An improved protein fold recognition with support vector machines

Predicting the three‐dimensional structure (fold) of a protein is a key problem in molecular biology. It is also interesting issue for statistical methods recognition. In this paper a multi‐class support vector machine (SVM) classifier is used on a real world data set. The SVM is a binary classifier, but protein fold recognition is a multi‐class problem. So several new approaches to deal with this issue are presented including a modification of the well‐known one‐versus‐one strategy. However, in this strategy the number of different binary classifiers that must be trained is quickly increasing with the number of classes. The methods proposed in this paper show how this problem can be overcome.     

A hybrid discriminative/generative approach to protein fold recognition

There are two standard approaches to the classification task: generative, which use training data to estimate a probability model for each class, and discriminative, which try to construct flexible decision boundaries between the classes. An ideal classifier should combine these two approaches. In this paper a classifier combining the well-known support vector machine (SVM) classifier with regularized discriminant analysis (RDA) classifier is presented. The hybrid classifier is used for protein structure prediction which is one of the most important goals pursued by bioinformatics. The obtained results are promising, the hybrid classifier achieves better result than the SVM or RDA classifiers alone. The proposed method achieves higher recognition ratio than other methods described in the literature.     

Switched Modeling and Task–Priority Motion Planning of Wheeled Mobile Robots Subject to Slipping

This study is devoted to the modelling and control of Wheeled Mobile Robots moving with longitudinal and lateral slips of all wheels. Due to wheel slippage we have to deal with systems with changing dynamics. Wheeled Mobile Robots can be thus modeled as switched systems with both autonomous switches (due to wheel slippage) and smooth controls (due to control algorithm). It is assumed that the slipping is counteracted by the slip reaction forces acting at contact points of the wheels with the ground. A model of these reaction forces, borrowed from the theory of automotive systems, has been adopted and included into the Lagrangian dynamic equations of the robot. A framework for designing motion planning schemes devoid of chattering effects for systems with changing dynamics is presented. A task–priority motion planning problem for wheeled mobile robots subject to slipping is addressed and solved by means of Jacobian motion planning algorithm based on the Endogenous Configuration Space Approach. Performance of the algorithm is presented in simulations of the Pioneer 2DX mobile platform. The robot dynamics equations are derived and 4 variants of motion are distinguished. The motion planning problem is composed of two sub-tasks: robot has to reach a desired point in the task space (proper motion planning) and the motion should minimize either the control energy expendinture or the wheel slippage. Performance of the motion planning algorithm is illustrated by a sort of the parking maneuver problem.     

An important step towards a prevascularized islet macroencapsulation device—effect of micropatterned membranes on development of endothelial cell network

The development of immune protective islet encapsulation devices could allow for islet transplantation in the absence of immunosuppression. However, the immune protective membrane / barrier introduced there could also impose limitations in transport of oxygen and nutrients to the encapsulated cells resulting to limited islet viability. In the last years, it is well understood that achieving prevascularization of the device in vitro could facilitate its connection to the host vasculature after implantation, and therefore could provide sufficient blood supply and oxygenation to the encapsulated islets. However, the microvascular networks created in vitro need to mimic well the highly organized vasculature of the native tissue. In earlier study, we developed a functional macroencapsulation device consisting of two polyethersulfone/polyvinylpyrrolidone (PES/PVP) membranes, where a bottom microwell membrane provides good separation of encapsulated islets and the top flat membrane acts as a lid. In this work, we investigate the possibility of creating early microvascular networks on the lid of this device by combining novel membrane microfabrication with co-culture of human umbilical vein endothelial cell (HUVEC) and fibroblasts. We create thin porous microstructured PES/PVP membranes with solid and intermittent line-patterns and investigate the effect of cell alignment and cell interconnectivity as a first step towards the development of a stable prevascularized layer in vitro. Our results show that, in contrast to non-patterned membranes where HUVECs form unorganized HUVEC branch-like structures, for the micropatterned membranes, we can achieve cell alignment and the co-culture of HUVECs on a monolayer of fibroblasts attached on the membranes with intermittent line-pattern allows for the creation of HUVEC branch-like structures over the membrane surface. This important step towards creating early microvascular networks was achieved without the addition of hydrogels, often used in angiogenesis assays, as gels could block the pores of the membrane and limit the transport properties of the islet encapsulation device.

