bluuebunny/crossref_metadata_2025_split huggingface dataset:
SMS 2.0: An Updated Database to Study the Structural Plasticity of Short Peptide Fragments in Non-Redundant Proteins
Authors: Ravella Dheeraj , Kumar Muthukumarasamy Uthaya , Sherlin Durairaj , Shankar Mani , Vaishnavi Marthandan Kirti , Sekar Kanagaraj 
Published: March 2012

Abstract
The function of a protein molecule is greatly influenced by its three-dimensional (3D) structure and therefore structure prediction will help identify its biological function. We have updated Sequence, Motif and Structure (SMS), the database of structurally rigid peptide fragments, by combining amino acid sequences and the corresponding 3D atomic coordinates of non-redundant (25%) and redundant (90%) protein chains available in the Protein Data Bank (PDB). SMS 2.0 provides information pertaining to the peptide fragments of length 5-14 residues. The entire dataset is divided into three categories, namely, same sequence motifs having similar, intermediate or dissimilar 3D structures. Further, options are provided to facilitate structural superposition using the program structural alignment of multiple proteins (STAMP) and the popular JAVA plug-in (Jmol) is deployed for visualization. In addition, functionalities are provided to search for the occurrences of the sequence motifs in other structural and sequence databases like PDB, Genome Database (GDB), Protein Information Resource (PIR) and Swiss-Prot. The updated database along with the search engine is available over the World Wide Web through the following URL http://cluster.physics.iisc.ernet.in/sms/.
Magnetohydrodynamic drift equations: from Langmuir circulations to magnetohydrodynamic dynamo?
Authors: Vladimirov V. A. 
Published: March 2012

AbstractWe derive the closed system of averaged magnetohydrodynamic (MHD) equations for general oscillating flows. The used small parameter of our asymptotic theory is the dimensionless inverse frequency, and the leading term for a velocity field is chosen to be purely oscillating. The employed mathematical approach combines the two-timing method and the notion of a distinguished limit. The properties of commutators are used to simplify calculations. The derived averaged equations are similar to the original MHD equations, but surprisingly (instead of the commonly expected Reynolds stresses) a drift velocity plays a part of an additional advection velocity. In the special case of a vanishing magnetic field $\mathbi{h}\equiv 0$, the averaged equations produce the Craik–Leibovich equations for Langmuir circulations (which can be called ‘vortex dynamo’). We suggest that, since the mathematical structure of the full averaged equations for $\mathbi{h}\not = 0$ is similar to those for $\mathbi{h}\equiv 0$, these full equations could lead to a possible mechanism of MHD dynamo, such as the generation of the magnetic field of the Earth.
On the Calculation of Two-Dimensional Added Mass Coefficients by the Taylor Theorem and the Method of Fundamental Solutions
Authors: Yang F.-L. , Wu C. T. , Young D. L. 
Published: March 2012

ABSTRACTThis work integrates the Taylor theorem and the method of fundamental solutions to develop a numerical tool for estimating the added mass coefficient tensor for a solid object of any convex shape moving in potential flow. In potential flow theory, the Taylor theorem calculates the added mass coefficient tensor for a Rankine body with algebraic manipulations of the properties of the internal singularities employed to generate the corresponding flow. To apply this theorem for objects in other shapes, the singularity strength and locations are required information which is facilitated numerically in this work by the method of fundamental solutions (MFS). The developed scheme is tested on a circle, an ellipse, a square, and a rhombus and the numerical results are in good agreement with the corresponding analytical values. A final example of a Cassini oval is also considered to show the potential applications on bio-engineering problems.
Theoretical Analysis of Cylindrical Microparticle Photophoresis in a Perpendicular Optical Field with Thermal Stress Slip Model
Authors: Tzeng P.-Y. , Liu C.-H. , Li W.-K. , Soong C.-Y. 
Published: March 2012

