Search results for: Filip Rusak

Authors: Filip Rusak, Yulia Arzhaeva, Dadong Wang

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Machine learning based Computer-Aided Diagnosis (CAD) is gaining much popularity in medical imaging and diagnostic radiology. However, it requires a large amount of high quality and labeled training image datasets. The training images may come from different sources and be acquired from different radiography machines produced by different manufacturers, digital or digitized copies of film radiographs, with various sizes as well as different pixel intensity distributions. In this paper, a content-aware image augmentation method is presented to deal with these variations. The results of the proposed method have been validated graphically by plotting the removed and added seams of pixels on original images. Two different chest X-ray (CXR) datasets are used in the experiments. The CXRs in the datasets defer in size, some are digital CXRs while the others are digitized from analog CXR films. With the proposed content-aware augmentation method, the Seam Carving algorithm is employed to resize CXRs and the corresponding labels in the form of image masks, followed by histogram matching used to normalize the pixel intensities of digital radiography, based on the pixel intensity values of digitized radiographs. We implemented the algorithms, resized the well-known Montgomery dataset, to the size of the most frequently used Japanese Society of Radiological Technology (JSRT) dataset and normalized our digital CXRs for testing. This work resulted in the unified off-the-shelf CXR dataset composed of radiographs included in both, Montgomery and JSRT datasets. The experimental results show that even though the amount of augmentation is large, our algorithm can preserve the important information in lung fields, local structures, and global visual effect adequately. The proposed method can be used to augment training and testing image data sets so that the trained machine learning model can be used to process CXRs from various sources, and it can be potentially used broadly in any medical imaging applications.

Keywords: computer-aided diagnosis, image augmentation, lung segmentation, medical imaging, seam carving

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Authors: Ewa Rusak, Sebastian Seget, Aleksandra Mroskowiak, Mirosław Partyka, Ewa Samulska, Julia Strózik, Anna Wilk, Przemysława Jarosz-Chobot

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Introduction: Various infections can affect children suffering from Type 1 Diabetes (T1D) because of dysfunctions of the immune system. The urinary tract and urethra of these children can be easily infected areas because of glycosuria. Aim: The microflora assessment of the urethra area of children with newly diagnosed T1D. Methods: The materials of the study were swabs taken prospectively from the urethral area of 63 children at the time of diagnosis of T1D (37 boys), then the results were correlated to the clinical parameters. In the statistical analysis, there were T student, Chi square, and U Mann-Whitney tests used. Results: The mean age was 9.4 years (6 months-17.4 years). The mean HbA1c value was 12.1% (5,6% - 20.1%). The mean value of glycosuria was 4463.2 mg/dl (0 - 9770 mg/dl). Ketoacidosis was diagnosed in 29 children (49%). The following microbial species were isolated in the collected materials: Staphylococcus epidermidis in 18 children (28.6%), Enterococcus faecalis in 17 children (27%), Candida albicans in 15 children (23.8%), coagulase-negative staphylococciin 11 children (17.5%), group B Streptococcus beta-hemolysis in 10 children (15.9%), S. aureus, E. coli, S. anginosus, C. glucuronolyticum, and A. urinae in 7 children each (11.1%), group B Streptococcus beta-hemolysis and S. hominis in 6 children each (9.5%), L. gasseri in 5 children (7.5%), C. dubliniensis in 4 children (6.3) and other, isolated cases. 2 of diagnosed patients were cultured negatively (3.2%). There were statistical correlations between the type of colonisation and patients’ sex and HbA1C value. Conclusions: It is extremely important to examine the urethral area at the time of diagnosis of T1D in order to detect inflammation and to undertake the appropriate and effective intervention.

Keywords: diabetology, skin disorders, microbiology, microflora

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Authors: Robert Prucek, Aleš Panáček, Jan Filip, Libor Kvítek, Radek Zbořil

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The preparation of Cu nanoparticles (NPs) through the reduction of copper ions by sodium borohydride in the presence of sodium polyacrylate with a molecular weight of 1200 is reported. Cu NPs were synthesized at a concentration of copper salt equal to 2.5, 5, and 10 mM, and at a molar ratio of copper ions and monomeric unit of polyacrylate equal to 1:2. The as-prepared Cu NPs have diameters of about 2.5–3 nm for copper concentrations of 2.5 and 5 mM, and 6 nm for copper concentration of 10 mM. Depending on the copper salt concentration and concentration of additionally added polyacrylate to Cu particle dispersion, primarily formed NPs grow through the process of aggregation and/or coalescence into clusters and/or particles with a diameter between 20–100 nm. The amount of additionally added sodium polyacrylate influences the stability of Cu particles against air oxidation. The catalytic efficiency of the prepared Cu particles for the reduction of 4-nitrophenol is discussed.

