bluuebunny/crossref_metadata_2025 huggingface dataset:
Meaning of resonator's coupling coefficient in bandpass filter design
Authors: Awai Ikuo
Published: May 2006

In the design of a bandpass filter, the mutual inductance M and the mutual capacitance Cm between two resonators are needed. In this paper, the speed of energy exchange between the coupled LC resonators is related to M and Cm and is defined as the coupling coefficient. Subsequently, the effective M and Cm are determined by deriving the coupling coefficient between the electromagnetic resonators. In this way, a basis is provided on which the filter design theory established previously for the LC resonator circuits is extended to the electromagnetic circuits. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 89(6): 1–7, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20241
Collimation field detection from digital radiographs using plane detection Hough transform
Authors: Kawashita Ikuo , Aoyama Masahito , Kajiyama Tomoaki , Asada Naoki , Awai Kazuo
Published: May 2006

There have been efforts to detect the collimation field of medical digital radiographs (x‐ray images), which is unnecessary in diagnosis. The method used in past studies is to detect the boundary of the collimation field as a straight line, using the edge detection on the two‐dimensional image. The boundary, however, is not an ideal step‐edge, as is seen from the principle of image generation, but is a ramp edge containing a blur (half‐shadow). This paper extends the radiograph to another dimension of brightness, to be considered as three‐dimensional data. A method is proposed in which the Hough transform is used to detect the boundary of the collimation field as a plane. In order to investigate the validity of the model and the effectiveness of the proposed method, a detection experiment is performed for the collimation field. The collimation field is correctly detected at a rate of 96.4% (324 cases) in 336 images. It is also shown that when the image is compressed by setting the brightness of the detected collimation field as 0, the amount of image data is smaller than the amount of image data obtained by compressing the original image. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 89(6): 22–33, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20268
Pattern recognition model with moving visual attention based on hypothesis and verification
Authors: Shimomura Masao , Satoh Shunji , Miyake Syogo , Aso Hirotomo
Published: May 2006

This paper proposes a method which can be used to extract and correctly recognize patterns by moving the attention point, even if less than the whole pattern is projected on the retina at the start of recognition. In the proposed model, a temporary result of pattern recognition (hypothesis) is generated on the basis of the features which are not affected by the presented position. Then, using the features that depend on the presented position, the attention point is moved while verifying the obtained hypothesis. By repeating the above procedure, the pattern is adequately extracted and recognized. It is shown by computer simulation of the proposed model that adequate extraction and recognition of the pattern are actually realized from its partial presentation. It is also shown that adequate recognition is achieved even if recognition is begun from a situation in which multiple patterns are mixed and presented, or noise is present in the pattern. © 2006 Wiley Periodicals, Inc. Electron Comm Jpn Pt 2, 89(6): 44–54, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/ecjb.20270
Two‐hourly surface change on supra‐tidal rock (Marengo, Victoria, Australia)
Authors: Gómez‐Pujol Lluís , Stephenson Wayne J. , Fornós Joan J.
Published: May 2006

A traversing micro‐erosion meter was used to measure rock surface micro‐topography over 40 cm2 on a supra‐tidal cliff face from early morning to late evening in late spring. From 06:00 hours to 22:00 hours the relative heights of 188 coordinates were obtained using the meter at 2‐hour intervals, resulting in a data set of 1607 readings. Monitoring shows that rock surfaces are dynamic entities, with significant rise and fall relative to the first measurement at shorter timescales than previously reported. The maximum positive rise between readings was 0·261 mm and lowering was 0·126 mm. The pattern of change did not relate as expected to environmental variables such as temperature or insolation. Rather, the surface showed greater surface change in the early morning and late afternoon. It is hypothesized that this pattern relates to the expansion and contraction of lichen thalli as moisture is absorbed during higher humidity in the morning and late afternoon. The implications of these results for weathering studies are considered. Copyright © 2006 John Wiley & Sons, Ltd.
Rock surface millimetre‐scale roughness and weathering of supratidal Mallorcan carbonate coasts (Balearic Islands)
Authors: Gómez‐Pujol Lluís , Fornós Joan J. , Swantesson Jan O. H.
Published: May 2006

Quantitative data on rock surface millimetre‐scale roughness are presented concerning the splash and spray geomorphologic domains of two coastal profiles developed on Mediterranean carbonate rocks. Differences of the roughness characteristics are attributed to rock properties, weathering agents and bioerosion. In the splash zone, roughness is related to sparsely distributed patterns of bioerosion, salt weathering and wave attack. In the spray zone, smooth surfaces seem to be the response to the solution processes that predominate, exerting a more homogenous influence on rock surface evolution. Copyright © 2006 John Wiley & Sons, Ltd.
Long‐memory forecasting of US monetary indices
Authors: Barkoulas John , Baum Christopher F.
Published: May 2006

Several studies have tested for long‐range dependence in macroeconomic and financial time series but very few have assessed the usefulness of long‐memory models as forecast‐generating mechanisms. This study tests for fractional differencing in the US monetary indices (simple sum and divisia) and compares the out‐of‐sample fractional forecasts to benchmark forecasts. The long‐memory parameter is estimated using Robinson's Gaussian semi‐parametric and multivariate log‐periodogram methods. The evidence amply suggests that the monetary series possess a fractional order between one and two. Fractional out‐of‐sample forecasts are consistently more accurate (with the exception of the M3 series) than benchmark autoregressive forecasts but the forecasting gains are not generally statistically significant. In terms of forecast encompassing, the fractional model encompasses the autoregressive model for the divisia series but neither model encompasses the other for the simple sum series.  Copyright © 2006 John Wiley & Sons, Ltd.
Nonlinear local electrovascular coupling. I: A theoretical model
Authors: Riera Jorge J. , Wan Xiaohong , Jimenez Juan Carlos , Kawashima Ryuta
Published: May 2006

