bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparisons of temperature response to solar forcing in the pre‐ and post periods of satellite data assimilation
Authors: Powell Alfred M. , Xu Jianjun
Published: October 2010

On the basis of both composite and multiple linear regression analysis, three temperature datasets from two reanalyses and one set of satellite observations have been used to evaluate the different responses in the winter [December–February (DJF)] period as they relate to solar forcing between the pre‐ and post periods of satellite data assimilation. The two periods are defined as 1958–1978 when no satellite data was available to be assimilated and the 1979–2002 period when satellite data was assimilated in the operational forecast models. The solar forcing signal for the two periods can be identified as significant in the extremes of the solar cycle (maximum and minimum). The composite analysis shows that the solar response of the DJF temperatures in the three datasets shows large‐scale similarities although there are differences over the southern middle‐high latitudes and some tropical areas. The stratospheric response showed the strongest DJF temperature anomalies related to solar variability occurring over the Arctic, but its sign is negative in 1979–2002 and positive in 1958–1978 for solar maximum activity. The stratospheric temperature response can be confirmed using a multiple regression analysis. The temperature features may be partially explained by the impacts of heating via ozone absorption, and is reinforced by the solar cycle, El‐Niño Southern Oscillation (ENSO), stratospheric quasi‐biennial oscillation (QBO), volcanic eruptions and other factors. In contrast, the tropospheric response, with a dynamic wavelike structure, occurs over the middle latitudes. The tropospheric differences between the two periods are not clearly resolved and raise questions about the efficacy of the observations and our ability to use the observations effectively. Copyright © 2010 Royal Meteorological Society
Preparation and characterization of molecularly imprinted microspheres for dibutyl phthalate recognition in aqueous environment
Authors: He Juan , Lv Ruihe , Cheng Jie , Li Yongxiang , Xue Jianfang , Lu Kui , Wang Fengcheng
Published: October 2010

Molecularly imprinted microspheres (MIMs) were prepared by suspension polymerization for the binding and recognition of dibutyl phthalate (DBP). DBP was used as the template molecule, methacrylic acid as the functional monomer, ethylene dimethacrylate (EDMA) as the linking agent, PVA as the dispersing agent, and Span 60 as the surfactant. The MIMs were characterized with electron microscope scanning and rebinding experiments. The Scatchard plot revealed that the template‐polymer system has a two‐site binding behavior with dissociation constants of 4.05 and 0.515 mmol/L. The MIMs exhibited the highest selective rebinding to DBP at 736.85 μg/g. The recoveries of the MIM‐SPE column for DBP extraction was 94.75–101.9% with the RSD of 1.5–7.3%, indicating the feasibility of the prepared MIMs for DBP extraction. Finally, the method developed was used to analyze the trace levels of phthalate in aqueous environment samples.
Application of liquid chromatography in polymer non‐ionic antistatic additives analysis
Authors: González‐Rodríguez M. Victoria , Dopico‐García M. Sonia , Noguerol‐Cal Rosalía , Carballeira‐Amarelo Tania , López‐Vilariño José M. , Fernández‐Martínez Gerado
Published: October 2010

This article investigates the applicability of HPLC‐UV, ultra performance LC‐evaporative light‐scattering detection (UPLC‐ELSD), HPLC‐ESI(+)‐MS and HPLC‐hybrid linear ion trap (LTQ) Orbitrap MS for the analysis of different non‐ionic antistatic additives, Span 20, Span 60, Span 65, Span 80, Span 85 (sorbitan fatty acid esters), Atmer 129 (glycerol fatty acid ester) and Atmer 163 (ethoxylated alkylamine). Several alkyl chain length or different degrees of esterification of polyol derivatives can be present in commercial mixtures of these polymer additives. Therefore, their identification and quantification is complicated. Qualitative composition of the studied compounds was analysed by MS. HPLC‐UV, UPLC‐ELSD and HPLC‐LTQ Orbitrap MS methods were applied to the quantitative determination of the different Spans, Atmer 129 and Atmer 163, respectively. Quality parameters of these methods were established and no derivatization was necessary.
The relationship between somatization and posttraumatic symptoms among immigrants receiving primary care services*
Authors: Aragona Massimiliano , Catino Elena , Pucci Daniela , Carrer Sara , Colosimo Francesco , Lafuente Montserrat , Mazzetti Marco , Maisano Bianca , Geraci Salvatore
Published: October 2010

