E-thesis repository – processes and data

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Repository and its place at the University of Pardubice

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Extracellular ATP in the lymphohematopoietic system: P2Z purinoceptors and membrane permeabilization

The effects of extracellular nucleosides and nucleotides on many organs and systems have been recognized for almost 50 years. The effects of extracellular ATP (ATPo), UTPo, ADPo, and other agonists are mediated by P2 purinoceptors. One of the most dramatic effects of ATPo is the permeabilization of plasma membranes to low molecular mass solutes of up to 900 Da. This effect is evident in several cells of the lymphohematopoietic system and is supposed to be mediated by P2Z, an ATP4--activated purinoceptor. Here, we review some basic information concerning P2 purinoceptors and focus our attention on P2Z-associated phenomena displayed by macrophages. Using fluorescent dye uptake, measurement of free intracellular Ca2+ concentration and electrophysiological recordings, we elucidate some of the events that follow the application of ATP to the extracellular surface of macrophages. We propose a regulatory mechanism for the P2Z-associated permeabilization pore. The presence of P2 purinoceptors in cells of the lymphohematopoietic system makes them potential candidates to mediate immunoregulatory events

Fever induction pathways: evidence from responses to systemic or local cytokine formation

The immune and central nervous systems are functionally connected and interacting. The concept that the immune signaling to the brain which induces fever during infection and inflammation is mediated by circulating cytokines has been traditionally accepted. Administration of bacterial lipopolysaccharide (LPS) induces the appearance of a so-termed "cytokine cascade" in the circulation more or less concomitantly to the developing febrile response. Also, LPS-like fever can be induced by systemic administration of key cytokines (IL-1ß, TNF-alpha, and others). However, anti-cytokine strategies against IL-1ß or TNF-alpha along with systemic injections of LPS frequently lead to attenuation of the later stages of the febrile response but not of the initial phase of fever, indicating that cytokines are rather involved in the maintenance than in the early induction of fever. Within the last years experimental evidence has accumulated indicating the existence of neural transport pathways of immune signals to the brain. Because subdiaphragmatic vagotomy prevents or attenuates fever in response to intraperitoneal or intravenous injections of LPS, a role for vagal afferent nerve fibers in fever induction has been proposed. Also other sensory nerves may participate in the manifestation of febrile responses under certain experimental conditions. Thus, injection of a small dose of LPS into an artificial subcutaneous chamber results in fever and formation of cytokines within the inflamed tissue around the site of injection. This febrile response can be blocked in part by injection of a local anesthetic into the subcutaneous chamber, indicating a participation of cutaneous afferent nerve signals in the manifestation of fever in this model. In conclusion, humoral signals and an inflammatory stimulation of afferent sensory nerves can participate in the generation and maintenance of a febrile response.

Cholinergic stimulation with pyridostigmine reduces the QTc interval in coronary artery disease

Parasympathetic dysfunction is an independent risk factor in patients with coronary artery disease; thus, cholinergic stimulation is a potential therapeutic measure that may be protective by acting on ventricular repolarization. The purpose of the present study was to determine the effects of pyridostigmine bromide (PYR), a reversible anticholinesterase agent, on the electrocardiographic variables, particularly QTc interval, in patients with stable coronary artery disease. In a randomized double-blind crossover placebo-controlled study, simultaneous 12-lead electrocardiographic tracings were obtained at rest from 10 patients with exercise-induced myocardial ischemia before and 2 h after the oral administration of 45 mg PYR or placebo. PYR increased the RR intervals (pre: 921 ± 27 ms vs post: 1127 ± 37 ms; P<0.01) and, in contrast with placebo, decreased the QTc interval (pre: 401 ± 3 ms vs post: 382 ± 3 ms; P<0.01). No other electrocardiographic variables were modified (PR segment, QT interval, QT and QTc dispersions). Cholinergic stimulation with PYR caused bradycardia and reduced the QTc interval without important side effects in patients with coronary disease. These effects, if confirmed in studies over longer periods of administration, may suggest a cardioprotection by cholinergic stimulation with PYR.

