Accelerating Industrial Applications: The Development of Basic GPU Kernels for the New Block AMG Algorithms for Solving SLE with Explicitly Calculated Sparse Basis

AbstractNowadays, GPU computations are playing significant role in supercomputing technologies. This work is a part of a project dealing with solving problems of modeling hydro- and aerodynamics where linear algebra operations are frequently used and occupy most of execution time. In despite of the fact that GPUs are traditionally used for solving high sized problems, in our project we need to solve many tasks of low sizes. Because of this, modern library's solutions such as cuBLAS (1) and cuSPARSE (2) are not suitable enough for that, so we have a task of implementation more efficient functions for concrete linear algebra operations taking into account its specialties

Meditation In The Emotional Intelligence Improvement Among Russian-Speakıng Migrants In Germany

The analysis of meditation as a factor of an individual’s psychological and emotional well-being as well as the comparison of main emotional intelligence quantitative measurement methods and the justification of the method used in the study were performed. Main features of the migrants’ social-psychological adaptation were considered. The key role of interpersonal emotional intelligence competency in migrants’ social-psychological adaptation process was identified. The interrelation between meditation practice and dynamics of migrants’ emotional intelligence was found

Gene expression analyses in Atlantic salmon challenged with infectious salmon anemia virus reveal differences between individuals with early, intermediate and late mortality

<p>Abstract</p> <p>Background</p> <p>Infectious salmon anemia virus (ISAV) causes a multisystemic disease responsible for severe losses in salmon aquaculture. Better understanding of factors that explain variations in resistance between individuals and families is essential for development of strategies for disease control. To approach this, we compared global gene expression using microarrays in fish dying early and late in the time course following infection from a highly pathogenic ISAV.</p> <p>Results</p> <p>Tissues (gill, heart, liver and spleen) from infected Atlantic salmon (cohabitation, ISAV Glesvaer 2/90 isolate) were collected from three stages over the time course of the experiment; early (EM, 0–10% cumulative mortality (CM), 21–25 days post-infection (DPI)), intermediate (IM, 35–55% CM, 28–31 DPI) and late (LM, 75–85% CM, 37–48 DPI) mortality. Viral loads were equal in EM and IM but dropped markedly in LM fish. Gene expression analyses using a 1.8 K salmonid fish cDNA microarray (SFA2.0) and real-time qPCR revealed a large group of genes highly up-regulated across tissues in EM, which were mainly implicated in innate antiviral responses and cellular stress. Despite equal levels of MHC class I in EM and LM, increase of splenic and cardiac expression of immunoglobulin-like genes was found only in LM while a suite of adaptive immunity markers were activated already in IM. The hepatic responses to ISAV were characterized by difference between EM and LM in expression of chaperones and genes involved in eicosanoid metabolism. To develop classification of high and low resistance phenotypes based on a small number of genes, we processed results from qPCR analyses of liver using a linear discriminant analysis. Four genes (5-lipoxygenase activating protein, cytochrome P450 2K4-1, galectin-9 and annexin A1) were sufficient for correct assignment of individuals to EM, LM and uninfected groups, while IM was inseparable from EM. Three of four prognostic markers are involved in metabolism of inflammatory regulators.</p> <p>Conclusion</p> <p>This study adds to the understanding of molecular determinants for resistance to acute ISAV infection. The most susceptible individuals were characterized by high viral replication and dramatic activation of innate immune responses, which did not provide protection. The ability to endure high levels of infection for sustained periods could be associated with lower inflammatory responses while subsequent protection and viral clearance was most likely conferred by activation of adaptive immunity.</p

