bluuebunny/crossref_metadata_2025_split huggingface dataset:
The White Paper: will GP consortia invest in mental health services?
Authors: Walton Ian , Hill Lisa 
Published: October 2010

AbstractNew governments have an obvious desire to demonstrate that they mean business, so the massive changes in the administration of the NHS proposed by the recent White Paper1 should come as no surprise. Many of us, however, will question whether its intentions can truly be carried out at the speed intended. The aim is to lead the change needed with GPs, the vast majority of whom have little experience of commissioning at the level the White Paper requires. With so much to focus on, how many GP commissioning
consortia will treat mental health as a priority and what will this mean for our patients and for those of us who work in mental health services?. Copyright © 2010 Wiley Interface Ltd
Copper(0)‐mediated living radical polymerization of acrylonitrile: SET‐LRP or AGET‐ATRP
Authors: Liu Xiao‐Hui , Zhang Gui‐Bao , Li Bai‐Xiang , Bai Yun‐Gang , Li Yue‐Sheng 
Published: October 2010

AbstractCu(0)‐mediated living radical polymerization was first extended to acrylonitrile (AN) to synthesize polyacrylonitrile with a high molecular weight and a low polydispersity index. This was achieved by using Cu(0)/hexamethylated tris(2‐aminoethyl)amine (Me6‐TREN) as the catalyst, 2‐bromopropionitrile as the initiator, and dimethyl sulfoxide (DMSO) as the solvent. The reaction was performed under mild reaction conditions at ambient temperature and thus biradical termination reaction was low. The rapid and extensive disproportionation of Cu(I)Br/Me6‐TREN in DMSO/AN supports a mechanism consistent with a single electron transfer‐living radical polymerization (SET‐LRP) rather than activators generated by electron transfer atom transfer radical polymerization (AGET ATRP). 1H NMR analysis and chain extension experiment confirm the high chain‐end functionality of the resultant polymer. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010
Managing social difficulties: roles and responsibilities of patients and staff
Authors: Wright Penny , Bingham Laura , Taylor Sally , Hanif Naheed , Podmore Emma , Velikova Galina 
Published: October 2010

AbstractBackground: Implementation of guidance on assessment and management of psychosocial and supportive‐care problems or needs will be successful only if consideration is given to existing skills, experience and expectations of staff and patients. This study examines the roles and responsibilities of staff, patients and families in relation to management of social difficulties and proposes a pathway for response.Methods: A qualitative study was performed using staff and patient interviews. Seventeen doctors and 16 nurses were interviewed using patient scenarios and a support service questionnaire. Patients (n = 41) completed a screening questionnaire (the Social Difficulties Inventory) and were interviewed. Interviews were audio‐recorded, transcribed and subjected to a Framework analysis. Analysis examined (1) actions taken by staff and patients in response to social difficulties, (2) reasons given for action taken and (3) perceptions of staff and patients of who was responsible for taking action.Results: Staff were confident concerning clinically related issues (i.e. mobility) but more hesitant concerning difficulties related to money, work and family concerns. Patients liked to cope with problems on their own where possible, would have liked information or support from staff but were uncertain how to access this. Results led to development of a hierarchy of interventions in response to detected social difficulties.Discussion: For routine assessment of social difficulties, patients, nurses and doctors will have to work collaboratively, with nurses taking a lead in discussion. For specific clinically related problems doctors would play a more primary role. Copyright © 2010 John Wiley & Sons, Ltd.
A differential association of Apolipoprotein E isoforms with the amyloid‐β oligomer in solution
Authors: Petrlova Jitka , Hong Hyun‐Seok , Bricarello Daniel A. , Harishchandra Ghimire , Lorigan Gary A. , Jin Lee‐Way , Voss John C. 
Published: October 2010

