bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling GPCR active state conformations: The β2‐adrenergic receptor
Authors: Simpson Lisa M. , Wall Ian D. , Blaney Frank E. , Reynolds Christopher A. 
Published: January 2011

AbstractThe recent publication of several G protein‐coupled receptor (GPCR) structures has increased the information available for homology modeling inactive class A GPCRs. Moreover, the opsin crystal structure shows some active features. We have therefore combined information from these two sources to generate an extensively validated model of the active conformation of the β2‐adrenergic receptor. Experimental information on fully active GPCRs from zinc binding studies, site‐directed spin labeling, and other spectroscopic techniques has been used in molecular dynamics simulations. The observed conformational changes reside mainly in transmembrane helix 6 (TM6), with additional small but significant changes in TM5 and TM7. The active model has been validated by manual docking and is in agreement with a large amount of experimental work, including site‐directed mutagenesis information. Virtual screening experiments show that the models are selective for β‐adrenergic agonists over other GPCR ligands, for (R)‐ over (S)‐β‐hydroxy agonists and for β2‐selective agonists over β1‐selective agonists. The virtual screens reproduce interactions similar to those generated by manual docking. The C‐terminal peptide from a model of the stimulatory G protein, readily docks into the active model in a similar manner to which the C‐terminal peptide from transducin, docks into opsin, as shown in a recent opsin crystal structure. This GPCR‐G protein model has been used to explain site‐directed mutagenesis data on activation. The agreement with experiment suggests a robust model of an active state of the β2‐adrenergic receptor has been produced. The methodology used here should be transferable to modeling the active state of other GPCRs. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Molecular dynamics of EF‐G during translocation
Authors: Li Wen , Trabuco Leonardo G. , Schulten Klaus , Frank Joachim 
Published: January 2011

AbstractElongation factor G (EF‐G) plays a crucial role in two stages of mRNA‐(tRNA)2 translocation. First, EF‐G•GTP enters the pre‐translocational ribosome in its intersubunit‐rotated state, with tRNAs in their hybrid (P/E and A/P) positions. Second, a conformational change in EF‐G's Domain IV induced by GTP hydrolysis disengages the mRNA‐anticodon stem‐loops of the tRNAs from the decoding center to advance relative to the small subunit when the ribosome undergoes a backward inter‐subunit rotation. These events take place as EF‐G undergoes a series of large conformational changes as visualized by cryo‐EM and X‐ray studies. The number and variety of these structures leave open many questions on how these different configurations form during the dynamic translocation process. To understand the molecular mechanism of translocation, we examined the molecular motions of EF‐G in solution by means of molecular dynamics simulations. Our results show: (1) rotations of the super‐domain formed by Domains III–V with respect to the super‐domain formed by I–II, and rotations of Domain IV with respect to Domain III; (2) flexible conformations of both 503‐ and 575‐loops; (3) large conformational variability in the bound form caused by the interaction between Domain V and the GTPase‐associated center; (4) after GTP hydrolysis, the Switch I region seems to be instrumental for effecting the conformational change at the end of Domain IV implicated in the disengagement of the codon‐anticodon helix from the decoding center. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Triathlon for energy functions: Who is the winner for design of protein–protein interactions?
Authors: Sharabi Oz , Dekel Ayelet , Shifman Julia M. 
Published: January 2011

AbstractComputational prediction of stabilizing mutations into monomeric proteins has become an almost ordinary task. Yet, computational stabilization of protein–protein complexes remains a challenge. Design of protein–protein interactions (PPIs) is impeded by the absence of an energy function that could reliably reproduce all favorable interactions between the binding partners. In this work, we present three energy functions: one function that was trained on monomeric proteins, while the other two were optimized by different techniques to predict side‐chain conformations in a dataset of PPIs. The performances of these energy functions are evaluated in three different tasks related to design of PPIs: predicting side‐chain conformations in PPIs, recovering native binding‐interface sequences, and predicting changes in free energy of binding due to mutations. Our findings show that both functions optimized on side‐chain repacking in PPIs are more suitable for PPI design compared to the function trained on monomeric proteins. Yet, no function performs best at all three tasks. Comparison of the three energy functions and their performances revealed that (1) burial of polar atoms should not be penalized significantly in PPI design as in single‐protein design and (2) contribution of electrostatic interactions should be increased several‐fold when switching from single‐protein to PPI design. In addition, the use of a softer van der Waals potential is beneficial in cases when backbone flexibility is important. All things considered, we define an energy function that captures most of the nuances of the binding energetics and hence, should be used in future for design of PPIs. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Indefinite noncooperative self‐association of chicken deoxy hemoglobin D
Authors: Rana Mitra S. , Riggs Austen F. 
Published: January 2011

