Showing papers by "Brno University of Technology published in 2014"

PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations.

Abstract: Single nucleotide variants represent a prevalent form of genetic variation. Mutations in the coding regions are frequently associated with the development of various genetic diseases. Computational tools for the prediction of the effects of mutations on protein function are very important for analysis of single nucleotide variants and their prioritization for experimental characterization. Many computational tools are already widely employed for this purpose. Unfortunately, their comparison and further improvement is hindered by large overlaps between the training datasets and benchmark datasets, which lead to biased and overly optimistic reported performances. In this study, we have constructed three independent datasets by removing all duplicities, inconsistencies and mutations previously used in the training of evaluated tools. The benchmark dataset containing over 43,000 mutations was employed for the unbiased evaluation of eight established prediction tools: MAPP, nsSNPAnalyzer, PANTHER, PhD-SNP, PolyPhen-1, PolyPhen-2, SIFT and SNAP. The six best performing tools were combined into a consensus classifier PredictSNP, resulting into significantly improved prediction performance, and at the same time returned results for all mutations, confirming that consensus prediction represents an accurate and robust alternative to the predictions delivered by individual tools. A user-friendly web interface enables easy access to all eight prediction tools, the consensus classifier PredictSNP and annotations from the Protein Mutant Database and the UniProt database. The web server and the datasets are freely available to the academic community at http://loschmidt.chemi.muni.cz/predictsnp.

Erratum to “New Optical Methods for Liveness Detection on Fingers”

Abstract: In the paper titled “New optical methods for liveness detection on fingers,” the address of the first author (Martin Drahansky) was incomplete; International Clinical Research Center, Center of Biomedical Engineering, St. Anne's University Hospital Brno, Pekarska 53, 656 91 Brno, Czech Republic was missing.

Automatic language identification using deep neural networks

Abstract: This work studies the use of deep neural networks (DNNs) to address automatic language identification (LID). Motivated by their recent success in acoustic modelling, we adapt DNNs to the problem of identifying the language of a given spoken utterance from short-term acoustic features. The proposed approach is compared to state-of-the-art i-vector based acoustic systems on two different datasets: Google 5M LID corpus and NIST LRE 2009. Results show how LID can largely benefit from using DNNs, especially when a large amount of training data is available. We found relative improvements up to 70%, in C avg , over the baseline system.

Multi-Scale Gaussian Normalization for Solar Image Processing

Abstract: Extreme ultra-violet images of the corona contain information over a wide range of spatial scales, and different structures such as active regions, quiet Sun, and filament channels contain information at very different brightness regimes. Processing of these images is important to reveal information, often hidden within the data, without introducing artefacts or bias. It is also important that any process be computationally efficient, particularly given the fine spatial and temporal resolution of Atmospheric Imaging Assembly on the Solar Dynamics Observatory (AIA/SDO), and consideration of future higher resolution observations. A very efficient process is described here, which is based on localised normalising of the data at many different spatial scales. The method reveals information at the finest scales whilst maintaining enough of the larger-scale information to provide context. It also intrinsically flattens noisy regions and can reveal structure in off-limb regions out to the edge of the field of view. We also applied the method successfully to a white-light coronagraph observation.

Inaccuracies in additive manufactured medical skull models caused by the DICOM to STL conversion process

Abstract: Introduction The process of fabricating physical medical skull models requires many steps, each of which is a potential source of geometric error. The aim of this study was to demonstrate inaccuracies and differences caused by DICOM to STL conversion in additively manufactured medical skull models. Material and methods Three different institutes were requested to perform an automatic reconstruction from an identical DICOM data set of a patients undergoing tumour surgery into an STL file format using their software of preference. The acquired digitized STL data sets were assessed and compared and subsequently used to fabricate physical medical skull models. The three fabricated skull models were then scanned, and differences in the model geometries were assessed using established CAD inspection software methods. Results A large variation was noted in size and anatomical geometries of the three physical skull models fabricated from an identical (or “a single”) DICOM data set. Conclusions A medical skull model of the same individual can vary markedly depending on the DICOM to STL conversion software and the technical parameters used. Clinicians should be aware of this inaccuracy in certain applications.