Here we present a detailed biophysical model of how brain electrical and vascular dynamics are generated within a basic cortical unit. The model was obtained from coupling a canonical neuronal mass and an expandable vasculature. In this proposal, we address several aspects related to electroencephalographic and functional magnetic resonance imaging data fusion: (1) the impact of the cerebral architecture (at different physical levels) on the observations; (2) the physiology involved in electrovascular coupling; and (3) energetic considerations to gain a better understanding of how the glucose budget is used during neuronal activity. The model has three components. The first is the canonical neural mass model of three subpopulations of neurons that respond to incoming excitatory synaptic inputs. The generation of the membrane potentials in the somas of these neurons and the electric currents flowing in the neuropil are modeled by this component. The second and third components model the electrovascular coupling and the dynamics of vascular states in an extended balloon approach, respectively. In the first part we describe, in some detail, the biophysical model and establish its face validity using simulations of visually evoked responses under different flickering frequencies and luminous contrasts. In a second part, a recursive optimization algorithm is developed and used to make statistical inferences about this forward/generative model from actual data. Hum. Brain Mapping 2006. © 2006 Wiley‐Liss, Inc.
Intelligence and EEG current density using low‐resolution electromagnetic tomography (LORETA)
Authors: Thatcher R.W. , North D. , Biver C.
Published: May 2006

The purpose of this study was to compare EEG current source densities in high IQ subjects vs. low IQ subjects. Resting eyes closed EEG was recorded from 19 scalp locations with a linked ears reference from 442 subjects ages 5 to 52 years. The Wechsler Intelligence Test was administered and subjects were divided into low IQ (≤90), middle IQ (>90 to <120) and high IQ (≥120) groups. Low‐resolution electromagnetic tomographic current densities (LORETA) from 2,394 cortical gray matter voxels were computed from 1–30 Hz based on each subject's EEG. Differences in current densities using t tests, multivariate analyses of covariance, and regression analyses were used to evaluate the relationships between IQ and current density in Brodmann area groupings of cortical gray matter voxels. Frontal, temporal, parietal, and occipital regions of interest (ROIs) consistently exhibited a direct relationship between LORETA current density and IQ. Maximal t test differences were present at 4 Hz, 9 Hz, 13 Hz, 18 Hz, and 30 Hz with different anatomical regions showing different maxima. Linear regression fits from low to high IQ groups were statistically significant (P < 0.0001). Intelligence is directly related to a general level of arousal and to the synchrony of neural populations driven by thalamo‐cortical resonances. A traveling frame model of sequential microstates is hypothesized to explain the results. Hum Brain Mapp, 2007. © 2006 Wiley‐Liss, Inc.
Mudanças not removalists: Rethinking the management of organizational change
Authors: Badham Richard J.
Published: May 2006

All successful innovation, including effective human factors interventions, needs to address the problems of organizational inertia as well as active opposition and resistance. Yet our common understanding of how to “manage” such problems—described in this article as the management of organizational change—embodies a restricted and ineffective view of change management. The author proposes an alternative approach, viewing change management as an activity of leading changing institutions. This approach captures the fluid character of change(ing) as an emergent process, the complex social character of human institutions, and the crucial role of leadership in constructing collective goals and purposes in situations of conflict and uncertainty. © 2006 Wiley Periodicals, Inc. Hum Factors Man 16: 229–245, 2006.
Mechanism of plasmid delivery by hydrodynamic tail vein injection. I. Hepatocyte uptake of various molecules
Authors: Sebestyén Magdolna G. , Budker Vladimir G. , Budker Tatiana , Subbotin Vladimir M. , Zhang Guofeng , Monahan Sean D. , Lewis David L. , Wong So C. , Hagstrom James E. , Wolff Jon A.
Published: May 2006

Background

The hydrodynamic tail vein (HTV) injection of naked plasmid DNA is a simple yet effectivein vivogene delivery method into hepatocytes. It is increasingly being used as a research tool to elucidate mechanisms of gene expression and the role of genes and their cognate proteins in the pathogenesis of disease in animal models. A greater understanding of its mechanism will aid these efforts and has relevance to macromolecular and nucleic acid delivery in general.

Methods

In an attempt to explore how naked DNA enters hepatocytes the fate of a variety of molecules and particles was followed over a 24‐h time frame using fluorescence microscopy. The uptake of some of these compounds was correlated with marker gene expression from a co‐injected plasmid DNA. In addition, the uptake of the injected compounds was correlated with the histologic appearance of hepatocytes.

Results

Out of the large number of nucleic acids, peptides, proteins, inert polymers and small molecules that we tested, most were efficiently delivered into hepatocytes independently of their size and charge. Even T7 phage and highly charged DNA/protein complexes of 60‐100 nm in size were able to enter the cytoplasm. In animals co‐injected with an enhanced yellow fluorescent protein (EYFP) expression vector and fluorescently labeled immunoglobulin (IgG), hepatocytes flooded with large amounts of IgG appeared permanently damaged and did not express EYFP‐Nuc. Hepatocytes expressing EYFP had only slight IgG uptake. In contrast, when an EYFP expression vector was co‐injected with a fluorescently labeled 200‐bp linear DNA fragment, both were mostly (in 91% of the observed cells) co‐localized to the same hepatocytes 24 h later.