AbstractThe minor tetrameric hemoglobin (Hb), Hb D, of chicken red blood cells self‐associates upon deoxygenation. This self‐association enhances the cooperativity of oxygen binding. The maximal Hill coefficient is greater than 4 at high Hb concentrations. Previous measurements at low Hb concentrations were consistent with a monomer‐to‐dimer equilibrium and an association constant of ∼1.3–1.6 × 104
M−1. Here, the Hb tetramer is considered as the monomer. However, new results indicate that the association extends beyond the dimer. We show by combination of Hb oligomer modeling and sedimentation velocity analyses that the data can be well described by an indefinite noncooperative or isodesmic association model. In this model, the deoxy Hb D associates noncooperatively to give a linear oligomeric chain with an equilibrium association constant of 1.42 × 104
M−1 at 20°C for each step. The data are also well described by a monomer–dimer–tetramer equilibrium model with monomer‐to‐dimer and dimer‐to‐tetramer association constants of 1.87 and 1.03 × 104
M−1 at 20°C, respectively. A hybrid recombinant Hb D was prepared with recombinant αD‐globin and native β‐globin to give a Hb D tetramer (αβ2). This rHb D undergoes decreased deoxygenation‐dependent self‐association compared with the native Hb D. Residue glutamate 138 has previously been proposed to influence intertetramer interactions. Our results with recombinant Hb D show that Glu138 plays no role in deoxy Hb D intertetramer interactions. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Modeling of the conformational flexibility and E/Z isomerism of thiazoximic acid and cefotaxime
Authors: Lerner Dan A. , Berthomieu Dorothée , Maia Elaine R. 
Published: January 2011

AbstractThe conformational flexibility of the Z and E isomers of cefotaxime (CFX) and thiazoximic acid, their ground‐state isomerization path and transition state, were all analyzed in depth. The modeling was carried at the semiempirical and DFT‐BLYP level with geometry optimization for gas phase conditions. That approach was used after a thorough analysis using classical molecular dynamics to initially define large families of conformers. The lowest energy conformers always have an E configuration, in contradiction to the behavior observed in solution, and the Z–E isomerization mechanism is a rotation. These results reveal the remarkable flexibility of these molecules, allow anticipating the role of water and of their target proteins in the redistribution of the conformers population, and provide the best geometry known for CFX. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Stable complex C2H4Al4Li3− and its similarity with bicyclo[2.2.0]hex‐2‐ene: A DFT study
Authors: Satpati Priyadarshi 
Published: January 2011

AbstractWe propose that complexation of all metal antiaromatic Al4Li with C2H4 may lead to stable C2H4Al4Li species [II(b)]. Complexation leads to the electron transfer from Al4Li moiety to C2H4 and development of aromatic character in the Al4 ring. Our proposed compound C2H4Al4Li [II(b)] is very similar to the existing organic compound bicyclo[2.2.0]hex‐2‐ene [I(b)]. The complex C2H4Al4Li [II(b)] can be imagined as an analogue of bicyclo[2.2.0]hex‐2‐ene [I(b)] achieved by a simple replacement of C4H4 in the later with π‐isoelectronic Al4Li moiety in the former. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Properties of hydrogen molecular ion with static screened coulomb and exponential cosine screened coulomb potentials
Authors: Ghoshal Arijit , Ho Y. K. 
Published: January 2011

