Evaluation and optimization of fMRI single-subject processing pipelines with NPAIRS and second-level CVA

In functional magnetic resonance imaging (fMRI) analysis, although the univariate general linear model (GLM) is currently the dominant approach to brain activation detection, there is growing interest in multivariate approaches such as principal component analysis, canonical variate analysis (CVA), independent component analysis and cluster analysis, which have the potential to reveal neural networks and functional connectivity in the brain. To understand the effect of processing options on performance of multivariate model-based fMRI processing pipelines with real fMRI data, we investigated the impact of commonly used fMRI preprocessing steps and optimized the associated multivariate CVA-based, single-subject processing pipelines with the NPAIRS (nonparametric prediction, activation, influence and reproducibility resampling) performance metrics [prediction accuracy and statistical parametric image (SPI) reproducibility] on the Fiswidgets platform. We also compared the single-subject SPIs of univariate GLM with multivariate CVA-based processing pipelines from SPM, FSL.FEAT, NPAIRS.GLM and NPAIRS.CVA software packages (or modules) using a novel second-level CVA. We found that for the block-design data, (a) slice timing correction and global intensity normalization have little consistent impact on the fMRI processing pipeline, but spatial smoothing, temporal detrending or high-pass filtering, and motion correction significantly improved pipeline performance across all subjects; (b) the combined optimization of spatial smoothing, temporal detrending and CVA model parameters on average improved between-subject reproducibility; and (c) the most important pipeline choices include univariate or multivariate statistical models and spatial smoothing. This study suggests that considering options other than simply using GLM with a fixed spatial filter may be of critical importance in determining activation patterns in BOLD fMRI studies.     

Coupling of simultaneously acquired electrophysiological and haemodynamic responses during visual stimulation

We investigate the relationship between the temporal variation in the magnitude of occipital visual evoked potentials (VEPs) and of haemodynamic measures of brain activity obtained using both blood oxygenation level dependent (BOLD) and perfusion sensitive (ASL) functional magnetic resonance imaging (fMRI). Volunteers underwent a continuous BOLD fMRI scan and/or a continuous perfusion-sensitive (gradient and spin echo readout) ASL scan, during which 30 second blocks of contrast reversing visual stimuli (at 4 Hz) were interleaved with 30 second blocks of rest (visual fixation). Electroencephalography (EEG) and fMRI were simultaneously recorded and following EEG artefact cleaning, VEPs were averaged across the whole stimulation block (120 reversals, VEP₁₂₀) and at a finer timescale (15 reversals, VEP₁₅). Both BOLD and ASL time-series were linearly modelled to establish: (1) the mean response to visual stimulation, (2) transient responses at the start and end of each stimulation block, (3) the linear decrease between blocks, (4) the nonlinear between-block variation (covariation with VEP₁₂₀), (5) the linear decrease within block and (6) the nonlinear variation within block (covariation with VEP₁₅).     

Single-Sequence Multi-Slice NMR in Strong Gradient Magnetic Fields

We describe and apply a scheme to obtain nuclear magnetic resonance (NMR) signals from multiple regions in space with a single pulse sequence in systems with strong, usually unavoidable, gradient magnetic fields. This is accomplished with multiple frequency irradiation and reception. Applications described include dual-slice NMR of a fluid to enhance S/N, T ₂ measurements of two different samples, and efficient T ₁ measurement sequence by interleaving shorter delays within a longer delay for different slices.     

CdxHg(1−x)Te Alloy Colloidal Quantum Dots: Tuning Optical Properties from the Visible to Near‐Infrared by Ion Exchange

The energy gap between valence and conduction levels in colloidal semiconductor quantum dots can be tuned via the nanoparticle diameter when this is comparable to or less than the Bohr radius. In materials such as cadmium mercury telluride, which readily forms a single phase ternary alloy, this quantum confinement tuning can also be augmented by compositional tuning, which brings a further degree of freedom in the bandgap engineering. Here it is shown that compositional control of 2.3 nm diameter Cd_xHg_(1?x)Te nanocrystals by exchange of Hg²⁺ in place of Cd²⁺ ions can be used to tune their optical properties across a technologically useful range, from 500 nm to almost 1200 nm. Data on composition‐dependent changes in the optical properties are provided, including bandgap, extinction coefficient, emission energy and spectral shape, Stokes shift, quantum efficiency, and radiative lifetimes as the exchange process occurs, which are highly relevant for those seeking to use these technologically important QD materials.     