Transcribed Tc1-like transposons in salmonid fish

BACKGROUND: Mobile genetic elements comprise a substantial fraction of vertebrate genomes. These genes are considered to be deleterious, and in vertebrates they are usually inactive. High throughput sequencing of salmonid fish cDNA libraries has revealed a large number of transposons, which remain transcribed despite inactivation of translation. This article reports on the structure and potential role of these genes. RESULTS: A search of EST showed the ratio of transcribed transposons in salmonid fish (i.e., 0.5% of all unique cDNA sequences) to be 2.4–32 times greater than in other vertebrate species, and 68% of these genes belonged to the Tc1-family of DNA transposons. A phylogenetic analysis of reading frames indicate repeated transposition of distantly related genes into the fish genome over protracted intervals of evolutionary time. Several copies of two new DNA transposons were cloned. These copies showed relatively little divergence (11.4% and 1.9%). The latter gene was transcribed at a high level in rainbow trout tissues, and was present in genomes of many phylogenetically remote fish species. A comparison of synonymous and non-synonymous divergence revealed remnants of divergent evolution in the younger gene, while the older gene evolved in a neutral mode. From a 1.2 MB fragment of genomic DNA, the salmonid genome contains approximately 10(5 )Tc1-like sequences, the major fraction of which is not transcribed. Our microarray studies showed that transcription of rainbow trout transposons is activated by external stimuli, such as toxicity, stress and bacterial antigens. The expression profiles of Tc1-like transposons gave a strong correlation (r(2 )= 0.63–0.88) with a group of genes implicated in defense response, signal transduction and regulation of transcription. CONCLUSION: Salmonid genomes contain a large quantity of transcribed mobile genetic elements. Divergent or neutral evolution within genomes and lateral transmission can account for the diversity and sustained persistence of Tc1-like transposons in lower vertebrates. A small part of transposons remain transcribed and their transcription is enhanced by responses to acute conditions

К ВОПРОСУ ОБ ОПРЕДЕЛЕНИИ ПОНЯТИЯ «СОЦИОКУЛЬТУРНОЕ ПРОСТРАНСТВО»

The relevance of the study is justified by the fact that in modern scientific literature there is no common understanding of the phenomenon of socio-cultural space. Works on the development of this concept in modern society is not enough. Often in scientific research it is used without definition and justification.Purpose. The article is devoted to the analysis of the main problems arising in the definition and application of the concept of “socio-cultural space” in research.Methodology. The basis of the research methodology is an analytical review of scientific literature devoted to the development and application of the concept of “socio-cultural space”, the method of dialectics.The theoretical significance of the work lies in the fact that it denotes the problems that need to be taken into account when using the category of “socio-cultural space” in modern studies of culture and society.Results. The results of the work are that the authors, having analyzed the main approaches to the definition and application of the concept of socio-cultural space in the scientific literature, have identified a number of problems faced by researchers: not the correct application of this concept as a universal, all encompassing categories that do not require justification for its use; the unjustified shift of emphasis between the basic concepts of “cultural” and “social”, which leads to a change in the meaning of the concept of “socio-cultural space”, and, consequently, to errors in the application of socio-cultural methodology; the ambiguous meaning of the concept of “socio-cultural space” makes it difficult to apply this category in the study of the phenomena of the information society.Актуальность исследования обоснована тем, что в современной научной литературе отсутствует единое понимание феномена социокультурного пространства. Работ, посвященных разработке этого понятия в условиях современного общества недостаточно. Часто в научных исследованиях оно используется без определения и обоснования.Цель. Статья посвящена анализу основных проблем, возникающих при определении и применении в исследованиях понятия «социокультурное пространство».Методология проведения работы. Основа методологии исследования – аналитический обзор научной литературы, посвященной разработке и применению понятия «социокультурное пространство», метод диалектики.Теоретическая значимость работы заключается в том, что она обозначает проблемы, возникновение которых необходимо учитывать при использовании категории «социокультурное пространство» в современных исследованиях культуры и общества.Результаты. Результаты работы заключаются в том, что авторы, проанализировав основные подходы к определению и применению понятия социокультурного пространства в научной литературе, выявили ряд проблем, с которыми сталкиваются исследователи: не корректное применение этого понятия как универсальной, все охватывающей категории, не требующей обоснования ее использования; необоснованное смещение акцентов между основными концептами «культурное» и «социальное», что приводит к изменению смысла понятия «социокультурное пространство», а, следовательно, и к ошибкам в применении социокультурной методологии; многозначный смысл понятия «социокультурное пространство» затрудняет применение этой категории в исследованиях феноменов информационного общества

A comprehensive transcriptional body map of Atlantic salmon unveils the vital role of the intestine in the immune system and highlights functional specialization within its compartments

