Опыт использования системы «ГиперМетод» при очной форме обучения

Current paper explain the experience of using the "HyperMethod" system at the full-time tuition in one semester of 2012-2013 academic year. The experience was gained when teaching different disciplines and when teaching for students with different levels of training. Authors believe that this information can be useful both future users and the team providing technical support.В работе изложен опыт использования системы «ГиперМетод» при очном обучении в 1 семестре 2012-2013 учебного года. Опыт приобретен при преподавании различных учебных дисциплин и при обучении различных по уровню подготовки студентов. Авторы считают, что данная публикация может быть полезна как будущим пользователям, так и коллективу, обеспечивающему техническую поддержку

Genome-wide analysis of nuclear magnetic resonance metabolites revealed parent-of-origin effect on triglycerides in medium very low-density lipoprotein in PTPRD gene

The aim of the study was to explore the parent-of-origin effects (POEs) on a range of human nuclear magnetic resonance metabolites. Materials & methods: We search for POEs in 14,815 unrelated individuals from Estonian and Finnish cohorts using POE method for the genotype data imputed with 1000 G reference panel and 82 nuclear magnetic resonance metabolites. Results: Meta-analysis revealed the evidence of POE for the variant rs1412727 in PTPRD gene for the metabolite: triglycerides in medium very low-density lipoprotein. No POEs were detected for genetic variants that were previously known to have main effect on circulating metabolites. Conclusion: We demonstrated possibility to detect POEs for human metabolites, but the POEs are weak, and therefore it is hard to detect those using currently available sample sizes.Peer reviewe

Исследование острой токсичности монокатионного производного хлорина е6 – перспективного фотосенсибилизатора для антимикробной и противоопухолевой фотодинамической терапии

In this experimental work the acute toxicity of a chemically modified derivative of the natural pigment chlorophyll a called monocationic chlorin e6, which is a promising photosensitizer (PS) for antimicrobial and antitumor photodynamic therapy, was studied using white rats. The advantages of the PS under investigation are an intense absorption in the long-wavelength region of the visible spectrum, a sufficiently high quantum yield of singlet oxygen generation, pronounced amphiphilic properties along with an appropriate solubility in water, and a high level of photocytotoxic- ity in relation to both malignant HeLa cells and antibiotic-resistant hospital strains of E. сoli bacteria., P. aerugenosa and others. It has been shown that the value of LD50 of the considered PS can be calculated as the value of 100 mg/kg. In the reproduced experimental model of acute toxicity, pathomorphological changes in the vital organs of laboratory animals indicate a pronounced vasopathic effect of the drug with the development of cerebral edema and respiratory distress syndrome, which have become the main signs of thanatogenesis.На белых крысах изучены особенности острой токсичности химически модифицированного производного природного пигмента хлорофилла а монокатионного хлорина e6 – перспективного фотосенсибилизатора (ФС) для антимикробной и противоопухолевой фотодинамической терапии. Преимуществами ФС являются интенсивное поглощение в длинноволновой области видимого спектра, достаточно высокий квантовый выход генерации синглетного кислорода, выраженные амфифильные свойства наряду с хорошей растворимостью в воде и высокий уровень фотоцитотоксичности в отношении как злокачественных клеток линии HeLa, так и антибиотикорезистентных госпитальных штаммов бактерий E. coli, P. Aerugenosa и других. Величина ЛД50 для монокатионного хлорина e6 составляет 100 мг/кг массы тела. В воспроизведенной экспериментальной модели острой токсичности патоморфологические изменения жизненно важных органов лабораторных животных свидетельствуют о выраженном вазопатическом действии препарата с развитием отека головного мозга и респираторного дистресс-синдрома, ставшими основными звеньями танатогенеза

Artificial Sequences and Complexity Measures

In this paper we exploit concepts of information theory to address the fundamental problem of identifying and defining the most suitable tools to extract, in a automatic and agnostic way, information from a generic string of characters. We introduce in particular a class of methods which use in a crucial way data compression techniques in order to define a measure of remoteness and distance between pairs of sequences of characters (e.g. texts) based on their relative information content. We also discuss in detail how specific features of data compression techniques could be used to introduce the notion of dictionary of a given sequence and of Artificial Text and we show how these new tools can be used for information extraction purposes. We point out the versatility and generality of our method that applies to any kind of corpora of character strings independently of the type of coding behind them. We consider as a case study linguistic motivated problems and we present results for automatic language recognition, authorship attribution and self consistent-classification.Comment: Revised version, with major changes, of previous "Data Compression approach to Information Extraction and Classification" by A. Baronchelli and V. Loreto. 15 pages; 5 figure

ОСОБЕННОСТИ МОРФОЛОГИИ, БИОХИМИЧЕСКОГО СОСТАВА И ГЕНЕТИЧЕСКОГО ПОЛИМОРФИЗМА КИТАЙСКОЙ БРОККОЛИ – НОВОЙ ДЛЯ РОССИИ ОВОЩНОЙ КУЛЬТУРЫ

