bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temperature and moisture trends in non‐sorted earth hummocks and stripes on the Old Man Range, New Zealand: implications for mechanisms of maintenance
Authors: Scott Matthew B. , Dickinson Katharine J. M. , Barratt Barbara I. P. , Sinclair Brent J. 
Published: August 2008

AbstractThe mechanisms of maintenance of earth hummocks and non‐sorted stripes in seasonally frozen ground on the Old Man Range, Otago, New Zealand were investigated. These landforms are hypothesised to be active periglacial landforms maintained by seasonal movement of moisture down an energy gradient. We tested three hypotheses: 1) freezing should occur predominantly in the crests of the stripes and hummocks; 2) differential freezing patterns should be consistent between years; and 3) in the presence of a temperature gradient (i.e. in winter), soil moisture content should be greater in crests than in furrows. An array of 39 thermistors at each of two sites was used to monitor soil temperature gradients during three winters, and replicate soil cores were taken in autumn and winter to determine soil moisture gradients. Freezing occurred mainly in the crests and sides (heavily influenced by aspect), and patterns of freezing showed strong interannual consistency, supporting our first two hypotheses. Soil in crests had a higher moisture content in both freezing and thawed seasons, which was inconclusive relative to the expected water gradient. Copyright © 2008 John Wiley & Sons, Ltd.
Molecular dynamic simulations of nanomechanic chaperone peptide and effects of in silico His mutations on nanostructured function
Authors: Barzegar Abolfazl , Moosavi‐Movahedi Ali Akbar , Mahnam Karim , Bahrami Homayoon , Sheibani Nader 
Published: August 2008

AbstractThe nanoscale peptide YSGVCHTDLHAWHGDWPLPVK exhibits molecular chaperone activity and prevents protein aggregation under chemical and/or thermal stress. Here, His mutations of this peptide and their impact on chaperone activity were evaluated using theoretical techniques. Molecular dynamic (MD) simulations with simulated annealing (SA) of different mutant nanopeptides were employed to determine the contribution of the scaffolding His residues (H45, H49, H52), when mutated to Pro, on chaperone action in vitro. The in silico mutations of His residues to Pro (H45P, H49P, H52P) revealed loss of secondary ordered strand structure. However, a small part of the strand conformation was formed in the middle region of the native chaperone peptide. The His‐to‐Pro mutations resulted in decreased gyration radius (Rg) values and surface accessibility of the mutant peptides under the simulation times. The invariant dihedral angle (ϕ) values and the disrupting effects of the Pro residues indicated the coil conformation of mutant peptides. The failure of the chaperone‐like action in the Pro mutant peptides was consistent with their decreased effective accessible surfaces. The high variation of Φ value for His residues in native chaperone peptide leads to high flexibility, such as a minichaperone acting as a nanomachine at the molecular level. Our findings demonstrate that the peptide strand conformation motif with high flexibility at nanoscale is critical for chaperone activity. Copyright © 2008 European Peptide Society and John Wiley & Sons, Ltd.
Estimating observation impact without adjoint model in an ensemble Kalman filter
Authors: Liu Junjie , Kalnay Eugenia 
Published: August 2008

AbstractWe propose an ensemble sensitivity method to calculate observation impacts similar to Langland and Baker (2004) but without the need for an adjoint model, which is not always available for numerical weather prediction models. The formulation is tested on the Lorenz 40‐variable model, and the results show that the observation impact estimated from the ensemble sensitivity method is similar to that from the adjoint method. Like the adjoint method, the ensemble sensitivity method is able to detect observations that have large random errors or biases. This sensitivity could be routinely calculated in an ensemble Kalman filter, thus providing a powerful tool to monitor the quality of observations and give quantitative estimations of observation impact on the forecasts. Copyright © 2008 Royal Meteorological Society
Theoretical study of the SH···O blue‐shifted hydrogen bond
Authors: Yang Yong 
Published: August 2008

