Correlation between gene expression for the DNA microarray and the RT-qPCR. Correlation for the e... more Correlation between gene expression for the DNA microarray and the RT-qPCR. Correlation for the expression of the 14 potential marker genes for stability between the DNA microarray and the RT-qPCR. (TIFF 41 kb)
Terrestrial isopods are a successful group of terrestrial crustaceans. Their exoskeletal cuticle ... more Terrestrial isopods are a successful group of terrestrial crustaceans. Their exoskeletal cuticle has been studied in several species. However, it is not known whether the cuticle of these animals becomes thicker or how its structure changes as the animals grow. We aimed to determine the principles of upscaling of the exoskeletal cuticle during growth in the terrestrial isopods Armadillidium vulgare (Latreille, 1804) and Porcellio scaber Latreille, 1804 with scanning electron microscopy. The tergal cuticle becomes thicker with increasing body length. In A. vulgare, which rolls into a ball in defense against predators, the rate of increase of tergite thickness was greater than in P. scaber, which clings to the substrate when threatened. As the cuticles of both species become thicker, the proportion of the endocuticle in the cuticle increases. There is a strong correlation between cuticle thickness and the thickness of endocuticular lamellae. This indicates that in thicker cuticles, chitin-protein fibers in sequential layers change their orientation by a smaller angle. We found no significant differences in morphometric parameters between the cuticles of A. vulgare and P. scaber when controlling for cuticle thickness. This suggests that known differences in cuticle structure and composition between these two species may result from differences in cuticle thickness.
The macrophytes of Lake Bled were studied from 1987 to 1990. Three main factors influenced the de... more The macrophytes of Lake Bled were studied from 1987 to 1990. Three main factors influenced the decline of the aquatic vegetation in the lake during that period: (1) reduced light in the littoral zone due to an increase in phytoplankton (2) grazing by herbivorous fish and waterfowl, and (3) direct human impact.
bioRxiv (Cold Spring Harbor Laboratory), Nov 21, 2021
We have developed pISA-tree, a straightforward and flexible data management solution for organisa... more We have developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. It enables on the fly creation of enriched directory tree structure (project/Investigation/Study/Assay), via a series of sequential batch files in a standardised manner based upon the ISA metadata framework. Metadata, according to the system-provided metadata templates, is generated in parallel at each level. The system supports reproducible research and is in accordance with the Open Science initiative and FAIR principles. Compared with similar frameworks, it does not require any systems administration and maintenance as it can be run on a personal computer or network drive. It is complemented with two R packages, pisar and seekr, where the former facilitates integration of the pISA-tree datasets into bioinformatic pipelines and the latter enables synchronisation with the FAIRDOMHub public repository using the SEEK API. Source code and detailed documentation of pISA-tree and its supporting R packages are available from https://github.com/NIB-SI/pISA-tree. We demonstrate the usability of pISA-tree with two examples of medium sized life science projects. Accordingly, it is suitable and also currently used to manage larger projects including several partners from different countries. Since pISA-tree was initiated by end user requirements with an emphasis on practicality, it will facilitate adoption of FAIR data management practices and open science principles.
Recent studies have revealed that at lower cultivation temperatures (25 °C) much higher percentag... more Recent studies have revealed that at lower cultivation temperatures (25 °C) much higher percentage of correctly folded recombinant hG-CSF protein can be extracted from inclusion bodies. Hence, the goal of our research was to investigate mechanisms determining characteristics of non-classical inclusion bodies production using gene expression profiling, focusing on proteases and chaperones gene expression. Statistical analysis of microarray data showed prominent changes in energy metabolism, in metabolism of amino acids and nucleotides, as well as in biosynthesis of cofactors and secondary metabolites if the culture was grown below its optimal temperature. Moreover, 24 differentially expressed up to now known genes classified among proteases, chaperones and other heat or stress related genes. Among chaperones UspE and among proteases YaeL and YeaZ might play an important role in accumulation of correctly folded recombinant proteins. Membrane localized protease yaeL gene was found to have higher activity at 25 °C and is thus potentially functionally related to the more efficient recombinant protein production at lower temperatures. The results of this study represent advance in the understanding of recombinant protein production in E. coli. Genes potentially influencing production of recombinant protein at lower growth temperature represent basis for further research towards improvement of E. coli production strains as well as fermentation process.
