Gene regulatory networks reconstruction from time series datasets using genetic programming: a comparison between tree-based and graph-based approaches

Genetic programming researchers have shown a growing interest in the study of gene regulatory networks in the last few years. Our team has also contributed to the field, by defining two systems for the automatic reverse engineering of gene regulatory networks called GRNGen and GeNet. In this paper, we revise this work by describing in detail the two approaches and empirically comparing them. The results we report, and in particular the fact that GeNet can be used on large networks while GRNGen cannot, encourage us to pursue the study of GeNet in the future. We conclude the paper by discussing the main research directions that we are planning to investigate to improve GeNet.     

A Lyapunov method for stability analysis of piecewise-affine systems over non-invariant domains

This paper analyses stability of discrete-time piecewise-affine systems, defined on possibly non-invariant domains, taking into account the possible presence of multiple dynamics in each of the polytopic regions of the system. An algorithm based on linear programming is proposed, in order to prove exponential stability of the origin and to find a positively invariant estimate of its region of attraction. The results are based on the definition of a piecewise-affine Lyapunov function, which is in general discontinuous on the boundaries of the regions. The proposed method is proven to lead to feasible solutions in a broader range of cases as compared to a previously proposed approach. Two numerical examples are shown, among which a case where the proposed method is applied to a closed-loop system, to which model predictive control was applied without a-priori guarantee of stability.     

Intrinsic Fluorescence of the Active and the Inactive Functional Forms of Human Thymidylate Synthase

The observables associated with protein intrinsic fluorescence – spectra, time decays, anisotropies – offer opportunities to monitor in real time and non-invasively a protein‘s functional form and its interchange with other forms with different functions. We employed these observables to sketch the fluorometric profiles of two functional forms of human thymidylate synthase (hTS), a homodimeric enzyme crucial for cell proliferation and thus targeted by anticancer drugs. The protein takes an active and an inactive form. Stabilization of the latter by peptides that, unlike classical hTS inhibitors, bind it at the monomer/monomer interface offers an alternative inhibition mechanism that promises to avoid the onset of drug resistance in anticancer therapy. The fluorescence features depicted herein can be used as tools to identify and quantify each of the two protein forms in solution, thus making it possible to investigate the kinetic and thermodynamic aspects of the active/inactive conformational interchange. Two examples of fluorometrically monitored interconversion kinetics are provided.     

Simultaneous Microwave Extraction and Separation of Volatile and Non-Volatile Organic Compounds of Boldo Leaves. From Lab to Industrial Scale

Microwave extraction and separation has been used to increase the concentration of the extract compared to the conventional method with the same solid/liquid ratio, reducing extraction time and separate at the same time Volatile Organic Compounds (VOC) from non-Volatile Organic Compounds (NVOC) of boldo leaves. As preliminary study, a response surface method has been used to optimize the extraction of soluble material and the separation of VOC from the plant in laboratory scale. The results from the statistical analysis revealed that the optimized conditions were: microwave power 200 W, extraction time 56 min and solid liquid ratio of 7.5% of plants in water. Lab scale optimized microwave method is compared to conventional distillation, and requires a power/mass ratio of 0.4 W/g of water engaged. This power/mass ratio is kept in order to upscale from lab to pilot plant.     

Integrated Inspection Scheduling and Maintenance Planning for Infrastructure Systems

Operation and maintenance of an infrastructure system rely on information collected on its components, which can provide the decision maker with an accurate assessment of their condition states. However, resources to be invested in data gathering are usually limited and observations should be collected based on their Value of Information (VoI). Assessing the VoI is computationally intractable for most applications involving sequential decisions, such as long‐term infrastructure maintenance. In this article, we propose an approach for integrating adaptive maintenance planning based on Partially Observable Markov Decision Process (POMDP) and inspection scheduling based on a tractable approximation of VoI. Two alternative myopic approaches, namely pessimistic and optimistic, are introduced, and compared theoretically and by numerical examples.     

A new hydroxyapatite-based biocomposite for bone replacement

Since the 1970s, various types of ceramic, glass and glass–ceramic materials have been proposed and used to replace damaged bone in many clinical applications. Among them, hydroxyapatite (HA) has been successfully employed thanks to its excellent biocompatibility. On the other hand, the bioactivity of HA and its reactivity with bone can be improved through the addition of proper amounts of bioactive glasses, thus obtaining HA-based composites. Unfortunately, high temperature treatments (1200 °C ÷ 1300 °C) are usually required in order to sinter these systems, causing the bioactive glass to crystallize into a glass–ceramic and hence inhibiting the bioactivity of the resulting composite. In the present study novel HA-based composites are realized and discussed. The samples can be sintered at a relatively low temperature (800 °C), thanks to the employment of a new glass (BG_Ca) with a reduced tendency to crystallize compared to the widely used 45S5 Bioglass®. The rich glassy phase, which can be preserved during the thermal treatment, has excellent effects in terms of in vitro bioactivity; moreover, compared to composites based on 45S5 Bioglass® having the same HA/glass proportions, the samples based on BG_Ca displayed an earlier response in terms of cell proliferation.     