Multicellular spheroids of bone marrow stromal cells: a three-dimensional in vitro culture system for the study of hematopoietic cell migration

Cell fate decisions are governed by a complex interplay between cell-autonomous signals and stimuli from the surrounding tissue. In vivo cells are connected to their neighbors and to the extracellular matrix forming a complex three-dimensional (3-D) microenvironment that is not reproduced in conventional in vitro systems. A large body of evidence indicates that mechanical tension applied to the cytoskeleton controls cell proliferation, differentiation and migration, suggesting that 3-D in vitro culture systems that mimic the in vivo situation would reveal biological subtleties. In hematopoietic tissues, the microenvironment plays a crucial role in stem and progenitor cell survival, differentiation, proliferation, and migration. In adults, hematopoiesis takes place inside the bone marrow cavity where hematopoietic cells are intimately associated with a specialized three 3-D scaffold of stromal cell surfaces and extracellular matrix that comprise specific niches. The relationship between hematopoietic cells and their niches is highly dynamic. Under steady-state conditions, hematopoietic cells migrate within the marrow cavity and circulate in the bloodstream. The mechanisms underlying hematopoietic stem/progenitor cell homing and mobilization have been studied in animal models, since conventional two-dimensional (2-D) bone marrow cell cultures do not reproduce the complex 3-D environment. In this review, we will highlight some of the mechanisms controlling hematopoietic cell migration and 3-D culture systems.

Correlation of serum leptin and insulin levels of pregnant protein-restricted rats with predictive obesity variables

During pregnancy and protein restriction, changes in serum insulin and leptin levels, food intake and several metabolic parameters normally result in enhanced adiposity. We evaluated serum leptin and insulin levels and their correlations with some predictive obesity variables in Wistar rats (90 days), up to the 14th day of pregnancy: control non-pregnant (N = 5) and pregnant (N = 7) groups (control diet: 17% protein), and low-protein non-pregnant (N = 5) and pregnant (N = 6) groups (low-protein diet: 6%). Independent of the protein content of the diet, pregnancy increased total (F1,19 = 22.28, P < 0.001) and relative (F1,19 = 5.57, P < 0.03) food intake, the variation of weight (F1,19 = 49.79, P < 0.000) and final body weight (F1,19 = 19.52, P < 0.001), but glycemia (F1,19 = 9.02, P = 0.01) and the relative weight of gonadal adipose tissue (F1,19 = 17.11, P < 0.001) were decreased. Pregnancy (F1,19 = 18.13, P < 0.001) and low-protein diet (F1,19 = 20.35, P < 0.001) increased the absolute weight of brown adipose tissue. However, the relative weight of this tissue was increased only by protein restriction (F1,19 = 15.20, P < 0.001) and the relative lipid in carcass was decreased in low-protein groups (F1,19 = 4.34, P = 0.05). Serum insulin and leptin levels were similar among groups and did not correlate with food intake. However, there was a positive relationship between serum insulin levels and carcass fat depots in low-protein groups (r = 0.37, P < 0.05), while in pregnancy serum leptin correlated with weight of gonadal (r = 0.39, P < 0.02) and retroperitoneal (r = 0.41, P < 0.01) adipose tissues. Unexpectedly, protein restriction during 14 days of pregnancy did not alter the serum profile of adiposity signals and their effects on food intake and adiposity, probably due to the short term of exposure to low-protein diet.

Effects of different general anesthetics on serum hemolysis and hepatic and muscular glycogenolysis in rats

