bluuebunny/crossref_metadata_2025_split huggingface dataset:
The biological and clinical value of p53 expression in pelvic high‐grade serous carcinomas
Authors: Köbel Martin , Reuss Alexander , Bois Andreas du , Kommoss Stefan , Kommoss Friedrich , Gao Dongxia , Kalloger Steve E , Huntsman David G , Gilks C Blake 
Published: June 2010

AbstractStudies on the p53 expression and outcome for women with ovarian carcinoma have produced conflicting results. The observed heterogeneity may be due to the range of cut‐offs used to define overexpression and the mix of histotypes of the study cohorts. We aimed to examine the association between p53 expression and biological properties of tumours as well as outcome in 502 pelvic high‐grade serous carcinomas (HGSCs) derived from two population‐based cohorts from British Columbia representing cases with or without residual tumour after initial surgery, respectively, and one clinical trial cohort from Germany (AGO‐OVAR‐3). p53 expression was assessed on tissue microarrays by immunohistochemistry using the DO‐7 antibody. p53 expression was scored in three tiers as complete loss of expression, focal expression or overexpression (defined as more than 50% positive tumour cell nuclei) and correlated with survival using multivariate Cox regression models. p53 was completely absent in 30.3%, focally expressed in 12.0%, and overexpressed in 57.7% of HGSCs, which was an inverse pattern compared to clear cell and endometrioid types of ovarian carcinomas, where 76% and 69% of cases showed focal expression, respectively (p < 0.001, chi square test). Pelvic HGSCs show either complete absence of p53 expression or p53 overexpression in 88% of cases; thus, aberrant p53 expression is a ubiquitous feature of HGSCs. HGSCs with p53 overexpression were associated with a reduced risk of recurrence compared to cases with complete absence of p53 in the British Columbia cohort with residual tumour (HR = 0.71, 95% CI 0.51–0.99) and for a combination of all three cohorts (HR = 0.70, 95% CI 0.55–0.89) in multivariate analysis including age, stage, residual tumour, and stratification by cohort. The association of complete absence of p53 expression with unfavourable outcome suggests functional differences of TP53 mutations underlying overexpression, compared to those underlying complete absence of expression. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
How do executive functions fit with the Cattell–Horn–Carroll model? Some evidence from a joint factor analysis of the Delis–Kaplan Executive Function System and the Woodcock–Johnson III tests of cognitive abilities
Authors: Floyd Randy G. , Bergeron Renee , Hamilton Gloria , Parra Gilbert R. 
Published: June 2010

AbstractThis study investigated the relations among executive functions and cognitive abilities through a joint exploratory factor analysis and joint confirmatory factor analysis of 25 test scores from the Delis–Kaplan Executive Function System and the Woodcock–Johnson III Tests of Cognitive Abilities. Participants were 100 children and adolescents recruited from general education classrooms. Principal axis factoring followed by an oblique rotation yielded a six‐factor solution. The Schmid–Leiman transformation was then used to examine the relations between specific cognitive ability factors and a general factor. A variety of hypothesis‐driven models were also tested using confirmatory factor analysis. Results indicated that all tests measure the general factor, and 24 tests measure at least one of five broad cognitive ability factors outlined by the Cattell–Horn–Carroll theory of cognitive abilities. These results, with limitations considered, add to the body of evidence supporting the confluence of measures of executive functions and measures of cognitive abilities derived from individual testing. © 2010 Wiley Periodicals, Inc.
Thermal state of permafrost in Russia
Authors: Romanovsky V. E. , Drozdov D. S. , Oberman N. G. , Malkova G. V. , Kholodov A. L. , Marchenko S. S. , Moskalenko N. G. , Sergeev D. O. , Ukraintseva N. G. , Abramov A. A. , Gilichinsky D. A. , Vasiliev A. A. 
Published: June 2010