Keywords: copper, nanoparticles, sodium polyacrylate, catalyst, 4-nitrophenol

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Authors: Mohsin Raza, Arne Bilberg, Thomas Ditlev Brunø, Ann-Louise Andersen, Filip SKärin

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Shifting from a dedicated or flexible manufacturing system to a reconfigurable manufacturing system (RMS) requires a significant amount of time, money, and effort. Therefore, it is vital to verify beforehand that the potential reconfigurable solution will be able to achieve the organizational objectives. Discrete event simulation offers the opportunity of assessing several reconfigurable alternatives against the set objectives. This study signifies the importance of using discrete-event simulation as a tool to verify several reconfiguration options. Two different industrial cases have been presented in the study to elaborate on the role of discrete event simulation in the implementation methodology of RMSs. The study concluded that discrete event simulation is one of the important tools to consider in the RMS implementation methodology.

Keywords: reconfigurable manufacturing system, discrete event simulation, Tecnomatix plant simulation, RMS

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Authors: Amelia Tero-Vescan, Camil-Eugen Vari, Laura Ciulea, Cristina Filip, Silvia Imre

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A HPLC –UV method for the identification of ephedrine (EPH), sibutramine (SB), yohimbine (Y) and caffeine (CF) was developed. Separation was performed on a Kromasil 100-RP8, 150 mm x 4.6 mm, 5 mm column equipped with a precolumn Kromasil RP 8. Mobile phase was a gradient of 80-35 % sodium dihydrogen phosphate pH=5 with NH4OH and acetonitrile over 15 minutes time of analysis. Based on the responses of 113 athletes about dietary supplements (DS) consumed for "fat burning" and weight loss which have a legal status in Romania, 28 supplements have been selected and investigated for their content in CF, Y, legal substances, and SB, EPH (prohibited substances in DS). The method allows quantitative determination of the four substances in a short analysis time and with minimum cost. The presence of SB and EPH in the analyzed DS was not detected while the content in CF and Y considering the dosage recommended by the manufacturer does not affect the health of the consumers. DS labeling (plant extracts with CF and Y content) allows manufacturers to avoid declaring correct and exact amounts per pharmaceutical form (pure CF or equivalent and Y, respectively).

Keywords: dietary supplements, sibutramine, ephedrine, yohimbine, caffeine, HPLC

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Authors: Mengfan Li, Filip Van Bockstaele, Wenyong Lou, Frank Devlighere

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The development of probiotics-encapsulated emulsions that maintain the viability of probiotics during processing, storage and human gastrointestinal (GI) tract environment receives great scientific and commercial interest. In this study, typical W/O and O/W emulsions with and without oil gelation were used to encapsulate L. plantarum. The effects of emulsion types on the viability of L. plantarum during storage and GI tract were investigated. Besides, the position of L. plantarum in emulsion system and its number of viable cells when threating by adverse environment was correlated in order to figure out which type of emulsion is more suitable as food carrier for probiotics encapsulation and protection. As a result, probiotics tend to migrate from oil to water phase due to the natural hydrophilicity; however, it’s harmful for cells viability when surrounding by water for a long time. Oil gelation in emulsions is one of the promising strategies for inhibiting the cells mobility and decreasing the contact with adverse factors (e.g., water, exogenous enzymes and gastric acid), thus enhancing the number of viable cells that enough to exert its beneficial effects in host.

Keywords: emulsion, gelation, encapsulation, probiotics

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Authors: Eleni Tsangouri, Xander Hillewaere, David Garoz Gómez, Dimitrios Aggelis, Filip Du Prez, Danny Van Hemelrijck

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Tapered Double Cantilever Beam (TDCB) is the most commonly used test set-up to evaluate the self-healing feature of thermoset polymers autonomously activated in the presence of crack. TDCB is a modification of the established fracture mechanics set-up of Double Cantilever Beam and is designed to provide constant strain energy release rate with crack length under stable load evolution (mode-I). In this study, the damage of virgin and autonomously healed TDCB polymer samples is evaluated considering the load-crack opening diagram, the strain maps provided by Digital Image Correlation technique and the fractography maps given by optical microscopy. It is shown that the pre-crack introduced prior to testing (razor blade tapping), the loading rate and the length of the side groove are the features that dominate the crack propagation and lead to inconstant fracture energy release rate.

Keywords: polymers, autonomous healing, fracture, tapered double cantilever beam

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Authors: Filip Dodigovic, Kreso Ivandic, Damir Stuhec, S. Strelec

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The general difference analysis between the former and new design concepts in geotechnical engineering is carried out. The application of new regulations results in the need for real adaptation of the computation principles of limit states, i.e. by providing a uniform way of analyzing engineering tasks. Generally, it is not possible to unambiguously match the limit state verification procedure with those in the construction engineering. The reasons are the inability to fully consistency of the common probabilistic basis of the analysis, and the fundamental effect of material properties on the value of actions and the influence of actions on resistance. Consequently, it is not possible to apply separate factorization with partial coefficients, as in construction engineering. For the slope stability analysis design procedures problems in the light of the use of limit states in relation to the concept of allowable stresses is detailed in. The quantifications of the safety margins in the slope stability analysis for both approaches is done. When analyzing the stability of the slope, by the strict application of the adopted forms from the new regulations for significant external temporary and/or seismic actions, the equivalent margin of safety is increased. The consequence is the emergence of more conservative solutions.