AbstractThe molecular pathogenesis of disorders arising from protein misfolding and aggregation is difficult to elucidate, involving a complex ensemble of intermediates, whose toxicity depends upon their state of progression along distinct processing pathways. To address the complex misfolding and aggregation that initiates the toxic cascade resulting in Alzheimer's disease (AD), we have developed a 2,2,6,6‐tetramethylpiperidine‐1‐oxyl‐4‐amino‐4‐carboxylic acid spin‐labeled amyloid‐β (Aβ) peptide to observe its isoform‐dependent interaction with the apoE protein. Although most individuals carry the E3 isoform of apoE, ∼15% of humans carry the E4 isoform, which is recognized as the most significant genetic determinant for Alzheimer's. ApoE is consistently associated with the amyloid plaque marker for AD. A vital question centers on the influence of the two predominant isoforms, E3 and E4, on Aβ peptide processing and hence Aβ toxicity. We used electron paramagnetic resonance (EPR) spectroscopy of incorporated spin labels to investigate the interaction of apoE with the toxic oligomeric species of Aβ in solution. EPR spectra of the spin‐labeled side chain report on side chain and backbone dynamics as well as the spatial proximity of spins in an assembly. Our results indicate oligomer binding involves the C‐terminal domain of apoE, with apoE3 reporting a much greater response through this conformational marker. Coupled with SPR binding measurements, apoE3 displays a higher affinity and capacity for the toxic Aβ oligomer. These findings support the hypothesis that apoE polymorphism and Alzheimer's risk can largely be attributed to the reduced ability of apoE4 to function as a clearance vehicle for the toxic form of Aβ. Proteins 2011. © 2010 Wiley‐Liss, Inc.
One‐bond and two‐bond j couplings help annotate protein secondary‐structure motifs: J‐coupling indexing applied to human endoplasmic reticulum protein ERp18
Authors: Schmidt Jürgen M. , Zhou Shen , Rowe Michelle L. , Howard Mark J. , Williamson Richard A. , Löhr Frank 
Published: October 2010

AbstractNMR coupling constants, both direct one‐bond (1J) and geminal two‐bond (2J), are employed to analyze the protein secondary structure of human oxidized ERp18. Coupling constants collected and evaluated for the 18 kDa protein comprise 1268 values of 1JCαHα, 1JCαCβ, 1JCαC′, 1JC′N′, 1JN′Cα, 1JN′HN, 2JCαN′, 2JHNCα, 2JC′HN, and 2JHαC′. Comparison with 1J and 2J data from reference proteins and pattern analysis on a per‐residue basis permitted main‐chain φ,ψ torsion‐angle combinations of many of the 149 amino‐acid residues in ERp18 to be narrowed to particular secondary‐structure motifs. J‐coupling indexing is here being developed on statistical criteria and used to devise a ternary grid for interpreting patterns of relative values of J. To account for the influence of the varying substituent pattern in different amino‐acid sidechains, a table of residue‐type specific threshold values was compiled for discriminating small, medium, and large categories of J. For the 15‐residue insertion that distinguishes the ERp18 fold from that of thioredoxin, the J‐coupling data hint at a succession of five isolated Type‐I β turns at progressively shorter sequence intervals, in agreement with the crystal structure. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Accounting for conformational entropy in predicting binding free energies of protein‐protein interactions
Authors: Kamisetty Hetunandan , Ramanathan Arvind , Bailey‐Kellogg Chris , Langmead Christopher James 
Published: October 2010

AbstractProtein‐protein interactions are governed by the change in free energy upon binding, ΔG = ΔH − TΔS. These interactions are often marginally stable, so one must examine the balance between the change in enthalpy, ΔH, and the change in entropy, ΔS, when investigating known complexes, characterizing the effects of mutations, or designing optimized variants. To perform a large‐scale study into the contribution of conformational entropy to binding free energy, we developed a technique called GOBLIN (Graphical mOdel for BiomoLecular INteractions) that performs physics‐based free energy calculations for protein‐protein complexes under both side‐chain and backbone flexibility. GOBLIN uses a probabilistic graphical model that exploits conditional independencies in the Boltzmann distribution and employs variational inference techniques that approximate the free energy of binding in only a few minutes. We examined the role of conformational entropy on a benchmark set of more than 700 mutants in eight large, well‐studied complexes. Our findings suggest that conformational entropy is important in protein‐protein interactions—the root mean square error (RMSE) between calculated and experimentally measured ΔΔGs decreases by 12% when explicit entropic contributions were incorporated. GOBLIN models all atoms of the protein complex and detects changes to the binding entropy along the interface as well as positions distal to the binding interface. Our results also suggest that a variational approach to entropy calculations may be quantitatively more accurate than the knowledge‐based approaches used by the well‐known programs FOLDX and ROSETTA—GOBLIN's RMSEs are 10 and 36% lower than these programs, respectively. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Design principles for chlorophyll‐binding sites in helical proteins
Authors: Braun Paula , Goldberg Eran , Negron Christopher , von Jan Mathias , Xu Fei , Nanda Vikas , Koder Ronald L. , Noy Dror 
Published: October 2010

