bluuebunny/crossref_metadata_2025_split huggingface dataset:
A neural network approach to evaluate fold recognition results
Authors: Juan D. , Graña O. , Pazos F. , Fariselli P. , Casadio R. , Valencia A. 
Published: February 2003

AbstractFold recognition techniques assist the exploration of protein structures, and web‐based servers are part of the standard set of tools used in the analysis of biochemical problems. Despite their success, current methods are only able to predict the correct fold in a relatively small number of cases. We propose an approach that improves the selection of correct folds from among the results of two methods implemented as web servers (SAMT99 and 3DPSSM). Our approach is based on the training of a system of neural networks with models generated by the servers and a set of associated characteristics such as the quality of the sequence‐structure alignment, distribution of sequence features (sequence‐conserved positions and apolar residues), and compactness of the resulting models. Our results show that it is possible to detect adequate folds to model 80% of the sequences with a high level of confidence. The improvements achieved by taking into account sequence characteristics open the door to future improvements by directly including such factors in the step of model generation. This approach has been implemented as an automatic system LIBELLULA, available as a public web server at http://www.pdg.cnb.uam.es/servers/libellula.html. Proteins 2003;50:600–608. © 2003 Wiley‐Liss, Inc.
Observation of residual dipolar couplings in short peptides
Authors: Ohnishi Satoshi , Shortle David 
Published: February 2003

AbstractResidual dipolar couplings provide information on the orientation of individual bond vectors with respect to a unique set of molecular axes. We report that short peptides from 2 to 15 amino acids in length of arbitrary sequence exhibit a modest range of residual dipolar couplings when aligned in either strained polyacrylamide gels or alkyl‐PEG bicelles. The absence of significant line broadening in gels suggests peptides align predominantly through steric interactions with the polyacrylamide matrix. However, broadening of NMR lines for a subset of residues aligned in bicelles indicates some peptides bind weakly to these lipid disks, yet a weak negative correlation between the couplings measured in gels and bicelles is consistent with steric hindrance playing a role in both media. The observation of dipolar couplings for peptides of length 10–15 suggests the statistical segment lengths of polypeptide chains must often be >10–15 residues, with data from denatured proteins indicating even larger values. Presumably, local side‐chain backbone interactions severely restrict chain flexibility, with the cumulative effect of many such restrictions giving rise to biases in chain direction that may persist for the entire length of a protein chain. Comparison of experimental dipolar couplings for peptides with couplings calculated for ensembles of conformations generated by molecular dynamics should permit evaluation of the accuracy of molecular mechanics potentials in reproducing sequence‐specific preferences for ϕ and ψ angles. Proteins 2003;50:546–551. © 2003 Wiley‐Liss, Inc.
Real value prediction of solvent accessibility from amino acid sequence
Authors: Ahmad Shandar , Gromiha M. Michael , Sarai Akinori 
Published: February 2003

AbstractThe solvent accessibility of amino acid residues has been predicted in the past by classifying them into exposure states with varying thresholds. This classification provides a wide range of values for the accessible surface area (ASA) within which a residue may fall. Thus far, no attempt has been made to predict real values of ASA from the sequence information without a priori classification into exposure states. Here, we present a new method with which to predict real value ASAs for residues, based on neighborhood information. Our real value prediction neural network could estimate the ASA for four different nonhomologous, nonredundant data sets of varying size, with 18.0–19.5% mean absolute error, defined as per residue absolute difference between the predicted and experimental values of relative ASA. Correlation between the predicted and experimental values ranged from 0.47 to 0.50. It was observed that the ASA of a residue could be predicted within a 23.7% mean absolute error, even when no information about its neighbors is included. Prediction of real values answers the issue of arbitrary choice of ASA state thresholds, and carries more information than category prediction. Prediction error for each residue type strongly correlates with the variability in its experimental ASA values. Proteins 2003;50:629–635. © 2003 Wiley‐Liss, Inc.
Shallow seismic surveying of an Alpine rock glacier
Authors: Musil Martin , Maurer Hansruedi , Green Alan G. , Horstmeyer Heinrich , Nitsche Frank O. , Mühll Daniel Vonder , Springman Sarah 
Published: February 2003

