Методические аспекты выделения семантических отношений для автоматической генерации специализированных тезаурусов и их оценки

The paper is devoted to analysis of methods for automatic generation of a specialized thesaurus. The main algorithm of generation consists of three stages: selection and preprocessing of a text corpus, recognition of thesaurus terms, and extraction of relations among terms. Our work is focused on exploring methods for semantic relation extraction. We developed a test bench that allow to test well-known algorithms for extraction of synonyms and hypernyms. These algorithms are based on different relation extraction techniques: lexico-syntactic patterns, morpho-syntactic rules, measurement of term information quantity, general-purpose thesaurus WordNet, and Levenstein distance. For analysis of the result thesaurus we proposed a complex assessment that includes the following metrics: precision of extracted terms, precision and recall of hierarchical and synonym relations, and characteristics of the thesaurus graph (the number of extracted terms and semantic relationships of different types, the number of connected components, and the number of vertices in the largest component). The proposed set of metrics allows to evaluate the quality of the thesaurus as a whole, reveal some drawbacks of standard relation extraction methods, and create more efficient hybrid methods that can generate thesauri with better characteristics than thesauri generated by using separate methods. In order to illustrate this fact, one of such hybrid methods is considered in the paper. It combines the best standard algorithms for hypernym and synonym extraction and generates a specialized medical thesaurus. The hybrid method leaves the thesaurus quality on the same level and finds more relations between terms than well-known algorithms.Работа посвящена анализу методов автоматической генерации специализированного тезауруса. Основной алгоритм генерации состоит из трех шагов: отбор и предварительная обработка корпуса текстов, формирование множества терминов для включения в тезаурус и выделение связей между терминами тезауруса. Данное исследование сфокусировано на изучении методов выделения семантических связей, для чего авторами был разработан программный стенд, который позволяет протестировать распространенные алгоритмы выделения гиперонимов и синонимов, использующие в своей работе лексико-синтаксические шаблоны, морфо-синтаксические правила, количество информации терминов, тезаурус общего назначения WordNet и расстояние Левенштейна. Для анализа результирующего тезауруса, созданного на стенде, авторами была разработана комплексная оценка, содержащая следующие характеристики качества: точность выделения терминов, точность и полнота выделения синонимических и гиперонимических связей, а также метрики графа тезауруса (количество выделенных терминов, количество семантических связей различных типов, число компонент связности и число вершин в наибольшей компоненте). Предлагаемый набор метрик позволяет оценить качество тезауруса в целом, выявить отдельные недостатки стандартных методов выделения связей и построить более эффективные гибридные методы, генерирующие тезаурус с лучшими характеристиками по сравнению с тезаурусами, генерируемыми при использовании отдельных методов. Для иллюстрации данного факта в статье рассмотрен один из таких гибридных методов. Он комбинирует лучшие стандартные алгоритмы построения гиперонимических и синонимических связей и строит специализированный тезаурус в области медицины с тем же уровнем качества, что и другие методы, но с большим количеством связей между терминами

