bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical, radiological, and physiological differences between obliterative bronchiolitis and problematic severe asthma in adolescents and young adults: The early origins of the overlap syndrome?
Authors: Bandeira Teresa , Negreiro Filipa , Ferreira Rosário , Salgueiro Marisa , Lobo Luísa , Aguiar Pedro , Trindade J.C. 
Published: January 2011

AbstractPurposeFew reports have compared chronic obstructive lung diseases (OLDs) starting in childhood.AimsTo describe functional, radiological, and biological features of obliterative bronchiolitis (OB) and further discriminate to problematic severe asthma (PSA) or to diagnose a group with overlapping features.ResultsPatients with OB showed a greater degree of obstructive lung defect and higher hyperinflation (P < 0.001). The most frequent high‐resolution computed tomography (HRCT) features (increased lung volume, inspiratory decreased attenuation, mosaic pattern, and expiratory air trapping) showed significantly greater scores in OB patients. Patients with PSA have shown a higher frequency of atopy (P < 0.05). ROC curve analysis demonstrated discriminative power for the LF variables, HRCT findings and for atopy between diagnoses. Further analysis released five final variables more accurate for the identification of a third diagnostic group (FVC%t, post‐bronchodilator ΔFEV1 in ml, HRCT mosaic pattern, SPT, and D. pteronyssinus‐specific IgE).ConclusionsWe found that OB and PSA possess identifiable characteristic features but overlapping values may turn them undistinguishable. Pediatr. Pulmonol. 2011; 46:580–580. © 2011 Wiley‐Liss, Inc.
NMR solution structure of a cyanovirin homolog from wheat head blight fungus
Authors: Matei Elena , Louis John M. , Jee JunGoo , Gronenborn Angela M. 
Published: January 2011

AbstractMembers of the cyanovirin‐N homolog (CVNH) lectin family are found in bacteria, fungi and plants. As part of our ongoing work on CVNH structure‐function studies, we determined the high‐resolution NMR solution structure of the homolog from the wheat head blight disease causing ascomycetous fungus Gibberella zeae (or Fusarium graminearum), hereafter called GzCVNH. Like cyanovirin‐N (CV‐N), GzCVNH comprises two tandem sequence repeats and the protein sequence exhibits 30% identity with CV‐N. The overall structure is similar to those of other members of the CVNH family, with the conserved pseudo‐symmetric halves of the structure, domains A and B, closely resembling recently determined structures of Tuber borchii, Neurospora crassa, and Ceratopteris richardii CVNH proteins. Although GzCVNH exhibits a similar glycan recognition profile to CV‐N and specifically binds to Manα(1‐2)Manα, its weak carbohydrate binding affinity to only one binding site is insufficient for conferring anti‐HIV activity. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Structure, dynamics, and Hck interaction of full‐length HIV‐1 Nef
Authors: Jung Jinwon , Byeon In‐Ja L. , Ahn Jinwoo , Gronenborn Angela M. 
Published: January 2011

AbstractNef is an HIV accessory protein that plays an important role in the progression of disease after viral infection. It interferes with numerous signaling pathways, one of which involves serine/threonine kinases. Here, we report the results of an NMR structural investigation on full‐length Nef and its interaction with the entire regulatory domain of Hck (residues 72–256; Hck32L). A helical conformation was found at the N‐terminus for residues 14–22, preceding the folded core domain. In contrast to the previously studied truncated Nef (Nef Δ1‐39), the full‐length Nef did not show any interactions of Trp57/Leu58 with the hydrophobic patch formed by helices α1 and α2. Upon Hck32L binding, the N‐terminal anchor domain as well as the well‐known SH3‐binding site of Nef exhibited significant chemical shift changes. Upon Nef binding, resonance changes in the Hck spectrum were confined mostly to the SH3 domain, with additional effects seen for the connector between SH3 and SH2, the N‐terminal region of SH2 and the linker region that contains the regulatory polyproline motif. The binding data suggest that in full‐length Nef more than the core domain partakes in the interaction. The solution conformation of Hck32L was modeled using RDC data and compared with the crystal structure of the equivalent region in the inactivated, full‐length Hck, revealing a notable difference in the relative orientations of the SH3 and SH2 domains. The RDC‐based model combined with 15N backbone dynamics data suggest that Hck32L adopts an open conformation without binding of the polyproline motif in the linker to the SH3 domain. Proteins 2011; © 2011 Wiley‐Liss, Inc.
New benchmark metrics for protein‐protein docking methods
Authors: Gao Mu , Skolnick Jeffrey 
Published: January 2011