The results of estimation of growth and development parameters, SSR analysis, electron microscopic examination of the surface of pollen and seeds, biochemical composition (ascorbic acid, carotenoids, carotenes, macro- and microelements content in the stem part of plant) of 8 Chinese broccoli, Brassica oleracea var. alboglabra samples grown in the unheated greenhouse of the Central Siberian Botanical Garden SB RAS, Novosibirsk (54°49′33″ N, 83°06′34″ E) and phy- totron of N. I. Vavilov Institute of Plant Genetic Resources (VIR) have been presented. Through the study, the large surface cellularity of B.oleracea var. alboglabra (cv. “Siji Xianggu jie lan” [“SX”]) seeds was similar with seed coat surface of B.oleraceae var. capitata f. alba cv. "Slava". A scanning electron microscopic study of Chinese broccoli pollen (cv. “SX”) revealed the formation of colpate pollen with ellipsoidal shape with a size of 32.9 ± 0.76 x 17.8 ± 0.42 μm, characterized by foveolate ornamentation with a length-to-diameter ratio – 1.85.The duration of the period from emergence stage to thickening of a stalk and flower-bud formation of cv. “SX” continued for 49-54 days. Сlose correlation was established between the largest diameter of the stem and the length of the leaf petiole (r=0,87, p < 0,001) and between the length of the leaf petiole and the weight of the stem (r=0,77, p < 0,001). As a result of molecular screening of Chinese broccoli using 5 SSR markers (Na10D09, Ol12F02, Ra2E12, BC 7 и BC 65) the greatest polymorphism was in the test with the BC 7 marker - five alleles from 160 to 295 bp in size. In the “SX” variety single flowering (10%) occurred on 59 ... 63 day and mass flowering (75%) – on 65 ... 68 day. The stem part of B. oleracea var. alboglabra is a fairly good source of vitamin C, accumulating as much as 32-46 mg/100 g, and also increased concentration of K, Ca, Mg and Cu. At the end of the season the fruits, together with the phytomass of stems are well-seasoned for 3-4 weeks forming viable seeds with germination above 85% corresponding to the Russian state standard (GOST 32592-2013) for white cabbage seeds. Приведены результаты оценки параметров роста и развития, SSR анализа, электронно-микроскопического исследования поверхности пыльцы и семян, биохимического состава, содержания макро- и микроэлементов в стеблевой части растений 8 образцов китайской брокколи Brassica oleracea var. alboglabra, выращенных в условиях необогреваемой пленочной теплицы ЦСБС СО РАН, г. Новосибирск (54°49′33″ с.ш. 83°06′34″ в.д.) и фитотрона. При исследовании поверхности семенной кожуры (спермодермы) семян видов рода Brassica L. установлено сходство крупной ячеистости поверхности семян B.oleracea var. alboglabra (сортобразец “Siji Xianggu jie lan” (“SX”) с семенами B.oleraceae var. сapitata f. alba, сv. Слава. При электронно-микроскопическом исследовании пыльцы китайской брокколи (“SX”) отмечено формирование в пыльниках кольпатной пыльцы эллипсоидного очертания, размером 32,9±0,76 х 17,8±0,42 мкм, характеризующейся фовеолятной орнаментацией, с соотношением длины к диаметру 1,85. Продолжительность периода от всходов до технической спелости, характеризующейся утолщением стебля китайской брокколи (“SX”) и переходом растений к бутонизации, продолжался 49-54 суток. Установлена тесная корреляционная связь между наибольшим диаметром стебля и длиной черешка листа (r=0,87, p < 0,001), а также между длиной черешка листа и массой товарной части стебля (r=0,77, p < 0,001). В результате молекулярно-генетического скрининга 5 SSR маркерами (Na10D09, Ol12F02, Ra2E12, BC 7 и BC 65) наибольший полиморфизм был при скринировании исследуемого материала маркером BC 7 – пять аллелей размером от 160 до 295 п.н. У образца “SX” цветение единичное (10%) наступало на 59-63 сутки, массовое цветение (75%) – на 65-68 сутки. Стеблевая часть B. oleracea var. alboglabra является достаточно хорошим источником витамина С, накапливая 32-46 мг%, также отличаясь повышенной концентрацией K, Ca, Mg и Сu. В конце сезона плоды вместе со срезанной фитомассой стеблей в течение 3-4 недель хорошо дозариваются, формируя полноценные семена со всхожестью выше 85%, соответствуя стандарту (ГОСТ 32592-2013) для семян капусты белокочанной

An integrative analysis of endometrial steroid metabolism and transcriptome in relation to endometrial receptivity in in vitro fertilization patients

