RNase footprinting demonstrates antigenomic hepatitis delta virus ribozyme structural rearrangement as a result of self-cleavage reaction

<p>Abstract</p> <p>Background</p> <p>Hepatitis delta virus (HDV) is a satellite virus of hepatitis B. During viral replication the 1700-nucleotide-long genomic RNA and its complement, the antigenomic RNA, undergo self-cleavage catalyzed by internal ribozyme motifs that are essential for propagation of the virus <it>in vivo</it>. These self-cleavage activities are provided by 85-nucleotide-long sequence elements, the genomic and antigenomic forms of HDV ribozyme. Recently four permuted variants of the antigenomic HDV <it>cis</it>-ribozyme with a self-cleavage site located at the 5' proximity, in the middle, or nearby the 3' end of the molecule were constructed and synthesized. These constructs exhibit equal activity, a bi-phasic kinetics of self-cleavage reaction and reaction products with low and high stability. We have used ribonuclease probing to footprint the structures of uncleaved and post-cleaved forms of the antigenomic HDV ribozymes in solution. Uncleaved ribozymes, associated and individual products of the self-cleavage reaction were analyzed using ribonuclease and Fe(II)-EDTA protection assays to reveal the differences in the structure of pre- and post-cleaved antigenomic HDV ribozyme in solution.</p> <p>Findings</p> <p>Our findings demonstrate that a significant conformational change accompanies catalysis in the antigenomic HDV ribozyme in solution, in contrast to minor conformational switch observed in crystals of the genomic form. This study indicates that changes in the structure of stem P1 and stem P4 are minor, those of the region ascribed to stem P2, stem P3 and loop l3 are dramatic, while stem P1.1 results from the self-cleavage reaction.</p> <p>Conclusion</p> <p>Our data agree with the structure of post-cleaved and disagree with that of pre-cleaved forms of HDV ribozyme published elsewhere.</p

Pilot Project «All-Russian Registry of Patients with Severe Bronchial Asthma.» The First Results in a Children’s Group of Patients (Moscow’s Observation Program)

The article presents the first results of the pilot observation program «The All-Russian Severe Asthma Patient Registry» which was started in Moscow. Objectives. The objective of this initiative is the accumulation of clinical data on patients with severe bronchial asthma in the Russian Federation. Methods. The chosen method was a registry, the rights holders of which were 3 professional associations — Interregional Public Organization «Russian Respiratory Society», Public Organization «Union of Pediatricians of Russia», All-Russian Public Organization «Association of Allergologists and Clinical Immunologists». Results. The results of the pilot project are presented by the data analysis of electronic case report forms of 36 children (totally, the project included 100 patients, 64 adults and 36 children) enrolled in the program from June to December 2016. Using the registry, a detailed analysis of the clinical characteristics of a group of children with severe atopic bronchial asthma was carried out, the results of a pharmacoepidemiological evaluation of therapy were given. Obtained by the researchers, a high frequency of the assignment of a genetically engineered biologic drug of omalizumab meets the international recommendations but does not reflect the all-Russian reality and can be explained by inclusion in the registry of pediatric patients observed only in the Federal State Autonomous Institution «National Scientific and Practical Center of Children’s Health» of the Ministry of Health of the Russian Federation. Conclusion. To determine true indicators that characterize bronchial asthma in children in the Russian Federation it is necessary, undoubtedly, to expand the geography of project participants

Пилотный проект «Общероссийский регистр пациентов с тяжелой бронхиальной астмой». Первые результаты в детской группе пациентов (наблюдательная программа г. Москвы)

