bluuebunny/crossref_metadata_2025 huggingface dataset:
A Grid-based solution for management and analysis of microarrays in distributed experiments
Authors: Porro Ivan , Torterolo Livia , Corradi Luca , Fato Marco , Papadimitropoulos Adam , Scaglione Silvia , Schenone Andrea , Viti Federica
Published: March 2007

Several systems have been presented in the last years in order to manage the complexity of large microarray experiments. Although good results have been achieved, most systems tend to lack in one or more fields. A Grid based approach may provide a shared, standardized and reliable solution for storage and analysis of biological data, in order to maximize the results of experimental efforts. A Grid framework has been therefore adopted due to the necessity of remotely accessing large amounts of distributed data as well as to scale computational performances for terabyte datasets. Two different biological studies have been planned in order to highlight the benefits that can emerge from our Grid based platform. The described environment relies on storage services and computational services provided by the gLite Grid middleware. The Grid environment is also able to exploit the added value of metadata in order to let users better classify and search experiments. A state-of-art Grid portal has been implemented in order to hide the complexity of framework from end users and to make them able to easily access available services and data. The functional architecture of the portal is described. As a first test of the system performances, a gene expression analysis has been performed on a dataset of Affymetrix GeneChip® Rat Expression Array RAE230A, from the ArrayExpress database. The sequence of analysis includes three steps: (i) group opening and image set uploading, (ii) normalization, and (iii) model based gene expression (based on PM/MM difference model). Two different Linux versions (sequential and parallel) of the dChip software have been developed to implement the analysis and have been tested on a cluster. From results, it emerges that the parallelization of the analysis process and the execution of parallel jobs on distributed computational resources actually improve the performances. Moreover, the Grid environment have been tested both against the possibility of uploading and accessing distributed datasets through the Grid middleware and against its ability in managing the execution of jobs on distributed computational resources. Results from the Grid test will be discussed in a further paper.
Gene models from ESTs (GeneModelEST): an application on the Solanum lycopersicum genome
Authors: D'Agostino Nunzio , Traini Alessandra , Frusciante Luigi , Chiusano Maria Luisa
Published: March 2007

Background

The structure annotation of a genome is based either on ab initio methodologies or on similaritiy searches versus molecules that have been already annotated. Ab initio gene predictions in a genome are based on a priori knowledge of species-specific features of genes. The training of ab initio gene finders is based on the definition of a data-set of gene models. To accomplish this task the common approach is to align species-specific full length cDNA and EST sequences along the genomic sequences in order to define exon/intron structure of mRNA coding genes.

Results

GeneModelEST is the software here proposed for defining a data-set of candidate gene models using exclusively evidence derived from cDNA/EST sequences.

GeneModelEST requires the genome coordinates of the spliced-alignments of ESTs and of contigs (tentative consensus sequences) generated by an EST clustering/assembling procedure to be formatted in a General Feature Format (GFF) standard file. Moreover, the alignments of the contigs versus a protein database are required as an NCBI BLAST formatted report file.

The GeneModelEST analysis aims to i) evaluate each exon as defined from contig spliced alignments onto the genome sequence; ii) classify the contigs according to quality levels in order to select candidate gene models; iii) assign to the candidate gene models preliminary functional annotations.

We discuss the application of the proposed methodology to build a data-set of gene models of Solanum lycopersicum, whose genome sequencing is an ongoing effort by the International Tomato Genome Sequencing Consortium.

Conclusion

The contig classification procedure used by GeneModelEST supports the detection of candidate gene models, the identification of potential alternative transcripts and it is useful to filter out ambiguous information. An automated procedure, such as the one proposed here, is fundamental to support large scale analysis in order to provide species-specific gene models, that could be useful as a training data-set for ab initio gene finders and/or as a reference gene list for a human curated annotation.
Matrix Metalloproteinase-9 (MMP-9) polymorphisms in patients with cutaneous malignant melanoma
Authors: Cotignola Javier , Reva Boris , Mitra Nandita , Ishill Nicole , Chuai Shaokun , Patel Ami , Shah Shivang , Vanderbeek Gretchen , Coit Daniel , Busam Klaus , Halpern Allan , Houghton Alan , Sander Chris , Berwick Marianne , Orlow Irene
Published: March 2007

Background

Cutaneous Malignant Melanoma causes over 75% of skin cancer-related deaths, and it is clear that many factors may contribute to the outcome. Matrix Metalloproteinases (MMPs) play an important role in the degradation and remodeling of the extracellular matrix and basement membrane that, in turn, modulate cell division, migration and angiogenesis. Some polymorphisms are known to influence gene expression, protein activity, stability, and interactions, and they were shown to be associated with certain tumor phenotypes and cancer risk.

Methods

We tested seven polymorphisms within the MMP-9 gene in 1002 patients with melanoma in order to evaluate germline genetic variants and their association with progression and known risk factors of melanoma. The polymorphisms were selected based on previously published reports and their known or potential functional relevance using in-silico methods. Germline DNA was then genotyped using pyrosequencing, melting temperature profiles, heteroduplex analysis, and fragment size analysis.