Utilization of oil extracted from spent coffee grounds for sustainable production of polyhydroxyalkanoates.

Abstract: Spent coffee grounds (SCG), an important waste product of the coffee industry, contain approximately 15 wt% of coffee oil. The aim of this work was to investigate the utilization of oil extracted from SCG as a substrate for the production of poly(3-hydroxybutyrate) (PHB) by Cupriavidus necator H16. When compared to other waste/inexpensive oils, the utilization of coffee oil resulted in the highest biomass as well as PHB yields. Since the correlation of PHB yields and the acid value of oil indicated a positive effect of the presence of free fatty acids in oil on PHB production (correlation coefficient R 2 = 0.9058), superior properties of coffee oil can be probably attributed to the high content of free fatty acids which can be simply utilized by the bacteria culture. Employing the fed-batch mode of cultivation, the PHB yields, the PHB content in biomass, the volumetric productivity, and the Y P/S yield coefficient reached 49.4 g/l, 89.1 wt%, 1.33 g/(l h), and 0.82 g per g of oil, respectively. SCG are annually produced worldwide in extensive amounts and are disposed as solid waste. Hence, the utilization of coffee oil extracted from SCG is likely to improve significantly the economic aspects of PHB production. Moreover, since oil extraction decreased the calorific value of SCG by only about 9 % (from 19.61 to 17.86 MJ/kg), residual SCG after oil extraction can be used as fuel to at least partially cover heat and energy demands of fermentation, which should even improve the economic feasibility of the process.

Size, Shape, Stability, and Color of Plasmonic Silver Nanoparticles

Abstract: The remarkable relationship between the size, shape, and optical properties of silver nanoparticles is proving to be very useful in a range of high performance applications. Considerable effort and investment are focused on delivering silver nanoparticles with precise morphologies. However, the reliability of these particles is contingent upon the morphological stability, particularly against variations in the thermodynamic environment, such as changes in temperature. Using a combination of computational and theoretical approaches, we have constructed a size- and shape-dependent phase diagram of nanoscale silver and projected the optical emission spectrum to produce a detailed structure/property map at thermal equilibrium. This map demonstrates that faceted near-spherical shapes and spheres are the predominant morphologies in a Ag NPs colloidal sample at low and high temperatures, showing a light yellow color. However, samples with more faceted shapes such as cubes or tetrahedrons, which gain stability at...

Succession and replacement of bacterial populations in the caecum of egg laying hens over their whole life.

Abstract: In this study we characterised the development of caecal microbiota in egg laying hens over their commercial production lifespan, from the day of hatching until 60 weeks of age. Using pyrosequencing of V3/V4 variable regions of 16S rRNA genes for microbiota characterisation, we were able to define 4 different stages of caecal microbiota development. The first stage lasted for the first week of life and was characterised by a high prevalence of Enterobacteriaceae (phylum Proteobacteria). The second stage lasted from week 2 to week 4 and was characterised by nearly an absolute dominance of Lachnospiraceae and Ruminococcaceae (both phylum Firmicutes). The third stage lasted from month 2 to month 6 and was characterised by the succession of Firmicutes at the expense of Bacteroidetes. The fourth stage was typical for adult hens in full egg production aged 7 months or more and was characterised by a constant ratio of Bacteroidetes and Firmicutes formed by equal numbers of the representatives of both phyla.

Wear Debris Characterization and Corresponding Biological Response: Artificial Hip and Knee Joints.

