APPLICATION OF INFORMATION SYSTEMS AND TOOLS IN BIOINFORMATICS

The pace at which scientific data is produced and disseminated has never been as high as it is currently. Modern sequencing technologies make it possible to obtain the genome of a specific organism in a few days, and the genome of a bacterial organism in less than a day, and therefore researchers from the field of life science are faced with a huge amount of data that needs to be analyzed. In this connection, various fields of science are converging with each other, giving rise to new disciplines. So, bioinformatics is one of these fields, it is a scientific discipline that has been actively developing over the past decades and uses IT tools and methods to solve problems related to the study of biological processes. In particular, a crucial role in the field of bioinformatics is played by the development of new algorithms, tools and the creation of new databases, as well as the integration of extremely large amounts of data. The rapid development of bioinformatics has made it possible to conduct modern biological research. Bioinformatics can help a biologist to extract valuable information from biological data by using tools to process them. Despite the fact that bioinformatics is a relatively new discipline, various web and computer tools already exist, most of which are freely available. This is a review article that provides an exhaustive overview of some of the tools for biological analysis available to a biologist, as well as describes the key role of information systems in this interdisciplinary field

The boundary integral equation based method for damages detection in multilayered elastic structures

For two kinds of defects – delamination and transversal failure in the multilayer composite the damages detection method is proposed. The inverse geometrical problems of crack’s parameters reconstruction were formulated as a sequence of boundary integral equations (BIE). These boundary integral equations were derived on the basis of the principle of works mutuality applied to the problem of the composite specimen stationary oscillations. To solve the integral equations the finite element method, the boundary element method, and the Tikhonov regularization method were used. As complementary information for inverse problems solving the displacement field measured on a mechanical stress free area of the specimen’s surface was served. The numerical examples of the interfacial cracks and transversal failure of the internal layers in the multilayered composite were considered in the framework of two-dimensional elasticity

The effect of dry extract of Geranium Palustre herb on coagulation system = Вплив сухого екстракту трави герані болотної на систему зсідання крові

