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PubMed2003

Processivity of the single-headed kinesin KIF1A through biased binding to tubulin.

Conventional isoforms of the motor protein kinesin behave functionally not as 'single molecules' but as 'two molecules' paired. This dimeric structure poses a barrier to solving its mechanism. To overcome this problem, we used an unconventional kinesin KIF1A (refs 5, 6) as a model molecule. KIF1A moves processively as an independent monomer, and can also work synergistically as a functional dimer. Here we show, by measuring its movement with an optical trapping system, that a single ATP hydrolysis triggers a single stepping movement of a single KIF1A monomer. The step size is distributed stochastically around multiples of 8 nm with a gaussian-like envelope and a standard deviation of 15 nm. On average, the step is directional to the microtubule's plus-end against a load force of up to 0.15 pN. As the source for this directional movement, we show that KIF1A moves to the microtubule's plus-end by approximately 3 nm on average on binding to the microtubule, presumably by preferential binding to tubulin on the plus-end side. We propose a simple physical formulation to explain the movement of KIF1A.

Adenosine Diphosphate↗

PubMed1998

Multiple-step method for making exceptionally well-oriented liquid-crystalline sols of macromolecular assemblies.

X-ray fiber diffraction is potentially powerful in solving the atomic structure of filamentous assemblies of macromolecules, as demonstrated for tobacco mosaic virus. However, it requires extremely well-oriented sols to allow for extraction of intensities on closely located layer-lines. A high degree of orientation requires a high filament concentration to restrain the orientational freedom, but orienting concentrated sols is hampered by their high viscosity. Here, we report a systematic method that reproducibly produces extremely good orientation, which involves three steps; liquid crystallization, centrifugation and magnetic orientation. We found that a slow centrifugation can trigger a dynamic self-orientation process to form perfectly homogeneous liquid-crystalline sols, and further centrifugation to concentrate sols followed by magnetic orientation produces exceptionally well-oriented sols. The best-oriented flagellar sol showed a disorientation angle of 0.6 degrees as 1sigma of its Gaussian distribution. The new method has been successfully applied to many other systems, such as tobacco mosaic virus and F-actin.

Actins↗

PubMed1995

Investigating simple and complex mechanisms in texture segregation using the speed-accuracy tradeoff method.

Several recent models of texture segregation have proposed two mechanisms: simple, linear channels (first-order, Fourier mechanisms) and complex channels (second-order, non-Fourier mechanisms). We used the speed-accuracy tradeoff (SAT) method to examine the time course of texture segregation processing in simple and complex channels. The stimuli were texture patterns designed to segregate primarily as a result of activity in one set of channels or the other. We presented subjects with textures that were checked or striped arrangements of either Gaussian-blob or Gabor-patch elements. Subjects were required to identify the orientation of a rectangular texture region embedded in a background field of a different texture. A range of contrasts and a control task were used to equate visibility of the Gabor and Gaussian textures. SAT functions were obtained by requiring subjects to respond within 200 msec after an auditory cue. We found that when segregation depended primarily on simple channels, performance was faster than when it depended primarily on complex channels: the 75% correct level was reached 100-200 msec sooner and this extra speed was reflected both in smaller delay and higher rate parameters.

Contrast Sensitivity↗

PubMed2003

Contrast sensitivity in subgroups of developmental dyslexia.

It has been proposed that developmental dyslexia is associated with a deficit in the magnocellular pathway of the visual system. Other research focuses upon the heterogeneous nature of developmental dyslexia, and evidence that subgroups of dyslexia may be identified based on selective deficits in specific component reading skills. This study tested the hypothesis that visual processing deficits may be present in different subgroups of developmental dyslexia by comparing the visual contrast sensitivity of three subgroups of dyslexic children (phonological, surface and mixed) and controls. The stimulus designed to measure magnocellular visual function was a low spatial frequency Gaussian blob, flickered sinusoidally at a temporal frequency of 8.33 Hz. The control stimulus, designed to measure parvocellular visual function, was a relatively high spatial frequency Gaussian windowed grating (8 c/deg) slowly ramped on and off. There were no significant differences between the groups of dyslexic and control children in contrast sensitivity to either stimulus. The findings do not support the existence of a magnocellular system deficit in dyslexia.

