bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling the interactions between polyoxometalates and their environment
Authors: Courcot Blandine , Bridgeman Adam J. 
Published: September 2011

AbstractTo develop a force field suitable both for polyoxometalates (POMs) and organic cations, the Merck molecular force field 94x (MMFF94x) has been selected to describe the counterions used in POMs synthesis and has been combined with our force field optimized for type‐II POMs with electrostatic and Van der Waals interactions included in the potential. Nontransferability of force fields is well‐known and, to overcome this limitation, a charge‐scaling factor (SF) has been introduced and optimized to tune the POMs force field parameters and adapt them to MMFF94x. The mixed MMFF94x/POMFF‐II force field has been optimized and tested on different clusters based on hepta‐molybdate. To validate our mixed force field comparison of the results obtained after molecular mechanics (MM), geometry optimizations with density‐functional (DFT) calculations have been performed on the smallest system of interest. This has enabled a study of the accuracy of different functionals, especially on the description of hydrogen bonding, to be made. Results are promising in terms of structural accuracy. MM geometry optimization can be used on small POM clusters, competing reasonably well with DFT. When quantum approaches increase considerably the computational cost because of the size of the system studied, MM can be used, with the small reservation that even if the charge SF introduced improves the performance of the force field, further optimizations of the nonbonded term and the model used for the atomic charges may be necessary in further studies. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Kinetic isotope effects calculated with the instanton method
Authors: Meisner Jan , Rommel Judith B. , Kästner Johannes 
Published: September 2011

AbstractThe ring‐opening reaction of the cyclopropylcarbinyl radical proceeds via heavy‐atom tunneling at low temperature. We used instanton theory to calculate tunneling rates and kinetic isotope effects with on‐the‐fly calculation of energies by density functional theory (B3LYP). The accuracy was verified by explicitly correlated coupled‐cluster calculations (UCCSD(T)‐F12). At cryogenic temperatures, we found protium/deuterium KIEs up to 13 and inverse KIEs down to 0.2. We also studied an intramolecular tautomerization reaction. A simple and computationally efficient method is proposed to calculate KIEs with the instanton method: the instanton path is assumed to be independent of the atomic masses. This results in surprisingly good estimates of the KIEs for the cyclopropylcarbinyl radical and for the secondary KIEs of the tautomerization. Challenges and capabilities of the instanton method for calculating KIEs are discussed. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011
Theoretical and practical barriers to practitioners' willingness to seek training in empirically supported treatments
Authors: Stewart Rebecca E. , Chambless Dianne L. , Baron Jonathan 
Published: September 2011

AbstractTo identify barriers to the dissemination of empirically supported treatments (ESTs), a random sample of psychologists in independent practice (N=1291) was asked to complete measures of attitudes towards ESTs and willingness to attend a 3‐hour, 1‐day, or 3‐day workshop in an EST of their choice. The strongest predictor of unwillingness to obtain EST training was the amount of time and cost required for the workshop, followed by objections to the need for EST training. Psychodynamic (compared to cognitive‐behavioral) and more experienced practitioners agreed more strongly with the objections to ESTs overall, as did those whose graduate schools had not emphasized psychotherapy research. Results suggest that both practical and theoretical barriers are significant obstacles to EST dissemination. © 2011 Wiley Periodicals, Inc. J Clin Psychol 67:1–16, 2011.
MRT letter: Segmentation and texture‐based classification of breast mammogram images
Authors: Naveed Nawazish , Jaffar M. Arfan , Choi Tae‐Sun 
Published: September 2011

AbstractBreast cancer is the most common cancer diagnosed among women. In this article, support vector machine is used to classify digital mammogram images into malignant and benign. Wiener filter is used to handle the possible quantum noise, which is more likely to occur in mammograms. Stack‐based connected component method is proposed for background removal, and the image is enhanced using retinax method. Seeded region growing algorithm is used to remove the pectoral muscle part of the mammogram. We have extracted 13 different multidomains' features for classification. Results show the superiority of the proposed algorithm in terms of sensitivity, specificity, and accuracy. We have used MIAS database of mammography for experimentation. Microsc. Res. Tech., 2011. © 2011 Wiley Periodicals, Inc.
Development of a hydroxyapatite coating containing silver for the prevention of peri‐prosthetic infection
Authors: Ghani Yaser , Coathup Melanie J. , Hing Karin A. , Blunn Gordon W. 
Published: September 2011

