bluuebunny/crossref_metadata_2025_split huggingface dataset:
Surfactant assisted polymerization of tetrafluoroethylene in supercritical carbon dioxide with a pilot scale batch reactor
Authors: Giaconia Alberto , Scialdone Onofrio , Apostolo Marco , Filardo Giuseppe , Galia Alessandro 
Published: November 2007

AbstractChain‐free radical polymerization of tetrafluoroethylene (TFE) was carried out in supercritical carbon dioxide (scCO2), at 50 °C and 121–133 bar, with tertiary‐amyl‐per‐pivalate as a free radical initiator, using a 5‐L pilot scale batch reactor. Experiments were carried out both in the absence and in the presence of perfluoropolyether (PFPE) carboxylate surfactants. Stabilizers were employed under the free acid form and as sodium and calcium salts. An expanded fibrillated poly(TFE) was obtained in all experiments. In the case of surfactant‐free polymerizations, the product was mainly constituted by irregular shape macroparticles having size in the range 200–500 μm. Quite interestingly, when the free acid surfactant was used, a clear acceleration of the polymerization rate was observed and smaller polymer particles with more regular quasi‐spherical morphology were obtained. Melt fusion crystallinity of as‐polymerized poly(TFE) seemed not substantially affected by the presence of the stabilizers and was rather high (80–86%) suggesting that polymerization mainly occurs at polymer particle surface. All these elements suggest that FLUOROLINK® 7004H PFPE carboxylic acid decreases coagulation of primary polymer particles leading to an increase in polymer surface area. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 257–266, 2008
Synthesis and characterization of water‐soluble gold nanoparticles stabilized by comb‐shaped copolymers
Authors: Han De‐Hui , Pan Cai‐Yuan 
Published: November 2007

AbstractThe water‐soluble gold nanoparticles stabilized by well‐defined comb‐shaped copolymers have been synthesized successfully. The hybrid nanoparticles consist of gold core and poly[poly(ethylene oxide) methyl ether acrylate]‐block‐poly(N‐isopropylacrylamide) [P(A‐MPEO)‐block‐PNIPAM] shell. The water‐soluble comb‐shaped copolymers, P(A‐MPEO)‐block‐PNIPAM with PNIPAM as a handle, were successfully synthesized via a macromonomer technique using reversible addition fragmentation chain transfer (RAFT) polymerization method. The terminal dithioester group of the comb‐shaped copolymer was reduced to a thiol end group forming SH‐terminated copolymers, P(A‐MPEO)‐block‐PNIPAM‐SH. Successively they were used to stabilize gold nanoparticles by the “grafting‐to” approach. The hybrid nanoparticles were characterized by TEM, UV–vis, and HRTEM. Because of the thermosensitive property of PNIPAM in aqueous solution, the comblike copolymer‐tethered gold nanoparticles show a sharp and reversible phase transition at 30 °C in aqueous solution, which was determined by microdifferential scanning calorimetry. © 2007 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 341–352, 2008
CO escape from myoglobin with metadynamics simulations
Authors: Ceccarelli Matteo , Anedda Roberto , Casu Mariano , Ruggerone Paolo 
Published: November 2007

AbstractThe relatively small size of myoglobin makes it suitable for the investigation of the ligand escape process in respiratory proteins and, in general, an ideal model system for the study of the more general structure‐function paradigm. In this work, we use Molecular Dynamics simulations combined with an accelerated algorithm, the metadynamics, to probe the escape of CO from myoglobin. Our approach permits to quantitatively describe the escape process via the reconstruction of the associated free energy surface. Additionally, hints on the involvement of a larger numbers of residues than hitherto assumed in the gating process are extracted from our data. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Modeling of metal interaction geometries for protein–ligand docking
Authors: Seebeck Birte , Reulecke Ingo , Kämper Andreas , Rarey Matthias 
Published: November 2007