Anesthetics can affect the structure and biological function of tissues and systems differentially. The aim of the present study was to compare three injectable anesthetics generally used in experiments with animals in terms of the degree of hemolysis and glycogenolysis occurring after profound anesthesia. Twenty-four male Wistar rats (330-440 g) were divided into three groups (N = 8): chloral hydrate (CH), ketamine + xylazine (KX), Zoletil 50® (zolazepam and tiletamine) + xylazine (ZTX). After deep anesthesia, total blood was collected. The liver and white (WG) and red gastrocnemius (RG) muscles were also immediately removed. The degree of serum hemolysis was quantified on the basis of hemoglobin concentration (g/L). Hepatic and muscular glycogen concentrations (mmol/kg wet tissue) were quantified by the phenol-sulfuric method. The CH and KX groups exhibited serum hemolysis (4.0 ± 2.2 and 1.9 ± 0.9 g/L, respectively; P < 0.05) compared to the ZTX group, which presented none. Only KX induced elevated glycogenolysis (mmol/kg wet tissue) in the liver (86.9 ± 63.2) and in WG (18.7 ± 9.0) and RG (15.2 ± 7.2; P < 0.05). The CH and ZTX groups exhibited no glycogenolysis in the liver (164.4 ± 41.1 and 176.8 ± 54.4, respectively), WG (28.8 ± 4.4, 32.0 ± 6.5, respectively) or RG (29.0 ± 4.9; 25.3 ± 8.6, respectively). Our data indicate that ZTX seems to be an appropriate general anesthetic for studies that seek to simultaneously quantify the concentration of glycogen and serum biochemical markers without interferences. ZTX is reasonably priced, found easily at veterinary markets, quickly induces deep anesthesia, and presents a low mortality rate.

Toxic effects of mercury, lead and gadolinium on vascular reactivity

Heavy metals have been used in a wide variety of human activities that have significantly increased both professional and environmental exposure. Unfortunately, disasters have highlighted the toxic effects of metals on different organs and systems. Over the last 50 years, the adverse effects of chronic lead, mercury and gadolinium exposure have been underscored. Mercury and lead induce hypertension in humans and animals, affecting endothelial function in addition to their other effects. Increased cardiovascular risk after exposure to metals has been reported, but the underlying mechanisms, mainly for short periods of time and at low concentrations, have not been well explored. The presence of other metals such as gadolinium has raised concerns about contrast-induced nephropathy and, interestingly, despite this negative action, gadolinium has not been defined as a toxic agent. The main actions of these metals, demonstrated in animal and human studies, are an increase of free radical production and oxidative stress and stimulation of angiotensin I-converting enzyme activity, among others. Increased vascular reactivity, highlighted in the present review, resulting from these actions might be an important mechanism underlying increased cardiovascular risk. Finally, the results described in this review suggest that mercury, lead and gadolinium, even at low doses or concentrations, affect vascular reactivity. Acting via the endothelium, by continuous exposure followed by their absorption, they can increase the production of free radicals and of angiotensin II, representing a hazard for cardiovascular function. In addition, the actual reference values, considered to pose no risk, need to be reduced.

The Falkland Islands War of 1982: a legal, diplomatic and strategic evaluation

The Falkland Islands War of 1982 was fought over competing claims to sovereignty over a group of islands off the east coast of South America. The dispute was between Argentina and the United Kingdom. Argentina claims the islands under rights to Spanish succession, the fact that they lie off the Argentine coast line and that in 1833 Great Britain took the islands illegally and by force. The United Kingdom claims the islands primarily through prescription--the fact that they have governed the islands in a peaceful, continuous and public manner since 1833. The British also hold that the population living on the islands, roughly eighteen hundred British descendants, should be able to decide their own future. The United Kingdom also lays claim to the islands through rights of discovery and settlement, although this claim has always been challenged by Spain who until 1811 governed the islands. Both claims have legal support, and the final decision if there will ever be one is difficult to predict. Sadly today the ultimate test of sovereignty does not come through international law but remains in the idea that "He is sovereign who can defend his sovereignty." The years preceding the Argentine invasion of 1982 witnessed many diplomatic exchanges between The United Kingdom and Argentina over the future of the islands. During this time the British sent signals to Argentina that ii implied a decline in British resolve to hold the islands and demonstrated that military action did more to further the talks along than did actual negotiations. The Argentine military junta read these signals and decided that they could take the islands in a quick military invasion and that the United Kingdom would consider the act as a fait accompli and would not protest the invasion. The British in response to this claimed that they never signaled to Argentina that a military solution was acceptable to them and launched a Royal Navy task force to liberate the islands. Both governments responded to an international crisis with means that were designed both to resolve the international crisis and increase the domestic popularity of the government. British Prime Minister Margaret Thatcher was facing an all-time low in popularity for post-War Prime Ministers while Argentine President General Galtieri needed to gain mass popular support so he could remain a viable President after he was scheduled to lose command of the army and a seat on the military junta that ran the country. The military war for the Falklands is indicative of the nature of modern warfare between Third World countries. It shows that the gap in military capabilities between Third and First World countries is narrowing significantly. Modern warfare between a First and Third World country is no longer a 'walk over' for the First World country.