Child↗

PubMed2003

High mass measurement accuracy determination for proteomics using multivariate regression fitting: application to electrospray ionization time-of-flight mass spectrometry.

Important factors that limit the mass measurement accuracy from a mass spectrometer are related to (1) the type of mass analyzer used and (2) the data processing/calibration methods used to obtain mass values from the raw data. Here, two data processing methods are presented that correct for systematic deviations when the mass of ions is measured using a time-of-flight (TOF) mass spectrometer. The first fitting method is one where m/z values are obtained from fitting peak distributions using double Gaussian functions. A second calibration method takes into account the slight nonlinear response of the TOF analyzer in addition to the drift in the calibration over time. Using multivariate regression, both of these two effects can be corrected for using a single calibration formula. Achievable performance was evaluated with a trypsin digestion of serum albumin and proteins from the organism D. radiodurans that was analyzed using gradient reversed-phase liquid chromatography combined with an electrospray ionization orthogonal TOF mass spectrometer. The root-mean-square deviation between the theoretical and experimental m/z values for serum albumin tryptic peptides was found to be 8 ppm using the double Gaussian-multivariate method compared to 29 ppm determined using linear calibration and normal peak centroiding. An advantage of the methods presented here is that no calibrant compounds need to be added to the mobile phase, thereby avoiding interference effects and signal suppression of analytes.

Bacterial Proteins↗

PubMed2004

Electron attachment and detachment: electron affinities of isomers of trifluoromethylbenzonitrile.

Rate constants for electron attachment to the three isomers of trifluoromethylbenzonitrile [(CF(3))(CN)C(6)H(4), or TFMBN] were measured over the temperature range of 303-463 K in a 133-Pa He buffer gas, using a flowing-afterglow Langmuir-probe apparatus. At 303 K, the measured attachment rate constants are 9.0 x 10(-8) (o-TFMBN), 5.5 x 10(-8) (m-TFMBN), and 8.9 x 10(-8) cm(3) s(-1) (p-TFMBN), estimated accurate to +/-25%. The attachment process formed only the parent anion in all three cases. Thermal electron detachment was observed for all three anion isomers, and rate constants for this reverse process were also measured. From the attachment and detachment results, the electron affinities of the three isomers of TFMBN were determined to be 0.70(o-TFMBN), 0.67(m-TFMBN), and 0.83 eV (p-TFMBN), all +/-0.05 eV. G3(MP2) [Gaussian-3 calculations with reduced Møller-Plesset orders (MP2)] calculations were carried out for the neutrals and anions. Electron affinities derived from these calculations are in good agreement with the experimental values.

Journal Article↗

PubMed2006

Nonequilibrium membrane fluctuations driven by active proteins.

We extend a model for nonthermal membrane undulations driven by active (adenosine triphosphate-dependent or light-harvesting) membrane proteins [N. Gov, Phys. Rev. Lett. 93, 268104 (2004)]. The present model accounts for the fact that proteins can diffuse laterally across the membrane surface and that individual proteins are expected to exert forces preferentially in one normal direction over the other (due to their orientation within the bilayer). The addition of these effects alters the scaling of fluctuation amplitudes with system size. Additionally, theoretical arguments and dynamic simulations both suggest that, in certain regimes, the probability distribution of fluctuation amplitudes is expected to be non-Gaussian (in contrast to thermal systems).

Biomechanical Phenomena↗

PubMed1998

Nitric oxide formation in an iron oxide pellet rotary kiln furnace.

A one-dimensional numerical model was developed to simulate the effects of heat and mass transfer on the formation of oxides of nitrogen (NOx) in a rotary kiln furnace for iron oxide pellet induration. The modeled kiln has a length-to-diameter ratio of approximately seven. The principal mechanism of heat transfer is radiation from the flame, which was described by the net radiation method. The well known Zeldovich mechanism was used to predict thermal NOx generation. Temperature fluctuations in the vicinity of the flame were estimated with a clipped Gaussian probability density function. The thermal energy and mass balance model equations were solved numerically. The model is capable of predicting temperature profiles and NOx production rates in agreement with observed plant performance. The model was used to explore the effects of process changes on the total NOx formation in the kiln. It was concluded that the gas temperature as well as the partial pressure of oxygen in the process gases controls the rate of NOx formation. Lowering the temperature of the kiln gases by increasing the secondary air flow rates requires simultaneously decreasing the pellet production rate in order to maintain the pellet temperatures needed for blast furnace conditions.

