bluuebunny/crossref_metadata_2025_split huggingface dataset:
The impact of psychological distress on exacerbation rates in COPD
Authors: Laurin Catherine , Moullec Grégory , Bacon Simon L. , Lavoie Kim L. 
Published: November 2010

Background: Exacerbations are common in chronic obstructive pulmonary disease (COPD) and contribute significantly to COPD morbidity and mortality. COPD is also associated with high levels of psychological distress, which has been shown to be associated with higher exacerbation rates. However, the existing literature on the association between psychological distress and exacerbation risk remains largely misunderstood. Objectives: To critically review the current literature on the association between psychological distress (defined as anxiety and depressive symptoms or anxiety and depressive disorders) and COPD exacerbations in COPD patients, to highlight the limitations of the existing literature, and to provide recommendations for future research. Methods: A critical review of English-language peer-reviewed longitudinal and retrospective studies was conducted. The Ovid portal to Medline, EMBASE, and PsycINFO databases were accessed. Results: Some acceptable evidence suggested that psychological distress confers greater risk for exacerbations, more specifically symptom-based exacerbations or those treated in the patient’s own environment. However, most studies showed an absence of a positive association, especially with exacerbations leading to hospitalization. Conclusions: Methodological weaknesses and the use of a wide range of psychological tools mean that there is an inconsistent association between psychological distress and exacerbations in the current literature. However, psychological distress may confer greater risk for symptom-based rather than event-based defined exacerbations. Further studies are needed to more comprehensively assess the question, particularly in light of the high levels of both anxiety and depression in COPD patients.
A role of ygfZ in the Escherichia coli response to plumbagin challenge
Authors: Lin Ching-Nan , Syu Wan-Jr , Sun Wei-Sheng W , Chen Jenn-Wei , Chen Tai-Hung , Don Ming-Jaw , Wang Shao-Hung 
Published: November 2010

Abstract
Plumbagin is found in many herbal plants and inhibits the growth of various bacteria. Escherichia coli strains are relatively resistant to this drug. The mechanism of resistance is not clear. Previous findings showed that plumbagin treatment triggered up-regulation of many genes in E. coli including ahpC, mdaB, nfnB, nfo, sodA, yggX and ygfZ. By analyzing minimal inhibition concentration and inhibition zones of plumbagin in various gene-disruption mutants, ygfZ and sodA were found critical for the bacteria to resist plumbagin toxicity. We also found that the roles of YgfZ and SodA in detoxifying plumbagin are independent of each other. This is because of the fact that ectopically expressed SodA reduced the superoxide stress but not restore the resistance of bacteria when encountering plumbagin at the absence of ygfZ. On the other hand, an ectopically expressed YgfZ was unable to complement and failed to rescue the plumbagin resistance when sodA was perturbed. Furthermore, mutagenesis analysis showed that residue Cys228 within YgfZ fingerprint region was critical for the resistance of E. coli to plumbagin. By solvent extraction and HPLC analysis to follow the fate of the chemical, it was found that plumbagin vanished apparently from the culture of YgfZ-expressing E. coli. A less toxic form, methylated plumbagin, which may represent one of the YgfZ-dependent metabolites, was found in the culture supernatant of the wild type E. coli but not in the ΔygfZ mutant. Our results showed that the presence of ygfZ is not only critical for the E coli resistance to plumbagin but also facilitates the plumbagin degradation.
A rapid and simple method for constructing stable mutants of Acinetobacter baumannii
Authors: Aranda Jesús , Poza Margarita , Pardo Belén G , Rumbo Soraya , Rumbo Carlos , Parreira José R , Rodríguez-Velo Patricia , Bou Germán 
Published: November 2010

Abstract

Background

Acinetobacter baumannii is a multidrug-resistant bacterium responsible for nosocomial infections in hospitals worldwide. Study of mutant phenotypes is fundamental for understanding gene function. The methodologies developed to inactivate A. baumannii genes are complicated and time-consuming; sometimes result in unstable mutants, and do not enable construction of double (or more) gene knockout mutant strains of A. baumannii.

