Evaluation of Bovine Embryo Biopsy Techniques according to Their Ability to Preserve Embryo Viability

The purpose of this research was to evaluate three embryo biopsy techniques used for preimplantation genetic diagnosis (PGD) in cattle and to recommend the least invasive one for current use, especially when PGD is followed by embryo cryopreservation. Three hundred bovine embryos were biopsied by either one of the needle, aspiration or microblade method, and then checked for viability by freezing/thawing and transplantation to recipient cows. The number of pregnancies obtained after the transfer of biopsied frozen/thawed embryos was assessed 30 days later using ultrasounds. The results were significantly different between the three biopsy methods: the pregnancy rate was of 57% in cows that received embryos biopsied by needle, 43% in cows that received embryos biopsied by aspiration, and 31% in cows that received embryos biopsied by microblade. Choosing an adequate biopsy method is therefore of great importance in embryos that will undergo subsequent cryopreservation, as it significantly influences their viability after thawing

Белково-липидный состав пыльцы березы бородавчатой (Betula verrucosa) и ее антиоксидантная активность в зависимости от места произрастания

Pollen has various effects on the human body. In order to study and compare the biological activity of the mature pollen grains of Betula verrucosa Ehrh. we investigated the protein-lipid composition and total antioxidant activity (TAA) of 10 samples from different habitats in the territory of Ukraine and the Slovak Republic. The collection sites are near highways and apartment blocks, as well as a nature reserve, forest and botanical garden. The protein content was determined by the Kjeldahl method. A chromatographic analysis of fatty acids from lipids was performed using a “Cvet 500” gas chromatograph, equipped with a flame-ionization detector in the isothermal mode. The bioactivity of aqueous, ethanol and methanol extracts of pollen grains was evaluated by the DPPH free radical scavenging method (2,2-diphenyl-1-picrylhydrazyl) by means spectrophotometry in vitro. The protein content of the pollen of B. verrucosa ranged from 17.9% to 25.6%, depending on the habitat. Unsaturated fatty acids were found in higher amounts than saturated fatty acids. The profile of fatty acids indicates a higher content of palmitic (33.9%), oleic (29.5%) and linoleic (27.8%) acids and a low content of arachidonic (0.4%) and pentadecanoic (0.8%) acids. We also established that silver birch pollen is characterized by high antioxidant activity. The measured value of TAA for aqueous pollen extracts was within 74.8–85.5%. For the ethanol extracts it was quantified within 60.3–95.0% and for the methanol extracts – 46.1–92.6%. The Tukey test was used to determine the differences between the means at a level of P < 0.05. A strong correlation coefficient (0.70) was defined between the protein content and the TAA of aqueous extracts. In general, the Ukrainian and Slovak samples of pollen differ in the fatty acid composition of lipids and aqueous and ethanol TAA extracts. Pollen of B. verrucosa should be used for diagnostic, therapeutic and prophylactic purposes as close as possible to the place of origin. Исследованы белковый и липидный состав и биологическая активность 10 образцов пыльцы Betula verrucosa Ehrh. из разных мест произрастания на территории Украины и Словакии. Определено содержание белков (17,9–25,6%) и 8 жирных кислот (с числом углеродных атомов от 14 до 20) в составе липидов. Выявлено преобладание ненасыщенных жирных кислот (58,6%) с доминированием пальмитиновой (33,9%), олеиновой (29,5%) и линолевой (27,8%). Оценена общая антиоксидантная активность водных, этаноловых и метаноловых экстрактов пыльцы березы бородавчатой с использованием свободного стабильного радикала дифенил­пикрилгидразила колориметрически в реакции in vitro. Установлены статистически достоверные различия между образцами как внутри украинских и словацких генотипов, так и между ними. Рассматриваются факторы влияния на вариации белково-липидного состава пыльцы и ее биологической активности.Исследованы белковый и липидный состав и биологическая активность 10 образцов пыльцы Betula verrucosa Ehrh. из разных мест произрастания на территории Украины и Словакии. Определено содержание белков (17,9–25,6%) и 8 жирных кислот (с числом углеродных атомов от 14 до 20) в составе липидов. Выявлено преобладание ненасыщенных жирных кислот (58,6%) с доминированием пальмитиновой (33,9%), олеиновой (29,5%) и линолевой (27,8%). Оценена общая антиоксидантная активность водных, этаноловых и метаноловых экстрактов пыльцы березы бородавчатой с использованием свободного стабильного радикала дифенил­пикрилгидразила колориметрически в реакции in vitro. Установлены статистически достоверные различия между образцами как внутри украинских и словацких генотипов, так и между ними. Рассматриваются факторы влияния на вариации белково-липидного состава пыльцы и ее биологической активности