AbstractThe results of the International Permafrost Association's International Polar Year Thermal State of Permafrost (TSP) project are presented based on field measurements from Russia during the IPY years (2007–09) and collected historical data. Most ground temperatures measured in existing and new boreholes show a substantial warming during the last 20 to 30 years. The magnitude of the warming varied with location, but was typically from 0.5°C to 2°C at the depth of zero annual amplitude. Thawing of Little Ice Age permafrost is ongoing at many locations. There are some indications that the late Holocene permafrost has begun to thaw at some undisturbed locations in northeastern Europe and northwest Siberia. Thawing of permafrost is most noticeable within the discontinuous permafrost domain. However, permafrost in Russia is also starting to thaw at some limited locations in the continuous permafrost zone. As a result, a northward displacement of the boundary between continuous and discontinuous permafrost zones was observed. This data set will serve as a baseline against which to measure changes of near‐surface permafrost temperatures and permafrost boundaries, to validate climate model scenarios, and for temperature reanalysis. Copyright © 2010 John Wiley & Sons, Ltd.
Potential remobilization of belowground permafrost carbon under future global warming
Authors: Kuhry P. , Dorrepaal E. , Hugelius G. , Schuur E. A. G. , Tarnocai C. 
Published: June 2010

AbstractResearch on permafrost carbon has dramatically increased in the past few years. A new estimate of 1672 Pg C of belowground organic carbon in the northern circumpolar permafrost region more than doubles the previous value and highlights the potential role of permafrost carbon in the Earth System. Uncertainties in this new estimate remain due to relatively few available pedon data for certain geographic sectors and the deeper cryoturbated soil horizons, and the large polygon size in the soil maps used for upscaling. The large permafrost carbon pool is not equally distributed across the landscape: peat deposits, cryoturbated soils and the loess‐like deposits of the yedoma complex contain disproportionately large amounts of soil organic matter, often exhibiting a low degree of decomposition. Recent findings in Alaska and northern Sweden provide strong evidence that the deeper soil carbon in permafrost terrain is starting to be released, supporting previous reports from Siberia. The permafrost carbon pool is not yet fully integrated in climate and ecosystem models and an important objective should be to define typical pedons appropriate for model setups. The thawing permafrost carbon feedback needs to be included in model projections of future climate change. Copyright © 2010 John Wiley & Sons, Ltd.
The thermal state of permafrost in the nordic area during the international polar year 2007–2009
Authors: Christiansen H. H. , Etzelmüller B. , Isaksen K. , Juliussen H. , Farbrot H. , Humlum O. , Johansson M. , Ingeman‐Nielsen T. , Kristensen L. , Hjort J. , Holmlund P. , Sannel A. B. K. , Sigsgaard C. , Åkerman H. J. , Foged N. , Blikra L. H. , Pernosky M. A. , Ødegård R. S. 
Published: June 2010

AbstractThis paper provides a snapshot of the permafrost thermal state in the Nordic area obtained during the International Polar Year (IPY) 2007–2009. Several intensive research campaigns were undertaken within a variety of projects in the Nordic countries to obtain this snapshot. We demonstrate for Scandinavia that both lowland permafrost in palsas and peat plateaus, and large areas of permafrost in the mountains are at temperatures close to 0°C, which makes them sensitive to climatic changes. In Svalbard and northeast Greenland, and also in the highest parts of the mountains in the rest of the Nordic area, the permafrost is somewhat colder, but still only a few degrees below the freezing point. The observations presented from the network of boreholes, more than half of which were established during the IPY, provide an important baseline to assess how future predicted climatic changes may affect the permafrost thermal state in the Nordic area. Time series of active‐layer thickness and permafrost temperature conditions in the Nordic area, which are generally only 10 years in length, show generally increasing active‐layer depths and rising permafrost temperatures. Copyright © 2010 John Wiley & Sons, Ltd.
Permafrost thermal state in the polar Northern Hemisphere during the international polar year 2007–2009: a synthesis
Authors: Romanovsky Vladimir E. , Smith Sharon L. , Christiansen Hanne H. 
Published: June 2010

