88 research outputs found

    Challenges in horizontal model integration

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    BACKGROUND: Systems Biology has motivated dynamic models of important intracellular processes at the pathway level, for example, in signal transduction and cell cycle control. To answer important biomedical questions, however, one has to go beyond the study of isolated pathways towards the joint study of interacting signaling pathways or the joint study of signal transduction and cell cycle control. Thereby the reuse of established models is preferable, as it will generally reduce the modeling effort and increase the acceptance of the combined model in the field. RESULTS: Obtaining a combined model can be challenging, especially if the submodels are large and/or come from different working groups (as is generally the case, when models stored in established repositories are used). To support this task, we describe a semi-automatic workflow based on established software tools. In particular, two frequent challenges are described: identification of the overlap and subsequent (re)parameterization of the integrated model. CONCLUSIONS: The reparameterization step is crucial, if the goal is to obtain a model that can reproduce the data explained by the individual models. For demonstration purposes we apply our workflow to integrate two signaling pathways (EGF and NGF) from the BioModels Database. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12918-016-0266-3) contains supplementary material, which is available to authorized users

    Investigations of Properties of Wax Mixtures Used in the Investment Casting Technology – New Investigation Methods

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    The results of testing of the selected group of wax mixtures used in the investment casting technology, are presented in the paper. Themeasurements of the kinetics of the mixtures shrinkage and changes of viscous-plastic properties as a temperature function wereperformed. The temperature influence on bending strength of wax mixtures was determined

    Histological and cytological analysis of microsporogenesis and microgametogenesis of the invasive species Galinsoga quadriradiata Ruiz & Pav. (Asteraceae)

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    Galinsoga quadriradiataRuiz & Pav. is an annual weedy plant that can be found all over the world. It belongsto the Asteraceae family and is recognised as one of the invasive foreign plants in Poland, which are native toCentral and South America. The aim of this study was to describe the reproductive features of Galinsoga quadri-radiatafocusing on the changes that occur during microsporogenesis and microgametogenesis along with themorphology of its pollen. As it is typical of the eudicot clade of Angiosperms, cytokinesis of G. quadriradiataissimultaneous. The pollen grains are tricolporate with spiny outer walls and the course of the microsporogenet-ic process is fairly typical of the Echinatae group of weed plants. The high viability of the pollen grains, whichmature unequally in the inflorescences, and the proper course of meiosis determine whether a plant has theinvasive character of Galinsoga quadriradiata

    The influence of the shape of wax pattern on the kinetics of drying of ceramic moulds

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    Multi-layer ceramic moulds are built of slurry and a refractory material forming their matrices. From the moment when the European Union introduced regulations concerning the environment protection requiring substitution of alcoholic binders by aqueous binders, several difficulties in making moulds occurred. The influence of selected factors on drying ceramic moulds applied in the investment casting technology was determined by the gravimetric method. It was found that each successive layer, of a similar thickness, is drying longer than the previous one. The drying time of layers forming a deep cavities is several times longer as compared with drying open surfaces (external). Extension scale of the drying time is a function of the slenderness of cavities

    Comparative anatomy of ovules in Galinsoga, Solidago and Ratibida (Asteraceae)

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    Many Asteraceae species have been introduced into horticulture as ornamental or interesting exotic plants. Some of them, including Solidago and Galinsoga, are now aggressive weeds; others such as Ratibida are not. Special modifications of the ovule tissue and the occurrence of nutritive tissue have been described in several Asteraceae species, including invasive Taraxacum species. This study examined whether such modifications might also occur in other genera. We found that the three genera examined – Galinsoga (G. quadriradiata), Solidago (S. canadensis, S. rigida, S. gigantea) and Ratibida (R. pinnata) – differed in their nutritive tissue structure. According to changes in the integument, we identified three types of ovules in Asteraceae: “Taraxacum” type (recorded in Taraxacum, Bellis, Solidago, Chondrilla), with well-developed nutritive tissue having very swollen cell walls of spongy structure; “Galinsoga” type (in Galinsoga), in which the nutritive tissue cells have more cytoplasm and thicker cell walls than the other integument parenchyma cells, and in which the most prominent character of the nutritive tissue cells is well-developed rough ER; and “Ratibida” type (in Ratibida), in which the nutritive tissue is only slightly developed and consists of large highly vacuolated cells. Our study and future investigations of ovule structure may be useful in phylogenetic analyses

    Ovule structure of Scotch thistle Onopordum acanthium L. (Cynareae, Asteraceae)

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    Studies concerning the ultrastructure of the periendothelial zone integumentary cells of Asteraceae species arescarce. The aim was to check whether and/or what kinds of integument modifications occur in Onopordum acanthium. Ovule structure was investigated using light microscopy, scanning electron microscopy, transmission electron microscopy and histochemistry. For visualization of calcium oxalate crystals, the polarizing microscopy was used. The periendothelial zone of integument in O. acanthium is well developed and composed of mucilage cells near the integumentary tapetum and large, highly vacuolated cells at the chalaza and therefore they differ from other integumentary cells. The cells of this zone lack starch and protein bodies. Periendothelial zone cells do not have calcium oxalate crystals, in contrast to other integument cells. The disintegration of periendothelial zone cells was observed in a mature ovule. The general ovule structure of O. acanthium is similar to other members of the subfamily Carduoideae, although it is different to “Taraxacum”, “Galinsoga” and “Ratibida” ovule types

    Reduced pollen viability and achene development in Solidago ×niederederi Khek from Poland

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    Pollen and achene characters of natural interspecific hybrid Solidago ×niederederi Khek were analyzed and compared with putative parental species S. virgaurea L. and S. canadensis L. to estimate the level of disturbances in generative reproduction resulting from its hybrid nature. Pollen viability (stainability) of Solidago ×niederederi from one newly discovered locality in NE Poland was evidently reduced to ~65% in both viability tests (acetocarmine and Alexander). The diameter of viable pollen (median 21.11 µm) fell between S. canadensis (median 19.52 µm) and S. virgaurea (median 23.48 µm). Both parental species produced normally developed achenes with high frequency (~90%) whereas in the hybrid, the seed set was dramatically low (6%). The results clearly indicated that sexual reproduction of hybridogenous taxon S. ×niederederi is disturbed, and its potential impact as an invasive species depends mainly on vegetative propagation
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