bluuebunny/crossref_metadata_2025 huggingface dataset:
Cell plasticity in homeostasis and regeneration
Authors: Galliot Brigitte , Ghila Luiza
Published: July 2010

Over the past decades, genetic analyses performed in vertebrate and invertebrate organisms deciphered numerous cellular and molecular mechanisms deployed during sexual development and identified genetic circuitries largely shared among bilaterians. In contrast, the functional analysis of the mechanisms that support regenerative processes in species randomly scattered among the animal kingdom, were limited by the lack of genetic tools. Consequently, unifying principles explaining how stress and injury can lead to the reactivation of a complete developmental program with restoration of original shape and function remained beyond reach of understanding. Recent data on cell plasticity suggest that beside the classical developmental approach, the analysis of homeostasis and asexual reproduction in adult organisms provides novel entry points to dissect the regenerative potential of a given species, a given organ or a given tissue. As a clue, both tissue homeostasis and regeneration dynamics rely on the availability of stem cells and/or on the plasticity of differentiated cells to replenish the missing structure. The freshwater Hydra polyp provides us with a unique model system to study the intricate relationships between the mechanisms that regulate the maintenance of homeostasis, even in extreme conditions (starvation and overfeeding) and the reactivation of developmental programs after bisection or during budding. Interestingly head regeneration in Hydra can follow several routes according to the level of amputation, suggesting that indeed the homeostatic background dramatically influences the route taken to bridge injury and regeneration. Mol. Reprod. Dev. 77:837–855, 2010. © 2010 Wiley‐Liss, Inc.
Superselective pseudocontinuous arterial spin labeling
Authors: Helle Michael , Norris David G. , Rüfer Susanne , Alfke Karsten , Jansen Olav , van Osch Matthias J. P.
Published: July 2010

A new technique for the imaging of flow territories of individual extra‐ and intracranial arteries is presented. The method is based on balanced pseudocontinuous arterial spin labeling but employs additional time‐varying gradients in between the radiofrequency pulses of the long labeling train. The direction of the additional gradient vector is perpendicular to the selected artery and its azimuthal angle is switched after every radiofrequency pulse. The phases of the radiofrequency pulses are adopted to cancel out the phase accrual of the spins at the center of the target vessel due to the extra applied gradients. This results in efficient inversion at the targeted position, whereas elsewhere time‐varying phase changes will result in marginal inversion efficiency. By changing the moment of the added gradients, the size of the labeling focus can be adjusted. Influence of the temporal order of the additional gradients on the labeling efficiency and on the selectivity was investigated by simulations and experimental measurements. In a volunteer study, the acquisition of high signal‐to‐noise ratio flow territory images of small branches of the anterior cerebral artery distal to the circle of Willis was demonstrated. This shows the method's flexibility for dealing with complicated arterial geometries and its ability to superselectively label small intracranial arteries. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Chemical shift–based water/fat separation: A comparison of signal models
Authors: Hernando Diego , Liang Zhi‐Pei , Kellman Peter
Published: July 2010

Quantitative water/fat separation in MRI requires careful modeling of the acquired signal. Multiple signal models have been proposed in recent years, but their relative performance has not yet been established. This article presents a comparative study of 12 signal models for quantitative water/fat separation. These models were selected according to three main criteria: magnitude or complex fitting, use of single‐peak or multipeak fat spectrum, and modeling of T decay. The models were compared based on an analysis of the bias and standard deviation of their resulting estimates. Results from theoretical analysis, simulation, phantom experiments, and in vivo data were in good agreement. These results show that (a) complex fitting is uniformly superior to magnitude fitting, (b) multipeak fat modeling is able to remove the bias present in single‐peak fat modeling, and (c) a single‐T model performs best over a range of clinically relevant signal‐to‐noise ratios (SNRs) and water/fat ratios. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Longitudinal tracking of human dendritic cells in murine models using magnetic resonance imaging
Authors: Briley‐Saebo Karen C. , Leboeuf Marylene , Dickson Stephen , Mani Venkatesh , Fayad Zahi A. , Karolina Palucka A. , Banchereau Jacques , Merad Miriam
Published: July 2010

Ex vivo generated dendritic cells are currently used to induce therapeutic immunity in solid tumors. Effective immune response requires dendritic cells to home and remain in lymphoid organs to allow for adequate interaction with T lymphocytes. The aim of the current study was to detect and track Feridex labeled human dendritic cells in murine models using magnetic resonance imaging. Human dendritic cells were incubated with Feridex and the effect of labeling on dendritic cells immune function was evaluated. Ex vivo dendritic cell phantoms were used to estimate sensitivity of the magnetic resonance methods and in vivo homing was evaluated after intravenous or subcutaneous injection. R2*‐maps of liver, spleen, and draining lymph nodes were obtained and inductively coupled plasma mass spectrometry or relaxometry methods were used to quantify the Feridex tissue concentrations. Correlations between in vivo R2* values and iron content were then determined. Feridex labeling did not affect dendritic cell maturation or function. Phantom results indicated that it was possible to detect 125 dendritic cells within a given slice. Strong correlation between in vivo R2* values and iron deposition was observed. Importantly, Feridex‐labeled dendritic cells were detected in the spleen for up to 2 weeks postintravenous injection. This study suggests that magnetic resonance imaging may be used to longitudinally track Feridex‐labeled human dendritic cells for up to 2 weeks after injection. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Visualization of inert gas wash‐out during high‐frequency oscillatory ventilation using fluorine‐19 MRI
Authors: Wolf Ursula , Scholz Alexander , Terekhov Maxim , Koebrich Rainer , David Matthias , Schreiber Laura Maria
Published: July 2010

