Quantification of in vivo short echo-time proton magnetic resonance spectra at 14.1 T using two different approaches of modelling the macromolecule spectrum

Reliable quantification of the macromolecule signals in short echo-time H-1 MRS spectra is particularly important at high magnetic fields for an accurate quantification of metabolite concentrations (the neurochemical profile) due to effectively increased spectral resolution of the macromolecule components. The purpose of the present study was to assess two approaches of quantification, which take the contribution of macromolecules into account in the quantification step. H-1 spectra were acquired on a 14.1 T/26 cm horizontal scanner on five rats using the ultra-short echo-time SPECIAL (spin echo full intensity acquired localization) spectroscopy sequence. Metabolite concentrations were estimated using LCModel, combined with a simulated basis set of metabolites using published spectral parameters and either the spectrum of macromolecules measured in vivo, using an inversion recovery technique, or baseline simulated by the built-in spline function. The fitted spline function resulted in a smooth approximation of the in vivo macromolecules, but in accordance with previous studies using Subtract-QUEST could not reproduce completely all features of the in vivo spectrum of macromolecules at 14.1 T. As a consequence, the measured macromolecular 'baseline' led to a more accurate and reliable quantification at higher field strengths.

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.

Shape resonance spectra of lignin subunits

We report integral cross sections for elastic electron scattering by the lignin subunits phenol, guaiacol, and p-coumaryl alcohol. Our calculations employed the Schwinger multichannel method with pseudopotentials and indicate three to four pi* shape resonances for each of these systems, suggesting that low-energy electrons could efficiently transfer energy into the lignin matrix. We also discuss dissociation mechanisms based on the calculated cross sections, available experimental data, virtual orbital analysis, and the knowledge on electron interactions with biomolecules. Our results point out a physical-chemical basis for electron-driven biomass delignification. The latter would be an essential step for efficient biofuel production from lignocellulosic materials.

Shape resonance spectra of uracil, 5-fluorouracil, and 5-chlorouracil.

We report on the shape resonance spectra of uracil, 5-fluorouracil, and 5-chlorouracil, as obtained from fixed-nuclei elastic scattering calculations performed with the Schwinger multichannel method with pseudopotentials. Our results are in good agreement with the available electron transmission spectroscopy data, and support the existence of three π* resonances in uracil and 5-fluorouracil. As expected, the anion states are more stable in the substituted molecules than in uracil. Since the stabilization is stronger in 5-chlorouracil, the lowest π* resonance in this system becomes a bound anion state. The present results also support the existence of a low-lying σ ∗ CCl shape resonance in 5- chlorouracil. Exploratory calculations performed at selected C–Cl bond lengths suggest that the σ ∗ CCl resonance could couple to the two lowest π* states, giving rise to a very rich dissociation dynamics. These facts would be compatible with the complex branching of the dissociative electron attachment cross sections, even though we cannot discuss any details of the vibration dynamics based only on the present fixed-nuclei results.

Two-dimensional linear-combination model fitting of magnetic resonance spectra to define the macromolecule baseline using FiTAID, a Fitting Tool for Arrays of Interrelated Datasets

To propose the determination of the macromolecular baseline (MMBL) in clinical 1H MR spectra based on T(1) and T(2) differentiation using 2D fitting in FiTAID, a general Fitting Tool for Arrays of Interrelated Datasets.

XSophe, a computer simulation software suite for the analysis of electron paramagnetic resonance spectra