Keywords: allowable pressure, Eurocode 7, limit states, slope stability

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Authors: Loredana G. Marcu, David Marcu, Sanda M. Filip

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Advanced head and neck cancers are aggressive tumours, which require aggressive treatment. Treatment efficiency is often hindered by cancer cell repopulation during radiotherapy, which is due to various mechanisms triggered by the loss of tumour cells and involves both stem and differentiated cells. The aim of the current paper is to present in silico simulations of radiotherapy schedules on a virtual head and neck tumour grown with biologically realistic kinetic parameters. Using the linear quadratic formalism of cell survival after radiotherapy, altered fractionation schedules employing various treatment breaks for normal tissue recovery are simulated and repopulation mechanism implemented in order to evaluate the impact of various cancer cell contribution on tumour behaviour during irradiation. The model has shown that the timing of treatment breaks is an important factor influencing tumour control in rapidly proliferating tissues such as squamous cell carcinomas of the head and neck. Furthermore, not only stem cells but also differentiated cells, via the mechanism of abortive division, can contribute to malignant cell repopulation during treatment.

Keywords: radiation, tumour repopulation, squamous cell carcinoma, stem cell

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Authors: Filip Jaroš

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The Swiss scholar Adolf Portmann (1897-1982) was an outstanding figure in the history of biology and the philosophy of the life sciences. Portmann’s biological theory is primarily focused on the problem of animal form (Gestalt), and it poses a significant counterpart to neo-Darwinian theories about the explanatory primacy of a genetic level over the outer appearance of animals. Besides that, Portmann’s morphological studies related to species-specific ontogeny and the influence of environmental surroundings can be classified as the antecedents of contemporary synthetic approaches such as “eco-evo-devo, “extended synthesis or biosemiotics. The most influential of Portmann’s concepts up to the present is his thesis of a social womb (Soziale Mutterschos): human children are born physiologically premature in comparison with other primates, and they find a second womb in a social environment nurturing their healthy development. It is during the first year of extra-uterine life when a specific human nature is formed, characterized by the strong tie between an individual and a broader historical, cultural whole. In my paper, I will closely analyze: a) the historical coordinates of Portmann’s philosophy of the life sciences (e.g., the philosophical anthropology of A. Gehlen, H. Plessner, and their concept of humans as beings “open to the world”), b) the relation of Portmann’s concept of the social womb to contemporary theories of infant birth evolution.

Keywords: adolf portmann, extended synthesis, philosophical anthropology, social womb

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Authors: Jan Jezek, Zdenek Pilat, Filip Smatlo, Pavel Zemanek

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We present a device that combines fluorescence spectroscopy with fiber optics and dielectrophoretic micromanipulation in PDMS (poly-(dimethylsiloxane)) microfluidic chips. The device allows high speed detection (in the order of kHz) of the fluorescence signal, which is coming from the sample by an inserted optical fiber, e.g. from a micro-droplet flow in a microfluidic chip, or even from the liquid flowing in the transparent capillary, etc. The device uses a laser diode at a wavelength suitable for excitation of fluorescence, excitation and emission filters, optics for focusing the laser radiation into the optical fiber, and a highly sensitive fast photodiode for detection of fluorescence. The device is combined with dielectrophoretic sorting on a chip for sorting of micro-droplets according to their fluorescence intensity. The electrodes are created by lift-off technology on a glass substrate, or by using channels filled with a soft metal alloy or an electrolyte. This device found its use in screening of enzymatic reactions and sorting of individual fluorescently labelled microorganisms. The authors acknowledge the support from the Grant Agency of the Czech Republic (GA16-07965S) and Ministry of Education, Youth and Sports of the Czech Republic (LO1212) together with the European Commission (ALISI No. CZ.1.05/2.1.00/01.0017).