Air Pollutants, Occupational↗

PubMed2006

Analysis of the CDR3 region of alpha/beta T-cell receptors (TCRs) and TCR BD gene double-stranded recombination signal sequence breaks end in peripheral blood mononuclear cells of T-lineage acute lymphoblastic leukemia.

Recently, numerous reports have highlighted the restriction of the CDR3 length of T-cell receptor (TCR) beta chain in T-cells infiltrating solid tumors and hematological malignancies. However, these studies ignored the restriction of CDR3 length of TCR alpha chain and few of them attempted to reveal the mechanisms of the oligo-clonal expansion of T cells in the tumors. The primary aims of this study were twofold to: (i) analyze the CDR3 length of TCR alpha and beta chain in peripheral blood mononuclear cells of T-lineage acute lymphoblastic leukemia (T-ALL); and (ii) discover the relationship between the clonality of T cells and the process of TCR rearrangement in peripheral T cells. To this end, we investigated the TCR BV and TCR AV family spectratypes of two T-ALL patients and healthy controls using the immunoscope spectratyping technique. We found that the spectratypes exhibited a Gaussian distribution in healthy controls. However, the TCR repertoires of the two patients were highly restricted in the number of different TCR BV and TCR AV family members present. Furthermore, we found that the peripheral blood mononuclear cells (PBMC) of two T-ALL patients had the recombination signal sequence (RSS) 5'- and 3'-breaks end in the TCR BD2 gene using a specialized ligation-mediated polymerase chain reaction, implying the ongoing recombination of the TCR beta gene. Analysis of the particular CDR3 length of TCR alpha/beta T cells might be helpful for further study of the individualized therapy of T-ALL. This information will also be helpful in exploring new immunological pathogenesis and facilitating the design of a T-ALL vaccine, as well as in improving our understanding of healthy human T-cell development.

Adolescent↗

PubMed1996

Practical Bayesian inference using mixtures of mixtures.

Discrete mixtures of normal distributions are widely used in modeling amplitude fluctuations of electrical potentials at synapses of human and other animal nervous systems. The usual framework has independent data values yj arising as yj = mu j + xn0 + j, where the means mu j come from some discrete prior G(mu) and the unknown xno + j's and observed xj, j = 1,...,n0, are Gaussian noise terms. A practically important development of the associated statistical methods is the issue of nonnormality of the noise terms, often the norm rather than the exception in the neurological context. We have recently developed models, based on convolutions of Dirichlet process mixtures, for such problems. Explicitly, we model the noise data values xj as arising from a Dirichlet process mixture of normals, in addition to modeling the location prior G(mu) as a Dirichlet process itself. This induces a Dirichlet mixture of mixtures of normals, whose analysis may be developed using Gibbs sampling techniques. We discuss these models and their analysis, and illustrate them in the context of neurological response analysis.

Animals↗

PubMed2005

A wavelet-based statistical analysis of FMRI data: I. motivation and data distribution modeling.

We propose a new method for statistical analysis of functional magnetic resonance imaging (fMRI) data. The discrete wavelet transformation is employed as a tool for efficient and robust signal representation. We use structural magnetic resonance imaging (MRI) and fMRI to empirically estimate the distribution of the wavelet coefficients of the data both across individuals and spatial locations. An anatomical subvolume probabilistic atlas is used to tessellate the structural and functional signals into smaller regions each of which is processed separately. A frequency-adaptive wavelet shrinkage scheme is employed to obtain essentially optimal estimations of the signals in the wavelet space. The empirical distributions of the signals on all the regions are computed in a compressed wavelet space. These are modeled by heavy-tail distributions because their histograms exhibit slower tail decay than the Gaussian. We discovered that the Cauchy, Bessel K Forms, and Pareto distributions provide the most accurate asymptotic models for the distribution of the wavelet coefficients of the data. Finally, we propose a new model for statistical analysis of functional MRI data using this atlas-based wavelet space representation. In the second part of our investigation, we will apply this technique to analyze a large fMRI dataset involving repeated presentation of sensory-motor response stimuli in young, elderly, and demented subjects.