The XSophe computer simulation software suite consisting of a daemon, the XSophe interface and the computational program Sophe is a state of the art package for the simulation of electron paramagnetic resonance spectra. The Sophe program performs the computer simulation and includes a number of new technologies including; the SOPHE partition and interpolation schemes, a field segmentation algorithm, homotopy, parallelisation and spectral optimisation. The SOPHE partition and interpolation scheme along with a field segmentation algorithm greatly increases the speed of simulations for most systems. Multidimensional homotopy provides an efficient method for accurately tracing energy levels and hence tracing transitions in the presence of energy level anticrossings and looping transitions and allowing computer simulations in frequency space. Recent enhancements to Sophe include the generalised treatment of distributions of orientational parameters, termed the mosaic misorientation linewidth model and a faster more efficient algorithm for the calculation of resonant field positions and transition probabilities. For complex systems the parallelisation enables the simulation of these systems on a parallel computer and the optimisation algorithms in the suite provide the experimentalist with the possibility of finding the spin Hamiltonian parameters in a systematic manner rather than a trial-and-error process. The XSophe software suite has been used to simulate multifrequency EPR spectra (200 MHz to 6 00 GHz) from isolated spin systems (S > ~½) and coupled centres (Si, Sj _> I/2). Griffin, M.; Muys, A.; Noble, C.; Wang, D.; Eldershaw, C.; Gates, K.E.; Burrage, K.; Hanson, G.R."XSophe, a Computer Simulation Software Suite for the Analysis of Electron Paramagnetic Resonance Spectra", 1999, Mol. Phys. Rep., 26, 60-84.

Evaluation of the sonically induced narrowing of nuclear magnetic resonance spectra of solids

The Nuclear Magnetic Resonance (NMR) spectra of liquids contain a wealth of quantitative information that may be derived, for instance, from chemical shifts and spin-spin couplings. The available information depends on the incoherent rapid molecular motion that causes complicating effects present in the solid state to average to zero. Whereas liquid state NMR spectra show narrow lines, the corresponding NMR spectra from the solid state are normally composed of exceedingly broad resonance lines due to highly restricted molecular motion. It is, therefore, difficult to obtain directly as detailed information from the spectra of solids as from those derived from the liquid state. Studies on a new technique (SINNMR, the sonically induced narrowing of the NMR spectra of solids) to remove line broadening effects in the NMR spectra of the solid state are reported within this thesis. SINNMR involves narrowing the NMR absorptions from solid particles by irradiating them with ultrasound when they are suspended in a support liquid. It is proposed that ultrasound induces incoherent motion of the suspended particles, producing motional characteristics of the particles similar to those of rather large molecules. The first report of apparently successful experiments involving SINNMR[1] emphasised both the irreproducibility of the technique and the uncertainty regarding its true origin. If SINNMR can be made reproducible and the effect definitively attributed to the sonically induced incoherent motional averaging of particles, the technique could offer a simple alternative to the now classical magic-angle spinning (MAS) NMR[2] and the recently reported dynamic angle spinning (DAS)[3] and double rotation (DOR)[4] techniques. Evidence is presented in this thesis to support the proposal that ultrasound may be used to narrow the NMR spectral resonances from solids by inducing incoherent motion of particles suspended in support liquids and, additionally, for some solids, by inducing rotational motion of molecular constituents in the lattices of solids. Successful SINNMR line narrowing using 20 kHz ultrasound is reported for a variety of samples: including trisodium orthophosphate, polytetrafluoroethylene and aluminium alloys. Investigations of SINNMR line narrowing in trisodium phosphate have revealed the relationship between ultrasonic power, particle size and support liquid density for the production of optimum SINNMR conditions. It is also proposed that the incoherent motion of particles induced by 20 kHz ultrasound can originate from interactions between acoustically induced cavitation microjets and particles.

Hadronic resonance production in d+Au collisions at root S(NN) = 200 GeV measured at the BNL Relativistic Heavy Ion Collider

We present the first measurements of the rho(770)(0),K(*)(892),Delta(1232)(++),Sigma(1385), and Lambda(1520) resonances in d+Au collisions at s(NN)=200 GeV, reconstructed via their hadronic decay channels using the STAR detector (the solenoidal tracker at the BNL Relativistic Heavy Ion Collider). The masses and widths of these resonances are studied as a function of transverse momentum p(T). We observe that the resonance spectra follow a generalized scaling law with the transverse mass m(T). The < p(T)> of resonances in minimum bias collisions are compared with the < p(T)> of pi,K, and p. The rho(0)/pi(-),K(*)/K(-),Delta(++)/p,Sigma(1385)/Lambda, and Lambda(1520)/Lambda ratios in d+Au collisions are compared with the measurements in minimum bias p+p interactions, where we observe that both measurements are comparable. The nuclear modification factors (R(dAu)) of the rho(0),K(*), and Sigma(*) scale with the number of binary collisions (N(bin)) for p(T)> 1.2 GeV/c.