To map the internal structure and lower boundary of an alpine rock glacier, we recorded three shallow seismic profiles and drilled four ∼70‐m‐deep holes through to the underlying bedrock. Although analysis of the seismic data using standard reflection processing schemes did not yield conclusive results because of the dominantly low‐frequency returned signals and the presence of strong source‐generated noise, tomographic inversions of first‐arrival times were successful in mapping several critical subsurface features. A thin, low‐velocity layer of loose boulders, air voids, and snow was found to extend across the entire surveyed area. Below this layer, two distinct velocity regimes superimposed on a general increase in velocity with depth were identified. A broad regime of high velocities was interpreted to contain boulders with numerous ice‐filled voids, whereas an adjacent regime of relatively low velocities was explained in terms of boulders with air‐ and water‐filled voids. This latter region of degraded permafrost, which was unexpected, may be an early result of global warming. The transition from rock glacier to gneissic bedrock was delineated approximately by the 4300‐m/s isovelocity line. Although poorly resolved, its depth varied from ∼35 to ∼70 m beneath the surface of the rock glacier. The tomographic inversion results also provided an explanation for the occurrence of strong source‐generated noise in our data. Using the derived velocity distributions as input, synthetic shot gathers were calculated using a finite‐difference viscoelastic scheme that accounted for surface topography. The resultant synthetic data were dominated by the overwhelming effects of back‐ and side‐scattered waves from shallow heterogeneities and high‐amplitude guided phases that originated from the thin, surficial low‐velocity zone. Had the guided phases not been correctly identified and eliminated during processing, they would have appeared as reflections in the stacked sections. Since low‐velocity layers overlying heterogeneous media are common features of the shallow subsurface, our findings may have implications for a broad range of engineering‐scale seismic investigations (e.g., studies of landfills, rockslides, moraines, talus slopes, alluvial fans).
Borehole electrical resistivity modeling using neural networks
Authors: Zhang Lin , Poulton Mary M. , Wang Tsili 
Published: February 2003

A neural network approach has been applied to model downhole resistivity tools, i.e., to generate a synthetic tool response for a given earth resistivity model. The microlaterolog (MLL), shallow dual laterolog (DLLs), and deep dual laterolog (DLLd) tools are modeled using neural networks to demonstrate this approach. Efforts have been made to select various neural network parameters, including the type of neural network, the length of input data for training, the number of hidden nodes, and the number of training samples. A modular neural network (MNN) has been selected because it can facilitate the training and prediction of tool responses in formations with large resistivity variations. The input data for training are taken to be the model formation resistivity values sampled over a depth window. The window length is chosen based on the tool lengths. Three different window lengths are used for experiments: 6.1, 9.1, and 30.5 m. We found the longer window lengths generally have higher modeling accuracy for the three different types of logging tools. The number of hidden nodes needed to yield satisfactory training and prediction data varies from 8 to 25, depending on the type of tool and the window length. Up to 30 000 training samples have been collected to train the MNN. Our modeling examples show that the trained MNN can achieve about 90% accuracy for the MLL log response and about 83% accuracy for the DLLs and DLLd responses. The modeling errors can be described roughly with a Gaussian distribution.
Smooth fitting of geophysical data using continuous global surfaces
Authors: Billings Stephen D. , Newsam Garry N. , Beatson Rick K. 
Published: February 2003

Continuous global surfaces (CGS) are a general framework for interpolation and smoothing of geophysical data. The first of two smoothing techniques we consider in this paper is generalized cross validation (GCV), which is a bootstrap measure of the predictive error of a surface that requires no prior knowledge of noise levels. The second smoothing technique is to define the CGS surface with fewer centers than data points, and compute the fit by least squares (LSQR); the noise levels are implicitly estimated by the number and placement of the centers relative to the data points. We show that both smoothing methods can be implemented using extensions to the existing fast framework for interpolation, so that it is now possible to construct realistic smooth fits to the very large data sets typically collected in geophysics.Thin‐plate spline and kriging surfaces with GCV smoothing appear to produce realistic fits to noisy radiometric data. The resulting surfaces are similar, yet the thin‐plate spline required less parameterization. Given the simplicity and parsimony of GCV, this makes a combination of the two methods a reasonable default choice for the smoothing problem. LSQR smooth fitting with sinc functions defined on a regular grid of centers, effectively low‐pass filters the data and produces a reasonable surface, although one not as visually appealing as for splines and kriging.
Multicomponent prestack depth migration by scalar wavefield extrapolation
Authors: Hou Anning , Marfurt Kurt J. 
Published: February 2003

