On the contribution of deoxy-hemoglobin to MRI gray–white matter phase contrast at high field
High field (> or =7 T) MRI studies based on signal phase have been used to improve visualization of the fine structure of the brain, most notably the major white matter fiber bundles, the gray-white matter subdivision, and the laminar cortical architecture. The observed contrast has been attributed in part to local variations in magnetic susceptibility arising from iron in storage proteins and tissue lipid. Another contribution could come from the paramagnetic blood constituent deoxy-hemoglobin, the tissue concentration of which may vary through local variations in vascular density. To investigate this possibility, we examined phase contrast between gray and white matter in rats after intravenous administration of a superparamagnetic contrast agent at various dosages. At the maximum dosage (3 mg Fe/kg), which resulted in an estimated paramagnetic susceptibility shift 4-8 times larger than deoxy-hemoglobin, we observed a negligible increase in phase contrast between gray and white matter. This result suggests that endogenous deoxy-hemoglobin has no significant contribution to phase contrast between gray and white matter.

title: Improving contrast to noise ratio of resonance frequency contrast images (phase images) using balanced steady-state free precession
abstract: Recent MRI studies have exploited subtle magnetic susceptibility differences between brain tissues to improve anatomical contrast and resolution. These susceptibility differences lead to resonance frequency shifts which can be visualized by reconstructing the signal phase in conventional gradient echo (GRE) acquisition techniques. In this work, a method is proposed to improve the contrast to noise ratio per unit time (CNR efficiency) of anatomical MRI based on resonance frequency contrast. The method, based on the balanced steady-state free precession (bSSFP) MRI acquisition technique, was evaluated in its ability to generate contrast between gray and white matter in human brain at 3T and 7T. The results show substantially improved CNR efficiency of bSSFP phase images (2.85±0.21 times at 3 T and 1.71±0.11 times at 7 T) compared to the GRE data in a limited spatial area. This limited spatial coverage is attributed to the sensitivity of bSSFP to macroscopic B(0) inhomogeneities. With this CNR improvement, high resolution bSSFP phase images (resolution=0.3×0.3×2 mm(3), acquisition time=10min) acquired at 3T had sufficient CNR to allow the visualization of cortical laminar structures in invivo human primary visual cortex. Practical application of the proposed method may require improvement of B(0) homogeneity and stability by additional preparatory scans and/or compensation schemes such as respiration and drift compensation. Without these additions, the CNR benefits of the method may be limited to studies at low field or limited regions of interest.

title: Improved shim method based on the minimization of the maximum off-resonance frequency for balanced steady-state free precession (bSSFP).
abstract: In this work, a shim method that minimizes the maximum off-resonance frequency (min-max shim) in balanced steady-state free precession (bSSFP) is tested for brain imaging at 3T with constant and linear shim terms. The method demonstrates improvement of spatial coverage and banding artifact reduction over standard least-squares shimming. In addition, a new method (modified min-max shim) is introduced. This method reduces boundary band regions where the artifact is inevitable due to the excessive off-resonance frequency distribution. In comparison to standard least-squares shimming, the min-max based shim method either eliminates or reduces the size of banding artifacts. The method can be used to increase the signal-to-noise ratio (SNR) in bSSFP imaging or to increase the functional contrast in bSSFP functional MRI (fMRI) by allowing a longer usable repetition time (TR).

title: Microcanonical origin of the maximum entropy principle for open systems.
abstract: There are two distinct approaches for deriving the canonical ensemble. The canonical ensemble either follows as a special limit of the microcanonical ensemble or alternatively follows from the maximum entropy principle. We show the equivalence of these two approaches by applying the maximum entropy formulation to a closed universe consisting of an open system plus bath. We show that the target function for deriving the canonical distribution emerges as a natural consequence of partial maximization of the entropy over the bath degrees of freedom alone. By extending this mathematical formalism to dynamical paths rather than equilibrium ensembles, the result provides an alternative justification for the principle of path entropy maximization as well.