Abstract: Wear debris, of deferent sizes, shapes and quantities, generated in artificial hip and knees is largely confined to the bone and joint interface. This debris interacts with periprosthetic tissue and may cause aseptic loosening. The purpose of this review is to summarize and collate findings of the recent demonstrations on debris characterization and their biological response that influences the occurrence in implant migration. A systematic review of peer-reviewed literature is performed, based on inclusion and exclusion criteria addressing mainly debris isolation, characterization, and biologic responses. Results show that debris characterization largely depends on their appropriate and accurate isolation protocol. The particles are found to be non-uniform in size and non-homogeneously distributed into the periprosthetic tissues. In addition, the sizes, shapes, and volumes of the particles are influenced by the types of joints, bearing geometry, material combination, and lubricant. Phagocytosis of wear debris is size dependent; high doses of submicron-sized particles induce significant level of secretion of bone resorbing factors. However, articles on wear debris from engineered surfaces (patterned and coated) are lacking. The findings suggest considering debris morphology as an important parameter to evaluate joint simulator and newly developed implant materials.

Adaptation of multilingual stacked bottle-neck neural network structure for new language

Abstract: The neural network based features became an inseparable part of state-of-the-art LVCSR systems. In order to perform well, the network has to be trained on a large amount of in-domain data. With the increasing emphasis on fast development of ASR system on limited resources, there is an effort to alleviate the need of in-domain data. To evaluate the effectiveness of other resources, we have trained the Stacked Bottle-Neck neural networks structure on multilingual data investigating several training strategies while treating the target language as the unseen one. Further, the systems were adapted to the target language by re-training. Finally, we evaluated the effect of adaptation of individual NNs in the Stacked Bottle-Neck structure to find out the optimal adaptation strategy. We have shown that the adaptation can significantly improve system performance over both, the multilingual network and network trained only on target data. The experiments were performed on Babel Year 1 data.

Automatic Camera Calibration for Traffic Understanding.

Abstract: We propose a method for fully automatic calibration of traffic surveillance cameras. This method allows for calibration of the camera – including scale – without any user input, only from several minutes of input surveillance video. The targeted applications include speed measurement, measurement of vehicle dimensions, vehicle classification, etc. The first step of our approach is camera calibration by determining three vanishing points defining the stream of vehicles. The second step is construction of 3D bounding boxes of individual vehicles and their measurement up to scale. We propose to first construct the projection of the bounding boxes and then, by using the camera calibration obtained earlier, create their 3D representation. In the third step, we use the dimensions of the 3D bounding boxes for calibration of the scene scale. We collected a dataset with ground truth speed and distance measurements and evaluate our approach on it. The achieved mean accuracy of speed and distance measurement is below 2%. Our efficient C++ implementation runs in real time on a low-end processor (Core i3) with a safe margin even for full-HD videos.

Serum and tissue zinc in epithelial malignancies: a meta-analysis.

Abstract: Background and Objectives: Current studies give us inconsistent results regarding the association of neoplasms and zinc(II) serum and tissues concentrations The results of to-date studies using meta-analysis are summarized in this paper Methods: Web of Science (Science citation index expanded), PubMed (Medline), Embase and CENTRAL were searched Articles were reviewed by two evaluators; quality was assessed by Newcastle-Ottawa scale; meta-analysis was performed including meta-regression and publication bias analysis Results: Analysis was performed on 114 case control, cohort and cross-sectional studies of 22737 participants Decreased serum zinc level was found in patients with lung (effect size = -104), head and neck (effect size = -143), breast (effect size = -093), liver (effect size = -229), stomach (effect size = -159), and prostate (effect size = -136) cancers; elevation was not proven in any tumor More specific zinc patterns are evident at tissue level, showing increase in breast cancer tissue (effect size = 180) and decrease in prostatic (effect size = -390), liver (effect size = -826), lung (effect size = -312), and thyroid cancer (effect size = -284) The rest of the included tumors brought ambiguous results, both in serum and tissue zinc levels across the studies The association between zinc level and stage or grade of tumor has not been revealed by meta-regression Conclusion: This study provides evidence on cancer-specific tissue zinc level alteration Although serum zinc decrease was associated with most tumors mentioned herein, further - prospective - studies are needed

Ink-and-ray: Bas-relief meshes for adding global illumination effects to hand-drawn characters

Abstract: We present a new approach for generating global illumination renderings of hand-drawn characters using only a small set of simple annotations. Our system exploits the concept of bas-relief sculptures, making it possible to generate 3D proxies suitable for rendering without requiring side-views or extensive user input. We formulate an optimization process that automatically constructs approximate geometry sufficient to evoke the impression of a consistent 3D shape. The resulting renders provide the richer stylization capabilities of 3D global illumination while still retaining the 2D hand-drawn look-and-feel. We demonstrate our approach on a varied set of hand-drawn images and animations, showing that even in comparison to ground-truth renderings of full 3D objects, our bas-relief approximation is able to produce convincing global illumination effects, including self-shadowing, glossy reflections, and diffuse color bleeding.