AbstractWe have investigated the properties of hydrogen molecular ion (H) interacting with screened Coulomb potentials. Two types of potentials have been considered, namely, static screened Coulomb potential and exponential cosine‐screened Coulomb potential. Simulating the localized motion of the nuclei by using high powers of the internuclear coordinate in the generalized Hylleraas‐type wave function we have been able to obtain reasonably accurate binding energies for 11S(J = 0, ν = 0) and 21S(J = 0, ν = 1) states for various values of the screening parameter within the frame work of Ritz variational method. Borromean bindings are found to exist in the ion for a wide range of the screening parameter. Furthermore, expectation values for various operators and cusp condition have been calculated. Results for the unscreened case are in nice agreement with some of the accurate results available in the literature. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Electronic structure of the ground and low‐lying electronic states of MoB and MoB+
Authors: Borin Antonio Carlos , Gobbo João Paulo 
Published: January 2011

AbstractMulticonfigurational second‐order perturbation theory (CASSCF//CASPT2) and quadruple‐ζ ANO‐RCC basis sets were employed to investigate the ground and low‐lying electronic states of MoB and MoB+. Spectroscopic constants, potential energy curves, wavefunctions, Mulliken population analyses, and ionization energies are given. The ground state of MoB is of X6Π symmetry (Re = 1.968 Å, ωe = 664 cm−1, and μ = 2.7 D), giving rise to a Ω = 7/2 ground state after including spin‐orbit coupling. For MoB+, the ground state is computed to be of X7 Σ+ symmetry (Re = 2.224 Å, ωe = 141 cm−1, and μ = 1.2 D), with an adiabatic ionization energy of 7.19 eV and a vertical one of 7.53 eV. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 111:3362–3370, 2010
Symbolic missing data imputation in principal component analysis
Authors: Zuccolotto Paola 
Published: January 2011

AbstractThe concept of symbolic data has been developed with the aim of representing variables whose measurement is affected by some internal variation. This idea has been mainly concerned with the need of aggregating individuals in order to summarize large datasets into smaller matrices of manageable size, retaining as much of the original knowledge as possible. Nevertheless it is often applied also with variables structured from their outset as symbolic variables, although measured on single individuals. This paper deals with the latter framework, and aims at showing that symbolic data analysis techniques can be applied to the field of missing values treatment. The algorithm for a symbolic imputation technique in principal component analysis is presented as a generalization of the basic strategy called interval imputation. An illustrative example and a real data case study show how the proposed technique works. © 2011 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 171–183, 2011
Trellis display for modeling data from designed experiments
Authors: Fuentes Montserrat , Xi Bowei , Cleveland William S. 
Published: January 2011

AbstractVisualizing data by graphing a response against certain factors, and conditioning on other factors, has arisen independently in many contexts. One is the interaction plots used in the analysis of data from designed experiments; these plots show conditional dependence based on the output of methods and models applied to the data. Trellis display, a framework for the visualization of multivariable data, allows conditioning to be readily carried out in a general way. It was developed initially in the context of data sets with a moderate or large number of observations to support the conditioning. This article demonstrates through examples that trellis display is also a highly useful visualization framework for designed experiments with a small number of runs. Trellis allows the visualization of conditional dependence, not only based on the output of models and methods, but also based on the raw data directly, which greatly aids the model building process. Trellis can even succeed for highly fractionated designs. The reason appears to be that for success, such designs require an engineering practice that keeps error variability small, which allows interpretable patterns to emerge on conditioning displays with a limited number of plotted points. © 2010 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 4: 133–145 2011
Videobased lesson analysis: Effective science PD for teacher and student learning
Authors: Roth Kathleen J. , Garnier Helen E. , Chen Catherine , Lemmens Meike , Schwille Kathleen , Wickler Nicole I.Z. 
Published: January 2011

AbstractThe Science Teachers Learning from Lesson Analysis (STeLLA) project is a videobased analysis‐of‐practice PD program aimed at improving teacher and student learning at the upper elementary level. The PD program developed and utilized two “lenses,” a Science Content Storyline Lens and a Student Thinking Lens, to help teachers analyze science teaching and learning and to improve teaching practices in this year‐long program. Participants included 48 teachers (n = 32 experimental, n = 16 control) and 1,490 students. The STeLLA program significantly improved teachers' science content knowledge and their ability to analyze science teaching. Notably, the STeLLA teachers further increased their classroom use of science teaching strategies associated with both lenses while their students increased their science content knowledge. Multi‐level HLM analyses linked higher average gains in student learning with teachers' science content knowledge, teachers' pedagogical content knowledge about student thinking, and teaching practices aimed at improving the coherence of the science content storyline. This paper highlights the importance of the science content storyline in the STeLLA program and discusses its potential significance in science teaching and professional development more broadly. © 2011 Wiley Periodicals, Inc., J Res Sci Teach 48: 117–148, 2011
A novel halogen‐free intumescent flame retardant containing phosphorus and nitrogen and its application in polypropylene systems
Authors: Xiang Haiwang , Sun Caiying , Jiang Dawei , Zhang Qingbo , Dong Chunmei , Liu Lei 
Published: January 2011