Objective: To study the relationship between the steroid concentration in the endometrium, in serum, and the gene expression level of steroid-metabolizing enzymes in the context of endometrial receptivity in in vitro fertilization (IVF) patients. Design: Case-control study of 40 IVF patients recruited in the SCRaTCH study (NTR5342), a randomized controlled trial investigating pregnancy outcome after “endometrial scratching.” Endometrial biopsies and serum were obtained from patients with a first failed IVF cycle randomized to the endometrial scratch in the midluteal phase of the natural cycle before the next fresh embryo transfer during the second IVF cycle. Setting: University hopsital. Patients: Twenty women with clinical pregnancy were compared with 20 women who did not conceive after fresh embryo transfer. Cases and controls were matched for primary vs. secondary infertility, embryo quality, and age. Intervention: None. Main Outcome Measure(s): Steroid concentrations in endometrial tissue homogenates and serum were measured with liquid chromatography-mass spectrometry. The endometrial transcriptome was profiled by RNA-sequencing, followed by principal component analysis and differential expression analysis. False discovery rate-adjusted and log-fold change >|0.5| were selected as the threshold for differentially expressed genes. Result(s): Estrogen levels were comparable in both serum (n = 16) and endometrium (n = 40). Androgens and 17-hydroxyprogesterone were higher in serum than that in endometrium. Although steroid levels did not vary between pregnant and nonpregnant groups, subgroup analysis of primary women with infertility showed a significantly lower estrone concentration and estrone:androstenedione ratio in serum of the pregnant group (n = 5) compared with the nonpregnant group (n = 2). Expression of 34 out of 46 genes encoding the enzymes controlling the local steroid metabolism was detected, and estrogen receptor β gene was differentially expressed between pregnant and nonpregnant women. When only the primary infertile group was considered, 28 genes were differentially expressed between pregnant and nonpregnant women, including HSD11B2, that catalyzes the conversion of cortisol into cortisone. Conclusion(s): Steroidomic and transcriptomic analyses show that steroid concentrations are regulated by the local metabolism in the endometrium. Although no differences were found in endometrial steroid concentration in the pregnant and nonpregnant IVF patients, primary women with infertility showed deviations in steroid levels and gene expression, indicating that a more homogeneous patient group is required to uncover the exact role of steroid metabolism in endometrial receptivity. Clinical Trial Registration Number: The study was registered in the Dutch trial registry (www.trialregister.nl), registration number NL5193/NTR5342, available at https://trialsearch.who.int/Trial2.aspx?TrialID=NTR6687. The date of registration is July 31, 2015. The first enrollment is on January 1, 2016

Genomics of 1 million parent lifespans implicates novel pathways and common diseases and distinguishes survival chances

We use a genome-wide association of 1 million parental lifespans of genotyped subjects and data on mortality risk factors to validate previously unreplicated findings near CDKN2B-AS1, ATXN2/BRAP, FURIN/FES, ZW10, PSORS1C3, and 13q21.31, and identify and replicate novel findings near ABO, ZC3HC1, and IGF2R. We also validate previous findings near 5q33.3/EBF1 and FOXO3, whilst finding contradictory evidence at other loci. Gene set and cell-specific analyses show that expression in foetal brain cells and adult dorsolateral prefrontal cortex is enriched for lifespan variation, as are gene pathways involving lipid proteins and homeostasis, vesicle-mediated transport, and synaptic function. Individual genetic variants that increase dementia, cardiovascular disease, and lung cancer - but not other cancers - explain the most variance. Resulting polygenic scores show a mean lifespan difference of around five years of life across the deciles.Peer reviewe

Genome-wide association analyses identify 143 risk variants and putative regulatory mechanisms for type 2 diabetes

Type 2 diabetes (T2D) is a very common disease in humans. Here we conduct a meta-analysis of genome-wide association studies (GWAS) with ~16 million genetic variants in 62,892 T2D cases and 596,424 controls of European ancestry. We identify 139 common and 4 rare variants associated with T2D, 42 of which (39 common and 3 rare variants) are independent of the known variants. Integration of the gene expression data from blood (n = 14,115 and 2765) with the GWAS results identifies 33 putative functional genes for T2D, 3 of which were targeted by approved drugs. A further integration of DNA methylation (n = 1980) and epigenomic annotation data highlight 3 genes (CAMK1D, TP53INP1, and ATP5G1) with plausible regulatory mechanisms, whereby a genetic variant exerts an effect on T2D through epigenetic regulation of gene expression. Our study uncovers additional loci, proposes putative genetic regulatory mechanisms for T2D, and provides evidence of purifying selection for T2D-associated variants

COMPARISON OF REACTOGENICITY AND IMMUNOGENICITY OF LIVE VACCINES AGAINST INFECTIOUS LARYNGOTRACHEITIS

Humoral immune response and ciliary activity of tracheal mucosa of poultry, vaccinated against infectious laryngotracheitis using ciliostatic test, was studied. Regardless of the vaccination route the vaccines decreased the ciliary activity by 5–9 % on Days 3 to 7 post vaccination. Herewith the vaccine ocular application in some chicks induced oneeye serous conjunctivitis, which resolved subsequently. Oral vaccination did not cause any clinical changes. Serological monitoring revealed an earlier and stronger immunity in poultry vaccinated by ocular route. The required seroprotection level in test groups was higher than the minimal value (80%) starting from Day 16 post vaccination. The period of immunity development after oral vaccination correlated with the vaccine dose volume. Moreover the domestic vaccine was highly competitive with foreign vaccines in immunogenicity and reactogenicity