophagy candidates. We also believe that functionalising the microrobots with living cells or suitable chemicals will make it possible to perform on-chip biological experiments in future.

Background Quantitative analysis of mitochondrial morphology plays important roles in studies of mitochondrial biology. The analysis depends critically on segmentation of mitochondria, the image analysis process of extracting mitochondrial morphology from images. The main goal of this study is to characterize the performance of convolutional neural networks (CNNs) in segmentation of mitochondria from fluorescence microscopy images. Recently, CNNs have achieved remarkable success in challenging image segmentation tasks in several disciplines. So far, however, our knowledge of their performance in segmenting biological images remains limited. In particular, we know little about their robustness, which defines their capability of segmenting biological images of different conditions, and their sensitivity, which defines their capability of detecting subtle morphological changes of biological objects.

This review addresses questions of the specific characteristics of power supply to implanted devices (ID), including the service life of supply elements and the level of power consumption of contemporary devices, the acceptable weight and size characteristics of ID, and priority areas for implantation. Known methods of energy transmission and transformation are compared and the ranges of potential specific power for these are determined −0.1-100 mW/cm2 for wireless energy transmission, 0.0001-0.1 mW/cm2 for transformation of energy for sources specific to biological objects, and less than 0.0001 mW/cm2 for isotope power sources.

In the past, algorithms exploiting varying semantics in interactions between biological objects such as genes and diseases have been used in bioinformatics to uncover latent relationships within biological datasets. In this paper, we consider the algorithm Medusa in parallel with binary classification in order to find potential compounds to inhibit oral cancer. Oral cancer affects the mouth and pharynx and has a high mortality rate due to its late discovery. Current methods of oral cancer treatment, such as chemoradiation and surgery, fail to provide better chances for survival, warranting an alternative approach. By running Medusa on a data fusion graph consisting of biological objects, we incorporate binary classification to model the algorithm's association detection to discover compounds with the potential to mitigate the effects of oral cancer.

Purpose: To determine frequency-dependent impedance characteristics of the brains of the experimental animals. Material and methods: The developed by us 2-microphone interferometer technology was used in the acoustic impedance characteristics determination. The two standard microphones mounted stationary on a lateral surface of the interferometer measure the sound pressure levels and the phase difference between them. According to these data, the complex reflection coefficient and the impedance components of the test sample mounted on the end of the interferometer are calculated. The electrical impedance characteristics were measured by two electrodes method with the usage of parallel electrodes. The sample was placed between two electrodes and values of electrical impedance were detected by the electric current flowing through them. The object of the investigation was the rabbit brain. Results: The maximum acoustic absorption coefficient of the rabbit’s brain, on average, is registered at a frequency of 160–180 Hz and reaches 0.7. Then, as the frequency increases, the absorption coefficient decreases and at an average frequency of 760 Hz is 0.43. It can be noted that the spread in the data is maximum in the frequency range up to 240 Hz. The coefficient of variation varies from 23 to 10 %. At frequencies above 300 Hz, the coefficient of variation is less than 5 %. A low value of the coefficient of variation indicates a sufficiently accurate and reliable data. The difference in the magnitude of the spread between low frequencies in comparison with the spreads at medium and high frequencies reaches 2–4 times. This difference is caused by methodological errors. First of all, this is due to the fact that the waveguide is round with a diameter equal to 3.3 cm, and the whole brain of the rabbit resembles in a greater degree an oval. It is impossible for the rabbit’s whole brain to completely cover the circular surface of the waveguide section, there will always be gaps that bring in an element of uncertainty at low frequencies. At higher frequencies, this circumstance no longer affects the measurement error significantly. The presence of a maximum at frequencies of 160–180 Hz does not correspond to theoretical concepts. With the help of additional experiments with non-biological samples, it was possible to establish that this maximum is caused by an irregular geometric shape of the rabbit’s whole brain. Depending on the position of small dimples in the brain tissue and other irregularities, the maximum of the absorption coefficient appears. Those it is also a methodological error that characterizes rather the degree of overlapping of the waveguide section and the contact surface of the sound wave with the brain. In this series of experiments, it was also estimated how the values of the acoustic characteristics of the brain of rabbits vary with time. The first measurements were made 10–15 minutes after the extraction of the brain, the second measurement after 20 minutes, the third after 1 hour. It can be noted that the average values are almost identical starting from frequencies from 300 Hz and higher. There are small deviations in the readings at low frequencies. Over time, the absorption coefficient at low frequencies increased from 0.65 to 0.75. The analysis of the electrical impedance characteristics and loss factor calculations indicates that the range of the loss factor variation at a frequency of 1 kHz, for all experimental animals ranges from 0.04 to 0.07 and at a frequency of 100 kHz – from 0.06 to 0.09. Conclusion: The represented measuring systems allow obtaining the necessary acoustic and electrical impedance characteristics of biotissues; these data are important for the physical and mathematical modelling of the sound and EM waves’ interaction with the human body.

The advanced instrumental technique for research and control of the motivation of the experimental animals under the weak microwave electromagnetic radiation are suggested. The microwave is modulated by interval patterns. The results of these physiological and metabolites experiments showed that long-distance low-intensive, special coded microwave exposition can change the current motivations and corresponding behavior of animals. These results can be used in the studies of the fundamental brain mechanisms and in the medicine.