bluuebunny/crossref_metadata_2025 huggingface dataset:
Significance analysis of microarray transcript levels in time series experiments
Authors: Di Camillo Barbara , Toffolo Gianna , Nair Sreekumaran K , Greenlund Laura J , Cobelli Claudio
Published: March 2007

Background

Microarray time series studies are essential to understand the dynamics of molecular events. In order to limit the analysis to those genes that change expression over time, a first necessary step is to select differentially expressed transcripts. A variety of methods have been proposed to this purpose; however, these methods are seldom applicable in practice since they require a large number of replicates, often available only for a limited number of samples. In this data-poor context, we evaluate the performance of three selection methods, using synthetic data, over a range of experimental conditions. Application to real data is also discussed.

Results

Three methods are considered, to assess differentially expressed genes in data-poor conditions. Method 1 uses a threshold on individual samples based on a model of the experimental error. Method 2 calculates the area of the region bounded by the time series expression profiles, and considers the gene differentially expressed if the area exceeds a threshold based on a model of the experimental error. These two methods are compared to Method 3, recently proposed in the literature, which exploits splines fit to compare time series profiles. Application of the three methods to synthetic data indicates that Method 2 outperforms the other two both in Precision and Recall when short time series are analyzed, while Method 3 outperforms the other two for long time series.

Conclusion

These results help to address the choice of the algorithm to be used in data-poor time series expression study, depending on the length of the time series.
Correlation analysis reveals the emergence of coherence in the gene expression dynamics following system perturbation
Authors: Neretti Nicola , Remondini Daniel , Tatar Marc , Sedivy John M , Pierini Michela , Mazzatti Dawn , Powell Jonathan , Franceschi Claudio , Castellani Gastrone C
Published: March 2007

Time course gene expression experiments are a popular means to infer co-expression. Many methods have been proposed to cluster genes or to build networks based on similarity measures of their expression dynamics. In this paper we apply a correlation based approach to network reconstruction to three datasets of time series gene expression following system perturbation: 1) Conditional, Tamoxifen dependent, activation of the cMyc proto-oncogene in rat fibroblast; 2) Genomic response to nutrition changes inD. melanogaster; 3) Patterns of gene activity as a consequence of ageing occurring over a life-span time series (25y–90y) sampled from T-cells of human donors.

We show that the three datasets undergo similar transitions from an "uncorrelated" regime to a positively or negatively correlated one that is symptomatic of a shift from a "ground" or "basal" state to a "polarized" state.

In addition, we show that a similar transition is conserved at the pathway level, and that this information can be used for the construction of "meta-networks" where it is possible to assess new relations among functionally distant sets of molecular functions.
Developmental expression of the receptor for advanced glycation end-products (RAGE) and its response to hyperoxia in the neonatal rat lung
Authors: Lizotte Pierre-Paul , Hanford Lana E , Enghild Jan J , Nozik-Grayck Eva , Giles Brenda-Louise , Oury Tim D
Published: March 2007

Background

The receptor for advanced glycation end products (mRAGE) is associated with pathology in most tissues, while its soluble form (sRAGE) acts as a decoy receptor. The adult lung is unique in that it expresses high amounts of RAGE under normal conditions while other tissues express low amounts normally and up-regulate RAGE during pathologic processes. We sought to determine the regulation of the soluble and membrane isoforms of RAGE in the developing lung, and its expression under hyperoxic conditions in the neonatal lung.

Results

Fetal (E19), term, 4 day, 8 day and adult rat lung protein and mRNA were analyzed, as well as lungs from neonatal (0–24 hrs) 2 day and 8 day hyperoxic (95% O2) exposed animals. mRAGE transcripts in the adult rat lung were 23% greater than in neonatal (0–24 hrs) lungs. On the protein level, rat adult mRAGE expression was 2.2-fold higher relative to neonatal mRAGE expression, and adult sRAGE protein expression was 2-fold higher compared to neonatal sRAGE. Fetal, term, 4 day and 8 day old rats had a steady increase in both membrane and sRAGE protein expression evaluated by Western Blot and immunohistochemistry. Newborn rats exposed to chronic hyperoxia showed significantly decreased total RAGE expression compared to room air controls.

Conclusion

Taken together, these data show that rat pulmonary RAGE expression increases with age beginning from birth, and interestingly, this increase is counteracted under hyperoxic conditions. These results support the emerging concept that RAGE plays a novel and homeostatic role in lung physiology.
Radiation of the Tnt1 retrotransposon superfamily in three Solanaceae genera
Authors: Manetti Maria E , Rossi Magdalena , Costa Ana PP , Clausen Andrea M , Van Sluys Marie-Anne
Published: March 2007

Background

Tnt1 was the first active plant retrotransposon identified in tobacco after nitrate reductase gene disruption. The Tnt1 superfamily comprises elements from Nicotiana (Tnt1 and Tto1) and Lycopersicon (Retrolyc1 and Tlc1) species. The study presented here was conducted to characterise Tnt1-related sequences in 20 wild species of Solanum and five cultivars of Solanum tuberosum.