We present a new multicomponent prestack depth migration methodology based on successive application of conventional scalar wave equation migration. We do not separate the data into PP‐ and PS‐waves; rather, we migrate each x‐, y‐, and z‐component of the data using both P and S propagation velocities, followed by polarization filtering in the depth domain. By generating intermediate images in the depth domain, we can account for polarity reversals of the PS reflection for all dips. Since the polarization angles are calculated from the data, it is straightforward to accommodate anisotropic effects (quasi‐P and quasi‐S) into multicomponent migration.The multicomponent migration results in our synthetic examples demonstrate that even for a single shot gather, we can obtain clean PP‐ and PS‐wave images over complex structures and resolve the problem of PS‐wave polarity reversals.
Processing‐induced anisotropy
Authors: Grechka Vladimir , Tsvankin Ilya 
Published: February 2003

Processing of seismic data is often performed under the assumption that the velocity distribution in the subsurface can be approximated by a macromodel composed of isotropic homogeneous layers or blocks. Despite being physically unrealistic, such models are believed to be sufficient for describing the kinematics of reflection arrivals.In this paper, we examine the distortions in normal‐moveout (NMO) velocities caused by the intralayer vertical heterogeneity unaccounted for in velocity analysis. To match P‐wave moveout measurements from a horizontal or a dipping reflector overlaid by a vertically heterogeneous isotropic medium, the effective homogeneous overburden has to be anisotropic. This apparent anisotropy is caused not only by velocity monotonically increasing with depth, but also by random velocity variations similar to those routinely observed in well logs.Assuming that the effective homogeneous medium is transversely isotropic with a vertical symmetry axis (VTI), we express the VTI parameters through the actual depth‐dependent isotropic velocity function. If the reflector is horizontal, combining the NMO and vertical velocities always results in nonnegative values of Thomsen's coefficient δ. For a dipping reflector, the inversion of the P‐wave NMO ellipse yields a nonnegative Alkhalifah‐Tsvankin coefficient η that increases with dip. The values of η obtained by two other methods (2‐D dip‐moveout inversion and nonhyperbolic moveout analysis) are also nonnegative but generally differ from that needed to fit the NMO ellipse. For truly anisotropic (VTI) media, the influence of vertical heterogeneity above the reflector can lead to a bias toward positive δ and η estimates in velocity analysis.
PP + PS = SS
Authors: Grechka Vladimir , Tsvankin Ilya 
Published: February 2003

Converted (PS) waves can provide important information about shear‐wave velocity and, in the presence of anisotropy, about the medium parameters responsible for both P‐ and S‐wave propagation. Kinematics and amplitudes of reflected PS‐waves, however, possess such undesirable features as moveout asymmetry, reflection point dispersal, and polarity reversal, which preclude application of conventional velocity‐analysis methods to mode conversions.Rather than using PS‐wave kinematics directly, here we propose a method for reconstructing SS‐wave reflection traveltimes from PP and PS data. The required preprocessing steps include picking of PP and PS traveltimes on prestack data and identification (correlation) of the PP and PS events from the same interfaces. The key idea of the method is to match the reflection slopes (horizontal slownesses) on common‐receiver PP and PS gathers. This procedure allows us to find the coordinates of receivers that record PP‐ and PS‐waves reflected at exactly the same (albeit unknown) subsurface points and to determine the shear‐wave reflection traveltime tSSas a simple combination of the PP and PS traveltimes. The reconstructed SS‐wave moveout can then be processed by velocity‐analysis methods designed for pure reflection modes. The developed technique, however, cannot be used to compute the true amplitudes of the reflected SS‐waves.Our method has the following attractive features:1) No information about the velocity field or anisotropic parameters is required to obtain SS‐wave traveltimes from PP and PS data. If the input PP and PS arrivals are picked correctly and correspond to the same reflector, the method produces exact traveltimes tSS.2) The estimates of traveltimes and reflection slopes are local, which makes reflection‐point dispersal irrelevant.3) Another consequence of the local nature of this procedure is that the portion of PS data in the vicinity of the polarity reversal (where the PS amplitudes are small) can be muted out without compromising the quality of tSSestimates for source–receiver pairs with high PS amplitudes.
Perturbation analysis of an explicit wavefield separation scheme for P‐ and S‐waves
Authors: Muijs Remco , Holliger Klaus , Robertsson Johan O. A. 
Published: February 2003