AbstractA novel halogen‐free intumescent flame retardant, pentaerythritol spirobisphosphoryl‐dicyandiamide (SPDC), was synthesized and characterized by FTIR, 1H NMR, and 31P NMR spectra. The new flame retardant was used in polypropylene (PP) to prepare flame‐retardant materials whose flammability and thermal behavior were studied by the limiting oxygen index (LOI) method, thermogravimetric analysis (TGA), and cone calorimetry (CONE). The mechanical properties were also investigated. The results indicated that when the addition of SPDC reached 30 wt%, the material showed both excellent flame retardancy and anti‐dripping abilities for PP. Moreover, the LOI value of the PP‐IFR(30%) was 32.5, and it passed the UL‐94 V‐0 rating test. The CONE results revealed that in PP, SPDC(30%) significantly decreased the peak heat release, total heat release, and smoke relative to their values for pure PP. The morphological structures observed by SEM demonstrated that SPDC could promote the formation of a homogeneous and compact intumescent char layer. The TGA data showed that SPDC could enhance the thermal stability of PP and effectively increase the char residue formation. J. VINYL ADDIT. TECHNOL., 2010. © 2010 Society of Plastics Engineers
Model‐free data screening and cleaning
Authors: Tarter Michael E. 
Published: January 2011

AbstractCategories of data screening and cleaning issues are reviewed and discussed. Bivariate model‐free approaches, specialized model‐free regression techniques, together with order statistic‐based (OSB) approaches are illustrated and shown to be of particular value for a variety of data screening and cleaning applications. It is shown how a combination of curve estimation with OSB approaches can help screen a progression to AIDS data set.WIREs Comp Stat2011 3 168–176 DOI: 10.1002/wics.140This article is categorized under:Statistical and Graphical Methods of Data Analysis > Density EstimationStatistical and Graphical Methods of Data Analysis > Data Reduction, Smoothing, and FilteringStatistical and Graphical Methods of Data Analysis > Nonparametric Methods
A Comparison of Prognosis between Patients with Hepatitis B and C Virus‐related Hepatocellular Carcinoma Undergoing Resection Surgery
Authors: Kao Wei‐Yu , Su Chien‐Wei , Chau Gar‐Yang , Lui Wing‐Yiu , Wu Chew‐Wun , Wu Jaw‐Ching 
Published: January 2011

AbstractBackgroundThe impact of viral factors on the prognosis of hepatocellular carcinoma (HCC) remains controversial because of heterogeneous populations included in previous reports. This study aims to compare clinicopathologic features and prognoses between patients with hepatitis B‐ and hepatitis C‐related HCC who underwent resection surgery.MethodsWe enrolled 609 patients with positive serum hepatitis B virus (HBV) surface antigen (HBsAg) and negative serum antibody against hepatitis C virus (anti‐HCV) as the B‐HCC group and 206 patients with negative serum HBsAg and positive anti‐HCV as the C‐HCC group. The overall survival rates and cumulative recurrence rates were compared between these two groups.ResultsB‐HCC patients were significantly younger, predominantly male, had better liver functional reserve, but more advanced tumor stage than C‐HCC patients. After a median follow‐up period of 40.6 months, 427 patients had died. Furthermore, 501 patients had tumor recurrence after surgery. The postoperative overall survival rates (p = 0.640) and recurrence rates (p = 0.387) of the two groups were comparable. However, the overall survival rate was higher in the B‐HCC group than in the C‐HCC group in the cases of transplantable HCC (p = 0.021) and Barcelona‐Clinic Liver Cancer stage A HCC (p = 0.040).ConclusionsViral etiologies were not apparent in determining outcomes of HCC patients who underwent resection due to heterogeneous studied populations. In early‐stage HCC, B‐HCC patients had better outcomes than C‐HCC patients did because of better liver reserve and less hepatic inflammation.
Factors Influencing Career Choice After Initial Training in Surgery
Authors: McHugh Seamus , Corrigan Mark , Sheikh Athar , Lehane Elaine , Tanner William , Hill Arnold 
Published: January 2011