High‐frequency oscillatory ventilation is looked upon as a lung‐protective ventilation strategy. For a further clarification of the physical processes promoting gas transport, a visualization of gas flow and the distribution of ventilation are of considerable interest. Therefore, fluorine‐19 magnetic resonance imaging of the imaging gas octafluorocyclobutane (C4F8) during high‐frequency oscillatory ventilation was performed in five healthy pigs. For that, a mutually compatible ventilation‐imaging system was set up and transverse images were acquired every 5 sec using FLASH sequences on a 1.5 T scanner. Despite a drop in signal‐to‐noise ratio after the onset of high‐frequency oscillatory ventilation, for each pig, the four experiments could be analyzed. A mean wash‐out time (τ) at 5 Hz of 52.7 ± 18 sec and 125.9 ± 39 sec at 10 Hz, respectively, were found for regions of interest including the whole lung. This is in agreement with the clinical findings, in that wash‐out of respiratory gases is significantly prolonged for increased high‐frequency oscillatory ventilation frequencies. Our study could be a good starting‐point for a further optimization of high‐frequency oscillatory ventilation. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Measurement of N‐acetylaspartylglutamate in the human frontal brain by 1H‐MRS at 7 T
Authors: Choi Changho , Ghose Subroto , Uh Jinsoo , Patel Aditya , Dimitrov Ivan E. , Lu Hanzhang , Douglas Deborah , Ganji Sandeep
Published: July 2010

N‐Acetylaspartylglutamate in human brain has been measured with difference editing at 7 T. The CH2 proton resonances (∼2.5 ppm) of the aspartyl groups of N‐acetylaspartylglutamate and N‐acetylaspartate were difference edited (MEGA) using 20‐msec gaussian radiofrequency pulses for selective 180° rotations of the coupling partners at 4.61 and 4.38 ppm, respectively. The echo time of the editing sequence, 108 msec, was obtained in phantom tests. Single‐voxel localized in vivo measurements were conducted in the medial prefrontal and right frontal cortices of five healthy volunteers. The gray and white matter fractions within the voxels were obtained from T1‐weighted image segmentation. Using linear regression of the metabolite concentration vs. fractional white matter contents within the voxels, the N‐acetylaspartylglutamate‐to‐N‐acetylaspartate concentration ratios in gray and white matter were estimated to be 0.13 and 0.28 by difference editing (95% confidence intervals 0.07–0.19 and 0.22–0.34), respectively, assuming identical relaxation effects between the metabolites. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Comparison of spectral fitting methods for overlapping J‐coupled metabolite resonances
Authors: Gonenc A. , Govind V. , Sheriff S. , Maudsley A. A.
Published: July 2010

There is increasing interest in the use of two‐dimensional J‐resolved spectroscopic acquisition (multiecho) methods for in vivo proton magnetic resonance spectroscopy due to the improved discrimination of overlapping J‐coupled multiplet resonances that is provided. Of particular interest is the potential for discrimination of the overlapping resonances of glutamate and glutamine. In this study, a new time‐domain parametric spectral model that makes use of all available data is described for fitting the complete two‐dimensional multiecho data, and the performance of this method was compared with fitting of one‐dimensional spectra obtained following averaging multiecho data (echo time‐averaged) and single‐echo time PRESS (Point Resolved Spectroscopy) acquired spectra. These methods were compared using data obtained from a phantom containing typical brain metabolites and a human brain. Results indicate that improved performance and accuracy is obtained for the two‐dimensional acquisition and spectral fitting model. Magn Reson Med, 2010. © 2010 Wiley‐Liss, Inc.
Adaptive finite element approximation of multiphysics problems: A fluid–structure interaction model problem
Authors: Bengzon Fredrik , Larson Mats G.
Published: July 2010

In this paper we consider finite element simulation of the mechanical response of an elastic solid immersed into a viscous incompressible fluid flow. For simplicity, we assume that the mechanics of the solid is governed by linear elasticity and the motion of the fluid by the Stokes equation. For this one‐way coupled multiphysics problem we derive ana posteriorierror estimate using duality techniques. Based on the estimate we propose an adaptive algorithm that automatically constructs a suitable mesh for the fluid and solid computational domains given a specific goal quantity for the elastic problem. Copyright © 2010 John Wiley & Sons, Ltd.
Variational surface reconstruction based on Delaunay triangulation and graph cut
Authors: Wan Min , Wang Yu , Wang Desheng
Published: July 2010

A novel method for surface reconstruction from an unorganized point set is presented. An energy functional based on a weighted minimal surface model is proposed for surface reconstruction, which is efficiently minimized by graph cut methods. By solving the minimization problem on the graph dual to a Delaunay‐based tetrahedral mesh, the advantages of explicit and implicit methods for surface reconstruction are well integrated. A triangular surface mesh homeomorphic to the original surface can be extracted directly from the tetrahedral mesh provided a sufficient sampling density exists. Difficult cases involving undersampling, non‐uniformity, noises and topological complexities can be handled effectively as well. Furthermore, for the first time, multi‐phase surface reconstruction is realized based on the graph cut methods. Various examples are included for demonstrating the efficiency and effectiveness of the proposed method. Copyright © 2010 John Wiley & Sons, Ltd.
Tailoring unstructured meshes for use with a 3D time domain co‐volume algorithm for computational electromagnetics
Authors: Xie Z. Q. , Hassan O. , Morgan K.
Published: July 2010

