Classifier combination for in vivo magnetic resonance spectra of brain tumours

Peer-reviewed

Classifier combination for in vivo magnetic resonance spectra of brain tumours

In this paper we present a multi-stage classifier for magnetic resonance spectra of human brain tumours which is being developed as part of a decision support system for radiologists. The basic idea is to decompose a complex classification scheme into a sequence of classifiers, each specialising in different classes of tumours and trying to reproducepart of the WHO classification hierarchy. Each stage uses a particular set of classification features, which are selected using a combination of classical statistical analysis, splitting performance and previous knowledge.Classifiers with different behaviour are combined using a simple voting scheme in order to extract different error patterns: LDA, decision trees and the k-NN classifier. A special label named "unknown¿ is used when the outcomes of the different classifiers disagree. Cascading is alsoused to incorporate class distances computed using LDA into decision trees. Both cascading and voting are effective tools to improve classification accuracy. Experiments also show that it is possible to extract useful information from the classification process itself in order to helpusers (clinicians and radiologists) to make more accurate predictions and reduce the number of possible classification mistakes.

Monte Carlo simulation of x-ray spectra generated by kilo-electron-volt electrons

We present a general algorithm for the simulation of x-ray spectra emitted from targets of arbitrary composition bombarded with kilovolt electron beams. Electron and photon transport is simulated by means of the general-purpose Monte Carlo code PENELOPE, using the standard, detailed simulation scheme. Bremsstrahlung emission is described by using a recently proposed algorithm, in which the energy of emitted photons is sampled from numerical cross-section tables, while the angular distribution of the photons is represented by an analytical expression with parameters determined by fitting benchmark shape functions obtained from partial-wave calculations. Ionization of K and L shells by electron impact is accounted for by means of ionization cross sections calculated from the distorted-wave Born approximation. The relaxation of the excited atoms following the ionization of an inner shell, which proceeds through emission of characteristic x rays and Auger electrons, is simulated until all vacancies have migrated to M and outer shells. For comparison, measurements of x-ray emission spectra generated by 20 keV electrons impinging normally on multiple bulk targets of pure elements, which span the periodic system, have been performed using an electron microprobe. Simulation results are shown to be in close agreement with these measurements.

Computer-aided discovery of biological activity spectra for anti-aging and anti-cancer olive oil oleuropeins

Aging is associated with common conditions, including cancer, diabetes, cardiovascular disease, and Alzheimer"s disease. The type of multi‐targeted pharmacological approach necessary to address a complex multifaceted disease such as aging might take advantage of pleiotropic natural polyphenols affecting a wide variety of biological processes. We have recently postulated that the secoiridoids oleuropein aglycone (OA) and decarboxymethyl oleuropein aglycone (DOA), two complex polyphenols present in health‐promoting extra virgin olive oil (EVOO), might constitute a new family of plant‐produced gerosuppressant agents. This paper describes an analysis of the biological activity spectra (BAS) of OA and DOA using PASS (Prediction of Activity Spectra for Substances) software. PASS can predict thousands of biological activities, as the BAS of a compound is an intrinsic property that is largely dependent on the compound"s structure and reflects pharmacological effects, physiological and biochemical mechanisms of action, and specific toxicities. Using Pharmaexpert, a tool that analyzes the PASS‐predicted BAS of substances based on thousands of"mechanism‐ effect" and"effect‐mechanism" relationships, we illuminate hypothesis‐generating pharmacological effects, mechanisms of action, and targets that might underlie the anti‐aging/anti‐cancer activities of the gerosuppressant EVOO oleuropeins.

Determination of three ultraviolet filters in sunscreen formulations and from skin penetration studies by high-performance liquid chromatography

An analytical procedure to quantify 3-benzophenone, octylmethoxycinnamate and octylsalicylate was validated and employed to assess these ultraviolet filters in sunscreen formulations and from skin penetration studies. The effect of the vehicle on the skin retention of these filters was investigated. HPLC and extraction procedure were found to be reliable when obtaining data for the sunscreen formulations and for evaluation skin penetration. The results demonstrated that a cream gel generated higher epidermal concentrations of these filters than a lotion or cream-based formulation. Additionally, when comparing the skin retentions of each filter using the same formulation, 3-benzophenone showed the highest skin retention.

Estudo da decomposição fotoquímica por exposição à luz UV de fotorresinas positivas

Positive photoresists are widely used in lithographic process in microelectronics and in optics for the fabrication of relief components. With the aim of identifying molecular modifications among positive photoresists unexposed and previously exposed to ultraviolet light the electron stimulated ion desorption technique coupled to time-of-flight mass spectrometry was employed in the study of the AZ-1518 photoresist. Mass spectra were obtained as a function of the electron beam energy, showing specific changes related to the photochemical decomposition of the photoresist. This reinforces the applicability of the technique to investigate and characterize structural changes in photosensitive materials.