Term-BLAST-like alignment tool for concept recognition in noisy clinical texts.

MOTIVATION: Methods for concept recognition (CR) in clinical texts have largely been tested on abstracts or articles from the medical literature. However, texts from electronic health records (EHRs) frequently contain spelling errors, abbreviations, and other nonstandard ways of representing clinical concepts. RESULTS: Here, we present a method inspired by the BLAST algorithm for biosequence alignment that screens texts for potential matches on the basis of matching k-mer counts and scores candidates based on conformance to typical patterns of spelling errors derived from 2.9 million clinical notes. Our method, the Term-BLAST-like alignment tool (TBLAT) leverages a gold standard corpus for typographical errors to implement a sequence alignment-inspired method for efficient entity linkage. We present a comprehensive experimental comparison of TBLAT with five widely used tools. Experimental results show an increase of 10% in recall on scientific publications and 20% increase in recall on EHR records (when compared against the next best method), hence supporting a significant enhancement of the entity linking task. The method can be used stand-alone or as a complement to existing approaches. AVAILABILITY AND IMPLEMENTATION: Fenominal is a Java library that implements TBLAT for named CR of Human Phenotype Ontology terms and is available at https://github.com/monarch-initiative/fenominal under the GNU General Public License v3.0

Thiol-Mediated Uptake of a Cysteine-Containing Nanobody for Anticancer Drug Delivery

The identification of tumor-specific biomarkers is one of the bottlenecks in the development of cancer therapies. Previous work revealed altered surface levels of reduced/oxidized cysteines in many cancers due to overexpression of redox-controlling proteins such as protein disulfide isomerases on the cell surface. Alterations in surface thiols can promote cell adhesion and metastasis, making thiols attractive targets for treatment. Few tools are available to study surface thiols on cancer cells and exploit them for theranostics. Here, we describe a nanobody (CB2) that specifically recognizes B cell lymphoma and breast cancer in a thiol-dependent manner. CB2 binding strictly requires the presence of a nonconserved cysteine in the antigen-binding region and correlates with elevated surface levels of free thiols on B cell lymphoma compared to healthy lymphocytes. Nanobody CB2 can induce complement-dependent cytotoxicity against lymphoma cells when functionalized with synthetic rhamnose trimers. Lymphoma cells internalize CB2 via thiol-mediated endocytosis which can be exploited to deliver cytotoxic agents. CB2 internalization combined with functionalization forms the basis for a wide range of diagnostic and therapeutic applications, rendering thiol-reactive nanobodies promising tools for targeting cancer

Espon-Interstrat. Espon in Integrated Territorial Strategies.

The INTERSTRAT project’s overall aim is “to encourage and facilitate the use of ESPON 2013 Programme findings in the creation and monitoring of Integrated Territorial Development Strategies (ITDS) and to support transnational learning about the actual and potential contribution of ESPON to integrated policy-making.” We defined integrated territorial development as ‘the process of shaping economic, social and environmental change through spatially sensitive policies and programmes’