Soft X‐ray absorption spectroscopy and resonant inelastic X‐ray scattering spectroscopy below 100 eV: probing first‐row transition‐metal M‐edges in chemical complexes

X‐ray absorption and scattering spectroscopies involving the 3d transition‐metal K‐ and L‐edges have a long history in studying inorganic and bioinorganic molecules. However, there have been very few studies using the M‐edges, which are below 100 eV. Synchrotron‐based X‐ray sources can have higher energy resolution at M‐edges. M‐edge X‐ray absorption spectroscopy (XAS) and resonant inelastic X‐ray scattering (RIXS) could therefore provide complementary information to K‐ and L‐edge spectroscopies. In this study, M_2,3‐edge XAS on several Co, Ni and Cu complexes are measured and their spectral information, such as chemical shifts and covalency effects, are analyzed and discussed. In addition, M_2,3‐edge RIXS on NiO, NiF₂ and two other covalent complexes have been performed and different d–d transition patterns have been observed. Although still preliminary, this work on 3d metal complexes demonstrates the potential to use M‐edge XAS and RIXS on more complicated 3d metal complexes in the future. The potential for using high‐sensitivity and high‐resolution superconducting tunnel junction X‐ray detectors below 100 eV is also illustrated and discussed.     

Measurement of στ product of solid state laser materials by an alternative method: Application to Nd3+ doped YVO4 crystal for 4 F 3/2→4 I 11/2 transition

In this paper an alternative approach for measurement of στ product for ⁴ F _3/2→⁴ I _11/2 transition of Nd³⁺ doped YVO₄ crystal is reported. In this method a microchip laser is formed by keeping a small piece of the sample in plane-plane resonator and a diode laser (808 nm) is used for pumping. The pump power induced thermal lensing effect is used to make the cavity stable. The cavity mode area is estimated by measuring the thermal lens focal length at the threshold and the average pump area is measured by Gaussian fit to the intensity profiles of the pump beam. The value of στ product of Nd:YVO₄ crystal obtained by this method is within 10% of the reported values. The advantage of this method is that it is a simple method for direct measurement of στ product of laser crystals.     

Interacting Field Theories in Robertson-Walker Spacetimes: Analytic Approximations

The renormalization of a scalar field theory with a quartic self-coupling via adiabatic regularization in a Robertson-Walker spacetime is discussed. The adiabatic counterterms are presented in a way that is most conducive to numerical computations. A variation of the adiabatic regularization method is presented which leads to analytic approximations for the energy–momentum tensor of the quantum field and the quantum contribution to the effective mass of the mean field. Conservation of the energy–momentum tensor for the field is discussed and it is shown that the part of the energy–momentum tensor which depends only on the mean field is not conserved but the full renormalized energy–momentum tensor is conserved, as expected and required by the semiclassical Einstein's equation. It is also shown that if the analytic approximations are used the resulting approximate energy–momentum tensor is conserved. This allows a self-consistent backreaction calculation to be performed using the analytic approximations. The usefulness of the approximations is discussed.     