Determination of fipronil in bovine plasma by solid-phase extraction and liquid chromatography with ultraviolet detection

A fast and efficient method has been developed and validated for the determination of fipronil in bovine plasma. Samples were subjected to solid-phase extraction (SPE) followed by reversed phase liquid chromatography (LC) separation, using acetonitrile/water (60:40 v/v) as the mobile phase with a flow rate of 1.0 mL/min and ultraviolet (UV) detection at 210 nm. Ethiprole was used as the internal standard (IS). The method was found to be linear over the range 5-500 ng/mL (r = 0.999). The limit of quantitation (LOQ) was validated at 5 ng/mL. The method was successfully applied to monitor plasma concentrations following subcutaneous administration of fipronil in cattle.

Resistance spectra of wheat cultivars and virulence diversity of Magnaporthe grisea isolates in Brazil

Seventy-two monoconidial isolates of Magnaporthe grisea were obtained from the States of Mato Grosso do Sul and Paraná. The isolates were inoculated on seedlings of 20 wheat (Triticum aestivum) cultivars under greenhouse conditions. The virulence diversity of M. grisea was assessed based on compatible and incompatible reactions of leaf blast on wheat cultivars. Fifty-four distinct virulence patterns were identified on test cultivars among the isolates collected from the two wheat growing States. Sixteen of these isolates corresponding to 22.2% showed similar virulence pattern. None of the wheat cultivars was resistant to all isolates of M. grisea, but the cultivars differed in degree of resistance as measured by the relative spectrum of resistance (RSR) and disease index (DI). Among the cultivars the RSR ranged from 0 to 53.3% and DI from 0.4662 to 0.9662 (0 to 1 scale). The wheat cultivar BR18 exhibited a broad resistance spectrum in relation to the rest of the tested cultivars to the isolates of M. grisea, and can be used in wheat resistance breeding.

Photoinhibition of Photosystem II. Kinetics, Photoprotection and Mechanism

Photosystem II (PSII) is susceptible to light-induced damage defined as photoinhibition. In natural conditions, plants are capable of repairing the photoinhibited PSII by on-going degradation and re-synthesis of the D1 reaction centre protein of PSII. Photoinhibition is induced by both visible and ultraviolet light and photoinhibition occurs under all light intensities with the same efficiency per photon. In my thesis work, I studied the reaction kinetics and mechanism of photoinhibition of PSII, as well as photoprotection in leaves of higher plants. Action spectroscopy was used to identify photoreceptors of photoinhibition. I found that the action spectrum of photoinhibition in vivo shows resemblance to the absorption spectra of manganese model compounds of the oxygen evolving complex (OEC) suggesting a role for manganese as a photoreceptor of photoinhibition under UV and visible light. In order to study the protective effect of non-photochemical quenching, the action spectrum was measured from leaves of wild type Arabidopsis thaliana and two mutants impaired in nonphotochemical quenching of chlorophyll a excitations. The findings of action spectroscopy and simulations of chlorophyll-based photoinhibition mechanisms suggested that quenching of antenna excitations protects less efficiently than would be expected if antenna chlorophylls were the only photoreceptors of photoinhibition. The reaction kinetics of prolonged photoinhibition was studied in leaves of Cucurbita maxima and Capsicum annuum. The results indicated that photoinhibitory decrease in both the oxygen evolution activity and ratio of variable to maximum fluorescence follows firstorder kinetics in vivo. The persistence of first-order kinetics suggests that already photoinhibited reaction centres do not protect against photoinhibition and that the mechanism of photoinhibition does not have a reversible intermediate. When Cucurbita maxima leaves were photoinhibited with saturating single-turnover flashes and continuous light, the light response curve of photoinhibition was found to be essentially a straight line with both types of illumination, suggesting that similar photoinhibition mechanisms might function during illumination with continuous light and during illumination with short flashes.

Experimental and theoretical investigation of the IR spectra and thermochemistry of four isomers of 2-N,N-dimethylaminecyclohexyl 1-N',N'-dimethylcarbamate

A combined experimental and Density functional theory (DFT) B3LYP/6-311+G* study on the IR spectra of four stable isomers of 2-N,N-dimethylaminecyclohexyl 1-N',N'-dimethylcarbamate was performed. Our theoretical calculations reveal that two new isomers of this compound exist and may be more stable than the known isomers. In addition the entropy, heat capacity, and the enthalpy content of the stable isomers are computed by fitting the calculated data to a standard Shomate equation and IR spectra for the two new isomers are presented.