Results

We found that reference alleles were present in higher frequency in patients who tend to sunburn, have family history of melanoma, higher melanoma stage, intransit metastasis and desmoplastic melanomas among others. However, after adjustment for age, sex, phenotypic index, moles, and freckles only Q279R, P574R and R668Q had significant associations with intransit metastasis, propensity to tan/sunburn and primary melanoma site.

Conclusion

This study does not provide strong evidence for further investigation into the role of the MMP-9 SNPs in melanoma progression.
Single chain Fab (scFab) fragment
Authors: Hust Michael , Jostock Thomas , Menzel Christian , Voedisch Bernd , Mohr Anja , Brenneis Mariam , Kirsch Martina I , Meier Doris , Dübel Stefan
Published: March 2007

Background

The connection of the variable part of the heavy chain (VH) and and the variable part of the light chain (VL) by a peptide linker to form a consecutive polypeptide chain (single chain antibody, scFv) was a breakthrough for the functional production of antibody fragments inEscherichia coli. Being double the size of fragment variable (Fv) fragments and requiring assembly of two independent polypeptide chains, functional Fab fragments are usually produced with significantly lower yields inE. coli. An antibody design combining stability and assay compatibility of the fragment antigen binding (Fab) with high level bacterial expression of single chain Fv fragments would be desirable. The desired antibody fragment should be both suitable for expression as soluble antibody inE. coliand antibody phage display.

Results

Here, we demonstrate that the introduction of a polypeptide linker between the fragment difficult (Fd) and the light chain (LC), resulting in the formation of a single chain Fab fragment (scFab), can lead to improved production of functional molecules. We tested the impact of various linker designs and modifications of the constant regions on both phage display efficiency and the yield of soluble antibody fragments. A scFab variant without cysteins (scFabΔC) connecting the constant part 1 of the heavy chain (CH1) and the constant part of the light chain (CL) were best suited for phage display and production of soluble antibody fragments. Beside the expression systemE. coli, the new antibody format was also expressed inPichia pastoris. Monovalent and divalent fragments (DiFabodies) as well as multimers were characterised.

Conclusion

A new antibody design offers the generation of bivalent Fab derivates for antibody phage display and production of soluble antibody fragments. This antibody format is of particular value for high throughput proteome binder generation projects, due to the avidity effect and the possible use of common standard sera for detection.
High mobility group box-1 protein in patients with suspected community-acquired infections and sepsis: a prospective study
Authors: Gaïni Shahin , Pedersen Svend Stenvang , Koldkjær Ole Græsbøll , Pedersen Court , Møller Holger Jon
Published: March 2007

Introduction

Sepsis is a serious condition with a significant morbidity and mortality. New insight into the immunopathogenesis of sepsis could promote the development of new strategies for diagnosis and therapy. High mobility group box-1 protein (HMGB1) has been known for many years as a nuclear chromosomal protein. Its role as a pro-inflammatory cytokine in sepsis and rheumatoid arthritis has been described recently. The aim of our study was to evaluate HMGB1 as a molecular marker in patients with community-acquired infections.

Methods

Patients suspected of having infections/sepsis and admitted to a department of internal medicine were included in the study in a prospective manner. Demographic data, comorbidity, routine biochemistry, microbiological data, infection focus, severity score, and mortality on day 28 were recorded. Plasma and serum were sampled at the time of admission. HMGB1 levels were measured with a commercially available enzyme-linked immunosorbent assay (ELISA). Procalcitonin levels were measured with a TRACE (time-resolved amplified cryptate emission) assay. Lipopolysaccharide-binding protein and interleukin-6 were measured with a chemiluminiscent immunometric assay. Soluble haemoglobin scavenger receptor (sCD163) levels were measured with an in-house ELISA.

Results

One hundred and ninety-four patients were included in the study. Levels of HMGB1 are presented as medians and interquartile ranges: healthy controls (0.77 ng/ml, 0.6 to 1.46), non-infected patients (1.54 ng/ml, 0.79 to 2.88), infected patients without systemic inflammatory response syndrome (2.41 ng/ml, 0.63 to 3.44), patients with sepsis (2.24 ng/ml, 1.30 to 3.75), and patients with severe sepsis (2.18 ng/ml, 0.91 to 3.85). In a receiver operator characteristic curve analysis discriminating between non-infected patients and all infected patients, the area under the curve for HMGB1 was 0.59 (P < 0.0001). HMGB1 correlated only weakly to levels of white blood cell count, neutrophils, C-reactive protein, interleukin-6, procalcitonin, and lipopolysaccharide-binding protein (P < 0.001). HMGB1 did not correlate to sCD163.

