Electrospray ionization mass spectrometry and tandem mass spectrometry of clodronate and related bisphosphonate and phosphonate compounds

The bisphosphonate family with a P-C-P structure is a broad class of drugs, widely investigated as potential inhibitors in bone diseases and calcium metabolic disorders. In this study, the mass spectrometric (MS) behavior and fragmentation of clodronate and related bisphosphonate and phosphonate compounds was studied by using negative ion electrospray ionization (ESI) with triple quadrupole and ion trap instruments. The effect of pH on the degree of deprotonation of the polyprotic bisphosphonic and phosphonic acids in negative ion ESI-MS was investigated, and the degree of deprotonation in the ESI mass spectra and the dissociation in the liquid phase were compared. The results provide evidence that the measured ESI mass spectra do not correlate with the chemistry in the liquid phase owing to the decrease in the pH of the solvent droplets during the ion evaporation process and the charge state neutralization in the gas phase. Ion trap MS(n) provided useful information on the fragmentation study of clodronate and related bisphosphonate and phosphonate compounds, in which interesting fragmentation pathways including the direct elimination of carbon monoxide from deprotonated bisphosphonates and formation of a P-P bond were observed. Reactions between the product ions with a -PO(2) group and residual water in the ion trap or in the high-pressure region of the triple quadrupole instrument formed other unexpected fragmentation paths for all the bisphosphonates studied.     

Mass spectrometric studies of benzoxazine resorcarenes

Eleven differently substituted 3,4-dihydro-2H-1,3-benzoxazine resorcarenes were studied by electrospray ionisation (ESI) and matrix-assisted laser desorption/ionisation (MALDI) mass spectrometry, using Fourier transform ion cyclotron resonance (FT-ICR) and time-of-flight (TOF) mass spectrometers, respectively. Under ESI conditions it was possible to transfer the intact resorcarenes from solution to the gas phase, yielding [M + H](+) and [M + 2H](+) ions as the main ions observed. Energy increase of the ions induced ready decomposition through successive eliminations of four CH(2)NR groups. Ion-molecule reactions showed that the ionising proton was situated somewhere inside the molecule and could not be reached with neutral reagent gases. In the host-guest complexation experiments, the benzoxazine resorcarenes studied turned out to be poor hosts for alkali metal and ammonium ions. In MALDI experiments, 2,5-dihydroxybenzoic acid proved to be the best matrix for these compounds. However, the intensity of the [M + H](+) ions was low for all compounds, and extensive fragmentation with consecutive elimination of CH(2)NR groups was observed.     

High Temperature Gas Chromatography with a Glass Capillary Column for the Analysis of High Molecular Weight Tracers in Smoke Samples from Biomass Burning

A custom-made glass capillary column coated with OV-1701-OH (88% methyl, 7% cyanopropyl, 5% phenylpolysiloxane) was used to analyze smoke samples from biomass combustion of different species of plants collected in the Amazon forest. CS₂ was used as solvent in order to enhance the dissolution and analysis of the heavier molecular weight components. The performance of the column was monitored during the experiments and a moderate increase in activity was observed after taking the column to high analytical temperatures (390°C). Trennzahl values typically dropped 20–30% from 1.7/m to the average of 1.35/m. In general, the performance of the custom-made column was satisfactory and comparable to the commercial high temperature columns. The high temperature high resolution GC and GC-MS analyses revealed the presence of a number of high molecular weight components reported to occur in smoke aerosols for the first time. These components consisted of series of wax esters (long chain alcohols esterified with long chain fatty acids) with up to 58 carbon numbers, aliphatic hydrocarbons, triglycerides, triterpenyl esters (e.g. α- and β-amyryl stearate). Although other types of compounds were also detected, their complete structure elucidation solely by electron impact MS was not adequate and other techniques will be required.     

Application of High Temperature High Resolution Gas Chromatography to Crude Extracts of Propolis

The underivatized acetone and hexane fractions from propolis samples (predominant flora Citrus spp. and Vernonia polyanthes) were analyzed by HT-HRGC (high temperature high resolution gas chromatography) and HT-HRGC coupled to mass spectrometry (HT-HRGC-MS). Several compounds, including flavonoid aglycones, phenolic acids, and high molecular weight compounds were characterized in crude extracts by HT-HRGC-MS. HT-HRGC and HT-HRGC-MS were shown to be quick and informative tools for rapid analysis of crude extracts without need for prior derivatization and purification.     