AbstractWe hypothesized that the electrochemical deposition of hydroxyapatite (EHA) can be used to incorporate silver (Ag), providing a controlled and sustained release of Ag ions at a bactericidal concentration. Six groups were investigated: electrochemical co‐precipitation of HA and Ag (EHA/Ag); EHA pre‐coated discs treated in AgN03 (EHA/AgN03); plasma sprayed HA (PHA) pre‐coated discs treated in AgN03 (PHA/AgN03); EHA with 2 “layers” of Ag (EHA/Ag/2 layers); EHA coating only; and PHA coating only. Scanning electron microscopy (SEM) and energy dispersive X‐ray (EDX) and X‐ray diffraction (XRD) analyses quantified coating thickness, calcium/phosphorous ratio, and % atomic silver content, respectively. Inductively coupled plasma‐mass spectrometry quantified the amount of Ag released in phosphate‐buffered saline, and zone of inhibition tests on agar plates using a lawn of Staph aureus were quantified in each group. XRD and EDX analysis confirmed the presence of Ag in all coatings. EHA coated discs with two layers of Ag and the EHA discs soaked in AgN03 showed significantly higher zones of inhibition at all time points when compared with all other groups (except PHA/AgN03 on day 0). This study demonstrated that Ag ions can be incorporated into a HA coating using an electrochemical technique. © 2011 Orthopaedic Research Society Published by Wiley Periodicals, Inc. J Orthop Res 30:356–363, 2012
Late Holocene vertical land motion and relative sea‐level changes: lessons from the British Isles
Authors: Shennan Ian , Milne Glenn , Bradley Sarah 
Published: September 2011

AbstractVertical land motion caused by continuing glacial isostatic adjustment is one of several important components of sea‐level change and is not limited just to previously glaciated regions. A national‐scale analysis for the British Isles shows an ellipse of present‐day relative uplift (relative sea‐level fall), ∼1.2 mm a−1, broadly centred on the deglaciated mountains of Scotland. The pattern of three foci of relative subsidence, ∼1 mm a−1, results from the additional interactions of the deglacial meltwater load on the Atlantic basin and the continental shelf, and the signal due to far‐field ice sheets. At a local scale, sediment compaction can more than double the rate of relative land subsidence. Relative land‐level change (the negative of relative sea‐level change) is not the same as vertical land motion. There is a spatial pattern in the difference between relative land‐level change and vertical land motion, with differences at present of approximately −0.1 to −0.3 mm a−1 around the British Isles and +2.5 to −1.5 mm a−1 globally. For the wider scientific and user community, whether or not the differences are considered significant will depend upon the location, time frame and spatial scale of the study that uses such information. Copyright © 2011 John Wiley & Sons, Ltd.
Novel Glycopolymer Brushes via ATRP: 2. Thermal and Mechanical Properties
Authors: Fleet Reda , van den Dungen Eric T. A. , Klumperman Bert 
Published: September 2011

AbstractThe thermal and mechanical properties of a series of novel glycopolymer brushes with various degrees of polymerization of the backbone and various grafting densities are established. Modulated differential scanning calorimetry (MDSC) is found to be an effective tool for the characterization of the thermal behavior of these glycopolymer brushes. There is little difference among the glass transition temperatures of the different glycopolymer brushes. The elastic features of each glycopolymer predominate (G′ > G″) at low frequency, while at higher frequencies the G″ curve overtakes the G′ curve, indicating the predominance of the viscous response.
m‐isometries on Banach spaces
Authors: Bayart Frédéric 
Published: September 2011

AbstractWe introduce the notion of an m‐isometry of a Banach space, following a definition of Agler and Stankus in the Hilbert space setting. We give a first approach to the general theory of these maps. Then, we focus on the dynamics of m‐isometries, showing that they are never N‐supercyclic. This result is new even on a Hilbert space, and even for isometries on a general Banach space.
Identification of Novel Inhibitors of UDP‐Galactopyranose Mutase by Structure‐Based Virtual Screening
Authors: Karunan Partha Sarathy , Sadeghi‐Khomami Ali , Cren Sylvaine , Robinson Richard I. , Woodward Simon , Slowski Kate , Berast Lindsey , Zheng Blake , Thomas Neil R. , Sanders David A. R. 
Published: September 2011