Conclusion

In a cohort of patients with suspected community-acquired infections and sepsis, HMGB1 levels were statistically significantly higher in patients compared to the healthy controls. There was no statistically significant difference between the infected and the non-infected patients. Levels of HMGB1 correlated only very weakly to other pro-inflammatory markers and did not correlate to the anti-inflammatory marker sCD163.
GOTax: investigating biological processes and biochemical activities along the taxonomic tree
Authors: Schlicker Andreas , Rahnenführer Jörg , Albrecht Mario , Lengauer Thomas , Domingues Francisco S
Published: March 2007

We describe GOTax, a comparative genomics platform that integrates protein annotation with protein family classification and taxonomy. User-defined sets of proteins, protein families, annotation terms or taxonomic groups can be selected and compared, allowing for the analysis of distribution of biological processes and molecular activities over different taxonomic groups. In particular, a measure of functional similarity is available for comparing proteins and protein families, establishing functional relationships independent of evolution.
Induction-response functions for frequency-domain electromagnetic mapping system for airborne and ground configurations
Authors: Fraser Douglas C. , Hodges Greg
Published: March 2007

A helicopter-towed electromagnetic (EM) sensor of the type typically flown in frequency-domain surveys may be towed over the ground on a trailer. The in-phase and quadrature components measured by a trailer-towed sensor will be dramatically different from those determined when the sensor is flown. For the airborne case, the in-phase and quadrature curves of the induction-response function are governed by the superposed-dipole behavior, in which flying height substantially exceeds the transmitting-receiving coil separation. In contrast, for a ground-based sensor, the coil separation substantially exceeds the sensor height, yielding the infinitely separated dipole case in which the sensor height is negligible compared to the coil separation. These two end cases — the superposed dipole and the infinitely separated dipole —yield EM amplitudes and phase angles that are very different from each other. For the superposed-dipole case of the airborne sensor, the in-phase component reaches a high positive value as the EM response approaches the inductive limit, whereas for the infinitely separated dipole case of the ground sensor, the in-phase component reaches a large negative value. Consequently, there must be a sensor height where the in-phase becomes zero at the inductive limit. This critical height is approximately 35% of the coil separation for the maximum coupled horizontal coplanar coils of the helicopter-towed EM system. The resolution of the ground sensor is superior to that of the airborne sensor, whereas the depth of exploration for the airborne sensor is superior to that of the ground sensor. This finding is to be expected from a consideration of the size of the footprint of the sensor.
Multiple prediction through inversion: Theoretical advancements and real data application
Authors: Wang Yanghua
Published: March 2007

Wave-equation-based multiple attenuation seismic methods may be divided into the two distinct phases of multiple modeling and multiple subtraction. These two are interrelated and must be optimized in order to produce an optimal final result. The multiple prediction through inversion (MPI) scheme updates the multiple model iteratively, as we usually do in a linearized inverse problem. The scheme models the multiple wavefield without an explicit knowledge of surface and subsurface structures or of the source signature; both are generally unknown in seismic surveys. However, compared to a conventional surface-related multiple attenuation method, the accuracy of the multiple model is improved both kinematically and dynamically. It is because the MPI scheme implicitly takes account of the spatial variation of the surface reflectivity, the source signature, the detector patterns and receiver ghosts, and other effects included in the so-called surface operator. When the MPI scheme is used in the first phase it also significantly reduces the nonlinearity of the problem in the second phase that involves attenuating multiples without removing or altering primaries. The effectiveness of the MPI scheme is demonstrated by examples involving real marine seismic data.
A comparison of Heelan and exact solutions for seismic radiation from a short cylindrical charge
Authors: Blair Dane Peter
Published: March 2007

A numerical comparison is made between the Heelan approximation and an exact (full-field) solution for the radiation of seismic waves at a distance [Formula: see text], produced by a short cylindrical charge in a dry borehole of radius [Formula: see text]. The explosive source model is based on direct pressure measurements within the blast hole, and its spectral output classified by a mean frequency [Formula: see text]. To generalize comparisons, this source model is incorporated within a scale-independent treatment of the Heelan and full-field solutions. If [Formula: see text] is the material P-wave velocity, then a mean dimensionless source frequency may be defined by [Formula: see text]. For sufficiently large [Formula: see text], the Heelan solution is a valid far-field approximation only, provided [Formula: see text]. However, for the present radiation model, the far-field condition is given by [Formula: see text] (approximately), which implies that the Heelan solution is never valid if [Formula: see text], irrespective of [Formula: see text]. If [Formula: see text], the Heelan solution significantly overestimates the true seismic motion, irrespective of [Formula: see text].
Prestack depth migration of primary and surface-related multiple reflections: Part II — Identification and removal of residual multiples
Authors: Muijs Remco , Robertsson Johan O. , Holliger Klaus
Published: March 2007