ABSTRACTThe present study is concerned with a theoretical analysis of the photophoresis of a microsized long cylinder in a perpendicular optical field. Different from previous studies of photophoresis, thermal stress slip usually neglected is taken into account in the analysis. The gaseous fluid relative to the microparticle in photophoretic motion falls into slip-flow regime. Asymmetric distribution of the absorbed heat energy within the particle becomes the driving force for photophoretic motion of the cylinder-shaped particle. By evaluating heat source function distributions at various conditions, the study focuses on the effects of particle size and optical properties on the energy distribution and the resultant influences on the photophoresis. The photophoretic mobility is developed by the slip flow model with consideration of thermal stress slip. The results reveal that the photophoretic mobility decreases with the increase of particle thermal conductivity (k*) and increases with Knudsen number (Kn). The thermal stress slip effect on photophoretic velocity is more noticeable at highKn, but disappears at the continuum limit. A long cylinder-shaped particle has higher photophoretic velocity than a spherical particle at lowk*, while the situation reverses at highk*. With thermal stress slip considered, the critical condition for crossing of the photophoretic velocity curves of cylindrical and spherical particles is mildly influenced byKn.
Modified Kastner Formula for Cylindrical Cavity Contraction in Mohr-Coulomb Medium for Circular Tunnel in Isotropic Medium
Authors: Cheng Y. M. 
Published: March 2012

ABSTRACTThe Kastner formula for cavity contraction is one of the commonly used formulae for the cavity contraction problem in tunnel excavation, and it is based on the assumption of small displacement around the cavity with no volume change in the plastic zone. In this paper, the errors arising from these assumptions are discussed, and the volume change of the plastic zone is considered. It can be seen that this assumption is reasonable for normal situations, but for rock with weak shear strength, the Kastner formula should be used with care, especially in situations where there will be relatively large volume changes in the plastic zone.
Fourier Expansion to Elastic Vector Wave Functions and Applications of Wave Bases to Scattering in Half-Space
Authors: Shih P.-J. , Teng T.-J. , Yeh C.-S. 
Published: March 2012

ABSTRACTThis paper proposes a complete basis set for analyzing elastic wave scattering in half-space. The half-space is an isotropic, linear, and homogeneous medium except for a finite inhomogeneity. The wave bases are obtained by combining buried source functions and their reflected counter-waves generated from the infinite-plane boundary. The source functions are the vector wave functions of infinite-space. Based on the source functions expressed in the Fourier expansion form, the reflected counter-waves are easily obtained by solving the infinite-plane boundary conditions. Few representations adopt Wely's integration, but the Fourier expansion is developed from it and applied to decouple the angular-differential terms of the vector wave functions. In addition to the scattering of the finite inhomogeneity, the transition matrix method is extended to express the surface boundary conditions. For the numerical application in this paper, the P- and the SV- waves are assumed as the incoming fields. As an example, this paper computes stress concentrations around a cavity. The steepest-descent path method yielding the optimum integral paths is used to ensure the numerical convergence of the wave bases in the Fourier expansion. The resultant patterns from these approaches are compared with those obtained from numerical simulations.
Aerodynamic Investigations of Low-Aspect-Ratio Thin Plate Wings at Low Reynolds Numbers
Authors: Liu Y.-C. , Hsiao F.-B. 
Published: March 2012

ABSTRACTTo realize the relationship between flow structures of wingtip vortices and post stall characteristics of low aspect-ratio wings, this paper experimentally studies the aerodynamic characteristics and the corresponding flow structures of the rectangular thin-plate wings at Reynolds numbers between 104 and 105. The aerodynamic properties to be studied include lift, drag, slopes at linear and nonlinear range of the lift curves and lift-to-drag ratios of the tested wings with the aspect ratio varying from 1.0 to 3.0. The flow structures regarding the leading-edge separation vortices and wingtip vortices at upper surface and near-wake regions of the wings are also investigated by smoke-wire visualization. Results indicate that the high stall angle of attack and vortex lift are clearly manifested to induce the nonlinear increase in the lift curves as the aspect ratio reaches less than 1.6. This phenomenon is specifically observed to augment the aerodynamic properties with the decrease of the aspect ratio. Additionally, the corresponding flow visualization also indicates that the wingtip vortices and the areas of highly affected regions are duly increased with the increase of the angle of attack up to 40°, which makes certain that the extra increase of the nonlinear lift results from these vortices. This result can be practically applied to the planform design for unmanned aerial vehicles.
ON PAIRS OF LINEAR EQUATIONS IN FOUR PRIME VARIABLES AND POWERS OF TWO
Authors: KONG YAFANG 
Published: March 2012