Conclusions

The appearance of permanently damaged cells with increased uptake of some molecules such as endogenous IgG raised the possibility that a molecule could be present in a hepatocyte but its transport would not be indicative of the transport process that can lead to foreign gene expression. The HTV procedure enables the uptake of a variety of molecules (as previous studies also found), but the uptake process for some of these molecules may be associated with a more disruptive process to the hepatocytes that is not compatible with successful gene delivery. Copyright © 2006 John Wiley & Sons, Ltd.
In vivo diffusion tensor imaging of the human calf muscle
Authors: Sinha Shantanu , Sinha Usha , Edgerton V. Reggie
Published: May 2006

Purpose

To demonstrate the feasibility of in vivo calf muscle fiber tracking in human subjects.

Materials and Methods

An EPI‐based diffusion tensor imaging (DTI) sequence with six‐direction diffusion gradient sensitization was implemented, and DT images were acquired at 3 Tesla on five subjects using an extremity coil. The mean diffusivity, fractional anisotropy (FA), and fiber angle (with respect to the magnet z‐axis) were measured in different muscles, and fibers were tracked from several regions of interest (ROIs).

Results

The fiber orientations in the current DTI studies agree well with those determined in previous spectroscopic studies. The orientation angles ranged from 13.4° in the lateral gastrocnemius to 48.5° in the medial soleus. The diffusion ellipsoid in muscle tissue is anisotropic and approximates a prolate model, as shown by color maps of the anisotropy. Fibers were tracked from the different muscle regions, and the unipennate and bipennate structure of muscle fibers was visualized.

Conclusion

The study clearly shows that in vivo fiber tracking of muscle fibers is feasible and could potentially be applied to study muscle structure function relationships. J. Magn. Reson. Imaging 2006. © 2006 Wiley‐Liss, Inc.
High‐resolution renal MRA: Comparison of image quality and vessel depiction with different parallel imaging acceleration factors
Authors: Michaely Henrik J. , Herrmann Karin A. , Kramer Harald , Dietrich Olaf , Laub Gerhard , Reiser Maximilian F. , Schoenberg Stefan O.
Published: May 2006

Purpose

To investigate the image quality and vessel depiction of renal MRA with integrated parallel imaging techniques (iPAT) using acceleration factors of 2 and 3.

Materials and Methods

In this prospective study renal MRA was performed on 14 and 12 patients with acceleration factors of 3 and 2, respectively. For the MRA a 3D‐GRE sequence with an acquired spatial resolution of 0.9 × 0.8 × 1.0 mm3 was applied (TR/TE = 3.79 msec/1.39 msec, FOV = 400 mm × 320 mm, acquired matrix = 512 × 384, flip angle = 25°) on a 32‐channel 1.5T MR scanner. The acquisition time was 26 seconds with iPAT 2, and 19 seconds with iPAT3. All parameters other than acquisition time and acceleration factor were kept constant. To assess the signal‐to‐noise ratio (SNR) we performed repetitive phantom measurements using iPAT 2 and 3. The images were rated by two radiologists in terms of noise, artifacts, and the quality of vessel depiction for the proximal, segmental, and subsegmental renal artery. A Mann‐Whitney U‐test and kappa‐test were used for statistical analysis.

Results

SNR decreased significantly with iPAT 3 in the phantom measurements. The two readers found no difference in noise, but significantly fewer artifacts with iPAT 3. The depiction of segmental vessels was significantly better for both readers with iPAT 3, and the subsegmental vessels were rated significantly better by one reader. iPAT 3 also resulted in a better interreader agreement.

Conclusion

The use of iPAT 3 for renal MRA enables a better depiction of the distal parts of the renal artery. The decrease in SNR is not diagnostically impairing. J. Magn. Reson. Imaging 2006. © 2006 Wiley‐Liss, Inc.
Two isomeric epoxysitosterols from Rhododendron formosanum: 1H and 13C NMR chemical shift assignments
Authors: Krishna Vivek , Chang Chi‐I , Chou Chang‐Hung
Published: May 2006

1H and 13C NMR assignments of the two isomeric epoxysitosterols, 5,6α‐epoxy‐5α‐stigmastan‐3β‐ol (1) and 5,6β‐epoxy‐5β‐stigmastan‐3β‐ol (2), isolated from the leaves of Rhododendron formosanum Hemsl were achieved by 1D and 2D techniques such as DEPT, HMBC, HMQC, COSY and NOESY. Copyright © 2006 John Wiley & Sons, Ltd.
Structure elucidation of the intermediate in triethylborane‐mediated radical addition of oxime ethers with 2D‐ and 3D‐DOSY NMR
Authors: Nakakoshi Masamichi , Ueda Masafumi , Sakurai Satoshi , Miyata Okiko , Sugiura Makiko , Naito Takeaki
Published: May 2006