Molecular diagnostics of primary immunodeficiencies in Sverdlovsk region

The article presents the results of the work performed by the laboratory of molecular diagnostics at the Medical Center “Health Care of Mother and Child” for the diagnosis of primary immunodeficiency in Sverdlovsk region over 5 years. The laboratory was organized in 2009 to verify the diagnosis of monogenic hereditary diseases included in the Neonatal Screening Program in the Russian Federation, e.g., phenylketonuria, cystic fibrosis, classical galactosemia. Over time, the range of diagnosed nosologies expanded, and since 2014, the laboratory has included in studies of a new group of disorders, i.e., congenital errors of immunity. Every year the Regional Registry of patients with primary immunodeficiencies (PIDs) replenished by 20 to 70 persons, thus comprising 15 to 43% of the entire Russian Registry for these conditions. As of 03/01/2020, the registry of patients with a clinical diagnosis of “primary immunodeficiency” consisted of 526 people, more than half of them (275) being children under 18 years of age. According to the expert calculations, the frequency of detected PID cases in the Sverdlovsk region is 1:10 480 inhabitants, which indicates not only high level of the existing clinical immunology service, but also the high expected frequency of PID in the region. Until 2014, verification of the “primary immunodeficiency” diagnosis in the patients from Sverdlovsk region was traditionally carried out in Moscow clinics (Dmitry Rogachev National Medical Research Center of Pediatric Hematology, Oncology and Immunology, Moscow Research Centre for Medical Genetics). Over 6 years of cooperation between regional immunological service with the medical genetic center, 47 children received molecular genetic confirmation of the diagnosis of congenital immunity errors at the laboratory of Regional Medical Center “Health Care of Mother and Child”. The authors present the data of Regional Registry of patients, classified into nosological forms of immune-dependent pathology and provide a detailed description of diagnostic procedures for the patients with various PIDs. A deletion of chromosome 22 (Di Giorgi syndrome) was found in 43 people, mutations in the Btk gene (X-linked agammaglobulinemia) were revealed in 7 patients and 6 members of their families, Nijmegen syndrome was confirmed in 1 child, a familial case of ADA-deficiency, difficult for diagnostics, was decided. The results of the study encourage the authors for further expansion of the spectrum of detectable disorders diagnosis, and give a hope that development of regional laboratories at this level may improve the diagnostic algorithm for PID diagnostic procedures in Russia, i.e., from prenatal and neonatal screening to the development of gene therapy for certain forms of immune-dependent disorders

Разработка алгоритма измерения частоты пульса человека с помощью камеры мобильного телефона

Nowadays there exist many different ways to measure a person’s heart rate. One of them assumes the usage of a mobile phone built-in camera. This method is easy to use and does not require any additional skills or special devices for heart rate measurement. It requires only a mobile cellphone with a built-in camera and a flash. The main idea of the method is to detect changes in finger skin color that occur due to blood pulsation. The measurement process is simple: the user covers the camera lens with a finger and the application on the mobile phone starts catching and analyzing frames from the camera. Heart rate can be calculated by analyzing average red component values of frames taken by the mobile cellphone camera that contain images of an area of the skin.In this paper the authors review the existing algorithms for heart rate measurement with the help of a mobile phone camera and propose their own algorithm which is more efficient than the reviewed algorithms.В настоящее время существует большое количество различных способов измерения частоты пульса человека. Один из таких способов связан с использованием камеры мобильного телефона. Он удобен и прост с точки зрения пользователя и не требует дополнительных знаний или покупки специальных устройств для измерения пульса. Все, что необходимо, — это мобильный телефон со встроенной камерой и вспышкой. Основная идея данного способа заключается в том, чтобы детектировать изменения цвета кожи пальца руки, которые возникают из-за пульсации крови. Процесс измерения выглядит очень просто: пользователь прикладывает палец к камере, после чего приложение на мобильном телефоне начинает захватывать и анализировать кадры, полученные с камеры. Анализируя средние значения красной компоненты кадров с камеры мобильного телефона, содержащих изображение участка кожи, можно сделать вывод о частоте пульса.В данной статье авторы делают обзор существующих алгоритмов для измерения частоты пульса с помощью мобильного телефона и предлагают собственный алгоритм, который более эффективен, чем рассмотренные.

Алгоритм замещения агентов dataflow-сети на платформе Smart-M3

The paper presents an agent substitution algorithm for a dataflow network implemented on the Smart-M3 platform. Such a substitution allows to transfer control and computational context from an unexpectedly disconnected agent to a programmable substitute agent for the period of absence of the first agent in the network. It also guarantees integrity of the information flow, i.e. the functioning of all dependent services is not disrupted after the agent disconnection. When the agent returns to the network the reverse substitution occurs also with keeping integrity of the information flow. The paper gives a description of the dataflow network implementation and substitution mechanism structure on the Smart-M3 platform. The detailed description of the substitution algorithm including initialization, registration, and bidirectional substitution phases is given. The proposed substitution algorithm was implemented by the authors in the substitution mechanism as a part of the RedSIB semantic information broker on the Smart-M3 platform.Рассматривается алгоритм замещения агента dataflow-сети, реализованной на платформе Smart-M3. Такое замещение позволяет перенести управление и контекст вычислений от преждевременно отключившегося агента к программируемому агенту-заместителю на время отсутствия первого агента в сети. При этом гарантируется целостность информационных потоков, то есть функционирование всех зависимых сервисов не нарушается при отключении агента. При возвращении агента в сеть происходит обратное замещение также с сохранением целостности всех информационных потоков. Приведено описание реализации dataflow-сети и структуры механизма замещения агентов для платформы Smart-M3. Дано детальное описание алгоритма замещения, включающее процедуры инициализации, регистрации и двунаправленного замещения агентов. Предложенный алгоритм замещения реализован авторами в механизме замещения в брокере семантической информации RedSIB на платформе Smart-M3.