AbstractThe permafrost monitoring network in the polar regions of the Northern Hemisphere was enhanced during the International Polar Year (IPY), and new information on permafrost thermal state was collected for regions where there was little available. This augmented monitoring network is an important legacy of the IPY, as is the updated baseline of current permafrost conditions against which future changes may be measured. Within the Northern Hemisphere polar region, ground temperatures are currently being measured in about 575 boreholes in North America, the Nordic region and Russia. These show that in the discontinuous permafrost zone, permafrost temperatures fall within a narrow range, with the mean annual ground temperature (MAGT) at most sites being higher than −2°C. A greater range in MAGT is present within the continuous permafrost zone, from above −1°C at some locations to as low as −15°C. The latest results indicate that the permafrost warming which started two to three decades ago has generally continued into the IPY period. Warming rates are much smaller for permafrost already at temperatures close to 0°C compared with colder permafrost, especially for ice‐rich permafrost where latent heat effects dominate the ground thermal regime. Colder permafrost sites are warming more rapidly. This improved knowledge about the permafrost thermal state and its dynamics is important for multidisciplinary polar research, but also for many of the 4 million people living in the Arctic. In particular, this knowledge is required for designing effective adaptation strategies for the local communities under warmer climatic conditions. Copyright © 2010 John Wiley & Sons, Ltd.
Fold homology detection using sequence fragment composition profiles of proteins
Authors: Solis Armando D. , Rackovsky Shalom R. 
Published: June 2010

AbstractThe effectiveness of sequence alignment in detecting structural homology among protein sequences decreases markedly when pairwise sequence identity is low (the so‐called “twilight zone” problem of sequence alignment). Alternative sequence comparison strategies able to detect structural kinship among highly divergent sequences are necessary to address this need. Among them are alignment‐free methods, which use global sequence properties (such as amino acid composition) to identify structural homology in a rapid and straightforward way. We explore the viability of using tetramer sequence fragment composition profiles in finding structural relationships that lie undetected by traditional alignment. We establish a strategy to recast any given protein sequence into a tetramer sequence fragment composition profile, using a series of amino acid clustering steps that have been optimized for mutual information. Our method has the effect of compressing the set of 160,000 unique tetramers (if using the 20‐letter amino acid alphabet) into a more tractable number of reduced tetramers (∼15–30), so that a meaningful tetramer composition profile can be constructed. We test remote homology detection at the topology and fold superfamily levels using a comprehensive set of fold homologs, culled from the CATH database that share low pairwise sequence similarity. Using the receiver‐operating characteristic measure, we demonstrate potentially significant improvement in using information‐optimized reduced tetramer composition, over methods relying only on the raw amino acid composition or on traditional sequence alignment, in homology detection at or below the “twilight zone”. Proteins 2010. © 2010 Wiley‐Liss, Inc.
An integrated suite of fast docking algorithms
Authors: Mashiach Efrat , Schneidman‐Duhovny Dina , Peri Aviyah , Shavit Yoli , Nussinov Ruth , Wolfson Haim J. 
Published: June 2010

AbstractThe CAPRI experiment (Critical Assessment of Predicted Interactions) simulates realistic and diverse docking challenges, each case having specific properties that may be exploited by docking algorithms. Motivated by the different CAPRI challenges, we developed and implemented a comprehensive suite of docking algorithms. These were incorporated into a dynamic docking protocol, consisting of four main stages: (1) Biological and bioinformatics research aiming to predict the binding site residues, to define distance constraints between interface atoms and to analyze the flexibility of molecules; (2) Rigid or flexible docking, performed by the PatchDock or FlexDock method, which utilizes the information gathered in the previous step. Symmetric complexes are predicted by the SymmDock method; (3) Flexible refinement and reranking of the rigid docking solution candidates, performed by FiberDock; and finally, (4) clustering and filtering the results based on energy funnels. We analyzed the performance of our docking protocol on a large benchmark and on recent CAPRI targets. The analysis has demonstrated the importance of biological information gathering prior to docking, which significantly increased the docking success rate, and of the refinement and rescoring stage that significantly improved the ranking of the rigid docking solutions. Our failures were mostly a result of mishandling backbone flexibility, inaccurate homology modeling, or incorrect biological assumptions. Most of the methods are available at http://bioinfo3d.cs.tau.ac.il/. Proteins 2010. © 2010 Wiley‐Liss, Inc.
A review of nanomaterial safety concerns
Authors: Lavoie Joseph H. 
Published: June 2010