AbstractUDP‐galactopyranose mutase (UGM) is a flavo‐enzyme involved in the bacterial cell wall biosynthesis. UGM catalyzes the reversible isomerization of UDP‐galactopyranose (UDP‐Galp) to UDP‐galactofuranose (UDP‐Galf). UDP‐Galf is the activated precursor of galactofuranose (Galf) residues that are essential components of the cell wall of certain pathogenic bacteria such as Klebsiella pneumoniae and Mycobacterium tuberculosis. Neither UGM nor Galf residues are found in humans, making Galf biosynthesis a potential drug target for developing antibacterial agents. We report the identification of novel inhibitors of UGM by in silico docking of the LeadQuest compound database against UGM from Escherichia coli. The 13 most promising inhibitors were then evaluated against K. pneumonia and M. tuberculosis UGMs by enzyme inhibition studies. Two inhibitors were identified with IC50 values of ∼1 µM and subsequently these compounds were docked into the recently solved X‐ray structure of Deinococcus radiodurans UGM. The structure‐activity relationships of the initial 13 compounds evaluated as inhibitors are discussed.
A Microarray Tool Provides Pathway and GO Term Analysis
Authors: Koch Martin , Royer Hans‐Dieter , Wiese Michael 
Published: September 2011

AbstractAnalysis of gene expression profiles is no longer exclusively a task for bioinformatic experts. However, gaining statistically significant results is challenging and requires both biological knowledge and computational know‐how. Here we present a novel, user‐friendly microarray reporting tool called maRt. The software provides access to bioinformatic resources, like gene ontology terms and biological pathways by use of the DAVID and the BioMart web‐service. Results are summarized in structured HTML reports, each presenting a different layer of information. In these report, contents of diverse sources are integrated and interlinked. To speed up processing, maRt takes advantage of the multi‐core technology of modern desktop computers by using parallel processing. Since the software is built upon a RCP infrastructure it might be an outset for developers aiming to integrate novel R based applications. Availability: Installer, documentation and various kinds of tutorials are available under LGPL license at the website of our institute http://www.pharma.uni‐bonn.de/www/mart. This software is free for academic use.
SAHA Capture Compound – A novel tool for the profiling of histone deacetylases and the identification of additional vorinostat binders
Authors: Fischer Jenny J. , Michaelis Simon , Schrey Anna K. , Diehl Anne , Graebner Olivia Y. , Ungewiss Jan , Horzowski Sabine , Glinski Mirko , Kroll Friedrich , Dreger Mathias , Koester Hubert 
Published: September 2011

AbstractSuberoylanilide hydroxamic acid (SAHA) is a potent histone deacetylase (HDAC) inhibitor. Inhibitors of HDACs are used in cancer therapy based on the role HDACs play in transcription by regulating chromatin compaction and non‐histone proteins such as transcription factors. Profiling of HDAC expression is of interest in the functional proteomics analysis of cancer. Also, non‐HDAC proteins may interact with HDAC inhibitor drugs and contribute to the drug mode of action. We here present a tool for the unbiased chemical proteomic profiling of proteins that specifically interact with SAHA. We designed and synthesized a trifunctional Capture Compound containing SAHA as selectivity and identified HDACs1, 2, 3 and 6, known and predicted HDAC interactors from human‐derived HepG2 cell lysate, as well as a set of new potential non‐HDAC targets of SAHA. One of these non‐HDAC targets, isochorismatase domain‐containing protein 2 (ISOC2) is putative hydrolase associated with the negative regulation of the tumor‐suppressor p16(INK4a). We demonstrated the direct and dose‐dependent interaction of SAHA to the purified recombinant ISOC2 protein. Using SAHA Capture Compound mass spectrometry, we thus identified potential new SAHA target proteins in an entirely unbiased chemical proteomics approach.
Autoimmune polyendocrine syndrome type 1: Utility of KCNRG autoantibodies as a marker of active pulmonary disease and successful treatment with rituximab
Authors: Popler Jonathan , Alimohammadi Mohammad , Kämpe Olle , Dalin Frida , Dishop Megan K. , Barker Jennifer M. , Moriarty‐Kelsey Margaret , Soep Jennifer B. , Deterding Robin R. 
Published: September 2011