AbstractWith the development of many computational methods that predict the structural models of protein‐protein complexes, there is a pressing need to benchmark their performance. As was the case for protein monomers, assessing the quality of models of protein complexes is not straightforward. An effective scoring scheme should be able to detect substructure similarity and estimate its statistical significance. Here, we focus on characterizing the similarity of the interfaces of the complex and introduce two scoring functions. The first, the interfacial Template Modeling score (iTM‐score), measures the geometric distance between the interfaces, while the second, the Interface Similarity score (IS‐score), evaluates their residue‐residue contact similarity in addition to their geometric similarity. We first demonstrate that the IS‐score is more suitable for assessing docking models than the iTM‐score. The IS‐score is then validated in a large‐scale benchmark test on 1562 dimeric complexes. Finally, the scoring function is applied to evaluate docking models submitted to the Critical Assessment of Prediction of Interactions (CAPRI) experiments. While the results according to the new scoring scheme are generally consistent with the original CAPRI assessment, the IS‐score identifies models whose significance was previously underestimated. Proteins 2011. © 2011 Wiley‐Liss, Inc.
Mechanism of reactant and product dissociation from the anthrax edema factor: A locally enhanced sampling and steered molecular dynamics study
Authors: Martínez Leandro , Malliavin Thérèse E. , Blondel Arnaud 
Published: January 2011

AbstractThe anthrax edema factor is a toxin overproducing damaging levels of cyclic adenosine mono‐phosphate (cAMP) and pyrophosphate (PPi) from ATP. Here, mechanisms of dissociation of ATP and products (cAMP, PPi) from the active site are studied using locally enhanced sampling (LES) and steered molecular dynamics simulations. Various substrate conformations and ionic binding modes found in crystallographic structures are considered. LES simulations show that PPi and cAMP dissociate through different solvent accessible channels, while ATP dissociation requires significant active site exposure to solvent. The ionic content of the active site directly affects the dissociation of ATP and products. Only one ion dissociates along with ATP in the two‐Mg2+ binding site, suggesting that the other ion binds EF prior to ATP association. Dissociation of reaction products cAMP and PPi is impaired by direct electrostatic interactions between products and Mg2+ ions. This provides an explanation for the inhibitory effect of high Mg2+ concentrations on EF enzymatic activity. Breaking of electrostatic interactions is dependent on a competitive binding of water molecules to the ions, and thus on the solvent accessibility of the active site. Consequently, product dissociation seems to be a two‐step process. First, ligands are progressively solvated while preserving the most important electrostatic interactions, in a process that is dependent on the flexibility of the active site. Second, breakage of the electrostatic bonds follows, and ligands diffuse into solvent. In agreement with this mecanism, product protonation facilitates dissociation. Proteins 2011; © 2011 Wiley‐Liss, Inc.
Dissociation curves and binding energies of diatomic transition metal carbides from density functional theory
Authors: Goel Satyender , Masunov Artëm E. 
Published: January 2011

AbstractThe computational description of the catalytic processes on the surface of transition metals (TMs) requires methods capable of accurate prediction of the bond forming and breaking between the atoms of metal and other elements. In our previous report [Goel and Masunov, J Chem Phys, 129, 214302, 2008], we studied TM hydrides and found that Boese–Martin functional for kinetics (BMK) combined with broken symmetry approach described dissociation process more accurately than multireference wavefunction theory (WFT) methods and some other functionals. Here, we investigate the binding energy, geometry, electronic structure, and potential energy curves for diatomic TM carbides using several exchange‐correlation functionals. The functionals that include explicit dependence on the kinetic energy density (τ‐functionals) are considered, among others. We have found M05‐2x performance to be the best, followed by BMK, when compared with experimental and high level WFT energetics. This agreement deteriorates quickly for other functionals when the fraction of the Hartree–Fock exchange is decreased. Scalar relativistic corrections yield mixed results for bond lengths and bond energies. The natural bond orbital analysis provides useful insight in description of stable spin state over others in these diatomics. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Theoretical study of the kojic acid structure in gas phase and aqueous solution
Authors: Kakkar Rita , Singh Chayannika 
Published: January 2011