Depth imaging using primary and multiple reflections (DIPMR), as described in Part I of this study, allows subsurface information carried by multiple reflections to be utilized. In the presence of strong lateral heterogeneity, however, the migration results may be distorted by artifacts originating from reflections associated with layers above the imaging plane that are commonly referred to as crosstalk. We present an image enhancement procedure that allows such artifacts to be effectively suppressed by predicting the initial crosstalk in a second migration phase. This second migration uses reflections imaged at shallower depth levels and requires knowledge of the total and primary downgoing wavefield at the receiver level. The predicted crosstalk image it-self may assist the interpretational effort by indicating areas where artifacts may result in incorrect identification of geologic structures or may cause local distortions of amplitude informa-tion. Furthermore, a clean depth image can be obtained by adap-tively subtracting the predicted crosstalk-related noise from the original image. The proposed method is an extension of the DIPMR procedure outlined in Part I of this study. However, it is also applicable to seismic data imaged by using conventional mi gration techniques that are based exclusively on primary reflec-tions. In the latter case, the enhancement procedure allows the ef-fects of imperfect multiple removal during preprocessing to be revealed in the migrated sections. When applied to synthetic data simulated for a complex salt model, the proposed enhancement procedure proved to be valid and effective.
Instantaneous spectral attributes to detect channels
Authors: Liu Jianlei , Marfurt Kurt J.
Published: March 2007

Channels filled with porous rock and encased in a nonporous matrix constitute one of the more important stratigraphic exploration plays. Although attributes such as coherence can be used to map channel width, they are relatively insensitive to channel thickness. In contrast, spectral decomposition can be used to map subtle changes in channel thickness. The peak spectral frequency derived by using the short-window, discrete Fourier transform (SWDFT) is an excellent tool for mapping such changes along an interpreted horizon. We show that by use of instantaneous spectral attributes, we can generate equivalent maps for complete seismic volumes. Because we are often interested in mapping high-reflectivity channels encased in a lower-reflectivity matrix, we find that a composite plot of the peak frequency and the above-average peak amplitude accentuates highly tuned channels. Finally, by generating a composite volume using peak frequency, peak amplitude, and coherence, we can establish not only the channel thickness, but also its width. We demonstrate the value of such 3D volumetric estimates through application to (1) a marine survey acquired over Tertiary channels from the Gulf of Mexico and (2) a land data survey acquired over Paleozoic channels from the Central Basin Platform, west Texas, United States. The channels in both marine and land surveys can be highlighted through composite-volume analysis.
True amplitude corrections for a narrow-angle one-way elastic wave equation
Authors: Angus D. A.
Published: March 2007

Wavefield extrapolators using one-way wave equations are computationally efficient methods for accurate traveltime modeling in laterally heterogeneous media, and have been used extensively in many seismic forward modeling and migration problems. However, most leading-order, one-way wave equations do not simulate waveform amplitudes accurately and this is primarily because energy flux is not accounted for correctly. I review the derivation of a leading-order, narrow-angle, one-way elastic wave equation for 3D media. I derive correction terms that enable energy-flux normalization and introduce a new higher-order, narrow-angle, one-way elastic wave extrapolator. By implementing these correction terms, the new true amplitude wave extrapolator allows accurate amplitude estimates in the presence of strong gradients. I present numerical examples for 1D velocity transition models to show that (1) the leading-order, narrow-angle propagator accurately models traveltimes, but overestimates transmitted- or primary-wave amplitudes and (2) the new amplitude corrected narrow-angle propagator accurately models both the traveltimes and amplitudes of all forward-traveling waves.
An introduction to marine controlled-source electromagnetic methods for hydrocarbon exploration
Authors: Constable Steven , Srnka Leonard J.
Published: March 2007

Early development of marine electromagnetic methods, dating back about 80 years, was driven largely by defense/military applications, and use for these purposes continues to this day. Deepwater, frequency-domain, electric dipole-dipole, controlled-source electromagnetic (CSEM) methods arose from academic studies of the oceanic lithosphere in the 1980s, and although the hydrocarbon exploration industry was aware of this work, the shallow-water environments being explored at that time were not ideally suited for its use. Low oil prices and increasingly successful results from 3D seismic methods further discouraged investment in costly alternative geophysical data streams. These circumstances changed in the late 1990s, when both Statoil and ExxonMobil began modeling studies and fieldtrials of CSEM surveying in deep water (around [Formula: see text] or deeper), specifically for characterizing the resistivity of previously identified drilling targets. Trials offshore Angola in 2000–2002 by both these companies showed that CSEM data can successfully be used to evaluate reservoir resistivity for targets as deep as several thousand meters. Both companies leveraged instrumentation and expertise from the academic community to make swift progress. The resulting rapid growth in the use of marine EM methods for exploration has created a demand for trained personnel that is difficult to meet; nevertheless, at this time, CSEM data represent a commercial commodity within the exploration business, and acquisition services are offered by three companies. The ability to determine the resistivity of deep drilling targets from the seafloor may well make marine CSEM the most important geophysical technique to emerge since 3D reflection seismology.
Shaping regularization in geophysical-estimation problems
Authors: Fomel Sergey
Published: March 2007

