bluuebunny/crossref_metadata_2025 huggingface dataset:
Over‐expression of human DNA polymerase lambda in E. coli and characterization of the recombinant enzyme
Authors: Shimazaki Noriko , Yoshida Kenta , Kobayashi Toshiko , Toji Shingo , Tamai Katsuyuki , Koiwai Osamu
Published: March 2003

Background: DNA polymerase lambda (Pol λ) was recently identified as a new member of the family X of DNA polymerases in eukaryotic cells. Pol λ contains a nuclear localization signal (NLS), a BRCA1‐C terminal (BRCT) domain, a proline‐rich region, helix‐hairpin‐helix (HhH) and pol X motifs. Since the amino acid sequence for Pol λ shares a high degree of homology to Pol β, Pol λ is considered to have a similar enzymatic nature to Pol β.

Results: Recombinant human Pol λ was shown to possess template‐directed DNA polymerase activity in its monomeric form. Pol λ required either Mn2+ or Mg2+ as a metal co‐factor to catalyse this activity, and optimal activity was detected at pH 8.5–9.0. Pol λ was insensitive to aphidicolin, but was sensitive to dideoxynucleoside triphosphates or N‐ethylmaleimide. By constructing the truncated Pol λ, the proline rich region was shown to act in a suppression of its polymerization activity. A chimeric enzyme comprised of the Pol λ N‐terminal region and Pol β also showed a reduced Pol β activity. Proliferating cell nuclear antigen (PCNA) directly interacts with Pol λ through its Pol β like region in vitro.

Conclusions: Pol λ possesses similar enzymatic nature to Pol β; requirements of cations and optimal conditions for pH and NaCl concentration, aside from sensitivity to N‐ethylmaleimide and template preference. The proline rich region of Pol λ functions as a suppressor domain for its polymerization activity (SDPA). Pol λ interacts directly with PCNA through its Pol β like region. The functional consequence of this interaction is the negative regulation of Pol λ activity.
Characterization of the chicken L‐Maf, MafB and c‐Maf in crystallin gene regulation and lens differentiation
Authors: Yoshida Tomonori , Yasuda Kunio
Published: March 2003

Background: Members of the Maf family, including L‐Maf, MafB and c‐Maf, are ‘basic region/leucine zipper’ (bZIP) transcription factors. Maf proteins contain a highly conserved acidic transactivation domain (AD), and a bZIP region that mediates DNA‐binding activity. The hinge region between AD and bZIP varies considerably in length between different proteins. Recent studies reveal that L‐Maf, c‐Maf and MafB play key roles in vertebrate lens development.

Results: We investigated the transactivation activity of individual factors in culture cells to analyse their specific functions. In transient transfection assays with a reporter gene containing Maf responsive elements, MafB and c‐Maf activated higher levels of the reporter gene than L‐Maf. However, L‐Maf transactivated the αA‐crystallin promoter as effectively as MafB and c‐Maf, and induced the expression of the endogenous δ‐crystallin gene more efficiently than the other two proteins. Domain‐swapping experiments reveal that the bZIP region of MafB takes part in strong transcriptional activity, while the acidic and hinge regions (AH) of c‐Maf collectively serve as a strong transactivation domain. The AH region of L‐Maf (but not c‐Maf) conferred transactivation activity to induce δ‐crystallin gene expression.

Conclusions: These results suggest that despite their similar DNA binding properties, L‐Maf, MafB and c‐Maf regulate different sets of target genes by complex interactions with multiple factors that recognize cis‐elements in promoters. The AH region of L‐Maf has a distinct role in inducing endogenous δ‐crystallin gene.
Targeted elimination of the follicular label‐retaining cells by photo‐induced cell killing caused a defect on follicular renewal on mice
Authors: Kameda Takashi , Hatakeyama Shin , Ma Ying‐Zhe , Kawarada Yoshihiko , Kawamata Makiko , Terada Kunihiko , Sugiyama Toshihiro
Published: March 2003

Background: One of the most well‐known ways to identify stem cells is to search for the slow‐cycling cells (label‐retaining cells; LRCs), by labelling their DNA. The bulge of hair follicle is assumed to identify the location of the follicular stem cells. While this assumption was supported by previous analyses of cell tracing, it is still not clear whether the LRCs are critical for follicular renewal.