The Yee algorithm is a highly efficient time domain co‐volume method for computational electromagnetics using a pair of staggered orthogonal cartesian meshes. An equivalent unstructured mesh process is readily implemented on a primal Delaunay tetrahedral mesh and its orthogonal Voronoï dual. The difficulty, for practical applications, is ensuring that both the Delaunay and the Voronoï meshes possess the necessary properties to enable an accurate and efficient solution to be obtained by this approach. This is a mesh generation problem and it is addressed here by using a combination of a point distribution provided by an ideal tetrahedral mesh, a constrained centroidal Voronoï tessellation method and a mesh quality optimization procedure. For the selected application area of electromagnetic wave scattering problems, the computational efficiency is enhanced by using a hybrid primal mesh, consisting of tetrahedral elements in the vicinity of the scatterer and hexahedral elements elsewhere. Three examples are included to demonstrate the viability of the proposed approach and to indicate the numerical performance that can be achieved. Copyright © 2010 John Wiley & Sons, Ltd.
Study on elastic modulus of crosslinked polyurethane/organoclay nanocomposites
Authors: Joulazadeh Mehrnaz , Navarchian Amir. H.
Published: July 2010

In this paper, two polyurethane/clay nanocomposite systems with crosslinked structure were synthesized via in situ polymerization of a polyether‐ as well as a polyester‐based prepolymer with methylene‐bis‐ortho‐chloroanilline (MOCA). Two types of modified clays with different organic modifiers were used in order to see the effect of compatibility between polymer matrix and clays on elastic modulus of nanocomposites. The morphology and the dispersion of clay layers in polyurethanes have been characterized by X‐ray diffraction (XRD) and microscopic techniques. The changes of elastic modulus of nanocomposites with clay content were examined and compared with those predicted by some conventional composite models. The results showed a reasonable fitting of experimental and theoretical values only at very low clay contents. As the clay content exceeds 1.5 wt% in this system, a reduction in elastic modulus was experimentally observed due to insufficient dispersion degree of silicate layers throughout the crosslinked matrix. This behavior was not predicted with the conventional composite theories. A new model on the basis of Wu model was then developed in order to predict the reduction of elastic modulus at various clay contents in crosslinked PU matrix. This model fitted reasonably the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.
Sam68 up‐regulation correlates with, and its down‐regulation inhibits, proliferation and tumourigenicity of breast cancer cells
Authors: Song Libing , Wang Lan , Li Yun , Xiong Huaping , Wu Jueheng , Li Jun , Li Mengfeng
Published: July 2010

The biosynthesis and metabolism of RNA play important roles in regulating gene expression. On the other hand, it has been shown that RNA expression profiling is differentially distinct between cancer and normal cells, suggesting the possibility that aberrant regulation of RNA metabolism might be associated with the development and progression of cancer. In the current study, we found that Sam68, an RNA‐binding protein that links cellular signalling to RNA processing, was markedly overexpressed in breast cancer cells and tissues. Immunohistochemical analysis showed that the expression and cytoplasmic localization of Sam68 significantly correlated with clinical characteristics of patients, including clinical stage, tumour‐nodule‐metastasis (TNM) classification, histological grade, and ER expression. Univariate and multivariate analyses showed that the expression level and cytoplasmic localization of Sam68 were identified as independent prognostic factors. Furthermore, we found that siRNA knockdown of endogenous Sam68 inhibited cell proliferation and tumourigenicity of breast cancer cells in vitro, through blocking the G1 to S phase transition. Moreover, we demonstrated that the anti‐proliferative effect of silencing Sam68 on breast cancer cells was associated with up‐regulation of cyclin‐dependent kinase inhibitor p21Cip1 and p27Kip1, enhanced transactivation of FOXO factors, and attenuation of Akt/GSK‐3β signalling. Taken together, our results suggest that Sam68 might play an important role in promoting the proliferation and carcinogenesis of human breast cancer, and thereby might be a novel and useful prognostic marker and a potential target for human breast cancer treatment. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Assessment of the influence of different sample processing and cold storage duration on plant free proline content analyses
Authors: Teklić Tihana , Špoljarević Marija , Stanisavljević Aleksandar , Lisjak Miroslav , Vinković Tomislav , Parađiković Nada , Andrić Luka , Hancock John T.
Published: July 2010

Introduction – A method which is widely accepted for the analysis of free proline content in plant tissues is based on the use of 3% sulfosalicylic acid as an extractant, followed by spectrophotometric quantification of a proline–ninhydrin complex in toluene. However, sample preparation and storage may influence the proline actually measured. This may give misleading or difficult to compare data.

Objective and Methodology – To evaluate free proline levels fresh and frozen strawberry (Fragaria × ananassa Duch.) leaves and soybean [Glycine max (L.) Merr.] hypocotyl tissues were used. These were ground with or without liquid nitrogen and proline extracted with sulfosalicylic acid. A particular focus was the influence of plant sample cold storage duration (1, 4 and 12 weeks at −20°C) on tissue proline levels measured.