The article presents the first results of the pilot observation program «The All-Russian Severe Asthma Patient Registry» which was started in Moscow. Objectives. The objective of this initiative is the accumulation of clinical data on patients with severe bronchial asthma in the Russian Federation. Methods. The chosen method was a registry, the rights holders of which were 3 professional associations — Interregional Public Organization «Russian Respiratory Society», Public Organization «Union of Pediatricians of Russia», All-Russian Public Organization «Association of Allergologists and Clinical Immunologists». Results. The results of the pilot project are presented by the data analysis of electronic case report forms of 36 children (totally, the project included 100 patients, 64 adults and 36 children) enrolled in the program from June to December 2016. Using the registry, a detailed analysis of the clinical characteristics of a group of children with severe atopic bronchial asthma was carried out, the results of a pharmacoepidemiological evaluation of therapy were given. Obtained by the researchers, a high frequency of the assignment of a genetically engineered biologic drug of omalizumab meets the international recommendations but does not reflect the all-Russian reality and can be explained by inclusion in the registry of pediatric patients observed only in the Federal State Autonomous Institution «National Scientific and Practical Center of Children’s Health» of the Ministry of Health of the Russian Federation. Conclusion. To determine true indicators that characterize bronchial asthma in children in the Russian Federation it is necessary, undoubtedly, to expand the geography of project participants.В статье представлены первые результаты пилотной наблюдательной программы «Общероссийский регистр пациентов с тяжелой бронхиальной астмой», стартовавшей в Москве. Цель данной инициативы — аккумуляция клинических сведений о больных тяжелой бронхиальной астмой в Российской Федерации. Методы. Методом был выбран регистр, правообладателями которого стали 3 профессиональные ассоциации — Межрегиональная общественная организация «Российское респираторное общество», Общественная организация «Союз педиатров России», Всероссийская общественная организация «Ассоциация аллергологов и клинических иммунологов». Результаты пилотного проекта, представлены анализом данных электронных индивидуальных регистрационных карт 36 пациентов детского возраста (всего в проект было включено 100 больных, из них 64 взрослых и 36 детей), прошедших регистрацию в программе с июня по декабрь 2016 г. С использованием регистра проведен подробный анализ клинической характеристики группы детей с тяжелой атопической бронхиальной астмой, даны результаты фармакоэпидемиологической оценки терапии. Полученная исследователями высокая частота назначения генно- инженерного биологического препарата омализумаба соответствует международным рекомендациям, однако не отражает общероссийской действительности и может быть объяснена включением в регистр пациентов детского возраста, наблюдающихся только в ФГАУ «ННПЦЗД» Минздрава России. Заключение. Для определения истинных показателей, характеризующих бронхиальную астму у детей в Российской Федерации, несомненно, необходимо расширение географии участников проекта.

Automatic enrichment of word lists with morphological derivatives for computer-assisted learning of vocabulary: Design-based research

Vocabulary is one of the biggest challenges in learning a second language. Computer-assisted language learning (CALL) of new vocabulary items is an effective and widely used approach to this challenge. One CALL application that has been empirically demonstrated to be highly effective is Linguatorium Lexis. Unlike off-the-shelf vocabulary learning software (e.g., bundled with textbooks), Lexis gives the instructor full control over the contents of word lists and the parameters of student experience. Additionally, Lexis leverages natural language processing (NLP) and adaptive learner modeling to generate more effective exercises. One downside of the approach of the Lexis system is that the instructors are required to spend considerable time on entering word lists: Each word needs to be entered along with its part of speech, WordNet synsets, images, usage examples, etc. While all these elements are needed for exercise generation, increased instructor time commitment negatively affects practicality. To address this limitation, this paper presents the two iterations of a design-based research (DBR) study wherein Linguatorium Lexis is extended with automatically generated activities that present the learners with morphological derivatives of the words included in teacher-provided word lists. With the proposed innovation, the teacher only needs to enter a single word from a “word family,” allowing the system to deliver fully automatic instruction on this word’s derivatives. NLP techniques are used to retrieve example sentences from a corpus and to generate exercises, which are then delivered to the user within the Linguatorium Lexis system. The computational performance of the proposed NLP techniques is evaluated, and the practicality and the language learning potential of the proposed exercise are addressed. The thesis concludes with design principles for developing such activity types