Results

Tnt1-related sequences were amplified from total genomic DNA using a PCR-based approach. Purified fragments were cloned and sequenced, and clustering analysis revealed three groups that differ in their U3 region. Using a network approach with a total of 453 non-redundant sequences isolated from Solanum (197), Nicotiana (140) and Lycopersicon (116) species, it is demonstrated that the Tnt1 superfamily can be treated as a population to resolve previous phylogenetic multifurcations. The resulting RNAseH network revealed that sequences group according to the Solanaceae genus, supporting a strong association with the host genome, whereas tracing the U3 region sequence association characterises the modular evolutionary pattern within the Tnt1 superfamily. Within each genus, and irrespective of species, nearly 20% of Tnt1 sequences analysed are identical, indicative of being part of an active copy. The network approach enabled the identification of putative "master" sequences and provided evidence that within a genus these master sequences are associated with distinct U3 regions.

Conclusion

The results presented here support the hypothesis that the Tnt1 superfamily was present early in the evolution of Solanaceae. The evidence also suggests that the RNAseH region of Tnt1 became fixed at the host genus level whereas, within each genus, propagation was ensured by the diversification of the U3 region. Different selection pressures seemed to have acted on the U3 and RNAseH modules of ancestral Tnt1 elements, probably due to the distinct functions of these regions in the retrotransposon life cycle, resulting in both co evolution and adaptation of the element population with its host.
Characterization of Escherichia coli MG1655 grown in a low-shear modeled microgravity environment
Authors: Tucker Don L , Ott C Mark , Huff Stephen , Fofanov Yuriy , Pierson Duane L , Willson Richard C , Fox George E
Published: March 2007

Background

Extra-cellular shear force is an important environmental parameter that is significant both medically and in the space environment. Escherichia coli cells grown in a low-shear modeled microgravity (LSMMG) environment produced in a high aspect rotating vessel (HARV) were subjected to transcriptional and physiological analysis.

Results

Aerobic LSMMG cultures were grown in rich (LB) and minimal (MOPS + glucose) medium with a normal gravity vector HARV control. Reproducible changes in transcription were seen, but no specific LSMMG responsive genes were identified. Instead, absence of shear and a randomized gravity vector appears to cause local extra-cellular environmental changes, which elicit reproducible cellular responses. In minimal media, the majority of the significantly up- or down-regulated genes of known function were associated with the cell envelope. In rich medium, most LSMMG down-regulated genes were involved in translation. No observable changes in post-culture stress responses and antibiotic sensitivity were seen in cells immediately after exposure to LSMMG. Comparison with earlier studies of Salmonella enterica serovar Typhimurium conducted under similar growth conditions, revealed essentially no similarity in the genes that were significantly up- or down-regulated.

Conclusion

Comparison of these results to previous studies suggests that different organisms may dramatically differ in their responses to medically significant low-shear and space environments. Depending on their specific response, some organisms, such as Salmonella, may become preadapted in a manner that predisposes them to increased virulence.
Importance of c-Type cytochromes for U(VI) reduction by Geobacter sulfurreducens
Authors: Shelobolina Evgenya S , Coppi Maddalena V , Korenevsky Anton A , DiDonato Laurie N , Sullivan Sara A , Konishi Hiromi , Xu Huifang , Leang Ching , Butler Jessica E , Kim Byoung-Chan , Lovley Derek R
Published: March 2007

Background

In order to study the mechanism of U(VI) reduction, the effect of deletingc-type cytochrome genes on the capacity ofGeobacter sulfurreducensto reduce U(VI) with acetate serving as the electron donor was investigated.

Results

The ability of severalc-type cytochrome deficient mutants to reduce U(VI) was lower than that of the wild type strain. Elimination of two confirmed outer membrane cytochromes and two putative outer membrane cytochromes significantly decreased (ca. 50–60%) the ability ofG. sulfurreducensto reduce U(VI). Involvement in U(VI) reduction did not appear to be a general property of outer membrane cytochromes, as elimination of two other confirmed outer membrane cytochromes, OmcB and OmcC, had very little impact on U(VI) reduction. Among the periplasmic cytochromes, only MacA, proposed to transfer electrons from the inner membrane to the periplasm, appeared to play a significant role in U(VI) reduction. A subpopulation of both wild type and U(VI) reduction-impaired cells, 24–30%, accumulated amorphous uranium in the periplasm. Comparison of uranium-accumulating cells demonstrated a similar amount of periplasmic uranium accumulation in U(VI) reduction-impaired and wild typeG. sulfurreducens. Assessment of the ability of the various suspensions to reduce Fe(III) revealed no correlation between the impact of cytochrome deletion on U(VI) reduction and reduction of Fe(III) hydroxide and chelated Fe(III).