AbstractIn this paper, we consider the simultaneous representation of pairs of positive integers. We show that every pair of large positive even integers can be represented in the form of a pair of linear equations in four prime variables and k powers of two. Here, k=63 in general and k=31 under the generalised Riemann hypothesis.
Cryptostatin, a chagasin-family cysteine protease inhibitor ofCryptosporidium parvum
Authors: KANG J.-M. , JU H.-L. , YU J.-R. , SOHN W.-M. , NA B.-K. 
Published: March 2012

SUMMARYCysteine proteases of pathogenic protozoan parasites play pivotal roles in the life cycle of parasites, but strict regulation of their activities is also essential for maintenance of parasite physiology and interaction with hosts. In this study, we identified and characterized cryptostatin, a novel inhibitor of cysteine protease (ICP) ofCryptosporidium parvum. Cryptostatin showed low sequence identity to other chagasin-family ICPs, but 3 motifs (NPTTG, GXGG, and RPW/F motifs), which are evolutionarily conserved in chagasin-family ICPs, were found in the sequence. The overall structure of cryptostatin consisted of 8β-strands that progressed in parallel and closely resembled the immunoglobulin fold. Recombinant cryptostatin inhibited various cysteine proteases, including papain, human cathepsin B, human cathepsin L, and cryptopain-1, withKi's in the picomolar range. Cryptostatin was active over a wide pH range and was highly stable under physiological conditions. The protein was thermostable and retained its inhibitory activity even after incubation at 95°C. Cryptostatin formed tight complexes with cysteine proteases, so the complexes remained intact in the presence of sodium dodecyl sulfate andβ-mercaptoethanol, but they were disassembled by boiling. An immunogold electron microscopy analysis demonstrated diffused localization of cryptostatin within oocystes and meronts, but not within trophozoites, which suggests a possible role for cryptostatin in host cell invasion byC. parvum.
Intensity of parasitic mite infection decreases with hibernation duration of the host snail
Authors: HAEUSSLER E. M. , PIZÁ J. , SCHMERA D. , BAUR B. 
Published: March 2012

SUMMARYTemperature can be a limiting factor on parasite development.Riccardoella limacum, a haematophagous mite, lives in the mantle cavity of helicid land snails. The prevalence of infection byR. limacumin populations of the land snailArianta arbustorumis highly variable (0–78%) in Switzerland. However, parasitic mites do not occur in host populations at altitudes of 1290 m or higher. It has been hypothesized that the host's hibernation period might be too long at high elevations for mites and their eggs to survive. To test this hypothesis, we experimentally infected snails and allowed them to hibernate at 4°C for periods of 4–7 months. Winter survival of host snails was negatively affected byR. limacum. The intensity of mite infection decreased with increasing hibernation duration. Another experiment with shorter recording intervals revealed that mites do not leave the host when it buries in the soil at the beginning of hibernation. The number of mites decreased after 24 days of hibernation, whereas the number of eggs attached to the lung tissue remained constant throughout hibernation. Thus,R. limacumsurvives the winter in the egg stage in the host. Low temperature at high altitudes may limit the occurrence ofR. limacum.
The relationship between executive functions and fluid intelligence in Parkinson's disease
Authors: Roca M. , Manes F. , Chade A. , Gleichgerrcht E. , Gershanik O. , Arévalo G. G. , Torralva T. , Duncan J. 
Published: March 2012

