First experiences with the Polish Optical Internet

The paper describes the new development programme of the Polish information infrastructure. The programme, called in Polish PIONIER: (English—PIONEER) Polish Optical Internet, Advanced Applications, Services and Technologies for the Information Society, has been proposed to the Polish State Committee for Scientific Research and has been accepted. The aim of the programme is to create an advanced infrastructure together with tools, services and applications available to the entire scientific community and eventually to government and local administrations as well as society in general. Services and applications are expected to appear as selected pilot realizations in order to verify deployed technologies. Some of the pilot realizations and testbeds are also presented in the paper.     

Verification of bounded Petri nets using integer programming

Model checking based on the causal partial order semantics of Petri nets is an approach widely applied to cope with the state space explosion problem. One of the ways to exploit such a semantics is to consider (finite prefixes of) net unfoldings—themselves a class of acyclic Petri nets—which contain enough information, albeit implicit, to reason about the reachable markings of the original Petri nets. In [19], a verification technique for net unfoldings was proposed, in which deadlock detection was reduced to a mixed integer linear programming problem. In this paper, we present a further development of this approach. The essence of the proposed modifications is to transfer the information about causality and conflicts between the events involved in an unfolding, into a relationship between the corresponding integer variables in the system of linear constraints. Moreover, we present some problem-specific optimisation rules, reducing the search space. To solve other verification problems, such as mutual exclusion or marking reachability and coverability, we adopt Contejean and Devie's algorithm for solving systems of linear constraints over the natural numbers domain and refine it, by taking advantage of the specific properties of systems of linear constraints to be solved. Another contribution of this paper is a method of re-formulating some problems specified in terms of Petri nets as problems defined for their unfoldings. Using this method, we obtain a memory efficient translation of a deadlock detection problem for a safe Petri net into an LP problem. We also propose an on-the-fly deadlock detection method. Experimental results demonstrate that the resulting algorithms can achieve significant speedups.

Intelligent product search with soft-boundary preference relaxation

This paper proposes a novel method for preference relaxation in online product search, which enables consumers to make quality choices without suffering from the commonly experienced information overload. In online shopping scenarios that involve multi-attribute choice tasks, it can be difficult for consumers to process the vast amounts of information available and to make satisfactory buying decisions. In such situations consumers are likely to eliminate potentially good choices early on, using hard-constraint filtering tools. Our approach uses edge sets to identify the alternatives on the soft boundary and the principle of alternative domination to suppress the alternatives on this boundary that are irrelevant. We demonstrate how our approach outperforms existing methods for product search in a set of simulations using two sets of 2650 car advertisements and 1813 digital cameras gathered from a popular online store.     

SDF classifier revisited

This paper is addressing problems related to the construction of classifiers based on the Similarity Discriminant Function (SDF), in which the traditional vector representation of a pattern is replaced with matrix data. We introduce potential modifications of the matrix data structure and propose new variants of the SDF. The algorithms that we present were tested on images of handwritten digits and on photographs of human faces, taken from the ORL and CMU‐PIE databases. The results of experiments show that our modifications significantly improved the performance of the original SDF classifier.     

Fabrication of biocompatible hydrogel coatings for implantable medical devices using Fenton-type reaction

In this paper the authors present a simple method of coating polyurethane (PU) surface with poly(vinyl pirrolidone) (PVP) hydrogel. The hydrogel-coated materials were designed for use in biomedical applications, especially in blood-contacting devices. The coating is formed due to free radical macromolecular grafting–crosslinking. Polymer surface was first immersed in an organic solution containing radical source: cumene hydroperoxide (CHP) with an addition of a branching and anchoring agent: ethylene glycol dimethylacrylate (EGDMA). In the second step, the substrate was immersed in a water solution containing given concentration of PVP and Fe²⁺. The novelty of the process consists in the fact that free radicals are formed mostly at the polymer/solution interface, what assures high grafting efficiency together with the formation of covalent bonds between polymer substrate and modifying layer.The process was optimized for reagents concentrations. The coating properties: thickness and the swelling ratio were strongly influenced by CHP, Fe²⁺, PVP and EGMDA concentrations. The chemical composition of the surface analyzed with FTIR-ATR spectroscopy confirmed the presence of PVP coating. In vitro biocompatibility tests with L929 fibroblasts confirmed non-cytotoxicity of the coatings. Hydrogel coating significantly improved polyurethane hemocompatibility. Studies with human whole blood revealed that both, the platelet consumption and the level of platelet activation were as low as for negative control.     