The work deals with two series of male students measured in the years 1927 and 1987/88. The first... more The work deals with two series of male students measured in the years 1927 and 1987/88. The first group was presented in the work of B. Skerlj Prispevek k antropologii Jihoslovanu. He measured 34 parameters on 60 Jugoslave students, studied in the University of Prague before 2nd World war. Their age was between 17 and 31 years. The second group was the representative series of first year students of the University of Ljubljana included in the research project: Morphological variability of the students of the University of Ljubljana in the years 1987/88. There were 344 male students between 19 and 21 years. We could compare only the parameters for which we were sure that was taken by the same technique - Martin's technique. Those were the following parameters: stature, sitting height jugular height, iliospinale height, biacromial, bicristal and bitrochanteric breadth, saggital and transverzal dimensions of chest, length and breadth of hand and foot and weight. We calculated basic statistics mean value, standard deviation and as in the work of Skerlj arranged the material according to Martin to five groups: type T (mean value) and -B, -A +A and +B calculated with + or -1/2 or 1 SD. The 60 years differences between both series of students show positive secular trend in stature with 4.7 cm increase, sitting height with 1.6 cm, jugular height with 4.2 cm and iliospinale height with 4.4 cm higher mean values. Those results indicates that the intensity of changes was greater on extremities than on the trunk. Except biacromial breadth, other breadths decreased. In the serie 1927 also parameters of hand and foot were greater except hand length, which was greater in 1987 for 2.3 cm. The difference of 9.3 kg in mean value of weight was greater than we expected. The reason for this could be the fact, that students in Prague loosed about 10 kg during first weeks of their stay in the new environment. Our analysis has shown, that nowadays students in Ljubljana follows the trend and intensity of last decades changes. Further systematic researches on students population will be necessary. The results are shown in Table 1, Table 2 and Table 3.
To identify transcription markers that uniquely determine specific Chinese hamster ovary (CHO) ce... more To identify transcription markers that uniquely determine specific Chinese hamster ovary (CHO) cell lines and can be used for the identification of cell lines in the process of biopharmaceutical cell-line development. Five CHO cell lines with different origins were extensively characterised at the transcriptomic level and the results were compared to their karyotype characterisation. The analysed cell lines differ in their karyotype but, due to the genome instability observed during parental and recombinant cell-line establishment, karyotyping is not the preferred method for accurate identification of the various CHO cell lines. Marker genes unique to a specific cell line were identified by microarrays, and their expression was validated by reverse-transcription quantitative real-time PCR. The analysed cell lines can be differentiated by the presence/absence of detectable marker gene expression. Additionally, the similarity of the transcriptional profiles is dependent on cell-line history but independent of the manipulation steps involved in the recombinant cell-line development process. Certain transcripts can be used as markers for the identification of a CHO cell line undergoing recombinant development and thus represent a powerful tool for ensuring the maintenance of high quality standards.
ABSTRACT The primary patterns of racial differentiation in the water louse, Asellus aquaticus (L.... more ABSTRACT The primary patterns of racial differentiation in the water louse, Asellus aquaticus (L.) sensu RACOVITZA, were assessed by the analysis of geographic variation in 59 morphometric characters. Males from 20 localities in Slovenia and 18 in other countries were analyzed. In Multivariate Discriminant Function Analysis, Minimum Spanning Tree and in Cluster Analysis, samples comprising specimens without eye and body pigmentation are separated from the samples with pigmented specimens, even though these two troglomorphic traits are not being considered. Only 7 traits are needed for the separation. In the cline of the samples with pigmented specimens, 3 groups of samples with the concentric distribution ranges may be distinguished. The results confirm the existence of extensive racial diversification in Slovenia and indicate some inconsistencies in the presently applied classification. The results of separate analysis of male gonopod structure are consistent with the results of multivariate statistical analysis.