The law of the sea: the United States, Canada and the deep seabed

The Falkland Islands War of 1982 was fought over competing claims to sovereignty over a group of islands off the east coast of South America. The dispute was between Argentina and the United Kingdom. Argentina claims the islands under rights to Spanish succession, the fact that they lie off the Argentine coast line and that in 1833 Great Britain took the islands illegally and by force. The United Kingdom claims the islands primarily through prescription--the fact that they have governed the islands in a peaceful, continuous and public manner since 1833. The British also hold that the population living on the islands, roughly eighteen hundred British descendants, should be able to decide their own future. The United Kingdom also lays claim to the islands through rights of discovery and settlement, although this claim has always been challenged by Spain who until 1811 governed the islands. Both claims have legal support, and the final decision if there will ever be one is difficult to predict. Sadly today the ultimate test of sovereignty does not come through international law but remains in the idea that "He is sovereign who can defend his sovereignty." The years preceding the Argentine invasion of 1982 witnessed many diplomatic exchanges between The United Kingdom and Argentina over the future of the islands. During this time the British sent signals to Argentina that ii implied a decline in British resolve to hold the islands and demonstrated that military action did more to further the talks along than did actual negotiations. The Argentine military junta read these signals and decided that they could take the islands in a quick military invasion and that the United Kingdom would consider the act as a fait accompli and would not protest the invasion. The British in response to this claimed that they never signaled to Argentina that a military solution was acceptable to them and launched a Royal Navy task force to liberate the islands. Both governments responded to an international crisis with means that were designed both to resolve the international crisis and increase the domestic popularity of the government. British Prime Minister Margaret Thatcher was facing an all-time low in popularity for post-War Prime Ministers while Argentine President General Galtieri needed to gain mass popular support so he could remain a viable President after he was scheduled to lose command of the army and a seat on the military junta that ran the country. The military war for the Falklands is indicative of the nature of modern warfare between Third World countries. It shows that the gap in military capabilities between Third and First World countries is narrowing significantly. Modern warfare between a First and Third World country is no longer a 'walk over' for the First World country.

Feature Selection and Classification Using Age Layered Population Structure Genetic Programming

The curse of dimensionality is a major problem in the fields of machine learning, data mining and knowledge discovery. Exhaustive search for the most optimal subset of relevant features from a high dimensional dataset is NP hard. Sub–optimal population based stochastic algorithms such as GP and GA are good choices for searching through large search spaces, and are usually more feasible than exhaustive and deterministic search algorithms. On the other hand, population based stochastic algorithms often suffer from premature convergence on mediocre sub–optimal solutions. The Age Layered Population Structure (ALPS) is a novel metaheuristic for overcoming the problem of premature convergence in evolutionary algorithms, and for improving search in the fitness landscape. The ALPS paradigm uses an age–measure to control breeding and competition between individuals in the population. This thesis uses a modification of the ALPS GP strategy called Feature Selection ALPS (FSALPS) for feature subset selection and classification of varied supervised learning tasks. FSALPS uses a novel frequency count system to rank features in the GP population based on evolved feature frequencies. The ranked features are translated into probabilities, which are used to control evolutionary processes such as terminal–symbol selection for the construction of GP trees/sub-trees. The FSALPS metaheuristic continuously refines the feature subset selection process whiles simultaneously evolving efficient classifiers through a non–converging evolutionary process that favors selection of features with high discrimination of class labels. We investigated and compared the performance of canonical GP, ALPS and FSALPS on high–dimensional benchmark classification datasets, including a hyperspectral image. Using Tukey’s HSD ANOVA test at a 95% confidence interval, ALPS and FSALPS dominated canonical GP in evolving smaller but efficient trees with less bloat expressions. FSALPS significantly outperformed canonical GP and ALPS and some reported feature selection strategies in related literature on dimensionality reduction.