Adult↗

PubMed2002

Iterative reconstruction methods for high-throughput PET tomographs.

A fast iterative method is described for processing clinical PET scans acquired in three dimensions, that is, with no inter-plane septa, using standard computers to replace dedicated processors used until the late 1990s. The method is based on sinogram resampling, Fourier rebinning, Monte Carlo scatter simulation and iterative reconstruction using the attenuation-weighted OSEM method and a projector based on a Gaussian pixel model. Resampling of measured sinogram values occurs before Fourier rebinning, to minimize parallax and geometric distortions due to the circular geometry, and also to reduce the size of the sinogram. We analyse the geometrical and statistical effects of resampling, showing that the lines of response are positioned correctly and that resampling is equivalent to about 4 mm of post-reconstruction filtering. We also present phantom and patient results. In this approach, multi-bed clinical oncology scans can be ready for diagnosis within minutes.

Algorithms↗

PubMed1994

In vivo tissue characterization of human brain by chisquares parameter maps: multiparameter proton T2-relaxation analysis.

The heterogeneous proton MR relaxation decay process in human brain has been investigated by performing region-of-interest and pixel-by-pixel calculations on the multiecho MR images with different repetition times (TR) of human brains using a clinical 1.5-T whole-body superconducting MR scanner. Based on the monoexponential, biexponential, and continuous gaussian distribution relaxation models, first-order proton relaxation parameters (proton density, T1 and T2) and higher-order transverse proton relaxation parameters (T2-long, T2-short, T2-long fraction, T2-average, and T2-distribution width) were calculated. On the basis of an F test (p < .01), the statistical significance of the higher-order (biexponential and distribution) fits over the monoexponential fit was evaluated. Here, a significant improvement in the biexponential fit was found for some of the regions containing the ventricular cerebrospinal fluid (CSF) (T2-long = 2780 +/- 570 ms; T2-short = 159 +/- 42 ms; T2-long fraction = 0.51 +/- 0.08 ms) due to the partial volume effect but not for most of the white matter (WM). On the other hand, an improvement of fit to WM was obtained when distribution (T2-average = 80 +/- 8 ms; T2-distribution half-width = 21 +/- 4 ms) as opposed to monoexponential (T2 = 89 +/- 10 ms) fit was used. As internal controls, tubes of CuSO4 solution (T2 = 1293 +/- 128 ms) and agarose gel (T2 = 111 +/- 10 ms) which have similar T2 values as the CSF and WM of the brain, respectively, were attached to the human head and imaged concomitantly. No significance improvements in either the biexponential or distribution fits over the monoexponential fit were found for all the controls. In addition to the first-order and higher-order relaxation parameter maps, the monoexponential chisquares, as well as the chisquares ratio (chisquares of the monoexponential fit divided by that of the higher-order fit), maps were also generated. Unlike the higher-order T2-relaxation parameter maps, the chisquares parameter maps required no selection of any predetermined statistical confidence level. Therefore, these chisquares parameter maps provided a somewhat nonsubjective spatial profile of the heterogeneous transverse relaxation process in the brain. Our results led us to propose that the use of chisquares parameter maps, together with the first-and higher-order relaxation parameter maps, may further improve the in vivo tissue characterization capability of MRI in future clinical diagnosis and staging of intracranial diseases.

Adult↗

PubMedDate not supplied

Universality in visual cortical pattern formation.

During ontogenetic development, the visual cortical circuitry is remodeled by activity-dependent mechanisms of synaptic plasticity. From a dynamical systems perspective this is a process of dynamic pattern formation. The emerging cortical network supports functional activity patterns that are used to guide the further improvement of the network's structure. In this picture, spontaneous symmetry breaking in the developmental dynamics of the cortical network underlies the emergence of cortical selectivities such as orientation preference. Here universal properties of this process depending only on basic biological symmetries of the cortical network are analyzed. In particular, we discuss the description of the development of orientation preference columns in terms of a dynamics of abstract order parameter fields, connect this description to the theory of Gaussian random fields, and show how the theory of Gaussian random fields can be used to obtain quantitative information on the generation and motion of pinwheels, in the two dimensional pattern of visual cortical orientation columns.