AbstractThe cyclic tetrapyrroles, viz. chlorophylls (Chl), their bacterial analogs bacteriochlorophylls, and hemes are ubiquitous cofactors of biological catalysis that are involved in a multitude of reactions. One systematic approach for understanding how Nature achieves functional diversity with only this handful of cofactors is by designing de novo simple and robust protein scaffolds with heme and/or (bacterio)chlorophyll [(B)Chls]‐binding sites. This strategy is currently mostly implemented for heme‐binding proteins. To gain more insight into the factors that determine heme‐/(B)Chl‐binding selectivity, we explored the geometric parameters of (B)Chl‐binding sites in a nonredundant subset of natural (B)Chl protein structures. Comparing our analysis to the study of a nonredundant database of heme‐binding helical histidines by Negron et al. (Proteins 2009;74:400–416), we found a preference for the m‐rotamer in (B)Chl‐binding helical histidines, in contrast to the preferred t‐rotamer in heme‐binding helical histidines. This may be used for the design of specific heme‐ or (B)Chl‐binding sites in water‐soluble helical bundles, because the rotamer type defines the positioning of the bound cofactor with respect to the helix interface and thus the protein‐binding site. Consensus sequences for (B)Chl binding were identified by combining a computational and database‐derived approach and shown to be significantly different from the consensus sequences recommended by Negron et al. (Proteins 2009;74:400–416) for heme‐binding helical proteins. The insights gained in this work on helix‐ (B)Chls‐binding pockets provide useful guidelines for the construction of reasonable (B)Chl‐binding protein templates that can be optimized by computational tools. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Studies on the inference of protein binding regions across fold space based on structural similarities
Authors: Teyra Joan , Hawkins John , Zhu Hongbo , Pisabarro M. Teresa 
Published: October 2010

AbstractThe emerging picture of a continuous protein fold space highlights the existence of non obvious structural similarities between proteins with apparent different topologies. The identification of structure resemblances across fold space and the analysis of similar recognition regions may be a valuable source of information towards protein structure‐based functional characterization. In this work, we use non‐sequential structural alignment methods (ns‐SAs) to identify structural similarities between protein pairs independently of their SCOP hierarchy, and we calculate the significance of binding region conservation using the interacting residues overlap in the ns‐SA. We cluster the binding inferences for each family to distinguish already known family binding regions from putative new ones. Our methodology exploits the enormous amount of data available in the PDB to identify binding region similarities within protein families and to propose putative binding regions. Our results indicate that there is a plethora of structurally common binding regions among proteins, independently of current fold classifications. We obtain a 6‐ to 8‐fold enrichment of novel binding regions, and identify binding inferences for 728 protein families that so far lack binding information in the PDB. We explore binding mode analogies between ligands from commonly clustered binding regions to investigate the utility of our methodology. A comprehensive analysis of the obtained binding inferences may help in the functional characterization of protein recognition and assist rational engineering. The data obtained in this work is available in the download link at www.scowlp.org. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Conformational flexibility and binding interactions of the G protein βγ heterodimer
Authors: Park Min‐Sun , Smrcka Alan V. , Stern Harry A. 
Published: October 2010

AbstractPrevious NMR experiments on unbound G protein βγ heterodimer suggested that particular residues in the binding interface are mobile on the nanosecond timescale. In this work we performed nanosecond‐timescale molecular dynamics simulations to investigate conformational changes and dynamics of Gβγ in the presence of several binding partners: a high‐affinity peptide (SIGK), phosducin, and the GDP‐bound α subunit. In these simulations, the high mobility of GβW99 was reduced by SIGK, and it appeared that a tyrosine might stabilize GβW99 by hydrophobic or aromatic stacking interactions in addition to hydrogen bonds. Simulations of the phosducin‐Gβγ complex showed that the mobility of GβW99 was restricted, consistent with inferences from NMR. However, large‐scale conformational changes of Gβγ due to binding, which were hypothesized in the NMR study, were not observed in the simulations, most likely due to their short (nanosecond) duration. A pocket consisting of hydrophobic amino acids on Gα appears to restrict GβW99 mobility in the crystal structure of the Gαβγ? heterotrimer. The simulation trajectories are consistent with this idea. However, local conformational changes of residues GβW63, GβW211, GβW297, GβW332, and GβW339 were detected during the MD simulations. As expected, the magnitude of atomic fluctuations observed in simulations was greater for α than for the βγ subunits, suggesting that α has greater flexibility. These observations support the notion that to maintain the high mobility of GβW99 observed by solution NMR requires that the Gβ–α interface must open up on time scale longer than can be observed in nanosecond scale simulations. Proteins 2011. © 2010 Wiley‐Liss, Inc.
Correlation effects for a quasi‐one‐dimensional polaron gas
Authors: Machado Paulo César Miranda , Borges Antônio Newton , Osório Francisco Aparecido Pinto 
Published: October 2010