A method for the study of surface corrosion beneath protective layers

This work is concerned with the development of a technique to observe the onset of corrosion as it occurs beneath a temporary protective layer. Such temporary protectives include paints, varnishes, greases and oils that are applied to metal surfaces to give short-term protection from corrosion. The objective of this project was to develop a technique that could be used to evaluate the effectiveness of various temporary protectives in different environments, without the need to remove the protective layer, thus eliminating the possibility of any chemical changes or loss of corrosion products occurring as a result of removal. The temporary protective layers are typically 25Μm for paints and 15Μm per layer for varnishes. The 6.3 keV fluorescence X-ray is able to penetrate such layers, but the large escape depth (∼10Μm) of the X-rays means that for a thin protective layer a large proportion of the X-rays detected will originate from deep within the substrate and the resultant spectrum will be representative of the bulk rather than the surface. To enhance the surface sensitivity of the CXMS technique, the near surface region must be enriched in the isotope Fe-57. To achieve this, Fe-57 was vacuum evaporated onto the surface of mild steel substrates and subsequently diffused into the near surface region. An approximate 20 nm Fe-57 layer was deposited onto mild steel samples. The surface enriched samples were then annealed to allow the Fe-57 to diffuse into the near surface region of the mild steel substrate, and also to allow back diffusion of the substrate. A diffusion model was developed to predict the surface distribution of Fe-57 as a function of annealing parameters. The computer diffusion model allowed the ideal annealing conditions to be estimated to obtain a required near surface environment. It was essential that the annealing conditions did not result in any surface oxidation, and did result in a surface that was characteristic of mild steel. CEMS and CXMS spectra were recorded of samples before and after annealing, and also dynamic Secondary Ion Mass Spectrometry (SIMS) was used to monitor the enrichment and diffusion process. Energy Dispersive X-ray Analysis (EDXA) was also used to characterize the surface. A number of enriched samples were prepared and treated with a variety of surface temporary protectives. The CXMS spectra were recorded before and after exposure of the coated samples to various aggressive environments.     

Magnetic resonance studies of laryngeal tumors implanted in nude mice: effect of treatment with bleomycin and electroporation

Recently, a new type of cancer treatment has been introduced that combines pulsed electric fields (PEF) with anticancer drugs. The proposed mode of action is that PEF create transient pores in the membranes which allow entry of drugs into the cells. This method increases cytotoxicity of some anticancer drugs like bleomycin (BLM) by 2-3 orders of magnitude, which, in turn, reduces systemic drug dosage without decreasing efficacy. In the present study, magnetic resonance imaging (MRI) was used to determine changes in apparent water self-diffusion coefficients (ADC) and spin-lattice (T(1)) and spin-spin (T(2)) relaxation times that occur in an animal laryngeal tumor (HEp-2 cells) model with BLM delivered by PEF. A Bruker 14 Tesla (600 MHz) wide-bore spectrometer with micro-imaging capability was used to generate all the data. Mice carrying approximately 8 mm tumors were treated with several combinations of drug and PEF. All measurements were made on tumor samples excised from mice 24 and 48 hours after treatment with (i) saline, intratumor injection (i.t.), (ii) BLM, i.t., (iii) saline with PEF, and (iv) BLM, i.t., followed by PEF. Although T(1) does not differ between the controls (i, ii, and iii) and full treatment (iv) 6.72 +/- 0.20 s vs. 6.31 +/- 1.7 s, T(2) for (iv) at 24 hours is significantly different from the controls 52.4 +/- 0.91 ms vs. 46.5 +/- 1.54 ms. T(2) differences between treatment and controls disappear at 48 hours. ADC increases significantly from 24 to 48 hours (7.31 +/- 0.16 x 10(-6) to 8.28 +/- 0.28 x 10(-6) cm(2)/sec, p = 0.05). Longer T(2) values may reflect early apoptosis and tumor death when the tumor is structurally less dense. Higher ADC's, associated with the periphery of the tumors and the central region, may indicate loose structural organization and necrosis resulting from the combination treatment.     

Optimum and standard beam widths for numerical modeling of interface scattering problems

Gaussian beams provide a useful insonifying field for surface or interface scattering problems such as encountered in electromagnetics, acoustics and seismology. Gaussian beams have these advantages: (i) They give a finite size for the scattering region on the interface. (ii) The incident energy is restricted to a small range of grazing angles. (iii) They do not have side lobes. (iv) They have a convenient mathematical expression. The major disadvantages are: (i) Insonification of an interface is nonuniform. The scattered field will depend on the location of the scatterers within the beam. (ii) The beams spread, so that propagation becomes an integral component of the scattering problem. A standard beam parameterization is proposed which keeps propagation effects uniform among various models so that the effects of scattering only can be compared. In continuous wave problems, for a given angle of incidence and incident amplitude threshold, there will be an optimum Gaussian beam which keeps the insonified area as small as possible. For numerical solutions of pulse beams, these standard parameters provide an estimate of the smallest truncated domain necessary for a physically meaningful result.