Keywords: dielectrophoretic sorting, fiber optics, laser, microfluidic chips, microdroplets, spectroscopy

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Authors: Kreso Ivandic, Filip Dodigovic, Damir Stuhec

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The paper deals with the proposed 'Material' and 'Action-resistance factor' design methods in designing the embedded retaining walls. The parametric analysis of evaluating the differences of the output values mutually and compared with classic approach computation was performed. There is a challenge with the criteria for choosing the proposed calculation design methods in Eurocode 7 with respect to current technical regulations and regular engineering practice. The basic criterion for applying a particular design method is to ensure minimum an equal degree of reliability in relation to the current practice. The procedure of combining the relevant partial coefficients according to design methods was carried out. The use of mentioned partial coefficients should result in the same level of safety, regardless of load combinations, material characteristics and problem geometry. This proposed approach of the partial coefficients related to the material and/or action-resistance should aimed at building a bridge between calculations used so far and pure probability analysis. The measure to compare the results was to determine an equivalent safety factor for each analysis. The results show a visible wide span of equivalent values of the classic safety factors.

Keywords: action-resistance factor design, classic approach, embedded retaining wall, Eurocode 7, limit states, material factor design

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Authors: Filip Stojcevski, Tim Hilditch, Luke Henderson

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Although carbon fibre composites are becoming ever more prominent in the engineering industry, interfacial failure still remains one of the most common limitations to material performance. Carbon fiber surface treatments have played a major role in advancing composite properties however research into the influence of manufacturing variables on a fiber manufacturing line is lacking. This project investigates the impact of altering carbon fiber manufacturing conditions on a production line (specifically electrochemical oxidization and sizing variables) to assess fiber-matrix adhesion. Pristine virgin fibers were manufactured and interfacial adhesion systematically assessed from a microscale (single fiber) to a mesoscale (12k tow), and ultimately a macroscale (laminate). Correlations between interfacial shear strength (IFSS) at each level is explored as a function of known interfacial bonding mechanisms; namely mechanical interlocking, chemical adhesion and fiber wetting. Impact of these bonding mechanisms is assessed through extensive mechanical, topological and chemical characterisation. They are correlated to performance as a function of IFSS. Ultimately this study provides a bottoms up approach to improving composite laminates. By understanding the scaling effects from a singular fiber to a composite laminate and linking this knowledge to specific bonding mechanisms, material scientists can make an informed decision on the manufacturing conditions most beneficial for interfacial adhesion.

Keywords: carbon fibers, interfacial adhesion, surface treatment, sizing

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Authors: Filip Buruiana, Alexander Hall, Reimar Hofmann, Thomas Hofmann, Silviu Ganceanu, Alexandru Tudorica

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In-memory column-stores make interactive analysis feasible for many big data scenarios. PowerDrill is a system used internally at Google for exploration in logs data. Even though it is a highly parallelized column-store and uses in memory caching, interactive response times cannot be achieved for all datasets (note that it is common to analyze data with 50 billion records in PowerDrill). In this paper, we investigate two orthogonal approaches to optimize performance at the expense of an acceptable loss of accuracy. Both approaches can be implemented as outer wrappers around existing database engines and so they should be easily applicable to other systems. For the first optimization we show that memory is the limiting factor in executing queries at speed and therefore explore possibilities to improve memory efficiency. We adapt some of the theory behind data sketches to reduce the size of particularly expensive fields in our largest tables by a factor of 4.5 when compared to a standard compression algorithm. This saves 37% of the overall memory in PowerDrill and introduces a 0.4% relative error in the 90th percentile for results of queries with the expensive fields. We additionally evaluate the effects of using sampling on accuracy and propose a simple heuristic for annotating individual result-values as accurate (or not). Based on measurements of user behavior in our real production system, we show that these estimates are essential for interpreting intermediate results before final results are available. For a large set of queries this effectively brings down the 95th latency percentile from 30 to 4 seconds.

Keywords: big data, in-memory column-store, high-performance SQL queries, approximate SQL queries

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Authors: Filip Franciszek Karuga, Szymon Turkiewicz, Marta Ditmer, Marcin Sochal, Piotr Białasiewicz, Agata Gabryelska

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Circadian rhythm, an internal coordinator of physiological processes is composed of a set of semi-autonomous clocks. Clocks are regulated through the expression of circadian clock genes which form feedback loops, creating an oscillator. The primary loop consists of activators: CLOCK, BMAL1 and repressors: CRY, PER. CLOCK can be substituted by the Neuronal PAS Domain Protein 2 (NPAS2). Orphan nuclear receptor (REV-ERB-α) is a component of the secondary major loop, modulating the expression of BMAL1. Circadian clocks might be disrupted by the obstructive sleep apnea (OSA), which has also been associated with type II diabetes mellitus (DM2). Interestingly, studies suggest that dysregulation of NPAS2 and REV-ERB-α might contribute to the pathophysiology of DM2 as well. The goal of our study was to examine the role of NPAS2 and REV-ERB-α in DM2 in OSA patients. After examination of the clinical data, all participants underwent polysomnography (PSG) to assess their apnea-hypopnea index (AHI). Based on the acquired data participants were assigned to one of 3 groups: OSA (AHI>30, no DM2; n=17 for NPAS2 and 34 for REV-ERB-α), DM2 (AHI>30 + DM2; n=7 for NPAS2 and 15 for REV-ERB-α) and control group (AHI<5, no DM2; n=16 for NPAS2 and 31 for REV-ERB-α). ELISA immunoassay was performed to assess the serum protein level of REV-ERB-α and NPAS2. The only statistically significant difference between groups was observed in NPAS2 protein level (p=0.037). Post-hoc analysis showed significant differences between the OSA and the control group (p=0.017). AHI and NPAS2 level was significantly correlated (r=-0.478, p=0.002) in all groups. A significant correlation was observed between the REV-ERB-α level and sleep efficiency (r=0.617, p=0.005) as well as sleep maintenance efficiency (r=0.645, p=0.003) in the OSA group. We conclude, that NPAS2 is associated with OSA severity and might contribute to metabolic sequelae of this disease. REV-ERB-α on the other hand can influence sleep continuity and efficiency.