Results – The free proline content analyses, carried out in leaves of Fragaria × ananassa Duch. as well as in hypocotyls of Glycine max (L.) Merr., showed a significant influence of the sample preparation method and cold storage period. Long‐term storage of up to 12 weeks at −20°C led to a significant increase in the measured proline in all samples analysed.

Conclusion – The observed changes in proline content in plant tissue samples stored at −20°C indicate the likelihood of the over‐estimation of the proline content if the proline analyses are delayed. Plant sample processing and cold storage duration seem to have an important influence on results of proline analyses. Therefore it is recommended that samples should be ground fresh and analysed immediately. Copyright © 2010 John Wiley & Sons, Ltd.
Preimplantation genetic diagnosis in Saudi Arabia: parents' experience and attitudes
Authors: Alsulaiman Ayman , Al‐Odaib Ali , Rijjal Al , Hewison Jenny
Published: July 2010

Background

Preimplantation genetic diagnosis (PGD) has been proposed as an alternative to prenatal diagnosis (PND). This study compares the attitudes towards PGD of four groups of parents in Saudi Arabia: two groups at genetic risk for different conditions but with no experience of PGD procedures and two groups who had experience, either of PGD or of in vitro fertilisation (IVF) for infertility.

Methods

One hundred and eighty four participants attending the King Faisal Specialist Hospital and Research Centre (KFSH&RC) in Riyadh were interviewed using a semi‐structured questionnaire: 49 had children affected by a haemoglobin disorder, 48 had children with non‐syndromic deafness, 37 were attending the PGD service and 50 were attending IVF services for infertility.

Results

Opinions in the two genetic groups were very similar: families were enthusiastic about PGD and relatively unconcerned about its technical limitations or the desirability of a confirmatory PND. The technical limitations of PGD and the moral status of embryos were of greatest concern to the PGD group. Waiting for the pregnancy result was the most commonly mentioned concern in the PGD and IVF groups.

Conclusion

PGD might be considered for a range of conditions in Saudi Arabia. However, it is not an easy option, and couples must be selected and counselled appropriately. Copyright © 2010 John Wiley & Sons, Ltd.
A quantitative evaluation of the regulatory assessment of the benefits and risks of rofecoxib relative to naproxen: an application of the incremental net‐benefit framework
Authors: Lynd Larry D. , Marra Carlo A. , Najafzadeh Mehdi , Sadatsafavi Mohsen
Published: July 2010

Purpose

To undertake a quantitative benefit–risk analysis of rofecoxib relative to naproxen using an incremental net‐benefit (INB) analysis from the societal perspective, using the same data evaluated by the Health Canada and US FDA expert advisory panels.

Methods

We developed a discrete event simulation model to calculate the INB of rofecoxib relative to naproxen in arthritis patients over a 1‐year time horizon. All outcomes were weighted using societal utilities for each health state which facilitated the use of quality‐adjusted life years (QALYs) as the outcome. Probability distributions were incorporated for each model parameter to facilitate a probabilistic analysis using second‐order Monte Carlo simulation.

Results

In the base case analysis, the mean INB (SD) of rofecoxib relative to naproxen was 0.0002 (0.415) QALYs per patient over 12 months of treatment, or 0.2 QALYs per 1000 patients treated. The probabilistic sensitivity analysis resulted in a mean INB of 0.0022 QALYs (95%CI −0.0005, 0.0051). Overall, the INB associated with rofecoxib relative to naproxen was ≥0 in 94% of the iterations of the model.

Conclusions

This analysis illustrates the application of the incremental net‐benefit framework to quantitative benefit–risk evaluation, and suggests that the potential benefits of rofecoxib outweigh the potential harms relative to naproxen over 1 year from the societal perspective under the assumptions of this model. Copyright © 2010 John Wiley & Sons, Ltd.
Linking a pharmaceutical claims database with a birth defects registry to investigate birth defect rates of suspected teratogens
Authors: Colvin Lyn , Slack‐Smith Linda , Stanley Fiona J. , Bower Carol
Published: July 2010

Purpose

Data linkage of population administrative data is being investigated as a tool for pharmacovigilance in pregnancy in Australia. Records of prescriptions of known or suspected teratogens dispensed to pregnant women have been linked to a birth defects registry to determine if defects associated with medicine exposure can be detected.

Methods

The Pharmaceutical Benefits Scheme is a national claims database that has been linked with population‐based data to extract linkages for women with a pregnancy event in Western Australia from 2002 to 2005 (n = 106 074). Records of births to the women who were dispensed medicines in categories D or X of the Australian ADEC pregnancy risk category were linked to the Birth Defects Registry of Western Australia. Population rates of registered birth defects per 1000 births were calculated for each medicine.

Results

There were 47 medicines dispensed at least once during pregnancy with 23 associated with a registered birth defect to a woman dispensed the medicine. When the birth defect rate for each medicine was compared with the rate for all other women not dispensed that medicine, most medicines showed an increased risk. Medicines with the higher risks were medroxyprogesterone acetate (OR: 1.8; 95%CI: 1.4–2.3), follitropin alfa (OR: 2.5; 95%CI: 1.2–5.0), carbamazepine (OR: 3.1; 95%CI: 1.7–5.6) and enalapril maleate (OR: 8.1; 95%CI: 1.6–41.7).