Полиненасыщенные жирные кислоты как универсальные эндогенные биорегуляторы

Studying of a physiological role of natural polyunsaturated fatty acids (PUFAs) at a new step of development of scientific and technical progress is actual. The present review is devoted questions of biosynthesis PUFAs, their regulatory functions, distribution in tissues lipids of an animal organism. In the review new effective methods of isolation and identification of unsaturated fatty acids and their metabolites from biological objects, such as extraction under pressure, a capillary nuclear magnetic resonance, a combination of a liquid chromatography and mass spectrometry also are considered.Изучение физиологической роли природных полиненасыщенных жирных кислот (ПНЖК) на новой ступени развития научно-технического прогресса является весьма актуальным. Настоящий обзор посвящен вопросам биосинтеза ПНЖК, их регуляторных функций, распределения в липидах тканей животного организма. В обзоре также рассмотрены новые эффективные методы выделения и идентификации ненасыщенных жирных кислот и их метаболитов из биообъектов, такие как экстракция под давлением, капиллярный ЯМР, жидкостная хроматография в сочетании с масс-спектрометрией

Specific features of designing a database for neuro-oncological 3D MRI images to be used in training artificial intelligence

The research was aimed at analyzing current approaches to the organization and design methodology of visualization database built on the basis of computer vision. Such approaches are necessary for effective development of diagnostic systems using artificial intelligence (AI). A training data set of high quality is a mandatory prerequisite for that. Material and methods. The paper presents the technology for designing an annotated database (SBT Dataset) that contains about 1000 clinical cases based on the archived data acquired by the Federal Neurosurgical Center, Novosibirsk, Russia including data on patients with astrocytoma, glioblastoma, meningioma, neurinoma, and patients with metastases of somatic tumors. Each case is represented by a preoperative MRI. The Results and Discussion. The dataset was built (SBT Dataset) containing segmented 3D MRI images of 5 types of brain tumors with 991 verified observations. Each case is represented by four MRI sequences T1-WI, T1C (with Gd-contrast), T2-WI and T2-FLAIR with histological and histochemical postoperative confirmation. Tumors segmentation with verification of the tumor core elements boundaries and perifocal edema was approved by two certified experienced neuroradiologists. Conclusion. The database built during the research is comparable in its volume and quality (verification level) with the state-of-the-art databases. The methodological approaches proposed in this paper were focused on designing the high-quality medical computer vision systems. The database was used to create artificial intelligence systems with the “physician assistant” functions for preoperative MRI diagnostics in neurosurgery

GA4GH Phenopackets: A Practical Introduction.

The Global Alliance for Genomics and Health (GA4GH) is developing a suite of coordinated standards for genomics for healthcare. The Phenopacket is a new GA4GH standard for sharing disease and phenotype information that characterizes an individual person, linking that individual to detailed phenotypic descriptions, genetic information, diagnoses, and treatments. A detailed example is presented that illustrates how to use the schema to represent the clinical course of a patient with retinoblastoma, including demographic information, the clinical diagnosis, phenotypic features and clinical measurements, an examination of the extirpated tumor, therapies, and the results of genomic analysis. The Phenopacket Schema, together with other GA4GH data and technical standards, will enable data exchange and provide a foundation for the computational analysis of disease and phenotype information to improve our ability to diagnose and conduct research on all types of disorders, including cancer and rare diseases

Term-BLAST-like alignment tool for concept recognition in noisy clinical texts

Motivation: Methods for concept recognition (CR) in clinical texts have largely been tested on abstracts or articles from the medical literature. However, texts from electronic health records (EHRs) frequently contain spelling errors, abbreviations, and other nonstandard ways of representing clinical concepts. Results: Here, we present a method inspired by the BLAST algorithm for biosequence alignment that screens texts for potential matches on the basis of matching k-mer counts and scores candidates based on conformance to typical patterns of spelling errors derived from 2.9 million clinical notes. Our method, the Term-BLAST-like alignment tool (TBLAT) leverages a gold standard corpus for typographical errors to implement a sequence alignment-inspired method for efficient entity linkage. We present a comprehensive experimental comparison of TBLAT with five widely used tools. Experimental results show an increase of 10% in recall on scientific publications and 20% increase in recall on EHR records (when compared against the next best method), hence supporting a significant enhancement of the entity linking task. The method can be used stand-alone or as a complement to existing approaches. Availability and implementation: Fenominal is a Java library that implements TBLAT for named CR of Human Phenotype Ontology terms and is available at https://github.com/monarch-initiative/fenominal under the GNU General Public License v3.0