AbstractDensity functional calculations at the B3LYP/6‐311++G** level have been performed to determine the ground‐state conformational preference for kojic acid, a widely used skin‐whitening, antibrowning, and antibacterial agent. It is found that the gas phase consists almost entirely of the 5‐hydroxy‐2‐(hydroxymethyl)‐4H‐pyran‐4‐one tautomer, although several rotamers of this are prevalent. In aqueous solution, however, other tautomers are also present. The validity of the calculations is confirmed by the observed FTIR, NMR, and UV–vis spectra, which show good correspondence with the theoretical spectra. The electronic interactions are interpreted in terms of charge and bond order analysis as well as the composition of the HOMO and LUMO. The calculations show that kojic acid has partial aromatic character and is a good nucleophile. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Quantum chemical studies on the structure and detonation properties of the fused polynitrodiazoles: New high energy density molecules
Authors: Ravi P. , Gore G.M. , Tewari Surya P. , Sikder A. K. 
Published: January 2011

AbstractIn this study, we explore the possibility that fused polynitrodiazoles act as high energy density materials. Density functional theory calculations at the B3LYP/aug‐cc‐pVDZ level were performed to predict the structure, energy of explosion (≈1.68 kcal g−1), density (≈1.98 g cm−3), detonation velocity (≈9.50 km s−1), and detonation pressure (≈41.50 GPa) of model molecules. The predicted properties have been found to be promising compared with 3,4,5‐trinitro‐1H‐pyrazole, 1,3,5‐trinitro‐1,3,5‐triazinane, and octahydro‐1,3,5,7‐tetranitro‐l,3,5,7‐tetraazocane. The nature of azoles of the molecule presumably determines the geometry, stability, sensitivity, density, and detonation performance. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Performance evaluation of MIMO–WCDMA cellular networks in multiuser frequency selective fading environments
Authors: Gkonis P. K. , Tsoulos G. V. , Kaklamani D. I. 
Published: January 2011

ABSTRACTThis paper investigates the performance of different transmission strategies for multiple input multiple output (MIMO) networks with the wideband code division multiple access (WCDMA) air interface as the physical layer protocol. Performance is evaluated statistically with extended Monte Carlo (MC) simulations in terms of achievable bit‐error (BER) rate in frequency selective fading cellular environments. As results indicate, for a MIMO configuration withMtantennas at the base station (BS),Mrantennas per mobile station (MS) andLresolvable multipath components, the transmission strategy based on signal to noise ratio (SNR) enhancement is the optimum transmit solution forMt ≤ Mr. However, the pre‐RAKE maximal ratio combining transmission strategy outerperforms the SNR enhancement strategy with post‐RAKE processing forMt > Mr, high number of resolvable multipath components and channel estimation error up to 40%. Moreover, a transmission scheme based on the maximization of the ratio of the desired MS's signal to the total amount of interference that causes to the network is proposed, and is shown that outerperforms the conventional transmission schemes for high data rate services. For symmetric MIMO configurations (Mt = Mr) and two resolvable multipath components, this strategy provides 30% BER gain compared to the maximization of SNR strategy. This gain can be further improved by 25% with a proposed adjacent sector cooperation algorithm. Copyright © 2011 John Wiley & Sons, Ltd.
Milk composition in free‐ranging polar bears (Ursus maritimus) as a model for captive rearing milk formula
Authors: Hedberg Gail E. , Derocher Andrew E. , Andersen Magnus , Rogers Quinton R. , DePeters Edward J. , Lönnerdal Bo , Mazzaro Lisa , Chesney Russell W. , Hollis Bruce 
Published: January 2011