Traumatic experiences and somatization are related in studies on complex trauma, though this relation is rarely studied in immigrants. The relationship between somatization and self‐reported traumatic experiences and posttraumatic symptoms in patients attending a primary care service for immigrants was studied. The sample consisted of 101 patients attending a primary healthcare service dedicated to immigrants. Participants completed two self‐assessment questionnaires specifically designed for use in transcultural research: the Bradford Somatic Inventory and the Harvard Trauma Questionnaire. Both were translated and back‐translated into eight languages. Somatization was significantly related to traumatic events and posttraumatic symptoms. In primary care centers for immigrants, physicians should give particular attention to somatization as a possible sign of unreported posttraumatic symptoms.
Morphological Transition Induced by Nanoparticles in Dynamically Asymmetric PS/PVME Blends
Authors: Xia Tian , Huang Yajiang , Peng Xiaojuan , Li Guangxian
Published: October 2010

The influence of hydrophilic SiO2 nanoparticles on the morphology of polystyrene (PS)/poly(vinyl methyl ether) (PVME) (10/90) blends in an unstable region has been investigated using optical microscopy and dynamic rheology techniques. For PS/PVME (10/90) blends annealed at 120 °C, the formation of a transient network structure and subsequent phase inversion indicates that a typical viscoelastic phase separation has occurred. However, for PS/PVME (10/90) blends filled with 4 wt.‐% SiO2 nanoparticles, a droplet‐like structure was formed immediately without the appearance of a network‐like structure. The rheological relaxation time of the blends suggested that the morphology transition observed in the PS/PVME/SiO2 (10/90/4) blend was related to the change in the dynamic asymmetry between the PS‐rich phase and the PVME‐rich phase, which was induced by the selective affinity of the SiO2 nanoparticles for PVME. After the incorporation of SiO2 nanoparticles, the PVME‐rich majority phase, which is originally the dynamically fast phase, became the slow phase, and led to a dynamic inversion compared with those unfilled blends.

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Lipidomics era: Accomplishments and challenges
Authors: Bou Khalil Maroun , Hou Weimin , Zhou Hu , Elisma Fred , Swayne Leigh Anne , Blanchard Alexandre P. , Yao Zemin , Bennett Steffany A.L. , Figeys Daniel
Published: October 2010

Lipid mediators participate in signal transduction pathways, proliferation, apoptosis, and membrane trafficking in the cell. Lipids are highly complex and diverse owing to the various combinations of polar headgroups, fatty acyl chains, and backbone structures. This structural diversity continues to pose a challenge for lipid analysis. Here we review the current state of the art in lipidomics research and discuss the challenges facing this field. The latest technological developments in mass spectrometry, the role of bioinformatics, and the applications of lipidomics in lipid metabolism and cellular physiology and pathology are also discussed. © 2010 Wiley Periodicals, Inc. Mass Spec Rev 29:877–929, 2010
Subcellular phosphoproteomics
Authors: Trost Matthias , Bridon Gaëlle , Desjardins Michel , Thibault Pierre
Published: October 2010

Protein phosphorylation represents one of the most extensively studied post‐translational modifications, primarily due to the emergence of sensitive methods enabling the detection of this modification bothin vitroandin vivo. The availability of enrichment methods combined with sensitive mass spectrometry instrumentation has played a crucial role in uncovering the dynamic changes and the large expanding repertoire of this reversible modification. The structural changes imparted by the phosphorylation of specific residues afford exquisite mechanisms for the regulation of protein functions by modulating new binding sites on scaffold proteins or by abrogating protein–protein interactions. However, the dynamic interplay of protein phosphorylation is not occurring randomly within the cell but is rather finely orchestrated by specific kinases and phosphatases that are unevenly distributed across subcellular compartments. This spatial separation not only regulates protein phosphorylation but can also control the activity of other enzymes and the transfer of other post‐translational modifications. While numerous large‐scale phosphoproteomics studies highlighted the extent and diversity of phosphoproteins present in total cell lysates, the further understanding of their regulation and biological activities require a spatio‐temporal resolution only achievable through subcellular fractionation. This review presents a first account of the emerging field of subcellular phosphoproteomics where cell fractionation approaches are combined with sensitive mass spectrometry methods to facilitate the identification of low abundance proteins and to unravel the intricate regulation of protein phosphorylation. © 2010 Wiley Periodicals, Inc. Mass Spec Rev 29:962–990, 2010
Scales to assess sleep impairment in Parkinson's disease: Critique and recommendations
Authors: Högl Birgit , Arnulf Isabelle , Comella Cynthia , Ferreira Joaquim , Iranzo Alex , Tilley Barbara , Trenkwalder Claudia , Poewe Werner , Rascol Olivier , Sampaio Cristina , Stebbins Glenn T. , Schrag Anette , Goetz Christopher G.
Published: October 2010

