A linear-encoding model explains the variability of the target morphology in regeneration

A fundamental assumption of today''s molecular genetics paradigm is that complex morphology emerges from the combined activity of low-level processes involving proteins and nucleic acids. An inherent characteristic of such nonlinear encodings is the difficulty of creating the genetic and epigenetic information that will produce a given self-assembling complex morphology. This ‘inverse problem’ is vital not only for understanding the evolution, development and regeneration of bodyplans, but also for synthetic biology efforts that seek to engineer biological shapes. Importantly, the regenerative mechanisms in deer antlers, planarian worms and fiddler crabs can solve an inverse problem: their target morphology can be altered specifically and stably by injuries in particular locations. Here, we discuss the class of models that use pre-specified morphological goal states and propose the existence of a linear encoding of the target morphology, making the inverse problem easy for these organisms to solve. Indeed, many model organisms such as Drosophila, hydra and Xenopus also develop according to nonlinear encodings producing linear encodings of their final morphologies. We propose the development of testable models of regeneration regulation that combine emergence with a top-down specification of shape by linear encodings of target morphology, driving transformative applications in biomedicine and synthetic bioengineering.     

Water Penetration—Its Effect on the Strength and Toughness of Silica Glass

When a crack forms in silica glass, the surrounding environment flows into the crack opening, and water from the environment reacts with the glass to promote crack growth. A chemical reaction between water and the strained crack-tip bonds is commonly regarded as the cause of subcritical crack growth in glass. In silica glass, water can also have a secondary effect on crack growth. By penetrating into the glass, water generates a zone of swelling and, hence, creates a compression zone around the crack tip and on the newly formed fracture surfaces. This zone of compression acts as a fracture mechanics shield to the stresses at the crack tip, modifying both the strength and subcritical crack growth resistance of the glass. Water penetration is especially apparent in silica glass because of its low density and the fact that it contains no modifier ions. Using diffusion data from the literature, we show that the diffusion of water into silica glass can explain several significant experimental observations that have been reported on silica glass, including (1) the strengthening of silica glass by soaking the glass in water at elevated temperatures, (2) the observation of permanent crack face displacements near the crack tip of a silica specimen that had been soaked in water under load, and (3) the observation of high concentrations of water close to the fracture surfaces that had been formed in water. These effects are consistent with a model suggesting that crack growth in silica glass is modified by a physical swelling of the glass around the crack tip. An implication of water-induced swelling during fracture is that silica glass is more resistant to crack growth than it would be if swelling did not occur.     

Volatile fraction of commercial thyme honeys produced in Mediterranean regions and key volatile compounds for geographical discrimination: A chemometric approach

The aim of the present study was to investigate the volatile fraction and discriminate 34 commercial thyme honeys from Morocco, Egypt, Spain, and Greece according to geographical origin, using key volatile compounds in combination with chemometrics. Sixty-two volatile compounds belonging to different classes were identified and semi-quantified using headspace solid phase micro-extraction coupled to gas chromatography/mass spectrometry (HS-SPME-GC/MS). Applying chemometric analyses to 17 volatiles (p < 0.05), honeys were successfully discriminated according to geographical origin. Correct classification rate was 88.2% using the cross-validation method. Volatile compounds proved to be a powerful tool for discriminating commercial thyme honeys from different countries.     

Porous concrete as a template for the synthesis of porous carbon materials

The potential of industrial porous concrete for using as a template for the synthesis of porous carbon materials has been investigated. Carbon replicas of porous concrete have been prepared by carbonization of sucrose. The pores of the resulting carbon materials range from the macropore to the micropore region, pointing to a hierarchy.     

Calculation of double layer interaction between colloidal aggregates

This paper examines the interaction between the electric double layers of aggregates. Commonly, rather simplified models are used like the approximation of primary particle interaction (APPI), which just considers the interaction of the closest pair of primary particles having a double layer as if they were isolated. However, for nanoparticles the double layer thickness may be in the same order of magnitude as the particle size or even larger, what leads to a considerable double layer overlap inside the aggregates and between two interacting aggregates. Consequently, such approximations will fail. The paper presents a numerical scheme for the double layer interaction of arbitrarily shaped aggregates, which can e.g. help to establish criteria for the applicability of approximate models. The calculation employs a singularity method, which is based on the linearised Poisson–Boltzmann equation. Additionally, a linear model for charge regulation is implemented. The impact of charge regulation and double layer thickness were studied for fractal DLCA aggregates and hexagonal closed-packed aggregates.     