Analysis of the structure and vibrational spectra of glucose and fructose

Molecular modelling using semiempirical methods AM1, PM3, PM5 and, MINDO as well as the Density Functional Theory method BLYP/DZVP respectively were used to calculate the structure and vibrational spectra of d-glucose and d-fructose in their open chain, alpha-anomer and beta-anomer monohydrate forms. The calculated data show that both molecules are not linear; ground state and the number for the point-group C is equal to 1. Generally, the results indicate that there are similarities in bond lengths and vibrational modes of both molecules. It is concluded that DFT could be used to study both the structural and vibrational spectra of glucose and fructose.

Spectrophotometric study of the chromium(III)/azide system in the ultraviolet region and its analytical application

A sensitive and alternative method for the spectrophotometric determination of chromium(III) based on the formation of chromium(III)/azide complexes was established by investigating a new band in the ultraviolet region. The best experimental conditions for the analytical determination of this metallic ion were: ligand and perchloric acid analytical concentration = 493 and 12.0 mmol L-1, respectively; aqueous medium; T = 25.0 ºC; contact time = 1 hour. The maximum molar absorptivity coefficient occurred at 287 nm (average 1.481 ± 0.008 ´ 10(4) L mol-1 cm-1), leading to the determination of metal ion concentrations one hundred times lower than the ones formerly determined in the visible region. The system obeys Beer's Law and is suitable for chromium determination in the 0.702-2.81 mg L-1 concentration range (15-65% T, 1.00 cm-width quartz cells). Analytical applications of the current method were tested with a nutritional supplement containing chromium. Results were compared with those obtained with atomic absorption spectrometry.

Evaluation of group electronegativities and hardness (softness) of group 14 elements and containing functional groups through density functional theory and correlation with NMR spectra data

Quantum Chemical calculations for group 14 elements of Periodic Table (C, Si, Ge, Sn, Pb) and their functional groups have been carried out using Density Functional Theory (DFT) based reactivity descriptors such as group electronegativities, hardness and softness. DFT calculations were performed for a large series of tetracoordinated Sn compounds of the CH3SnRR'X type, where X is a halogen and R and R' are alkyl, halogenated alkyl, alkoxy, or alkyl thio groups. The results were interpreted in terms of calculated electronegativity and hardness of the SnRR'X groups, applying a methodology previously developed by Geerlings and coworkers (J. Phys. Chem. 1993, 97, 1826). These calculations allowed to see the regularities concerning the influence of the nature of organic groups RR' and inorganic group X on electronegativities and hardness of the SnRR'X groups; in this case, it was found a very good correlation between the electronegativity of the fragment and experimental 119Sn chemical shifts, a property that sensitively reflects the change in the valence electronic structure of molecules. This work was complemented with the study of some compounds of the EX and ER types, where E= C, Si, Ge, Sn and R= CH3, H, which was performed to study the influence that the central atom has on the electronegativity and hardness of molecules, or whether these properties are mainly affected for the type of ligand bound to the central atom. All these calculations were performed using the B3PW91 functional together with the 6-311++G** basis set level for H, C, Si, Ge, F, Cl and Br atoms and the 3-21G for Sn and I atoms.

Mössbauer spectra of iron oxides in the bulk and nanocrystalline states

Magnetic nanoparticles are very important in modern industry. These particles are used in many different spheres of life. Nanoparticles have unusual physical and chemical properties connected both with quantum dimensional effects and with the increased role of the surface atoms. Most clearly the difference between the properties of bulk materials and nanoparticles can be seen in the magnetic properties of these materials. The most typical magnetic properties of nanomaterials are superparamagnetism with the size of the cluster from 1 to 10 nm; single-domain magnetic state of nanoclusters and nanostructures up to 20 nm; magnetization processes connected with magnetic cluster ordering and with its forms and sizes; quantum magnetic tunneling effects when magnetization changes by jumps and giant magnetoresistance effects. For research of the magnetic properties of iron-containing nanostructures, it is convenient to apply Mӧssbauer spectroscopy. In this work a number of nano-sized samples of iron oxides were examined by Mössbauer spectroscopy. The Mössbauer spectra of nanoparticles with various sizes were obtained. Mössbauer spectra of iron oxide nanoparticles were compared with the spectra of bulk samples. It was shown how the spectra of iron oxide nanoparticles change depending on the particle sizes.

Side peaks in Nb and NbTi point-contact spectra

Superconductor – normal metal point contacts were investigated, using different combinations of Cu, brass, Nb and NbTi. The resulting spectra contained side peaks. The currents at which these side peaks appeared, depended on the radii of the contacts. For contacts with Nb this dependence was quadratic, while for contacts with NbTi it was linear. Based on this, we argue that the side peaks in the case of the Nb contacts are due to the critical current density being exceeded. In contrast, side peaks of the NbTi contacts are caused by the self-magnetic field exceeding the lower critical field of NbTi. The NbTi contacts did not show the expected contribution from the vanishing Maxwell resistance of the superconductor, a question which remained open.