It has been suggested that both niche-based and neutral mechanisms are important for biological c... more It has been suggested that both niche-based and neutral mechanisms are important for biological communities to evolve and persist. For communities in extreme and isolated environments such as caves, theoretical and empirical considerations (low species turnover, high stress, strong convergence owing to strong directional selection) predict neutral mechanisms and functional equivalence of species. We tested this prediction using subterranean amphipod communities from caves and interstitial groundwater. Contrary to expectations, functional morphological diversity within communities in both habitats turned out to be significantly higher than the null model of randomly assembled communities. This suggests that even the most extreme, energy-poor environments still maintain the potential for diversification via differentiation of niches.
In many instances only the approximation curve to experimental or field data is of interest. Appl... more In many instances only the approximation curve to experimental or field data is of interest. Application of Bernstein-Bézier polynomials for smoothing of noisy data is shown. Bezier curves provide a simple yet efficient way to approximate (or smooth) arbitrarily spaced vector valued functions without explicit model specification. To evaluate the efficiency of Bézier curves some simulated cases are presented .
Some properties of Bernstein-Bezier polynomials for approximation of functions with added error t... more Some properties of Bernstein-Bezier polynomials for approximation of functions with added error term are investigated. Slow convergence of Bernstein polynomials makes them efficient for smoothing of noisy data. Application of Bezier curves for smoothing of arbitrarily spaced vector valued functions is shown.
In nature the aerial trace of pheromone used by male moths to find a female appears as a train of... more In nature the aerial trace of pheromone used by male moths to find a female appears as a train of discontinuous pulses separated by gaps among a complex odorant background constituted of plant volatiles. We investigated the effect of such background odor on behavior and coding of temporal parameters of pheromone pulse trains in the pheromone olfactory receptor neurons of Spodoptera littoralis. Effects of linalool background were tested by measuring walking behavior towards a source of pheromone. While velocity and orientation index did drop when linalool was turned on, both parameters recovered back to pre-background values after 40 s with linalool still present. Photo-ionization detector was used to characterize pulse delivery by our stimulator. The photo-ionization detector signal reached 71% of maximum amplitude at 50 ms pulses and followed the stimulus period at repetition rates up to 10 pulses/s. However, at high pulse rates the concentration of the odorant did not return to base level during inter-pulse intervals. Linalool decreased the intensity and shortened the response of receptor neurons to pulses. High contrast (.10 dB) in firing rate between pulses and inter-pulse intervals was observed for 1 and 4 pulses/s, both with and without background. Significantly more neurons followed the 4 pulses/s pattern when delivered over linalool; at the same time the information content was preserved almost to the control values. Rapid recovery of behavior shows that change of perceived intensity is more important than absolute stimulus intensity. While decreasing the response intensity, background odor preserved the temporal parameters of the specific signal.
Understanding statistical concepts is important for proper use of statistics. The idea of using s... more Understanding statistical concepts is important for proper use of statistics. The idea of using simulations and dynamic graphics to foster understanding of statistical concepts is not new. In recent years, R became the lingua franca for statistical data analysis. While R graphical devices are not meant for display of animated graphics, my aim is to use base R graphics for display of animated graphical sequences. To enable dynamic graphics in R, I developed a package animatoR, which supports smooth transitions of graphical elements and simplifies preparation of animated displays. I will show some animations that can be useful for statistics teaching and present basic features of the animatoR package. The animatoR package is freely available at .
Simple probabilistic simulations, such as flipping a coin or rolling a dice, are used for illustr... more Simple probabilistic simulations, such as flipping a coin or rolling a dice, are used for illustration of statistical concepts and stochastic properties of modeled processes. With availability of personal computers in past decade, computer supported statistical simulations were introduced to statistics teaching. Such simulations -usually combined with graphic presentation of results and simulation itself -can be used for more obvious demonstration of statistical phenomena. With the advent of the Internet, new dimensions were introduced to teaching. The simulation software is easily available for those that are connected to the Internet, regardless of physical distance. Internet also brought cross-platform compatibility of teaching material, which was sometimes limited to one or another type of operating system. But there are some cultural and language barriers, usually combined with low availability of computers and Internet in some countries.