The structures of the components in the triethylborane‐mediated radical addition reaction of oxime ether were investigated by 1H‐ and 3D‐DOSY NMR methods. It has been impossible to physically separate the unstable intermediates; therefore, the structures were thus far unidentified. It has been possible to elucidate the structures of these unstable intermediates using Diffusion‐Ordered Spectroscopy (DOSY) methods for the reaction in an NMR tube. The DOSY methods resolved the spectra of each starting compound, intermediate and product having different diffusion coefficients. The structure of the intermediate was shown to be due to the bonding of diethylborane to the nitrogen atom of the alkoxyamino group. Copyright © 2006 John Wiley & Sons, Ltd.
Numerical analysis of the stochastic Stokes equations of Wick type
Authors: Manouzi H. , Theting T.G.
Published: May 2006

We propose a finite element method for the numerical solution of the stochastic Stokes equations of the Wick type. We give existence and uniqueness results for the continuous problem and its approximation. Optimal error estimates are derived and algorithmic aspects of the method are discussed. Our method will reduce the problem of solving stochastic Stokes equations to solving a set of deterministic ones. Moreover, one can reconstruct particular realizations of the solution directly from Wiener chaos expansions once the coefficients are available. © 2006 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2007
On the maximum principle and its application to diffusion equations
Authors: Stys̆ T. , Motsumi T. , Daman O.
Published: May 2006

In this article, an analog of the maximum principle has been established for an ordinary differential operator associated with a semi‐discrete approximation of parabolic equations. In applications, the maximum principle is used to prove O(h2) and O(h4) uniform convergence of the method of lines for the diffusion Equation (1). The system of ordinary differential equations obtained by the method of lines is solved by an implicit predictor corrector method. The method is tested by examples with the use of the enclosed Mathematica module solveDiffusion. The module solveDiffusion gives the solution by O(h2) uniformly convergent discrete scheme or by O(h4) uniformly convergent discrete scheme. © 2006 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2007
Domain decomposition for time‐dependent problems using radial based meshless methods
Authors: Chinchapatnam Phani P. , Djidjeli K. , Nair Prasanth B.
Published: May 2006

In this article, we present meshless overlapping Schwarz additive and multiplicative domain decomposition schemes for time‐dependent problems using radial basis functions. The proposed schemes are compared with the global radial basis function collocation method and an explicit multizone domain decomposition method (Wong et al.,Comput Math Appl 37 (1999), 23–43) by solving an unsteady convection‐diffusion problem for various Peclet numbers. Stability analysis of the presented schemes suggest that for radial basis functions incorporating a free shape parameter, the freedom of varying the shape parameter decreases with increase in the number of collocation points. Numerical studies show that the ill‐conditioning problem of global radial basis function collocation method is reduced by the proposed Schwarz schemes. Also, with an increase in the number of subdomains the efficiency of the Schwarz schemes increases with a slight loss in the accuracy. © 2006 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2007
The pattern of vertebral osteophyte development in a South African population
Authors: Van der Merwe A. E. , Işcan M. Y. , L'Abbè E. N.
Published: May 2006

Vertebral osteophytosis is recognised by outgrowths of bone on the margins of the vertebral body. These spurs have been shown to increase with age and are usually caused by increased spinal pressure. The purpose of this paper is to describe the pattern and severity of osteophyte development in the vertebral columns of male and female South Africans. A total of 101 male and 117 female morphologically normal vertebral columns were investigated. Osteophytes were visually assessed and scored between 0 (no osteophytosis present) and 4 (osteophytes fused together). The highest frequency and degree of projections was on C5, T11, T12, L3, L4 and L5, whereas the lowest frequency was observed on T2 and L1 in females and T2 in males. In both the cervical and lumbar regions, osteophyte development was significantly more pronounced in males than females. Possible reasons for differential osteophytic development throughout the vertebral column include the position of the vertebrae in relation to the line of gravity, mobility of the joint and weight bearing. A description of the normal pattern of osteophytic development across the spine is of great importance for the future development of reliable age‐at‐death techniques for South African groups. Copyright © 2006 John Wiley & Sons, Ltd.
Variation in the decision to terminate pregnancy in the setting of fetal aneuploidy
Authors: Shaffer Brian L. , Caughey Aaron B. , Norton Mary E.
Published: May 2006

Objective

To investigate the rate of pregnancy termination for various fetal aneuploidies, and to evaluate predictors of this choice.

Methods

A retrospective cohort study identified all patients with any of seven common fetal aneuploidies (trisomies 21, 18, and 13; 45,X, 47,XXX, 47,XXY, and 47,XYY) at a referral prenatal diagnosis unit from 1983 to 2003. We abstracted type of aneuploidy, time and type of diagnostic procedure, maternal age, and ethnicity as predictors of the decision to terminate. Statistical comparisons were made using the chi‐square test. Potential confounding variables were controlled for using multivariate logistic regression.

Results

Overall, there were 833 patients who had fetuses with aneuploidy. In our study population, the overall rate of termination was 81%: 86% in cases of autosomal trisomy and 60% in cases of sex chromosome aneuploidy (SCA) (p < 0.001). Rates were lowest in cases with the least severe prognosis, 47,XYY (57%) and 47,XXX (40%) compared with 45,X (65%) and 47,XXY (70%) (p = 0.05). Patients with SCA detected by chorionic villus sampling (CVS) had a higher termination rate than those who had undergone amniocentesis (77% vs 55%, p = 0.015). Increased maternal age was associated with higher termination rates in autosomal trisomy (88% vs 76% p < 0.001) and a trend toward decreased rates in those with SCA (55% vs 71%, p = 0.06). Hispanic women were less likely to terminate pregnancy (69%, p = 0.01) than those from other racial/ethnic groups.