AbstractThe goals of this study were to have an improved understanding of milk composition and to help create a suitable milk formula for cubs raised in captivity. Milk samples were evaluated for fat, fatty acids, carbohydrate, vitamin D3, 25(OH)D3, vitamin A (retinol), vitamin E (α‐tocopherol), protein, and amino acids. Total lipids in milk did not differ for cubs (mean ± SEM = 26.60 ± 1.88 g/100 ml vs. yearlings 27.80 ± 2.20 g/100 ml). Milk lipids were of 23.6% saturated fatty acid for cubs and 22.4% for yearlings. Milk consumed by cubs and yearlings contained 43.8 and 42.0% mono‐unsaturated fatty acids and 23.4 and 21.9% polyunsaturated fatty acids, respectively. Carbohydrate content was higher in milk for cubs (4.60 ± 0.64 g/100 ml) than for yearlings (2.60 ± 0.40 g/100 ml). Vitamin D3concentration of milk was 18.40 ± 5.00 ng/ml in early lactation compared with 7.60 ± 2.00 ng/ml for mid‐lactation. 25(OH)D3was lower in milk consumed by cubs (162.00 ± 6.70 pg/ml) than in milk consumed by yearlings (205.00 ± 45.70 pg/ml). Vitamin A concentrations were 0.06 ± 0.01 and 0.03 ± 0.01 µg/ml for cubs and yearlings, respectively. Vitamin E was higher in milk consumed by cubs (20.16 ± 4.46 µg/ml) than by yearlings (7.30 ± 1.50 µg/ml). Protein content did not differ in milk available to cubs (11.40 ± 0.80 g/100 ml compared with milk for yearlings 11.80 ± 0.40 g/100 ml). Taurine was the most abundant free amino acid at 3,165.90 ± 192.90 nmol/ml (0.04% as fed basis). Zoo Biol 30:550–565, 2011. © 2011 Wiley Periodicals, Inc.
Emergency contraception in the context of marriage in Upper Egypt
Authors: Shaaban Omar M. , Fathalla Mohamed M.F. , Shahin Ahmed Y. , Nasr Ahmed 
Published: January 2011

AbstractObjectiveTo explore the degree of knowledge, perception, and practice of emergency contraception (EC) within marital relations in Egypt.MethodsThe present study was a pilot cross‐sectional survey. Eligible participants were randomly selected from 4 governorates in Upper Egypt. A questionnaire was designed by the investigators and administered to an unselected sample of healthcare providers and potential users of EC. The questionnaire collected information in 4 domains: demographics; knowledge about EC; attitudes toward EC; and practice of EC in Egypt.ResultsIn total, 240 healthcare providers and 60 potential users of EC completed the questionnaire. Approximately 85% of healthcare providers and 30% of potential users had heard about EC. A similar proportion of study participants said that EC methods are needed. Only 32.7% of healthcare providers and very few potential users had actually used EC.ConclusionThere is a need for EC in Egypt. However, a big gap in knowledge leads to nonuse or incorrect use of EC and negative attitude toward it. If health service planners and policy makers could fill this gap, a considerable decline in the prevalence of unwanted pregnancy may be achieved by using EC.
Half a century of “muddling”: Are we there yet?
Authors: Rothmayr Allison Christine , Saint-Martin Denis 
Published: January 2011

Abstract
Half a century after the publication of Lindblom's seminal article “The Science of Muddling Through”, we revisit the heritage of incrementalism in this special issue, analyzing its legacy in public policy and public administration. The articles discuss the extent to which recent theoretical developments have transformed the original idea, reinforced it, or possibly rendered it obsolete. In this introductory article, we provide a short overview over the core elements of incrementalism and assess how the concept is used in scholarly publications and research today. We thereby focus on incrementalism as an analytical concept rather then a prescriptive theory. We argue that even after a half a century of “muddling”, we are not yet through with incrementalism. Some of the ideas that underpin the concept of incrementalism continue to drive research, often in combination with more recent theoretical approaches to the policy process. After half a century, incrementalism is still part of the policy scholar's tool kit.
Cryostratigraphy of late Pleistocene syngenetic permafrost (yedoma) in northern Alaska, Itkillik River exposure
Authors: Kanevskiy M. , Shur Y. , Fortier D. , Jorgenson M.T. , Stephani E. 
Published: January 2011

AbstractExtremely ice-rich syngenetic permafrost, or yedoma, developed extensively under the cold climate of the Pleistocene in unglaciated regions of Eurasia and North America. In Alaska, yedoma occurs in the Arctic Foothills, the northern part of the Seward Peninsula, and in interior Alaska. A remarkable 33-m-high exposure along the lower Itkillik River in northern Alaska opened an opportunity to study the unmodified yedoma, including stratigraphy, particle-size distribution, soil carbon contents, morphology and quantity of segregated, wedge, and thermokarst-cave ice. The exposed permafrost sequence comprised seven cryostratigraphic units, which formed over a period from > 48,000 to 5,00014C yr BP, including: 1) active layer; 2) intermediate layer of the upper permafrost; 3–4) two yedoma silt units with different thicknesses of syngenetic ice wedges; 5) buried peat layer; 6) buried intermediate layer beneath the peat; and 7) silt layer with short ice wedges. This exposure is comparable to the well known Mus-Khaya and Duvanny Yar yedoma exposures in Russia. Based on our field observations, literature sources, and interpretation of satellite images and aerial photography, we have developed a preliminary map of yedoma distribution in Alaska.
Changes in meal pattern among Norwegian children from 2001 to 2008
Authors: Øverby Nina , Stea Tonje H , Vik Frøydis N , Klepp Knut-Inge , Bere Elling 
Published: January 2011