Animals↗

PubMed2002

Significance and statistical errors in the analysis of DNA microarray data.

DNA microarrays are important devices for high throughput measurements of gene expression, but no rational foundation has been established for understanding the sources of within-chip statistical error. We designed a specialized chip and protocol to investigate the distribution and magnitude of within-chip errors and discovered that, as expected from theoretical expectations, measurement errors follow a Lorentzian-like distribution, which explains the widely observed but unexplained ill-reproducibility in microarray data. Using this specially designed chip, we examined a data set of repeated measurements to extract estimates of the distribution and magnitude of statistical errors in DNA microarray measurements. Using the common "ratio of medians" method, we find that the measurements follow a Lorentzian-like distribution, which is problematic for subsequent analysis. We show that a method of analysis dubbed "median of ratios" yields a more Gaussian-like distribution of errors. Finally, we show that the bootstrap algorithm can be used to extract the best estimates of the error in the measurement. Quantifying the statistical error in such measurements has important applications for estimating significance levels, clustering algorithms, and process optimization.

Algorithms↗

PubMed2004

Effect of quantum collapse on the distribution of work in driven single molecules.

Two sources of quantum deviations from Jarzynski's celebrated classical relation between the free energy change and the distribution of work are analyzed using an exactly solvable harmonic model: Quantum dynamics retains the Gaussian profile of the distribution and merely gives rise to analytic corrections in variant Planck's over 2pi, whereas quantum measurements (wave function collapse) induce extended power-law tails which fundamentally alter the distribution. These results may be observed in quantum information processing and in experiments involving mechanically or optically driven single quantum objects.

Journal Article↗

PubMed1994

Two-dimensional random arrays for real time volumetric imaging.

Two-dimensional arrays are necessary for a variety of ultrasonic imaging techniques, including elevation focusing, 2-D phase aberration correction, and real time volumetric imaging. In order to reduce system cost and complexity, sparse 2-D arrays have been considered with element geometries selected ad hoc, by algorithm, or by random process. Two random sparse array geometries and a sparse array with a Mills cross receive pattern were simulated and compared to a fully sampled aperture with the same overall dimensions. The sparse arrays were designed to the constraints of the Duke University real time volumetric imaging system, which employs a wide transmit beam and receive mode parallel processing to increase image frame rate. Depth-of-field comparisons were made from simulated on-axis and off-axis beamplots at ranges from 30 to 160 mm for both coaxial and offset transmit and receive beams. A random array with Gaussian distribution of transmitters and uniform distribution of receivers was found to have better resolution and depth-of-field than both a Mills cross array and a random array with uniform distribution of both transmit and receive elements. The Gaussian random array was constructed and experimental system response measurements were made at several ranges. Comparisons of B-scan images of a tissue mimicking phantom show improvement in resolution and depth-of-field consistent with simulation results.

Ultrasonography↗

PubMed2005

Ab initio calculation of interatomic decay rates by a combination of the Fano ansatz, Green's-function methods, and the Stieltjes imaging technique.

A new computational technique is introduced for the ab initio calculation of the rates of interatomic and intermolecular nonradiative decay processes occurring due to electronic correlation. These recently discovered phenomena are described theoretically using the configuration-interaction formalism first introduced by Fano [Phys. Rev. 124, 1866 (1961)] and later adapted to an Auger decay by Howat et al. [J. Phys. B 11, 1575 (1978)]. The boundlike and the continuumlike components of the wave function of the decaying state are constructed using a Green's-function method known as algebraic diagrammatic construction. A combination of atomic and distributed Gaussian basis sets is shown to provide an adequate description of both boundlike and continuumlike wave-function components. The problem of the normalization of the continuum (final state) wave function is addressed using the Stieltjes imaging technique. The new method is applied to the calculation of the rates of interatomic decay in alkaline-earth-rare-gas clusters. The obtained results help to verify our earlier conclusions [Phys. Rev. Lett. 93, 263002 (2004)] regarding the validity of the virtual-photon transfer model for the interatomic Coulombic decay. In addition, we demonstrate that the process of electron-transfer-mediated decay is responsible for the finite lifetimes of the outer valence vacancies in alkaline-earth-rare-gas clusters.

Journal Article↗