Conclusion

Type and severity of aneuploidy, type of diagnostic procedure, maternal age, and ethnicity contribute to patients' decision‐making in the setting of fetal aneuploidy. Copyright © 2006 John Wiley & Sons, Ltd.
Personality and team performance: a meta‐analysis
Authors: Peeters Miranda A. G. , van Tuijl Harrie F. J. M. , Rutte Christel G. , Reymen Isabelle M. M. J.
Published: May 2006

Using a meta‐analytical procedure, the relationship between team composition in terms of the Big‐Five personality traits (trait elevation and variability) and team performance were researched. The number of teams upon which analyses were performed ranged from 106 to 527. For the total sample, significant effects were found for elevation in agreeableness (ρ = 0.24) and conscientiousness (ρ = 0.20), and for variability in agreeableness (ρ = −0.12) and conscientiousness (ρ = −0.24). Moderation by type of team was tested for professional teams versus student teams. Moderation results for agreeableness and conscientiousness were in line with the total sample results. However, student and professional teams differed in effects for emotional stability and openness to experience. Based on these results, suggestions for future team composition research are presented. Copyright © 2006 John Wiley & Sons, Ltd.
Nonuniversal transport behavior in heterogeneous high‐density polyethylene/graphite nanosheet composites
Authors: Lu Wei , Lin Hongfei , Chen Guohua
Published: May 2006

The direct‐current resistivity of high‐density polyethylene/graphite nanosheet composites above the percolation threshold has been measured and fitted to a power law, which gives a conductivity critical exponent (0.10 ± 0.01) and a percolation threshold (2.97 ± 0.03). These fitted parameters are in disagreement with universal theoretical predictions, and plausible explanations of the observed discrepancies are given. The sample‐to‐sample fluctuations in the relative resistivity seem to obey a power law. This fluctuation behavior, if interpreted in terms of correlation‐length fluctuations, yields a correlation‐length critical exponent, 0.52 ± 0.06, that is consistent with the mean‐field value of 1/2. Interpretations of these experimental results imply that nonuniversal transport behavior in disordered composites is caused by composites being in a nonuniversal scaling regime. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1846–1852, 2006
Error distribution derived NOE distance restraints
Authors: Nilges Michael , Habeck Michael , O'Donoghue Seán I. , Rieping Wolfgang
Published: May 2006

Errors and imprecisions in distance restraints derived from NOESY peak volumes are usually accounted for by generous lower and upper bounds on the distances. In this paper, we propose a new form of distance restraints, replacing the subjective bounds by a potential function obtained from the error distribution of the distances. We derived the shape of the potential from molecular dynamics calculations and by comparison of NMR data with X‐ray crystal structures. We used complete cross‐validation to derive the optimal weight for the data in the calculation. In a model system with synthetic restraints, the accuracy of the structures improved significantly compared to calculations with the usual form of restraints. For experimental data sets, the structures systematically approach the X‐ray crystal structures of the same protein. Also standard quality indicators improve compared to standard calculations. The results did not depend critically on the exact shape of the potential. The new approach is less subjective and uses fewer assumptions in the interpretation of NOESY peak volumes as distance restraints than the usual approach. Figures of merit for the structures, such as the RMS difference from the average structure or the RMS difference from the data, are therefore less biased and more meaningful measures of structure quality than with the usual form of restraints. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Ab initio computational modeling of loops in G‐protein‐coupled receptors: Lessons from the crystal structure of rhodopsin
Authors: Mehler Ernest L. , Hassan Sergio A. , Kortagere Sandhya , Weinstein Harel
Published: May 2006

With the help of the crystal structure of rhodopsin an ab initio method has been developed to calculate the three‐dimensional structure of the loops that connect the transmembrane helices (TMHs). The goal of this procedure is to calculate the loop structures in other G‐protein coupled receptors (GPCRs) for which only model coordinates of the TMHs are available. To mimic this situation a construct of rhodopsin was used that only includes the experimental coordinates of the TMHs while the rest of the structure, including the terminal domains, has been removed. To calculate the structure of the loops a method was designed based on Monte Carlo (MC) simulations which use a temperature annealing protocol, and a scaled collective variables (SCV) technique with proper structural constraints. Because only part of the protein is used in the calculations the usual approach of modeling loops, which consists of finding a single, lowest energy conformation of the system, is abandoned because such a single structure may not be a representative member of the native ensemble. Instead, the method was designed to generate structural ensembles from which the single lowest free energy ensemble is identified as representative of the native folding of the loop. To find the native ensemble a successive series of SCV‐MC simulations are carried out to allow the loops to undergo structural changes in a controlled manner. To increase the chances of finding the native funnel for the loop, some of the SCV‐MC simulations are carried out at elevated temperatures. The native ensemble can be identified by an MC search starting from any conformation already in the native funnel. The hypothesis is that native structures are trapped in the conformational space because of the high‐energy barriers that surround the native funnel. The existence of such ensembles is demonstrated by generating multiple copies of the loops from their crystal structures in rhodopsin and carrying out an extended SCV‐MC search. For the extracellular loops e1 and e3, and the intracellular loop i1 that were used in this work, the procedure resulted in dense clusters of structures with Cα‐RMSD ∼0.5 Å. To test the predictive power of the method the crystal structure of each loop was replaced by its extended conformations. For e1 and i1 the procedure identifies native clusters with Cα‐RMSD ∼0.5 Å and good structural overlap of the side chains; for e3, two clusters were found with Cα‐RMSD ∼1.1 Å each, but with poor overlap of the side chains. Further searching led to a single cluster with lower Cα‐RMSD but higher energy than the two previous clusters. This discrepancy was found to be due to the missing elements in the constructs available from experiment for use in the calculations. Because this problem will likely appear whenever parts of the structural information are missing, possible solutions are discussed. Proteins 2006. © 2006 Wiley‐Liss, Inc.
Züchtung von dreidimensionalen Knorpeltransplantaten
Authors: Martin
Published: May 2006