Results
We describe here a rapid and simple method of obtaining A. baumannii mutants by gene replacement via double crossover recombination, by use of a PCR product that carries an antibiotic resistance cassette flanked by regions homologous to the target locus. To demonstrate the reproducibility of the approach, we produced mutants of three different chromosomal genes (omp33, oxyR, and soxR) by this method. In addition, we disrupted one of these genes (omp33) by integration of a plasmid into the chromosome by single crossover recombination, the most widely used method of obtaining A. baumannii mutants. Comparison of the different techniques revealed absolute stability when the gene was replaced by a double recombination event, whereas up to 40% of the population reverted to wild-type when the plasmid was disrupting the target gene after 10 passages in broth without selective pressure. Moreover, we demonstrate that the combination of both gene disruption and gene replacement techniques is an easy and useful procedure for obtaining double gene knockout mutants in A. baumannii.

Conclusions
This study provides a rapid and simple method of obtaining stable mutants of A. baumannii free of foreign plasmidic DNA, which does not require cloning steps, and enables construction of multiple gene knockout mutants.
Polymorphisms in regulatory regions of Cyclooxygenase-2 gene and breast cancer risk in Brazilians: a case-control study
Authors: Piranda Diogo N , Festa-Vasconcellos Juliana S , Amaral Laura M , Bergmann Anke , Vianna-Jorge Rosane 
Published: November 2010

AbstractBackgroundCyclooxygenase-2 (COX-2) is up-regulated in several types of cancer, and it is hypothesized that COX-2 expression may be genetically influenced. Here, we evaluate the association between single-nucleotide polymorphisms (SNPs) in the COX-2 gene (PTGS2) and the occurrence of breast cancer among Brazilian women.MethodsThe study was conducted prospectively in two steps: First, we screened the promoter region and three fragments of the 3'-untranslated region ofPTGS2from 67 healthy Brazilians to identify SNPs and to select those with a minor allele frequency (MAF) of at least 0.10. The MAF of these selected SNPs was further characterized in 402 healthy volunteers to evaluate potential differences related to heterogeneous racial admixture and to estimate the existence of linkage disequilibrium among the SNPs. The second step was a case-control study with 318 patients and 273 controls designed to evaluatePTGS2genotype- or haplotype-associated risk of breast cancer.ResultsThe screening analysis indicated nine SNPs with the following MAFs: rs689465 (0.22), rs689466 (0.15), rs20415 (0.007), rs20417 (0.32), rs20419 (0.015), rs5270 (0.02), rs20424 (0.007), rs5275 (0.22) and rs4648298 (0.01). The SNPs rs689465, rs689466, rs20417 and rs5275 were further studied: Their genotypic distributions followed Hardy-Weinberg equilibrium and the MAFs were not affected by gender or skin color. Strong linkage disequilibrium was detected for rs689465, rs20417 and rs5275 in the three possible pairwise combinations. In the case-control study, there was a significant increase of rs5275TC heterozygotes in cases compared to controls (OR = 1.44, 95% CI = 1.01-2.06; P = 0.043), and the haplotype formed by rs689465G, rs689466A, rs20417G and rs5275C was only detected in cases. The apparent association with breast cancer was not confirmed for rs5275CC homozygotes or for the most frequent rs5275C-containing haplotypes.ConclusionsOur results indicate no strong association between the four most frequentPTGS2SNPs and the risk of breast cancer.
A study on the compatibility and physical properties of chlorinated polyethylene rubber/nitrile rubber blends
Authors: Zhang Zhen Xiu , Chen Chun Hua , Gao Xin Wen , Kim Jin Kuk , Xin Zhen Xiang 
Published: November 2010