Results: To solve this problem, we tried to selectively eliminate the bromodeoxyuridine (BrdU)‐labelled follicular LRCs by a photo‐induced cell killing method, in combination with Hoechst 33258 treatment. We labelled the slow‐cycling cells in the follicular bulge by repeated administration of the BrdU, followed by a chase period. When the labelled mice skin was irradiated at the telogen phase after the Hoechst 33258 treatment, we observed apoptotic cells in the bulge area 18 h after the irradiation and a defect on the follicular renewal at the next anagen phase. The time course of appearance of hair defect suggests that only the late telogen follicle is sensitive to irradiation.

Conclusions: This finding suggests that the LRCs contribute to the renewal of the hair follicle, and they might proliferate at a restricted point in the hair cycle to supply hair germinative cells as previously predicted.
Zebrafish DAZ‐like protein controls translation via the sequence ‘GUUC’
Authors: Maegawa Shingo , Yamashita Masakane , Yasuda Kunio , Inoue Kunio
Published: March 2003

Background: In many species, DAZ homologous genes encode RNA‐binding proteins containing two conserved motifs, namely the RNA‐recognition motif (RRM) and the DAZ motif. Genetic analysis and gene disruption studies have demonstrated that DAZ family proteins play important roles in gametogenesis. However, little is known about the biochemical functions of DAZ family proteins.

Results: Using in vitro selection and UV‐crosslinking experiments, we identified the sequence ‘GUUC’ as the target RNA sequence of zebrafish DAZ‐like protein (zDAZL). In transfection experiments, zDAZL protein activated translation in a manner dependent on the binding sequence in the 3′UTR of the Drosophila twine gene or zDazl gene. Moreover, it is highly likely that the zDAZL protein associates with polysomes through the DAZ motif in vivo, and that the association with polysomes is indispensable for translational activation.

Conclusions: This is the first report that the DAZ family protein directly promotes the translation of the target mRNAs in vertebrates. This study provides important insights into the molecular mechanisms underlying the post‐transcriptional regulation of DAZ family proteins in gametogenesis.
Naso‐maxillary deformity due to frontonasal expression of human transthyretin gene in transgenic mice
Authors: Noguchi Hiromitsu , Kaname Tadashi , Sekimoto Tomohisa , Senba Kei , Nagata Yasushi , Araki Masatake , Abe Makoto , Nakagata Naomi , Ono Tomomichi , Yamamura Ken‐ichi , Araki Kimi
Published: March 2003

Background Retinoic acid, a metabolic product of retinol, is essential for craniofacial morphogenesis. Transthyretin (TTR) is a plasma protein delivering retinol to tissues. We produced several transgenic mouse lines using the human mutant TTR (hTTRMet30) gene to establish a mouse model of familial amyloidotic polyneuropathy. One of the lines showed an autosomal dominant inheritance of naso‐maxillary deformity termed Nax.

Results: The Nax malformation was characterized by a hypoplastic developmental defect of the frontonasal region. Homozygous mice with higher transgene expressions showed more severe phenotypes, but a subline, in which the copy number and expression of the transgene was reduced, showed a normal phenotype, indicating that the hTTRMet30 expression caused the malformation. Nax mice began to express the hTTRMet30 gene in the nasal placode from embryonic day 10.5 (E10.5), which was 2 days earlier than in the other transgenic lines with a normal phenotype. Excessive cell death was observed in the nasal placode of the E10.5 Nax embryos. In addition, the forced expression of hTTRMet30 in the nasal placode of transgenic mice resulted in similar phenotypes.

Conclusion: The expression of the hTTRMet30 gene in the nasal placode at E10.5 induced apoptotic cell death, leading to hypoplastic deformity in the frontonasal region.
Simultaneous acceleration of the cell cycle and suppression of apoptosis by splice variant delta‐6 of the candidate tumour suppressor LUCA‐15/RBM5
Authors: Mourtada‐Maarabouni Mirna , Sutherland Leslie C. , Meredith Janet M. , Williams Gwyn T.
Published: March 2003

Background: The short arm of chromosome 3 is thought to include one or more tumour suppressor genes (TSGs), since carcinoma of various tissues display deletions in this region. Many genes mapping to this region have recently been identified, including the LUCA‐15/RBM5 gene.