On the conditions for the existence of a plane of symmetry for anisotropic elastic material

We consider the problem of determining necessary and sufficient conditions for the existence of symmetry planes of an anisotropic elastic material. These conditions are given in several equivalent forms, and are used to determine special coordinate systems where the number of non-zero components in the elasticity tensor is minimized. By the method presented here it is also shown that an elastic solid has at least six coordinate systems with respect to which there are only 18 non-zero elastic constants and cannot possess more then ten traditional and distinct symmetrics by planes of symmetry.     

Objective Supervised Machine Learning-Based Classification and Inference of Biological Neuronal Networks

The classification of biological neuron types and networks poses challenges to the full understanding of the human brain’s organisation and functioning. In this paper, we develop a novel objective classification model of biological neuronal morphology and electrical types and their networks, based on the attributes of neuronal communication using supervised machine learning solutions. This presents advantages compared to the existing approaches in neuroinformatics since the data related to mutual information or delay between neurons obtained from spike trains are more abundant than conventional morphological data. We constructed two open-access computational platforms of various neuronal circuits from the Blue Brain Project realistic models, named Neurpy and Neurgen. Then, we investigated how we could perform network tomography with cortical neuronal circuits for the morphological, topological and electrical classification of neurons. We extracted the simulated data of 10,000 network topology combinations with five layers, 25 morphological type (m-type) cells, and 14 electrical type (e-type) cells. We applied the data to several different classifiers (including Support Vector Machine (SVM), Decision Trees, Random Forest, and Artificial Neural Networks). We achieved accuracies of up to 70%, and the inference of biological network structures using network tomography reached up to 65% of accuracy. Objective classification of biological networks can be achieved with cascaded machine learning methods using neuron communication data. SVM methods seem to perform better amongst used techniques. Our research not only contributes to existing classification efforts but sets the road-map for future usage of brain–machine interfaces towards an in vivo objective classification of neurons as a sensing mechanism of the brain’s structure.     

Numerical Comparison of Some Penalty-Based Constraint Handling Techniques in Genetic Algorithms

We study five penalty function-based constraint handling techniques to be used with genetic algorithms in global optimization. Three of them, the method of superiority of feasible points, the method of parameter free penalties and the method of adaptive penalties have already been considered in the literature. In addition, we introduce two new modifications of these methods. We compare all the five methods numerically in 33 test problems and report and analyze the results obtained in terms of accuracy, efficiency and reliability. The method of adaptive penalties turned out to be most efficient while the method of parameter free penalties was the most reliable.     

Determination of wood grain direction from laser light scattering pattern

Laser light scattering patterns from the grains of wood are investigated in detail to gain information about the characteristics of scattering patterns related to the direction of the grains. For this purpose, wood samples of Scots pine (Pinus sylvestris L.) and silver birch (Betula pubescens) were investigated. The orientation and shape of the scattering pattern of laser light in wood was found to correlate well with the direction of grain angles in a three-dimensional domain. The proposed method was also experimentally verified.     

Blocking the lateral film growth at the nanoscale in area-selective atomic layer deposition

Area-selective atomic layer deposition (ALD) allows the growth of highly uniform thin inorganic films on certain parts of the substrate while preventing the film growth on other parts. Although the selective ALD growth is working well at the micron and submicron scale, it has failed at the nanoscale, especially near the interface where there is growth on one side and no-growth on the other side. The reason is that methods so far solely rely on the chemical modification of the substrate, while neglecting the occurrence of lateral ALD growth at the nanoscale. Here we present a proof-of-concept for blocking the lateral ALD growth also at the nanoscale by combining the chemical surface modification with topographical features. We demonstrate that area-selective ALD of ZnO occurs by applying the diethylzinc/water ALD process on cicada wings that contain a dense array of nanoscopic pillars. The sizes of the features in the inorganic film are down to 25 nm which is, to the best of our knowledge, the smallest obtained by area-selective ALD. Importantly, our concept allows the synthesis of such small features even though the film is multiple times thicker.