Conclusion

This study indicates thatc-type cytochromes are involved in U(VI) reduction byGeobacter sulfurreducens. The data provide new evidence for extracellular uranium reduction byG. sulfurreducensbut do not rule out the possibility of periplasmic uranium reduction. Occurrence of U(VI) reduction at the cell surface is supported by the significant impact of elimination of outer membrane cytochromes on U(VI) reduction and the lack of correlation between periplasmic uranium accumulation and the capacity for uranium reduction. Periplasmic uranium accumulation may reflect the ability of uranium to penetrate the outer membrane rather than the occurrence of enzymatic U(VI) reduction. Elimination of cytochromes rarely had a similar impact on both Fe(III) and U(VI) reduction, suggesting that there are differences in the routes of electron transfer to U(VI) and Fe(III). Further studies are required to clarify the pathways leading to U(VI) reduction inG. sulfurreducens.
Microsatellite analysis of Damask rose (Rosa damascena Mill.) accessions from various regions in Iran reveals multiple genotypes
Authors: Babaei Alireza , Tabaei-Aghdaei Seyed Reza , Khosh-Khui Morteza , Omidbaigi Reza , Naghavi Mohammad Reza , Esselink Gerhard D , Smulders Marinus JM
Published: March 2007

Background

Damask roses (Rosa damascena Mill.) are mainly used for essential oil production. Previous studies have indicated that all production material in Bulgaria and Turkey consists of only one genotype. Nine polymorphic microsatellite markers were used to analyze the genetic diversity of 40 accessions of R. damascena collected across major and minor rose oil production areas in Iran.

Results

All microsatellite markers showed a high level of polymorphism (5–15 alleles per microsatellite marker, with an average of 9.11 alleles per locus). Cluster analysis of genetic similarities revealed that these microsatellites identified a total of nine different genotypes. The genotype from Isfahan province, which is the major production area, was by far the most common genotype (27/40 accessions). It was identical to the Bulgarian genotype. Other genotypes (each represented by 1–4 accessions) were collected from minor production areas in several provinces, notably in the mountainous Northwest of Iran.

Conclusion

This is the first study that uncovered genetic diversity within Damask rose. Our results will guide new collection activities to establish larger collections and manage the Iranian Damask rose genetic resources. The genotypes identified here may be directly useful for breeding.
Lack of Influence of GTP Cyclohydrolase Gene (GCH1) Variations on Pain Sensitivity in Humans
Authors: Kim Hyungsuk , Dionne Raymond A
Published: March 2007

Objectives:

To assess the effect of variations in GTP cyclohydrolase gene ( GCH1) on pain sensitivity in humans.

Methods:

Thermal and cold pain sensitivity were evaluated in a cohort of 735 healthy volunteers. Among this cohort, the clinical pain responses of 221 subjects after the surgical removal of impacted third molars were evaluated. Genotyping was done for 38 single nucleotide polymorphisms (SNPs) whose heterozygosity > 0.2 in GCH1. Influence of the genetic variations including SNPs and haplotypes on pain sensitivity were analyzed.

Results:

Minor allele frequencies and linkage disequilibrium show significant differences in European Americans, African Americans, Hispanic Americans and Asian Americans. Association analyses in European Americans do not replicate the previously reported important influence of GCH1 variations on pain sensitivity.

Conclusion:

Considering population stratification, previously reported associations between GCH1 genetic variations and pain sensitivity appear weak or negligible in this well characterized model of pain.
Predicting the connectivity of primate cortical networks from topological and spatial node properties
Authors: Costa Lucianoda F , Kaiser Marcus , Hilgetag Claus C
Published: March 2007

Background

The organization of the connectivity between mammalian cortical areas has become a major subject of study, because of its important role in scaffolding the macroscopic aspects of animal behavior and intelligence. In this study we present a computational reconstruction approach to the problem of network organization, by considering the topological and spatial features of each area in the primate cerebral cortex as subsidy for the reconstruction of the global cortical network connectivity. Starting with all areas being disconnected, pairs of areas with similar sets of features are linked together, in an attempt to recover the original network structure.

Results

Inferring primate cortical connectivity from the properties of the nodes, remarkably good reconstructions of the global network organization could be obtained, with the topological features allowing slightly superior accuracy to the spatial ones. Analogous reconstruction attempts for the C. elegans neuronal network resulted in substantially poorer recovery, indicating that cortical area interconnections are relatively stronger related to the considered topological and spatial properties than neuronal projections in the nematode.

Conclusion

The close relationship between area-based features and global connectivity may hint on developmental rules and constraints for cortical networks. Particularly, differences between the predictions from topological and spatial properties, together with the poorer recovery resulting from spatial properties, indicate that the organization of cortical networks is not entirely determined by spatial constraints.
Prestack and poststack migration of crooked-line seismic reflection data: A case study from the South Portuguese Zone fold belt, southwestern Iberia
Authors: Schmelzbach C. , Juhlin C. , Carbonell R. , Simancas J. F.
Published: March 2007