AbstractTheoretical calculations were performed to study the nature of the hydrogen bonds in the complexes HCHO···HSO, HCOOH···HSO, HCHO···HOO, and HCOOH···HOO. The geometric structures and vibrational frequencies of these four complexes at the MP2/6‐31G(d,p) and MP2/6‐311+G(d,p) levels are calculated by standard and counterpoise‐corrected methods, respectively. The results indicate that in the complexes HCHO···HSO and HCOOH···HSO the SH bond is strongly contracted. In the SH···O hydrogen bonds, the calculated blue shifts for the SH stretching frequencies are in the vicinity of 50 cm−1. While in the complexes HCHO···HOO and HCOOH···HOO, the OH bond is elongated and OH···O red‐shifted hydrogen bonds are found. From the natural bond orbital analysis it can be seen that the XH bond length in the XH···Y hydrogen bond is controlled by a balance of four main factors in the opposite directions: hyperconjugation, electron density redistribution, rehybridization, and structural reorganization. Among them hyperconjugation has the effect of elongating the XH bond. Electron density redistribution and rehybridization belong to the bond shortening effects, while structural reorganization has an uncertain influence on the XH bond length. In the complexes HCHO···HSO and HCOOH···HSO, the shortening effects dominate which lead to the blue shift of the SH stretching frequencies. In the complexes HCHO···HOO and HCOOH···HOO where elongating effects are dominant, the OH···O hydrogen bonds are red‐shifted. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Reconstruction of the (011) surface on α‐quartz: A semiclassical Ab initio molecular dynamics study
Authors: Lopes Pedro E. M. , Demchuk Eugene , Mackerell Alexander D. 
Published: August 2008

AbstractAb initio molecular dynamics simulations have been performed on the (011) surface of α‐quartz at room‐temperature using density functional theory. Pristine surface was obtained by homolytic fracture of α‐quartz crystal, leaving exposed SiO· radicals, following which the surface was allowed to spontaneously reconstruct during the simulation. Reconstruction events occurred at different timings but in most cases produced similar geometries. The most common motif consisted of a fused seven‐member ring. Formation of this structure proceeded through reaction of two adjacent O· radicals, followed by linking of one of the reactive O· with a nearby silicon. Other structures, like Si2O2, were also observed. In the newly formed structures some of the silicon atoms had pentacoordinated geometry, usually distorted between pure bipyramidal, trigonal, and square pyramidal. In a few cases oxygen atoms also became tricoordinated. Formation of new bonds was investigated by analyzing the electronic structure of the system along the reaction path, and specifically the localization of unpaired electrons was deduced from the spin‐density. Because most reactions involved triplet → singlet transitions, a time‐dependent density functional theory was used to determine the crossing point of the two potential energy surfaces. Plotted density of states was also used to compare the electronic structures of the initial and reconstructed surfaces. Reconstruction originated new states from O‐px and O‐pz orbitals. Stability analysis of the reconstructed surface was performed at the PBE level and 7‐member rings were found to be more stable than fused rings with pentacoordinated silicon. Hypervalent silicon and oxygen atoms were also found to exist. Nevertheless, specialization of (011) surface appears to be less reactive compared to (001), which suggests a lesser toxicity of rhombohedral form on crystalline silica. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
π‐π Stacking of curved carbon networks: The corannulene dimer
Authors: Sygula Andrzej , Saebø Svein 
Published: August 2008

AbstractDimers of corannulene, a curved, saucer shaped molecule, were studied by theoretical calculations using second order Møller‐Plesset perturbation theory and a large polarized triple zeta basis set. Three dimer motifs were investigated: the “native” dimer is the concave‐convex stacking of two monomers with the geometries of both monomers conserved; the “planar” motif with both monomers forced to be planar; and the “C60‐like” dimer where the outer monomer has the native geometry while the inner one has the curvature of buckminsterfullerene C60. Both staggered and eclipsed conformations of the dimers were investigated. Our calculations show that the binding energy of the native concave‐convex corannulene dimer is quite substantial (17.2 kcal/mole at the “best” SCS‐MP2/cc‐pvtz level of theory) with an equilibrium distance of about 3.64 Å. Surprisingly, there are only minor differences in both binding energies and equilibrium distances between the three different dimer motifs. This suggests that the curvature of the conjugated carbon networks does not disable their ability to form π‐π stacked assemblies similar to the planar systems. However, in contrast to the planar systems, at least part of the binding energies in the stacked curved systems can be attributed to attractive electrostatic dipole‐dipole contributions since buckybowls exhibit significant dipole moments. For the “planar” dimer, a staggered arrangement of the two monomers is preferred, while eclipsed conformations are the most stable for all curved dimers. For all systems, the basis set superposition errors are large (ca. 7 kcal/mol) at the equilibrium distance even with our largest basis sets. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Decomposition mechanisms of dinitrotoluene
Authors: Tanaka Genzo , Weatherford Charles 
Published: August 2008