AbstractThe accurate modeling of metal coordination geometries plays an important role for structure‐based drug design applied to metalloenzymes. For the development of a new metal interaction model, we perform a statistical analysis of metal interaction geometries that are relevant to protein–ligand complexes. A total of 43,061 metal sites of the Protein Data Bank (PDB), containing amongst others magnesium, calcium, zinc, iron, manganese, copper, cadmium, cobalt, and nickel, were evaluated according to their metal coordination geometry. Based on statistical analysis, we derived a model for the automatic calculation and definition of metal interaction geometries for the purpose of molecular docking analyses. It includes the identification of the metal‐coordinating ligands, the calculation of the coordination geometry and the superposition of ideal polyhedra to identify the optimal positions for free coordination sites. The new interaction model was integrated in the docking software FlexX and evaluated on a data set of 103 metalloprotein‐ligand complexes, which were extracted from the PDB. In a first step, the quality of the automatic calculation of the metal coordination geometry was analyzed. In 74% of the cases, the correct prediction of the coordination geometry could be determined on the basis of the protein structure alone. Secondly, the new metal interaction model was tested in terms of predicting protein–ligand complexes. In the majority of test cases, the new interaction model resulted in an improved docking accuracy of the top ranking placements. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Estimating quality of template‐based protein models by alignment stability
Authors: Chen Hao , Kihara Daisuke 
Published: November 2007

AbstractThe error in protein tertiary structure prediction is unavoidable, but it is not explicitly shown in most of the current prediction algorithms. Estimated error of a predicted structure is crucial information for experimental biologists to use the prediction model for design and interpretation of experiments. Here, we propose a method to estimate errors in predicted structures based on the stability of the optimal target‐template alignment when compared with a set of suboptimal alignments. The stability of the optimal alignment is quantified by an index named the SuboPtimal Alignment Diversity (SPAD). We implemented SPAD in a profile‐based threading algorithm and investigated how well SPAD can indicate errors in threading models using a large benchmark dataset of 5232 alignments. SPAD shows a very good correlation not only to alignment shift errors but also structure‐level errors, the root mean square deviation (RMSD) of predicted structure models to the native structures (i.e. global errors), and local errors at each residue position. We have further compared SPAD with seven other quality measures, six from sequence alignment‐based measures and one atomic statistical potential, discrete optimized protein energy (DOPE), in terms of the correlation coefficient to the global and local structure‐level errors. In terms of the correlation to the RMSD of structure models, when a target and a template are in the same SCOP family, the sequence identity showed a best correlation to the RMSD; in the superfamily level, SPAD was the best; and in the fold level, DOPE was best. However, in a head‐to‐head comparison, SPAD wins over the other measures. Next, SPAD is compared with three other measures of local errors. In this comparison, SPAD was best in all of the family, the superfamily and the fold levels. Using the discovered correlation, we have also predicted the global and local error of our predicted structures of CASP7 targets by the SPAD. Finally, we proposed a sausage representation of predicted tertiary structures which intuitively indicate the predicted structure and the estimated error range of the structure simultaneously. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Stabilization of antibody structure upon association to a human carbonic anhydrase IX epitope studied by X‐ray crystallography, microcalorimetry, and molecular dynamics simulations
Authors: Král Vlastimil , Mader Pavel , Collard Renata , Fábry Milan , Hořejší Magdaléna , Řezáčová Pavlína , Kožíšek Milan , Závada Jan , Sedláček Juraj , Rulíšek Lubomír , Brynda Jiří 
Published: November 2007