Keywords: OSA, diabetes mellitus, endocrinology, chronobiology

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Authors: Sammy Kibor, Filip Huyghe, Marc Kochzius, James Kairo

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Goldstripe Sardinella, Sardinella gibbosa, (Bleeker, 1849) is a commercially and ecologically important small pelagic fish common in the Western Indian Ocean region. The present study aimed to assess genetic diversity and population structure of the species in the Kenya-Tanzania transboundary area using mtDNA and msDNA markers. Some 630 bp sequence in the mitochondrial DNA (mtDNA) Cytochrome C Oxidase I (COI) and five polymorphic microsatellite DNA loci were analyzed. Fin clips of 309 individuals from eight locations within the transboundary area were collected between July and December 2018. The S. gibbosa individuals from the different locations were distinguishable from one another based on the mtDNA variation, as demonstrated with a neighbor-joining tree and minimum spanning network analysis. None of the identified 22 haplotypes were shared between Kenya and Tanzania. Gene diversity per locus was relatively high (0.271-0.751), highest Fis was 0.391. The structure analysis, discriminant analysis of Principal component (DAPC) and the pair-wise (FST = 0.136 P < 0.001) values after Bonferroni correction using five microsatellite loci provided clear inference on genetic differentiation and thus evidence of population structure of S. gibbosa along the Kenya-Tanzania coast. This study shows a high level of genetic diversity and the presence of population structure (Φst =0.078 P < 0.001) resulting to the existence of four populations giving a clear indication of minimum gene flow among the population. This information has application in the designing of marine protected areas, an important tool for marine conservation.

Keywords: marine connectivity, microsatellites, population genetics, transboundary

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Authors: Nicolò Vaiana, Filip C. Filippou, Giorgio Serino

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The solution of the nonlinear dynamic equilibrium equations of base-isolated structures adopting a conventional monolithic solution approach, i.e. an implicit single-step time integration method employed with an iteration procedure, and the use of existing nonlinear analytical models, such as differential equation models, to simulate the dynamic behavior of seismic isolators can require a significant computational effort. In order to reduce numerical computations, a partitioned solution method and a one dimensional nonlinear analytical model are presented in this paper. A partitioned solution approach can be easily applied to base-isolated structures in which the base isolation system is much more flexible than the superstructure. Thus, in this work, the explicit conditionally stable central difference method is used to evaluate the base isolation system nonlinear response and the implicit unconditionally stable Newmark’s constant average acceleration method is adopted to predict the superstructure linear response with the benefit in avoiding iterations in each time step of a nonlinear dynamic analysis. The proposed mathematical model is able to simulate the dynamic behavior of seismic isolators without requiring the solution of a nonlinear differential equation, as in the case of widely used differential equation model. The proposed mixed explicit-implicit time integration method and nonlinear exponential model are adopted to analyze a three dimensional seismically isolated structure with a lead rubber bearing system subjected to earthquake excitation. The numerical results show the good accuracy and the significant computational efficiency of the proposed solution approach and analytical model compared to the conventional solution method and mathematical model adopted in this work. Furthermore, the low stiffness value of the base isolation system with lead rubber bearings allows to have a critical time step considerably larger than the imposed ground acceleration time step, thus avoiding stability problems in the proposed mixed method.