Conclusion

Many known associations between medicines and birth defects were identified, suggesting that linked administrative data could be an important means of pharmacovigilance in pregnancy in Australia. Copyright © 2010 John Wiley & Sons, Ltd.
Educational performance and attitudes toward school as risk‐protective factors for violence: A study of the Asian/Pacific Islander Youth Violence Prevention Center
Authors: Wegner Eldon L. , Garcia‐Santiago Orlando , Nishimura Stephanie T. , Hishinuma Earl S.
Published: July 2010

The purpose of this study was to examine whether school experiences, school performance, and other risk‐protective factors were related to violence among Hawaiian, Filipino, and Samoan youths residing in Hawai'i. This study analyzed survey data (N = 325) collected in three high schools having concentrations of Filipino, Hawaiian, and Samoan youths, as well as a smaller number of Japanese students, which served as a comparison group. The analyses consisted of bivariate and multivariate analyses of risk protection for violence. Two‐ and three‐way interactions were tested to examine whether there were specific gender and/or ethnic effects. The final model explained 29.3% of the variance in violent behavior. Five variables were significant: grade point average, pressure to choose between school and friends, favorable school attitude, feeling safe, and importance of college. Schools serving these populations should focus on fostering positive bonds between teachers and students and building bridges to families and neighborhoods. © 2010 Wiley Periodicals, Inc.
Comparison of correlates of classroom behavior problems in schools with and without a school‐wide character education program
Authors: Parker David C. , Nelson Jennifer S. , Burns Matthew K.
Published: July 2010

System‐wide practices in schools should diminish the occurrence of children's problem behavior that is deleterious to academic achievement. The current study examined the relationship between variables that affect classroom behavior and observed behavior in schools with and without a theoretically based character education program. Observational data from 12 elementary schools compared control and treatment conditions on classroom disruption, and examined the influences of class size and percentage of students receiving a free or reduced price lunch (FRL). Results showed a weaker relationship between class size, FRL, and behavior problems within the character education schools than in control schools and that the character education program may have had a stronger influence in schools with a high percentage of students eligible for FRL. © 2010 Wiley Periodicals, Inc.
Protecs, a comprehensive and powerful storage and analysis system for OMICS data, applied for profiling the anaerobiosis response of Staphylococcus aureus COL
Authors: Fuchs Stephan , Mehlan Henry , Kusch Harald , Teumer Alexander , Zühlke Daniela , Berth Matthias , Wolf Carmen , Dandekar Thomas , Hecker Michael , Engelmann Susanne , Bernhardt Jörg
Published: July 2010

Broad functional genomic studies call for comprehensive and powerful data repositories for storage of genome sequences, experimental information, protein identification data, protein properties and expression values. The better such data repositories can integrate and display complex data in a clear and structured way the more biologically meaningful conclusions or novel hypotheses can be derived from extensive omics data sets. This work presents the web accessible database system Protecs and how it was used to support analysis of 50 samples drawn from four Staphylococcus aureus cultivations under anaerobiosis. Protecs incorporates findings from visualization science, e.g. micro charts and heat maps in the user interface. Its integrated tools for expression data analysis in combination with TIGR Multi Experiment Viewer were used to highlight similar gene expression profiles in single or multiple experiments based on the continuously updated S. aureus master gel. Raw data analysis results are available online at www.protecs.uni‐greifswald.de. Our meta‐study revealed that S. aureus responds in different anaerobiotic experimental setups (growth without oxygen; growth without oxygen but with supplemental pyruvate and uracil; growth without oxygen but with NO; growth without oxygen but with NO and without functional nreABC genes) with a general anaerobiosis response. Among others, this response is characterized by an induction of fermentation enzymes (PflB, Ldh1, SACOL0135, SACOL0660) as well as the response regulator SrrA. Interestingly, especially genes with a high codon adaptation index highly overlap with anaerobically induced genes.
Shotgun proteome analysis utilising mixed mode (reversed phase‐anion exchange chromatography) in conjunction with reversed phase liquid chromatography mass spectrometry analysis
Authors: Phillips Helen L. , Williamson James C. , van Elburg Karin A. , Snijders Ambrosius P. L. , Wright Phillip C. , Dickman Mark J.
Published: July 2010

The 2‐D peptide separations employing mixed mode reversed phase anion exchange (MM (RP‐AX)) HPLC in the first dimension in conjunction with RP chromatography in the second dimension were developed and utilised for shotgun proteome analysis. Compared with strong cation exchange (SCX) typically employed for shotgun proteomic analysis, peptide separations using MM (RP‐AX) revealed improved separation efficiency and increased peptide distribution across the elution gradient. In addition, improved sample handling, with no significant reduction in the orthogonality of the peptide separations was observed. The shotgun proteomic analysis of a mammalian nuclear cell lysate revealed additional proteome coverage (2818 versus 1125 unique peptides and 602 versus 238 proteins) using the MM (RP‐AX) compared with the traditional SCX hyphenated to RP‐LC‐MS/MS. The MM analysis resulted in approximately 90% of the unique peptides identified present in only one fraction, with a heterogeneous peptide distribution across all fractions. No clustering of the predominant peptide charge states was observed during the gradient elution. The application of MM (RP‐AX) for 2‐D LC proteomic studies was also extended in the analysis of iTRAQ‐labelled HeLa and cyanobacterial proteomes using nano‐flow chromatography interfaced to the MS/MS. We demonstrate MM (RP‐AX) HPLC as an alternative approach for shotgun proteomic studies that offers significant advantages over traditional SCX peptide separations.
Analyzing protease specificity and detecting in vivo proteolytic events using tandem mass spectrometry
Authors: Gupta Nitin , Hixson Kim K. , Culley David E. , Smith Richard D. , Pevzner Pavel A.
Published: July 2010