AbstractObjectiveThe present study aimed to analyse changes in meal pattern among Norwegian children from 2001 to 2008 in general; to analyse associations between meal pattern and gender, parental educational level and number of parents in the household; and to analyse the association between intake of unhealthy snacks, meal pattern and the mentioned variables.DesignWithin the Fruits and Vegetables Make the Marks (FVMM) project, two cross-sectional studies were conducted, one in 2001 and one in 2008, where participants from the same schools filled in a questionnaire on meals eaten the previous day.SubjectsParticipants were 6th and 7th grade pupils,n1488 in 2001 andn1339 in 2008.SettingTwenty-seven elementary schools in two Norwegian counties.ResultsThere were no significant changes in children's meal pattern from 2001 to 2008. For both years more than 90 % of the participants reported that they had breakfast yesterday, while 95 % had lunch, 94 % had dinner and 82 % had supper. More girls than boys reported that they had lunch yesterday (96 %v. 94 %,P= 0·03). More children with higherv. lower educated parents reported that they had breakfast yesterday (93 %v. 88 %,P< 0·001). More children living with two parentsv. one parent had breakfast (93 %v. 88 %,P= 0·001) and lunch yesterday (97 %v. 93 %,P< 0·001).ConclusionsThere were no changes in meal pattern from 2001 to 2008 among Norwegian children. Characteristics associated with skipping meals were living in a one-parent family and having lower educated parents.
Comparison of physical and technical performance in European soccer match‐play: FA Premier League and La Liga
Authors: Dellal Alexandre , Chamari Karim , Wong Del P. , Ahmaidi Said , Keller Dominique , Barros Ricardo , Bisciotti Gian Nicola , Carling Christopher 
Published: January 2011

AbstractThe aim of this study was to compare match performance in professional soccer players across two major European championships: Spanish La Liga and English FA Premier League (FAPL). Data were collected using a computerized match analysis system. A total of 5938 analyses were recorded during the 2006–2007 season. The players were classified into six positional roles: central defenders, full backs, central defensive midfielders, wide midfielders, central attacking midfielders, and forwards. The match performance variables analysed included: (i) physical activity – total distance covered, distances covered at high‐intensities both with and without possession of the ball; (ii) technical actions – heading and ground duels, passing, time in possession, and ball touches. Comparison of the total distance covered by FAPL and La Liga players showed no difference across individual playing positions but FAPL players generally covered greater distances in sprinting. In contrast, more of the total distance in sprinting was covered by La Liga players when their team was in possession (values from P < 0.05 to P < 0.001), while an equal total sprint distance, irrespective of possession, was observed in FAPL players. La Liga players won more heading duels (49.32% vs. 48.68%) and performed the same proportion of successful passes (76.17%). FAPL wide midfielders had ~20% more ball touches per possession than their La Liga counterparts (2.24±0.54 vs. 2.03±0.55, P < 0.001). In conclusion, our results show that FAPL and La Liga teams present differences in various physical and technical aspects of match‐play, suggesting that cultural differences may exist across professional soccer leagues and playing positions.
What determines carbon partitioning between competing sinks?
Authors: Minchin P.E.H. , Thorpe M.R. 
Published: January 2011

Carbohydrate sinks have been described by their ability to attract photosynthate, denoted by sink strength, and by their priority rank ordering for supply in the presence of a reduced availability of photosynthate. Sink strength has been defined as the rate of carbohydrate flow into a sink, but this flow rate is also dependent upon supply, other sinks, and resistance to flow of the transport pathway, so it is not a property of the sink alone. It is a property of the entire system. Hence sink strength defined as a flow rate is not a valid descriptor of a sink.
However, a simple model of phloem flow based upon Münch's ideas and with saturable unloading has many properties similar to a plant's carbohydrate source-sink relations, including priorities of sinks, and leads to a set of sink descriptors. This model's ability to mimic observed source-sink relations is reviewed here.