We present a simple statistical method for detection and identification of firing rate changes in... more We present a simple statistical method for detection and identification of firing rate changes in spontaneously active neurons. Spontaneously active neurons (such as olfactory neurons) can be, in response to stimulation, either excited or suppressed and thus increase or decrease the spike firing rate. The described method is based on the detection of changes in slope of cumulative spike time distribution and efficiently detects excitations and suppressions. Using the simulated spike trains we examined the method's power in relation to response strength and duration.
Proceedings of the First Scientific Meeting of the IASE Satellite Conference
Computers were invented and constructed to compute. Since statistical analyses are computing inte... more Computers were invented and constructed to compute. Since statistical analyses are computing intensive it is natural that computers are widely used in statistical research and applications. Statistical applications, such as census with its problems of sorting, counting and tabulating, were among the motives for constructing the ancestors of modern computers.
In vitro cell-based models are important tools for assessing efficacies of new leads in early pha... more In vitro cell-based models are important tools for assessing efficacies of new leads in early phases of drug development. Human osteoarthritic chondrocytes (OACs), obtained from biomedical waste material, represent a valuable, relatively accessible cellular source that could be used for this purpose. By employing reverse transcription-polymerase chain reaction (qRT-PCR) we compared gene expression profiles of key anabolic, catabolic and inflammatory genes of freshly isolated vs. monolayer cultured OACs (passages P0-P2) and non-stimulated vs. tumor necrosis factor alpha (TNF-a) stimulated P2 OACs. After expansion of OACs in monolayer cultures, the expression of almost all analyzed genes significantly decreased. The subsequent addition of TNF-a to OACs at P2 significantly increased expressions of all catabolic and inflammatory genes, leaving the anabolic profile almost unchanged. TNF-a-treated OACs were later utilized for efficacy testing of anti-TNF-a drugs infliximab and etanercept and both significantly reduced the expressions of all catabolic and inflammatory genes tested.
Correlation between gene expression for the DNA microarray and the RT-qPCR. Correlation for the e... more Correlation between gene expression for the DNA microarray and the RT-qPCR. Correlation for the expression of the 14 potential marker genes for stability between the DNA microarray and the RT-qPCR. (TIFF 41 kb)
Terrestrial isopods are a successful group of terrestrial crustaceans. Their exoskeletal cuticle ... more Terrestrial isopods are a successful group of terrestrial crustaceans. Their exoskeletal cuticle has been studied in several species. However, it is not known whether the cuticle of these animals becomes thicker or how its structure changes as the animals grow. We aimed to determine the principles of upscaling of the exoskeletal cuticle during growth in the terrestrial isopods Armadillidium vulgare (Latreille, 1804) and Porcellio scaber Latreille, 1804 with scanning electron microscopy. The tergal cuticle becomes thicker with increasing body length. In A. vulgare, which rolls into a ball in defense against predators, the rate of increase of tergite thickness was greater than in P. scaber, which clings to the substrate when threatened. As the cuticles of both species become thicker, the proportion of the endocuticle in the cuticle increases. There is a strong correlation between cuticle thickness and the thickness of endocuticular lamellae. This indicates that in thicker cuticles, chitin-protein fibers in sequential layers change their orientation by a smaller angle. We found no significant differences in morphometric parameters between the cuticles of A. vulgare and P. scaber when controlling for cuticle thickness. This suggests that known differences in cuticle structure and composition between these two species may result from differences in cuticle thickness.