String Constraints for Verification

Abstract: We present a decision procedure for a logic that combines (i)aword equations over string variables denoting words of arbitrary lengths, together with (ii)aconstraints on the length of words, and on (iii)athe regular languages to which words belong. Decidability of this general logic is still open. Our procedure is sound for the general logic, and a decision procedure for a particularly rich fragment that restricts the form in which word equations are written. In contrast to many existing procedures, our method does not make assumptions about the maximum length of words. We have developed a prototypical implementation of our decision procedure, and integrated it into a CEGAR-based model checker for the analysis of programs encoded as Horn clauses. Our tool is able to automatically establish the correctness of several programs that are beyond the reach of existing methods.

Modelling elastic wave propagation using the k-Wave MATLAB Toolbox

Abstract: A new model for simulating elastic wave propagation using the open-source k-Wave MATLAB Toolbox is described. The model is based on two coupled first-order equations describing the stress and particle velocity within an isotropic medium. For absorbing media, the Kelvin-Voigt model of viscoelasticity is used. The equations are discretised in 2D and 3D using an efficient time-stepping pseudospectral scheme. This uses the Fourier collocation spectral method to compute spatial derivatives and a leapfrog finite-difference scheme to integrate forwards in time. A multi-axial perfectly matched layer (M-PML) is implemented to allow free-field simulations using a finite-sized computational grid. Acceleration using a graphics processing unit (GPU) is supported via the MATLAB Parallel Computing Toolbox. An overview of the simulation functions and their theoretical and numerical foundations is described.

Bulk-driven floating-gate and bulk-driven quasi-floating-gate techniques for low-voltage low-power analog circuits design

Abstract: In this paper, novel non-conventional techniques, 1 named by the author of this paper “bulk-driven floating-gate (BD-FG)” MOS transistor (MOST) and “bulk-driven quasi-floating-gate (BD-QFG) MOST” for low-voltage (LV) low-power (LP) analog circuit design are presented. These novel techniques appear as a good solution to merge the advantages of floating-gate (FG) and quasi-floating-gate (QFG) with the advantages of bulk-driven (BD) technique and suppress their disadvantages. Consequently, the transconductance and transient frequency of BD-FG and BD-QFG MOSTs approach the conventional gate driven (GD) MOST values. Furthermore, a novel LV LP class AB second generation current conveyor based on BD-FG MOST is presented in this paper as an example. The supply voltage is only ±0.4 V with a rail-to-rail voltage swing capability and total power consumption of mere 10 μW. PSpice simulation results using the 0.18 μm P-well CMOS technology are included to confirm the attractive properties of these new techniques.

Pilot study of the wrist orthosis design process

Abstract: Purpose – The purpose of this paper is to describe a manufacturing methodology for a wrist orthosis. The case study aims to offer new approaches in the area of human orthoses. Design/methodology/approach – The article describes the utilization of rapid prototyping (RP), passive stereo photogrammetry and software tools for the orthosis design process. This study shows the key points of the design and manufacturing methodology. The approach uses specific technologies, such as 3D digitizing, reverse engineering and polygonal-surface software, FDM RP and 3D printing. Findings – The results show that the used technologies reflect the patient's requirements and also they could be an alternative solution to the standard method of orthosis design. Research limitations/implications – The methodology provides a good position for further development issues. Practical implications – The methodology could be usable for clinical practice and allows the manufacturing of the perfect orthosis of the upper limb. The usage ...