AbstractSpecific antibodies interfere with the function of human tumor‐associated carbonic anhydrase IX (CA IX), and show potential as tools for anticancer interventions. In this work, a correlation between structural elements and thermodynamic parameters of the association of antibody fragment Fab M75 to a peptide corresponding to its epitope in the proteoglycan‐like domain of CA IX, is presented. Comparisons of the crystal structures of free Fab M75 and its complex with the epitope peptide reveal major readjustments of CDR‐H1 and CDR‐H3. In contrast, the overall conformations and positions of CDR‐H2 and CDR‐L2 remain unaltered, and their positively charged residues may thus present a fixed frame for epitope recognition. Adoption of the altered CDR‐H3 conformation in the structure of the complex is accompanied by an apparent local stabilization. Analysis of domain mobility with translation‐libration‐screw (TLS) method shows that librations of the entire heavy chain variable domain (VH) decrease and reorient in the complex, which correlates well with participation of the heavy chain in ligand binding. Isothermal titration microcalorimetry (ITC) experiments revealed a highly unfavorable entropy term, which can be attributed mainly to the decrease in the degrees of freedom of the system, the loss of conformational freedom of peptide and partially to a local stabilization of CDR‐H3. Moreover, it was observed that one proton is transferred from the environment to the protein‐ligand complex upon binding. Molecular dynamics simulations followed by molecular mechanics/generalized Born surface area (MM‐GBSA) calculations of the ligand (epitope peptide) binding energy yielded energy values that were in agreement with the ITC measurements and indicated that the charged residues play crucial role in the epitope binding. Theoretical arguments presented in this work indicate that two adjacent arginine residues (ArgH50 and ArgH52) are responsible for the observed proton transfer. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Large scale analysis of protein‐binding cavities using self‐organizing maps and wavelet‐based surface patches to describe functional properties, selectivity discrimination, and putative cross‐reactivity
Authors: Kupas Katrin , Ultsch Alfred , Klebe Gerhard 
Published: November 2007

AbstractA new method to discover similar substructures in protein binding pockets, independently of sequence and folding patterns or secondary structure elements, is introduced. The solvent‐accessible surface of a binding pocket, automatically detected as a depression on the protein surface, is divided into a set of surface patches. Each surface patch is characterized by its shape as well as by its physicochemical characteristics. Wavelets defined on surfaces are used for the description of the shape, as they have the great advantage of allowing a comparison at different resolutions. The number of coefficients to describe the wavelets can be chosen with respect to the size of the considered data set. The physicochemical characteristics of the patches are described by the assignment of the exposed amino acid residues to one or more of five different properties determinant for molecular recognition. A self‐organizing neural network is used to project the high‐dimensional feature vectors onto a two‐dimensional layer of neurons, called a map. To find similarities between the binding pockets, in both geometrical and physicochemical features, a clustering of the projected feature vector is performed using an automatic distance‐ and density‐based clustering algorithm. The method was validated with a small training data set of 109 binding cavities originating from a set of enzymes covering 12 different EC numbers. A second test data set of 1378 binding cavities, extracted from enzymes of 13 different EC numbers, was then used to prove the discriminating power of the algorithm and to demonstrate its applicability to large scale analyses. In all cases, members of the data set with the same EC number were placed into coherent regions on the map, with small distances between them. Different EC numbers are separated by large distances between the feature vectors. A third data set comprising three subfamilies of endopeptidases is used to demonstrate the ability of the algorithm to detect similar substructures between functionally related active sites. The algorithm can also be used to predict the function of novel proteins not considered in training data set. Proteins 2008. © 2007 Wiley‐Liss, Inc.
Artificial Neural Networks: Useful Aid in Diagnosing Acute Appendicitis
Authors: Prabhudesai S. G. , Gould S. , Rekhraj S. , Tekkis P. P. , Glazer G. , Ziprin P. 
Published: November 2007

AbstractBackroundThe purpose of the study was to assess the role of artificial neural networks (ANNs) in the diagnosis of appendicitis in patients presenting with acute right iliac fossa (RIF) pain and comparing its performance with the assessment made by experienced clinicians and the Alvarado score.MethodsAfter training and testing an ANN, data from 60 patients presenting with suspected appendicitis over a 6‐month period to a teaching hospital was collected prospectively. Accuracy of diagnosing appendicitis by the clinician, the Alvarado score, and the ANN was compared.ResultsThe sensitivity, specificity, and positive and negative predictive values of the ANN were 100%, 97.2%, 96.0%, and 100% respectively. The ability of the ANN to exclude accurately the diagnosis of appendicitis in patients without true appendicitis was statistically significant compared to the clinical performance (p = 0.031) and Alvarado score of ≥6 (p = 0.004) and nearly significant compared to the Alvarado score of ≥7 (p = 0.063).ConclusionsANNs can be an effective tool for accurately diagnosing appendicitis and may reduce unnecessary appendectomies.
Family Support and Cardiac Rehabilitation: A Comparative Study of the Experiences of South Asian and White-European Patients and Their Carer's Living in the United Kingdom
Authors: Astin Felicity , Atkin Karl , Darr Aliya 
Published: November 2007