AbstractThe miscibility and some physicomechanical characteristics of chlorinated polyethylene rubber (CPE) and nitrile rubber (NBR) blends have been investigated. Calculation of the heat of mixing, differential scanning calorimetry, and scanning electron microscopy analysis showed that CPE was miscible with NBR in all proportions. The cure and scorch times decreased with the increase in NBR content, whereas the maximum torque increased. The tensile strength, 100% modulus, elongation at break, tear strength, and compression set decreased with increasing of NBR content. After aging, hardness and tensile strength increased, and there was no drastic change in elongation at break on aging. The thermal aging resistance and the abrasion resistance of NBR are improved after blending with CPE, but the oil resistance decreased. © 2010 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Ultra‐Slow Molecular Motion in Polymers: 1D and 2D NMR Spectroscopy
Authors: Blümich B. , Hagemeyer A. , Schmidt‐Rohr K. , Spiess H. W. 
Published: November 2010

AbstractDifferent approaches of 1 D and 2 D solid state NMR spectroscopy for the detection of ultraslow molecular reorientation are reviewed with examples from 13C NMR: 2 D exchange spectroscopy of static powders is applicable generally for simple molecules only, because of spectral overlap. But the resulting spectra are readily interpreted in terms of jump and diffusive motion. More complex systems can be investigated with 1 D “inverse hole burning” spectroscopy or the 1 D magic angle spinning (MAS) method of exchange induced sidebands (EIS). 2 D MAS exchange spectra provide more specific information but are hard to interpret without computer simulations. The combination of 1 D EIS spectroscopy with rotor synchronization leads to 2 D spectra which correlate order and motion. The phase cycle for the TOSS (total suppression of sidebands) sequence needed in these experiments is given. The advantages of MAS and static exchange spectroscopy are combined in 2 D spectroscopy with sample spinning off the magic angle. 2 D exchange spectra similar to those of static samples are obtained for each chemical shift, however, the anisotropy is scaled down by the offset from the magic angle, resulting in increased spectral resolution.
Can Enantioselectivity be Computed in Enthalpic Barrierless Reactions? The Case of CuI‐Catalyzed Cyclopropanation of Alkenes
Authors: García José I. , Jiménez‐Osés Gonzalo , Mayoral José A. 
Published: November 2010

AbstractAn extensive computational study has been carried out on different catalytic systems for cyclopropanation reactions based on copper. Most DFT schemes used present drawbacks that preclude the calculation of accurate absolute kinetic properties (energy barriers) of such systems, excepting the M05 and M06 suites of density functionals. On the other hand, there is a wide range of DFT methods capable of reproducing relative energy values, which can be easily translated into selectivities. Most of the theoretical levels used tend to overestimate activation barriers, allowing the location of the transition state (TS) on the potential‐energy surface (PES) of the most reactive systems, which are probably artifacts of the method. However, after a thorough analysis of the calculated PES, and the origin of the energy differences obtained for the different alkene approaches in chiral systems, it is found that energy differences are almost constant over a wide range of geometries covering the reaction channel zone in which the true TS on the Gibbs free‐energy surface (GFES) lies. Therefore, many computational schemes can still be used confidently to explain and predict enantioselectivities in these systems.
Selection of simplified models: I. Analysis of model‐selection criteria using mean‐squared error
Authors: Wu Shaohua , McAuley K. B. , Harris T. J. 
Published: November 2010

AbstractMean‐squared error (MSE) is used to analyse nine commonly used model‐selection criteria (MSC) for their performance when selecting simplified models (SMs). Expressions are derived to enable exact calculations of the probability that a particular MSC will select a SM. For several common MSC, the relative propensities to select SMs are independent of model structure and data. It is shown that MSC that are effective in preventing overfitting are prone to underfitting when information content of the data is low. In a subsequent article, results are extended to develop a new MSE‐based MSC for selecting nonlinear multi‐response SMs.
Numerical simulation of the tissue ablation in high‐intensity focused ultrasound therapy with array transducer
Authors: Okita Kohei , Ono Kenji , Takagi Shu , Matsumoto Yoichiro 
Published: November 2010