Crooked-line 2D seismic reflection survey geometries violate underlying assumptions of 2D imaging routines, affecting our ability to resolve the subsurface reliably. We compare three crooked-line imaging schemes involving prestack and poststack time migration using the 2D IBERSEIS deep seismic reflection profile running over the South Portuguese Zone thrust-and-fold belt to obtain crisp high-resolution images of the shallow crust. The crust is characterized by a complex subsurface geometry with conflicting dips of up to [Formula: see text]. In summary, the three schemes are (1) normal-moveout (NMO) corrections, dip-moveout (DMO) corrections, common-midpoint (CMP) stacking, CMP projection, and poststack time migration; (2) NMO corrections, DMO corrections, CMP projection, zero-offset time migration of the common-offset gathers, and CMP stacking; (3) CMP projection, prestack time migration in the common-offset domain, and CMP stacking. An essential element of all three schemes is a CMP projection routine, projecting the CMPs first binned along individual segments for preprocessing onto one straight line, which is parallel to the general dip direction of the subsurface structures. After CMP projection, the data satisfy the straight-line assumption of 2D imaging routines more closely. We observe that the prestack time-migration scheme yields comparable or more coherent synthetic and field-data images than the other two DMO-based schemes along the parts of the profile where the acquisition overall follows a straight line. However, the schemes involving DMO corrections are less plagued by migration artifacts than the prestack time-migration scheme along profile parts where the acquisition line is crooked. In particular, prominent migration artifacts on the prestack migrated synthetic data can be related to significant variations in source-receiver azimuths for which 2D prestack migration cannot account. Thus, the processing scheme including DMO corrections, CMP projection, and zero-offset migration of common-offset gathers offers a reliable and effective alternative to prestack migration for crooked-line 2D seismic reflection processing.
Sensitivity functions of frequency-domain magnetic dipole-dipole systems
Authors: Tølbøll Rasmus Juhl , Christensen Niels Bøie
Published: March 2007

The resolution capabilities of airborne electromagnetic (AEM) frequency-domain systems are traditionally analyzed in terms of the footprint, which provides a simple measure of the lateral extent of the earth volume involved in a given measurement. However, considerably more detailed insight into the system resolution capabilities can be obtained by studying the 3D sensitivity distribution as defined by the Fréchet derivatives. A qualitative analysis of the 3D sensitivity distributions for six typical magnetic dipole-dipole configurations demonstrates that the spatial resolution characteristics differ widely and that the optimal coil configuration for practical investigations depends on the expected target characteristics. For all six coil configurations, the 3D sensitivity distributions reveal significant sign changesdownwards and outwards from the center, stressing the necessity of reliable starting models for successful inversion of frequency-domain AEM data. Likewise, the central zone of sensitivity for the in-phase component is always larger than for the quadrature, indicating an inferior lateral resolution of the former. A new sensitivity footprint is defined, based on the at-surface behavior of the sensitivity distribution, simply as the area where the sensitivity is at least 10% of its maximum value. For the vertical coaxial (VCA) coil configuration, the size of the sensitivity footprint in the [Formula: see text]-direction (perpendicular to the flight path) is approximately a factor of two larger than in the [Formula: see text]-direction (along the flight path), while there is virtually no difference for the horizontal coplanar (HCP) coil configuration. The ratio of the HCP to VCA sensitivity footprint exceeds one in both [Formula: see text]- and [Formula: see text]-directions, suggesting that the VCA coil configuration has the best lateral resolution.
Seismoelectric data processing for surface surveys of shallow targets
Authors: Haines Seth S. , Guitton Antoine , Biondi Biondo
Published: March 2007

The utility of the seismoelectric method relies on the development of methods to extract the signal of interest from background and source-generated coherent noise that may be several orders-of-magnitude stronger. We compare data processing approaches to develop a sequence of preprocessing and signal/noise separation and to quantify the noise level from which we can extract signal events. Our preferred sequence begins with the removal of power line harmonic noise and the use of frequency filters to minimize random and source-generated noise. Mapping to the linear Radon domain with an inverse process incorporating a sparseness constraint provides good separation of signal from noise, though it is ineffective on noise that shows the same dip as the signal. Similarly, the seismoelectric signal and noise do not separate cleanly in the Fourier domain, so [Formula: see text]-[Formula: see text] filtering can not remove all of the source-generated noise and it also disrupts signal amplitude patterns. We find that prediction-error filters provide the most effective method to separate signal and noise, while also preserving amplitude information, assuming that adequate pattern models can be determined for the signal and noise. These Radon-domain and prediction-error-filter methods successfully separate signal from [Formula: see text] stronger noise in our test data.
The effect of pore pressure depletion and injection cycles on ultrasonic velocity and quality factor in a quartz sandstone
Authors: Frempong P. , Donald A. , Butt S. D.
Published: March 2007

