| 1. |
- Navakauskiene, Ruta, et al.
(författare)
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Alpha-Dystrobrevin and its associated proteins in human promyelocytic leukemia cells induced to apoptosis
- 2012
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Ingår i: Journal of Proteomics. - : Elsevier. - 1874-3919 .- 1876-7737. ; 75:11, s. 3291-3303
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Tidskriftsartikel (refereegranskat)abstract
- Dystrobrevin is a dystrophin-related component of the dystrophin-associated protein complex (DAPC). Using alpha-dystrobrevin as indicator, we aimed to elucidate the interaction network of the DAPC with other proteins during apoptosis of promyelocytic HL-60 cells. The precise role(s) of DBs are not known, but we and others have shown that they play a role in intracellular signal transduction and cellular organization. Apoptosis was induced with etoposide in the absence or presence of Z-VAD to block caspase activity, and we then followed the cellular distribution of alpha-DB and its association with other proteins, using confocal imaging and cell fractions analyses after immune-precipitation with anti-alpha-DB and mass spectrometry. Confocal imaging revealed distinct spatial relocalizations of alpha-DB between the cell membrane, cytosol and nucleus after induction of apoptosis. The expression levels of the identified proteins were evaluated with computer-assisted image analysis of the gels. We thus identified associations with structural and transport proteins (tropomyosin, myosin), membrane (ADAM21, syntrophin), ER-Golgi (TGN51, eIF38) and nuclear (Lamins, ribonucleoprotein C1/C2) proteins. These results suggest that apoptosis-induction in HL-60 cells involves not only classical markers of apoptosis but also a network alpha-DB-associated proteins at the cell membrane, the cytoplasm and nucleus, affecting key cellular transport processes and cellular structure.
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| 2. |
- Navakauskiene, Ruta, et al.
(författare)
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Epigenetic changes during hematopoietic cell granulocytic differentiation - comparative analysis of primary CD34+cells, KG1 myeloid cells and mature neutrophils
- 2014
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Ingår i: BMC Cell Biology. - : BioMed Central. - 1471-2121. ; 15:4
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Tidskriftsartikel (refereegranskat)abstract
- Background: Epigenetic regulation is known to affect gene expression, and recent research shows that aberrant DNA methylation patterning and histone modifications may play a role in leukemogenesis. In order to highlight the co-operation of epigenetic mechanisms acting during the latter process it is important to clarify their potential as biomarkers of granulocytic differentiation. Results: In this study we investigated epigenetic alterations in human hematopoietic cells at a distinct differentiation stages: primary hematopoietic CD34+ cells, KG1 myeloid leukemic cells, whose development is stopped at early stage of differentiation, and mature neutrophils. We focused on the epigenetic status of cell cycle regulating (p15, p16) and differentiation related (E-cadherin and RAR beta) genes. We found that the methylation level in promoter regions of some of these genes was considerably higher in KG1 cells and lower in CD34+ cells and human neutrophils. As examined and evaluated by computer-assisted methods, histone H3 and H4 modifications, i.e. H3K4Me3, H3K9Ac, H3K9Ac/S10Ph and H4 hyperAc, were similar in CD34+ cells and human mature neutrophils. By contrast, in the KG1 cells, histone H3 and H4 modifications were quite high and increased after induction of granulocytic differentiation with the HDAC inhibitor phenyl butyrate. Conclusions: We found the methylation status of the examined gene promoters and histone modifications to be characteristically associated with the hematopoietic cell progenitor state, induced to differentiate myeloid KG1 cells and normal blood neutrophils. This could be achieved through epigenetic regulation of E-cadherin, p15, p16 and RAR beta genes expression caused by DNA methylation/demethylation, core and linker histones distribution in stem hematopoietic cells, induced to differentiation KG1 cells and mature human neutrophils, as well as the histone modifications H3K4Me3, H3K9Ac, H3K9Ac/S10Ph and H4 hyperAc in relation to hematopoietic cell differentiation to granulocyte. These findings also suggest them as potentially important biomarkers of hematopoietic cell granulocytic differentiation and could be valuable for leukemia induced differentiation therapy.
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| 3. |
- Pivoriunas, Augustas, et al.
(författare)
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Proteomic Analysis of Stromal Cells Derived from the Dental Pulp of Human Exfoliated Deciduous Teeth
- 2010
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Ingår i: STEM CELLS AND DEVELOPMENT. - : Mary Ann Leibert. - 1547-3287 .- 1557-8534. ; 19:7, s. 1081-1093
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Tidskriftsartikel (refereegranskat)abstract
- Human dental pulp derived from exfoliated deciduous teeth has been described as a promising alternative source of multipotent stem cells. While these cells share certain similarities with mesenchymal stem-like cells (MSC) isolated from other tissues, basically they are still poorly characterized. In this study, for the first time, a proteomic map of abundantly expressed proteins in stromal cells derived from the dental pulp of human exfoliated deciduous teeth (SHED) was established. We also analyzed proteomic signatures of 2 clonal strains derived from SHEDs by single-cell cloning. The SHEDs were established from enzyme-disaggregated deciduous dental pulp from 6-year-old children. They had typical fibroblastoid morphology and high colony-forming efficiency index (16.4%). Cloning was performed at the second passage using limiting dilution in a 96-well plate (0.3 cell/well). Differentiation assessment revealed strong osteogenic but no adipogenic potential of the SHEDs in either clonal strain. The cells expressed characteristic antigens of MSC-like cells, including CD73, CD90, CD105, CD146, and did not express hematopoietic markers CD14, CD34, and CD45, as assessed with FACS analysis. For proteomic studies, cytosolic and nuclear proteins were analyzed with 2-dimensional gel electrophoresis (2-DE) and identified using matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF)-mass spectrometry (MS). All proteins were identified with high level of confidence (the lowest sequence coverage was 27%). Identification of highly expressed proteins in SHEDs revealed proteomic profiles very similar to that of MSC-like cells derived from other tissues. We also found a high degree of similarity between proteomic signatures of primary SHEDs and clonal cell strains. Thus, our data confirm a close resemblance between SHEDs and MSC-like cells from other tissues and may serve as starting point for creating-comprehensive proteomic maps.