Durch die Ex-vivo-Züchtung von Knorpelgewebe mit vordefinierten Formen aus autologen Zellen wird orthopädischen Chirurgen die Möglichkeit gegeben, Knorpelverletzungen mit funktionellen Transplantaten zu versorgen. Trotz der erzielten Fortschritte bei der Generierung und Validierung von aus tierischen Vorläuferzellen gezüchtetem Knorpel steht man jedoch bei der Übertragung dieser Ergebnisse auf humane Chondrozyten weiterhin vor zahlreichen Herausforderungen. Ziel dieser Übersichtsarbeit ist es, die Notwendigkeit einer hoch interdisziplinären Vorgehensweise aufzuzeigen, um gezüchtete Knorpeltransplantate effektiv in den klinischen Alltag einzuführen. Neben Fragestellungen im Hinblick auf die Chondrozytenbiologie, die Eigenschaften von porösen dreidimensionalen Gerüsten und die Anwendung physikalischer Stimuli wird auch die Entwicklung ökonomischer und praktikabler Herstellungssysteme erörtert.
Wie reagiert das Gehirn auf Konflikt und Irrtum?
Authors: Mager  , Falkenstein
Published: May 2006

In der Informationsverarbeitung des menschlichen Gehirns besteht eine wesentliche adaptive Funktion darin, aktuelle Kognitionen und Geschehnisse zu erfassen und in der Folge das Verhalten so anzupassen, dass das Individuum möglichst zielgerichtet handeln kann und keinen Schaden erleidet. In den letzten Jahren konnten über verschiedene experimentelle Zugänge vorwiegend präfrontale Strukturen als Kandidaten für eine solche Supervisionstätigkeit identifiziert werden. Zum einen führen konflikthafte oder widersprüchliche Informationen zu einer Aktivierung dieser Strukturen, zum anderen wird eine Aktivierung bevorzugt dann gesehen, wenn eine Erwartung durch die eintretende Realität widerlegt wird (Irrtum). Diese Supervisionszentren üben neben der Detektion von Konflikt und Irrtum eine Kontrollfunktion aus. Dabei nehmen sie Einfluss auf laufende Kognitionen und leiten notwendige Handlungsveränderungen ein, um effizienter agieren zu können. Diese Prozesse laufen zum Teil unbewusst ab, sodass die Forschung hier heute einen Zugang zu «vor- bzw. unbewussten» Kognitionen hat. Dieser Zugang wird zunehmend zur Erforschung psychiatrischer und neurologischer Erkrankungen genutzt.
Hörverlust nach Myelographie
Authors: Schiffer  , Podvinec  , Hasler
Published: May 2006

Hörverlust ist eine mögliche Folge der Myelographie. Wir beschreiben einen beidseitigen Hörverlust von –60 dB, der sich nach einem epiduralen Blutpatch vollständig erholte. Bei einem Hörverlust oder Tinnitus in Assoziation mit einem möglichen Liquorverlust nach einer Punktion des lumbalen Duralsackes zu diagnostischen oder therapeutischen Zwecken ist der epidurale Blutpatch die heute empfohlene therapeutische Option.
Source and transport of terrigenous organic matter in the upper Yukon River: Evidence from isotope (δ13C, Δ14C, and δ15N) composition of dissolved, colloidal, and particulate phases
Authors: Guo Laodong , Macdonald Robie W.
Published: May 2006