AbstractTo develop a viable detection system for 2,4‐dinitrotoluene (DNT), its unimolecular decomposition mechanisms were studied by using the density functional theory. Three decomposition mechanisms were investigated: (1) homolytic cleavage; (2) migration of one of the O atoms in the NO2 groups to its neighboring C atoms; (3) migration of one of the H atoms in the methyl group to a neighboring O atom in the NO2 group. Only homolytic cleavage of the CN bond yields NO2 radicals with a total energy of 61 kcal/mol or more. Initial migration of the O atom to its second‐nearest‐neighbor C atom requires about 56 kcal/mol, but subsequent homolysis produces NO fragments with less energy ∼15 kcal/mol. NO formation from both NO2 groups in 2,4‐DNT is possible with a total energy of ∼63 kcal/mol. The H‐migration has the lowest energy barrier of 39 kcal/mol among the three initial decomposition mechanisms. Removing O directly from 2,4‐DNT requires ∼90 kcal/mol, while NO2 radical decomposes to NO and O with ∼73 kcal/mol. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Investigations of structure and dynamics of water solvation of the type I antifreeze protein
Authors: Cui Jun , Battle Keith , Wierzbicki Andrzej , Madura Jeffry D. 
Published: August 2008

AbstractWe use molecular dynamics simulations to study the water structure and dynamics around the winter flounder antifreeze protein (AFP) and its two mutant forms in which the four key threonine residues of the winter flounder AFP are mutated to alanines and serines, respectively. The TIP4P‐Ew water model is used to better describe the water interactions and water structure; all simulations are performed at 245.5 K, a temperature near the freezing point of the TIP4P‐Ew water model. Analysis of structural and dynamic properties of the water around the threonines in the winter flounder AFP reveals that the water structure is ordered around the threonine residues, especially in the second‐solvation shell. Alanine and serine mutations instead promote water hydration in the first‐solvation shell. Also our calculations show that in the close vicinity of the threonine residues of the wild‐type AFP, the mobility of water molecules is substantially decreased. A smaller effect is observed for the weakly active alanine‐substituted mutant, and no effect is observed for the inactive serine‐substituted mutant. The results of this study suggest that water ordering and immobilization play important roles in the recognition and adsorption of the antifreeze protein to ice. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Equivalent non‐linear single‐degree‐of‐freedom system of spatial asymmetric multi‐storey buildings in pushover procedure: theory and applications
Authors: Makarios Triantafyllos K. 
Published: August 2008

AbstractIn the present paper, the issue of the approximate definition of a new equivalent non‐linear single‐degree‐of‐freedom (NLSDF) system on spatial asymmetric reinforced concrete (r/c) tall multi‐storey buildings is presented. In order to achieve this goal, three different types of r/c systems are examined: the first type refers to multi‐storey planar r/c frames; the second type refers to asymmetric single‐storey r/c building; and the third type refers to asymmetric multi‐storey r/c buildings. The definition of the NLSDF system is mathematically derived, considering suitable dynamic loadings on the masses of each r/c system using simplified assumptions. The NLSDF system is very useful in the seismic design of the r/c systems, since it is widely used in all forms of various pushover analyses that have been published in the past. The use of the equivalent NLSDF system in combination with the inelastic design spectra can give an acceptable evaluation of the maximum required seismic floor displacement for a known design earthquake. The present paper concludes the total theory of definition of the optimum equivalent NLSDF system for the above three types of buildings that possess the required normality by the contemporary seismic codes in elevation. In order to illustrate the theory, three numerical examples are presented, respectively. The final numerical required displacement results by the use of the equivalent NLSDF system are verified and checked by non‐linear response history analyses. Copyright © 2008 John Wiley & Sons, Ltd.
Shaking table model tests on a complex high‐rise building with two towers of different height connected by trusses
Authors: Lu Xilin , Chen Linzhi , Zhou Ying , Huang Zhihua 
Published: August 2008

