bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improved side‐chain torsion potentials for the Amber ff99SB protein force field
Authors: Lindorff‐Larsen Kresten , Piana Stefano , Palmo Kim , Maragakis Paul , Klepeis John L. , Dror Ron O. , Shaw David E. 
Published: March 2010

AbstractRecent advances in hardware and software have enabled increasingly long molecular dynamics (MD) simulations of biomolecules, exposing certain limitations in the accuracy of the force fields used for such simulations and spurring efforts to refine these force fields. Recent modifications to the Amber and CHARMM protein force fields, for example, have improved the backbone torsion potentials, remedying deficiencies in earlier versions. Here, we further advance simulation accuracy by improving the amino acid side‐chain torsion potentials of the Amber ff99SB force field. First, we used simulations of model alpha‐helical systems to identify the four residue types whose rotamer distribution differed the most from expectations based on Protein Data Bank statistics. Second, we optimized the side‐chain torsion potentials of these residues to match new, high‐level quantum‐mechanical calculations. Finally, we used microsecond‐timescale MD simulations in explicit solvent to validate the resulting force field against a large set of experimental NMR measurements that directly probe side‐chain conformations. The new force field, which we have termed Amber ff99SB‐ILDN, exhibits considerably better agreement with the NMR data. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Recent advances in InN‐based solar cells: status and challenges in InGaN and InAlN solar cells
Authors: Yamamoto Akio , Islam Md. R. , Kang Ting‐Ting , Hashimoto Akihiro 
Published: March 2010

AbstractIn this paper, we review and discuss the recent advances in InN‐based solar cells. Before the discussion on InN‐based solar cells, two major losses in a solar cell, transparency loss and excess excitation loss, are explained and the effectiveness of a multi‐junction tandem cell in reducing the both losses simultaneously is described. Then, the status and issues for multi‐junction tandem solar cells using the conventional III‐V materials (InGaP/InGaAs systems) are reviewed briefly in order to understand the advantages of InN‐based material as a multi‐junction solar cell material. It is shown that main problem in the conventional III‐V multi‐junction solar cell is the current mismatching between sub‐cells, which reduces significantly the conversion efficiency of the tandem cells. The main advantage of InGaN and InAlN as a multi‐junction solar cell is that a wanted band‐gap between 0.7 and 2.5 eV is realized by changing only their composition.This means that current matching between sub‐cells will be easily achieved using InGaN and InAlN systems. After the status of InGaN solar cell research is summarized, the results on the MOVPE growth of InGaN with an In content up to 0.4, Mg doping using Cp2Mg, and the formation of an n+‐p homo‐junction are described. The insertion of step‐graded InxGa1‐xN interlayer between the GaN and InGaN epilayer is also shown to be effective to improve the epilayer quality. The study on InAlN solar cell is on the stage of the growth of In‐rich InAlN. Single‐crystalline InAlN films with an Al content from 0 (Eg = 0.7 eV) to 0.43 (2 eV) have been successfully grown by employing atmospheric‐pressure MOVPE. The study on Mg‐doping for InAlN will be the next step. Finally, we will summarize and discuss the challenges in InGaN and InAlN solar cells. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
In‐clustering induced anomalous behavior of band gap in InAlN and InGaN
Authors: Gorczyca I. , Suski T. , Christensen N. E. , Svane A. 
Published: March 2010

AbstractElectronic band structure calculations of In containing ternary nitride alloys are presented showing a strong modification of the band gap, EG and its pressure coefficient, dEG/dp, as a function of In‐content. Two different arrangements of In atoms are considered: uniform and clustered. It is shown that Indium clustering is the additional, large factor leading to the unusual bowings of the band gaps and their pressure coefficients. The theoretical results are compared with experimental data on variations of EG with In content. In the analysis of observed phenomena we point out the particular role of the uppermost valence band (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Electron microscopy of InGaN nanopillars spontaneously grown on Si(111) substrates
Authors: Kehagias Th. , Kerasiotis I. , Vajpeyi A. P. , Hausler I. , Neumann W. , Georgakilas A. , Dimitrakopulos G. P. , Komnninou Ph. 
Published: March 2010