The macrophytes of Lake Bled were studied from 1987 to 1990. Three main factors influenced the de... more The macrophytes of Lake Bled were studied from 1987 to 1990. Three main factors influenced the decline of the aquatic vegetation in the lake during that period: (1) reduced light in the littoral zone due to an increase in phytoplankton (2) grazing by herbivorous fish and waterfowl, and (3) direct human impact.
bioRxiv (Cold Spring Harbor Laboratory), Nov 21, 2021
We have developed pISA-tree, a straightforward and flexible data management solution for organisa... more We have developed pISA-tree, a straightforward and flexible data management solution for organisation of life science project-associated research data and metadata. It enables on the fly creation of enriched directory tree structure (project/Investigation/Study/Assay), via a series of sequential batch files in a standardised manner based upon the ISA metadata framework. Metadata, according to the system-provided metadata templates, is generated in parallel at each level. The system supports reproducible research and is in accordance with the Open Science initiative and FAIR principles. Compared with similar frameworks, it does not require any systems administration and maintenance as it can be run on a personal computer or network drive. It is complemented with two R packages, pisar and seekr, where the former facilitates integration of the pISA-tree datasets into bioinformatic pipelines and the latter enables synchronisation with the FAIRDOMHub public repository using the SEEK API. Source code and detailed documentation of pISA-tree and its supporting R packages are available from https://github.com/NIB-SI/pISA-tree. We demonstrate the usability of pISA-tree with two examples of medium sized life science projects. Accordingly, it is suitable and also currently used to manage larger projects including several partners from different countries. Since pISA-tree was initiated by end user requirements with an emphasis on practicality, it will facilitate adoption of FAIR data management practices and open science principles.
Recent studies have revealed that at lower cultivation temperatures (25 °C) much higher percentag... more Recent studies have revealed that at lower cultivation temperatures (25 °C) much higher percentage of correctly folded recombinant hG-CSF protein can be extracted from inclusion bodies. Hence, the goal of our research was to investigate mechanisms determining characteristics of non-classical inclusion bodies production using gene expression profiling, focusing on proteases and chaperones gene expression. Statistical analysis of microarray data showed prominent changes in energy metabolism, in metabolism of amino acids and nucleotides, as well as in biosynthesis of cofactors and secondary metabolites if the culture was grown below its optimal temperature. Moreover, 24 differentially expressed up to now known genes classified among proteases, chaperones and other heat or stress related genes. Among chaperones UspE and among proteases YaeL and YeaZ might play an important role in accumulation of correctly folded recombinant proteins. Membrane localized protease yaeL gene was found to have higher activity at 25 °C and is thus potentially functionally related to the more efficient recombinant protein production at lower temperatures. The results of this study represent advance in the understanding of recombinant protein production in E. coli. Genes potentially influencing production of recombinant protein at lower growth temperature represent basis for further research towards improvement of E. coli production strains as well as fermentation process.
The work deals with two series of male students measured in the years 1927 and 1987/88. The first... more The work deals with two series of male students measured in the years 1927 and 1987/88. The first group was presented in the work of B. Skerlj Prispevek k antropologii Jihoslovanu. He measured 34 parameters on 60 Jugoslave students, studied in the University of Prague before 2nd World war. Their age was between 17 and 31 years. The second group was the representative series of first year students of the University of Ljubljana included in the research project: Morphological variability of the students of the University of Ljubljana in the years 1987/88. There were 344 male students between 19 and 21 years. We could compare only the parameters for which we were sure that was taken by the same technique - Martin's technique. Those were the following parameters: stature, sitting height jugular height, iliospinale height, biacromial, bicristal and bitrochanteric breadth, saggital and transverzal dimensions of chest, length and breadth of hand and foot and weight. We calculated basic statistics mean value, standard deviation and as in the work of Skerlj arranged the material according to Martin to five groups: type T (mean value) and -B, -A +A and +B calculated with + or -1/2 or 1 SD. The 60 years differences between both series of students show positive secular trend in stature with 4.7 cm increase, sitting height with 1.6 cm, jugular height with 4.2 cm and iliospinale height with 4.4 cm higher mean values. Those results indicates that the intensity of changes was greater on extremities than on the trunk. Except biacromial breadth, other breadths decreased. In the serie 1927 also parameters of hand and foot were greater except hand length, which was greater in 1987 for 2.3 cm. The difference of 9.3 kg in mean value of weight was greater than we expected. The reason for this could be the fact, that students in Prague loosed about 10 kg during first weeks of their stay in the new environment. Our analysis has shown, that nowadays students in Ljubljana follows the trend and intensity of last decades changes. Further systematic researches on students population will be necessary. The results are shown in Table 1, Table 2 and Table 3.