Although trypsin remains the most commonly used protease in MS, other proteases may be employed for increasing peptide coverage or generating overlapping peptides. Knowledge of the accurate specificity rules of these proteases is helpful for database search tools to detect peptides, and becomes crucial when label‐free MS is used to discover in vivo proteolytic cleavages. Since in vivo cleavages are inferred by subtracting digestion‐induced cleavages from all observed cleavages, it is important to ensure that the specificity rule used to identify digestion‐induced cleavages are broad enough to capture even minor cleavages produced in digestion, to avoid erroneously identifying them as in vivo cleavages. In this study, we describe MS‐Proteolysis, a software tool for identifying putative sites of in vivo proteolytic cleavage using label‐free MS. The tool is used in conjunction with digestion by trypsin and three other proteases, whose specificity rules are revised and extended before inferring proteolytic cleavages. Finally, we show that comparative analysis of multiple proteases can be used to detect putative in vivo proteolytic sites on a proteome‐wide scale.
An Exploratory Study of Gender in Project Management: Interrelationships with Role, Location, Technology, and Project Cost
Authors: Henderson Linda S. , Stackman Richard W.
Published: July 2010

This study explores whether gender differences in project managers are related to gender differences in their team members. Gender differences are explored in the context of project managers’ and team members’ location to one another, the project team's use of technology, and the cost and size of the project teams. Using log-linear analysis of 563 project team members’ responses, several significant findings are reported-including the likelihood of same-gender project manager and team member dyads as well as gender differences in project contextual factors. Implications for organizational and project management researchers and decision makers conclude the article.
Complete basis set, hybrid‐DFT study and NBO interpretations of conformational behaviors of trans‐2,3‐ and trans‐2,5‐dihalo‐1,4‐dithianes
Authors: Nori‐Shargh Davood , Boggs James E.
Published: July 2010

The conformational behaviors of trans‐2,3‐dihalo‐1,4‐dithiane [halo = F (1), Cl (2), Br (3)] and trans‐2,5‐dihalo‐1,4‐dithiane [halo = F (4), Cl (5), Br (6)] have been analyzed by means of complete basis set CBS‐4, hybrid‐density functional theory (B3LYP/6‐311 + G**//B3LYP/6‐311 + G**) based methods, and natural bond orbital (NBO) interpretation. Both methods showed that the axial conformations of compounds 1–5 are more stable than their equatorial conformations but CBS‐4 resulted in an equatorial preference for compound 6. The Gibbs free energy difference (Geq−Gax) values (i.e., ΔGeq–ax) at 298.15 K and 1 atm between the axial and equatorial conformations decrease from compound 1 to compound 2 but increase from compound 2 to compound 3. Also, the calculated ΔGeq–ax values decrease from compound 4 to compound 6. The NBO analysis of donor–acceptor (LP → σ*) interactions showed that the anomeric effect (AE) increase from compound 1 to compound 3 and also from compound 4 to compound 6. On the other hand, the calculated dipole moment values between the axial and equatorial conformations [Δ(µeq−µax)] decrease from compound 1 to compound 3. The conflict between the increase of AE and the decrease of Δ(µeq−µax) values could explain the variation of the calculated ΔGeq–ax for compounds 1–3. The Gibbs free energy difference values between the axial and equatorial conformations (i.e., ΔGax–ax and ΔGeq–eq) of compounds 1 and 4, 2 and 5 and also 3 and 6 have been calculated. The correlations between the AE, bond orders, pairwise steric exchange energies (PSEE), ΔGeq–ax, ΔGax–ax, ΔGeq–eq, dipole–dipole interactions, structural parameters, and conformational behaviors of compounds 1–6 have been investigated. Copyright © 2010 John Wiley & Sons, Ltd.
Plasma Surface Modification of Polycarbonate and Poly(propylene) Substrates for Biomedical Electrodes
Authors: Pedrosa Paulo , Chappé Jean‐Marie , Fonseca Carlos , Machado Ana Vera , Nóbrega João Miguel , Vaz Filipe
Published: July 2010

The effects of surface plasma treatments on the properties of PP and PC substrates were studied. Main results showed that the 0.48 Pa Ar treatment promoted the most favorable changes: roughness increased from 15 to 17 nm for PC and from 12 to 30 nm for PP, while the CA lowered from 95° to 59° and from 87° to 35° for PC and PP, respectively. The effects of the activation treatment on adhesion were checked by depositing a thin layer of TiNx on both untreated and 0.48 Pa Ar plasma treated PC samples, and the adhesion to both substrates compared using the standard X‐cut tape test. The Ar activated samples displayed better adhesion of the TiNx film than the untreated ones, confirming the benefits of the surface changes induced by the plasma treatments.