title: Measures for the assessment of fuzzy predictions of protein secondary structure.
abstract: Many of the recent secondary structure prediction methods incorporate the idea of fuzzy set theory, where instead of assigning a definite secondary structure to a query residue, probability for the residue being in each of the conformational states is estimated. Moreover, continuous assignment of conformational states to the experimentally observed protein structures can be performed in order to reflect inherent flexibility. Although various measures have been developed for evaluating performances of secondary structure prediction methods, they depend only on the most probable secondary structures. They do not assess the accuracy of the probabilities produced by fuzzy prediction methods, and they cannot incorporate information contained in continuous assignments of conformational states to observed structures. Three important measures for evaluating performance of a secondary structure prediction algorithm, Q score, Segment OVerlap (SOV) measure, and the k-state correlation coefficient (Corr), are deformed into fuzzy measures F score, Fuzzy OVerlap (FOV) measure, and the fuzzy correlation coefficient (Forr), so that the new measures not only assess probabilistic outputs of fuzzy prediction methods, but also incorporate information from continuous assignments of secondary structure. As an example of application, prediction results of four fuzzy secondary structure prediction methods, PSIPRED, PROFking, SABLE, and PREDICT, are assessed using the new fuzzy measures.

title: Motion correction for phase-resolved dynamic optical coherence tomography imaging of rodent cerebral cortex
abstract: Cardiac and respiratory motions in animals are the primary source of image quality degradation in dynamic imaging studies, especially when using phase-resolved imaging modalities such as spectral-domain optical coherence tomography (SD-OCT), whose phase signal is very sensitive to movements of the sample. This study demonstrates a method with which to compensate for motion artifacts in dynamic SD-OCT imaging of the rodent cerebral cortex. We observed that respiratory and cardiac motions mainly caused, respectively, bulk image shifts (BISs) and global phase fluctuations (GPFs). A cross-correlation maximization-based shift correction algorithm was effective in suppressing BISs, while GPFs were significantly reduced by removing axial and lateral global phase variations. In addition, a non-origin-centered GPF correction algorithm was examined. Several combinations of these algorithms were tested to find an optimized approach that improved image stability from 0.5 to 0.8 in terms of the cross-correlation over 4 s of dynamic imaging, and reduced phase noise by two orders of magnitude in ~8% voxels.

title: Nanoparticle assemblies with molecular springs: a nanoscale thermometer.
abstract: aretypicallystatic:Theyshowa limitedresponsetoenvironmentalparametersanddonotexhibitsmoothrever-sible transitions of their three-dimensional organization orgeometry in response to external stimuli. Dynamic NPsuperstructures with gradual structural adaptation tocommon physical parameters may reveal interesting analo-gies to biological entities of similar scale.

title: Spectrum measurement of fast optical signal of neural activity in brain tissue and its theoretical origin
abstract: Functional brain imaging technologies have enabled recent advances in understanding human brain function. In particular, a noninvasive and fast optical technique will become one of the most promising tools for future studies. As a fundamental ex vivo study for the development of such a technique, this paper demonstrates the spectral measurement of fast optical changes associated with neural activity in bulk brain tissue. For this purpose, a high-speed confocal near-infrared spectrometer was built and used. The results verified that observed transient optical responses (tORs) are associated with neural activity by showing that the following: tORs were concurrent and correlated with local field potentials (LFPs); tORs disappeared following tetrodotoxin application; and tORs were reproducibly observed across preparations. In addition, the amplitude of tORs was statistically significantly larger in longer wavelengths (approximately 1200 nm). The time course of tORs, however, is quite different from that of LFPs. Since this difference implies that tORs may originate not directly from the electric potential variation but from other neurophysiological events accompanying excitation, this paper tested the hypothesis that tORs are attributed to transient cellular volume changes (tCVCs). With no previous dynamic equation to elucidate such different temporal dynamics of the optical responses, a novel mathematical neuron model to describe tCVCs was developed. This neuron model, along with finite-difference time-domain simulations, showed that tCVCs and tORs were similar in the temporal dynamics, order of magnitude, response direction, and detectability in the bulk tissue; thus supporting the hypothesis.