AbstractIn this work, we investigate the plasmon–LO phonon interaction effects on the intrasubband structure factor, electron–electron effective potential, and plasmon energy associated with the lowest subband in a GaAs‐AlGaAs rectangular quantum‐well wire (QWW) as a function of the electronic density. Our calculations are performed using the self‐consistent field approximation, which includes the local‐field correction (LFC) within the Singwi, Tosi, Land, and Sjolander (STLS) theory, at zero temperature and assuming a three‐subband model, where only the first subband is occupied by electrons. We report for the first time dips in the structure factor spectra as a function of the quasi‐one‐dimensional (Q1D) plasmon–LO phonon wavevector that are directly related with the resonant split of the collective excitation energy into two branches due to the polaronic effects.
In vivo and in vitro antibacterial activity of acanthospermal B, a sesquiterpene lactone isolated from Acanthospermum hispidum
Authors: Arena Mario E. , Cartagena Elena , Gobbato Nadia , Baigori Mario , Valdez Juan C. , Bardon Alicia 
Published: October 2010

AbstractAcanthospermal B (AcB), the major sesquiterpene lactone (SL) of Acanthospermum hispidum, an herb widely spread in Argentina, is a selective antibacterial agent against Enterococcus faecalis and Staphylococcus aureus, but inactive on Gram‐negative and Lactobacillus. Methicillin‐resistant Staphylococcus aureus (MRSA) is one of the main microorganisms involved in human chronic infection. A balb\c mouse skin infection model was developed to reproduce the lesions caused by acute and chronic infections produced by MRSA. After determination of the maximum concentration of AcB unable to produce tissular injury after intradermal injection, the anti‐MRSA effect of AcB was evaluated on skin, liver and spleen tissues of infected mice. AcB, at doses of 2.5 mg/kg, produced a ten times decrease of MRSA growth in skin infection. In addition, the same dose prevented the dissemination to liver and/or spleen. AcB also displayed a bacteriostatic effect, in vitro, on MRSA cultures at 50 µg/mL that seems to be caused by partial denaturation of total bacterial DNA and/or inhibition of the PCR reaction in not denaturized DNA. Finally, total MRSA cell wall lysis occurred at a concentration of 100 µg/mL of AcB after 2 h of exposure. Copyright © 2010 John Wiley & Sons, Ltd.
The formation of a multicell thunderstorm behind a sea‐breeze front
Authors: Wissmeier Ulrike , Smith Roger K. , Goler Robert 
Published: October 2010

AbstractIdealized three‐dimensional numerical simulations are used to investigate the influence of sea breezes on the evolution of multicell thunderstorms in the Tropics. The study is motivated by a desire to understand a particular type of severe storm system that occurs occasionally over the ‘Top End’ region of northern Australia, but the results should have wider applicability. The calculations are carried out using Bryan's cloud model.The simulations reproduce the main features of the evolution of an observed storm system. New cells develop on the gust front of the initial updraught, behind the sea‐breeze front, and subsequently merge to form a multicell thunderstorm. The propagation speed and direction, the orientation, and length of the line of updraught cells are all similar to those observed. The sea breezes in the model play an important role in the evolution of the storm. In general, the low‐level convergence at the gust front produced by the initial cell needs to be strong enough and to persist for a sufficiently long time to allow new cells to develop near this front. A strong cold pool occurs if the initial updraught is sufficiently tilted so that the downdraught does not fall into it, but supplies cold air close to the gust front. A generalized form of the Rotunno–Klemp–Weisman criterion was used to test whether the new updraughts developed at locations where the cold pool circulation was largely opposed by that of the environmental shear. The comparison of the shear components normal to the gust front showed that new cells develop even though this criterion is not fulfilled, suggesting that the criterion is not applicable to the more complex flow configurations studied here. Copyright © 2010 Royal Meteorological Society
A compression‐based distance measure for texture
Authors: Campana Bilson J. L. , Keogh Eamonn J. 
Published: October 2010