Background: Effective lifestyle modification facilitated by cardiac rehabilitation is known to reduce the occurrence of adverse coronary events and mortality. South Asians have poorer outcomes after a myocardial infarction than the general UK population, but little is known about their experiences of family support, cardiac rehabilitation and lifestyle change. Aims: To explore the nature of family support available to a sample of South Asian and White-European cardiac patients and to highlight similarities and differences between these groups with regard to cardiac rehabilitation and lifestyle modification. Methods: Using a qualitative approach, semi-structured interviews (in 1 of 6 languages) were conducted by researchers with; 45 South Asian patients and 37 carers and 20 White-European patients and 17 carers. Interviews were conducted in a home setting, up to eighteen months after discharge from hospital following myocardial infarction, coronary artery bypass surgery or unstable angina. Results: The main themes that emerged related to the provision of advice and information, family support and burden, dietary change and exercise regimes. Conclusions: Several cultural and ethnic differences were identified between patients and their families alongside similarities, irrespective of ethnicity. These may represent generic characteristics of recovery after a cardiac event. Health professionals should develop a cultural repertoire to engage with diversity and difference. Not every difficulty a person encounters as they try to access appropriate service delivery can be attributed to ethnic background. By improving services generally, support for South Asian populations can be improved. The challenge is to know when ethnicity makes a difference and mediates a person's relationship with service support and when it does not.
Antenatal detection of arteriovenous anastomoses in monochorionic twin pregnancy
Authors: Sau A. , Weber M. , Shennan A.H. , Maxwell D. 
Published: November 2007

AbstractObjectivesTo revalidate the detection technique for arteriovenous anastomoses in an unselected group of monochorionic twins, and to make recommendations about its applicability for more widespread use.MethodsWomen with monochorionic diamniotic (MCDA) twins were recruited and underwent placental mapping by color Doppler ultrasound. Images of placental maps showing the location and type of anastomoses were saved as digital video clips. After delivery, dye injection study of all the placentas was performed to delineate the site and type of anastomoses. A digital photograph of each injection study was taken and saved. The antenatal ultrasound images and postnatal dye injection studies were compared.Results18 sets MCDA twins were evaluated. In 3 cases there was evidence of twin‐to‐twin transfusion syndrome. Dye injection of 18 placentas revealed 21 arterio‐arterial anastomoses (AAA), 21 arteriovenous anastomoses (AVA) and 4 veno‐venous anastomoses (VVA). Of these, 10 (48%) AAAs and 5 (24%) AVAs were detected antenatally by color Doppler. In all cases, where an AVA was detected, the placenta was located anteriorly.ConclusionAntenatal detection of AVA was feasible when the placenta was located anteriorly, but proved difficult in posteriorly situated placentas.
Effect of vitamins C and E supplementation on peripheral oxidative stress markers and pregnancy rate in women with endometriosis
Authors: Mier‐Cabrera Jennifer , Genera‐García Mercedes , De la Jara‐Díaz Julio , Perichart‐Perera Otilia , Vadillo‐Ortega Felipe , Hernández‐Guerrero Cesar 
Published: November 2007

AbstractObjectiveTo determine whether vitamins C and E supplementation lowers oxidative stress marker levels and improves pregnancy rate in women with endometriosis.MethodsThirty‐four women with endometriosis received a bar containing vitamins C and E (343 mg and 84 mg, respectively) or placebo for 6 months. Plasma and peritoneal fluid levels of malondialdehyde (MDA) and lipid hydroperoxides (LOOHs) were measured for all women and compared between the 2 groups. Data were analyzed by the t test or 1‐way analysis of variance for parametric data and the Mann–Whitney rank sum test or Kruskall–Wallis test for nonparametric data. The Fisher exact test was used to compare pregnancy rates.ResultsAfter 4 months, the study group had lower levels of MDA and LOOHs than the control group, and the difference became statistically significant in the fourth month for MDA levels and in the sixth month for LOOH levels. The postintervention pregnancy rates were 19% and 12% in the supplementation and placebo groups, respectively, but the difference was not significant.ConclusionsVitamins C and E supplementation was associated with a decrease in the concentration of oxidative stress markers in women with endometriosis. The pregnancy rate, however, did not improve during or after the intervention.
An assessment of the onset and duration of action of olopatadine nasal spray
Authors: Patel Piyush , Roland Peter S. , Marple Bradley F. , Benninger Paul J. , Margalias Harriet , Brubaker Michael , Drake Margaret , Potts Susan L. , Wall G. Michael , Michael Brubaker 
Published: November 2007