Feature Selection and Classification Using Age Layered Population Structure Genetic Programming

The curse of dimensionality is a major problem in the fields of machine learning, data mining and knowledge discovery. Exhaustive search for the most optimal subset of relevant features from a high dimensional dataset is NP hard. Sub–optimal population based stochastic algorithms such as GP and GA are good choices for searching through large search spaces, and are usually more feasible than exhaustive and determinis- tic search algorithms. On the other hand, population based stochastic algorithms often suffer from premature convergence on mediocre sub–optimal solutions. The Age Layered Population Structure (ALPS) is a novel meta–heuristic for overcoming the problem of premature convergence in evolutionary algorithms, and for improving search in the fitness landscape. The ALPS paradigm uses an age–measure to control breeding and competition between individuals in the population. This thesis uses a modification of the ALPS GP strategy called Feature Selection ALPS (FSALPS) for feature subset selection and classification of varied supervised learning tasks. FSALPS uses a novel frequency count system to rank features in the GP population based on evolved feature frequencies. The ranked features are translated into probabilities, which are used to control evolutionary processes such as terminal–symbol selection for the construction of GP trees/sub-trees. The FSALPS meta–heuristic continuously refines the feature subset selection process whiles simultaneously evolving efficient classifiers through a non–converging evolutionary process that favors selection of features with high discrimination of class labels. We investigated and compared the performance of canonical GP, ALPS and FSALPS on high–dimensional benchmark classification datasets, including a hyperspectral image. Using Tukey’s HSD ANOVA test at a 95% confidence interval, ALPS and FSALPS dominated canonical GP in evolving smaller but efficient trees with less bloat expressions. FSALPS significantly outperformed canonical GP and ALPS and some reported feature selection strategies in related literature on dimensionality reduction.

Modelling software quality : a multidimensional approach

Les sociétés modernes dépendent de plus en plus sur les systèmes informatiques et ainsi, il y a de plus en plus de pression sur les équipes de développement pour produire des logiciels de bonne qualité. Plusieurs compagnies utilisent des modèles de qualité, des suites de programmes qui analysent et évaluent la qualité d'autres programmes, mais la construction de modèles de qualité est difficile parce qu'il existe plusieurs questions qui n'ont pas été répondues dans la littérature. Nous avons étudié les pratiques de modélisation de la qualité auprès d'une grande entreprise et avons identifié les trois dimensions où une recherche additionnelle est désirable : Le support de la subjectivité de la qualité, les techniques pour faire le suivi de la qualité lors de l'évolution des logiciels, et la composition de la qualité entre différents niveaux d'abstraction. Concernant la subjectivité, nous avons proposé l'utilisation de modèles bayésiens parce qu'ils sont capables de traiter des données ambiguës. Nous avons appliqué nos modèles au problème de la détection des défauts de conception. Dans une étude de deux logiciels libres, nous avons trouvé que notre approche est supérieure aux techniques décrites dans l'état de l'art, qui sont basées sur des règles. Pour supporter l'évolution des logiciels, nous avons considéré que les scores produits par un modèle de qualité sont des signaux qui peuvent être analysés en utilisant des techniques d'exploration de données pour identifier des patrons d'évolution de la qualité. Nous avons étudié comment les défauts de conception apparaissent et disparaissent des logiciels. Un logiciel est typiquement conçu comme une hiérarchie de composants, mais les modèles de qualité ne tiennent pas compte de cette organisation. Dans la dernière partie de la dissertation, nous présentons un modèle de qualité à deux niveaux. Ces modèles ont trois parties: un modèle au niveau du composant, un modèle qui évalue l'importance de chacun des composants, et un autre qui évalue la qualité d'un composé en combinant la qualité de ses composants. L'approche a été testée sur la prédiction de classes à fort changement à partir de la qualité des méthodes. Nous avons trouvé que nos modèles à deux niveaux permettent une meilleure identification des classes à fort changement. Pour terminer, nous avons appliqué nos modèles à deux niveaux pour l'évaluation de la navigabilité des sites web à partir de la qualité des pages. Nos modèles étaient capables de distinguer entre des sites de très bonne qualité et des sites choisis aléatoirement. Au cours de la dissertation, nous présentons non seulement des problèmes théoriques et leurs solutions, mais nous avons également mené des expériences pour démontrer les avantages et les limitations de nos solutions. Nos résultats indiquent qu'on peut espérer améliorer l'état de l'art dans les trois dimensions présentées. En particulier, notre travail sur la composition de la qualité et la modélisation de l'importance est le premier à cibler ce problème. Nous croyons que nos modèles à deux niveaux sont un point de départ intéressant pour des travaux de recherche plus approfondis.

