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.

Excitação eletrônica das moléculas de metacrilato de metila e estireno na região do ultravioleta de vácuo

Angle-resolved electron energy-loss spectra have been measured for the methyl methacrylate (MMA) and styrene molecules in the 0 - 50 eV energy range. The spectra have been obtained at 1 keV incident energy, with an energy resolution of 0.8 eV and covering an angular range of 2.0 to 7.0 degrees. Within our knowledge, this is the first gas-phase excitation spectrum for MMA and styrene in this energy range. The spectra of MMA at small scattering angles are dominated by an intense peak at 6.7 eV followed by a broad band centered at about 16 eV. In the case of styrene, six bands can be observed in the spectra. Based on the angular behaviour of the excitation spectra of these molecules, the low-lying peaks observed are considered to be associated predominantly with dipole-allowed processes. In both cases, new bands can be observed for excitation energies greater than 20 eV. This could be associated with dipole-forbidden transitions to shake-up and doubly-excited states.

Estudo de métodos de aumento de resolução de espectros de FTIR para análise de estruturas secundárias de proteínas

The FTIR spectroscopy has been used to quantify the secondary structures of proteins, using amide I band (1600 - 1700 cm-1). The resolution enhancement methods have been used to resolve the individual components of this band that correlate to the secondary structure. In this paper we discuss the methods of derivative, Fourier deconvolution and fitting with simulated spectra. The results shows that they have serious problems and can be used only as a qualitative or semiquatitative method.

Separação de espectros simulados e de luminescência total através do método generalizado de anulação do posto (GRAM)

A multivariate curve resolution method, "GENERALIZED RANK ANNIHILATION METHOD (GRAM)", is discussed and tested with simulated and experimental data. The analysis of simulated data provides general guidelines concerning the condition for uniqueness of a solution for a given problem. The second-order emission-excitation spectra of human and animal dental calculus deposits were used as an experimental data to estimate the performance of the above method. Three porphyrinic spectral profiles, for both human and cat, were obtained by the use of GRAM.

Surface Studies of Thiolate Adsorbates on Some Metals

The results and discussions in this thesis are based on my studies about selfassembled thiol layers on gold, platinum, silver and copper surfaces. These kinds of layers are two-dimensional, one molecule thick and covalently organized at the surface. They are an easy way to modify surface properties. Self-assembly is today an intensive research field because of the promise it holds for producing new technology at nanoscale, the scale of atoms and molecules. These kinds of films have applications for example, in the fields of physics, biology, engineering, chemistry and computer science. Compared to the extensive literature concerning self-assembled monolayers (SAMs) on gold, little is known about the structure and properties of thiolbased SAMs on other metals. In this thesis I have focused on thiol layers on gold, platinum, silver and copper substrates. These studies can be regarded as a basic study of SAMs. Nevertheless, an understanding of the physical and chemical nature of SAMs allows the correlation between atomic structure and macroscopic properties. The results can be used as a starting point for many practical applications. X-ray photoelectron spectroscopy (XPS) and synchrotron radiation excited high resolution photoelectron spectroscopy (HR-XPS) together with time-offlight secondary ion mass spectrometry (ToF-SIMS) were applied to investigate thin organic films formed by the spontaneous adsorption of molecules on metal surfaces. Photoelectron spectroscopy was the main method used in these studies. In photoelectron spectroscopy, the sample is irradiated with photons and emitted photoelectrons are energy-analyzed. The obtained spectra give information about the atomic composition of the surface and about the chemical state of the detected elements. It is widely used in the study of thin layers and is a very powerful tool for this purpose. Some XPS results were complemented with ToF-SIMS measurements. It provides information on the chemical composition and molecular structure of the samples. Thiol (1-Dodecanethiol, CH3(CH2)11SH) solution was used to create SAMs on metal substrates. Uniform layers were formed on most of the studied metal surfaces. On platinum, surface aligned molecules were also detected in investigations by XPS and ToF-SIMS. The influence of radiation on the layer structure was studied, leading to the conclusion that parts of the hydrocarbon chains break off due to radiation and the rest of the layer is deformed. The results obtained showed differences depending on the substrate material. The influence of oxygen on layer formation was also studied. Thiol molecules were found to replace some of the oxygen from the metal surfaces.

Identification of metabolites and thermal transformation products of quinolones in raw cow milk by liquid chromatography coupled to high resolution mass spectrometry.

The presence of residues of antibiotics, metabolites, and thermal transformation products (TPs), produced during thermal treatment to eliminate pathogenic microorganisms in milk, could represent a risk for people. Cow"s milk samples spiked with enrofloxacin (ENR), ciprofloxacin (CIP), difloxacin (DIF), and sarafloxacin (SAR) and milk samples from cows medicated with ENR were submitted to several thermal treatments. The milk samples were analyzed by liquid chromatography-mass spectrometry (LC-MS) to find and identify TPs and metabolites. In this work, 27 TPs of 4 quinolones and 24 metabolites of ENR were found. Some of these compounds had been reported previously, but others were characterized for the first time, including lactose-conjugated CIP, the formamidation reaction for CIP and SAR, and hydroxylation or ketone formation to produce three different isomers for all quinolones studied.

