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.     

Water soluble trehalose-derived oligoamides

A new family of oligotrehaluronamides was synthesized through the polycondensation of α,α-trehaluronic acid dimethyl ester and different diamines or polyamines. In particular, diamines with different molecular structure (1,n-alkylene diamines, aromatic diamine, and alkyleneoxydiamine) were used in order to modulate the molecular weights and the physical characteristics of the products, such as T_g, hydrophilic or hydrophobic properties, and solubility. α,α-Trehaluronic acid was obtained from a renewable source as α,α-trehalose. The syntheses of oligotrehaluronamides were carried out in different solvents such as ethanol, methanol, THF and DMSO, using triethylamine as catalyst. All the compounds obtained in this study were characterized through FT-IR and NMR spectroscopy. The molecular weights were evaluated by ¹H-NMR and in some cases compared with those obtained from ESI-MS spectrometry. Glass transition temperatures and melting points were detected by differential scanning calorimetry. Low molecular weight oligoamides, containing several hydroxyl groups, are water-soluble and could be used in water-based formulations.     

A variational integrators approach to second order modeling and identification of linear mechanical systems

The theory of variational integration provides a systematic procedure to discretize the equations of motion of a mechanical system, preserving key properties of the continuous time flow. The discrete-time model obtained by variational integration theory inherits structural conditions which in general are not guaranteed under general discretization procedures. We discuss a simple class of variational integrators for linear second order mechanical systems and propose a constrained identification technique which employs simple linear transformation formulas to recover the continuous time parameters of the system from the discrete-time identified model. We test this approach on a simulated eight degrees of freedom system and show that the new procedure leads to an accurate identification of the continuous-time parameters of second-order mechanical systems starting from discrete measured data.     

DNA barcoding as a new tool for food traceability

Food safety and quality are nowadays a major concern. Any case of food alteration, especially when reported by the media, has a great impact on public opinion. There is an increasing demand for the improvement of quality controls, hence addressing scientific research towards the development of reliable molecular tools for food analysis. DNA barcoding is a widely used molecular-based system, which can identify biological specimens, and is used for the identification of both raw materials and processed food. In this review the results of several researches are critically analyzed, in order to exploit the effectiveness of DNA barcoding in food traceability, and to delineate some best practices in the application of DNA barcoding throughout the industrial pipeline. The use of DNA barcoding for food safety and in the identification of commercial fraud is also discussed.     

HF Formation through Dissociative Electron Attachment—A Combined Experimental and Theoretical Study on Pentafluorothiophenol and 2-Fluorothiophenol

In chemoradiation therapy, dissociative electron attachment (DEA) may play an important role with respect to the efficiency of the radiosensitizers used. The rational tailoring of such radiosensitizers to be more susceptive to DEA may thus offer a path to increase their efficiency. Potentially, this may be achieved by tailoring rearrangement reactions into the DEA process such that these may proceed at low incident electron energies, where DEA is most effective. Favorably altering the orbital structure of the respective molecules through substitution is another path that may be taken to promote dissociation up on electron capture. Here we present a combined experimental and theoretical study on DEA in relation to pentafluorothiophenol (PFTP) and 2-fluorothiophenol (2-FTP). We investigate the thermochemistry and dynamics of neutral HF formation through DEA as means to lower the threshold for dissociation up on electron capture to these compounds, and we explore the influence of perfluorination on their orbital structure. Fragment ion yield curves are presented, and the thermochemical thresholds for the respective DEA processes are computed as well as the minimum energy paths for HF formation up on electron capture and the underlying orbital structure of the respective molecular anions. We show that perfluorination of the aromatic ring in these compounds plays an important role in enabling HF formation by further lowering the threshold for this process and through favorable influence on the orbital structure, such that DEA is promoted. We argue that this approach may offer a path for tailoring new and efficient radiosensitizers.     

Surface properties of phenolic compounds and their influence on the dispersion degree and oxidative stability of olive oil O/W emulsions

The surface and interfacial properties of gallic acid, catechin and quercetin, and their effect on the dispersion degree and the oxidative stability of olive oil oil-in-water (O/W) emulsions prepared using β-lactoglobulin and Tween 20 were studied.Gallic acid showed no effect on the surface properties while catechin was proven to be able to accumulate at the air/water interface, decreasing the surface tension values with increasing its concentration. All the phenolic antioxidants caused a decrease in the interfacial tension at the oil/water interface, even though only catechin and quercetin showed a concentration dependent behaviour.In emulsions, gallic acid did not affect the droplet size of the systems, catechin caused the formation of oil droplets bigger than those of the control, whilst quercetin improved the dispersion state of the emulsions with the increasing of its concentration. Gallic acid, despite its partitioning in the water phase due to its polarity, delayed the formation of both the hydroperoxides and TBARs and limited their accumulation. Catechin did not affect the formation of oxidation products whilst quercetin, among the tested antioxidants, caused the lowest formation of both hydroperoxides and TBARs through 33 days of storage.     

Solvent‐stable UV‐cured acrylic polysulfone membranes

A systematic investigation of the effect of the presence of acrylate resin on polysulfone‐based membranes was performed with the aim of obtaining chemically stable crosslinked membranes without affecting their flux performances. The membranes were prepared via UV curing of the polymer dope followed by a non‐solvent‐induced phase separation process. Two different acrylic monomers were investigated and their amount was varied in the polymer dope, to study the influence of concentration on final results. High crosslinking degrees were achieved by irradiating the solution for one minute. Morphological investigations of the active surface and of the cross‐sections of the fabricated membranes showed that the typical porosity of ultrafiltration membranes was obtained starting from solutions containing a low amount of crosslinker (10 wt%), which is consistent with the water flux values which were comparable to that of the pristine polysulfone membrane. High concentrations of crosslinker resin in the initial polymer dope produced denser membranes with lower permeability. High rejection of 27 nm particles (>90%) was measured for all samples having measurable flux. The addition of the crosslinker allowed one to obtain stability in various solvents without affecting the flux and rejection performance of the porous membranes. © 2016 Society of Chemical Industry     

Quantitative Assessment of a Peer-to-peer Cooperative Infrastructure Using Stochastic Well-Formed Nets

Traditional support tools for software engineers, normally based on a client-server architecture, are unsuitable to deal with the new issues emerging from the current (and future) cooperative work scenarios (where connectivity is intrinsically transient, the number of interacting partners dynamically changes, etc.). This paper presents a quantitative assessment of a fully decentralized, peer-to-peer, cooperative infrastructure. Stochastic Well-Formed Nets (SWNs) modelling the new peer-to-peer architecture, and a traditional (client-server) one, are developed and analysed: we used SWNs for their ability to directly exploit the symmetries intrinsically present in the modelled systems, thus greatly reducing the complexity of the analysis. The main goal is to compare the impact of the two alternative protocols on the collaborative work. Together with the performance figures of interest, methodological issues concerning the choice of the most appropriate model abstraction level, the adoption of a compositional modelling approach, and the management of the model complexity are also discussed.