Keywords: base-isolated structures, earthquake engineering, mixed time integration, nonlinear exponential model

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Authors: Nicolò Vaiana, Filip C. Filippou, Giorgio Serino

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In order to reduce numerical computations in the nonlinear dynamic analysis of seismically base-isolated structures, a Mixed Explicit-Implicit time integration Method (MEIM) has been proposed. Adopting the explicit conditionally stable central difference method to compute the nonlinear response of the base isolation system, and the implicit unconditionally stable Newmark’s constant average acceleration method to determine the superstructure linear response, the proposed MEIM, which is conditionally stable due to the use of the central difference method, allows to avoid the iterative procedure generally required by conventional monolithic solution approaches within each time step of the analysis. The main aim of this paper is to investigate the stability and computational efficiency of the MEIM when employed to perform the nonlinear time history analysis of base-isolated structures with sliding bearings. Indeed, in this case, the critical time step could become smaller than the one used to define accurately the earthquake excitation due to the very high initial stiffness values of such devices. The numerical results obtained from nonlinear dynamic analyses of a base-isolated structure with a friction pendulum bearing system, performed by using the proposed MEIM, are compared to those obtained adopting a conventional monolithic solution approach, i.e. the implicit unconditionally stable Newmark’s constant acceleration method employed in conjunction with the iterative pseudo-force procedure. According to the numerical results, in the presented numerical application, the MEIM does not have stability problems being the critical time step larger than the ground acceleration one despite of the high initial stiffness of the friction pendulum bearings. In addition, compared to the conventional monolithic solution approach, the proposed algorithm preserves its computational efficiency even when it is adopted to perform the nonlinear dynamic analysis using a smaller time step.

Keywords: base isolation, computational efficiency, mixed explicit-implicit method, partitioned solution approach, stability

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Authors: Ante Turudic, Filip Varga, Zlatko Liber, Jernej Jakse, Zlatko Satovic, Ivan Radosavljevic, Martina Grdisa

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Microsatellites (SSRs) are highly informative repetitive sequences of 2-6 base pairs, which are the most used molecular markers in assessing the genetic diversity of plant species. Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir./ Sch. Bip) is an outcrossing diploid (2n = 18) endemic to the eastern Adriatic coast and source of the natural insecticide pyrethrin. Due to the high repetitiveness and large size of the genome (haploid genome size of 9,58 pg), previous attempts to develop microsatellite markers using the standard methods were unsuccessful. A next-generation sequencing (NGS) approach was applied on genomic DNA extracted from fresh leaves of Dalmatian pyrethrum. The sequencing was conducted using NovaSeq6000 Illumina sequencer, after which almost 400 million high-quality paired-end reads were obtained, with a read length of 150 base pairs. Short reads were assembled by combining two approaches; (1) de-novo assembly and (2) joining of overlapped pair-end reads. In total, 6.909.675 contigs were obtained, with the contig average length of 249 base pairs. Of the resulting contigs, 31.380 contained one or multiple microsatellite sequences, in total 35.556 microsatellite loci were identified. Out of detected microsatellites, dinucleotide repeats were the most frequent, accounting for more than half of all microsatellites identifies (21,212; 59.7%), followed by trinucleotide repeats (9,204; 25.9%). Tetra-, penta- and hexanucleotides had similar frequency of 1,822 (5.1%), 1,472 (4.1%), and 1,846 (5.2%), respectively. Contigs containing microsatellites were further filtered by SSR pattern type, transposon occurrences, assembly characteristics, GC content, and the number of occurrences against the draft genome of T. cinerariifolium published previously. After the selection process, 50 microsatellite loci were used for primer design. Designed primers were tested on samples from five distinct populations, and 25 of them showed a high degree of polymorphism. The selected loci were then genotyped on 20 samples belonging to one population resulting in 17 microsatellite markers. Availability of codominant SSR markers will significantly improve the knowledge on population genetic diversity and structure as well as complex genetics and biochemistry of this species. Acknowledgment: This work has been fully supported by the Croatian Science Foundation under the project ‘Genetic background of Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir/ Sch. Bip.) insecticidal potential’ - (PyrDiv) (IP-06-2016-9034).

Keywords: genome assembly, NGS, SSR, Tanacetum cinerariifolium

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Authors: Filip Ščerba, Veronika Pochylá

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Performing of the acts within criminal proceedings usually takes too long and thus this phenomenon can be regarded as one of the most burning problems which have plagued the criminal justice not only in the Czech Republic but at least all over Europe for the last few decades. This problem obviously has to be dealt with and thus the need to tackle this issue has resulted in the trend which is sometimes called Criminal Justice Rationalization, i.e. introducing and enforcing methods supporting the increase in efficiency of the criminal justice in order to make the criminal proceedings shorter and administrative procedure easier. This resulted in the introduction of institutes such as e.g. diversions in criminal proceedings or other forms of shortened pre-trial proceedings, which may be used primarily for dealing with less serious crimes. But also the institute, which was originally mentioned in connection with the system of criminal law in the countries belonging to the Anglo-Saxon legal order where it is frequently called of plea bargaining, has been introduced into the criminal law of many European countries, and it may be applied also in cases of serious crimes. All these special and shortened forms of criminal proceedings are connected with limited extent of process of evidence; in fact, some of these specific forms of criminal proceedings are designed for the purpose to simplify the process of evidence. That is also the reason, why some of these procedures are conditioned with the defendant’s confession. Main hypothesis: Limited process of evidence represents also a potential conflict with certain fundamental principles upon which the criminal proceeding in the Continental legal system is based. (A conflict with principle of material truth may be considered as the most important problem. This principle states that the bodies in criminal proceedings must clarify the facts of the case beyond reasonable doubt to such extent that a decision can be made; the defendant’s confession does not mean that these bodies are freed from the duty to review all the circumstances and facts of the case. Such principle is typical for criminal law in Central European region.) Basic methodologies: The paper is going to analyze such a problem of weakening of the principle of material truth in modern criminal law. Such analysis will be provided primarily on the base of the Czech criminal law, but also other legal regulations will be taken into consideration, and its result may have some relevance for all legal regulations belonging to the Continental legal system, so the paper offers also a comparison with legal systems of other Central European countries.