The intestine is a barrier organ that plays an important role in the immune system of Atlantic salmon. The immune functions are distributed among the diffuse gut lymphoid tissue containing diverse immune cells, and other cell types. Comparison of intestinal transcriptomes with those of other organs and tissues offers an opportunity to elucidate the specific roles of the intestine and its relationship with other parts of the body. In this work, a meta-analysis was performed on a large volume of data obtained using a genome-wide DNA oligonucleotide microarray. The intestine ranks third by the expression level of immune genes after the spleen and head kidney. The activity of antigen presentation and innate antiviral immunity is higher in the intestine than in any other tissue. By comparing transcriptome profiles, intestine shows the greatest similarity with the gill, head kidney, spleen, epidermis, and olfactory rosette (descending order), which emphasizes the integrity of the peripheral mucosal system and its strong connections with the major lymphoid organs. T cells-specific genes dominate among the genes co-expressed in these tissues. The transcription signature of CD8+ (86 genes, r > 0.9) includes a master gene of immune tolerance foxp3 and other negative regulators. Different segments of the intestine were compared in a separate experiment, in which expression gradients along the intestine were found across several functional groups of genes. The expression of luminal and intracellular (lysosome) proteases is markedly higher in pyloric caeca and distal intestine respectively. Steroid metabolism and cytochromes P450 are highly expressed in pyloric caeca and mid intestine while the distal intestine harbors genes related to vitamin and iron metabolism. The expression of genes for antigen presenting proteins and immunoglobulins shows a gradual increase towards the distal intestine.publishedVersio

Estrogen Modulates Hepatic Gene Expression and Survival of Rainbow Trout Infected with Pathogenic Bacteria Yersinia ruckeri

In the aquatic environment, fish are exposed to various stimuli at once and have developed different response mechanisms to deal with these multiple stimuli. The current study assessed the combined impacts of estrogens and bacterial infection on the physiological status of fish. Juvenile rainbow trout were exposed to two different concentrations of 17β-estradiol (E2) (2 or 20mg/kg feed) and then infected with three concentrations of Yersinia ruckeri, a bacterial pathogen causing massive losses in wild and farmed salmonid populations. Organism-level endpoints to assess the impact of the single and combined treatments included hepatic vitellogenin transcript expression to evaluate the E2 exposure efficiency and survival rate of pathogen-challenged fish. The two E2 doses increased vitellogenin levels within the physiological range. Infection with Y. ruckeri caused mortality of trout, and this effect was significantly enhanced by a simultaneous exposure to high E2 dose. The hormone reduced survival at intermediate and high (104 and 106 colony forming units, cfu) bacterial concentrations, but not for a low one (102cfu). Analysis of hepatic gene expression profiles by a salmonid 2k cDNA microarray chip revealed complex regulations of pathways involved in immune responses, stress responses, and detoxicification pathways. E2 markedly reduced the expression of several genes implicated in xenobiotic metabolism. The results suggest that the interaction between pathogen and E2 interfered with the fish's capability of clearing toxic compounds. The findings of the current study add to our understanding of multiple exposure responses in fis

Developmental disturbances in early life stage mortality (M74) of Baltic salmon fry as studied by changes in gene expression

BACKGROUND: We have studied alterations of gene expression associated with naturally-occurring early life stage mortality (M74) in Baltic salmon using a cDNA microarray and real time PCR. M74-affected fry have several typical neurological, cardiovascular and pathological symptoms. They are also characterized by low thiamine content and show signs of oxidative stress. RESULTS: Affected fry can be divided into three major groups with early, intermediate or late onset of mortality. If mortality starts during the first third of the yolk-sac stage, virtually all the responses are compatible with stress, which rapidly leads to the common terminal responses. If death occurs during the second third of the yolk sac stage, the terminal stage is preceded by a decrease in globin gene expression, which leads to internal hypoxia when the animals grow and shift from skin- to gill-breathing. Fry will eventually proceed to the terminal responses. The group developing M74 most slowly appears to compensate for reduced oxygen delivery by downregulation of metabolism, and hence some fry can escape death. CONCLUSION: Our study is the first demonstration of diverse transcriptional responses to a naturally-occurring developmental disturbance. Since many of the genes differentially expressed in M74-fry are evolutionarily conserved, the M74 of Baltic salmon can serve as a model for developmental disturbances and environmental stress responses in vertebrates in general

Evaluation of Immune Status in Two Cohorts of Atlantic Salmon Raised in Different Aquaculture Systems (Case Study)

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