Challenges in horizontal model integration

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

The Process-Interaction-Model: a common representation of rule-based and logical models allows studying signal transduction on different levels of detail

BACKGROUND: Signaling systems typically involve large, structured molecules each consisting of a large number of subunits called molecule domains. In modeling such systems these domains can be considered as the main players. In order to handle the resulting combinatorial complexity, rule-based modeling has been established as the tool of choice. In contrast to the detailed quantitative rule-based modeling, qualitative modeling approaches like logical modeling rely solely on the network structure and are particularly useful for analyzing structural and functional properties of signaling systems. RESULTS: We introduce the Process-Interaction-Model (PIM) concept. It defines a common representation (or basis) of rule-based models and site-specific logical models, and, furthermore, includes methods to derive models of both types from a given PIM. A PIM is based on directed graphs with nodes representing processes like post-translational modifications or binding processes and edges representing the interactions among processes. The applicability of the concept has been demonstrated by applying it to a model describing EGF insulin crosstalk. A prototypic implementation of the PIM concept has been integrated in the modeling software ProMoT. CONCLUSIONS: The PIM concept provides a common basis for two modeling formalisms tailored to the study of signaling systems: a quantitative (rule-based) and a qualitative (logical) modeling formalism. Every PIM is a compact specification of a rule-based model and facilitates the systematic set-up of a rule-based model, while at the same time facilitating the automatic generation of a site-specific logical model. Consequently, modifications can be made on the underlying basis and then be propagated into the different model specifications – ensuring consistency of all models, regardless of the modeling formalism. This facilitates the analysis of a system on different levels of detail as it guarantees the application of established simulation and analysis methods to consistent descriptions (rule-based and logical) of a particular signaling system

Spectrophotometric data of the Re(VII) adsorption process on activated carbon

The data show the UV-Vis spectra obtained during the adsorption of Re (VII) ions on activated carbon. 200 mlof the solution was used in each ester, 3 ml of the solution was taken for analysis after a specified time, and then it was returned to the system. The data were used to determine the kinetic curves of adsorption depending on the amount of adsorbent, temperature, mixing speed of the solution, initial concentration of Re (VII) ions and pH.THIS DATASET IS ARCHIVED AT DANS/EASY, BUT NOT ACCESSIBLE HERE. TO VIEW A LIST OF FILES AND ACCESS THE FILES IN THIS DATASET CLICK ON THE DOI-LINK ABOV

Influence of the glassy carbon admixtures on useful properties of surgical cement

W pracy przeprowadzono badania procesu polimeryzacji cementu chirurgicznego na bazie PMMA domieszką węgla szklistego w postaci proszku. Określono podstawowe charakterystyki mechaniczne otrzymanego kompozytu polimerowego. Podjęto próbę oceny właściwości użytkowych tego biomateriału pod względem możliwości jego zastosowania w ortopedii.In this study has been carried examination of polymerization process bone cement modified with glassy carbon powder. It has been described mechanical characteristics of received polymer’s composite. We tried to assess useful properties of this biomaterial under possibility use it in orthopeady