AbstractAutoimmune polyendocrine syndrome type 1 (APS‐1), also known as Autoimmune Polyendocrinopathy Candidiasis and Ectodermal Dysplasia (APECD) is a disorder caused by mutations in the autoimmune regulator (AIRE) gene. In some APS‐1 patients, significant pulmonary disease is observed. Autoantibodies directed against the potassium channel regulatory protein (KCNRG), found in epithelial cells of terminal bronchioles, have been suggested as a marker for pulmonary disease in APS‐1 patients. We report two patients with APS‐1; one with and one without lung disease. Patient 1 had multiple admissions for pneumonia and respiratory insufficiency, required non‐invasive ventilation, and had findings of bronchiectasis on thoracic imaging and significant lymphocytic infiltrates of the airways on lung biopsy. To verify the autoimmune cause of pulmonary symptoms APS‐1 patients, both were tested in a blinded manner for the presence of autoantibodies to KCNRG in serum. We found that only Patient 1 had autoantibodies present. Additionally, Patient 1 had progressive disease despite treatment with several immunomodulating agents, including corticosteroids, azathioprine, and mycophenolate. Patient 1 had a lung biopsy performed which was consistent with B cell lymphocytic aggregates. Rituximab treatment was initiated with apparent good response. This report illustrates the practical use of KCNRG autoantibodies to identify APS‐1 patients with pulmonary risk and the successful use of the monoclonal antibody, Rituximab, to treat pulmonary disease in APS‐1 patients. Pediatr Pulmonol. Pediatr Pulmonol. 2012; 47:84–87. © 2010 Wiley Periodicals, Inc.
Hospital readmissions for newly discharged pediatric home mechanical ventilation patients
Authors: Kun Sheila S. , Edwards Jeffrey D. , Davidson Ward Sally L. , Keens Thomas G. 
Published: September 2011

AbstractBackgroundVentilator‐dependent children have complex chronic conditions that put them at risk for acute illness and repeated hospitalizations.ObjectivesTo determine the 12‐month incidence of and risk factors for non‐elective readmission in children with chronic respiratory failure (CRF) after initiation on home mechanical ventilation (HMV) via tracheostomy.MethodsA retrospective cohort study of 109 HMV patients initiated and followed at an university‐affiliated children's hospital between 2003 and 2009. Patient characteristics are presented using descriptive statistics; generalized estimated equations are used to estimate adjusted odds ratios of select predictor variables for readmission.ResultsThe 12‐month incidence of non‐elective readmission was 40%. Close to half of these readmissions occurred within the first 3 months post‐index discharge. Pneumonia and tracheitis were the most common reasons for readmission; 64% were pulmonary‐ or tracheostomy‐related. Most demographic and clinical patient characteristics were not statistically associated with non‐elective readmissions. Although, a change in the child's management within 7 days before discharge was associated readmissions shortly after index discharge.ConclusionNon‐elective readmissions of newly initiated pediatric HMV patients were common and likely multifactorial. Many of these readmissions were airway‐related, and some may have been potentially preventable. Pediatr Pulmonol. 2012; 47:409–414. © 2011 Wiley Periodicals, Inc.
Lower airway microbiology and cellularity in children with newly diagnosed non‐CF bronchiectasis
Authors: Kapur Nitin , Grimwood Keith , Masters I. Brent , Morris Peter S. , Chang Anne B. 
Published: September 2011