AbstractThe development of high‐intensity focused ultrasound (HIFU) therapy for deeply situated cancer has been desired. One problem is focal point displacement due to the inhomogeneity of the human body. The objectives are the realization of appropriate phase control of an array transducer and support for preoperative planning of HIFU therapy by the computational prediction of ablation regions. To these ends, in this study we have developed an HIFU simulator that employs a voxel phantom constructed from CT/MRI data of a living human body. To reproduce the pressure propagation through an inhomogeneous medium, the mass and momentum equations for a mixture with the equation of state of the medium are solved. The ablation of tissue is modeled as a phase transition by using the phase field model. Then, the heat equation with viscous dissipation as a heat source and the Allen–Cahn equation with a free energy model are solved to predict the development of the ablation region. The basic equations are discretized by the finite difference method. HIFU therapy with an array transducer for liver cancer is reproduced numerically. Although the results without phase control show displacement and diffusion of the focal point due to the inhomogeneity of the human body, a clear focal point is obtained by using the array transducer with an appropriate phase delay obtained from pre‐computation. The HIFU simulator predicts that the ablation region will develop close to the target, owing to the phase control of the array transducer. Copyright © 2010 John Wiley & Sons, Ltd.
Proof interpretations with truth
Authors: Gaspar Jaime , Oliva Paulo 
Published: November 2010

AbstractThis article systematically investigates so‐called “truth variants” of several functional interpretations. We start by showing a close relation between two variants of modified realizability, namely modified realizability with truth and q‐modified realizability. Both variants are shown tobe derived from a single “functional interpretation with truth” of intuitionistic linear logic. This analysis suggests that several functional interpretations have truth and q‐variants. These variants, however, require a more involved modification than the ones previously considered. Following this lead we present truth and q‐variants of the Diller‐Nahm interpretation, the bounded modified realizability and the bounded functional interpretation (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Vibronic coupling in Frenkel and charge‐transfer states of oligothiophene crystals
Authors: Stradomska Anna , Kulig Waldemar , Petelenz Piotr 
Published: November 2010

AbstractA novel approach, recently proposed to describe exciton–phonon coupling in Frenkel states of an infinite molecular crystal, is generalized to incorporate charge‐transfer (CT) excitons. Both types of electronic excitations are treated on the same footing. The corresponding Hamiltonian in the Lang–Firsov representation is subdivided into subspaces representing one‐particle, two‐particle, etc., excitations, and (after truncating the basis set to manageable size) numerically diagonalized to yield the absorption as well as the electroabsorption (EA) spectrum. The emphasis is on the latter, previously reproduced only in the limiting cases of weak or strong vibronic coupling. The calculations are presented for the sexithiophene crystal, with parameterization based on independent experimental and theoretical estimates.
Photoluminescence study of LaF3:Eu3+ nanoparticles capped with different ligands
Authors: Janssens Stefaan , Williams Grant , Clarke David , Sharp Matt 
Published: November 2010

AbstractTemperature dependent photoluminescence (PL) measurements have been done on LaF3:Eu3+ nanoparticles capped with sensitizing or nonsensitizing ligands. The LaF3:Eu3+ nanoparticles containing a sensitizing ligand display a large enhancement of the PL intensity as well as an additional PL decay mechanism that is not seen in the LaF3:Eu3+ nanoparticles capped with nonsensitizing ligands. We also demonstrate that it is possible to obtain transparent discs, which is advantageous for device applications.The image in the abstract shows cuvettes containing solutions of LaF3:Eu3+ capped with OA (left) and LaF3:Eu3+ capped with TTA/OA (right) in CHCl3 and excited at 365 nm.magnified image
Value of autofluorescence bronchoscopy in patients with laryngeal cancer
Authors: Çetınkaya E , Veyseller B , Yildirim Y S , Aksoy F , Özgül M A , Gençoğlu A , Altin S 
Published: November 2010