Results: In this study we report the cloning from human bone marrow library of a splice variant of LUCA‐15 which lacks exon 6, resulting in a frameshift and producing a truncated protein of 150 amino acids instead of 815 amino acids. This variant is widely expressed at a low level in normal tissues and is expressed at increased levels in T‐leukaemic cell lines. Over‐expression of this splice variant after electroporation both shortened the cell cycle and inhibited CD95‐mediated apoptosis in CEM‐C7 T‐cells. In marked contrast, over‐expression of the full length LUCA‐15/RBM5 suppressed cell proliferation both by inducing apoptosis and by extending the G1 phase of the cell cycle.

Conclusion: These results, taken together with previous observations from ourselves and others, suggest that LUCA‐15 is involved in the control of both apoptosis and the cell cycle. Since oncogenesis often relies on separate changes in molecules regulating apoptosis on the one hand, and proliferation, on the other, the discovery of a candidate tumour suppressor gene which affects both processes simultaneously is likely to be of major significance.
Overproduction of a conserved domain of fission yeast and mammalian translation initiation factor eIF4G causes aberrant cell morphology and results in disruption of the localization of F‐actin and the organization of microtubules
Authors: Hashemzadeh‐Bonehi Lida , Curtis Penelope S. , Morley Simon J. , Thorpe Julian R. , Pain Virginia M.
Published: March 2003

Background: The recruitment of mRNA for translation involves the assembly at the 5′cap of a complex of three initiation factors: the cap binding protein eIF4E, the ATP‐dependent RNA helicase eIF4A and the scaffold protein eIF4G. eIF4G mediates the binding of this mRNA–protein complex to the 43S ribosomal preinitiation complex. There is growing recognition that the components of the translational apparatus interact functionally with cytoskeletal components. Here we report specific effects of the over‐expression of human and fission yeast eIF4G domains on cell morphology in Schizosaccharomyces pombe.

Results: A single gene encoding fission yeast eIF4G was identified and demonstrated to be essential. We have over‐expressed fragments corresponding to the conserved functional domains of eIF4G. At expression levels that did not disrupt rates of overall translation or protein accumulation, a fragment of S. pombe eIF4G, 4G‐NOB, corresponding to the minimal region of human eIF4G required to support cap‐independent mRNA recruitment, was found to impair cell proliferation in fission yeast. This resulted from defects in cytokinesis, and was associated with the disruption of both microtubules and actin microfilaments. The over‐expressed fragment was itself localized to the cell ends, the nuclear periphery and the septum.

Conclusions: This is the first demonstration of a link between a translation initiation factor and mechanisms controlling cell morphology. The data suggest a direct or indirect interaction between the functional domains of eIF4G and cellular structures involved in cytokinesis.
Guess who's coming to dinner: A portrait of Tyrannosaurus as a predator
Authors: LINGHAM‐SOLIAR THEAGARTEN
Published: March 2003

The debate over whether Tyrannosaurus was a scavenger or an active predator has raged for almost a hundred years. Biomechanical studies show that the king of the tyrant lizards lived up to its name and actively hunted its prey.
The geology of Lulworth Cove, Dorset
Authors: NOWELL
Published: March 2003

A classic British geological locality revisited.
High‐Arctic glaciers as analogues for glacial landform development in Britain
Authors: Hambrey Michael J. , Bennett Matthew R. , Glasser Neil F. , Huddart David
Published: March 2003

Applying the principles of structural geology and sedimentology to glacial depositional features indicates that the High‐Arctic provides the best analogues for late glacial landforms in the British uplands.
John Whitehurst (1713–1788): philosopher, geologist, horologist and engineer
Authors: Ford Trevor D.
Published: March 2003

Among the late 18th‐century pioneers of geological science was John Whitehurst. He set the scene for the early Derbyshire geologists, White Watson and John Farey, whose books were not published until 1811, long after Whitehurst's death. But Whitehurst's ideas went beyond Derbyshire; he looked at the global situation in his book An Inquiry into the Original State & Formation of the Earth (1778, 1786). Whitehurst was a founder member of the influential Lunar Society and a close friend of many philosophers of the period.
Geophysical inversion with a neighbourhood algorithm—I. Searching a parameter space
Authors: Sambridge Malcolm
Published: March 2003

This paper presents a new derivative-free search method for finding models of acceptable data fit in a multidimensional parameter space. It falls into the same class of method as simulated annealing and genetic algorithms, which are commonly used for global optimization problems. The objective here is to find an ensemble of models that preferentially sample the good data-fitting regions of parameter space, rather than seeking a single optimal model. (A related paper deals with the quantitative appraisal of the ensemble.)