AbstractThe past decades have witnessed a flourish of novel high‐rise structures throughout the world under the requirement of a ceaselessly progressing architectural aesthetics, resulting in a complex plan and elevation of a building. Shanghai International Design Center is such a high‐rise building with two towers of different heights connected by trusses, and the structural system is composed of steel frame, reinforced concrete (RC) core wall and shear walls. The great irregularity in plan and elevation, according to Chinese code, necessitates a detailed study, which usually includes refined structural analysis, scaled structural model test and large size member or joint test. As recommended by the peer review committee, the shaking table tests of the 1:15‐scale structural model were performed. Based on the analysis and shaking table model testing, it was found that the stiffness of the connecting trusses is capable of coordinating the two towers to resist lateral forces jointly even under strong earthquakes. As a result of stiffening action brought by the connecting trusses, whipping‐lash effect in longitudinal direction develops sharply on top storeys. Structural responses at storeys around the connecting trusses vary remarkably due to sudden change in lateral stiffness. Through comparison between tests and numerical analysis, weak positions of the structure are identified, and some corresponding measures for improving the design of this structure are also put forward. Copyright © 2008 John Wiley & Sons, Ltd.
Photogrammetry of fetal breathing movements during the third trimester of pregnancy: observations in normal and abnormal pregnancies
Authors: Florido J. , Padilla M. C. , Soto V. , Camacho A. , Moscoso G. , Navarrete L. 
Published: August 2008

AbstractObjectiveTo evaluate parameters of fetal breathing movements—displacement of the fetal abdominal wall during inspiration and expiration, time of inspiration and expiration and speed of inspiration and expiration—between 30 and 36 weeks' gestation in normal pregnancies, and in those complicated by gestational diabetes or maternal hypertension.MethodsThree categories of pregnancy were investigated: 49 were normal, 16 had pregnancy‐induced diabetes and 10 were hypertensive. According to their gestational age, the patients were divided into two groups: Group A between 30 and 32 weeks' gestation and Group B between 33 and 36 weeks. Using photogrammetry and a computer‐operated algorithm, six parameters of fetal breathing movements were investigated.ResultsThere were significant differences in the various fetal parameters measured among the three categories of pregnant women. Up until 32 weeks of gestation, the displacements during inspiration and expiration were larger, the speeds of inspiration and expiration were higher, and the times for inspiration and expiration were shorter in the diabetic and hypertensive groups than in the normal group. In the later period, between 33 and 36 weeks, fetuses of pregnancy‐induced diabetic patients showed the lowest inspiration and expiration times and the highest speeds of inspiration and expiration.ConclusionsPhotogrammetry in conjunction with a computer‐operated algorithm can be used to assess fetal breathing movements. There are significant differences in fetal breathing movements between normal pregnancies and those that are complicated by gestational diabetes or hypertension. Copyright © 2008 ISUOG. Published by John Wiley & Sons, Ltd.
Surgical Margin Status and Prognosis of Gastrointestinal Stromal Tumor
Authors: Gouveia António M. , Pimenta Amadeu P. , Capelinha Ana F. , de la Cruz Dionísio , Silva Paula , Lopes José M. 
Published: August 2008

AbstractBackgroundSurgery is the best treatment for primary GIST and may be curative, but resection extension/completeness impact on the prognosis remains controversial. The authors aim was to evaluate the clinicopathological (CP) parameters and surgical margins status influence on GIST patients’ outcome.Materials and methodsThe study evaluated 113 consecutive patients with sporadic GIST; the influence of CP parameters on recurrence‐free survival (RFS) and disease‐specific survival (DSS) was determined by univariate analysis (UA) and multivariate analysis (MA).ResultsOf 104 cases, macroscopically complete resection was achieved in 96: R0 surgical margin status in 78 and R1 in 18. Recurrence rates (12.5%) were significantly lower in R0 (9.0%) than in R1 (27.8%). Tumor >10 cm, mitotic count >5/50 high power field (HPF), and high‐risk GIST predicted poor RFS and DSS (UA). Disease‐specific survival was significantly shorter after macroscopic incomplete (R2) resection, for mixed cellular morphology, and in tumors with necrosis (UA). High‐risk GIST (p = 0.016) and R2 resection (p = 0.013) predicted poor DSS of patients (MA).ConclusionsHigh risk and positive macroscopic surgical margin status are parameters associated with poor disease‐specific survival in GIST patients.
Ipsilateral femoral neck and shaft fractures: a retrospective analysis of two treatment methods
Authors: Singh Roop , Rohilla Rajesh , Magu Narender Kumar , Siwach Ramchander , Kadian Virender , Sangwan Sukhbir Singh 
Published: August 2008