Evaluation of susceptibility to ageing of the polymer surgical cement

W pracy badano wpływ starzenia na właściwości polimerowego cementu kostnego. Proces starzenia cementu kostnego realizowano poprzez zastosowanie naświetlania promieniami rentgenowskimi oraz moczenia w roztworze Ringera. Przeprowadzono badania statycznego ściskania i zginania zgodnie z wymogami normy ISO 5833 oraz badania zmęczeniowe niskocyklowe. Na podstawie badań zmęczeniowych opracowano krzywe cyklicznego pełzania i charakterystykę dynamicznego modułu sprężystości. Po starzeniu cementu kostnego stwierdzono spadek wytrzymałości na zginanie odpowiednio po naświetlaniu promieniami rtg i moczeniu w roztworze Ringera o 23% i o 32% a modułu sprężystości na zginanie o 20% i o 21%. Wytrzymałość na ściskanie cementu kostnego po promieniowaniu rtg spadła o 4% a po moczeniu w roztworze Ringera wzrosła o 9%. Moduł sprężystości wzrósł o 7% po starzeniu w środowisku wodnym a po promieniowaniu rtg pozostał bez zmian. Zaobserwowano również wpływ starzenia na właściwości lepkosprężyste cementu kostnego po promieniowaniu rtg. Stwierdzono wzrost dynamicznego modułu sprężystości cementu kostnego oraz uzyskanie mniejszych odkształceń podczas pełzania.The paper describes the research into the influence of ageing on the properties of the polymer surgical cement. The process of ageing of the surgical cement was performed using X-ray radiation and soaking in Ringer’s solution. The studies of static compression and bending in compliance with ISO 5833 requirements and low-cycle fatigue tests were carried out. Based on the fatigue tests performed, the curves of cyclic creep were obtained and characteristics of dynamic elasticity modulus developed. After ageing of the surgical cement, a decrease of bending strength was identified after X-ray radiation and soaking in Ringer’s solution, by 23% and 32% respectively, while the modulus of bending elasticity by 20% and 21%. Compression strength of surgical cement after X-ray radiation decreased by 4%, and increased by 9% after soaking in Ringer’s solution. The modulus of compression elasticity increased by 7% after ageing in a wet environment, while after X-ray radiation it remained almost unchanged. Also, the influence of ageing on viscoelastic properties of surgical cement after X-ray radiation was observed. A decrease in the dynamic elasticity modulus of surgical cement was identified, while the deformations obtained during creep were smaller

Examination of time's influence on mechanical properties of polyethylene hip cup endoprostheses

W pracy badano wpływ czasu na właściwości polietylenowych panewek endoprotez stawu biodrowego. Badaniom poddano oryginalne panewki z wysokocząsteczkowego polietylenu, wyprodukowane w latach od 1991 do 2003. Przeprowadzono pomiar twardości oraz statyczną próbę rozciągania próbek wykonanych z panewek. Stwierdzono niekorzystny wpływ czasu na właściwości mechaniczne panewek polietylenowych. Wraz z upływem czasu wystąpił wzrost twardości i modułu sprężystości E oraz spadek wytrzymałości na rozciąganie Rm polietylenu, z którego wykonane były panewki. Zmiany właściwości mechanicznych polietylenowych panewek mogą prowadzić do kruchego pękania materiału.The paper refers to the study of the influence of time on the properties of polyethylene hip joint cups. Original cups made of a high-molecular-weight polyethylene, produced in the years 1991-2003, were used for the study. Hardness measurement and a static tensile test of cup specimens were carried out. A disadvantageous impact of time upon the polyethylene cups' mechanical properties was observed. Over time, an increase in hardness and elasticity modulus E was observed coupled with a decrease in tensile strength Rm of the polyethylene of which the cups were made. Changes in the polyethylene cups' mechanical properties may lead to material's brittle cracking

Self-Assembled Monolayers Assisted all Wet Metallization of SU-8 Negative Tone Photoresist

The present work investigates the application of a Self-Assembled Monolayer (SAM) on the widely used negative photoresist SU-8. (3-Aminopropyl) trimethoxysilane (APTMS) is employed to form SAMs on the surface of the polymer through wet silanization in ethanol. The treatment process of SU-8 resin surface is optimized to achieve a well-formed, high quality SAM. Wettability measurements, atomic force microscopy (AFM) and infrared (IR) spectroscopy are employed to follow and optimize the silanization process. Following silanization, the resulting SAMs are employed as adhesion layers for electroless plated metallic layers. For this purpose, the superior affinity of APTMS amine terminal groups towards Pd2+ ions is exploited to activate the surface. Metallic coatings such as Cu, Ni-P or Co-Ni-P are thus deposited by mean of autocatalytic deposition. The surface of metallized samples is analyzed using AFM, scanning electron microscopy (SEM) and glow discharge optical emission spectroscopy (GDOES). Finally, Ni-P is deposited on a micropatterned SU-8 surface to demonstrate the potential of the presented metallization approach for microfabrication