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Search Results: 1 - 10 of 160 matches for " Bozena Kaminska "
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Is Glioblastoma an Epigenetic Malignancy?
Marta Maleszewska,Bozena Kaminska
Cancers , 2013, DOI: 10.3390/cancers5031120
Abstract: Epigenetic modifications control gene expression by regulating the access of nuclear proteins to their target DNA and have been implicated in both normal cell differentiation and oncogenic transformation. Epigenetic abnormalities can occur both as a cause and as a consequence of cancer. Oncogenic transformation can deeply alter the epigenetic information enclosed in the pattern of DNA methylation or histone modifications. In addition, in some cancers epigenetic dysfunctions can drive oncogenic transformation. Growing evidence emphasizes the interplay between metabolic disturbances, epigenomic changes and cancer, i.e., mutations in the metabolic enzymes SDH, FH, and IDH may contribute to cancer development. Epigenetic-based mechanisms are reversible and the possibility of “resetting” the abnormal cancer epigenome by applying pharmacological or genetic strategies is an attractive, novel approach. Gliomas are incurable with all current therapeutic approaches and new strategies are urgently needed. Increasing evidence suggests the role of epigenetic events in development and/or progression of gliomas. In this review, we summarize current data on the occurrence and significance of mutations in the epigenetic and metabolic enzymes in pathobiology of gliomas. We discuss emerging therapies targeting specific epigenetic modifications or chromatin modifying enzymes either alone or in combination with other treatment regimens.
On Reliable Transmission of Data over Simple Wireless Channels
Pawel Gburzynski,Bozena Kaminska,Ashikur Rahman
Journal of Computer Networks and Communications , 2009, DOI: 10.1155/2009/409853
Abstract: Standard protocols for reliable data transmission over unreliable channels are based on various Automatic Repeat reQuest (ARQ) schemes, whereby the sending node receives feedback from the receiver and retransmits the missing data. We discuss this issue in the context of one-way data transmission over simple wireless channels characteristic of many sensing and monitoring applications. Using a specific project as an example, we demonstrate how the constraints of a low-cost embedded wireless system get in the way of a workable solution precluding the use of popular schemes based on windows and periodic acknowledgments. We also propose an efficient solution to the problem and demonstrate its advantage over the traditional protocols.
Prediction of a key role of motifs binding E2F and NR2F in down-regulation of numerous genes during the development of the mouse hippocampus
Michal Dabrowski, Stein Aerts, Bozena Kaminska
BMC Bioinformatics , 2006, DOI: 10.1186/1471-2105-7-367
Abstract: In the current work, we used a novel approach of analyzing cis-regulation of gene expression in a subspace of a single SVD mode of temporal expression profiles. In the putative upstream regulatory sequences identified by mouse-human homology for all the genes represented in either dataset, we searched for simple features (motifs and pairs of motifs) associated with either sign of the loading of Mode 2. Using a cross-system training-test set approach, we identified E2F binding sites as predictors of down-regulation of gene expression during hippocampal development. NR2F binding sites, for the transcription factors Nr2f/COUP and Hnf4, and also NR2F_SP1 pairs of binding sites, were predictors of down-regulation of expression both during hippocampal development and neuronal differentiation. Analysis of another dataset, from gene profiling of myoblast differentiation in vitro, shows that the conservation of Mode 2 extends to the differentiation of mesenchymal cells. This permitted the identification of two more pairs of motifs, one of which included the CDE/CHR tandem element, as features associated with down-regulation both in the differentiating myoblasts and in the developing hippocampus. Of the features we identified, the E2F and CDE/CHR motifs may be associated with the cycling progenitor cell status, while NR2F may be related to the entry into differentiation along the neuronal pathway.Our results constitute the first prediction of an expression pattern from the genomic sequence for the developing mammalian brain, and demonstrate a potential for the analysis of gene regulation in a subspace of a single SVD mode of expression.Transcriptome profiling experiments documented changes in gene expresion in several areas or cellular populations of the developing mammalian brain [1-4]. The availability of genomic sequences of an increasing number of vertebrate species, including human and mouse, permits – by their comparison – the identification of putative regulatory seque
An automatic hierarchical delay analysis tool
An Automatic Hierarchical Delay Analysis Tool

Farid Mheir-El-Saadi,Bozena Kaminska,
Farid Mheir-ELSaadi
,Bozena Kaminska

计算机科学技术学报 , 1994,
Abstract: The performance analysis of VLSI integrated circuits (ICs) with flat tools is slow and even sometimes impossible to complete. Some hierarchical tools have been developed to speed up the analysis of these large ICs. However, these hierarchical tools suffer from a poor interaction with the CAD database and poorly automatized operations. We introduce a general hierarchical framework for performance analysis to solve these problems. The circuit analysis is automatic under the proposed framework. Information that has been automatically abstracted in the hierarchy is kept in database properties along with the topological information. A limited software implementation of the framework, PREDICT, has also been developed to analyze the delay performance. Experimental results show that hierarchical analysis CPU time and memory requirements are low if heuristics are used during the abstraction process. This work is supported by grants from the Natural Sciences and Engineering Research Council (Canada) (NSERC) and the Ministry of Higher Education (Québec).
