The effect of artifacts on dependence measurement in fMRI

The study of effective connectivity by means of neuroimaging depends on the measurement of similarity between activity patterns at different locations in the brain, without necessarily presupposing a particular model for this dependence. When these interactions are measured using functional magnetic resonance imaging (fMRI) techniques, however, imaging and physiological artifacts create patterns of dependence that may be unrelated to cortical activity. We demonstrate some of these effects through the measurement of short-range dependencies present in fMRI scans of the primary visual cortex (V1) in the anaesthetized macaque monkey. High-field (4.7 T) fMRI scans were conducted to measure responses based on the blood oxygen level-dependent contrast mechanism, during periods of no sensory stimulation and of visual stimulation with rotating polar-transformed checkerboard gratings. Dependence between the haemodynamic activity at different spatial locations (i.e., different voxels) was measured using correlation, mutual information and functional covariance. Particular attention was paid to understanding the sources of spurious dependence that may be observed during such investigations. Two main effects were detected: (a) short-range correlations introduced by the process of image reconstruction and (b) perturbations in the haemodynamic response caused by breathing. The image reconstruction artifacts were shown to create an artificially high short-range dependence in the readout direction of the scan, and the breathing artifacts caused enhanced short-range dependence in both the readout and phase-encode directions. Additional dependence in the phase-encode direction due to image-ghosting is also possible but will not be discussed in this report, as it can be alleviated by fine adjustment of preemphasis (elimination of eddy currents). A technique is described for removing breathing artifacts, and the effect of breathing on the apparent dependence between voxels is illustrated. The correlation of haemodynamic activity with the stimulus was found to be affected by breathing, although this effect can be neutralised by averaging the haemodynamic responses over many repetitions of the stimulus. Nonetheless, patterns of dependent activity between voxels may be lost in this averaging process, which makes the removal of breathing artifacts necessary if statistical dependence and the study of effective connectivity is the primary aim of an investigation.     

Extensive limit of a non-extensive entanglement entropy

We report wide-range optical investigations on transparent conducting networks made from separated (semiconducting, metallic) and reference (mixed) single-walled carbon nanotubes, complemented by transport measurements. Comparing the intrinsic frequency-dependent conductivity of the nanotubes with that of the networks, we conclude that higher intrinsic conductivity results in better transport properties, indicating that the properties of the nanotubes are at least as much important as the contacts. We find that HNO₃ doping offers a larger improvement in transparent conductive quality than separation. Spontaneous dedoping occurs in all samples but is most effective in films made of doped metallic tubes, where the sheet conductance returns close to its original value within 24 h.     

Single enzyme studies reveal the existence of discrete functional states for monomeric enzymes and how they are "selected" upon allosteric regulation

Allosteric regulation of enzymatic activity forms the basis for controlling a plethora of vital cellular processes. While the mechanism underlying regulation of multimeric enzymes is generally well understood and proposed to primarily operate via conformational selection, the mechanism underlying allosteric regulation of monomeric enzymes is poorly understood. Here we monitored for the first time allosteric regulation of enzymatic activity at the single molecule level. We measured single stochastic catalytic turnovers of a monomeric metabolic enzyme (Thermomyces lanuginosus Lipase) while titrating its proximity to a lipid membrane that acts as an allosteric effector. The single molecule measurements revealed the existence of discrete binary functional states that could not be identified in macroscopic measurements due to ensemble averaging. The discrete functional states correlate with the enzyme's major conformational states and are redistributed in the presence of the regulatory effector. Thus, our data support allosteric regulation of monomeric enzymes to operate via selection of preexisting functional states and not via induction of new ones.     

Mean-field gauge interactions in five dimensions II. The orbifold

We study Gauge–Higgs Unification in five dimensions on the lattice by means of the mean-field expansion. We formulate it for the case of an SU(2)$\mathit{SU}(2)$ pure gauge theory and orbifold boundary conditions along the extra dimension, which explicitly break the gauge symmetry to U(1)$U(1)$ on the boundaries. Our main result is that the gauge boson mass computed from the static potential along four-dimensional hyperplanes is non-zero implying spontaneous symmetry breaking. This observation supports earlier data from Monte Carlo simulations in Irges and Knechtli (2007) [12].     

Electronic transport between Au surface and scanning tunnelling microscope tip via a multipodal cyclodextrin host–metallo‐guest supramolecular system

An elementary supramolecular conducting system was constructed using a novel (±)‐thioctic acid‐functionalized β‐cyclodextrin host deposited on a gold (Au) surface and an iridium‐bearing guest molecule with biphenyl tails to insert specifically into the cyclodextrin cavity. The resulting supramolecular system was used to investigate remote electron communication between the flat Au surface and the platinum (Pt)/iridium (Ir) tip of a scanning tunnelling microscope. The morphology of the surfaces after successive deposition of host molecules followed by guest molecules was investigated. Formation of features of 2 nm size was shown on the Au surface functionalised with the supramolecular system. I–V spectroscopic analysis of the tunnelling current through this supramolecular layer revealed the relation between the effective barrier height and tunnelling distance. Thus, in the supramolecular host–metallo‐guest system, a small increase of conductance is observed, compared to the layer without the guest. This can be attributed to the presence of the Ir‐guest, which eventually creates intermediate energy states between the Au substrate and the Pt/Ir tip. Copyright © 2011 John Wiley & Sons, Ltd.     