Natural organic matter was collected from the upper Yukon River and size fractionated into the <1 kDa low‐molecular‐weight dissolved (LMW‐DOC), colloidal (COC, 1 kDa to 0.45 μm) and particulate organic carbon (POC, >0.45 μm) phases for characterization of elemental (C and N) and isotopic (13C, 14C and 15N) composition to examine their sources and transport. Concentrations of total organic carbon (TOC) decreased from 3010 μM in mid‐May to 608 μM in September, accompanying an increase in river water δ18O from the snowmelt to summer and early fall. COC was the predominant OC species, comprising, on average, 63 ± 8% of the TOC, with 23 ± 5% partitioned in the LMW‐DOC and 14 ± 5% in the POC fraction. Annual riverine export flux to the ocean was 2.02 × 1012 g‐C for TOC, 7.66 × 1010 g‐N for total organic nitrogen (TON), and 3.53 × 1012 g‐C for dissolved inorganic carbon (DIC), respectively. The C/N molar ratios were distinctly different between colloidal organic matter (COM, 46 ± 3) and particulate organic matter (POM, 15 ± 1.4). Similar δ13C values were found for LMW‐DOM (−27.9 ± 0.5‰), COM (−27.4 ± 0.2‰), and POM (−26.2 ± 0.7‰), although there was a general increase with increasing size, suggesting a common terrigenous organic source. In contrast, distinct Δ14C values were found for LMW‐DOC (−155 to +91‰), COC (40 to 140‰), and POC (−467 to −253‰) with a decreasing trend from snowmelt to ice‐open season, suggesting that turnover pathways and transport mechanisms vary with organic matter size fractions. The high abundance of COC and its contemporary 14C ages points to a predominant source from modern terrestrial primary production, likely from the leaching/decomposition of fresh plant litter in the upper soil horizon. The predominately old POC (average 3698 ± 902 years B.P.), in contrast, was largely derived from riverbank erosion and melting of permafrost. These results imply that ice‐opening Yukon River flows are dominated by snowmelt (low δ18O) with high DOC (high Δ14C) but low DIC and Si(OH)4 concentrations, whereas late summer flows contain more products of permafrost or ice melt and rain (high δ18O), with low DOC (low Δ14C) but high DIC and Si(OH)4 concentrations. A warming climate with a deeper permafrost active layer in the Yukon River watershed would enhance the mobilization and export of old terrestrial OC, but largely in the particulate form into the Bering Sea and Arctic Ocean.
Solar flare signatures of the ionospheric GPS total electron content
Authors: Liu J. Y. , Lin C. H. , Chen Y. I. , Lin Y. C. , Fang T. W. , Chen C. H. , Chen Y. C. , Hwang J. J.
Published: May 2006

In this study, ionospheric solar flare effects on the total electron content (TEC) and associated time rate of change (rTEC) derived from ground‐based global positioning system (GPS) receivers in the midday region are examined. The occurrence times and locations of 11 solar flares are isolated from the 1–8 Å X‐ray radiations of the geosynchronous operational environmental satellite (GOES) and the SOHO Extreme Ultraviolet Imaging Telescope (EIT) images, respectively, while the TEC and rTEC are obtained from the international GPS services (IGS). Results show that the maximum value of the TEC increase solely depends on the flare class, while the maximum value of the rTEC increase is related to not only the flare class but also the time rate of change in flare radiations. A statistical analysis further demonstrates that the two maximum values are inversely proportional to the cosine of the great circle angle between the center and flare locations on the solar disc.
Major geomagnetic storms (Dst ≤ −100 nT) generated by corotating interaction regions
Authors: Richardson I. G. , Webb D. F. , Zhang J. , Berdichevsky D. B. , Biesecker D. A. , Kasper J. C. , Kataoka R. , Steinberg J. T. , Thompson B. J. , Wu C.‐C. , Zhukov A. N.
Published: May 2006

Seventy‐nine major geomagnetic storms (minimum Dst ≤ −100 nT) observed in 1996 to 2004 were the focus of a “Living with a Star” Coordinated Data Analysis Workshop (CDAW) in March 2005. In nine cases, the storm driver appears to have been purely a corotating interaction region (CIR) without any contribution from coronal mass ejection‐related material (interplanetary coronal mass ejections (ICMEs)). These storms were generated by structures within CIRs located both before and/or after the stream interface that included persistently southward magnetic fields for intervals of several hours. We compare their geomagnetic effects with those of 159 CIRs observed during 1996–2005. The major storms form the extreme tail of a continuous distribution of CIR geoeffectiveness which peaks at Dst ∼ −40 nT but is subject to a prominent seasonal variation of ∼40 nT which is ordered by the spring and fall equinoxes and the solar wind magnetic field direction toward or away from the Sun. The O'Brien and McPherron (2000) equations, which estimate Dst by integrating the incident solar wind electric field and incorporating a ring current loss term, largely account for the variation in storm size. They tend to underestimate the size of the larger CIR‐associated storms by Dst ∼ 20 nT. This suggests that injection into the ring current may be more efficient than expected in such storms. Four of the nine major storms in 1996–2004 occurred during a period of less than three solar rotations in September to November 2002, also the time of maximum mean IMF and solar magnetic field intensity during the current solar cycle. The maximum CIR‐storm strength found in our sample of events, plus additional 23 probable CIR‐associated Dst ≤ −100 nT storms in 1972–1995, is (Dst = −161 nT). This is consistent with the maximum storm strength (Dst ∼ −180 nT) expected from the O'Brien and McPherron equations for the typical range of solar wind electric fields associated with CIRs. This suggests that CIRs alone are unlikely to generate geomagnetic storms that exceed these levels.
Simulation and analysis of secondary organic aerosol dynamics in the South Coast Air Basin of California
Authors: Vutukuru Satish , Griffin Robert J. , Dabdub Donald
Published: May 2006

The dynamics of secondary organic aerosol (SOA) formation are analyzed using a species‐resolved SOA model for the South Coast Air Basin of California (SoCAB). Updated versions of the Caltech Atmospheric Chemistry Mechanism (CACM) and the Model to Predict the Multiphase Partitioning of Organics (MPMPO) are integrated with the CIT airshed model. The simulations are performed using input data from the 8–9 September 1993 episode. Results show that urban areas with major volatile organic compound (VOC) emission sites experience peaks in SOA levels during morning hours. Downwind locations, such as Azusa and Claremont, experience sustained levels of high SOA concentrations in comparison with coastal areas such as central Los Angeles and Long Beach. Concentrations of condensible organics are higher in inland locations compared to those in coastal locations because of high oxidation capacity and transport of pollutants. Furthermore, SOA constitutes up to 30% of simulated organic particulate matter at inland locations, with maximum contributions occurring during afternoon hours. Anthropogenic sources contribute over 90% of simulated SOA at most locations in the basin. Oxidation products of aromatic compounds from anthropogenic sources constitute over 70% of total simulated SOA. Sensitivity runs indicate strong dependence of SOA on VOC emissions and temperature. Overall, model predictions are in qualitative agreement with recent observations in the SoCAB.
Transient thermal response in ocean bottom pressure measurement
Authors: Hirata Kenji , Baba Toshitaka
Published: May 2006