Dense spatial recording patterns of three‐component (3C) receivers allow for direct wavefield decomposition through explicit calculation of divergence and curl of the recorded elastic wavefield. Since this approach is based upon the observation of small phase shifts, it requires highly accurate deployment of the receiver configurations. To study the feasibility of a recently proposed P/S‐wave separation scheme, we systematically assess the effects of position and orientation errors of one or several geophones within the recording pattern on technique performance. We find that realistic deployment errors can significantly affect estimates of the divergence and curl of particle velocity. The errors induced by mispositioned or misoriented geophones differ for each of the geophones that make up a pattern. Moreover, the inaccuracies vary with the angle of incidence, potentially affecting analysis procedures applied to the data at a later stage, such as amplitude variation with offset (AVO). Based on a relative L1‐criterion, the position of each receiver needs to be accurate within 10% of the length of the sides of the configuration to obtain meaningful divergence and curl estimates. Furthermore, the output is particularly sensitive to misorientations of geophones, requiring that the orientations of all geophones be accurate within 2°. These observations point to significant difficulties when applying this technique. To alleviate this problem, we present an approach to detect and compensate for such deployment‐related inaccuracies prior to explicit P/S‐wave separation. This strategy is based on a pyramid‐shaped receiver configuration and relies on minimizing the differences between the divergence and curl estimates calculated over the pyramid and each of the four subtetrahedra that comprise the pyramid.
Toward optimal spatial filters for demultiple and wavefield splitting of ocean‐bottom seismic data
Authors: Osen Are , Amundsen Lasse , Reitan Arne 
Published: February 2003

Suppressing the receiver‐side sea‐surface ghost with its accompanying water‐layer reverberations in multicomponent sea‐floor data can be performed in both the frequency–wavenumber and the frequency–space domains. Similarly, separation of ocean‐bottom seismic (OBS) data into upgoing P‐ and S‐mode responses can be formulated in both domains. The frequency–space domain algorithms can be attractive when the sea‐floor medium has lateral velocity variations or the data are irregularly sampled along the sea floor, which requires that the data be processed with local, compact decomposition filters having optimal angular (wavenumber) response.By deriving the frequency–space domain formulas, we find an exact representation for the demultipled pressure response. This formula involves filter convolutions over the data, with filters having a long spatial impulse response. The filtering can be approximated in the wavenumber domain by, for example, power series, Chebyshev polynonomial fitting, Pade approximants, or continued fraction expansions. The filters must then be Fourier transformed back to the frequency–space domain, where the resulting filter is convolved with the data. The implies that the demultipled OBS data must be computed by numerical solution of a differential equation.Alternatively, the spatial filtering can be formulated as a filter design problem, where the filtering is performed by an optimal filter. This latter formulation can to some extent handle local variations in the medium properties along the sea floor, and it does not require solving a differential equation for the multiple suppressed pressure.
Rough‐sea deghosting using a single streamer and a pressure gradient approximation
Authors: Robertsson Johan O. A. , Kragh Ed 
Published: February 2003

