Dalius Navakauskas

Dalius Navakauskas
Vilnius Gediminas Technical University | VGTU · Department of Electronic Systems

Prof HP Dr EE

About

128
Publications
11,099
Reads
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447
Citations
Additional affiliations
September 2016 - present
Vilnius Gediminas Technical University
Position
  • Head of Department
August 2006 - present
Vilnius Gediminas Technical University
Position
  • Professor (Full)
August 2006 - present
Vilnius Gediminas Technical University
Position
  • Professor (Full)
Education
February 2006 - February 2006
Vilnius Gediminas Technical University
Field of study
  • Informatics Engineering
September 1994 - September 1999
Vilnius Gediminas Technical University
Field of study
  • Electrical and Electronic Engineering
August 1992 - June 1994
Vilnius (Gediminas) Technical University
Field of study
  • Electronics

Publications

Publications (128)
Article
Full-text available
Mass spectrometry-based proteomics have become a valued tool for conducting comprehensive analyses in amniotic fluid samples with pathologies. Our research interest is the finding and characterization of proteins related to normal vs. polyhydramnios (non-immune hydrops) pregnancy. Proteomic analysis was performed on proteins isolated from fresh amn...
Article
Full-text available
The study reports a first comprehensive approach to the proteome analysis done by comparing the protein profiles characteristic of bee- and manually-collected common dandelion (Taraxacum officinale) pollen. Proteins isolated from the bee- and manually-collected pollen was fractionated by two-dimensional electrophoresis, visualized by staining with...
Chapter
We exploited the proteomic approach to identify proteins whose expression changed during leukemia cell differentiation. The determination of protein expression differences in leukemia and normal blood cells can help identify novel cancer signaling mechanisms. In Chap. 4 are presented proteomic studies in order to identify proteins characteristic fo...
Chapter
Understanding of the genetic and epigenetic factors contributing to the pathogenesis of leukemia has a high impact on blood cancer therapy. In Chap. 1 we review the hematopoiesis process—formation of blood cells from fetus development throughout adulthood. The number of genetic and epigenetic alterations that arise in normal cells during the many y...
Chapter
Protein moves between cell compartments as cells develop and functioning. This is closely related to signal transmission from cell surface into the nucleus. In the Chap. 7 we have described a method for the study of protein translocation from the cytoplasm into the nucleus. And we provided a method for estimating where protein phosphorylation occur...
Chapter
Chromatin dynamic during normal cell development and differentiation plays a pivotal role in cell functioning. Cellular processes such as DNA replication, transcription, and translation depend on chromatin structure. Therefore modifications of DNA and nuclear proteins—histones—play a key role in these processes and consequently in cell functioning...
Chapter
It seems quite unlikely that any adult cancer may arise as the result of single gene defect. Epigenetic alterations have been described in AML and also play an important role in cancer formation. Chapter 2 includes a description of chromatin modifiers (HDACi, HMTi, and DNMTi) alone or in combination with all-trans retinoic acid, inhibitors of prote...
Chapter
Fluorescence microscopy has enabled imaging of spatial proteome (morphological pattern of subcellular protein localization). Automated (and even manual) high-resolution fluorescence image acquisition generates a large amount of complex image data, and manual analysis of such data in order to distill biologically meaningful information is challengin...
Chapter
Alterations in histone modifications have been linked to deregulation of many genes expression important for cancer development and unregulated cancer progression. Therefore, epigenetic modifiers used in cancer therapy have an impact to remodel chromatin with replacement of histone modifications and thus restore the normal state of cells. In Chap....
Chapter
The importance of two-dimensional electrophoresis (2DE) in the life sciences, more precisely protein studies, is large. Although the 2DE technology has shortcomings, however, due to significant 2DE possibilities, this technology still is irreplaceable. Thus we focus on the analysis of 2DE gels (2DEG) and its automation capabilities. In Chapter 6 ar...
Chapter
Despite the growing volume of studies demonstrating the importance of post-translational modifications modulating protein functions we still need to reveal its impact to normal and pathogenic cell development. Protein tyrosine phosphorylation is the protein modification that plays an essential role in cellular signaling and function regulation. In...
Book
This book reviews the current state of epigenetics and proteomics of leukemia and introduces the methods that are important to process and evaluate these factors in leukemia. In particular, epigenetic modifiers and their inhibitors in leukemia treatment as well as approaches to the epigenetic treatment of leukemia are covered. Various computational...