Sélection et polymorphisme chez des grenouilles mimétiques du Pérou (Dendrobatidae)

La diversification des signaux aposématiques dans un cadre de mimétisme müllérien est un phénomène intrigant. Alors que la théorie relative à l'aposématisme et au mimétisme suggère l'évolution vers un signal aposématique unique, d'impressionnantes variations peuvent être observées entre les populations, et cela à petite échelle spatiale. Il a été supposé que la variation spatiale des pressions de sélection engendrées par différents prédateurs puisse être à l'origine de ce phénomène. Afin de tester cette hypothèse, nous avons étudié la transition entre deux systèmes géographiques caractérisés par des patrons aposématiques distincts chez des grenouilles mimétiques et toxiques du nord du Pérou (Dendrobatidae) en combinant les outils de génétique des populations aux outils écologiques. Dans chacun de ces systèmes, Ranitomeya imitator vit en sympatrie avec R. ventrimaculata ou R. variabilis. Il s'agit du principal exemple empirique suggérant que dans un cadre de mimétisme müllérien, il n'y a pas convergence des signaux aposématiques des deux espèces, mais plutôt convergence unidirectionnelle où R. imitator, étant polymorphe, imite des espèces monomorphes avec lesquelles elle est sympatrique. Premièrement, les résultats réfutent les prémisses qui suggèrent que R. imitator converge vers le signal aposématique d’une autre espèce. La haute similarité génétique entre les espèces modèles suggère qu'elles ont divergé plus récemment que les populations de R. imitator ou qu'elles sont encore connectées par du flux génique. Ces résultats indiquent que ces espèces ont été identifiées à tort comme des espèces différentes. De fait, l'identification de l'espèce imitatrice basée sur la variabilité phénotypique est invalidée dans ce système puisque R. imitator et R. variabilis/ventrimaculata démontrent la même variabilité. Deuxièmement, nos résultats démontrent que la prédation varie spatialement, autant en intensité qu'en direction, créant ainsi un paysage hétérogène de pressions de sélection. Ainsi, de fortes pressions de prédation stabilisatrice permettent le maintien de l'organisation géographique de différents signaux aposématiques et expliquent l'uniformité de ces signaux ainsi que les relations mimétiques. Par contre, le relâchement temporaire des pressions de prédation permet l'apparition de nouveaux phénotypes aposématiques via les processus évolutifs neutres, conduisant à un haut polymorphisme au niveau de ces populations. L'interaction de ces modes sélectifs nous a permis de démontrer pour la première fois comment la théorie évolutive de Wright (shifting balance theory) permet la diversification adaptative dans un système naturel. Pour conclure, cette étude a permis de mettre en évidence à quel point les systèmes de mimétisme müllérien peuvent être dynamiques. L'alternance spatiale entre les processus évolutifs neutres et la sélection naturelle permet l'émergence de nouveaux phénotypes aposématiques à une échelle locale, ainsi que l'apparition d'une organisation géographique des signaux d'avertissement et des relations de mimétisme müllérien.