Liquid Chromatography–Hybrid Linear Ion Trap–High-Resolution Mass Spectrometry (LTQ-Orbitrap) Method for the Determination of Glycoalkaloids and Their Aglycons in Potato Samples

Potatoes produce biologically active secondary metabolites like glycoalkaloids and their aglycons, which may have both adverse and beneficial effects in the diet. A new analytical method that uses liquid chromatography–mass spectrometry (LTQ-Orbitrap) has been developed for the analysis of glycoalkaloids and their aglycons in potato samples. Two glycoalkaloids, α-solanine and α-chaconine, and two aglycons, demissidine and solasodine, were quantified in potato samples. Samples were extracted using methanol, purified on an SPE Strata C₁₈ cartridge, and then analyzed in HPLC–mass spectrometry (LTQ-Orbitrap) with the FTMS operating in full scan at a resolving power of 30,000 (FWHM), enabling the detection and accurate mass measurement and with the ITMS mode operating in MRM (multiple reaction monitoring) for glycoalkaloids and their aglycons using the [M + H]⁺ ions and their optimized collision energies. After validation, the method was applied to screen different type of potatoes, and some cooking experiment were conducted.     

Dynamic attribute based vehicle authentication

Modern vehicles are proficient in establishing a spontaneous connection over a wireless radio channel, synchronizing actions and information. Security infrastructure is most important in such a sensitive scope of vehicle communication for coordinating actions and avoiding accidents on the road. One of the first security issues that need to be established is authentication via IEEE 1609.2 security infrastructure. According to our preliminary work, vehicle owners are bound to preprocess a certificate from the certificate authority. The certificate carries vehicle static attributes (e.g., licence number, brand and color) certified together with the vehicle public key in a monolithic manner. Nevertheless, a malicious vehicle might clone the static attributes to impersonate a specific vehicle. Therefore, in this paper we consider a resource expensive attack scenario involving multiple malicious vehicles with identical visual static attributes. Apparently, dynamic attributes (e.g., location and direction) can uniquely define a vehicle and can be utilized to resolve the true identity of the vehicle. However, unlike static attributes, dynamic attributes cannot be signed by a trusted authority beforehand. We propose an approach to verify the coupling between non-certified dynamic attributes and certified static attributes on an auxiliary communication channel, for example, a modulated laser beam. Furthermore, we illustrate that the proposed approach can be used to facilitate the usage of existing authentication protocols such as NAXOS, in the new scope of ad-hoc vehicle networks. We use BAN logic to verify the security claims of the protocol against the passive and active interception.     

Reprint of “Pharmacokinetic modelling of the anti-malarial drug artesunate and its active metabolite dihydroartemisinin”

A four compartment mechanistic mathematical model is developed for the pharmacokinetics of the commonly used anti-malarial drug artesunate and its principle metabolite dihydroartemisinin following oral administration of artesunate. The model is structurally unidentifiable unless additional constraints are imposed. Combinations of mechanistically derived constraints are considered to assess their effects on structural identifiability and on model fits. Certain combinations of the constraints give rise to locally or globally identifiable model structures.     

A note on the time travel approach for handling time windows in vehicle routing problems

In this paper, we identify two cases in which the proposition for calculating time window penalties presented in Nagata, Y., Bräysy, O. and Dullaert, W. A penalty-based edge assembly memetic algorithm for the vehicle routing problem with time windows, Computers & Operations Research 2010;37(4): 724–37 yields incorrect results. We derive the corrected proposition and use numerical studies to show that a significant proportion of the evaluations performed by a Tabu Search for VRPTW falls under the two incorrect cases. Moreover, we demonstrate that the incorrect time window handling has a significant negative impact on the solution quality of the Tabu Search.