Article
Full-text available
Upcoming 5G technology and the demand for near real-time response services raise the need for optimizing current IoT solutions. The aim of this paper is to model and execute the performance analysis of network structures suitable for Edge Computing in IoT. The prior research into different topology and parameter sets have not provided sufficient cl...
Article
Full-text available
The Internet of Things (IoT) is a critical part of current information technology. When designing IoT data routes, device limited resources such as the computation speed, available amount of memory, remaining battery power or channel bandwidth, to name a few, must be considered. Since the Ant Colony System (ACS) is successfully applied to solving d...
Article
Full-text available
Proteins from hand- and bee- collected pollen were isolated and separated in sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional gel electrophoresis (2DE) system as well by direct gel-free mass spectrometry (MS) analysis. Total thirty six plant proteins with known functions and three uncharacterized were identi...
Article
Full-text available
Background and objectives: Human amniotic fluid-derived mesenchymal stem cells (AF-MSCs) may be a valuable source for cardiovascular tissue engineering and cell therapy. The aim of this study is to verify angiotensin II and transforming growth factor-beta 1 (TGF-β1) as potential cardiomyogenic differentiation inducers of AF-MSCs. Methods and resu...
Article
Full-text available
It is assumed that at some time moment, in wireless sensor networks the new set of current samples of input and system impulse response enter a digital memory replacing the previous samples. It is urgent for each new sample or for a small part of new samples to update a convolution as well. Therefore, a recursive fast convolution algorithm is propo...
Article
Full-text available
The aim of the investigation presented in this paper was to develop a software-based assistant for the protein analysis workflow. The prior characterization of the unknown protein in two-dimensional electrophoresis gel images is performed according to the molecular weight and isoelectric point of each protein spot estimated from the gel image befor...
Article
Human amniotic fluid (AF)-derived mesenchymal stem cells (MSCs) sharing embryonic and adult stem cells characteristics are interesting by their multipotency and the usage for regenerative medicine. However, the usefulness of these cells for revealing the fetal diseases still needs to be assessed. Here, we have analyzed the epigenetic environment in...
Article
Full-text available
In the study, honey from oilseed rape Brassica napus L., and both hand-collected (winter rape Visby and Cult) and bee-collected pollen of oilseed rape were analyzed for their proteome content, in order to see if any plant proteins were present to allow the proteo-typing of the oilseed rape honey. Proteins were fractionated by two-dimensional gel el...
Conference Paper
Metabolic P (MP) system formalism is already proven to be applicable and useful in various fields of science, however knowledge about possibilities of MP system implementation in a hardware is limited. The use of a reconfigurable hardware empowers investigation in a search of the best implementation strategy for specified computing. Thus in the pap...
Article
Background: Amniotic fluid is a complex mixture and reflects the physiological status of the developing fetus. Many proteins presented in amniotic fluid are of exceptional interest because their expression reflects physiological and pathological conditions of the fetus and/or pregnancy. Objective: In the present study, we performed proteomics-based...
Article
Full-text available
An original Very High Speed Integrated Circuit Hardware Description Language (VHDL) code generation tool that can be used to automate Metabolic P (MP) system implementation in hardware such as Field Programmable Gate Arrays (FPGA) is described. Unlike P systems, MP systems use a single membrane in their computations. Nevertheless, there are many bi...
Article
FPGA implementation of hyperbolic tangent activation function for multilayer perceptron structure seems attractive; however, there is a lack of preliminary results on the choice of memory size particularly, when LUT of the function is stored in dedicated on-chip block RAM. The aim of this investigation was to get insights on the distortions of the...
Article
Xenograft models are suitable for in vivo study of leukemia’s pathogenesis and the preclinical development of anti-leukemia agents but understanding of epigenetic regulatory mechanisms linking to adult cell functions in pathological conditions during different in vivo treatments is yet unknown. In this study, for the first time epigenetic chromatin...
Conference Paper
The FPGA implementation of lattice-ladder multilayer perceptron with its training algorithm seems attractive, however there is a lack of experimental results on its efficiency. The main aim of this investigation was to optimize the latency and DSP block usage for the normalized lattice-ladder neuron (LLN) and its simple gradient training algorithm...