Passing seismic waves generate transient pore-pressure changes that influence the velocity and attenuation characteristics of porous rocks. Compressional ultrasonic wave velocities [Formula: see text] and quality factors [Formula: see text] in a quartz sandstone were measured under cycled pore pressure and uniaxial strain conditions during a laboratory simulated injection and depletion process. The objectives were to study the influence of cyclical loading on the acoustic characteristics of a reservoir sandstone and to evaluate the potential to estimate pore-fluid pressure from acoustic measurements. The values of [Formula: see text] and [Formula: see text] were confirmed to increase with effective stress increase, but it was also observed that [Formula: see text] and [Formula: see text] increased with increasing pore pressure at constant effective stress. The effective stress coefficient [Formula: see text] was found to be less thanone and dependent on the pore pressure, confining stress, and load. At low pore pressures, [Formula: see text] approached one and reduced nonlinearly at high pore pressures. The change in [Formula: see text] and [Formula: see text] with respect to pore pressure was more pronounced at low versus high pore pressures. However, the [Formula: see text] variation with pore pressure followed a three-parameter exponential rise to a maximum limit whereas [Formula: see text] had no clear limit and followed a two-parameter exponential growth. Axial strain measurements during the pore-pressure depletion and injection cycles indicated progressive viscoelastic deformation in the rock. This resulted in an increased influence on [Formula: see text] and [Formula: see text] with increasing pore-pressure cycling. The value [Formula: see text] was more sensitive in responding to the loading cycle and changes in pore pressures than [Formula: see text]; thus, [Formula: see text] may be a better indicator for time-lapse reservoir monitoring than [Formula: see text]. However, under the experimental conditions, [Formula: see text] was unstable and difficult to measure at low effective stress.
A nonsplit complex frequency-shifted PML based on recursive integration for FDTD modeling of elastic waves
Authors: Drossaert Francis H. , Giannopoulos Antonios
Published: March 2007

In finite-difference time-domain (FDTD) modeling of elastic waves, absorbing boundary conditions are used to mitigate undesired reflections that can arise at the model’s truncation boundaries. The perfectly matched layer (PML) is generally considered to be the best available absorbing boundary condition. An important but rarely addressed limitation of current PML implementations is that their performance is severely reduced when waves are incident on the PML interface at near-grazing angles. In addition, very low frequency waves as well as evanescent waves could cause spurious reflections at the PML interface. In electromagnetic modeling, similar problems are circumvented by using a complex frequency-shifted stretching function in the PML formulas. However, in elastic-wave modeling using the conventional PML formulation — based on splitting the velocityand stressfields — it is difficult to adopt a complex frequency--shifted stretching function. We present an alternative implemen-tation of a PML that is based on recursive integration and does not require splitting of the velocity and stress fields. Modeling re-sults show that the performance of our implementation using a standard stretching function is identical to that of the convention-al split-field PML. Then we show that the new PML can be modi-fied easily to include the complex frequency-shifted stretching function. Results of models with an elongated domain show that this modification can substantially improve the performance of the PML boundary condition. An efficient implementation of the new PML requires less memory than the conventional split-field PML, and, therefore, is a very attractive alternative to the con-ventional PML. By adopting the complex frequency-shifted stretching function, the PML can accommodate a wide variety of model problems, and hence it is more generic.
Residual moveout in anisotropic angle-domain common-image gathers
Authors: Biondi Biondo
Published: March 2007

I develop the fundamental concepts for quantitatively relating perturbations in anisotropic parameters to the corresponding reflector movements in angle-domain common-image gathers (ADCIGs) after anisotropic wavefield-continuation migration. The proposed theory potentially enables the application of residual moveout (RMO) analysis of ADCIGs to velocity estimation in realistic anisotropic conditions. I demonstrate that linearization of the relationship between anisotropic velocity parameters and reflector movements can be derived by assuming stationary raypaths. This assumption leads to a fairly simple analytical derivation. I then apply the general method to the particular case of RMO analysis of reflections from flat reflectors in a vertical transverse isotropic (VTI) medium. This analysis yields expressions to predict RMO curves in migrated ADCIGs. These RMO expressions are functions of both the phase aperture angle and the group aperture angle. Several numerical examples demonstrate the accuracy of the RMO curves predicted by my kinematic analysis. The synthetic examples also show that approximating the group angles with the phase angles in the application of the RMO expressions may lead to substantial errors for events reflected at wide aperture angles. The results obtained by migrating a 2D line extracted from a Gulf of Mexico 3D data set confirm the accuracy of the proposed method. The RMO curves predicted by the theory match the RMO function observed in the ADCIGs computed from the real data.
Virtual shear source makes shear waves with air guns
Authors: Bakulin Andrey , Mateeva Albena , Calvert Rodney , Jorgensen Patsy , Lopez Jorge
Published: March 2007

We demonstrate a novel application of the virtual source method to create shear-wave sources at the location of buried geophones. These virtual downhole sources excite shear waves with a different radiation pattern than known sources. They can be useful in various shear-wave applications. Here we focus on the virtual shear check shot to generate accurate shear-velocity profiles in offshore environments using typical acquisition for marine walkaway vertical seismic profiling (VSP). The virtual source method is applied to walkaway VSP data to obtain new traces resembling seismograms acquired with downhole seismic sources at geophone locations, thus bypassing any overburden complexity. The virtual sources can be synthesized to radiate predominantly shear waves by collecting converted-wave energy scattered throughout the overburden. We illustrate the concept in a synthetic layered model and demonstrate the method by estimating accurate P- and S-wave velocity profiles below salt using a walkaway VSP from the deepwater Gulf of Mexico.
Effect of cementation on ultrasonic velocities in sandstones
Authors: Al-Tahini Ashraf M. , Sondergeld Carl H. , Rai Chandra S.
Published: March 2007