The new search algorithm makes use of the geometrical constructs known as Voronoi cells to derive the search in parameter space. These are nearest neighbour regions defined under a suitable distance norm. The algorithm is conceptually simple, requires just two ‘tuning parameters’, and makes use of only the rank of a data fit criterion rather than the numerical value. In this way all difficulties associated with the scaling of a data misfit function are avoided, and any combination of data fit criteria can be used. It is also shown how Voronoi cells can be used to enhance any existing direct search algorithm, by intermittently replacing the forward modelling calculations with nearest neighbour calculations.

The new direct search algorithm is illustrated with an application to a synthetic problem involving the inversion of receiver functions for crustal seismic structure. This is known to be a non-linear problem, where linearized inversion techniques suffer from a strong dependence on the starting solution. It is shown that the new algorithm produces a sophisticated type of ‘self-adaptive’ search behaviour, which to our knowledge has not been demonstrated in any previous technique of this kind.
Local Bayesian inversion: theoretical developments
Authors: Moraes Fernando S. , Scales John A.
Published: March 2003

We derive a new Bayesian formulation for the discrete geophysical inverse problem that can significantly reduce the cost of the computations. The Bayesian approach focuses on obtaining a probability distribution (the posterior distribution), assimilating three kinds of information: physical theories (data modelling), observations (data measurements) and prior information on models. Once this goal is achieved, all inferences can be obtained from the posterior by computing statistics relative to individual parameters (e.g. marginal distributions), a daunting computational problem in high dimensions.

Our formulation is developed from the working hypothesis that the local (subsurface) prior information on model parameters supercedes any additional information from other parts of the model. Based on this hypothesis, we propose an approximation that permits a reduction of the dimensionality involved in the calculations via marginalization of the probability distributions. The marginalization facilitates the tasks of incorporating diverse prior information and conducting inferences on individual parameters, because the final result is a collection of 1-D posterior distributions. Parameters are considered individually, one at a time. The approximation involves throwing away, at each step, cross-moment information of order higher than two, while preserving all marginal information about the parameter being estimated. The main advantage of the method is allowing for systematic integration of prior information while maintaining practical feasibility. This is achieved by combining (1) probability density estimation methods to derive marginal prior distributions from available local information, and (2) the use of multidimensional Gaussian distributions, which can be marginalized in closed form.

Using a six-parameter problem, we illustrate how the proposed methodology works. In the example, the marginal prior distributions are derived from the application of the principle of maximum entropy, which allows one to solve the entire problem analytically. Both random and modelling errors are considered. The uncertainty measure for estimated parameters is provided by 95 per cent probability intervals calculated from the marginal posterior distributions.
Thin‐bed AVO effects
Authors: Bakke N. E. , Ursin B.
Published: March 2003

Tuning caused by closely spaced impedance boundaries affects seismic amplitudes. At zero‐offset the shape of the composite reflected signal approaches the time‐derivative of the original pulse as the layer thickness decreases. For layers thinner than half of the tuning thickness, the reflected amplitude is modified by a factor equal to twice the time‐thickness of the thin layer. Offset‐dependent tuning can be approximated by the time differences between primary reflections. For high‐velocity contrasts locally converted waves will also affect the total reflected seismic response. The contribution from intrabed multiples can, in most cases, be ignored. Correction for offset‐dependent tuning should be considered before conventional AVO analysis.
Reflection moveout inversion in azimuthally anisotropic media: accuracy, limitations and acquisition
Authors: Al‐Dajani AbdulFattah , Alkhalifah Tariq , Morgan Frank Dale
Published: March 2003