There is a broad spectrum of sleep disturbances observed in Parkinson's disease (PD). A variety of scales have been applied to the evaluation of PD sleep and wakefulness, but only a small number have been assessed specifically for clinimetric properties in the PD population. The movement disorder society has commissioned this task force to examine these scales and to assess their use in PD. A systematic literature review was conducted to explore the use of sleep scales in PD and to determine which scales qualified for a detailed critique. The task force members, all of whom have extensive experience in assessing sleep in PD reviewed each of the scales using a structured proforma. Scales were categorized into recommended, suggested and listed according to predefined criteria. A total of 48 potential scales were identified from the search and reviewed. Twenty‐nine were excluded because they did not meet review criteria or were variations of scales already included, leaving 19 scales that were critiqued and rated by the task force based on the rating criteria. Only six were found to meet criteria for recommendation or suggestion by the task force: the PD sleep scale (PDSS) and the Pittsburgh sleep quality index (PSQI) are recommended for rating overall sleep problems to screen and to measure severity, the SCOPA‐sleep (SCOPA) is recommended for rating overall sleep problems both to screen and to measure severity, and for rating daytime sleepiness; the Epworth sleepiness scale (ESS) is recommended for rating daytime sleepiness to screen and to measure severity; the inappropriate sleep composite score (ISCS) is suggested for rating severe daytime sleepiness or sleep attacks to screen and to measure severity; and the Stanford sleepiness scale (SSS) is suggested for rating sleepiness and to measure severity at a specific moment. The task force does not recommend the development of new scales, but emphasizes the need for educational efforts to train physicians in sleep interview techniques and polysomnography. © 2010 Movement Disorder Society
Motor complications in Parkinson's disease: Ten year follow‐up study
Authors: López Iria Cabo , Ruiz Pedro J. García , del Pozo Silvia Vázquez Fernández , Bernardos Vicenta Sánchez
Published: October 2010

Parkinson's disease (PD) can be symptomatically controlled with standard treatments; however, after a few years, this response typically declines and most patients develop motor complications. We carried out a prospective practice‐based study to evaluate the evolution appearance and evolution of motor complications in 64 de novo PD patients over 5 years and in 38 PD patients over 10 years. We studied untreated patients from initial assessment at basal conditions and evaluated every 6 months thereafter with treatment (levodopa versus other drugs). The follow‐up assessments were performed with the Unified Parkinson's Disease Rating Scale (UPDRS). At each assessment, patients were monitored regarding the development of dyskinesias, motor fluctuations, freezing, loss of postural reflexes, and cognitive impairment. We observed a significant improvement in UPDRS scores during the first year, then a progressive decline, more evident after the third year. Motor complications increased after the third year, and at the end of the survey (tenth year); drug‐induced dyskinesias and motor fluctuations were experienced (71.1 and 94.7%, respectively). After the first decade, many complications arose from the non‐levodopa–responsive features of the disease (cognitive impairment was present in 52.6% and gait freezing in 71.1%). Initial medication may influence medium‐term complications but not long‐term problems. Most long‐term disabling problems of PD were related to non‐levodopa‐responsive features. © 2010 Movement Disorder Society.
Prescriptions from general practitioners and in hospital physicians requiring pharmacists' interventions
Authors: Haavik Svein , Soeviknes Silje , Erdal Hilde , Kjonniksen Inge , Guttormsen Anne Berit , Granas Anne Gerd
Published: October 2010

Purpose

To study prescribing errors requiring pharmacists' interventions and to evaluate the potential clinical significance of the errors and omissions detected.