Transported snapshot model order reduction approach for parametric,steady-state fluid flows containing parameter-dependent shocks

A new model order reduction approach is proposed for parametric steady-state nonlinear fluid flows characterized by shocks and discontinuities whose spatial locations and orientations are strongly parameter dependent. In this method, solutions in the predictive regime are approximated using a linear superposition of parameter-dependent basis. The sought-after parametric reduced bases are obtained by transporting the snapshots in a spatially and parametrically dependent transport field. Key to the proposed approach is the observation that the transport fields are typically smooth and continuous, despite the solution themselves not being so. As a result, the transport fields can be accurately expressed using a low-order polynomial expansion. Similar to traditional projection-based model order reduction approaches, the proposed method is formulated mathematically as a residual minimization problem for the generalized coordinates. The proposed approach is also integrated with well-known hyper-reduction strategies to obtain significant computational speedups. The method is successfully applied to the reduction of a parametric one-dimensional flow in a converging-diverging nozzle, a parametric two-dimensional supersonic flow over a forward-facing step, and a parametric two-dimensional jet diffusion flame in a combustor.     

Multipose Binding in Molecular Docking

Molecular docking has been extensively applied in virtual screening of small molecule libraries for lead identification and optimization. A necessary prerequisite for successful differentiation between active and non-active ligands is the accurate prediction of their binding affinities in the complex by use of docking scoring functions. However, many studies have shown rather poor correlations between docking scores and experimental binding affinities. Our work aimed to improve this correlation by implementing a multipose binding concept in the docking scoring scheme. Multipose binding, i.e., the property of certain protein-ligand complexes to exhibit different ligand binding modes, has been shown to occur in nature for a variety of molecules. We conducted a high-throughput docking study and implemented multipose binding in the scoring procedure by considering multiple docking solutions in binding affinity prediction. In general, improvement of the agreement between docking scores and experimental data was observed, and this was most pronounced in complexes with large and flexible ligands and high binding affinities. Further developments of the selection criteria for docking solutions for each individual complex are still necessary for a general utilization of the multipose binding concept for accurate binding affinity prediction by molecular docking.     

Piperine Targets Different Drug Resistance Mechanisms in Human Ovarian Cancer Cell Lines Leading to Increased Sensitivity to Cytotoxic Drugs

Our goal was to examine the anticancer effects of piperine against the resistant human ovarian cancer cells and to explore the molecular mechanisms responsible for its anticancer effects. Our study used drug-sensitive ovarian cancer cell line W1 and its sublines resistant to paclitaxel (PAC) and topotecan (TOP). We analyzed the cytotoxic effect of piperine and cytostatic drugs using an MTT assay. The impact of piperine on protein expression was determined by immunofluorescence and Western blot. We also examined its effect on cell proliferation and migration. We noticed a different level of piperine resistance between cell lines. Piperine increases the cytotoxic effect of PAC and TOP in drug-resistant cells. We observed an increase in PTPRK expression correlated with decreased pTYR level after piperine treatment and downregulation of P-gp and BCRP expression. We also noted a decrease in COL3A1 and TGFBI expression in investigated cell lines and increased COL3A1 expression in media from W1PR2 cells. The expression of Ki67 protein and cell proliferation rate decreased after piperine treatment. Piperine markedly inhibited W1TR cell migration. Piperine can be considered a potential anticancer agent that can increase chemotherapy effectiveness in cancer patients.     

Innovative method of Transthoracic Lung Cancer Biopsy of Parietal Lung Tumors under US Guidance after CT Pre-biopsy Planning as an Alternative to CT- Guided Biopsy

The authors compared their earlier results of the tumor biopsies performed under computer tomography （CT） guidance against the results of their recently modified-combined method of visualization and measurement of lung tumor parameters by CT imaging followed by US guided biopsy. In 238 （6.36%） of 3,745 patients in CT examination, the lung tumor was located peripherally, and obtaining histopathological confirmation was crucial to start the proper treatment. The patients were divided into two groups, the division was based on the biopsy method. Within the first group in I 18 patients, parietal lung tumor was confirmed and CT guided biopsy was performed. Within the second group, parietal lung tumor was confirmed in 120 patients and combined method of CT pre- biopsy planning and US guided biopsy were used. Pre-biopsy planning was performed using CT, measurements such as depth and distance of the tumor were made, obtained data were then saved on CT image and patient＇s skin was marked. Then obtained results were analyzed using test for two proportions. The analysis of the results confirmed the higher efficacy of the combined method taking into account the number of complications （p 〈 0.01） and diagnostic histopathological results （P 〈 0.001）. Suggested innovative method, involving both CT pre-biopsy planning and US guided biopsy, allows to analyze simultaneously static CT and dynamic US images and it is considered to be an easy and effective method comparing to relying on static in nature CT images only. Our method is related to a lower complication risk rate.