Effect of sugar, citric acid and egg white type on the microstructural and mechanical properties of meringues

Meringues are characterized by a predominant air phase and their overall quality is intimately related with microstructure. The formation of meringues microstructure relies on the capacity of egg white (EW) proteins to form voluminous and stable foams and it is ultimately related with the chemical properties of proteins and with the addition of ingredients such as sugars, salts, acids and surfactants.The study aimed at assessing the influence of sugar/EW ratio, citric acid and EW type on the microstructural and mechanical properties of meringues. Meringues prepared with different sugar/EW, citric acid level and different EW type were subjected to microstructural analysis by X-ray microtomography and to mechanical assessment by compression tests.Results demonstrate the ability of X-ray microtomography to reconstruct the 3D microstructure of meringues allowing the measurement of porosity, size, shape and distribution of pores. Citric acid, sugar concentration and EW type play a fundamental role on meringues microstructural parameters and mechanical properties. Low sugar/EW ratios as well as increasing citric acid levels increase the air phase and result in a softer texture of meringues. Moreover, low sugar/EW ratios and increasing citric acid in the meringue result in a reduction of pore size and also influence the shape of pores. Meringues microstructural and mechanical properties are affected by the EW quality: fresh and pasteurized EWs and EWs stored at refrigerated temperatures scored the highest structural and mechanical performances, while powdered and frozen EWs and albumens from old eggs showed the worst results. Not only the balance among ingredients but also the choice of raw materials can strongly affect the final quality of meringues.     

Shelf life of ready‐to‐cook cauliflower mixtures as affected by packaging film mass transport properties

In this work, the influence of packaging mass transport properties on quality loss of fresh‐cut cauliflower mixtures was addressed. The study was organised in two subsequent experimental steps; first, the selection of micro‐perforated packaging films was carried out by monitoring the package headspace gas concentrations of fresh‐cut white, green cauliflower and roman cabbage. Then, the effects of the barrier properties of the selected micro‐perforated film on shelf life of two different fresh‐cut cauliflower mixtures, stored at 4 ± 1 °C, were addressed. Results suggested that, among the investigated films, the micro‐perforated polymeric matrix with the lowest oxygen transmission rate value showed the best performance as it created the optimum headspace gas composition for each cauliflower variety, as well as, for the product mixtures. The appearance of visible moulds was the factor limiting product shelf life that accounted for about 18 days for both the investigated cauliflower mixtures.     

Eumelanin for nature‐inspired UV‐absorption enhancement of plastics

In the human body, the black‐brown biopigment eumelanin blocks harmful ultraviolet (UV) radiation. In the plastics industry, additives are often added to polymers to increase their UV‐absorption properties. We herein report an assessment of the biopigment eumelanin as a nature‐inspired additive for plastics to enhance their UV absorption. Since eumelanin is produced by natural sources and is nontoxic, it is an interesting candidate in the field of sustainable plastic additives. In this work, the eumelanin‐containing films of commercial ethylene–vinyl acetate copolymer, a plastic used for packaging applications, were obtained by melt compounding and compression molding. The biopigment dispersion in the films was improved by means of the melanin free acid treatment. It was observed that eumelanin amounts as low as 0.8 wt% caused an increase of the UV absorption, up to one order of magnitude in the UVA range. We also evaluated the effect of eumelanin on the thermal stability and photostability of the films: the biopigment proved to be double‐edged, working both as UV‐absorption enhancer and photo‐prooxidant, as thermogravimetric analysis and infrared spectroscopy revealed. © 2019 Society of Chemical Industry     

A proportional share allocation mechanism for coordination of plug-in electric vehiclecharging

The near-future penetration of plug-in electric vehicles is expected to be large enough to have a significant impact on the power grid. If PEVs were allowed to charge simultaneously at the maximum power rate, the distribution grid would face serious problems of stability. Therefore, mechanisms are needed to coordinate various PEVs that charge simultaneously. In this paper we propose an allocation mechanism that aims at balancing allocative efficiency and fairness, providing preferential treatment to the PEVs that have a high valuation of the available power, while guaranteeing a fair share of this power to all thePEVs.