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| 4. |
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2012 2nd Baltic Congress on Future Internet Communications
- 2012
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Proceedings (redaktörskap) (refereegranskat)abstract
- The following topics are dealt with: smart applications; next generation WLAN; broadband infrastructure; network performance; network security; user-centric solutions; wireless systems; Internet of things; smart spaces; analog integrated circuits; traffic analysis; SoC; routing; and protocols. © 2012 IEEE
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| 5. |
- Navakauskas, Dalius
(författare)
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A New Lattice-Ladder Neural Network
- 1997
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- An idea to incorporate FIR or IIR filters in the common structure with Artificial Neural Network (ANN) is motivated by the need to process with ANN time-varying signals. Employment of static ANNs with input data windowing in time in this case is also possible, however experimental studies showed unsatisfactory results. In the common structures of filters and ANNs, IIR filters are more advantageous than FIR filters, as they require less coefficients and can handle long duration signals. However, non-guaranteed stability of IIR filters requires special attention. Both structures suffer from the long training time, because it is proportional to input data correlation which usually is big, e.g., in speech signals.We propose new ANN structure, which is based on the Lattice-Ladder realization of IIR filters incorporated as Multi-layer Perceptron (MLP) synapses. It is of small size because redundant ladder parts of filters are removed, has simple monitoring of filters stability, trains rapidly, and is easy expandable in filter orders. Last two properties are guaranteed because of orthogonality of signals inside of Lattice-Ladder filters. Comparison of proposed ANN structure with MLPs having full Lattice-Ladder or FIR filters in their synapses, and MLP with input data windowing in time in nonlinear system identification and speech signal prediction frameworks is given and confirms the new structure reasonability.
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| 6. |
- Navakauskas, Dalius, et al.
(författare)
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Multirate Implementation Scheme for Restoration of Voiced Speech Signals
- 2003
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Recently iterative procedure for the restoration of speech signals when prosodic elements: stress and accent, of comparatively long duration are missing was developed. Alternatively, it could be cast in a signal generation framework. Basing on that view the paper presents the efficient implementation scheme for the restoration of voiced speech signals. It enjoys parallel order of multirate processing utilizing interpolation and decimation filters parameterized by specific to problem coefficients.Presented simulation results confirm feasibility of developed implementation.
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| 7. |
- Navakauskas, Dalius
(författare)
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Speeding up the Training of Lattice-Ladder Multilayer Perceptrons
- 2002
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- A lattice-ladder multilayer perceptron (LLMLP) is an appealing structure for advanced signal processing in a sense that it is nonlinear, possesses infinite impulse response and stability monitoring of it during training is simple. However, even moderate implementation of LLMLP training hinders the fact that a lot of storage and computation power must be allocated. In this paper we deal with the problem of computational efficiency of LLMLP training algorithms that are based on computation of gradients, e.g., backpropagation, conjugate-gradient or Levenberg-Marquardt.The paper aims to explore most computationally demanding calculations---computation of gradients for lattice (rotation)parameters. Here we find and propose to use for training of several LLMLP architectures a simplest in terms of storage and number of delay elements computation of exact gradients, assuming that the coefficients of the lattice-ladder filter are held stationary.
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| 8. |
- Navakauskas, Dalius
(författare)
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Training Algorithm for Extra Reduced Size Lattice-Ladder Multilayer Perceptrons
- 2003
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- A quick gradient training algorithm for a specific neural network structure called an extra reduced size lattice-ladder multilayer perceptron is introduced. Presented derivation of the algorithm utilizes recently found by author simplest way of exact computation of gradients for rotation parameters of lattice-ladder filter. Developed neural network training algorithm is optimal in terms of minimal number of constants, multiplication and addition operations, while the regularity of the structure is also preserved.
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| 9. |
- Pupeikis, Rimantas, et al.
(författare)
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Identification of Wiener Systems with Hard and Discontinuous Nonlinearities
- 2003
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The problem of identification of Wiener systems with special types of hard and discontinuous nonlinearities in the presence of process and measurements noises in observations to be processed has been considered. It is shown, that the original problem could be reduced to the problem of determination of the subsystem from the auxiliary network of subsystems, equivalent to the true linear system (linear part of the Wiener system). A technique based on the ordinary least squares, to be used in a case of missing data, and on the expectation maximization algorithm is proposed here. The results of numerical simulation of the discrete-time Wiener systems with various hard and discontinuous nonlinearities by computer are given.
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| 10. |
- Pupeikis, Rimantas, et al.
(författare)
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Recursive Parameter Estimation Using Closed-Loop Observations
- 2003
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- The aim of the given paper is development of a joint input-output approach in the case of an additive correlated noise acting on the output of the open-loop system. Here the ordinary prediction error method is applied to solve the closed-loop identification problem by processing observations. In the case of the known regulator, the two-stage method, which belongs to the ordinary joint input-output approach, reduces to the one-stage method. In such a case, the open-loop system could be easily determined after some extended rational transfer function has been identified. In the case of the unknown regulator, the estimate of the extended transfer function is used to generate an auxiliary input. The form of an additive noise filter, that ensures the minimal value of the mean square criterion, is determined. The results of numerical simulation and identification of the open-loop system by computer, using the two-stage method and closed-loop observations are given.
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