ObjectiveSeasonal allergic rhinitis (SAR) is a highly prevalent disease. This study was conducted to evaluate the onset and duration of action of three concentrations of olopatadine nasal spray.METHODSThis was a randomized, double‐blind, single‐dose, placebo‐controlled study, conducted in an environmental exposure chamber in patients with SAR. A total of 320 patients were exposed to ragweed allergen in the chamber and randomized to olopatadine nasal spray 0.2%, 0.4%, 0.6%, or placebo nasal spray. Symptoms (sneezing, runny, itchy, and stuffy nose) were self‐assessed during a 12‐hour study period.RESULTSAll concentrations of olopatadine nasal spray provided clinically meaningful reductions in total nasal symptom scores at 30 minutes compared to the placebo. Olopatadine nasal spray 0.6% was significantly more effective (P<0.05) than placebo nasal spray at all time‐points starting at 90 minutes postdose and continuing over 12 hours.CONCLUSIONSOlopatadine nasal spray 0.6% demonstrated a fast onset of action and maintained an effect for at least 12 hours after dosing.
Long‐term improvements in quality‐of‐life after surgical therapy for pediatric sinonasal disease
Authors: Rudnick Emily F. , Mitchell Ron B. 
Published: November 2007

ObjectiveTo study long‐term changes in quality‐of‐life (QOL) in children after surgery for chronic sinonasal disease.DESIGNProspective, nonrandomized.METHODSCaregivers completed the SN‐5 QOL instrument before surgery. Children underwent either adenoidectomy or endoscopic sinus surgery (ESS). Caregivers then completed a survey <6 months (short‐term) and between six and 24 months after surgery (long‐term). Scores were compared using a paired t test.RESULTSTwenty‐two children were enrolled (mean age, 5.7 years). The majority (59%) of children underwent ESS. The mean preoperative total score was 25.6. Postoperatively, the mean total score was 11.7 at short‐term (P < 0.0001) and 11.5 at long‐term follow‐up (P < 0.0001). Short‐ and long‐term postoperative scores for all domains were significantly different from preoperative scores. In the long‐term scores, the domain with the greatest change was “emotional distress” (SRM 1.9) and with the smallest change was “allergy symptoms” (SRM 1.0). There were no significant differences between children who underwent adenoidectomy compared with ESS.CONCLUSIONSAfter adenoidectomy or ESS, caregivers observe a long‐term improvement in QOL of children with sinonasal disease.
Early experience with minimally invasive esophagectomy in head and neck surgical patients
Authors: Morris Luc G. T. , Tran Theresa N. , DeLacure Mark D. 
Published: November 2007

BackgroundMinimally invasive esophagectomy (MIE) via thoracoscopy and laparoscopy have reduced the morbidity and mortality of total esophagectomy at experienced centers. MIE has not been evaluated in combination with major head and neck surgery, or in the otolaryngology literature.MethodsCase series of 11 consecutive patients undergoing either open or MIE with an ablative neck procedure.ResultsComparing 4 MIEs and 7 open operations, similar operative time, blood loss, and ICU and hospital length of stay were observed. There was one mortality in the open group. A 100% rate of major complications was observed in the MIE group.ConclusionOur multidisciplinary team was unable to achieve improved outcomes in a series of head and neck surgical patients undergoing MIE. This result may represent an early stage of the learning curve for MIE, but may also be attributed to the escalated surgical requirements of head and neck patients.