Conference Paper
Metabolic P (MP) systems were proposed by V. Manca in 2005. They evolved from and are based on membrane computing, also known as P systems. P systems have been implemented already, however there are no known equivalent implementations of MP systems. We have developed software written in Python interpreted programming language to convert the MP syst...
Conference Paper
Full-text available
We are very pleased to welcome our colleagues - young scientists and researchers from Lithuania, Latvia, United Kingdom, Spain, Czech Republic, Ukraine and Turkey to the 4th IEEE Workshop on Advances in Information, Electronic and Electrical Engineering (AIEEE), held in Vilnius, Lithuania, 10 – 12 November 2016.
Article
Intra-reference and inter-reference distances can be used for evaluation and comparison of reference templates in template based speech recognition. Hence decision on quality of reference template can be done and the reference set can be updated if necessary. In this paper a new reference set update technique based on analysis of vocabulary distanc...
Conference Paper
Full-text available
The speed and precision of the prototype of voice control unit was optimized and it was proven that: It is possible to recognize 2.6 times more words without the loose of precision by the use of global constrains in optimized DTWc IP module. Hardware optimized isolated word matching (DTWc) is executed in 128 µs achieving ~7800 word/s comparison spe...
Conference Paper
FPGA implementation of a lattice-ladder multilayer perceptron structure together with its training algorithm in a full scale seems attractive, however there is a lack of preliminary results on the choice of implementation architecture. The aim of this investigation was to get insights on the selected neuron model fixed-point architecture (necessary...
Article
Paper focuses on the new vocabulary renewal algorithm designed for the hardware implemented Lithuanian speech recognizer. The isolated word recognition is performed using dynamic time warping of the Mel-frequency cepstrum coefficients (MFCC) estimated during short-time analysis of speech signals. A self-organizing feature map is used to extract the...
Article
Full-text available
The article reports on the investigation of augmented reality system which is designed for identification and augmentation of 100 different square markers. Marker recognition efficiency was investigated by rotating markers along x and y axis directions in range from −90° to 90°. Virtual simulations of four environments were developed: a) an intense...
Article
Full-text available
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 leukemia-genesis. 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 granu...
Article
Full-text available
We consider the biggest challenge in speech recognition – noise reduction. Traditionally detected transient noise pulses are removed with the corrupted speech using pulse models. In this paper we propose to cope with the problem directly in Dynamic Time Warping domain. Bidirectional Dynamic Time Warping algorithm for the recognition of isolated wor...
Article
The article reports on the upgrading of the FPGA based isolated word recognition system for real-time tasks. All recognition system components (except some feature calculation steps) were implemented using VHDL. Some high precision calculations were implemented on soft core processor. The employed Dynamic time warping algorithm was speeded-up 2.8 t...
Conference Paper
Full-text available
Paper presents an algorithm for acceleration of the dynamic time warping (DTW) based isolated word recognition algorithm. The number of matching operations directly depends on the size of vocabulary. A set of perceptual cepstrum features is calculated for each word and stored in the vocabulary as a reference. Additionally all words (references) are...
Conference Paper
The article presents the Lithuanian isolated word recognition system implementation in a FPGA hard-core. The pursued objective is the acceleration of the previous soft-core implementation at both key stages: feature extraction and recognition. The 12-th order cepstral analysis is used to extract speech signal features, while for isolated word recog...
Article
Full-text available
Paper presents an comparative evaluation of features extraction algorithm for a real-time isolated word recognition system based on FPGA. The Mel-frequency cepstral, linear frequency cepstral, linear predictive and their cepstral coefficients were implemented in hardware/software design. The proposed system was investigated in speaker dependent mod...
Article
Full-text available
The article reports on the upgrading of the FPGA based isolated word recognition system for real-time tasks. All recognition system components (except some feature calculation steps) were implemented using VHDL. Some high precision calculations were implemented on soft core processor. The employed Dynamic time warping algorithm was speeded-up 2.8 t...
Article
The conventional, Finite Impulse Response and Lattice-Ladder multilayer perceptron (MLP) structures with 4, 8 and 16 hidden neurons were verified for speaker identification. The experiments were performed on 10 speakers, 3 Lithuanian words, 7 sessions' database. Identification performance was compared against two baseline methods: Vector Quantizati...