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An important step towards a prevascularized islet microencapsulation device: in vivo prevascularization by combination of mesenchymal stem cells on micropatterned membranes

Extrahepatic transplantation of islets of Langerhans could aid in better survival of islets after transplantation. When islets are transfused into the liver 60-70% of them are lost immediately after transplantation. An important factor for a successful extrahepatic transplantation is a well-vascularized tissue surrounding the implant. There are many strategies known for enhancing vessel formation such as adding cells with endothelial potential, the combination with angiogenic factors and / or applying surface topography at the exposed surface of the device. Previously we developed porous, micropatterned membranes which can be applied as a lid for an islet encapsulation device and we showed that the surface topography induces human umbilical vein endothelial cell (HUVEC) alignment and interconnection. This was achieved without the addition of hydrogels, often used in angiogenesis assays. In this work, we went one step further towards clinical implementation of the device by combining this micropatterned lid with Mesenchymal Stem Cells (MSCs) to facilitate prevascularization in vivo. As for HUVECs, the micropatterned membranes induced MSC alignment and organization in vitro, an important contributor to vessel formation, whereas in vivo (subcutaneous rat model) they contributed to improved implant prevascularization. In fact, the combination of MSCs seeded on the micropatterned membrane induced the highest vessel formation score in 80% of the sections.

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A new insight into in vitro behaviour of poly(ε-caprolactone)/bioactive glass composites in biologically related fluids

In the present work, the role of content, size and chemical composition of gel-derived bioactive glass particles from the SiO₂–CaO–P₂O₅ system in modulating the in vitro bioactivity, osteoinductive properties and long-term (up to 15 months) degradation behaviour of poly(ε-caprolactone)-based composite films was investigated. Bioactivity was assessed in simulated body fluid (SBF) and HEPES-free Dulbecco’s modified Eagle medium (DMEM) supplemented with 10% foetal bovine serum (FBS), while hydrolytic degradation tests were performed in phosphate buffer saline. Obtained composite films showed excellent calcium phosphate (CaP) layer forming ability in both SBF and DMEM-10% FBS. However, kinetics of bioactivity process strongly depended on the type of medium used. The layer of amino acids and proteins, derived from cell culture medium, on the surfaces of composites created barrier that inhibited release of the ions on the one hand, while increasing nucleation density of calcium phosphates, affecting the morphology of formed CaP layers on the other. The presence of bioactive glass fillers was shown to impart osteoinductive properties to obtained films, supporting osteoblast attachment and proliferation, as well as stimulating cell differentiation and also matrix mineralization process in vitro. We showed that kinetics of bioactivity process and also osteoinductive properties of composite films could be easily modulated with the use of different contents and chemical compositions of fillers. The results showed that modification of PCL matrix with bioactive glass particles accelerated its degradation. We proved that the degradation rate of composites could be controlled and optimized for bone regeneration, in particular by using bioactive fillers causing different calcium phosphate layer forming ability on the surfaces of composites, depending on particle size and chemical composition. We have presented new opportunities to design and obtain multifunctional composites with tunable degradation and bioactivity kinetics, as well as biological properties that can meet complex requirements of bone tissue engineering.     

Bacterial cell killing properties of silver-loaded polysiloxane microspheres

Cross-linked polysiloxane microspheres containing a large number of SiOH groups were modified by introduction of organic thiol groups, which were further used for the functionalization of the microspheres with silver thiolate groups. The microspheres were characterized by ²⁹Si MAS NMR, ¹³C MAS NMR, SEM, XPS and elemental analysis. They were tested as biocides against selected Gram-positive and Gram-negative bacteria strains and exhibited high bactericidal activity. Separately, linear polysiloxane polymers equipped with organothiol groups and loaded with silver were synthesized. Their antibacterial activity was compared with that of silver thiolate-functionalized microspheres. Different shape of particles and a different form of silver explained somewhat lower activity of polymers.     