AbstractBackgroundInfection and inflammation are important in the pathogenesis of bronchiectasis. However, there are few published data describing the lower airway microbiology and cellularity in children.MethodsChildren with non‐cystic fibrosis (CF) bronchiectasis who underwent bronchoalveolar lavage (BAL) within 4 weeks of diagnosis were identified by a retrospective patient‐record review. The effects of infection (≥105 colony‐forming units of respiratory bacteria/ml; or detectable Pseudomonas aeruginosa; mycobacteria, fungi, mycoplasma, or respiratory viruses) on airway cellularity and the impact of age, gender, indigenous status, immune function, radiographic involvement and antibiotic usage on infection risk were evaluated.ResultsOf 113 children [median age 63 months (IQR 32–95)] with newly diagnosed bronchiectasis, 77 (68%) had positive BAL cultures for respiratory bacterial pathogens. Haemophilus influenzae was most commonly detected, being present in 53 (47%) BAL specimens. P. aeruginosa was found in just 7 (6%) children, five of whom had an underlying disorder, while mycobacterial and fungal species were not detected. Respiratory viruses were identified in 14 (12%) children and Mycoplasma pneumoniae in two others. Overall, 56 (49.5%) children fulfilled our definition of a lower airway infection and of these, 35 (63%) had more than one pathogen present. Compared to children without infection, children with infection had higher total cell counts (610 vs. 280 × 106/L), neutrophil counts (351 vs. 70 × 106/L), and neutrophil percentages (69% vs. 34%). Age at diagnosis was most strongly associated with infection.ConclusionsBAL microbiology of children with newly diagnosed bronchiectasis is dominated by H. influenzae. In the absence of CF, isolation of P. aeruginosa may suggest a serious co‐morbidity in this group. Airway neutrophilia is common, especially with higher bacterial loads. Pediatr Pulmonol. 2012; 47:300–307. © 2011 Wiley Periodicals, Inc.
Respiratory effects associated with wood fuel use: A cross‐sectional biomarker study among adolescents
Authors: Van Miert Erik , Sardella Antonia , Nickmilder Marc , Bernard Alfred 
Published: September 2011

AbstractThe use of wood as heating and cooking fuel can result in elevated levels of indoor air pollution, but to what extent this is related to respiratory diseases and allergies is still inconclusive. Here, we report a cross‐sectional study among 744 school adolescents (median age 15 years) using as main outcomes respiratory symptoms and diseases, exhaled nitric oxide, total and aeroallergen‐specific IgE in serum, and two epithelial biomarkers in nasal lavage fluid (NALF) or serum, that is, Clara cell protein (CC16) and surfactant‐associated protein D (SPD). Information about the wood fuel use and potential confounders was collected via a personal interview of the adolescent and a questionnaire filled out by the parents. Two approaches were used to limit the possible influence of confounders, that is, multivariate analysis using the complete study population or pairwise analysis of matched sub‐populations obtained using an automated procedure. Wood fuel use was associated with a decrease of CC16 and an increase of SPD in serum, which resulted in a decreased serum CC16/SPD ratio (median −9%, P = 0.001). No consistent differences were observed for the biomarkers measured in exhaled breath or NALF. Wood fuel use was also associated with increased odds for asthma [odds ratio (OR) 2.2, 95% CI: 1.1–4.4, P = 0.02], hay fever (OR = 2.4, 95% CI: 1.4–4.3, P = 0.002), and sensitization against pollen allergens (OR = 2.1, 95% CI: 1.3–3.4, P = 0.002). The risks of respiratory tract infections, self‐reported symptoms, and sensitization against house‐dust mite were not increased by wood fuel use. The increased risks of asthma, hay fever and aeroallergen sensitization, and the changes of lung‐specific biomarkers consistently pointed towards respiratory effects associated with the use of wood fuel. Pediatr Pulmonol. 2012; 47:358–366. © 2011 Wiley Periodicals, Inc.
The linear interaction energy method for the prediction of protein stability changes upon mutation
Authors: Wickstrom Lauren , Gallicchio Emilio , Levy Ronald M. 
Published: September 2011

AbstractThe coupling of protein energetics and sequence changes is a critical aspect of computational protein design, as well as for the understanding of protein evolution, human disease, and drug resistance. To study the molecular basis for this coupling, computational tools must be sufficiently accurate and computationally inexpensive enough to handle large amounts of sequence data. We have developed a computational approach based on the linear interaction energy (LIE) approximation to predict the changes in the free‐energy of the native state induced by a single mutation. This approach was applied to a set of 822 mutations in 10 proteins which resulted in an average unsigned error of 0.82 kcal/mol and a correlation coefficient of 0.72 between the calculated and experimental ΔΔG values. The method is able to accurately identify destabilizing hot spot mutations; however, it has difficulty in distinguishing between stabilizing and destabilizing mutations because of the distribution of stability changes for the set of mutations used to parameterize the model. In addition, the model also performs quite well in initial tests on a small set of double mutations. On the basis of these promising results, we can begin to examine the relationship between protein stability and fitness, correlated mutations, and drug resistance. Proteins 2012; © 2011 Wiley Periodicals, Inc.