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Risk Factors for Aspergillus Colonization and Allergic Bronchopulmonary Aspergillosis in Children With Cystic Fibrosis
Authors: Jubin Virginie , Ranque Stéphane , Stremler Le bel Nathalie , Sarles Jacques , Dubus Jean‐Christophe
Published: July 2010

Background

The annual prevalence of Aspergillus colonization (AC) and allergic bronchopulmonary aspergillosis (ABPA) has recently increased in pediatric patients with cystic fibrosis (CF). The reasons remain unclear although a number of factors have been suggested to be involved. This study was set up to investigate the association between potential predisposing factors, including new therapies recommended in CF, and the occurrence of AC or ABPA in children with CF.

Methods

The medical records of 85 children monitored regularly in the Pediatric Reference Centre for Cystic Fibrosis Care (RCCFC) of the University Hospital of Marseille (France) were analyzed from the first time they attended the RCCFC until either the occurrence of an end event, or their last visit to the RCCFC. Risk factors for AC or ABPA were analyzed by univariate and multivariate logistic regression.

Results

Eight children developed ABPA and 18 had AC. In univariate analysis, ABPA was significantly associated with RhDNase therapy, sensitization to Alternaria and Candida, and a low body mass index (BMI). Multivariate analysis identified an independent association between low BMI and ABPA (OR = 10.6, 95% CI [2.2–51.8], P = 0.004), and for the first time, between long‐term azithromycin therapy and AC (OR = 6.4, 95% CI [2.1–19.5], P = 0.001). This latter association might be explained by the inhibitory effect of azithromycin on both the recruitment and the activation of neutrophils, which represent the first‐line defenses against Aspergillus.

Conclusions

The risk factors associated with AC and ABPA in children with CF identified in this comprehensive exploratory study now need to be confirmed in further prospective studies. Pediatr. Pulmonol. 2010; 45:764–771. © 2010 Wiley‐Liss, Inc.
Improved gas exchange and survival after KL‐4 surfactant in newborn pigs with severe acute lung injury
Authors: Zimmermann Anna M. , Roberts Kari D. , Lampland Andrea L. , Meyers Patricia A. , Worwa Cathy T. , Plumm Brenda , Pacheco M. Cristina , Wolfson Marla R. , Mammel Mark C.
Published: July 2010

Objective

To determine the effectiveness of artificial surfactant therapy using KL‐4 surfactant in newborn pigs with hydrochloric acid (HCl)‐induced acute lung injury (ALI).

Design

After induction of ALI via intratracheal HCl instillation, pigs were randomized to receive 5.8 ml/kg KL‐4 surfactant or no surfactant prior to extubation to bubble CPAP.

Setting

Clinical laboratory.

Subjects

Spontaneously breathing newborn pigs (<1 week of age).

Interventions

Treatment with KL‐4 surfactant on bubble CPAP with PEEP of 6 cmH2O for 3.5 hr after extubation compared with controls.

Measurements

Physiologic parameters and arterial blood gases were measured every 15 min. At the conclusion of the study, the lungs were excised for the analysis of histopathology and morphometric data.

Main Results

Pigs treated with KL‐4 surfactant had arterial blood gases with less acidosis (P < 0.001), higher PaO2 levels (P < 0.001), and lower PaCO2 levels (P < 0.001). Pigs treated with KL‐4 surfactant had improved survival compared with controls (6/12 KL‐4, 2/12 control, P < 0.05). Postmortem morphometric data demonstrated that pigs treated with KL‐4 surfactant had larger (P < 0.05) exchange units in the caudal‐dorsal lung as compared to relatively atelectatic region in the control animals.

Conclusions

In newborn pigs with severe HCl‐induced ALI, treatment with KL‐4 surfactant resulted in improved respiratory parameters, less dependent atelectasis, and improved short‐term survival. Pediatr. Pulmonol. 2010; 45:782–788. © 2010 Wiley‐Liss, Inc.
Pilot study: The effect of reducing treatment on exercise induced bronchoconstriction
Authors: Kersten E.T.G. , Driessen J.M.M. , van Leeuwen J.C. , Thio B.J.
Published: July 2010

Rationale

Asthma therapy should be stepped up or stepped down in response to changes in asthma control. However, there is little evidence available on the optimal timing, sequence, and degree of medication reductions. In this study we analyzed clinically stable asthmatic children who underwent a medication reduction from a combination preparation consisting of an inhaled corticosteroid (ICS) and long acting beta2‐agonist (LABA) to monotherapy with the same dose of the ICS. We hypothesized that the extent of exercise‐induced bronchoconstriction (EIB) would not increase after the cessation of the LABA.

Methods

Nineteen children, aged 8–16 years, with clinically stable asthma, receiving LABA/ICS combination therapy, were analyzed in this open‐label pilot study. Children performed an exercise challenge at baseline and 3 weeks after the medication reduction. Best values of spirometric measurements of the forced expiratory volume in 1 sec (FEV1) were used for statistical calculations.

Results

Maximum percent fall in FEV1 was significantly lower after 3 weeks of ICS monotherapy (P = 0.03). Eight of 19 children had a ≥15% fall in FEV1 after exercise at the initial exercise challenge. In this subgroup, maximum percent fall in FEV1 after the medication reduction was significantly lower (P < 0.01), and in six children it decreased to <15%, indicating they no longer had EIB.