Methods

The pharmacists at ten community pharmacies and two out‐patient hospital pharmacies recorded prescribing errors and corresponding interventions using a modified version of a previously developed registration scheme. Prescription errors with potential clinical significance were scored according to a modified version of Safety Assessment Code (SAC)‐score

Results

During the study period 85 475 prescriptions were dispensed. A total of 2385 prescribing errors were detected on 2226 (2.6%) prescriptions. The proportion of prescriptions with errors and omissions was more than four times higher on prescriptions from hospital physicians (7.1%) than on prescriptions from general practitioners (1.5%). The information on the majority (62.2%) of the prescriptions with inaccuracies had to be clarified before the drug could be dispensed. About 1/4 of the errors and omissions were of potential importance for the drug therapy. An expert panel of physicians and pharmacists judged 85% of these errors and omissions to be clinically significant. Individual physicians and pharmacists judged the clinical importance of the detected prescribing errors somewhat differently.

Conclusions

Pharmacists intervened on 2.6% of prescriptions, and the majority of the potentially clinically significant prescribing errors were judged as significant to the patient's drug therapy and safety. Copyright © 2010 John Wiley & Sons, Ltd.
Impact of drug interactions, dosage, and duration of therapy on the risk of hip fracture associated with benzodiazepine use in older adults
Authors: Zint Kristina , Haefeli Walter E. , Glynn Robert J , Mogun Helen , Avorn Jerry , Stürmer Til
Published: October 2010

Purpose

To determine how concomitant use of potentially interacting drugs, drug dosage, and duration of therapy modify the risk of hip fracture associated with use of benzodiazepines and benzodiazepine‐related drugs (BDZ) in older adults.

Methods

A nested case–control study was conducted in Medicare patients 65 years or older, enrolled in the Pennsylvania drug assistance program (PACE) between 1994 and 2005. We included 17 198 patients with a hip fracture leading to hospitalization and 85 990 controls matched on hospitalization (index date). BDZ and interacting drug use within 2 weeks preceding the index date was determined using information on date of drug dispensing, days supplied, quantity dispensed, and strength. Date of the first BDZ prescription within the year preceding the index date was used as surrogate for duration of therapy.

Results

While the adjusted relative risk (RR) for overall BDZ use and hip fracture was 1.2 (95% confidence interval 1.1, 1.2), the RRs for concomitant use of alprazolam, lorazepam, and zolpidem and their interacting drugs were 1.5 (1.3, 1.7), 1.9 (1.7, 2.2), and 1.7 (1.4, 2.0), and 2.1 (1.5, 2.8) for BDZ use initiated within 14 days preceding the index date. RR increased with increasing BDZ dose and was highest for defined daily BDZ doses >1 [RR: 1.3 (1.2, 1.5)].

Conclusions

BDZ associated hip fracture risk increases with concomitant use of interacting drugs, higher doses, and is highest at initiation. Clinicians should avoid concomitant use of BDZ and interacting drugs, because their impact on hip fracture risk is at least additive. Copyright © 2010 John Wiley & Sons, Ltd.
The White Paper: will GP consortia invest in mental health services?
Authors: Walton Ian , Hill Lisa
Published: October 2010

New 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

Cu(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

Background: 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

The 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

NMR 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

Protein‐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

The 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

The 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

Previous 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

In 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

Acanthospermal 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

Idealized 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

The 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

The 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

The 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.
XPS and AFM characterization of the self‐assembled molecular monolayers of a 3‐aminopropyltrimethoxysilane on silicon surface, and effects of substrate pretreatment by UV‐irradiation
Authors: Cui Nai‐Yi , Liu Chaozong , Yang Wantai
Published: October 2010

The self‐assembled (SA) molecular monolayers of a 3‐aminopropyltrimethoxysilane (3‐APTS) on a silicon (111) surface, and the effects of ultraviolet (UV) pre‐treatment for substrates on the assembling process have been studied using XPS and atomic force microscopy (AFM). The results show that the SA 3‐APTS molecules are bonded to the substrate surface in a nearly vertical orientation, with a thickness of the monolayer of about 0.8–1.5 nm. The SA molecular monolayers show a substantial degree of disorder in molecular packing, which are believed to result from the interactions of amine tails in the silane molecules used with surface functionalities of the substrates, and the oxygen‐containing species from the ambient. UV irradiation for silicon substrates prior to the self‐assembly reaction can enhance the assembly process and hence, significantly increase the coverage of the monolayer assembled for the substrates. Copyright © 2010 John Wiley & Sons, Ltd.
Insight, innovation, and the big picture in system design
Authors: Bonnema G. Maarten
Published: October 2010