Ostapets M. O., Shevtsov I. I., Karabut L. V., Bereznyakova M. E. The effect of dry extract of Geranium Palustre herb on coagulation system = Вплив сухого екстракту трави герані болотної на систему зсідання крові. Journal of Education, Health and Sport. 2015;5(8):119-125. ISSN 2391-8306. DOI 10.5281/zenodo.27484http://dx.doi.org/10.5281/zenodo.27484http://ojs.ukw.edu.pl/index.php/johs/article/view/2015%3B5%288%29%3A119-125https://pbn.nauka.gov.pl/works/605723Formerly Journal of Health Sciences. ISSN 1429-9623 / 2300-665X. Archives 2011–2014 http://journal.rsw.edu.pl/index.php/JHS/issue/archive Deklaracja.Specyfika i zawartość merytoryczna czasopisma nie ulega zmianie.Zgodnie z informacją MNiSW z dnia 2 czerwca 2014 r., że w roku 2014 nie będzie przeprowadzana ocena czasopism naukowych; czasopismo o zmienionym tytule otrzymuje tyle samo punktów co na wykazie czasopism naukowych z dnia 31 grudnia 2014 r.The journal has had 5 points in Ministry of Science and Higher Education of Poland parametric evaluation. Part B item 1089. (31.12.2014).© The Author (s) 2015;This article is published with open access at Licensee Open Journal Systems of Kazimierz Wielki University in Bydgoszcz, Poland and Radom University in Radom, PolandOpen Access. This article is distributed under the terms of the Creative Commons Attribution Noncommercial License which permits any noncommercial use, distribution, and reproduction in any medium, provided the original author(s) and source are credited. This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non commercial use, distribution and reproduction in any medium, provided the work is properly cited.This is an open access article licensed under the terms of the Creative Commons Attribution Non Commercial License (http://creativecommons.org/licenses/by-nc/3.0/) which permits unrestricted, non commercialuse, distribution and reproduction in any medium, provided the work is properly cited.The authors declare that there is no conflict of interests regarding the publication of this paper.Received: 05.06.2015. Revised 15.07.2015. Accepted: 25.07.2015. UDC 615.322:582.751:615.273 THE EFFECT OF DRY EXTRACT OF GERANIUM PALUSTRE HERB ON COAGULATION SYSTEMВПЛИВ СУХОГО ЕКСТРАКТУ ТРАВИ ГЕРАНІ БОЛОТНОЇ НА СИСТЕМУ ЗСІДАННЯ КРОВІ M. O. Ostapets, I. I. Shevtsov, L. V. Karabut, M. E. BereznyakovaМ. О. Остапець, І. І. Шевцов, Л. В. Карабут, М. Є. Березнякова National University of Pharmacy, Kharkiv, UkraineНаціональний фармацевтичний університет, Харків, Україна[email protected] AbstractThe article is devoted to the studying of mechanism action on coagulation system the dry extract of Geranium Palustre herb. Established, those during 20-ty days of introduction the investigation extract increasing the activity of platelet’s mechanism of hemostasis (increasing platelet’s amount, their aggregation activity and retraction of blood clotting). On the background of introduction the investigation extract decreasing indicators of I and III phase of coagulation cascade (activated partial thromboplastin time, thrombin time), increasing prothrombin time and level of fibrinogen. Obtaining result suggest about active action the dry extract of Geranium Palustre herb on «external» way activation of hemocoagulation by possibility effect of accelerate the formation of thromboplastin, causing the hypercoagulation.The mechanism of antihemmorhagic action of dry extract of Geranium Palustre herb due to the presence in the composition biological active substances (such as tannins, flavonoids, elagic, galic and ascorbinic organic acids) that acting complex on vascular-platelet and coagulation hemostasis at the expense of increasing the strength and sealing vascular-tissue barriers, P-vitamin activity – it is ability to reduce capillary fragility and permeability and increasing their resistance.Key words: dry extract of Geranium Palustre herb, platelets, coagulation, phenolic compounds.  РефератСтаття присвячена дослідженню механізму дії сухого екстракту трави герані болотної на систему зсідання крові. Встановлено, що протягом 20-ти денного введення досліджуваного екстракту підвищувалася активність тромбоцитарної ланки гемостазу (підвищувалася кількість тромбоцитів, їх агрегаційна здатність та ретракція кров’яного згустку). На фоні введення сухого екстракту трави герані болотної знижувалися показники I та III фази коагуляційного гемостазу (активований частковий тромбопластиновий час, тромбіновий час), підвищувався протромбіновий час та рівень фібриногену. Отримані дані свідчать про вплив сухого екстракту трави герані болотної на «внутрішній» шлях активації зсідання крові за рахунок прискорення формування тромбопластину, що призводить до гіперкоагуляції.Механізм антигеморагічної дії сухого екстракту трави герані болотної обумовлений наявністю у складі біологічно активних речовин (дубильних речовин, флавоноїдів, елагової, галової та аскорбінової органічних кислот), які діють комплексно як на судинно-тромбоцитарний, так і на коагуляційний гемостаз за рахунок ущільнення та збільшення міцності судинно-тканинних бар’єрів, Р-вітамінної активності – здатності зменшувати проникність та ламкість капілярів, підвищувати їх резистентність.Ключові слова: сухий екстракт трави герані болотної, тромбоцити, зсідання крові, фенольні сполуки. РефератВЛИЯНИЕ СУХОГО ЭКСТРАКТА ТРАВЫ ГЕРАНИ БОЛОТНОЙ НА СИСТЕМУ СВЕРТЫВАНИЯ КРОВИ. Статья посвящена исследованию механизма действия сухого экстракта травы герани болотной на систему свертывания крови. Установлено, что на протяжении 20-ти дневного введения исследуемого экстракта повышалась активность тромбоцитарного звена гемостаза (увеличивалось количество тромбоцитов, их агрегационная способность и ретракция кровяного сгустка). На фоне введения сухого экстракта травы герани болотной снижались показатели I и III фазы коагуляционного гемостаза (активированное частичное тромбопластиновое время, тромбиновое время), повышалось  протромбиновое время и уровень фибриногена. Полученные данные свидетельствуют о влиянии сухого экстракта травы герани болотной на «внутренний» путь активации свертывания крови за счет ускорения формирования тромбопластина, что приводит к гиперкоагуляции.Механизм антигеморрагического действия сухого экстракта травы герани болотной обусловлен наличием в составе биологически активных соединений (дубильных веществ, флавоноидов, эллаговой, галловой и аскорбиновой органических кислот), которые действуют комплексно как на сосудисто-тромбоцитарный, так и на коагуляционный гемостаз за счет уплотнения и увеличения прочности сосудисто-тканевых барьеров, Р-витаминной активности – способности уменьшать проницаемость и ломкость капилляров, повышать их резистентность.Ключевые слова: сухой экстракт травы герани болотной, тромбоциты, свертывание крови, фенольные соединения

SuperConga: an open-source framework for mesoscopic superconductivity

We present SuperConga, an open-source framework for simulating equilibrium properties of unconventional and ballistic singlet superconductors, confined to two-dimensional (2D) mesoscopic grains in a perpendicular external magnetic field, at arbitrary low temperature. It aims at being both fast and easy to use, enabling research without access to a computer cluster, and visualization in real-time with OpenGL. The core is written in C++ and CUDA, exploiting the embarrassingly parallel nature of the quasiclassical theory of superconductivity by utilizing the parallel computational power of modern GPUs. The framework self-consistently computes both the superconducting order-parameter and the induced vector potential, and finds the current density, free energy, induced flux density, local density of states, as well as the magnetic moment. A user-friendly Python frontend is provided, enabling simulation parameters to be defined via intuitive configuration files, or via the command-line interface, without requiring a deep understanding of implementation details. For example, complicated geometries can be created with relative ease. The framework ships with simple tools for analyzing and visualizing the results, including an interactive plotter for spectroscopy. An overview of the theory is presented, as well as examples showcasing the framework's capabilities and ease of use. The framework is free to download from https://gitlab.com/superconga/superconga, which also links to the extensive user manual, containing even more examples, tutorials and guides.Comment: Accepted version. Review-style article, 31 pages and link to software at https://gitlab.com/superconga/supercong