AbstractBackground:Patients with squamous cell carcinoma of the head and neck constitute a high risk group for synchronous and metachronous tumours.Objective:This study aimed to investigate the usefulness of white light and autofluorescence bronchoscopy in the evaluation of pre-malignant and early neoplastic lesions in patients with laryngeal cancer, who are at high risk of concomitant lung cancer.Methods:This prospective, cross-sectional study included 30 patients who had undergone total laryngectomy for squamous cell carcinoma of the larynx. The tracheobronchial system was investigated for the presence of pre-malignant and malignant lesions, using a combination of white light and autofluorescence bronchoscopy. Biopsies were obtained from areas with a pathological appearance, and histopathological studies were performed.Results:All patients had a permanent tracheostomy. Light and autofluorescence bronchoscopy indicated that the tracheobronchial system was normal in 11 patients. A total of 27 biopsies was taken from the remaining 19 patients, and revealed invasive squamous cell carcinoma in one patient and pre-malignant changes in six.Conclusion:Bronchoscopy is a valuable and practical tool for screening patients at high risk of lung cancer, and requires minimal intervention especially in patients with a permanent tracheostomy. Of the various bronchoscopic techniques becoming available, autofluorescence bronchoscopy shows promise for the detection of pre-invasive malignant changes of the tracheobronchial system in patients previously operated upon for laryngeal cancer.
A generic approach for representing complex structures in biological models
Authors: Muetzelfeldt Robert 
Published: November 2010

AbstractIncreasingly, the biological modelling community is looking for ways of handling complex and possibly dynamic structures in their models. On the one hand, the pathway-modelling groups (SBML and CellML) seek to move up levels of organisation, while on the other hand the "Virtual X" communities (where X is some organism or organ) need to represent the organisational structure within their object of study. To date, various approaches have been proposed, such as the SBML Level 3 'comp', 'spatial', 'array' and 'dyn' extension packages, and domain-specific elements in languages such as NeuroML, but there is no generic approach intended to be adopted by the various communities.We have designed and implemented such a generic approach in the Simile modelling environment ("http://www.simulistics.com":http://www.simulistics.com). Simile combines a diagrammatic notation for ODEs (in terms of stocks, flows and subsidiary equations), combined with a UML-like notation for representing classes of object and associations between them. No domain-specific concepts are built in, so the object classes can represent anything from molecules to planets, and the associations are specified by the modeller. For example, Simile has no spatial concepts built in, but the modeller can create a class called (perhaps) 'spatial unit', and specify a regular (2- or 4-neighbour) square grid, a 3D array, a hexagonal grid or arbitrary polygons, simply by changing the expression which defines when the association exists between any pair of spatial units. Containership is represented simply by drawing one class inside another (so you can easily show that molecules are inside cells, and cells are inside organs), and objects can be dynamically created and destroyed during the simulation. Because Simile generates compiled C++ code for simulating model behaviour, it is capable of handling very complex models (1 million+ objects).We thus consider that Simile demonstrates the feasibility of a generic approach for handling disaggregation in biological models. We suggest that the widespread adoption of such an approach across the various biological modelling communities would greatly improve the efficiency and effectiveness of future model development as the models become increasingly complex.
DNA vaccination targeting macrophage migration inhibitory factor prevents murine experimental colitis
Authors: Ohkawara T , Koyama Y , Onodera S , Takeda H , Kato M , Asaka M , Nishihira J 
Published: November 2010

SummaryPrevious studies have shown that neutralization of macrophage migration inhibitory factor (MIF) by anti-MIF antibody reduces intestinal inflammation in mice. In this study we tested whether or not anti-MIF autoantibody induced by DNA vaccine targeting MIF protects mice against experimental colitis. Mice were administered a MIF-deoxyribonucleic acid (DNA) vaccine by introducing oligonucleotides encoding helper T epitope into the cDNA sequence of murine MIF by in vivo electroporation. Preventive effects of this method against dextran sulphate sodium-induced (DSS) colitis were evaluated. Mice administered with MIF-DNA vaccine raised values of autoantibody significantly. The clinical and histological findings of colitis induced by 3·0% DSS solution were ameliorated significantly in mice treated with MIF-DNA vaccine compared with saline or pCAGGS-treated mice given DSS. Myeloperoxidase activity, infiltration of F4/80-positive staining cells and the levels of proinflammatory cytokines were suppressed in the colon of MIF-DNA vaccine treated mice compared with saline or pCAGGS-treated mice exposed to DSS. Our results suggest that immunization with helper T epitope DNA-vaccine targeting MIF may be a useful approach for the treatment of colitis including inflammatory bowel diseases.