We present a method for receiver ghost correction of towed streamer data that accounts for the rough sea surface. The method explicitly uses the fact that the pressure is zero at the free (sea) surface to estimate the vertical pressure gradient. Continuous elevation measurements of the wave height directly above the hydrophones are required—a measurement which is currently unavailable. The new deghosting method is fundamentally limited to frequencies below the first ghost notch. The lowest‐order implementation requires that the streamer is towed no deeper than approximately 6 m and a receiver spatial sampling interval of about 3 m or less. Using the lowest‐order and simplest implementation of the new method, the rough‐sea error is reduced from 1.5–2.5 dB to about 1–1.5 dB in amplitude and from 20° to 10° in phase, at 50 Hz in a 4‐m significant wave height sea. Higher‐order terms in the approximation promise to further reduce the error.
Structural characterization of oligomers from the polycondensation of citric acid with ethylene glycol and long‐chain aliphatic alcohols
Authors: Barroso‐Bujans Fabienne , Martínez Ricardo , Ortiz Pedro 
Published: February 2003

AbstractThe structural characterization of polyesters of citric acid (CA) with ethylene glycol and long‐chain aliphatic alcohols (ROH), prepared by the composition of the reaction mixture being adjusted slightly away from stoichiometric equivalence, was performed with 1H‐ and 13C‐NMR spectroscopy. The aliphatic alcohols employed were 1‐decanol, 1‐dodecanol, and 1‐octadecanol. The 13C‐NMR carbonyl region presented four groups of signals, two corresponding to the ester groups and two corresponding to the acid groups. However, symmetric and asymmetric groups of CA moieties were identified in the 13C‐NMR spectra. The ester yield from ROH decreased as the number of carbon atoms in the alcohols increased. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 302–306, 2003
Low addition of melamine salts for improved melamine‐urea‐formaldehyde adhesive water resistance
Authors: Zanetti M. , Pizzi A. 
Published: February 2003

AbstractThe addition of melamine acetate salts to an adhesive glue mix can allow the use of melamine–urea–formaldehyde (MUF) resins of lower melamine contents (rather than just urea–formaldehyde resins) and lower total amounts of melamine. Performances can be obtained that are characteristic of the top‐of‐the‐line, generally higher melamine content MUF adhesive resins for the preparation of wood particleboard panels. Improvements in the panel internal‐bond strength of greater than 30% can be obtained by the addition of melamine acetate salts to top‐of‐the‐line MUF resins. The approach to the concept of increased melamine solubility with a melamine salt is compatible with the approach of increasing melamine solubility with solvents such as acetals (e.g., methylal). However, the synergy advantage of using the two approaches jointly is not very marked. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 287–292, 2003
Kinetic study on the reaction of 2,4‐ and 2,6‐tolylene diisocyanate with 1‐butanol in the presence of styrene, as a model reaction for the process that yields interpenetrating polyurethane–polyester networks
Authors: Król Piotr , Wojturska Joanna 
Published: February 2003

AbstractA classical method was utilized for determination of free isocyanates to study the kinetics of a model reaction of 2,4‐ and 2,6‐tolylene diisocyanate (TDI) with 1‐butanol, which was run in the reaction medium of liquid aliphatic hydrocarbons. Such conditions made it possible to find rate constants and activation energy values for the second‐order reactions under isothermal conditions. Those reactions can be employed to produce isocyanate prepolymers, which make intermediates for downstream polyurethanes. The findings are commented upon against the background of earlier kinetic data that can widely be found in the research reports published. Further, part of our work utilized the findings to provide interpretation of kinetic parameters for analogous reactions, the kinetic data being found in the presence of styrene—the monomer employed when producing polyurethane–polyester interpenetrating polymer network (IPN) systems. The hypothesis was put forward that styrene and isocyanate component(s) could react at the final stages of the process when the system becomes short in the hydroxyl substrate. That hypothesis was based on disturbances observed in the reactivity of NCO groups (in 2,4‐TDI) in the reaction system studied. The rate constants and activation energy values were determined and presented for the urethanization reaction of 1‐butanol. © 2003 Wiley Periodicals, Inc. J Appl Polym Sci 88: 327–336, 2003