Number of Confirmation Blocks for Bitcoin and GHOST Consensus Protocols on Networks with Delayed Message Delivery

A specific number of transaction confirmation blocks determines average time of receiving and accepting payments at cryptocurrencies, and the shortest confirmation time for the same level of blockchain security provides the best user properties. Existing papers on transaction confirmation blocks for Bitcoin use implicit assumption of prompt spreading of Bitcoin blocks over the network (that is not always the case for the real world conditions). The newer publications with rigorous analysis and proofs of Bitcoin blockchain properties that take into account network delays provide asymptotic estimates, with no specific numbers for transaction confirmation blocks. We propose three methods for determination of required number of confirmation blocks for Bitcoin and GHOST on networks with delayed message delivery with different models that take into account the possibility of faster adversarial node syncronization. For the GHOST we propose the first (to our knowledge) strict theoretical method that allows to get required number of confirmation blocks for a given attacker’s hashrate and attack success probability

Pharmacological sequestration of mitochondrial calcium uptake protects against dementia and β-amyloid neurotoxicity

All forms of dementia including Alzheimer's disease are currently incurable. Mitochondrial dysfunction and calcium alterations are shown to be involved in the mechanism of neurodegeneration in Alzheimer's disease. Previously we have described the ability of compound Tg-2112x to protect neurons via sequestration of mitochondrial calcium uptake and we suggest that it can also be protective against neurodegeneration and development of dementia. Using primary co-culture neurons and astrocytes we studied the effect of Tg-2112x and its derivative Tg-2113x on β-amyloid-induced changes in calcium signal, mitochondrial membrane potential, mitochondrial calcium, and cell death. We have found that both compounds had no effect on β-amyloid or acetylcholine-induced calcium changes in the cytosol although Tg2113x, but not Tg2112x reduced glutamate-induced calcium signal. Both compounds were able to reduce mitochondrial calcium uptake and protected cells against β-amyloid-induced mitochondrial depolarization and cell death. Behavioral effects of Tg-2113x on learning and memory in fear conditioning were also studied in 3 mouse models of neurodegeneration: aged (16-month-old) C57Bl/6j mice, scopolamine-induced amnesia (3-month-old mice), and 9-month-old 5xFAD mice. It was found that Tg-2113x prevented age-, scopolamine- and cerebral amyloidosis-induced decrease in fear conditioning. In addition, Tg-2113x restored fear extinction of aged mice. Thus, reduction of the mitochondrial calcium uptake protects neurons and astrocytes against β-amyloid-induced cell death and contributes to protection against dementia of different ethology. These compounds could be used as background for the developing of a novel generation of disease-modifying neuroprotective agents

Techniques of blood sampling for detection of African swine fever virus in wild boar and domestic pigs in the field conditions

It is thought that due to the high virulence of the African swine fever virus its circulation in the Russian Federation is accompanied by a low seroprevalence. However taking into account a long-term ASF unfavourable situation, the introduction of the virus into the wild boar population, and the occurrence of attenuated viral variants, the significance of serological testing aimed at the detection of viral antibodies is increasing. To collect field samples of biological material from animals for molecular genetic, virological, and serological tests, filter paper, as well as swabs, can be used. The specificity and sensitivity of enzyme-linked immunosorbent assay when testing blood absorbed by filter paper are worse than those shown when testing sera, but they allow effective detection of African swine fever virus antibodies. It was demonstrated that blood absorbed on filter paper can be used for the immunoblot analysis, but the optimum performance could be achieved when the immunoperoxidase technique in combination with samples, taken by swabs was used. When comparing results of enzyme-linked immunosorbent assay performed on sera collected from domestic pigs (infected with ASFV isolates Antonovo 07/14 and Sobinka 07/15), and blood from ear veins absorbed on filter paper the sensitivity was 88.9%, specificity – 90.6%. However, the use of the immunoperoxidase technique for testing blood from swabs showed 100% coincidence with ELISA, while testing of sera with immunoperoxidase technique was superior to ELISA in sensitivity. This means blood sampling using swabs may be recommended for tests after proper validation. This technique can be especially useful for collecting data about infected wild boars because effective eradication strategies are impossible without such data