Electron paramagnetic resonance of Ni(II) doped tris(ethylenediamine)zinc(II) dinitrate

Variable temperature electron paramagnetic resonance spectra of tris(ethylenediamine)zinc(II) dinitrate single crystals doped with NI(II) have been measured. The host crystal undergoes a trigonal to monoclinic phase transition at 146 K. Above the transition temperature the zero field splitting tensor is axially symmetric with D = -0.831 cm(-1) and below it becomes rhombic with D = -0.785 cm(-1), E = -0.088 cm(-1). The low temperature spectrum is characterised by the pattern repeating every 60 degrees when the crystal is rotated about the high temperature c axis. The analysis shows that the Zn(II) site retains a C-2 symmetry axis and that the distortion away from the D-3 site symmetry observed for high temperatures is small, the principal axes being tilted by 2.6 degrees. This implies that the phase transition involves the flipping of the C-C backbone in one of the ethylenediamine ligands of the complex, resulting in a A delta delta delta to Lambda delta delta lambda type conformational change.

Magnetic Resonance Experiments with Atomic Hydrogen

In this thesis three experiments with atomic hydrogen (H) at low temperatures T<1 K are presented. Experiments were carried out with two- (2D) and three-dimensional (3D) H gas, and with H atoms trapped in solid H2 matrix. The main focus of this work is on interatomic interactions, which have certain specific features in these three systems considered. A common feature is the very high density of atomic hydrogen, the systems are close to quantum degeneracy. Short range interactions in collisions between atoms are important in gaseous H. The system of H in H₂ differ dramatically because atoms remain fixed in the H₂ lattice and properties are governed by long-range interactions with the solid matrix and with H atoms. The main tools in our studies were the methods of magnetic resonance, with electron spin resonance (ESR) at 128 GHz being used as the principal detection method. For the first time in experiments with H in high magnetic fields and at low temperatures we combined ESR and NMR to perform electron-nuclear double resonance (ENDOR) as well as coherent two-photon spectroscopy. This allowed to distinguish between different types of interactions in the magnetic resonance spectra. Experiments with 2D H gas utilized the thermal compression method in homogeneous magnetic field, developed in our laboratory. In this work methods were developed for direct studies of 3D H at high density, and for creating high density samples of H in H₂. We measured magnetic resonance line shifts due to collisions in the 2D and 3D H gases. First we observed that the cold collision shift in 2D H gas composed of atoms in a single hyperfine state is much smaller than predicted by the mean-field theory. This motivated us to carry out similar experiments with 3D H. In 3D H the cold collision shift was found to be an order of magnitude smaller for atoms in a single hyperfine state than that for a mixture of atoms in two different hyperfine states. The collisional shifts were found to be in fair agreement with the theory, which takes into account symmetrization of the wave functions of the colliding atoms. The origin of the small shift in the 2D H composed of single hyperfine state atoms is not yet understood. The measurement of the shift in 3D H provides experimental determination for the difference of the scattering lengths of ground state atoms. The experiment with H atoms captured in H2 matrix at temperatures below 1 K originated from our work with H gas. We found out that samples of H in H2 were formed during recombination of gas phase H, enabling sample preparation at temperatures below 0.5 K. Alternatively, we created the samples by electron impact dissociation of H₂ molecules in situ in the solid. By the latter method we reached highest densities of H atoms reported so far, 3.5(5)x10¹⁹ cm^-3. The H atoms were found to be stable for weeks at temperatures below 0.5 K. The observation of dipolar interaction effects provides a verification for the density measurement. Our results point to two different sites for H atoms in H2 lattice. The steady-state nuclear polarizations of the atoms were found to be non-thermal. The possibility for further increase of the impurity H density is considered. At higher densities and lower temperatures it might be possible to observe phenomena related to quantum degeneracy in solid.