AbstractThe analysis of texture is an important subroutine in application areas as diverse as biology, medicine, robotics, and forensic science. While the last three decades have seen extensive research in algorithms to measure texture similarity, almost all existing methods require the careful setting of many parameters. There are many problems associated with a lot of parameters, the most obvious of which is that with many parameters to fit, it is very difficult to avoid overfitting. In this work, we propose to extend recent advances in Kolmogorov complexity‐based similarity measures to texture matching problems. These Kolmogorov‐based methods have been shown to be very useful in intrinsically discrete domains such as DNA, protein sequences, MIDI music, and natural languages; however, they are not well defined for real‐valued data. To address this, we introduce a very simple idea, the Campana‐Keogh (CK) video compression‐based method for texture measures. These measures utilize video compressors to approximate the Kolmogorov complexity. Using the parameter‐free CK method, we novely utilize lossy compression to create an efficient and robust parameter‐lite texture similarity measure: the CK‐1 distance measure. We demonstrate the utility of our measure with extensive empirical evaluations on real‐world case studies drawn from nematology, arachnology, entomology, medicine, forensics, texture analysis benchmarks, and many other domains. Copyright © 2010 Wiley Periodicals, Inc. Statistical Analysis and Data Mining 3: 381‐398, 2010
Microstructure analysis of sol‐gel‐derived nanocrystalline ITO thin films
Authors: Li Ying , Zhao Gaoyang , Ren Yang , Chen Dichun 
Published: October 2010

AbstractThe technique for ITO (Tin‐doped indium oxide) thin films by sol‐gel process is presented in this paper. After annealing at 500° for 15 min, ITO gel films get transformed into nanocrystallined indium tin oxide films. We studied the microstructure of ITO thin film which is closely related to optical and electrical properties. The microstructure of ITO thin film can be observed through high‐resolution transmission electronic spectroscopy (HRTEM) and the Fast Fourier Transform (FFT) technique. The film is nanocrystallite with grain sizes about 20 nm. Also, the surface chemical components were studied by XPS spectra. The transmission and the resistivity of ITO films is 97.0% and 3.5 × 10−3 Ω•cm, respectively. Copyright © 2010 John Wiley & Sons, Ltd.
Physicochemical study of the ‘anatase/electrolyte solution’ interface in suspension and closely packed particles of the solid
Authors: Kamarianakis George , Tsevis Athanasios , Spanos Nikos 
Published: October 2010

AbstractThe electric double layer (EDL) developed at the interface of anatase in contact with aqueous electrolyte solutions was investigated at 25 °C. Potentiometric titrations (PT), measurements of the electrophoretic mobility (EM) in suspensions, and streaming potential (SP) measurements were taken. The surface charge over a wide pH range (ca. 3–10) and the point of zero charge (pzc = 6.3 ± 0.1) of anatase was easily determined by means of the suspension titration curve and the blank one, obtained at a single ionic strength value. Streaming potential measurements were conducted in anatase particles appropriately packed to form plugs. Two different plugs were prepared differing in the degree of particles' packing and, consequently, in the respective porosities. It was found that surface conductivity is lower at higher packing (lower porosity), because of the reduction of the total surface area in contact with the electrolyte. Moreover, it was found that the surface conductivity of the anatase samples increased at pH values away from pzc, while the mobility of the counter ions behind the shear plane decreased. This trend was attributed to the increase of the absolute surface charge. This increase caused an increase in the amount of the counter ions and, therefore, in the conductivity due to these ions. On the other hand, stronger electrostatic interactions between the surface of the solid and the counter ions reduced their mobility. The packing density of the anatase particles in the respective plugs, affected the values of ζ‐potential calculated from SP measurements when the effect of surface conductivity was neglected. Copyright © 2010 John Wiley & Sons, Ltd.