Blood flow simulation in neck veins

The goal of this thesis is an overview of the vast field of existing computational fluid dynamics solvers for a three-dimensional model and integration of the most suitable into a web application, with the vision to integrate it into the existing Med3D program. The simulation is to be run through a blood vessel, that was generated by assembling medical images in NeckVeins. In the paper we get briefly acquainted with the physical background of the Lattice Boltzmann method, on which the chosen solution from the overview of existing solutions is based on. We inspect the file formats, that are needed for a successful integration of different interfaces, that the existing software already defines. Presented is also the final implementation of the developed program, the algorithms used for supporting the preparation of the model for the simulation, and design decisions met during the development

Ping Pong Balayage and Convexity of Equilibrium Measures

In this presentation we prove that the equilibrium measure of a finite union of intervals on the real line or arcs on the unit circle has convex density. This is true for both, the classical logarithmic case, and the Riesz case. The electrostatic interpretation is the following: if we have a finite union of subintervals on the real line, or arcs on the unit circle, the electrostatic distribution of many “electrons” will have convex density on every subinterval. Applications to external field problems and constrained energy problems are presented

SymGRASS: a database of sugarcane orthologous genes involved in arbuscular mycorrhiza and root nodule symbiosis : from Seventh International Meeting on Computational Intelligence Methods for Bioinformatics and Biostatistics, (CIBB 2010), Palermo, Italy, 16 - 18 September 2010

Background: The rationale for gathering information from plants procuring nitrogen through symbiotic interactions controlled by a common genetic program for a sustainable biofuel production is the high energy demanding application of synthetic nitrogen fertilizers. We curated sequence information publicly available for the biofuel plant sugarcane, performed an analysis of the common SYM pathway known to control symbiosis in other plants, and provide results, sequences and literature links as an online database. Methods: Sugarcane sequences and informations were downloaded from the nucEST database, cleaned and trimmed with seqclean, assembled with TGICL plus translating mapping method, and annotated. The annotation is based on BLAST searches against a local formatted plant Uniprot90 generated with CD-HIT for functional assignment, rpsBLAST to CDD database for conserved domain analysis, and BLAST search to sorghum's for Gene Ontology (GO) assignment. Gene expression was normalized according the Unigene standard, presented as ESTs/100 kb. Protein sequences known in the SYM pathway were used as queries to search the SymGRASS sequence database. Additionally, antimicrobial peptides described in the PhytAMP database served as queries to retrieve and generate expression profiles of these defense genes in the libraries compared to the libraries obtained under symbiotic interactions. Results: We describe the SymGRASS, a database of sugarcane orthologous genes involved in arbuscular mycorrhiza (AM) and root nodule (RN) symbiosis. The database aggregates knowledge about sequences, tissues, organ, developmental stages and experimental conditions, and provides annotation and level of gene expression for sugarcane transcripts and SYM orthologous genes in sugarcane through a web interface. Several candidate genes were found for all nodes in the pathway, and interestingly a set of symbiosis specific genes was found. Conclusions: The knowledge integrated in SymGRASS may guide studies on molecular, cellular and physiological mechanisms by which sugarcane controls the establishment and efficiency of endophytic associations. We believe that the candidate sequences for the SYM pathway together with the pool of exclusively expressed tentative consensus (TC) sequences are crucial for the design of molecular studies to unravel the mechanisms controlling the establishment of symbioses in sugarcane, ultimately serving as a basis for the improvement of grass crops

Monitoring by HPLC of Chamomile Flavonoids Exposed to Rat Liver Microsomal Metabolism

Three major flavonoid chamomile components (quercetin, apigenin-7-O-glucoside and rutin) were subjected to oxidative metabolism by cytochrome P-450 of rat liver microsomal preparations. Changes over time in their respective concentrations were followed using reversed-phase HPLC with UV detection. No clean-up had to be applied as only the specific flavonoid had to be separated from the background components originating from the rat liver microsome. Neither the concentration of apigenin-7-O-glucoside nor that of the diglycoside rutin decreased during one hour of exposure to rat microsomal treatment. In contrast, the concentration of quercetin, a lipophilic aglycon, decreased. Our analytical HPLC results complement the in silico calculated lipophilicity (logP) of these compounds; the relatively high lipophilicity of quercetin appears to predispose it to oxidative metabolism in order to decrease its fat solubility. In contrast the much less lipophilic compounds apigenin-7-O-glucoside and rutin were resistant in vitro to microsomal treatment

Web usage analysis of Pillar 3 disclosed information by deposit customers in turbulent times