AbstractIntroductionIrish general surgery faces a recruitment crisis with only 87 of 145 (60%) basic surgical training (BST) places filled in 2009. We assessed basic surgical trainees to identify objective, and potentially modifiable, factors that influence ultimate recruitment into a general surgical career.MethodsCandidates commencing BST training during a 5‐year period between 2004 and 2008 were included in a quantitative study. In addition a total of 2,536 candidates, representing all those who commenced surgical training in Ireland since 1960 were identified through the Royal College of Surgeons in Ireland (RCSI) database and invited to complete an online survey. Statistical analysis was performed using SPSS version 15, with p < 0.05 considered significant.ResultsDuring the 5‐year quantitative study period there were 381 BST trainees. Gender was a significant predictor of career choice with women more likely to ultimately choose a nonsurgical career after initial surgical training (p = 0.049). Passing surgical membership examinations (MRCS) also was predictive of remaining in surgery (p = 0.005). Training region was not a significant predictor of ultimate career choice. There were 418 survey respondents. The influence of role models was most commonly cited as influencing candidates in choosing to commence surgical training. Candidates who rated “academic opportunity” (p = 0.023) and “intellectual challenge” (p = 0.047) as factors that influenced their decision to commence surgical training were more likely to ultimately continue their careers in a surgical speciality.ConclusionsThis study describes the career pathway of surgical trainees and confirms the importance of academic achievement in discriminating between candidates applying for surgical training schemes.
Improvement of sexual function after transobturator tape procedure in women with stress urinary incontinence
Authors: Arts-de Jong M. , van Altena A. M. , Aalders C. I. M. , Dijkhuizen F. P. H. L. J. , van Balken M. R. 
Published: January 2011

AbstractSling procedures are a widely proven treatment for stress urinary incontinence. The aim of this prospective study was to evaluate the effect of the transobturator tape on female sexual functioning. Fifty-four women treated for stress urinary incontinence with transobturator tape filled out self-administered questionnaires on quality of life, urinary incontinence, and sexual function prior to surgery and 6 weeks and 12 months postoperatively. Preoperatively, 40 women (78%) were sexually active. There were no significant postoperative changes regarding frequency of sexual activity, sexual desire, and problems with lubrication or orgasm. Preoperatively, 55% reported urinary leakage during sexual activity and after surgery 6.5%. Sexual satisfaction was significantly improved 6 weeks (p = 0.05) and 12 months (p = 0.03) postoperatively. Pain during or after sexual activity was declined, only one patient reported worsening of pain. The transobturator tape procedure has a positive effect on female sexual functioning by reducing urinary leakage and pain during or after sexual activity. It seems to improve the overall sexual satisfaction. Further research is warranted to support these preliminary findings.
Changes in Fatty Acids, Tocochromanols, Carotenoids and Chlorophylls Content During Flaxseed Development
Authors: Herchi Wahid , Sakouhi Faouzi , Boukhchina Sadok , Kallel Habib , Pepe Claude 
Published: January 2011

AbstractA comparative study was performed to determine tocopherols, tocotrienols, fatty acids, and pigments content during the development of three varieties of flaxseed (H52, O116 and P129). Seed samples were collected at regular intervals from 7 to 56 days after flowering (DAF). The highest content of chlorophyll (89.72–130.5 mg/kg oil) was detected at 7 DAF. The maximum level of carotenoids (52.10–65.55 mg/kg oil) was reached at 21 DAF. During seed development, unsaturated fatty acids are the major component, reaching 85% of the total fatty acids while saturated fatty acids content were about 15%. The maximum level of γ‐tocopherol (585 mg/kg oil) was reached at 42 DAF in P129 variety. These results may be useful for evaluating the flaxseed quality and determining its optimal harvest period.