Article
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...
Article
Full-text available
In this paper Wiener class system consisting of infinite impulse response dynamic subsystem and sigmoid nonlinearity is employed for speech modelling. The experiments on Lithuanian vowel "u" with different initial phase of the signal are done. The average of mean square errors of prediction with the Wiener system model are smaller approximately by...
Conference Paper
Critical information that is related to vital processes of the cell can be revealed comparing several two-dimensional electrophoresis (2DE) gel images. Through up to 10 000 protein spots may appear in inevitably noisy gel thus 2DE gel image comparison and analysis protocols usually involve the work of experts. In this paper we demonstrate how the p...
Conference Paper
This paper presents a comparative investigation of distance measures that may be used in image registration algorithms specialized for two-dimensional electrophoresis gel images. Standard image registration techniques employ correlationbased similarity measures but they are not robust against geometric and large intensity distortions. Exploitation...
Conference Paper
Image processing for the comparison and matching of two images is usually based on classical cross-correlation technique. However matching of 2DE gel images requires more sophisticated approach. In this paper the preprocessing of 2DE gel images by self-organising map is proposed in order to improve results of image matching. Proposed technique divi...
Article
The paper describes a field programmable gate array implementation of the main part of speech recognition system - feature extraction. In order to accelerate recognition the whole cepstral analysis scheme is implemented in hardware by the use of intellectual property cores. Two field programmable gate array devices are used for evaluation. Comparat...
Article
Full-text available
In this paper biometric feature systems and multimodal databases for biometric recognition systems are analyzed on the basis of scientific publications in IEEE Xplore digital library. It is shown that wavelet transform coefficients are the most universal feature used in biometric person recognition systems - it is among five frequently used feature...
Article
Full-text available
Enhancement of FPGA implementation of Lithuanian isolated word recognition system is presented. Software based recognizer implementation was used as the basis for enhancement. The feature extraction (as the most time required process) and local distance calculation (as the most times performed process) were selected for hardware implementation. Red...
Article
The paper addresses the over-saturated protein spot detection and extraction problem in two-dimensional electrophoresis gel images. The effective technique for detection and reconstruction of over-saturated protein spots is proposed. The paper presents: an algorithm of the median filter mask adaptation for initial filtering of gel image; the models...
Article
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 o...
Article
Full-text available
The paper presents some preliminary results on efficiency study of Ant System implementation using software processor Microblaze. By the use of Monte-Carlo tests of number ? calculation the best use of Pseudo-Random Number Generator - implementation of Multiply-With-Carry algorithm in a single precision floating point numbers - is grounded. By expe...
Article
Full-text available
MAX-MIN Ant System (MMAS) application in image preprocessing is investigated. Standard MMAS model for traveling salesman problem is presented together with MMAS model modifications, applying it for image preprocessing. Two modifications of initial ant placement strategy introduced, one based on simplified MMAS without heuristic information (Mod1),...
Conference Paper
Two-dimensional gel electrophoresis is the powerful technique used by biochemists to resolve and visualize protein samples.Commonly gels produced from several samples are analyzed in order to detect changes of protein expression. Thus computer-aided gel image analysis for protein spot detection became the main step in the whole process.Nevertheless...
Article
Full-text available
Detection and quantification of proteins in two-dimensional electrophoresis get images is complicated but the same time important task for the development of modem diagnostics and prognostics systems. In this paper the solution of effective protein spot segmentation in two-dimensional electrophoresis gel images is proposed, It is based on the recon...
Article
Full-text available
Cardiovascular diseases are among the leading causes of mortality in the developing count­ ries. The cardiac conduction system consists of distinctive heart muscle cells that initiate and propagate the electric impulse required for coordinated contraction. This myogenic system per­ forms a distinguished function and has features not characteristic...
Article
The aim of this paper is to investigate the main existing 3D skeletonization methods, their properties and particularities with respect to centerline extraction of segmented blood vessels in human brain MRI images. Skeletonization of 3D objects may be performed using different approaches. Basically there are four main concepts of skeletonization al...
Article
Ant colony optimization application for two-dimensional electrophoresis gel image segmentation is investigated. Standard ACO model with one ants' colony is presented also provided ants' colony size control method. Presented modified ACO model for two-dimensional electrophoresis gel image segmentation. Created synthetic image and experimentally esti...