Regularization is a required component of geophysical-estimation problems that operate with insufficient data. The goal of regularization is to impose additional constraints on the estimated model. I introduce shaping regularization, a general method for imposing constraints by explicit mapping of the estimated model to the space of admissible models. Shaping regularization is integrated in a conjugate-gradient algorithm for iterative least-squares estimation. It provides the advantage of better control on the estimated model in comparison with traditional regularization methods and, in some cases, leads to a faster iterative convergence. Simple data interpolation and seismic-velocity estimation examples illustrate the concept.
Identification of image artifacts from internal multiples
Authors: Malcolm Alison E. , de Hoop Maarten V. , Calandra Henri
Published: March 2007

First-order internal multiples are a source of coherent noise in seismic images because they do not satisfy the single-scattering assumption fundamental to most seismic processing. There are a number of techniques to estimate internal multiples in data; in many cases, these algorithms leave some residual multiple energy in the data. This energy produces artifacts in the image, and the location of these artifacts is unknown because the multiples were estimated in the data before the image was formed. To avoid this problem, we propose a method by which the artifacts caused by internal multiples are estimated directly in the image. We use ideas from the generalized Bremmer series and the Lippmann-Schwinger scattering series to create a forward-scattering series to model multiples and an inverse-scattering series to describethe impact these multiples have on the common-image gather and the image. We present an algorithm that implements the third term of this series, responsible for the formation of first-order in-ternal multiples. The algorithm works as part of a wave-equation migration; the multiple estimation is made at each depth using a technique related to one used to estimate surface-related multi-ples. This method requires knowledge of the velocity model to the depth of the shallowest reflector involved in the generation of the multiple of interest. This information allows us to estimate internal multiples without assumptions inherent to other methods. In particular, we account for the formation of caustics. Results of the techniques on synthetic data illustrate the kinematic accuracy of predicted multiples, and results on field data illustrate the potential of estimating artifacts caused by internal multiples in the image rather than in the data.
Fast finite-difference time-domain modeling for marine-subsurface electromagnetic problems
Authors: Maaø Frank A.
Published: March 2007

In the low-frequency limit, the displacement currents in the Maxwell equations can be neglected. However, for numerical simulations, a small displacement current should be present to achieve numerical stability. This requirement leads to a large range of propagation velocities with high velocities for the high frequencies and low velocities for the low frequencies. As a consequence, the number of time steps may become large. I show that it is possible to transform mathematically the original physical problem to one that has propagation velocities with less frequency dependence. Hence, the number of time steps necessary for a signal to travel a certain distance with the lowest velocity is significantly reduced. A typical example shows a reduction in computational time by a factor of 40. A comparison of the solutions from plane-layered modeling in the frequency and wavenumber domain and the proposed method shows good agreement between the two. The proposed method can also be used for other systems of diffusive equations.
Crossline resistivity tomography for the delineation of anomalous seepage pathways in an embankment dam
Authors: Cho In-Ky , Yeom Ji-Yeon
Published: March 2007

Crossline resistivity tomography was developed to find out anomalous seepage pathways in an embankment dam. By applying crossline tomography to the investigation of embankment dams, leakage pathways can be effectively located because the crossline tomogram presents resistivity distribution in the horizontal plane of an embankment dam. To test the effectiveness of crossline tomography, we applied it to data from an experiment designed to delineate anomalous seepage pathways in the embankment dam. The method yields relatively accurate geoelectric structure of the dam when applied to synthetic data. In the crossline resistivity tomogram, abrupt discontinuities of a low resistivity band corresponding to the core of the dam can be interpreted as leakage pathways. Application to real data obtained from an embankment dam in Korea yields the result which accurately depicts two anomalous seepage pathways. The identified pathways were consistent with low resistivity zones in the dipole-dipole resistivity section obtained on the crest of the dam. One pathway was confirmed by visual inspection of the dam, and afterward, by trenching.
Seabed property estimation from ambient-noise recordings: Part I — Compliance and Scholte wave phase-velocity measurements
Authors: Muyzert Everhard
Published: March 2007

The ability to derive a near-surface shear-velocity profile from ambient-noise records is useful for seismic applications such as shear-wave statics estimation and geohazard prediction. Measurements of seafloor compliance and Scholte wave velocity and amplitude are all related to the near-surface shear-velocity profile. I analyzed a data set of [Formula: see text] of continuous noise records recorded by an ocean bottom cable deployed in [Formula: see text] deep water for seafloor compliance and Scholte waves. I failed to observe seafloor compliance because of limitations in the record length. I have detected Scholte waves on the inline and vertical component geophones and Love waves on the crossline component using [Formula: see text] spectra. Both the Scholte and Love wave phase-velocities can be explained by a simple 1D isotropic near-surface model. The Scholte waves may have been excited by acoustic energy from the recording vessel, while no satisfactory excitation mechanism has been found for the Love waves.
AVO inversion of BSRs in marine gas hydrate studies
Authors: Chen Marc-André P. , Riedel Michael , Hyndman Roy D. , Dosso Stan E.
Published: March 2007