We determine the acoustic velocities for samples cored from the Jauf and Unayzah sandstone formations of Saudi Arabia. We use microstructural analysis including thin sections and point counting to quantify cementation. Velocities in these formations are strongly controlled by the combination of porosity and cementation. Consequently, rocks of similar porosity but with different cementation materials display different velocities. The objective of this study is to understand the effect of cementation on the acoustic velocity. Cements in these two formations have variable compositions and properties. Pure quartz overgrowth plays a major role in increasing velocities while clay and clay coatings play a minor role. We found that clay coatings inhibit the quartz overgrowth cement leading to a decrease in velocities. Understanding the influence of various cementation types on velocity, and thus elastic properties in sandstone cores, enables an understanding of the variation of sonic velocities and moduli across these formations. The uniqueness of this study is that we emphasize the quantification of the role of cement and not just mineral volume.
Topographic corrections to slowness measurements in parsimonious migration of land data
Authors: Basi Ibrahim Z. , McMechan George A.
Published: March 2007

Parsimonious migration requires that incident and emergent angles be measured, via apparent slownesses, from the seismic data being migrated. When slownesses are measured from land data, it is the apparent slowness along the topography, not the horizontal slowness that is being measured. Thus, errors are introduced into the incident and emergent angle estimates, which are defined via horizontal slownesses. These errors can be corrected using the local topographic dips. A 2D field data example shows that, after correction, a migrated image has significantly improved coherency.
3D gravity inversion of basement relief — A depth-dependent density approach
Authors: Chakravarthi Vishnubhotla , Sundararajan Narasimman
Published: March 2007

We present a 3D gravity inversion technique, based on the Marquardt algorithm, to analyze gravity anomalies attributable to basement interfaces above which the density contrast varies continuously with depth. The salient feature of this inversion is that the initial depth of the basement is not a required input. The proposed inversion simultaneously estimates the depth of the basement interface and the regional gravity background. Applicability and efficacy of the inversion is demonstrated with a synthetic model of a density interface. We analyze the synthetic gravity anomalies (1) solely because of the structure, (2) in the presence of a regional gravity background, and (3) in the presence of both random noise and regional gravity background. The inverted structure remains more or less the same, regardless of whether the regional background is simulated with a second-degree polynomial or a bilinear equation. The depth of the structure and estimated regional background deviate only modestly from the assumed ones in the presence of random noise and regional background. The analyses of two sets of real field data, one over the Chintalpudi subbasin, India, and another over the Pannonian basin, eastern Austria, yield geologically plausible models with the estimated depths that compare well with drilling data.
Seismic signatures of partial saturation on acoustic borehole modes
Authors: Chao Gabriel , Smeulders D. M. J. , van Dongen M. E. H.
Published: March 2007

We present an exact theory of attenuation and dispersion of borehole Stoneley waves propagating along porous rocks containing spherical gas bubbles by using the Biot theory. An effective frequency-dependent fluid bulk modulus is introduced to describe the dynamic (oscillatory) behavior of the gas bubbles. The model includes viscous, thermal, and radiation damping. It is assumed that the gas pockets are larger than the pore size, but smaller than the wavelengths involved (mesoscopic inhomogeneity). A strong dependence of the attenuation of the Stoneley wave on gas fraction and bubble size is found. Attenuation increases with gas fraction over the complete range of studied frequencies [Formula: see text]. The dependence of the phase velocity on the gas fraction and bubble size is restricted to the lower frequency range. These results indicate that the interpretation of Stoneley wave properties for the determination of, for example, local permeability formation is not straightforward and could be influenced by the presence of gas in the near-wellbore zone. When mud-cake effects are included in the model, the same observations roughly hold, though dependence on the mud-cake stiffness is quite complex. In this case, a clear increase of the damping coefficient with saturation is predicted only at relatively high frequencies.
Fast line searches for the robust solution of linear systems in the hybrid ℓ1 ∕ ℓ2 and Huber norms
Authors: Bube Kenneth P. , Nemeth Tamas
Published: March 2007

Linear systems of equations arise in traveltime tomography, deconvolution, and many other geophysical applications. Nonlinear problems are often solved by successive linearization, leading to a sequence of linear systems. Overdetermined linear systems are solved by minimizing some measure of the size of the misfit or residual. The most commonly used measure is the [Formula: see text] norm (squared), leading to least squares problems. The advantage of least squares problems for linear systems is that they can be solved by methods (for example, [Formula: see text] factorization) that retain the linear behavior of the problem. The disadvantage of least squares solutions is that the solution is sensitive to outliers. More robust norms, approximating the [Formula: see text] norm, can be used to reduce the sensitivity to outliers. Unfortunately, these more robustnorms lead to nonlinear minimization problems, even for linear systems, and many efficient algorithms for nonlinear minimiza-tion problems require line searches. One iterative method for solving linear problems in these more robust norms is iteratively reweighted least squares (IRLS). Recently, the limited-memory Broyden, Fletcher, Goldfarb, and Shanno (BFGS) algorithm (LBFGS) has been applied efficiently to these problems. A vari-ety of nonlinear conjugate gradient algorithms (NLCG) can also be applied. LBFGS and NLCG methods require a line search in each iteration. We show that exact line searches for these meth-ods can be performed very efficiently for computing solutions to linear systems in these robust norms, thereby promoting fast con--vergence of these methods. We also compare LBFGS and NLCG (with and without exact line searches) to IRLS for a small number of iterations.
Direct multichannel predictive deconvolution
Authors: Porsani Milton J. , Ursin Bjørn
Published: March 2007