AbstractNanomaterials are quickly moving from research benches to the manufacturing environment and into product lines. These materials pose unique safety concerns, which should be made clear to both the workers and the consumers who are exposed to them. The following is a summary of documents concerning the dangers posed by a wide variety of nanomaterials as well as references, which may be useful to practicing process engineers and EHS professionals. © 2010 American Institute of Chemical Engineers Process Saf Prog, 2010
ZnO nanoparticles prepared by an electroexploding wire technique
Authors: Singh N. Kamal , Alqudami A. , Annapoorni S. 
Published: June 2010

AbstractZinc oxide (ZnO) nanoparticles have been successfully prepared by an electroexploding wire (EEW) technique from pure zinc (Zn). The system comprises of a wire‐plate and a series of 12 V batteries. The formation of ZnO and nature of the crystallinity have been studied using X‐ray diffraction (XRD) and Raman analyses. The polycrystalline nature of the prepared nanoparticles is confirmed from the XRD studies. The time‐dependent UV–Visible absorption and photoluminescence (PL) studies confirm the evolution of ZnO nanoparticles from Zn obtained by the EEW technique. The sizes of the as‐prepared and annealed nanoparticles as estimated using the effective mass theory from the UV–Visible absorption are 8.9 and 22.0 nm, respectively. These are in agreement with those obtained from TEM micrographs. A broad and intense PL emission centered about 508 nm that is in the green region is observed. It is characteristic of the presence of defect energy states due to oxygen deficiency. From the energy‐dependent analysis of the PL emission, the green emission observed is concluded to be due to the bulk contribution rather than surface defects.
Initial rise of transient electroluminescence in doped Alq3 films
Authors: Uddin A. , Lee C. B. , Andersson T. G. 
Published: June 2010

AbstractThe doping effect on initial rise of transient electroluminescence (EL) in organic light emitting diodes (OLEDs) is investigated. The dopants red light emitter 5,6,11,12‐tetraphenylnaphthacene (Rb) and 4‐(diacynomethylene)‐2‐methyl‐6‐(p‐dimethylaminostyryl)‐4H‐pyan (DCM), and yellow light emitter 3‐(2′‐benzothiazolyl)‐7‐diethylaminocoumarin (C‐6) were used in green light emitter tris‐(8‐hydroxyquinoline) aluminum (Alq3) film with various concentrations from 0.5 to 24 wt%. The increase of EL delay time and the slower rise of EL saturation were observed with doping concentrations. The values of EL delay time was found from 0.78 to 1.86 µs in doped OLED compared to 0.74 µs in pure Alq3 device. The EL saturation time was found from 1.2 to 2.8 µs for different doping concentration. We have also estimated the carrier mobility from the transient EL measurements. The charge‐carrier mobility was found as 0.5–1.2 × 10−5 cm2 V−1 s−1 in doped Alq3 films.
Gate voltage and structure parameter modulated spin splitting in AlGaN/GaN quantum wells
Authors: Li M. , Zhang R. , Zhang Z. , Liu B. , Fu Deyi , Zhao C. Z. , Xie Z. L. , Xiu X. Q. , Zheng Y. D. 
Published: June 2010

AbstractIn this paper, considerable magnitude of spin splitting for the conduction subband at the Fermi energy is obtained in AlGaN quantum wells (QWs) grown along the c‐axis. We have analyzed how the magnitude of spin splitting of the first electron subband in AlGaN QWs with different sheet carrier concentration changes as a function of applied gate voltage, well width, and Al content in the barrier. It is also found that the contribution to spin splitting from Dresselhaus term is much larger than that from Rashba term, the contribution of Dresselhaus term to the total spin splitting depends greatly on the carrier concentrations, the change of well width has little effect on total spin splitting, and the magnitude of spin splitting can be greatly modulated by Al content in the barrier, gate voltage, and sheet carrier concentration. The internal polarized electric field is crucial for considerable spin splitting in III‐nitride QWs. Moreover, the magnitude of total spin splitting calculated here is comparable with other theoretical and experimental values observed in III‐nitride heterostructures.
Surface enhanced infrared spectroscopy using gold nanoantennas
Authors: Pucci A. , Neubrech F. , Weber D. , Hong S. , Toury T. , de la Chapelle M. Lamy 
Published: June 2010