AbstractThe mopholological, structural and chemical properties of InxGa1–xN nanopillars directly grown on Si (111) substrates, by molecular beam epitaxy, were investigated employing transmission electron microscopy related techniques. Single crystalline, single phase nanopillars were observed exhibiting a low density of crystal defects, which contribute to good crystal quality. Initial nanostructures merge through subgrain boundaries to form final nanopillars. Energy dispersive X‐ray analysis revealed a very low InN mole fraction near the interface with the substrate, owing to high desorption rates from the elevated growth temperature, and gradually higher In incorporation rates near the tips of the nanopillars. This compositional fluctuation is maintained due to poor segregation of indium adatoms along the c‐axis of the nanopillars towards the Si interface. A second species of long and narrow nanopillars was found In‐free. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Meissner effect of superconducting InN
Authors: Inushima Takashi , Maude Duncan K. , Muto Daisuke , Nanishi Yasushi 
Published: March 2010

AbstractWe report on the BCS‐type superconductivity of InN. A sample with a carrier concentration ne of 7×1018cm–3 is found to become zero resistance at ∼0.8 K and show BCS type Meissner effect at 0.2 K onset. Though the vortex solid is melted by thermal fluctuation and by external magnetic field from ∼2.5 K, the occurrence of the Meissner phase is suppressed by localized carriers along [10$ \bar 1 $0], which changes the character of the superconductivity into BCS type and the coherent length becomes comparable to that of ideal metal In. A mechanism which causes superconductivity in InN is proposed on the basis of the residual carriers produced by the interaction among the second nearest neighbor In‐In atoms originating from In 4d and N 2s hybridization (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
TEM investigation of a processed InGaN based laser grown by PAMBE on bulk GaN substrate
Authors: Kret S. , Ivaldi F. , Żak M. , Feduniewicz‐Żmuda A. , Siekacz M. , Cywiński G. , Skierbiszewski C. 
Published: March 2010

AbstractThe structural investigation of the processed InGaN/GaN LDs and LEDs structures are performed by Transmission Electron Microscopy. A plasma assisted molecular beam epitaxy (PAMBE) process is used to fabricate laser structures on high pressure bulk GaN substrates. The indium composition inside the active multi quantum wells (MQW) region is measured by the analysis of the local lattice distortion using lattice fringes images. The characterization of different defects in the laser's structure is given in this paper. Defects, crossing the entire active region of the laser structure, have been detected. These defects can be related to the discontinuities of the Au/Ni contact. The local heating caused by the local non‐uniform current density can be the origin of these defects. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
The microstructure and properties of InN layers
Authors: Ruterana P. , Syrkin A. L. , Monroy E. , Valcheva E. , Kirilov K. 
Published: March 2010

AbstractA series of InN layers grown by different techniques has been investigated by transmission electron microscopy, photoluminescence and Raman spectroscopy. The polarity is shown to be determined by the underlying GaN template. In these In polar layers, the c ‐screw dislocations density is low and that of a ‐type dislocations is in the high‐109 cm‐2 range. The dislocation density tends to decrease towards the surface. Along the first 0.5 μm, and particularly in the samples grown by hydride vapour epitaxy, we observe a large number of stacking faults, which probably contribute to the dislocation density reduction. The optical band gap in MBE and MOVPE samples is between 0.6 and 0.7 eV, but that of the HVPE templates is above 1 eV. Estimations from Raman data show that this behaviour correlates well with the residual carrier concentration. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Quasi‐Biennial Modulation of the Southern Ocean Coherent Mode
Authors: Hibbert Angela , Leach Harry , Woodworth Philip , Hughes Chris W , Roussenov Vassil 
Published: March 2010