To identify transcription markers that uniquely determine specific Chinese hamster ovary (CHO) ce... more To identify transcription markers that uniquely determine specific Chinese hamster ovary (CHO) cell lines and can be used for the identification of cell lines in the process of biopharmaceutical cell-line development. Five CHO cell lines with different origins were extensively characterised at the transcriptomic level and the results were compared to their karyotype characterisation. The analysed cell lines differ in their karyotype but, due to the genome instability observed during parental and recombinant cell-line establishment, karyotyping is not the preferred method for accurate identification of the various CHO cell lines. Marker genes unique to a specific cell line were identified by microarrays, and their expression was validated by reverse-transcription quantitative real-time PCR. The analysed cell lines can be differentiated by the presence/absence of detectable marker gene expression. Additionally, the similarity of the transcriptional profiles is dependent on cell-line history but independent of the manipulation steps involved in the recombinant cell-line development process. Certain transcripts can be used as markers for the identification of a CHO cell line undergoing recombinant development and thus represent a powerful tool for ensuring the maintenance of high quality standards.
ABSTRACT The primary patterns of racial differentiation in the water louse, Asellus aquaticus (L.... more ABSTRACT The primary patterns of racial differentiation in the water louse, Asellus aquaticus (L.) sensu RACOVITZA, were assessed by the analysis of geographic variation in 59 morphometric characters. Males from 20 localities in Slovenia and 18 in other countries were analyzed. In Multivariate Discriminant Function Analysis, Minimum Spanning Tree and in Cluster Analysis, samples comprising specimens without eye and body pigmentation are separated from the samples with pigmented specimens, even though these two troglomorphic traits are not being considered. Only 7 traits are needed for the separation. In the cline of the samples with pigmented specimens, 3 groups of samples with the concentric distribution ranges may be distinguished. The results confirm the existence of extensive racial diversification in Slovenia and indicate some inconsistencies in the presently applied classification. The results of separate analysis of male gonopod structure are consistent with the results of multivariate statistical analysis.
It has been suggested that both niche-based and neutral mechanisms are important for biological c... more It has been suggested that both niche-based and neutral mechanisms are important for biological communities to evolve and persist. For communities in extreme and isolated environments such as caves, theoretical and empirical considerations (low species turnover, high stress, strong convergence owing to strong directional selection) predict neutral mechanisms and functional equivalence of species. We tested this prediction using subterranean amphipod communities from caves and interstitial groundwater. Contrary to expectations, functional morphological diversity within communities in both habitats turned out to be significantly higher than the null model of randomly assembled communities. This suggests that even the most extreme, energy-poor environments still maintain the potential for diversification via differentiation of niches.
In many instances only the approximation curve to experimental or field data is of interest. Appl... more In many instances only the approximation curve to experimental or field data is of interest. Application of Bernstein-Bézier polynomials for smoothing of noisy data is shown. Bezier curves provide a simple yet efficient way to approximate (or smooth) arbitrarily spaced vector valued functions without explicit model specification. To evaluate the efficiency of Bézier curves some simulated cases are presented .
Some properties of Bernstein-Bezier polynomials for approximation of functions with added error t... more Some properties of Bernstein-Bezier polynomials for approximation of functions with added error term are investigated. Slow convergence of Bernstein polynomials makes them efficient for smoothing of noisy data. Application of Bezier curves for smoothing of arbitrarily spaced vector valued functions is shown.
