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Search Results: 1 - 10 of 803 matches for " Jakub Mieczkowski "
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Identification of Pathway Deregulation – Gene Expression Based Analysis of Consistent Signal Transduction
Jakub Mieczkowski, Karolina Swiatek-Machado, Bozena Kaminska
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0041541
Abstract: Signaling pathways belong to a complex system of communication that governs cellular processes. They represent signal transduction from an extracellular stimulus via a receptor to intracellular mediators, as well as intracellular interactions. Perturbations in signaling cascade often lead to detrimental changes in cell function and cause many diseases, including cancer. Identification of deregulated pathways may advance the understanding of complex diseases and lead to improvement of therapeutic strategies. We propose Analysis of Consistent Signal Transduction (ACST), a novel method for analysis of signaling pathways. Our method incorporates information regarding pathway topology, as well as data on the position of every gene in each pathway. To preserve gene-gene interactions we use a subject-sampling permutation model to assess the significance of pathway perturbations. We applied our approach to nine independent datasets of global gene expression profiling. The results of ACST, as well as three other methods used to analyze signaling pathways, are presented in the context of biological significance and repeatability among similar, yet independent, datasets. We demonstrate the usefulness of using information of pathway structure as well as genes’ functions in the analysis of signaling pathways. We also show that ACST leads to biologically meaningful results and high repeatability.
Probe set filtering increases correlation between Affymetrix GeneChip and qRT-PCR expression measurements
Jakub Mieczkowski, Magdalena E Tyburczy, Michal Dabrowski, Piotr Pokarowski
BMC Bioinformatics , 2010, DOI: 10.1186/1471-2105-11-104
Abstract: We present a comprehensive analysis of agreement between Affymetrix GeneChip and qRT-PCR results. We analyzed the influence of filtering by fraction Present calls introduced by J.N. McClintick and H.J. Edenberg (2006) and 2 mapping procedures: updated probe sets definitions proposed by Dai et al. (2005) and our "naive mapping" method. Because of evolution of genome sequence annotations since the time when microarrays were designed, we also studied the effect of the annotation release date. These comparisons were prepared for 6 popular preprocessing algorithms (MAS5, PLIER, RMA, GC-RMA, MBEI, and MBEImm) in the 2 above-mentioned types of studies. We used data sets from 6 independent biological experiments. As a measure of reproducibility of microarray and qRT-PCR values, we used linear and rank correlation coefficients.We show that filtering by fraction Present calls increased correlations for all 6 preprocessing algorithms. We observed the difference in performance of PM-MM and PM-only methods: using MM probes increased correlations in fold change studies, but PM-only methods proved to perform better in detection of differential expression. We recommend using GC-RMA for detection of differential expression and PLIER for estimation of fold change. The use of the more recent annotation improves the results in both types of studies, encouraging re-analysis of old data.Affymetrix GeneChip microarrays (MA) are routinely used for genome-wide quantitative expression analysis. MA measure the expression of genes using probe sets. Probe sets are composed of multiple probes covering different regions of a particular transcript (Perfect-Match, PM), as well as probes designed to measure non-specific hybridization (Mismatch, MM).Preprocessing algorithms evaluate the signals from probes and combine them to get an expression measure for each probe set. As was shown in [1-4], the choice of the preprocessing algorithm has a strong impact on MA analysis. Irizarry et al. [5] presented
Comparative analysis of cis-regulation following stroke and seizures in subspaces of conserved eigensystems
Michal Dabrowski, Norbert Dojer, Malgorzata Zawadzka, Jakub Mieczkowski, Bozena Kaminska
BMC Systems Biology , 2010, DOI: 10.1186/1752-0509-4-86
Abstract: We applied SVD to time-series gene expression datasets from the rat experimental models of stroke and seizures. We demonstrate conservation of two eigensystems, reflecting inflammation and/or apoptosis (eigensystem 2) and neuronal synaptic activity (eigensystem 3), between the stroke and seizures. We analyzed cis-regulation of gene expression in the subspaces of the conserved eigensystems. Bayesian networks analysis was performed separately for either experimental model, with cross-system validation of the highest-ranking features. In this way, we correctly re-discovered the role of AP1 in the regulation of apoptosis, and the involvement of Creb and Egr in the regulation of synaptic activity-related genes.We identified a novel antagonistic effect of the motif recognized by the nuclear matrix attachment region-binding protein Satb1 on AP1-driven transcriptional activation, suggesting a link between chromatin loop structure and gene activation by AP1. The effects of motifs binding Satb1 and Creb on gene expression in brain conform to the assumption of the linear response model of gene regulation. Our data also suggest that numerous enhancers of neuronal-specific genes are important for their responsiveness to the synaptic activity.Eigensystems conserved between stroke and seizures separate effects of inflammation/apoptosis and neuronal synaptic activity, exerted by different transcription factors, on gene expression in rat brain.Stroke and seizures-induced neurodegeneration share a number of biological processes, including increased neuronal activity, neuronal plasticity, inflammation, and apoptosis [1,2]. Separation of effects of these processes on gene expression, identification of participating transcription factors, and comparison of transcriptional regulation between the two pathological conditions remain a challenging task. Global gene expression following stroke and seizures were compared before at a single time-point [3], but no comparison of time-series gene
Arithmetic of triangles
Edward Mieczkowski
Mathematics , 2013,
Abstract: The set of segments, each of the next is n times bigger than the first one is a simple geometric interpretation of the set $\mathbb{N}$ of natural numbers. In this paper we investigate the opposite situation. We give algebraic structure to the set of similar triangles with parallel sides. We present geometric construction of adding of triangles and use it to dissection of triangles into 15 triangles of different sides.