Market discipline has been a scrutinized area since the last financial crisis in 2008. Regulators strengthened their role particularly through Pillar 3 in Basel III. However, there are still some aspects of market discipline that deserve special attention to avoid future failures. This study focuses on the analysis of the interest and behaviour of deposit stakeholders based on website data dedicated to disclosures of commercial bank in Slovakia during and after turbulent times (period 2009–2012). The data consists of log files, and web mining techniques were applied (the modelling of web user behaviour in dependence on time - based on the proposals of the authors). The results show that also in turbulent times, stakeholders’ interest in Pillar 3 disclosures is low (in line with (Munk, Pilkova, Benko, & Blažeková, 2017)) and the highest interest was identified for the Pricing List category. After turbulent times, Pillar 3 categories (Pillar 3 related information and Pillar 3 disclosures) have weak interest, with peaks at the beginning of the year, and the highest increase was in the Business Conditions category. The results suggest that the enhancement of interest of key stakeholders in disclosures inevitably requires changes to deliver sufficient disclosure data structures and to design a disclosure policy that fulfils regulatory expectations. © 2021 The AuthorsScientific Grant Agency of the Ministry of Education of the Slovak Republic (ME SR); Slovak Academy of Sciences (SAS) [VEGA-1/0776/18, VEGA-1/0821/21]Slovenská Akadémia Vied, SAV: VEGA-1/0776/18, VEGA-1/0821/2

De novo steroidogenesis in tumor cells drives bone metastasis and osteoclastogenesis

Osteoclasts play a central role in cancer-cell-induced osteolysis, but the molecular mechanisms of osteoclast activation during bone metastasis formation are incompletely understood. By performing RNA sequencing on a mouse breast carcinoma cell line with higher bone-metastatic potential, here we identify the enzyme CYP11A1 strongly upregulated in osteotropic tumor cells. Genetic deletion of Cyp11a1 in tumor cells leads to a decreased number of bone metastases but does not alter primary tumor growth and lung metastasis formation in mice. The product of CYP11A1 activity, pregnenolone, increases the number and function of mouse and human osteoclasts in vitro but does not alter osteoclast-specific gene expression. Instead, tumor-derived pregnenolone strongly enhances the fusion of pre-osteoclasts via prolyl 4-hydroxylase subunit beta (P4HB), identified as a potential interaction partner of pregnenolone. Taken together, our results demonstrate that Cyp11a1-expressing tumor cells produce pregnenolone, which is capable of promoting bone metastasis formation and osteoclast development via P4HB

The NKCC1 ion transporter modulates microglial phenotype and inflammatory response to brain injury in a cell-autonomous manner

The NKCC1 ion transporter contributes to the pathophysiology of common neurological disorders, but its function in microglia, the main inflammatory cells of the brain, has remained unclear to date. Therefore, we generated a novel transgenic mouse line in which microglial NKCC1 was deleted. We show that microglial NKCC1 shapes both baseline and reactive microglia morphology, process recruitment to the site of injury, and adaptation to changes in cellular volume in a cell-autonomous manner via regulating membrane conductance. In addition, microglial NKCC1 deficiency results in NLRP3 inflammasome priming and increased production of interleukin-1 beta (IL-1 beta), rendering microglia prone to exaggerated inflammatory responses. In line with this, central (intracortical) administration of the NKCC1 blocker, bumetanide, potentiated intracortical lipopolysaccharide (LPS)-induced cytokine levels. In contrast, systemic bumetanide application decreased inflammation in the brain. Microglial NKCC1 KO animals exposed to experimental stroke showed significantly increased brain injury, inflammation, cerebral edema, and, worse, neurological outcome. Thus, NKCC1 emerges as an important player in controlling microglial ion homeostasis and inflammatory responses through which microglia modulate brain injury. The contribution of microglia to central NKCC1 actions is likely to be relevant for common neurological disorders.Peer reviewe

Conceptual framework for programming skilss development based on microlearning and automated source code evaluation in virtual learning environment

Understanding how software works and writing a program are currently frequent requirements when hiring employees. The complexity of learning programming often results in educational failures, student frustration and lack of motivation, because different students prefer different learning paths. Although e-learning courses have led to many improvements in the methodology and the supporting technology for more effective programming learning, misunderstanding of programming principles is one of the main reasons for students leaving school early. Universities face a challenging task: how to harmonise students’ education, focusing on advanced knowledge in the development of software applications, with students’ education in cases where writing code is a new skill. The article proposes a conceptual framework focused on the comprehensive training of future programmers using microlearning and automatic evaluation of source codes to achieve immediate feedback for students. This framework is designed to involve students in the software development of virtual learning environment software that will provide their education, thus ensuring the sustainability of the environment in line with modern development trends. The paper’s final part is devoted to verifying the contribution of the presented elements through quantitative research on the introductory parts of the framework. It turned out that although the application of interactive features did not lead to significant measurable progress during the first semester of study, it significantly improved the results of students in subsequent courses focused on advanced programming