We examine the usefulness of amplitude versus offset (AVO) analysis of bottom-simulating reflections (BSRs) for estimating associated marine gas hydrate and free-gas concentrations. A nonlinear Bayesian inversion is applied to estimate marginal probability distributions (MPDs) of physical parameters at a BSR interface, which are related to overlying gas hydrate and underlying free-gas concentrations via rock physics modeling. The problem is constrained further by prior information and re-parameterization of inversion results. Inversion of BSR AVO data from offshore Vancouver Island, Canada, shows that gas hydrate and free-gas concentrations are, respectively, 0%–23% and0%–2% of the pore volume, at a 90% credibility level. This result indicates that the data do not provide sufficient information to independently resolve gas hydrate and free-gas concentrations to useful accuracy. The study is directed primarily at AVO for gas-hydrate-related BSRs, but may have important applicability in testing the degree of constraint of formation characteristics in other AVO studies. The inversion method is applied also to syn-thetic AVO data generated from Ostrander’s gas-sand model. In this case, MPDs sufficiently constrain the relationship between P- and S-wave velocities in the sandstone unit to determine if it is gas-charged. The variable degree of model constraint obtained in this AVO study highlights the need to include rigorous quantita-tive uncertainty analysis in all AVO studies.
Local singular value decomposition for signal enhancement of seismic data
Authors: Bekara Maïza , Van der Baan Mirko
Published: March 2007

Singular value decomposition (SVD) is a coherency-based technique that provides both signal enhancement and noise suppression. It has been implemented in a variety of seismic applications — mostly on a global scale. In this paper, we use SVD to improve the signal-to-noise ratio of unstacked and stacked seismic sections, but apply it locally to cope with coherent events that vary with both time and offset. The local SVD technique is compared with [Formula: see text] deconvolution and median filtering on a set of synthetic and real-data sections. Local SVD is better than [Formula: see text] deconvolution and median filtering in removing background noise, but it performs less well in enhancing weak events or events with conflicting dips. Combining [Formula: see text] deconvolution or median filtering with local SVD overcomes the main weaknesses associated with each individual method and leads to the best results.
Application of the empirical mode decomposition and Hilbert-Huang transform to seismic reflection data
Authors: Battista Bradley Matthew , Knapp Camelia , McGee Tom , Goebel Vaughn
Published: March 2007

Advancements in signal processing may allow for improved imaging and analysis of complex geologic targets found in seismic reflection data. A recent contribution to signal processing is the empirical mode decomposition (EMD) which combines with the Hilbert transform as the Hilbert-Huang transform (HHT). The EMD empirically reduces a time series to several subsignals, each of which is input to the same time-frequency environment via the Hilbert transform. The HHT allows for signals describing stochastic or astochastic processes to be analyzed using instantaneous attributes in the time-frequency domain. The HHT is applied herein to seismic reflection data to: (1) assess the ability of the EMD and HHT to quantify meaningful geologic information in the time and time-frequency domains, and (2) use instantaneous attributes to develop superior filters for improving the signal-to-noise ratio. The objective of this work is to determine whether the HHT allows for empirically-derived characteristics to be used in filter design and application, resulting in better filter performance and enhanced signal-to-noise ratio. Two data sets are used to show successful application of the EMD and HHT to seismic reflection data processing. Nonlinear cable strum is removed from one data set while the other is used to show how the HHT compares to and outperforms Fourier-based processing under certain conditions.
Competence and Resilience in Development
Authors: MASTEN ANN S. , OBRADOVIĆ JELENA
Published: March 2007

Abstract:  The first three waves of research on resilience in development, largely behavioral in focus, contributed a compelling set of concepts and methods, a surprisingly consistent body of findings, provocative issues and controversies, and clues to promising areas for the next wave of resilience research linking biology and neuroscience to behavioral adaptation in development. Behavioral investigators honed the definitions and assessments of risk, adversity, competence, developmental tasks, protective factors, and other key aspects of resilience, as they sought to understand how some children overcome adversity to do well in life. Their findings implicate fundamental adaptive systems, which in turn suggest hot spots for the rising fourth wave of integrative research on resilience in children, focused on processes studied at multiple levels of analysis and across species.
Contributions of Temperament to Buffering and Sensitization Processes in Children's Development
Authors: WACHS THEODORE D.
Published: March 2007