A clinical case of post-COVID-19 myoendocarditis and arrhythmic syndrome at the outpatient stage

Background: Infection with the SARS-CoV-2 virus entails the development of complications which affect the prognosis of the underlying disease. More than 40% of COVID-19 complications represent diseases of the cardiovascular system, most of which are the rhythm and conduction disturbances. In order to avoid these complications, it is necessary to detect cases of infection in a timely manner at the outpatient stage. Clinical case description: A 40-year-old patient came to the clinic with complaints of interruptions in the heart rhythm that appeared after the coronavirus infection. The laboratory examination (CBC) revealed signs of systemic inflammation (leukocytosis 12.6×109 U/l; erythrocyte sedimentation rate 18 mm/h, C-reactive protein 18 mg/l); the instrumental examination of the heart revealed the rhythm disturbances in the form of frequent ventricular ectopic activity and weakness of the SA node. The patient received propafenone (150 mg, 3 times a day) as a therapy with a positive effect. Against the background of improvement in the patient’s condition and despite the history of myocarditis and a positive result of enzyme immunoassay for antibodies to SARS-CoV-2 (IgG, 10 BAU/ml), the patient was prescribed immunization with the CoviVac vaccine. After the immunization, the condition worsening was observed in the form of an increase in the rhythm disturbances, which required an inpatient treatment. A clinical diagnosis of recurrent ventricular arrhythmia — ventricular extrasystole was established, and the therapy was corrected. The outcome was favorable. Conclusion: Myocarditis is one of the most common complications of SARS-CoV-2 and should be kept in mind at all stages of medical care. This clinical case demonstrates the importance of the correct diagnosis and treatment of post-COVID myocarditis, as well as the need to assess contraindications for SARS-CoV-2 vaccination in patients with cardiac complications

SURF1 knockout cloned pigs : early onset of a severe lethal phenotype

Leigh syndrome (LS) associated with cytochrome c oxidase (COX) deficiency is an early onset, fatal mitochondrial encephalopathy, leading to multiple neurological failure and eventually death, usually in the first decade of life. Mutations in SURF1, a nuclear gene encoding a mitochondrial protein involved in COX assembly, are among the most common causes of LS. LSSURF1 patients display severe, isolated COX deficiency in all tissues, including cultured fibroblasts and skeletal muscle. Recombinant, constitutive SURF1 12/ 12 mice show diffuse COX deficiency, but fail to recapitulate the severity of the human clinical phenotype. Pigs are an attractive alternative model for human diseases, because of their size, as well as metabolic, physiological and genetic similarity to humans. Here, we determined the complete sequence of the swine SURF1 gene, disrupted it in pig primary fibroblast cell lines using both TALENs and CRISPR/Cas9 genome editing systems, before finally generating SURF1 12/ 12 and SURF1 12/+ pigs by Somatic Cell Nuclear Transfer (SCNT). SURF1 12/ 12 pigs were characterized by failure to thrive, muscle weakness and highly reduced life span with elevated perinatal mortality, compared to heterozygous SURF1 12/+ and wild type littermates. Surprisingly, no obvious COX deficiency was detected in SURF1 12/ 12 tissues, although histochemical analysis revealed the presence of COX deficiency in jejunum villi and total mRNA sequencing (RNAseq) showed that several COX subunit-encoding genes were significantly down-regulated in SURF1 12/ 12 skeletal muscles. In addition, neuropathological findings, indicated a delay in central nervous system development of newborn SURF1 12/ 12 piglets. Our results suggest a broader role of sSURF1 in mitochondrial bioenergetics