Synthesis of silver nanoparticles by Bacillus subtilis T‐1 growing on agro‐industrial wastes and producing biosurfactant

In this study, culture supernatnats of Bacillus subtilis T‐1 growing on brewery effluents and molasses was used for silver nanoparticles (Ag‐NPs) synthesis. The biosurfactant production of B. subtilis T‐1 was confirmed by the detection of genes in the genome and by the identification of the product in the supernatants. The genes for synthesis of surfactin (sfp, srfAA) and iturin (ituC) were noted by PCR reactions. Also, in examined culture supernatants the presence of C₁₃, C₁₄ and C₁₅ surfactin homologues with the sodiated molecules [M + Na]⁺ at m /z 1030, 1044 and 1058 was confirmed using LC/MS/MS analysis. The formation of NPs in the culture supernatants was confirmed by UV–vis spectroscopy. The dynamic light scattering measurements and transmission electron microscopy images showed the nanometric sizes of the biosynthesised Ag‐NPs which ranged from several nm to several tens of nm depending on the used culture supernatant. Biological properties of Ag‐NPs were evaluated by binding of Ag‐NPs with DNA isolated from the Escherichia coli ATCC 25922 and B. subtilis ATCC 6633. Biogenic Ag‐NPs were actively bound to DNA in increased concentration which could be the one important mode of antibacterial action of the Ag‐NPs.Inspec keywords: silver, nanoparticles, nanofabrication, materials preparation, microorganisms, antibacterial activity, industrial waste, agrochemicals, surfactants, breweries, genomics, genetics, chromatography, mass spectroscopic chemical analysis, ultraviolet spectroscopy, visible spectroscopy, spectrochemical analysis, light scattering, transmission electron microscopy, DNA, bonds (chemical), biochemistry, molecular biophysics, nanobiotechnology, biological techniques, particle size, enzymesOther keywords: silver nanoparticle synthesis, Bacillus subtilis T‐1 growth, agro‐industrial waste, biosurfactant production, brewery effluent, molasses, Ag‐NP synthesis, B. subtilis T‐1, gene detection, genome, supernatant product identification, surfactin synthesis, sfp, srfAA, iturin synthesis, ituC, PCR reaction, C₁₃ surfactin homologue, C₁₄ surfactin homologue, C₁₅ surfactin homologue, sodiated molecules, LC‐MS‐MS analysis, UV‐vis spectroscopy, dynamic light scattering measurement, transmission electron microscopy image, Ag‐NP nanometric size range, Ag‐NP biosynthesis, used culture supernatant dependence, biological properties, DNA isolation, Escherichia coli ATCC 25922, B. subtilis ATCC 6633, biogenic Ag‐NP‐DNA binding, Ag‐NP antibacterial action, Ag     

Nanoparticle Reshaping and Ion Migration in Nanocomposite Ultrafast Ionic Actuators: The Converse Piezo–Electro–Kinetic Effect

This article reports on the effect of silver nanoparticles (NPs), used as active fillers, on the piezoelectric response of polymer composites. In particular, it is demonstrated that the application of a periodic electric field drives a collective drift of surface atoms of the NPs along the field direction (“electrokinetic effect”) which, in turn, creates macroscopic reversible tensile states. Overdriving the system, in high‐field conditions, the electronic current is counterbalanced by a massive injection of Ag⁺ ions into the matrix, producing a metastable exceptional expansion of the device. For similitude with the converse piezoelectric effect, it has been called the converse piezo–electro–kinetic effect. By using in situ spectroscopy, vibrometric analysis, real‐time UV‐visible spectroscopy, in situ electrical transmission electron microscopy, and in qualitative form ab initio and finite element method numerical simulations, i) the injection of ions from the NPs to the matrix, ii) the surface migration‐induced NP reshaping, and iii) the NP migration and consequent percolation path adjustments are shown. The implications of this study are significant for the development of ultrafast soft ionic actuators and create the premises for a broad range of applications in smart materials and devices.