The Levinson principle generally can be used to compute recursively the solution of linear equations. It can also be used to update the error terms directly. This is used to do single-channel deconvolution directly on seismic data without computing or applying a digital filter. Multichannel predictive deconvolution is used for seismic multiple attenuation. In a standard procedure, the prediction-error filter matrices are computed with a Levinson recursive algorithm, using a covariance matrix of the input data. The filtered output is the prediction errors or the nonpredictable part of the data. Starting with the classical Levinson recursion,wehave derived new algorithms for direct recursive calculationof the prediction errors without computing the data covariance-matrix or computing the prediction-error filters. One algorithm generates recursively the one-step forward and backward predic-tion errors and the L-step forward prediction error, computing only the filter matrices with the highest index. A numerically more stable algorithm uses reduced QR decomposition or singular-value decomposition (SVD) in a direct recursive computation of the prediction errors without computing any filter matrix. The new, stable, predictive algorithms require more arithmetic opera-tions in the computer, but the computer programs and data flow are much simpler than for standard predictive deconvolution.
An effective medium algorithm for calculating water saturations at any salinity or frequency
Authors: Berg Charles
Published: March 2007

An algorithmic approach is used to mix the conductivities and geometric factors of the disperse components (the rock and hydrocarbon particles) with the host conductivity (formation water). The theoretical basis for the algorithm is the Hanai-Bruggeman (HB) equation, which itself incorporates only one disperse component. The new approach, the incremental model, accommodates geometric factors such as sand and shale porosity exponents, saturation exponent, and also accommodates the associated grain conductivities. Its advantage over previous methods is that it works at any water salinity or tool frequency while allowing saturation and porosity exponents to have values other than 1.5. The algorithm is general and is written to accommodate simultaneous mixing of up to three disperse components and the formation water, but it can be extended to accommodate any number of disperse components. In its application to shaley sands, hydrocarbon and sand elements are set to zero conductivity at low frequency, but they can be nonzero for calculating saturations at higher frequencies. The reason for this is that hydrocarbon and sand conductivities are real and very close to zero at low frequencies, but at high frequencies the dielectric constants become significant, making the complex conductivities nonzero. The incremental model compared well with the Waxman-Smits model on multiple water-conductivity saturation data from two published experimental data sets. The model is adaptable to other rock conductivity problems such as vuggy porosity, vuggy water saturation, and clay-coated sand grains. The potential exists for the algorithm to be part of a comprehensive computer program for calculating rock conductivities and saturations using many different combinations of rock fabrics and compositions.
2D marine controlled-source electromagnetic modeling: Part 1 — An adaptive finite-element algorithm
Authors: Li Yuguo , Key Kerry
Published: March 2007

In Part 1 of this work, we develop an adaptive finite-element algorithm for forward modeling of the frequency-domain, marine controlled-source electromagnetic (CSEM) response of a 2D conductivity structure that is excited by a horizontal electric dipole source. After transforming the governing equations for the secondary electromagnetic fields into the wavenumber domain, the coupled system of two partial differential equations for the strike-parallel electric and magnetic fields is approximated using the finite-element method. The model domain is discretized using an unstructured triangular element grid that readily accommodates arbitrarily complex structures. A numerical solution of the system of linear equations is obtained using the quasi-minimal residual (QMR) method, which requiresmuch less storagethan full matrix inversion methods. We implement an automatedadaptive grid refinement algorithm in which the finite-element solution is computed iteratively on successively refined grids. Grid refinement is guided by an a posteriori error estimator based on a recently developed gradient recovery operator. The error estimator uses the solution to a dual problem in order to bias refinement toward elements that affect the solution at the electromagnetic (EM) receiver locations and enables the computation of asymptotically exact solutions to the 2.5D partial differential equations. We validate the finite element formulation against the canonical 1D reservoir model and study the performance of the adaptive refinement algorithm. An example model study of a complex offshore structure of interest for petroleum exploration illustrates the utility of the adaptive finite-element method for CSEM modeling.
Preferred orientation and elastic anisotropy of illite-rich shale
Authors: Wenk Hans-Rudolf , Lonardelli Ivan , Franz Hermann , Nihei Kurt , Nakagawa Seiji
Published: March 2007