Systems architecting is the design phase where the top‐level functions and performance of a system are distributed over the system's parts, its environment, and its users. Up till now, system architects had to largely learn the required skills in practice. Some courses exist that teach the right attitude and mindset for the system architect. However, methods for architecting that can be implemented in a computer tool are virtually nonexistent. Earlier we presented a method, FunKey Architecting, which may aid the system architect in the early phase of design. In combination with TRIZ a design tool is created, which can be used to simplify and improve system architectures. It aims at supporting both the system designer and the specialist designers working on systems. The main topic of the paper is the application of the method in two industrial cases. The one case is an environment where new technology has to be developed and state of the art physics have to meet machine construction principles. The other case is in an industry where well‐proven technology is used in such a way that high‐performance machines are created. A third application of the FunKey tool is performed by students at the University of Twente. The context of each case and the results will be described. © 2010 Wiley Periodicals, Inc. Syst Eng 14
Harmonizing ABET accreditation and the certification of systems engineers
Authors: Chittister Clyde , Haimes Yacov Y.
Published: October 2010

The ever‐increasing complexity of technology‐based systems that are conceived, designed, constructed, operated and maintained, and managed places heavy civic and professional responsibilities on engineers of all disciplines. Furthermore, the ubiquitous involvement of systems engineers in almost every sector of the economy and in government attests to the growing recognition of their pivotal contributions to systems' safety and effectiveness. For example, the expertise of systems engineers is commonly required in the planning, design, testing, operation, and maintenance of most physical and cyber‐based infrastructures (e.g., transportation, telecommunication, and electric power). This paper explores the needs, requirements, and challenges associated with the academic‐baccalaureate and professional certification of systems engineers, given the breadth and depth required of them, and especially the specific domain knowledge and expertise required to supplement their competence in systems engineering. The authors of this paper take no position on the repeated reference made by several certification organizations to the requirement of being a licensed professional engineer (PE). Finally, a closer partnership between ABET and the two major professional societies—INCOSE and the IEEE—would enable us to reach agreement on what constitutes a Body of Knowledge (BoK) in systems engineering at the baccalaureate level, which would provide an invaluable benchmark to colleges and universities that offer such degrees. The joint initiative by ABET and the two societies would (a) harmonize and solidify the specific requirements for the accreditation of systems engineering programs in colleges and universities in the United States and abroad, and (b) guide the development of BoK requirements for any certification of systems engineers beyond the baccalaureate level. © 2010 Wiley Periodicals, Inc. Syst Eng 14
Synthesis and Crystal Structure of a Dinuclear Silver(I) Metallocyclophane with N‐Heterocyclic Carbene Linkage
Authors: Wan Xiangjian , Xu Fengbo , Zhang Zhengzhi , Song Haibin
Published: October 2010

Reaction of the carbene precursor 9,10‐bis(N‐ethylimidazoliummethyl)anthracene hexafluorophosphate (1) and Ag2O yielded the dinuclear metallocyclophane (2) in high yield. The structures of 1 and 2 were determined by X‐ray crystallography.
Synthesis and Characterization of a New Silaborazine Derivative
Authors: Cakmak Hasan , Jansen Martin
Published: October 2010

The synthesis and characterization of a new silaborazine derivative, namely 1,1,3,5‐tetrachloro‐2,6‐dimethyl‐4‐hydride‐1‐silaborazine (TDSB) are reported. The monomeric TDSB molecule is structurally characterized by NMR and FT‐IR spectroscopy and mass spectrometry, and additionally investigated by single crystal X‐ray diffraction (P$\bar{1}$ (No. 2); a = 7.2534(6) Å, b = 9.0788(7) Å, c = 9.1361(7) Å, α = 66.839(2)°, β = 89.348(2)°, γ = 80.502(2)°; Z = 2; R1 = 0.0425 [3443 observed reflections with I > 2σ(I)]). The structure of TDSB is composed of an essentially planar SiB2N3 ring.