Dual-functional probes towards in vivo studies of brain connectivity and plasticity

A Gd(3+) based paramagnetic dextran conjugate has been developed, which enables the tracking of neuroanatomical connectivity in the brain by both MR and optical imaging. Cell studies and subsequent in vivo experiments in rodents demonstrate efficient internalisation and transport properties of the new tracer molecule.     

Spectral methods for the equations of classical density-functional theory: relaxation dynamics of microscopic films

We propose a numerical scheme based on the Chebyshev pseudo-spectral collocation method for solving the integral and integro-differential equations of the density-functional theory and its dynamic extension. We demonstrate the exponential convergence of our scheme, which typically requires much fewer discretization points to achieve the same accuracy compared to conventional methods. This discretization scheme can also incorporate the asymptotic behavior of the density, which can be of interest in the investigation of open systems. Our scheme is complemented with a numerical continuation algorithm and an appropriate time stepping algorithm, thus constituting a complete tool for an efficient and accurate calculation of phase diagrams and dynamic phenomena. To illustrate the numerical methodology, we consider an argon-like fluid adsorbed on a Lennard-Jones planar wall. First, we obtain a set of phase diagrams corresponding to the equilibrium adsorption and compare our results obtained from different approximations to the hard sphere part of the free energy functional. Using principles from the theory of sub-critical dynamic phase field models, we formulate the time-dependent equations which describe the evolution of the adsorbed film. Through dynamic considerations we interpret the phase diagrams in terms of their stability. Simulations of various wetting and drying scenarios allow us to rationalize the dynamic behavior of the system and its relation to the equilibrium properties of wetting and drying.     

Electronic excitation spectra from time-dependent density functional response theory using plane-wave methods

The time-dependent density functional response theory method for the computation of electronic excitation spectra has been implemented in a plane-wave basis set/pseudo-potential formalism. We compare our test results for N₂ and H₂CO to literature atomic basis set calculations and find good agreement. We also discuss some of the technical complications specific to the use of plane-wave basis sets. As an application, the thermally broadened photoabsorption spectrum of formamide at room temperature is computed by averaging over a number of vibrational configurations sampled from an ab initio molecular dynamics run and compared to experiment.     

In-chain functionalized poly(ε-caprolactone): A valuable precursor towards the synthesis of 3-miktoarm star containing hyperbranched polyethylene

Well-defined 3-miktoarm star copolymer 3μ-HBPE(PCL)₂ (HBPE: hyperbranched polyethylene, PCL: poly[ε-caprolactone]) was synthesized by combining chain walking polymerization (CWP), ring-opening polymerization (ROP), and “click” chemistry. The synthetic methodology includes the following steps: (a) synthesis of in-chain ethynyl-functionalized PCL, (PCL)₂-C ≡ CH by ROP of ε-caprolactone (CL) with ethylene-functionalized solketal (3-[prop-2-yn-1-yloxy] propane-1,2-diol) as difunctional initiator and phosphazene superbase t-BuP₂ as catalyst; (b) synthesis of azido-functionalized hyperbranched PE (HBPE-N₃) by CWP of ethylene with α-diimine-Pd(II) catalyst, followed by quenching with excess 4-vinylbenzyl chloride and transformation of chloro to azide group with sodium azide; and (c) “clicking” HBPE-N₃ and (PCL)₂-C ≡ CH using copper(I)-catalyzed azide–alkyne cycloaddition. ¹H NMR spectroscopy, gel permeation chromatography, Fourier-transform infrared spectroscopy, and differential scanning calorimetry were used to determine the molecular characteristics and thermal properties of the polymers. Self-assembly behavior of 3μ-HBPE (PCL)₂ in petroleum ether, a selective solvent for HBPE, was investigated by dynamic light scattering, atomic force microscopy, and transmission electron microscopy. The in-chain alkyne-functionalized poly(ε-caprolactone) is a valuable precursor for PCL-based complex macromolecular architectures.     

Block copolymers of styrene and n‐alkyl methacrylates with long alkyl groups. Micellization behavior in selective solvents

The micellization properties of well‐defined block copolymers of styrene and decyl methacrylate (SDMA) were studied in two different solvents, methyl acetate (MAc) selective for the polystyrene (PS) block and dodecane, selective for the poly(decyl methacrylate) (PDMA) block. The results were compared with those obtained, in the same solvents, from block copolymers of styrene and stearyl methacrylate (SSMA). In MAc, SDMA copolymers with a decyl methacrylate (DMA) content of 15% or less formed unimolecular micelles, whereas those with a content of 18.5% or higher formed multimolecular micelles. The degrees of association were lower than the corresponding SSMA samples. In dodecane, SDMA form large, monodisperse, spherical, and thermally stable micelles with degrees of association higher than the corresponding SSMA samples. The different behaviors can be attributed to the steric hindrance effect and the ability of the long alkyl groups of the polymethacrylate, MA blocks to crystallize. When the MA blocks are in the soluble corona of the micelles, the steric hindrance effect prevails, thus leading to higher degrees of association for the less bulky alkyl group. In the case where the MA block is in the insoluble core of the micelles, the higher the tendency for crystallization the higher the degree of association. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4177–4188, 2004