Диагностика расслаивающей аневризмы аорты в условиях многопрофильного стационара

Рассмотрена проблема ранней диагностики расслаивающей аневризмы аорты (АА) в многопрофильном стационаре, продемонстрированы преимущества командной работы, проанализирована информационная значимость диагностических методов по данным литературы за 2014– 2017 гг. На примере клинического случая успешной ранней диагностики и хирургического лечения расслаивающей АА у пациента доказано, что внезапная боль в грудной клетке, независимо от локализации, у лиц старше 40 лет, особенно мужчин, требует дифференциальной диагностики для исключения острых кардиоваскулярных состояний специалистами любых профилей. Дополнительное обследование пациента выявило факторы риска расслаивающей АА: синдром дисплазии соединительной ткани и артериальную гипертензию. Ишемические изменения ЭКГ в сочетании с периодической болью в грудной клетке направили поиск в сторону острого коронарного синдрома, КТ-ангиография позволила выявить другое жизнеугрожающее состояние — расслаивающую АА и провести своевременное хирургическое лечение.Acute aortic dissection (AD) is one of important and crucial clinical problem due to difficulties of earlier diagnosis and high rate of severe adverse outcomes. It is known as part of acute aortic syndrome also including intramural hematoma, penetrating atherosclerotic ulcer, traumatic aortic injury, and aortic rupture. Acute AD is defined as disruption of the medial layer provoked by intramural bleeding, resulting in separation of the aortic wall layers and subsequent formation of a true lumen and a false lumen with or without communication. In most cases, an intimae tear is the initiating condition, resulting in tracking of the blood in a dissection plane within the media. The article draws the attention of specialists to the problem of optimizing the diagnosis of the AD in a multidisciplinary hospital and demonstrates the advantages of the teamwork of related specialists, provides an analysis of the information significance of diagnostic methods according to literature data for 2014–2017, and the clinical case of successful early diagnosis and complex, including surgical, treatment of AD in a young patient. The clinical case emphasizes that sudden pain in the chest, regardless of its location, in individuals over 40 years, especially in men, requires careful differential diagnosis to exclude acute cardiovascular conditions by specialists of any profile. Comprehensive examination and treatment of the patient helped to identify the RFs for AD: connective tissue dysplasia syndrome and hypertension. Ischemic type of ECG changes in the in combination with periodic chest pain sent a diagnostic opinion towards acute coronary syndrome, however an additional examination by a team of specialists of a multidisciplinary hospital revealed another acute life-threatening condition — AD, and to do surgical treatment timely

Deficient Induction Response in a Xenopus Nucleocytoplasmic Hybrid

Defects in induction signaling and response underlie the nucleocytoplasmic incompatibility between two evolutionarily distant frog species, while specific treatments partially restore this response in explants and whole embryos

Analysis of Imprinted Gene Expression in Normal Fertilized and Uniparental Preimplantation Porcine Embryos

In the present study quantitative real-time PCR was used to determine the expression status of eight imprinted genes (GRB10, H19, IGF2R, XIST, IGF2, NNAT, PEG1 and PEG10) during preimplantation development, in normal fertilized and uniparental porcine embryos. The results demonstrated that, in all observed embryo samples, a non imprinted gene expression pattern up to the 16-cell stage of development was common for most genes. This was true for all classes of embryo, regardless of parental-origins and the direction of imprint. However, several differentially expressed genes (H19, IGF2, XIST and PEG10) were detected amongst the classes at the blastocyst stage of development. Most interestingly and despite the fact that maternally and paternally expressed genes should not be expressed in androgenones and parthenogenones, respectively, both uniparental embryos expressed these genes when tested for in this study. In order to account for this phenomenon, we compared the expression patterns of eight imprinted genes along with the methylation status of the IGF2/H19 DMR3 in haploid and diploid parthenogenetic embryos. Our findings revealed that IGF2, NNAT and PEG10 were silenced in haploid but not diploid parthenogenetic blastocysts and differential methylation of the IGF2/H19 DMR3 was consistently observed between haploid and diploid parthenogenetic blastocysts. These results appear to suggest that there exists a process to adjust the expression status of imprinted genes in diploid parthenogenetic embryos and that this phenomenon may be associated with altered methylation at an imprinting control region. In addition we believe that imprinted expression occurs in at least four genes, namely H19, IGF2, XIST and PEG10 in porcine blastocyst stage embryos