Abstract:  Temperament refers to relatively stable, early appearing, biologically rooted individual differences in behavioral traits. Individual differences in temperament are multidetermined encompassing both biological and experiential influences. Evidence indicates that certain temperament traits, such as impulsivity, inhibition, and negative emotionality, can serve as developmental risk factors. Evidence also indicates that other temperament traits, such as flexible self‐regulation, sociability, and task orientation, can serve to increase children's resilience. Five potential mechanisms through which individual differences in temperament can increase vulnerability or facilitate resilience are presented: (1) Differential treatment of children with different temperaments by caregivers or teachers (reactive covariance). (2) Children with different temperament styles seeking out environments that may increase risk or promote resilience (active covariance). (3) Goodness or poorness of fit between child temperament characteristics and environmental demands. (4) Children with different temperaments reacting to similar levels or types of stress in different ways. (5) Different coping strategies used by children with different temperaments.
The Inherent Stress of Normal Daily Life and Social Interaction Leads to the Development of Coping and Resilience, and Variation in Resilience in Infants and Young Children
Authors: TRONICK ED
Published: March 2007

Abstract:  The hypothesis is advanced that behavioral and physiologic resilience develops in part from infants' and young children's experience coping with the inherent normal stress of daily life and social interaction. Data on the stress of normal social interactions and perturbated interactions from the Face‐to‐Face Still‐Face Paradigm (FFSF) are presented for young infants. These findings, including behavioral, heart rate and vagal tone, and electrodermal reactivity demonstrate the stress inherent in normal interaction and how coping with normal stress develops infants' coping with more intense environmental and social stressors.
Conceptual Issues in Studies of Resilience
Authors: LUTHAR SUNIYA S. , SAWYER JEANETTE A. , BROWN PAMELA J.
Published: March 2007

Abstract:  We begin this article by considering the following critical conceptual issues in research on resilience: (1) distinctions between protective, promotive, and vulnerability factors; (2) the need to unpack underlying processes; (3) the benefits of within‐group experimental designs; and (4) the advantages and potential pitfalls of an overwhelming scientific focus on biological and genetic factors (to the relative exclusion of familial and contextual ones). The next section of the article is focused on guidelines for the selection of vulnerability and protective processes in future research. From a basic science standpoint, it is useful and appropriate to investigate all types of processes that might significantly affect adjustment among at‐risk individuals. If the research is fundamentally applied in nature, however, it would be most expedient to focus on risk modifiers that have high potential to alter individuals' overall life circumstances. The final section of this article considers conceptual differences between contemporary resilience research on children versus adults. Issues include differences in the types and breadth of outcomes (e.g., the tendencies to focus on others' ratings of competence among children and on self‐reports of well‐being among adults respectively).
Psychosocial Constraints on the Development of Resilience
Authors: SAMEROFF ARNOLD J. , ROSENBLUM KATHERINE L.
Published: March 2007

Abstract:  Although resilience is usually thought to reside in individuals, developmental research is increasingly demonstrating that characteristics of the social context may be better predictors of resilience. When the relative contribution of early resilience and environmental challenges to later child mental health and academic achievement were compared in a longitudinal study from birth to adolescence, indicators of child resilience, such as the behavioral and emotional self‐regulation characteristic of good mental health, and the cognitive self‐regulation characteristic of high intelligence contributed to later competence. However, the effects of such individual resilience did not overcome the effects of high environmental challenge, such as poor parenting, antisocial peers, low‐resource communities, and economic hardship. The effects of single environmental challenges become very large when accumulated into multiple risk scores even affecting the development of offspring in the next generation.
Adolescents' Resilience as a Self‐Regulatory Process
Authors: DISHION THOMAS J. , CONNELL ARIN
Published: March 2007

Abstract:  This chapter focuses on the concept of self‐regulation as a measure of resilience in children and adolescents. Developmental psychology and neuroscience are converging on the role of attention control as a central ability underlying self‐regulation. We collected measures of adolescent attention control from parents and youth, and a measure of self‐regulation from teachers. The measures of effortful attention correlated highly with teacher ratings of self‐regulation. The composite measure of self‐regulation (youth, parent, teacher report) was found to moderate the impact of peer deviance on adolescent antisocial behavior, as well as stress on adolescent depression. These findings suggest that self‐regulation is a promising index of adolescent resilience. The construct of self‐regulation also provides an excellent target for strategies aimed to improve child and adolescent adjustment in problematic environments and stressful circumstances.
Prevention of Pediatric Bipolar Disorder
Authors: CHANG KIKI , HOWE MEGHAN , GALLELLI KIM , MIKLOWITZ DAVID
Published: March 2007