Shales display significant seismic anisotropy that is attributed in part to preferred orientation of constituent minerals. This orientation pattern has been difficult to quantify because of the poor crystallinity and small grain size of clay minerals. A new method is introduced that uses high-energy synchrotron X-rays to obtain diffraction images in transmission geometry and applies it to an illite-rich shale. The images are analyzed with the crystallographic Rietveld method to obtain quantitative information about phase proportions, crystal structure, grain size, and preferred orientation (texture) that is the focus of the study. Textures for illite are extremely strong, with a maximum of 10 multiples of a random distribution for (001) pole figures. From the three-dimensional orientation distribution of crystallites, and single-crystal elastic properties, the intrinsic anisotropic elastic constants of the illite aggregate (excluding contribution from aligned micropores) can be calculated by appropriate medium averaging. The illitic shale displays roughly transverse isotropy with [Formula: see text] close to [Formula: see text] and more than twice as strong as [Formula: see text]. This method will lend itself to investigate complex polymineralic shales and quantify the contribution of preferred orientation to macroscopic anisotropy.
Particle swarm optimization: A new tool to invert geophysical data
Authors: Shaw Ranjit , Srivastava Shalivahan
Published: March 2007

Particle swarm optimization (PSO) is a global optimization strategy that simulates the social behavior observed in a flock (swarm) of birds searching for food. A simple search strategy in PSO guides the algorithm toward the best solution through constant updating of the cognitive knowledge and social behavior of the particles in the swarm. To evaluate the applicability of PSO to inversion of geophysical data, we inverted three noise-corrupted synthetic sounding data sets over a multilayered 1D earth model by using DC, induced polarization (IP), and magnetotelluric (MT) methods. The results show that acceptable solutions can be obtained with a swarm of about 300 particles and that convergence occurs in less than 100 iterations. The time required to execute a PSO algorithm is comparable to that of a genetic algorithm (GA). Similarly, the models estimated from PSO and GA are close to the true solutions. Whereas a ridge regression (RR) algorithm converges in four to eight iterations, it yields satisfactory results only when the initial model is very close to the true model. Models estimated from PSO explain observed, vertical electric sounding (VES) and MT data, from Bhiwani district, Haryana, India, and the Chottanagpur gneissic complex, Dhanbad, India. The results are consistent with RR and GA inversions.
Spatial focusing of electrical resistivity surveys considering geologic and hydrologic layering
Authors: Furman Alex , Ferré Ty P. , Heath Gail L.
Published: March 2007

Electrical resistivity tomography (ERT) has shown great promise for monitoring transient hydrologic processes. One advantage of ERT under those conditions is the ability of a user to tailor the spatial sensitivity of an ERT survey through selection of electrode locations and electrode combinations. Recent research has shown that quadripoles can be selected in a manner that improves the independent inversion of ERT data. Our ultimate interest lies in using ERT data along with measurements from other sensors, which typically can provide high-quality data from shallow regions of the subsurface, in a joint inversion. As a result, we do not consider the selection of quadripoles specifically for inde-pendent ERT inversion. Rather, we present an approach to focusthe spatial sensitivity of ERT surveys in specificsubsurface regions with the assumption that those data, when interpreted along with other measurements that are sensitive to those regions, will lead to more complete hydrologic characterization. Because we are interested in monitoring rapid processes, our approach is designed to efficiently identify optimal quadripoles. This is achieved by separating the optimization from the inversion grid, significantly reducing computational effort. We extend our previous work to consider the use of both surface and borehole ERT electrodes and to consider the impacts of horizontally layered electrical conductivity conditions. Results confirm the ability of the method to focus survey sensitivity while showing the importance of incorporation of prior knowledge of the subsurface electric conductivity structure in designing optimal ERT surveys.
Convergence of traveltime power series for a layered VTI medium
Authors: Tygel Martin , Ursin Bjørn , Stovas Alexey
Published: March 2007

For a multiply reflected SH-wave or a multiply reflected and converted qP/qSV-wave in a layered VTI medium, traveltime and offset can be expressed by power series in horizontal slowness. As for a stack of isotropic layers, these can be used to express traveltime as a series of even powers of offset. The existence and behavior of this power series depend on the derivative of offset with respect to horizontal slowness, formally expressed as traveltime multiplied by NMO-velocity squared. When the NMO-velocity squared is different from zero, the power series always exists for sufficiently small offset. The NMO-velocity squared is always positive for SH-waves and for qP-waves in media with normal polarization, for which there are no triplications in traveltime as function of offset. For qSV-wave propagation insome layers, the NMO-velocity squared may be positive, zero, or negative. When it is positive, the power series exists, but there may be an off-axis triplication in traveltime. When the NMO-squared velocity is zero, the power series does not exist, and there is an incipient triplication on the vertical axis. When the NMO-velocity squared is negative, there is a triplication in traveltime on the vertical axis. The power series exists and represents the first-arrival traveltime branch. Numerical examples show that when the value of the NMO-velocity squared is small, the power series for a qSV-wave can be used only for very small values of offset. The series of traveltime squared in powers of offset al-ways exists when the series for traveltime exists; therefore, it must have the same or larger region of convergence.