Conclusion

In clinically stable asthmatic children on LABA/ICS combination therapy, the cessation of the LABA can reduce and in most cases abolish EIB. Pediatr. Pulmonol. 2010; 45:927–933. © 2010 Wiley‐Liss, Inc.
Spherical and hyperspherical representation of potential energy surfaces for intermolecular interactions
Authors: Palazzetti Federico , Munusamy Elango , Lombardi Andrea , Grossi Gaia , Aquilanti Vincenzo
Published: July 2010

The definition of a proper set of coordinates is desirable for the representation of the potential energy surfaces that accounts faithfully also for the symmetry properties of the systems. The expansion in harmonics corresponding to spherical and hyperspherical mapping for atomic and molecular interactions is considered in the present article. The choice of a few but significant configurations, “leading configurations,” relies upon considerations about the geometrical features of the systems. Their minimal number depends on the symmetry property and on the number of coordinates of the problem, and allows us to determine the expansion moments of the interaction potentials, to be used for bound state and dynamical calculations. Here, we report an outlook of prescriptions for the choice of leading configurations, which provides the expansion of the potential energy surface for interacting closed shell systems, such as linear‐molecule–linear‐molecule, floppy‐molecule–rare‐gas‐atom, and nonlinear‐molecule–linear‐molecule. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The role of rotational relaxation in the intersystem crossing between a triplet and a singlet electronic state
Authors: Rashev Svetoslav , Moule David C. , Judge Richard H.
Published: July 2010

A calculation of the rate of ISC (intersystem crossing) relaxation at 0 K requires a knowledge of the spin–orbit coupling and the vibrational overlap integrals (Franck‐Condon factors) between the T1 and S0 states. At elevated temperatures, the population of the rotational states needs to be taken into account through the overlap of the rotational wavefunctions between the interacting T1/S0 electronic states. Here, we discuss the effect of the ISC singlet–triplet selection rules on the number and magnitude of the rotational overlap factors for the J = 0, 5, and 10 rotational levels of thiophosgene, Cl2CS. Of equal importance is the influence of the spin–spin and spin‐rotation coupling on the rotational fragmentation factors and the ISC survival probability. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
The effects of counter cation on oxide ion conductivity: In the case of Sr‐doped LaAlO3 perovskite
Authors: Onishi Taku
Published: July 2010

Many research activities on the solid‐state oxide fuel cell (SOFC) have been performed for production of electronic energy without fossil fuel. To design the efficient SOFC electrolyte, we should clarify the detailed mechanism on oxide ion conduction. LaAlO3 perovskite has been much expected as the electrolyte material. It is known that strontium doping at lanthanum site lowers the activation energy for the oxide ion conduction. In this study, we have investigated the mechanism of the activation energy decrease in strontium‐doped LaAlO3 by the cluster model calculations based on hybrid density functional theory. It was concluded that the ionic and covalent bonds between counter cation and conductive oxide ion is responsible for the activation energy change. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Estimation problems for a class of impulsive systems
Authors: Belkoura L. , Floquet T. , Ibn Taarit K. , Perruquetti W. , Orlov Y.
Published: July 2010

This paper deals with on‐line identification of continuous‐time systems subject to impulsive terms. Using a distribution framework, a scheme is proposed in order to annihilate singular terms in differential equations representing a class of impulsive systems. As a result, an online estimation of unknown parameters is provided, regardless of the switching times or the impulse rules. Numerical simulations of physical processes with noisy data are illustrating our methodology and results. Copyright © 2010 John Wiley & Sons, Ltd.
An Approach of Adaptive Control for Robot Manipulators
Authors: Lee C. S. G. , Chung M. J. , Lee B. H.
Published: July 2010

This paper presents the study of an adaptive control which tracks a desired time‐based trajectory as closely as possible for all times over a wide range of manipulator motion and payloads both in joint‐variable coordinates and Cartesian coordinates. The proposed adaptive control is based on the linearized perturbation equations in the vicinity of a nominal trajectory. The controlled system is characterized by feedforward and feedback components which can be computed separately and simultaneously. The feedforward component computes the nominal torques from the Newton‐Euler equations of motion either using the resolved joint information or the joint information from the trajectory planning program. This computation can be completed in O(n) time. The feedback component consisting of recursive least square identification and one‐step optimal control algorithms for the linearized system computes the perturbation torques in O(n3) time. Because of the parallel structure, the computations of the adaptive control may be implemented in low‐cost microprocessors. A computer simulation study Was conducted to evaluate the performance of the adaptive control in joint‐variable coordinates for a three‐joint robot arm. The feasibility of implementing the adaptive control in Cartesian coordinates using present day low‐cost microprocessors is discussed.
Estimation of Three‐Dimensional Object Orientation for Computer Vision Systems with Feedback
Authors: Lin W. C. , Fu K. S. , Sederberg T.
Published: July 2010

The determination of orientation information of a 3D object is a crucial step in hypothesis‐verification approach to object recognition. In this paper. two approaches are presented to estimate the orientation parameters of a 3D object from a single image. The first one is based on camera model estimation and analysis. The second one is a hierarchical search method. Simulation experiments are conducted to evaluate the performance of the estimations.
Arm Dynamics Simulation
Authors: Swartz Neil M.
Published: July 2010

The ability to mathematically model the movement of a robot manipulator is a prerequisite to the understanding of the key factors that influence a manipulator's performance. This paper presents a manipulator model which has been used to simulate and control a real robot arm. A method of describing the arm by its rotational characteristics. a set of equations called the “Inverse Arm” and an algorithm called the “Forward Arm” are presented. The Forward Arm simulates the movement of an arm and the Inverse Arm provides a means of computing the correct voltages to apply to an arm to achieve a desired movement.