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.
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
Selected Papers from International Mixed Signals Testing and GHz/Gbps Test Workshop
Bozena Kaminska,Marcelo Lubaszewski,José Machado da Silva
VLSI Design , 2008, DOI: 10.1155/2008/165673
Development of a Novel Contactless Mechanocardiograph Device
Kouhyar Tavakolian,Faranak M. Zadeh,Yindar Chuo,Ali Vaseghi,Bozena Kaminska
International Journal of Telemedicine and Applications , 2008, DOI: 10.1155/2008/436870
Abstract: A novel method of detecting mechanical movement of the heart, Mechanocardiography (MCG), with no connection to the subject's body is presented. This measurement is based on radar technology and it has been proven through this research work that the acquired signal is highly correlated to the phonocardiograph signal and acceleration-based ballistocardiograph signal (BCG) recorded directly from the sternum. The heart rate and respiration rate have been extracted from the acquired signal as two possible physiological monitoring applications of the radar-based MCG device.
Characteristics of the Alternative Phenotype of Microglia/Macrophages and its Modulation in Experimental Gliomas
Konrad Gabrusiewicz, Aleksandra Ellert-Miklaszewska, Maciej Lipko, Malgorzata Sielska, Marta Frankowska, Bozena Kaminska
PLOS ONE , 2011, DOI: 10.1371/journal.pone.0023902
Abstract: Microglia (brain resident macrophages) accumulate in malignant gliomas and instead of initiating the anti-tumor response, they switch to a pro-invasive phenotype, support tumor growth, invasion, angiogenesis and immunosuppression by release of cytokines/chemokines and extracellular matrix proteases. Using immunofluorescence and flow cytometry, we demonstrate an early accumulation of activated microglia followed by accumulation of macrophages in experimental murine EGFP-GL261 gliomas. Those cells acquire the alternative phenotype, as evidenced by evaluation of the production of ten pro/anti-inflammatory cytokines and expression profiling of 28 genes in magnetically-sorted CD11b+ cells from tumor tissues. Furthermore, we show that infiltration of implanted gliomas by amoeboid, Iba1-positive cells can be reduced by a systematically injected cyclosporine A (CsA) two or eight days after cell inoculation. The up-regulated levels of IL-10 and GM-CSF, increased expression of genes characteristic for the alternative and pro-invasive phenotype (arg-1, mt1-mmp, cxcl14) in glioma-derived CD11b+ cells as well as enhanced angiogenesis and tumor growth were reduced in CsA-treated mice. Our findings define for the first time kinetics and biochemical characteristics of glioma-infiltrating microglia/macrophages. Inhibition of the alternative activation of tumor-infiltrating macrophages significantly reduced tumor growth. Thus, blockade of microglia/macrophage infiltration and their pro-invasive functions could be a novel therapeutic strategy in malignant gliomas.
Poverty in Poland and the United States: A Comparison of Key Characteristics, Composition, and Prospects  [PDF]
Bozena Leven
Modern Economy (ME) , 2016, DOI: 10.4236/me.2016.75057
Abstract: This study provides a comparative approach to assess the state of Polish poverty. To do so, poverty in Poland and the United States is presented in terms of selected general, shared characteristics and particularly vulnerable societal groups. Using official, primarily income based, statistics for Poland and the United States, we conclude that a higher percentage of the overall population in the United States is poor and, relative to median country-specific incomes, that the US poverty is deeper than in Poland. In addition, more children, the elderly, and the disabled are poor in America than in Poland; the breadth of poverty is wider in the United States and, perhaps most importantly, may in some important ways also be more intractable.
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