Abstract:  Bipolar disorder (BD) is a prevalent condition in the United States that typically begins before the age of 18 years and is being increasingly recognized in children and adolescents. Despite great efforts in discovering more effective treatments for BD, it remains a difficult‐to‐treat condition with high morbidity and mortality. Therefore, it appears prudent to focus energies into developing interventions designed to

prevent

individuals from ever fully developing BD. Such interventions early in the development of the illness might prevent inappropriate interventions that may worsen or hasten development of BD, delay the onset of first manic episode, and/or prevent development of full BD. Studies of populations at high‐risk for BD development have indicated that children with strong family histories of BD, who are themselves experiencing symptoms of attention‐deficit/hyperactive disorder (ADHD) and/or depression or have early mood dysregulation, may be experiencing prodromal states of BD. Understanding the neurobiological and genetic underpinnings that create risk for BD development would help with more accurate identification of this prodromal population, which could then lead to suitable preventative interventions. Such interventions could be pharmacologic or psychosocial in nature. Reductions in stress and increases in coping abilities through psychosocial interventions could decrease the chance of a future manic episode. Similarly, psychotropic medications may decrease negative sequelae of stress and have potential for neuroprotective and neurogenic effects that may contribute to prevention of fully expressed BD. Further research into the biologic and environmental mechanisms of BD development as well as controlled early intervention studies are needed to ameliorate this significant public health problem.
The Role of Verbal Competence and Multiple Risk on the Internalizing Behavior Problems of Costa Rican Youth
Authors: CORAPCI FEYZA , SMITH JULIA , LOZOFF BETSY
Published: March 2007

Abstract:  This longitudinal study examined internalizing behavior problems (anxiety/depression) in early adolescence in relation to adversity in early childhood and child verbal competence. We hypothesized that verbal competence would act as a protective factor in the face of early adversity, that is, high verbal IQ would predict relatively lower internalizing problems in early adolescence primarily for those children who experienced the greatest adversity. The sample was based on 191 Costa Rican children and their mothers, who were recruited in infancy from an urban community and assessed again at 5 and 11–14 years. Families were generally lower‐middle to working class. A total of 165 children (94 boys) participated in the early adolescent follow‐up (mean age = 12.3 years). Internalizing problems were based on maternal report (Spanish Child Behavior Checklist). Our cumulative risk index (CRI)_of adversity in early childhood consisted of home environment quality (HOME score), socioeconomic status, maternal depressed mood (CESD), and maternal IQ. Controlling for the effects of age, gender, internalizing problems at 5 years, and verbal IQ at 5 years, there was a significant interaction between early adversity and verbal IQ at age 11–14 years in predicting internalizing problems in early adolescence. Youth with high verbal IQ had comparable levels of internalizing problems regardless of high or low adversity in early childhood. In contrast, youth with low verbal IQ received higher internalizing problem ratings if they experienced high adversity early in life. The results raise the possibility that interventions to improve verbal competence might help lower the risk of internalizing problems in the face of early adversity.
Children Survivors of the 2004 Tsunami in Aceh, Indonesia
Authors: RATRIN HESTYANTI YOHANA
Published: March 2007

Abstract:  This exploratory study investigates factors contributing to resiliency of children in the age group of 11–15 years, survivors of the 2004 tsunami in Aceh, Indonesia, through qualitative methodology. Series of participative observation and interviews with children, parents, and local social workers were conducted. A group of 50 children from three camps of the tsunami‐affected areas in Banda Aceh and Great Aceh were involved and observed through several psychosocial activities conducted in coordination with local social workers in the community. Resilient children were identified based on criteria that were developed from the context of the tsunami‐affected children in Banda Aceh and Great Aceh. Six children were identified as resilient. They show absence of clinically significant levels of trauma‐related symptoms as measured by Trauma Symptom Checklist for Children‐A (TSCC‐A). They are able to live normally, such as participate in school activities, play with friends, perform daily chores, be involved in religious activities, and develop healthy relationships with caregivers and peers. They are also perceived as cooperative in psychosocial activities. Findings in internal protective factors of these children include: strong internal motivation to recover, good heart, open to other people, high motivation to bond to religiosity, self‐responsible, sense of humor, and easygoing. Contributing external factors include: support from significant others, able to do religious practice routinely, able to learn traditional dance in groups, have opportunities to be involved in structured play/psychosocial activities, and have access to natural resources for recreation, such as a river.
Frontal EEG Asymmetry and Regulation during Childhood
Authors: JEONG KIM KEE , ANN BELL MARTHA
Published: March 2007

Abstract:  Previous research suggests an association between frontal electroencephalographic (EEG) asymmetries and both positive and negative emotion reactivity. Specifically, right frontal EEG activation is associated with emotions of negative valence in both infants and adults, whereas left frontal EEG activation is associated with emotions of more positive valence. Relatively few studies have examined such associations in children. Moreover, research on mechanisms through which emotion reactivity is related to frontal EEG asymmetries is sparse. As one possible mechanism, we hypothesize that regulatory skills and behaviors developing rapidly during childhood play a critical role in linking frontal EEG asymmetries to emotion reactivity in children. To test the research hypothesis, 25 children were followed from early‐to‐middle childhood at two different points in time with a 4‐year interview interval. Results show that individual variations in a number of regulatory behaviors among children are significantly associated with frontal EEG asymmetries. Our results provide support for the possibility of frontal EEG asymmetry informing the study of the development of regulation in children. The discussion of the findings is centered on potential risk for and resilience to children's emotional reactivity and regulation.