BackgroundWe recently demonstrated that decline in fluid intelligence is a substantial contributor to frontal deficits. For some classical ‘executive’ tasks, such as the Wisconsin Card Sorting Test (WCST) and Verbal Fluency, frontal deficits were entirely explained by fluid intelligence. However, on a second set of frontal tasks, deficits remained even after statistically controlling for this factor. These tasks included tests of theory of mind and multitasking. As frontal dysfunction is the most frequent cognitive deficit observed in early Parkinson's disease (PD), the present study aimed to determine the role of fluid intelligence in such deficits.MethodWe assessed patients with PD (n=32) and control subjects (n=22) with the aforementioned frontal tests and with a test of fluid intelligence. Group performance was compared and fluid intelligence was introduced as a covariate to determine its role in frontal deficits shown by PD patients.ResultsIn line with our previous results, scores on the WCST and Verbal Fluency were closely linked to fluid intelligence. Significant patient–control differences were eliminated or at least substantially reduced once fluid intelligence was introduced as a covariate. However, for tasks of theory of mind and multitasking, deficits remained even after fluid intelligence was statistically controlled.ConclusionsThe present results suggest that clinical assessment of neuropsychological deficits in PD should include tests of fluid intelligence, together with one or more specific tasks that allow for the assessment of residual frontal deficits associated with theory of mind and multitasking.
Study of stimulated Brillouin scattering in extended paraxial region
Authors: Sharma Prerana , Bhardwaj A.K. , Sharma R.P. 
Published: March 2012

AbstractThis communication presents a comparison of two cases to study the process of laser beam propagation and Stimulated Brillouin Scattering (SBS) in laser plasma interaction. These two cases are, with imposing the restriction of paraxial approximation on the laser beam and, relaxing this restriction up to a certain extent. In this work, the study done by Sharma et al. (2009) using paraxial approximation is extended by taking contribution of the off-axial rays in the laser beam profile. The spitted profile of the laser beam is obtained due to uneven focusing of the off-axial rays and its effect on localization of the ion acoustic wave (IAW) has been studied. Including the off-axial part of the laser beam semi-analytical solution of the nonlinear coupled IAW equation has been found and this is examined that off-axial part affects background densities. The nonlinear coupling between the laser beam and IAW is severely affected by modified profile of the laser beam. Further, it is investigated that the SBS is also influenced by this coupling process. Therefore, the reflectivity of SBS has been compared with and without contribution of off-axial rays. A notable change is found in the magnitude of SBS reflectivity in modified-paraxial case in comparison to the paraxial case.
Children's ability to answer different types of questions
Authors: SALOMO DOROTHÉ , LIEVEN ELENA , TOMASELLO MICHAEL 
Published: March 2012

ABSTRACTYoung children answer many questions every day. The extent to which they do this in an adult-like way – following Grice's Maxim of Quantity by providing the requested information, no more no less – has been studied very little. In an experiment, we found that two-, three- and four-year-old children are quite skilled at answering argument-focus questions and predicate-focus questions with intransitives in which their response requires only a single element. But predicate-focus questions for transitives – requiring both the predicate and the direct object – are difficult for children below four years of age. Even more difficult for children this young are sentence-focus questions such as “What's happening?”, which give the child no anchor in given information around which to structure their answer. In addition, in a corpus study, we found that parents ask their children predicate-focus and sentence-focus questions very infrequently, thus giving children little experience with them.
The science on front-of-package food labels
Authors: Hawley Kristy L , Roberto Christina A , Bragg Marie A , Liu Peggy J , Schwartz Marlene B , Brownell Kelly D 
Published: March 2012

AbstractObjectiveThe US Food and Drug Administration and Institute of Medicine are currently investigating front-of-package (FOP) food labelling systems to provide science-based guidance to the food industry. The present paper reviews the literature on FOP labelling and supermarket shelf-labelling systems published or under review by February 2011 to inform current investigations and identify areas of future research.DesignA structured search was undertaken of research studies on consumer use, understanding of, preference for, perception of and behaviours relating to FOP/shelf labelling published between January 2004 and February 2011.ResultsTwenty-eight studies from a structured search met inclusion criteria. Reviewed studies examined consumer preferences, understanding and use of different labelling systems as well as label impact on purchasing patterns and industry product reformulation.ConclusionsThe findings indicate that the Multiple Traffic Light system has most consistently helped consumers identify healthier products; however, additional research on different labelling systems’ abilities to influence consumer behaviour is needed.
From seismic noise to ocean wave parameters: General methods and validation
Authors: Ardhuin Fabrice , Balanche Abel , Stutzmann E. , Obrebski Mathias 
Published: March 2012