The arithmetic of solids
Edward Mieczkowski
Mathematics , 2012,
Abstract: The set of segments, each of the next is n times bigger than the first one is a simple geometric interpretation of the set $\mathbb{N}$ of natural numbers. In this paper we investigate the opposite situation. We construct an algebraic structure similar to the set $\mathbb{N}$ which describes the set of congruent triangles, each of the next has the sides n times bigger than the first one. Later we do the same with the set of congruent tetrahedrons, and finally with a set of simplices of any dimension.
Where Do We Stand on Locating the Self?  [PDF]
Jakub Limanowski, Heiko Hecht
Psychology (PSYCH) , 2011, DOI: 10.4236/psych.2011.24049
Abstract: The subjective location of the Self in the body is a traditionally problematic question, and it can only be addressed from the first-person perspective. However, this does not preclude an empirical approach to the question. In the present study, we examined whether a large sample of participants would be willing and able to determine the perceived location of their Self. The main goal was to assess current beliefs about the nature of the Self and its assumed relation to specific bodily organs. Eighty-seven participants indicated the center of their Self by placing crosshairs on human silhouettes and abstract, non-human silhouettes with varying anatomy. Results show a clearly dominant role of the brain and the heart for Self-location in humans, but only of the brain for Self-location in abstract creatures. Moreover, results reveal that people believe there is one single point inside the human body where their Self is located.
Coordination Incentives in Cross-Border Macroprudential Regulation  [PDF]
Alexis Derviz, Jakub Seidler
Modern Economy (ME) , 2014, DOI: 10.4236/me.2014.511098

When national financial sector regulators need to mutually harmonize macroprudential policy decisions, imperfections of cross-border information exchange may undermine fair cooperation. Attempts to overcome the effects of informational distortions by delegating macroprudential policy to a supranational body are also likely to entail welfare losses. We study the tradeoff between macroprudential policy autonomy and centralization by means of a signaling game of imperfect information played by two national regulators. The model concentrates on informational frictions in an environment with otherwise fully aligned preferences. We show that even in the absence of evident conflicting goals, the non-transferable nature of some regulatory information creates misreporting incentives. Reporting accuracy is a part of a broader problem of strategic advantage-seeking by the national regulators. Therefore, cross-border coordination mechanisms, centralized or not, that limit strategic behavior are preferable to those allowing its full deployment. The results are applicable to systemic risk management by international organizations, including the relevant EU institutions.

Jak wygl da y lasy pierwotne Europy pod presj du ych ro lino erców?
Jakub Borkowski
Forest Research Papers , 2011, DOI: 10.2478/v10111-011-0018-5
Abstract: The long-standing received wisdom has been that primeval forests (before the development of agriculture) in temperate Europe were created by broad-leaved trees forming closed-canopies. However, a recent theory has challenged this perception by proposing that primeval forests were in fact wood pastures: a mosaic of grassland and forest patches. These forest patches were created mainly by oak and hazel. Grazing by large herbivores, mostly aurochs and tarpan, living at high densities, later replaced by cattle and horses in the agricultural epoc, allowed wood-pasture formation. The regeneration of trees in such conditions was possible thanks to the protective shelter offered by thorny shrubs. Several forest reserves created in Europe, serving as references for primeval forests, have been succeeding without pressure from large herbivores and therefore their character may be different than that of real primeval vegetation. Although some palaeoecological studies suggest that primeval forests had closed-canopies, other analyses indicate that closed canopy forests were interrupted by a remarkably large proportion of more open areas. It is hard to judge what was the true character of primeval forests, but the role of large herbivores in shaping primeval forest structure has been neglected. It is believed that there was a higher proportion of mega-herbivorous mammals in the temperate zone during the late Pleistocene than the proportion presently living in Africa. Given the evidence that large herbivores can effectively determine the openness of African landscapes, their potential to have shaped temperate primeval forests should not be under-estimated.
Squirrel cage induction motors with idle bars
Jakub Bernatt
Archives of Electrical Engineering , 2010, DOI: 10.2478/s10171-010-0006-z
Abstract: The paper describes high output induction motors driving large applications of heavy starting conditions. Heavy start is characterised by long accelerating time and occures in drives of hudge inertia torque, esspecially when performed at full load. The reliable operation of the motors depends on proper design and quality of rotor's cage. The aspects of thermal behaviour and electrodynamic forces have to be considered during the design of the motor for hard working conditions. In the paper the rotor with idle bars is investigated.
Hayek and Departure from Praxeology
Jakub Wozinski
Libertarian Papers , 2010,
Abstract: Friedrich von Hayek is mostly known as a staunch critic of naturalist fallacy. It is claimed in the article that having been heavily influenced by Epicurus, he commited an identical error that he himself criticized. This opinion is based on Hayek’s application of Ernst Mach mind-body dualism criticism, Epicurean theory of irrational ethics and falsificationistic theory of knowledge related with atomistic view of the universe.
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