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

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

Actual aspects of etiological diagnostics of tick-borne infections in Ural region

Etiological decoding was produced of infections transmitted by Ixodes ticks. 142 patients (adults and children) with a fever of unknown etiology or tick bite history of being in the hospital with symptoms of infection was investigate serological methods (ELISA, IgM and IgG). IgM of tick-borne encephalitis virus is found in 17 patients (35.4%), of Ixodes tick borreliosis agents in one (2%), of human granulocytic anaplasmosis pathogen in two (4%). IgM is not revealed of monocytic ehrlichiosis agents person. IgM were determined simultaneously not only to the tick-borne encephalitis virus and Ixodes tick borreliosis pathogens, but also to Anaplasma phagocytophilum in 8.3% patients.Произведена этиологическая расшифровка заболеваний, передающихся иксодовыми клещами, у 142 пациентов (детей и взрослых) с лихорадкой неясной этиологии или укусом клеща в анамнезе, находящихся в стационаре с признаками инфекционного заболевания, с помощью серологического метода (ИФА, IgM и IgG). IgM к вирусу клещевого энцефалита обнаружен у 17 пациентов (35,4%), к возбудителям иксодового клещевого боррелиоза — у одного (2%), к возбудителю гранулацитарного анаплазмоза человека — у двоих (4%). IgM к возбудителям моноцитарного эрлихиоза человека не выявлены. Одномоментно IgM определялись не только к вирусу клещевого энцефалита и возбудителям иксодового клещевого боррелиоза, но и к Anaplasma phagocytophilum у 8,3% пациентов

Aetiology of infectious complications in children with oncohematological diseases

The article presents the results of microbiological studies of different biomaterials in the diagnosis of infectious complications in children with oncohematologicaldiseases after bone marrow transplantation.Gram-negative bacteria both endogenous and possibly nosocomial origin are lead among the detected microorganisms.В статье приведены результаты микробиологических исследований различных биоматериалов, полученных при диагностике инфекционных осложнений у детей с онкогематологическими заболеваниями после трансплантации. Среди обнаруженных микроорганизмов лидируют грамотрицательные бактерии как эндогенного, так и, возможно, нозокомиального происхождения

Diagnosis of catheter-associated bloodstream infections

238 catheters from 220 children were studied mainly from the surgical, intensive care and oncohematological departments. For the diagnosis of catheter-associated bloodstream infections used semiquantitative method inoculation catheters by D. Maki and blood culture isolation of intact vein. Share colonized or locally infected catheters was 79.2%, catheter-associated bloodstream infections – 20.8%.Исследовано 238 проб катетеров от 220 детей, преимущественно из хирургических, реанимационных и онкогематологических отделений. Для диагностики катетер-ассоциированных инфекций кровотока применяли полуколичественный метод посева катетера по D. Maki и выделение гемокультуры из интактной вены. Доля колонизированных или локально инфицированных катетеров составила 79,2%, катетер-ассоциированных инфекций кровотока — 20,8%

Modern methods of diagnosis neuroinfections in children with hydrocephalus

104 samples of cerebrospinal fluid were studied from patients in the surgical departments. For the diagnosis of neuroinfections used analyzer with the technology of light scattering ALIFAX HB&L LIGHT (Alifax, Italy) and the culture method. The results of bacteriological tests in the analyzer and the conventional method coincided in 99% of cases. But in the case of ALIFAX HB&L LIGHT obtained at 8–10 hours earlier than conventional methods, and provide information on the presence or absence of antimicrobial drugs in the cerebrospinal fluid.Исследовано 104 пробы спинномозговой жидкости от больных, находящихся на лечении в хирургических отделениях. Для диагностики нейроинфекций применяли анализатор с технологией светорассеивания ALIFAX HB&L LIGHT (Alifax, Италия) и культуральный метод. Результаты бактериологического исследования на анализаторе и общепринятым методом совпали в 99% случаях, но в случае ALIFAX HB&L LIGHT получены на 8–10 часов раньше по сравнению с классическими методами и дают информацию о наличии или отсутствии антибактериальных препаратов в спинномозговой жидкости

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

Application of innovative methods for bacteriuria diagnostics of urinary tract infections

317 urine samples were tested by the analyzer ALIFAX HB&L LIGHT (Alifax, Italy), using a laser light scattering technology. Urine samples were obtained from children aged from one to 16 years with different pathologies. 281 sample showed a negative result (88.6%) three hours after inoculation, 36 samples positive (11.4%), of which 19 samples were correlated with the results of the traditional culture method (inoculation on blood agar for Eisenberg method). Bacteriuria definition it is crucial for the diagnostics of urinary tract infections in a short period of time (3 hours), especially for material obtained during surgical procedures and outpatients.Протестировано 317 образцов мочи от детей в возрасте от года до 16 лет с различной патологией при применении анализатора ALIFAX HB&L LIGHT (Alifax, Италия), использующего технологию лазерного светорассеивания. Через три часа после посева 281 проба показала отрицательный результат (88,6%), 36 образцов — положительный (11,4%), из них 19 образцов коррелировали с результатами традиционного культурального метода (посева на кровяной агар по методу Айзенберга). Для диагностики инфекций мочевыводящих путей определение бактериурии в более короткие сроки (3 часа) является принципиально важным, особенно при получении материала во время оперативных вмешательств и на амбулаторном приеме

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

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