AbstractThe sensitivity of infrared (IR) vibration spectroscopy can be enhanced by several orders of magnitude if plasmonic electromagnetic nearfield enhancement is exploited. For maximum enhancement the plasmonic resonance needs to be strong, which cannot be achieved by randomly grown metal island films that on average may show already signal enhancement of the order of 1000. Metal nanowires may give sufficiently strong antenna‐like plasmonic resonances in the IR that can be adjusted to the molecular vibration frequencies of interest via the wire length. With individual gold nanowires we obtained vibration‐signal enhancement up to 500,000 for molecular monolayers adsorbed on gold nanowires. The already obtained enhancement is not a limit. Since antennae coupled via nanogaps should enable strong electromagnetic nearfield enhancement in these gaps, respective arrays would be ideal for surface enhanced IR spectroscopy. First experiments prove the tendency of increasing vibration‐signal enhancement with decreasing gap size.
FP‐LAPW calculations of structural and elastic properties of tantalum under high pressure
Authors: Liu Zhong‐Li , Li Xiao‐Feng , Cai Ling‐Cang , Jing Fu‐Qian 
Published: June 2010

AbstractWe have revisited and refined the high‐pressure elastic properties of body‐centered‐cubic Ta using the accurate all‐electron full potential linearized augmented plane wave method (FP‐LAPW) within the framework of density functional theory (DFT). Based on the total energy calculations, we first deduced the accurate static equation of state (EOS) of Ta. Then we derived the elastic constants, C11, C12, and C44 under pressure up to 500 GPa using the pressure‐correction method which corrected the previous method theoretically, and the calculated elastic constants agree well with experiment under high pressure. From the accurately determined elastic constants, we also discussed the elastic anisotropy and the sound velocities of Ta at high pressure. The predicted Debye temperature at 0 GPa and 0 K is in good agreement with experiment, and the Debye temperature increases monotonously as pressure increases.
Zero temperature coefficient of frequency crystal cuts in monoclinic NdCa4O(BO3)3piezoelectric crystals
Authors: Yu Fapeng , Zhang Shujun , Zhao Xian , Yuan Duorong , Wang Qing‐Ming , Shrout Thomas R. 
Published: June 2010

AbstractThe temperature coefficient of frequency (TCF) was investigated in monoclinic NdCa4O(BO3)3(NdCOB) piezoelectric crystals over the temperature range of –140 °C to 200 °C. A zero TCF characteristic was achieved for the (ZXw) 15° crystal cut, with turnover point at 20 °C. The electromechanical couplingk26and piezoelectric coefficientd26, in shear vibration mode, were determined to be 25% and 13.5 pC/N, respectively. The zero TCF crystal cut, large coupling factor and high piezoelectric coefficient, together with a high mechanical quality factor (Q> 10,000), demonstrate NdCOB crystals promising candidates for bulk acoustic wave resonators over a wide temperature range. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Floodplain management strategies for flood attenuation in the river Po
Authors: Castellarin A. , Di Baldassarre G. , Brath A. 
Published: June 2010

AbstractThis paper analyses the effects of different floodplain management policies on flood hazard using a 350 km reach of the river Po (Italy) as a case study. The river Po is the longest Italian river, and the largest in terms of streamflow. The middle‐lower Po flows East some 350 km in the Pianura Padana (Po Valley), a very important agricultural region and industrial heart of Northern Italy. This portion of the river consists of a main channel (200–500 m wide) and a floodplain (overall width from 200 m to 5 km) confined by two continuous artificial embankments. Floodplains are densely cultivated, and a significant portion of these areas is protected against frequent flooding by a system of minor dykes, which impacts significantly the hydraulic behaviour of the middle‐lower Po during major flood events. This study aims at investigating the effects of the adoption of different floodplain management strategies (e.g. raising, lowering or removing the minor dyke system) on the hydrodynamics of the middle‐lower Po and, in particular, on flood‐risk mitigation. This is a crucial task for institutions and public bodies in charge of formulating robust flood risk management strategies for the river Po. Furthermore, the results of this study are of interest for other European water‐related public bodies managing large river basins, in the light of the recent European Directive 2007/60/EC on the assessment and management of flood risks. The analysis is performed by means of a quasi‐2D hydraulic model, which has been developed on the basis of a laser‐scanning DTM and a large amount of calibration data recorded during the significant flood event of October 2000. Copyright © 2010 John Wiley & Sons, Ltd.