Offshore ocean bottom pressures usually follow ocean tidal motion but sometimes deviate from it even when no tsunami occurs. Numerous observations suggest that such deviations highly correlate with sudden temperature changes, probably due to irregular deep ocean currents, around the pressure gauges regardless of static temperature compensation mechanism. We ascribe this deviation to the transient thermal response of the pressure gauges, which produce apparent pressure fluctuations when temperature change quickly so that temperature equilibrium condition of two quartz transducers is not valid. We put forward an empirical method to estimate the transient thermal response correctly. Such rapid temperature change may have to be corrected for a robust tsunami warning based on offshore tsunami observation with pressure gauges.
Area-scan camera for terahertz holography
Authors: Crawley David , Withington Stafford , Obradovic Jelena
Published: May 2006

Terahertz technology has shown great promise in recent years with a large number of applications being demonstrated, as well improvements in detectors, sources, imaging schemes. Many of the proposed applications, however, will require compact imaging systems that have the capability to capture two- or three-dimensional images. We propose an area-scan configuration that has the potential to meet this need that could be used to generate three-dimensional images through holographic techniques. We present data that verify the feasibility of our scheme.
Bond-orientational analysis of hard-disk and hard-sphere structures
Authors: Senthil Kumar V. , Kumaran V.
Published: May 2006

We report the bond-orientational analysis results for the thermodynamic, random, and homogeneously sheared inelastic structures of hard-disks and hard-spheres. The thermodynamic structures show a sharp rise in the order across the freezing transition. The random structures show the absence of crystallization. The homogeneously sheared structures get ordered at a packing fraction higher than the thermodynamic freezing packing fraction, due to the suppression of crystal nucleation. On shear ordering, strings of close-packed hard-disks in two dimensions and close-packed layers of hard-spheres in three dimensions, oriented along the velocity direction, slide past each other. Such a flow creates a considerable amount of fourfold order in two dimensions and body-centered-tetragonal (bct) structure in three dimensions. These transitions are the flow analogs of the martensitic transformations occurring in metals due to the stresses induced by a rapid quench. In hard-disk structures, using the bond-orientational analysis we show the presence of fourfold order. In sheared inelastic hard-sphere structures, even though the global bond-orientational analysis shows that the system is highly ordered, a third-order rotational invariant analysis shows that only about 40% of the spheres have face-centered-cubic (fcc) order, even in the dense and near-elastic limits, clearly indicating the coexistence of multiple crystalline orders. When layers of close-packed spheres slide past each other, in addition to the bct structure, the hexagonal-close-packed (hcp) structure is formed due to the random stacking faults. Using the Honeycutt-Andersen pair analysis and an analysis based on the 14-faceted polyhedra having six quadrilateral and eight hexagonal faces, we show the presence of bct and hcp signatures in shear ordered inelastic hard-spheres. Thus, our analysis shows that the dense sheared inelastic hard-spheres have a mixture of fcc, bct, and hcp structures.
Real time scanning force microscopy observation of a structural phase transition in self-assembled alkanethiols
Authors: Munuera C. , Ocal C.
Published: May 2006

We present here a new approach based on high resolution scanning force microscopy that permits molecular determination and frictional discrimination between coexisting molecular configurations of alkanethiols on Au(111). The method has allowed visualizing in real time a phase transition between two differently ordered self-assembled configurations, which spontaneously takes place with time at constant coverage and under ambient conditions. Frictional force measurements indicate that the molecular rearrangement observed occurs via an order-disorder-order process.
Free volume hypothetical scanning molecular dynamics method for the absolute free energy of liquids
Authors: White Ronald P. , Meirovitch Hagai
Published: May 2006

The hypothetical scanning (HS) method is a general approach for calculating the absolute entropy, S, and free energy, F, by analyzing Boltzmann samples obtained by Monte Carlo (MC) or molecular dynamics (MD) techniques. With HS applied to a fluid, each configuration i of the sample is reconstructed by gradually placing the molecules in their positions at i using transition probabilities (TPs). With our recent version of HS, called HSMC-EV, each TP is calculated from MC simulations, where the simulated particles are excluded from the volume reconstructed in previous steps. In this paper we remove the excluded volume (EV) restriction, replacing it by a “free volume” (FV) approach. For liquid argon, HSMC-FV leads to an improvement in efficiency over HSMC-EV by a factor of 2–3. Importantly, the FV treatment greatly simplifies the HS implementation for liquids, allowing a much more natural application of the method for MD simulations. Given the success and popularity of MD, the present development of the HSMD method for liquids is an important advancement for HS methodology. Results for the HSMD-FV approach presented here agree well with our HSMC and thermodynamic integration results. The efficiency of HSMD-FV is equivalent to HSMC-EV. The potential use of HSMC(MD)-FV in protein systems with explicit water is discussed.