AbstractEmpirical Orthogonal Function (EOF) analysis of two independent Southern Ocean sea‐level datasets for the period 1992–2002 shows that the coherent oceanic mode–a zonally symmetric counterpart to the atmospheric Southern Annular Mode (SAM)–consistently emerges as the predominant mode of variability and is revealed to be a reliable proxy for circumpolar transport upon subannual to interannual time‐scales. Cross‐validation of the coherent mode from each dataset and that of a global barotropic model demonstrates a high degree of correspondence between sea‐level observations and model estimations and also indicates that the coherent oceanic mode is largely barotropically driven upon subannual time‐scales, whilst baroclinic oceanic effects predominate at longer periods. Both the coherent mode and transport are shown to be modified by the stratospheric Quasi‐Biennial Oscillation (QBO) and a mechanism is described by which QBO‐dependent planetary wave activity may be guided from the stratosphere towards the surface by high‐latitude easterly and westerly jets, inducing wind anomalies that force sea‐level variability through equatorward Ekman transport. A longer (18‐year) tide‐gauge record from the Vernadsky/Faraday station and a 22‐year time series of sea‐level estimations from an ocean general circulation model are used to show that QBO‐induced sea‐level and transport variability may be modulated upon longer time‐scales by a quasi‐decadal cycle of solar activity. Copyright © 2010 Royal Meteorological Society
Dynamical derivation of Eyring equation and the second‐order kinetic law
Authors: Bonnet L. , Rayez J.‐C. 
Published: March 2010

AbstractElementary gas‐phase reactions of the bimolecular type A + B → Products are characterized by the second‐order kinetic law
$- {{d[{\rm A}]} \over {dt}} = k[{\rm A}][{\rm B}]$, where [A] and [B] are the concentrations of A and B species, t is the time, and k is the rate constant, usually estimated by means of Eyring equation. Here, we show that its dynamical derivation, as such, is not consistent with the second‐order law. This contradiction is however removed by introducing a correlation between what we call potentially reactive pairs. A new presentation of the dynamical derivation of Eyring equation is finally proposed on the basis of the previous findings. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2355–2359, 2010
Interaction of atoms with graphenic‐type surfaces for the chemistry of the interstellar medium: New properties of H dimers on the surface
Authors: Teillet‐Billy D. , Rougeau N. , Ivanovskaya V. V. , Sidis V. 
Published: March 2010

AbstractFollowing the works of Rougeau et al. (Chem Phys Lett 2006, 431,135) and Ferro et al. (Phys Rev B 2008, 78, 085417) on the one‐sided double chemisorption of H atoms on graphenic platelets, we investigate the two‐sided double chemisorption using DFT‐GGA PW91 calculations. Equilibrium characteristics and potential energy curves for chemisorption are reported for the ortho, meta, para, and bottom positions. Contrary to the one‐sided case, the two‐sided ortho chemisorption, as well as the bottom position, is barrier‐less, whereas the two‐sided para chemisorption exhibits an activation barrier. The highest occupied Kohn‐Sham orbital (HOKSO) of the H‐graphene radical is shown to signal the privileged barrier‐less double chemisorption sites. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Climate records from corals
Authors: Lough Janice M. 
Published: March 2010

AbstractUnderstanding the nature and causes of climate variability and change in the tropical oceans—the heat engine of the global climate system—is limited by the relatively short length of instrumental records. Certain massive reef‐building corals contain a wealth of historical proxy climate and environmental information locked in their calcium carbonate skeletons. This information is available from living corals that can be up to several hundred years old and from fossil corals, often well preserved after death, for well‐dated windows of the more distant past. Continuous, high‐resolution (annual to seasonal) information from such corals is provided by a range of measures that include growth characteristics which can document coral responses to unusual environmental conditions and various geochemical tracers whose incorporation into the skeleton is mediated by ambient seawater characteristics. The stable oxygen isotope ratio, δ18O, has been the most commonly measured coral environmental tracer and, although reflecting both sea surface temperature and seawater salinity, long records of this variable are providing new insights into interannual (e.g., El Niño‐Southern Oscillation), decadal, and longer time‐scale variability in the tropical oceans—information not accessible from the instrumental records—which complements other sources of high‐resolution proxy climate information (e.g., tree rings, ice cores, documentary records). The contribution of proxy climate records in corals to the global picture of past climates is being enhanced through efforts to reduce the various sources of uncertainty that can confound the interpretation of any source of proxy climate information. Copyright © 2010 John Wiley & Sons, Ltd.This article is categorized under:

Paleoclimates and Current Trends > Paleoclimate
A pseudoelastic model for mechanical twinning on the microscale
Authors: Glüge R. , Bertram A. , Böhlke T. , Specht E. 
Published: March 2010

AbstractA pseudoelastic model for the simulation of deformation twinning on the microscale is develope and coupled with a crystal plasticity model for crystallographic slip. The material parameters are adopted to $\{10\bar 1 2\}\langle \bar 1 0 1 1 \rangle$ twinning and basal glide in a magnesium alloy. Special attention is drawn to the energy invariance of conjugate twin systems that emerges when twinning is treated elastically. The model is tested in three characteristic FE simulations, namely a simple shear test parallel and inclined to a twin system and an elongation test of a notched band. The slip‐twin interaction is studied, as well as the practical implications of the strain energy invariance. Some characteristics of twinning could be reproduced. The most important observations are that the load drop at the twin nucleation, the cusp shape of the twin tip in the absence of slip and the kink patterns that evolve in slip‐twin interaction could be simulated.
Complete allocation sampling: an efficient and easily implemented adaptive sampling design
Authors: Salehi Mohammad , Brown Jennifer A. 
Published: March 2010

AbstractAdaptive sampling designs are becoming increasingly popular in environmental science, particularly for surveying rare and aggregated populations. An adaptive sample is one in which the survey design is modified, or adapted, in some way on the basis of information gained during the survey. There are many different adaptive survey designs that can be used to estimate animal and plant abundance. In adaptive cluster sampling, additional sample effort is allocated during the survey to the immediate neighborhood in which the species is found. In adaptive stratified sampling, additional sample effort is allocated during the survey to strata of high abundance. The appealing feature of these adaptive designs is that the field biologist gets to do what innately seems sensible when working with rare and aggregated populations—field effort is targeted around where the species is observed in the first wave of the survey. However, there are logistical challenges of applying this principle of targeted field effort while remaining in the framework of probability‐based sampling. We propose a simplified adaptive survey design that incorporates both targeting field effort and being logistically feasible. We show with a case study population of rockfish that complete allocation stratified sampling is a very efficient design.
Characterization of Nitrotyrosine-Modified Proteins in Cerebrospinal Fluid
Authors: Beasley Ashley S. , Anderson Caroline , McArthur Justin , Sacktor Ned , Nath Avindra , Cotter Robert J. 
Published: March 2010

Abstract

Background
HIV-associated neurocognitive disorders (HAND) has been associated with the up-regulation of various oxidative stress pathways. Previous studies have linked the neuronal damage observed in individuals diagnosed with HAND to increased nitrotyrosine modification of neuronal proteins.

Materials and methods
Tyrosine nitration alters protein structure and function, affects biological half-life, and potentially prevents the phosphorylation of key tyrosine residues involved in signal transduction pathways. Therefore, in this study we employed proteomics-based experimental approaches to investigate nitrotyrosine-modified proteins in pooled cerebrospinal fluid (CSF) of individuals diagnosed with HAND. To identify specific nitrotyrosine-modified proteins in the CSF of individuals diagnosed with HAND, affinity purification and high-performance tandem mass spectrometry are utilized in a “bottom-up” proteomics approach.