In nature the aerial trace of pheromone used by male moths to find a female appears as a train of... more In nature the aerial trace of pheromone used by male moths to find a female appears as a train of discontinuous pulses separated by gaps among a complex odorant background constituted of plant volatiles. We investigated the effect of such background odor on behavior and coding of temporal parameters of pheromone pulse trains in the pheromone olfactory receptor neurons of Spodoptera littoralis. Effects of linalool background were tested by measuring walking behavior towards a source of pheromone. While velocity and orientation index did drop when linalool was turned on, both parameters recovered back to pre-background values after 40 s with linalool still present. Photo-ionization detector was used to characterize pulse delivery by our stimulator. The photo-ionization detector signal reached 71% of maximum amplitude at 50 ms pulses and followed the stimulus period at repetition rates up to 10 pulses/s. However, at high pulse rates the concentration of the odorant did not return to base level during inter-pulse intervals. Linalool decreased the intensity and shortened the response of receptor neurons to pulses. High contrast (.10 dB) in firing rate between pulses and inter-pulse intervals was observed for 1 and 4 pulses/s, both with and without background. Significantly more neurons followed the 4 pulses/s pattern when delivered over linalool; at the same time the information content was preserved almost to the control values. Rapid recovery of behavior shows that change of perceived intensity is more important than absolute stimulus intensity. While decreasing the response intensity, background odor preserved the temporal parameters of the specific signal.
Understanding statistical concepts is important for proper use of statistics. The idea of using s... more Understanding statistical concepts is important for proper use of statistics. The idea of using simulations and dynamic graphics to foster understanding of statistical concepts is not new. In recent years, R became the lingua franca for statistical data analysis. While R graphical devices are not meant for display of animated graphics, my aim is to use base R graphics for display of animated graphical sequences. To enable dynamic graphics in R, I developed a package animatoR, which supports smooth transitions of graphical elements and simplifies preparation of animated displays. I will show some animations that can be useful for statistics teaching and present basic features of the animatoR package. The animatoR package is freely available at .
Simple probabilistic simulations, such as flipping a coin or rolling a dice, are used for illustr... more Simple probabilistic simulations, such as flipping a coin or rolling a dice, are used for illustration of statistical concepts and stochastic properties of modeled processes. With availability of personal computers in past decade, computer supported statistical simulations were introduced to statistics teaching. Such simulations -usually combined with graphic presentation of results and simulation itself -can be used for more obvious demonstration of statistical phenomena. With the advent of the Internet, new dimensions were introduced to teaching. The simulation software is easily available for those that are connected to the Internet, regardless of physical distance. Internet also brought cross-platform compatibility of teaching material, which was sometimes limited to one or another type of operating system. But there are some cultural and language barriers, usually combined with low availability of computers and Internet in some countries.
We present a simple statistical method for detection and identification of firing rate changes in... more We present a simple statistical method for detection and identification of firing rate changes in spontaneously active neurons. Spontaneously active neurons (such as olfactory neurons) can be, in response to stimulation, either excited or suppressed and thus increase or decrease the spike firing rate. The described method is based on the detection of changes in slope of cumulative spike time distribution and efficiently detects excitations and suppressions. Using the simulated spike trains we examined the method's power in relation to response strength and duration.
Proceedings of the First Scientific Meeting of the IASE Satellite Conference
Computers were invented and constructed to compute. Since statistical analyses are computing inte... more Computers were invented and constructed to compute. Since statistical analyses are computing intensive it is natural that computers are widely used in statistical research and applications. Statistical applications, such as census with its problems of sorting, counting and tabulating, were among the motives for constructing the ancestors of modern computers.
In vitro cell-based models are important tools for assessing efficacies of new leads in early pha... more In vitro cell-based models are important tools for assessing efficacies of new leads in early phases of drug development. Human osteoarthritic chondrocytes (OACs), obtained from biomedical waste material, represent a valuable, relatively accessible cellular source that could be used for this purpose. By employing reverse transcription-polymerase chain reaction (qRT-PCR) we compared gene expression profiles of key anabolic, catabolic and inflammatory genes of freshly isolated vs. monolayer cultured OACs (passages P0-P2) and non-stimulated vs. tumor necrosis factor alpha (TNF-a) stimulated P2 OACs. After expansion of OACs in monolayer cultures, the expression of almost all analyzed genes significantly decreased. The subsequent addition of TNF-a to OACs at P2 significantly increased expressions of all catabolic and inflammatory genes, leaving the anabolic profile almost unchanged. TNF-a-treated OACs were later utilized for efficacy testing of anti-TNF-a drugs infliximab and etanercept and both significantly reduced the expressions of all catabolic and inflammatory genes tested.
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Papers by Andrej Blejec