Keywords: burden of proof, central European countries, criminal justice rationalization, criminal proceeding, Czech legislation, Czech republic, defendant, diversions, evidence, fundamental principles, plea bargaining, pre-trial proceedings, principle of material truth, process of evidence, process of evidence

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Authors: Filip Majetić, Dražen Šimleša, Jelena Puđak, Anita Bušljeta Tonković, Svitlana Pinchuk

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This paper focuses on the self-sustainability aspect of social entrepreneurship (SE). We define SE as a form of entrepreneurship that is social/ecological mission oriented. It means SE organizations start and run businesses and use them to accomplish their social/ecological missions i.e. to solve social/ecological problems or fulfill social/ecological needs. Self-sustainability is defined as the capability of an SE organization to operate by relying on the money earned through trading its products in the free market. For various reasons, the achievement of self-sustainability represents a fundamental (business) challenge for many SE organizations. Those that are not able to operate using the money made through commercial activities, in order to remain active, rely on alternative, non-commercial streams of income such as grants, donations, and public subsidies. Starting from this widespread (business) challenge, we are interested in exploring elements that (could) influence the self-sustainability in SE organizations. Therefore, the research goal is to empirically investigate some of the self-sustainability factors of two notable SE organizations from different socio-economic contexts. A qualitative research, using the multiple case study approach, was conducted. ACT Group Čakovec (ACT) from Croatia was selected for the first case because it represents one of the leading and most self-sustainable SE organization in the region (in 2015 55% of the organization’s budget came from commercial activities); Friskis&Svettis Stockholm (F&S) from Sweden was selected for the second case because it is a rare example of completely self-sustainable SE organization in Europe (100% of the organization’s budget comes from commercial activities). The data collection primarily consists of conducting in-depth interviews. Additionally, the content of some of the organizations' official materials are analyzed (e.g. business reports, marketing materials). The interviewees are selected purposively and include: six highly ranked F&S members who represent five different levels in the hierarchy of their organization; five highly ranked ACT members who represent three different levels in the hierarchy of the organization. All of the interviews contain five themes: a) social values of the organization, b) organization of work, c) non-commercial income sources, d) marketing/collaborations, and e) familiarity with the industry characteristics and trends. The gathered data is thematically analyzed through the coding process for which Atlas.ti software for qualitative data analysis is used. For the purpose of creating thematic categories (codes), the open coding is used. The research results intend to provide new theoretical insights on factors of SE self-sustainability and, preferably, encourage practical improvements in the field.

Keywords: Friskis&Svettis, self-sustainability factors, social entrepreneurship, Stockholm

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Authors: Filip Varga, Nina Jeran, Martina Biosic, Zlatko Satovic, Martina Grdisa

Abstract:

Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir./ Sch. Bip.), a species endemic to the eastern Adriatic coastline, is the source of natural insecticide pyrethrin. Pyrethrin is a mixture of six compounds (pyrethrin I and II, cinerin I and II, jasmolin I and II) that exhibits high insecticidal activity with no detrimental effects to the environment. A recently optimized matrix-solid phase dispersion method (MSPD), using florisil as the sorbent, acetone-ethyl acetate (1:1, v/v) as the elution solvent, and sodium sulfate anhydrous as the drying agent was utilized to extract the pyrethrins from 10 wild populations (20 individuals per population) distributed along the Croatian coast. All six components in the extracts were qualitatively and quantitatively determined by high-performance liquid chromatography with a diode array detector (HPLC-DAD). Pearson’s correlation index was calculated between pyrethrin compounds, and differences between the populations using the analysis of variance were tested. Additionally, the correlation of each pyrethrin component with spatio-ecological variables (bioclimate, soil properties, elevation, solar radiation, and distance from the coastline) was calculated. Total pyrethrin content ranged from 0.10% to 1.35% of dry flower weight, averaging 0.58% across all individuals. Analysis of variance revealed significant differences between populations based on all six pyrethrin compounds and total pyrethrin content. On average, the lowest total pyrethrin content was found in the population from Pelješac peninsula (0.22% of dry flower weight) in which total pyrethrin content lower than 0.18% was detected in 55% of the individuals. The highest average total pyrethrin content was observed in the population from island Zlarin (0.87% of dry flower weight), in which total pyrethrin content higher than 1.00% was recorded in only 30% of the individuals. Pyrethrin I/pyrethrin II ratio as a measure of extract quality ranged from 0.21 (population from the island Čiovo) to 5.88 (population from island Mali Lošinj) with an average of 1.77 across all individuals. By far, the lowest quality of extracts was found in the population from Mt. Biokovo (pyrethrin I/II ratio lower than 0.72 in 40% of individuals) due to the high pyrethrin II content typical for this population. Pearson’s correlation index revealed a highly significant positive correlation between pyrethrin I content and total pyrethrin content and a strong negative correlation between pyrethrin I and pyrethrin II. The results of this research clearly indicate high intra- and interpopulation diversity of Dalmatian pyrethrum with regards to pyrethrin content and composition. The information obtained has potential use in plant genetic resources conservation and biodiversity monitoring. Possibly the largest potential lies in designing breeding programs aimed at increasing pyrethrin content in commercial breeding lines and reintroduction in agriculture in Croatia. Acknowledgment: This work has been fully supported by the Croatian Science Foundation under the project ‘Genetic background of Dalmatian pyrethrum (Tanacetum cinerariifolium /Trevir/ Sch. Bip.) insecticidal potential’ - (PyrDiv) (IP-06-2016-9034).

Keywords: Dalmatian pyrethrum, HPLC, MSPD, pyrethrin

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Authors: Martina Grdiša, Filip Varga, Nina Jeran, Ante Turudić, Zlatko Šatović

Abstract:

Dalmatian pyrethrum (Tanacetum cinerariifolium (Trevir.) Sch. Bip.) is a plant species that occurs naturally in the eastern Mediterranean. It is of immense economic importance as it synthesizes and accumulates the phytochemical compound pyrethrin. Pyrethrin consists of several monoterpene esters (pyrethrin I and II, cinerin I and II and jasmolin I and II), which have insecticidal and repellent activity through their synergistic action. In this study, 15 natural Dalmatian pyrethrum populations were sampled along their natural range in Croatia, Bosnia and Herzegovina and Montenegro to characterize and compare their pyrethrin profiles and to define the bioclimatic factors associated with the accumulation of each pyrethrin compound. Pyrethrins were extracted from the dried flower heads of Dalmatian pyrethrum using ultrasound-assisted extraction and the amount of each compound was quantified using high-performance liquid chromatography coupled to DAD-UV /VIS. The biochemical data were subjected to analysis of variance, correlation analysis and multivariate analysis. Quantitative variability within and among populations was found, with population P15 Vranjske Njive, Podgorica having the significantly highest pyrethrin I content (66.47% of total pyrethrin content), while the highest levels of total pyrethrin were found in P14 Budva (1.27% of dry flower weight; DW), followed by P08 Korčula (1.15% DW). Based on the environmental conditions at the sampling sites of the populations, five bioclimatic groups were distinguished, referred to as A, B, C, D, and E, each with rare chemical profile. The first group (A) consisted of the northern Adriatic population P01 Vrbnik, Krk and the population P06 Sevid - the coastal population of the central Adriatic, and generally differed significantly from the other bioclimatic groups by higher average jasmolin II values (2.13% of total pyrethrin). The second group (B) consisted of two central Adriatic island populations (P02 Telašćica, Dugi otok and P03 Žman, Dugi otok), while the remaining central Adriatic island populations were grouped in bioclimatic group C, which was characterized by the significantly highest average pyrethrin II (48.52% of total pyrethrin) and cinerin II (5.31% DW) content. The South Adriatic inland populations P10 Srđ and P11 Trebinje (Bosnia and Herzegovina), and the populations from Montenegro (P12 Grahovo, P13 Lovćen, P14 Budva and P15 Vranjske Njive, Podgorica) formed bioclimatic group E. This bioclimatic group was characterized by the highest average values for pyrethrin I (53.07 % of total pyrethrin), total pyrethrin content (1.06 % DW) and the ratio of pyrethrin I and II (1.85). Slightly lower values (although not significant) for the latter traits were detected in bioclimatic group D (southern Adriatic island populations P07 Vis, P08 Korčula and P09 Mljet). A weak but significant correlation was found between the levels of some pyrethrin compounds and bioclimatic variables (e.g., BIO03 Isothermality and BIO04 Temperature Seasonality), which explains part of the variability observed in the populations studied. This suggests the interconnection between bioclimatic variables and biochemical profiles either through the selection of adapted genotypes or through the ability of species to alter the expression of biochemical traits in response to environmental changes.

Keywords: biopesticides, biochemical variability, pyrethrin, Tanacetum cinerariifolium

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