AbstractBackgroundNo consensus exists regarding the optimal treatment of ipsilateral femoral neck and shaft fractures. The three major issues related to these fractures are the optimal timing of surgery, which fracture to stabilize first, and the optimal implant to use. In an effort to find answers to these three key issues, we report our experience of managing 27 patients with ipsilateral femoral neck and shaft fractures by using two different treatment methods, i.e., reconstruction-type intramedullary nailing and various plate combinations.Materials and methodsWe divided patients into two groups. Group I included 15 patients (13 males and 2 females) who were operated with cancellous lag screws or dynamic hip screws (DHS) for fractured neck and compression plate fixation for fractured shaft of the femur. Group II included 12 patients (11 males and 1 female) who were operated with reconstruction-type intramedullary nailing.ResultsMean age was 33.2 and 37.9 years in group I and II, respectively. Mean delay in surgery was 5.9 and 5.4 days in group I and II, respectively. Average union time for femoral neck fracture in groups I and II were 15.2 and 17.1 weeks, respectively; and for shaft fracture these times were 20.3 and 22.8 weeks, respectively. There were 13 (86.6%) good, 1 (6.7%) fair and 1 (6.7%) poor functional results in group I. There were 10 (83.3%) good, 1 (8.3%) fair and 1 (8.3%) poor functional results in group II.ConclusionsBoth of the treatment methods used in the present study achieved satisfactory functional outcome in these complex fractures. Fixation with plate for shaft and screws or DHS for hip is easy from a technical point of view. Choice of the treatment method should be dictated primarily by the type of femoral neck fracture and the surgeon’s familiarity with the treatment method chosen. The femoral neck fracture should preferably be stabilized first, and a delay of 5–6 days does not affect the ultimate functional outcome.
Preparation and Characterization of Stimuli-Responsive Magnetic Nanoparticles
Authors: Wang ShiXing , Zhou Yang , Guan Wen , Ding Bingjun 
Published: August 2008

Abstract
In this work, the main attention was focused on the synthesis of stimuli-responsive magnetic nanoparticles (SR-MNPs) and the influence of glutathione concentration on its cleavage efficiency. Magnetic nanoparticles (MNPs) were first modified with activated pyridyldithio. Then, MNPs modified with activated pyridyldithio (MNPs-PDT) were conjugated with 2, 4-diamino-6-mercaptopyrimidine (DMP) to form SR-MNPs via stimuli-responsive disulfide linkage. Fourier transform infrared spectra (FTIR), transmission electron microscopy (TEM), and X-ray photoelectron spectroscopy (XPS) were used to characterize MNPs-PDT. The disulfide linkage can be cleaved by reduced glutathione (GHS). The concentration of glutathione plays an important role in controlling the cleaved efficiency. The optimum concentration of GHS to release DMP is in the millimolar range. These results had provided an important insight into the design of new MNPs for biomedicine applications, such as drug delivery and bio-separation.
Analyses of velocity, acceleration, statics, and workspace of a 2(3-SPR) serial-parallel manipulator
Authors: Lu Yi , Hu Bo , Sun Tao 
Published: August 2008

SUMMARYThe kinematics, statics, and workspace of a 2(3-SPR) serial-parallel manipulator (S-PM) are studied systematically in this paper. First, a 2(3-SPR) S-PM including an upper 3-SPR parallel manipulator (PM) and a lower 3-SPR PM is constructed, and the inverse/forward displacements, velocity, acceleration, and statics of the lower and upper 3-SPR PMs are studied, respectively. Second, the kinematics and statics of the lower and upper 3-SPR PMs are combined and the displacement, velocity, acceleration, and statics of a 2(3-SPR) S-PM are analyzed systematically. Third, a workspace of the 2(3-SPR) S-PM is constructed and analyzed. Finally, the analytic solved results are given and verified by the simulation mechanism.