Results
From tandem mass spectrometric analysis, we identified major proteins that underwent nitration as a result of nitro-oxidative stress in the CSF of individuals diagnosed with HAND. We also utilized analytical and biochemical techniques to characterize the expression and modification site of in vivo nitrated lipocalin-type prostaglandin-D synthase in HAND CSF.
Catastrophizing moderates the effect of exposure in vivo for back pain patients with pain‐related fear
Authors: Flink Ida K. , Boersma Katja , Linton Steven J. 
Published: March 2010

AbstractThis investigation was an initial attempt to explore psychological factors that might help or hinder the effect of exposure in vivo for patients with musculoskeletal pain and pain‐related fear. The study was based on data from a randomized‐controlled trial for patients with non‐specific spinal pain (Linton et al., 2008).First, catastrophizing, anxiety, and depression were studied as possible treatment moderators. We found evidence that catastrophizing was a moderator of treatment outcome in exposure. When further exploring the nature of the relationship between catastrophizing and outcome, the results showed that the exposure was effective only for patients with low or moderate levels of catastrophizing. High catastrophizers did not improve from the treatment. On the other hand, anxiety was a general predictor of poor outcome, and not a specific moderator of outcome in exposure. In contrast, depression was not significantly related to outcome.Next, patients were divided into high change participants and low change participants based on their improvement in disability after treatment in order to investigate the change in psychological variables during treatment. Descriptive data indicated that high change participants had large improvements across treatment on depression, anxiety, catastrophizing, and fear‐avoidance beliefs whereas low change participants virtually did not change at all on these variables across treatment.These findings denote that catastrophizing is a moderator of treatment outcome in exposure whereas several psychological variables might be important for the treatment process.
Reproducibility and validity of a diet quality index for children assessed using a FFQ
Authors: Huybrechts Inge , Vereecken Carine , De Bacquer Dirk , Vandevijvere Stefanie , Van Oyen Herman , Maes Lea , Vanhauwaert Erika , Temme Liesbeth , De Backer Guy , De Henauw Stefaan 
Published: March 2010

The diet quality index (DQI) for preschool children is a new index developed to reflect compliance with four main food-based dietary guidelines for preschool children in Flanders. The present study investigates: (1) the validity of this index by comparing DQI scores for preschool children with nutrient intakes, both of which were derived from 3 d estimated diet records; (2) the reproducibility of the DQI for preschoolers based on a parentally reported forty-seven-item FFQ DQI, which was repeated after 5 weeks; (3) the relative validity of the FFQ DQI with 3 d record DQI scores as reference. The study sample included 510 and 58 preschoolers (2·5–6·5 years) for validity and reproducibility analyses, respectively. Increasing 3 d record DQI scores were associated with decreasing consumption of added sugars, and increasing intakes of fibre, water, Ca and many micronutrients. Mean FFQ DQI test–retest scores were not significantly different: 72 (sd11)v.71 (sd10) (P = 0·218) out of a maximum of 100. Mean 3 d record DQI score (66 (sd10)) was significantly lower than mean FFQ DQI (71 (sd10);P < 0·001). The reproducibility correlation was 0·88. Pearsons correlation (adjusted for within-person variability) between FFQ and 3 d record DQI scores was 0·82. Cross-classification analysis of the FFQ and 3 d record DQI classified 60 % of the subjects in the same category and 3 % in extreme tertiles. Cross-classification of repeated administrations classified 62 % of the subjects in the same category and 3 % in extreme categories. The FFQ-based DQI approach compared well with the 3 d record approach, and it can be used to determine diet quality among preschoolers.
Single, subcondylar mandibular osteotomy: a new access route for extensive, benign parapharyngeal neoplasms
Authors: Bianchi B , Ferri A , Ferrari S , Copelli C , Magri A S , Sesenna E 
Published: March 2010

AbstractObjective:We report a new approach to benign parapharyngeal space tumours: a single, subcondylar mandibular osteotomy.Method:Case report and review of the world literature concerning parapharyngeal space access and the various types of mandibular osteotomy.Results:The use of a single, subcondylar mandibular osteotomy achieves good exposure and satisfactory aesthetic and functional results, using a simple, easily performed technique that is fast and has minimal morbidity. In addition, this technique preserves the submandibular gland and avoids lip-splitting and post-operative intermaxillary fixation.Conclusion:To our knowledge, this is the first report of this approach to the parapharyngeal space. We propose this approach as the first choice for resection of benign neoplasms of the parapharyngeal space.