Seismic noise is an indirect source of information on ocean waves. Using a model of noise generation and propagation, seismic stations can be separated into those that are mostly sensitive to local sea states, and those that integrate sources from a large oceanic area. The model also provides a classification of noise‐generating sea states into three classes. The analysis of Central California seismic noise data, well correlated with local waves, reveals that class I events dominate in summer, caused by a single wind‐sea system, and for which ocean wave spectral levels are proportional to seismic spectral levels to an exponentb ≃ 0.9. In winter, noise is dominated by class II generation, for which coastal reflection is important, with a wave spectral density roughly proportional to the seismic spectral density to an exponent b ≃ 0.7. Sporadic events of class III probably produce some of the strongest noise events in Central California and need to be properly screened. These events are caused by opposed wave systems that are usually the wind‐sea and a swell. This noise classification can be used to improve on the correlation between measured and estimated wave heights (up tor = 0.93 for daily averages). For other locations, where remote oceanic sources are recorded, a significant wave height estimated from the seismic noise compares well with area‐averaged satellite data or wave model results (r > 0.85 for daily averages). These analyses pave the way for quantitative uses of seismic records, including the reconstruction of past wave climates, and the calibration of wave hindcasts.
Evaluation of SMOS retrievals of soil moisture over the central United States with currently available in situ observations
Authors: Collow Thomas W. , Robock Alan , Basara Jeffrey B. , Illston Bradley G. 
Published: March 2012

The European Space Agency launched the Soil Moisture Ocean Salinity (SMOS) satellite in November 2009. Using SMOS soil moisture retrievals for 2010 processed using algorithm V4.00, we evaluated SMOS retrievals by comparing them to in situ soil moisture observations for the top 5 cm at several stations in the Great Plains of the U.S. A major issue with comparing the satellite data with in situ data is that a SMOS footprint is about 40 km across and we compare to point observations. To address this issue, we chose locations in Oklahoma that have 10 to 25 different in situ observations within each SMOS footprint. The SMOS retrievals have a dry bias when compared to the average of all in situ stations in a footprint. Large differences exist between the in situ observations, even for probes only a few meters apart. Observations from different sensors within a SMOS footprint differ from each other by a larger amount than they differ from the SMOS retrieval. Removing the mean and normalizing the data bring the in situ observations into better agreement with each other and with SMOS but there are still substantial differences. Agricultural Research Service Micronet regions in Oklahoma had highly varying values of soil moisture despite being in close proximity to one another, but when averaged and compared to SMOS they had less of a bias than the other regions. Further north in the Great Plains, SMOS retrievals of top 5 cm soil moisture from descending orbits were consistently about 5% by volume wetter than ascending retrievals.
Mechanical versus kinematical shortening reconstructions of the Zagros High Folded Zone (Kurdistan region of Iraq)
Authors: Frehner Marcel , Reif Daniel , Grasemann Bernhard 
Published: March 2012

This paper compares kinematical and mechanical techniques for the palinspastic reconstruction of folded cross sections in collision orogens. The studied area and the reconstructed NE–SW trending, 55.5 km long cross section is located in the High Folded Zone of the Zagros fold‐and‐thrust belt in the Kurdistan region of Iraq. The present‐day geometry of the cross section has been constructed from field as well as remote sensing data. In a first step, the structures and the stratigraphy are simplified and summarized in eight units trying to identify the main geometric and mechanical parameters. In a second step, the shortening is kinematically estimated using the dip domain method to 11%–15%. Then the same cross section is used in a numerical finite element model to perform dynamical unfolding simulations taking various rheological parameters into account. The main factor allowing for an efficient dynamic unfolding is the presence of interfacial slip conditions between the mechanically strong units. Other factors, such as Newtonian versus power law viscous rheology or the presence of a basement, affect the numerical simulations much less strongly. If interfacial slip is accounted for, fold amplitudes are reduced efficiently during the dynamical unfolding simulations, while welded layer interfaces lead to unrealistic shortening estimates. It is suggested that interfacial slip and decoupling of the deformation along detachment horizons is an important mechanical parameter that controlled the folding processes in the Zagros High Folded Zone.