Aumento da resolução de espectros de RMN 13C de ácidos húmicos em solução através do tratamento prévio com KCl 0,03 mol L-1

High levels of Fe and Mn present in some soils and compost organic matter decrease the resolution of 13C NMR spectra of humic substances. Addition of KCl up to a concentration of 0,03 mol L-1 to humic substances extracts followed by centrifugation is an efficient method of eliminating clays and minerals containing high levels of paramagnetic metals such as Fe and Mn thus increasing the resolution of 13C NMR spectra.

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.

Aplicação de métodos quimiométricos na especiação de Cr(VI) em solução aquosa

The equilibria, the spectra and the identities of the species of Cr(VI) that are present in aqueous solution have long been an active subject of discussion in the literature. In this paper, three different chemometric methodologies are applied to sets of UV/Visible spectra of aqueous Cr(VI) solutions, in order to solve a chemical system where there is no available information concerning the composition of the samples nor spectral information about the pure species. Imbrie Q-mode factor analysis, followed by varimax rotation and Imbrie oblique projection, were used to estimate the composition of Cr(VI) equilibrium solutions and, by combining these results with the k-matrix method, to obtain the pure spectra of the species. Evolving factor analysis and self modeling curve resolution were used to confirm the number of the species and the resolution of the system, respectively. Sets of 3.3×10-4 and 3.3×10-5 mol L-1 Cr(VI) solutions, respectively, were analyzed in the pH range from 1 to 12. Two factors were identified, which were related to the chromate ion (CrO4(2-)) and bichromate ion (HCrO4-). The pK of the equilibrium was estimated as 5.8.

3D kinematics of the near-IR HH 223 outflow in L723

In this work, we derive the full 3D kinematics of the near-infrared outflow HH 223, located in the dark cloud Lynds 723 (L723), where a well-defined quadrupolar CO outflow is found. HH 223 appears projected on to the two lobes of the eastwest CO outflow. The radio continuum source VLA 2, towards the centre of the CO outflow, harbours a multiple system of low-mass young stellar objects. One of the components has been proposed to be the exciting source of the eastwest CO outflow. From the analysis of the kinematics, we get further evidence on the relationship between the near-infrared and CO outflows and on the location of their exciting source. The proper motions were derived using multi-epoch, narrow-band H2 (2.122 μm line) images. Radial velocities were derived from the 2.122 μm line of the spectra. Because of the extended (∼5 arcmin), S-shaped morphology of the target, the spectra were obtained with the multi-object-spectroscopy (MOS) observing mode using the instrument Long-Slit Intermediate Resolution Infrared Spectrograph (LIRIS) at the 4.2 m William Herschel Telescope. To our knowledge, this work is the first time that MOS observing mode has been successfully used in the near-infrared range for an extended target.

Fourier self-deconvolution in coherent anti-Stokes Raman scattering spectrum analysis

Coherent anti-Stokes Raman scattering (CARS) microscopy is rapidly developing into a unique microscopic tool in biophysics, biology and the material sciences. The nonlinear nature of CARS spectroscopy complicates the analysis of the received spectra. There were developed mathematical methods for signal processing and for calculations spectra. Fourier self-deconvolution is a special high pass FFT filter which synthetically narrows the effective trace bandwidth features. As Fourier self-deconvolution can effectively reduce the noise, which may be at a higher spatial frequency than the peaks, without losing peak resolution. The idea of the work is to experiment the possibility of using wavelet decomposition in spectroscopic for background and noise removal, and Fourier transformation for linenarrowing.

Espectroscopia de fotoelétrons de limiares de átomos e moléculas

A threshold photoelectron spectrometer applied to the study of atomic and molecular threshold photoionization processes is described. The spectrometer has been used in conjunction with a toroidal grating monochromator at the National Synchrotron Radiation Laboratory (LNLS), Brazil. It can be tuned to accept threshold electrons (< 20 meV) and work with a power resolution of 716 (~18 meV at 12 eV) with a high signal/noise ratio. The performance of this apparatus and some characteristics of the TGM (Toroidal Grating Monochromator) beam line of LNLS are described and discussed by means of argon, O2 and N2 threshold photoelectron spectra.

Probing quantum gravity using photons from a flare of the active galactic nucleus Markarian 501 observed by the MAGIC telescope

We analyze the timing of photons observed by the MAGIC telescope during a flare of the active galactic nucleus Mkn 501 for a possible correlation with energy, as suggested by some models of quantum gravity (QG), which predict a vacuum refractive index similar or equal to 1 + (E/M-QGn)(n), n = 1, 2. Parametrizing the delay between gamma-rays of different energies as Delta t = +/-tau E-1 or Delta t = +/-tau E-q(2), we find tau(1) = (0.030 +/- 0.012) s/GeV at the 2.5-sigma level, and tau(q) = (3.71 +/- 2.57) x 10(-6) s/GeV2, respectively. We use these results to establish lower limits M-QG1 > 0.21 X 10(18) GeV and M-QG2 > 0.26 x 10(11) GeV at the 95% C.L. Monte Carlo studies confirm the MAGIC sensitivity to propagation effects at these levels. Thermal plasma effects in the source are negligible, but we cannot exclude the importance of some other source effect.

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.