Parameter estimation from the elliptical variations in the normal‐moveout (NMO) velocity in azimuthally anisotropic media is sensitive to the angular separation between the survey lines in 2D, or equivalently, the source‐to‐receiver azimuth in 3D, and to the set of azimuths used in the inversion procedure. The accuracy in estimating the orientation of an NMO ellipse, in particular the parameter α, is also sensitive to the magnitude of anisotropy. On the other hand, the accuracy in estimating the semi‐axes of the NMO‐velocity ellipse is about the same for any magnitude of anisotropy.  To invert for the NMO ellipse parameters at least three NMO‐velocity measurements along distinct azimuth directions are needed. In order to maximize the accuracy and stability in parameter estimation, it is best to have the azimuths for the three source‐to‐receiver directions 60° apart. Having more than three distinct source‐to‐receiver azimuths (e.g. full azimuthal coverage) provides a useful data redundancy that enhances the quality of the estimates.  In order to maximize quality in the inversion process, it is recommended to design the seismic data acquisition such that it contains small sectors (≤10°) with adequate fold and offset distribution.  Using three NMO‐velocity measurements, 60° apart, an azimuthally anisotropic layer overlain by an azimuthally isotropic overburden (as might occur for fractured reservoirs) should have a relative thickness (in time) with respect to the total thickness at least equal to the ratio of the error in the NMO (stacking) velocity to the interval anisotropy of the fractured layer. Coverage along more than three azimuths, however, improves this limitation, which is imposed by Dix differentiation, by at most 50%, depending on the number of observations (NMO velocities) that enter the inversion procedure.
An efficient non‐linear least‐squares 1D inversion scheme for resistivity and IP sounding data
Authors: Roy Indrajit G
Published: March 2003

Non‐linear least‐squares inversion operates iteratively by updating the model parameters in each step by a correction vector which is the solution of a set of normal equations. Inversion of geoelectrical data is an ill‐posed problem. This and the ensuing suboptimality restrict the initial model to being in the near vicinity of the true model. The problem may be reduced by introducing damping into the system of equations. It is shown that an appropriate choice of the damping parameter obtained adaptively and the use of a conjugate‐gradient algorithm to solve the normal equations make the 1D inversion scheme efficient and robust. The scheme uses an optimal damping parameter that is dependent on the noise in the data, in each iterative step. The changes in the damping and relative residual error with iteration number are illustrated. A comparison of its efficacy over the conventional Marquardt and simulated annealing methods, tested on Inman's model, is made. Inversion of induced polarization (IP) sounding is obtained by inverting twice (true and modified) DC apparent resistivity data. The inversion of IP data presented here is generic and can be applied to any of the IP observables, such as chargeability, frequency effect, phase, etc., as long as these observables are explicitly related to the DC apparent resistivity. The scheme is used successfully in inverting noise‐free and noisy synthetic data and field data taken from the published literature.
Non‐linear three‐dimensional inversion of cross‐well electrical measurements
Authors: Abubakar Aria , Van Den Berg Peter M.
Published: March 2003

Cross‐well electrical measurement as known in the oil industry is a method for determining the electrical conductivity distribution between boreholes from the electrostatic field measurements in the boreholes. We discuss the reconstruction of the conductivity distribution of a three‐dimensional domain. The measured secondary electric potential field is represented in terms of an integral equation for the vector electric field. This integral equation is taken as the starting point to develop a non‐linear inversion method, the so‐called contrast source inversion (CSI) method. The CSI method considers the inverse scattering problem as an inverse source problem in which the unknown contrast source (the product of the total electric field and the conductivity contrast) in the object domain is reconstructed by minimizing the object and data error using a conjugate‐gradient step, after which the conductivity contrast is updated by minimizing only the error in the object. This method has been tested on a number of numerical examples using the synthetic ‘measured’ data with and without noise. Numerical tests indicate that the inversion method yields a reasonably good reconstruction result, and is fairly insensitive to added random noise.
2D multiscale non‐linear velocity inversion
Authors: Jin Side , Beydoun Wafik
Published: March 2003

An efficient and robust non‐linear inversion method for velocity optimization combining a global random search followed by a simplex technique is presented. The background velocity field is estimated at different spatial scales by analysing image gathers after iterative prestack depth migrations. First, the global random search is used to determine the main features/trends of the velocity model (large‐scale component). Then, the simplex technique improves the resolution of the velocity field by estimating smaller‐scale features. A measure of the quality of the velocity model (objective function) is based on flattening offset events in depth‐migrated image gathers. To help constrain the solution, the algorithm can incorporate a priori information about the model and a smoothness condition. This 2D velocity estimation offers the benefit of being semi‐automatic (requiring minimal human intervention) as well as providing a global and objective solution (which is a useful approach to an interpretation‐derived velocity‐estimation technique). The method is applied to a real data set where AVO analysis is carried out after prestack depth migration, as structural effects are non‐negligible. It is demonstrated that the method can successfully estimate a laterally inhomogeneous velocity model at a computational cost modest compared with an interpretation‐based iterative prestack depth velocity‐analysis technique.
A new concept in Euler deconvolution of isolated gravity anomalies
Authors: Roy  , Agarwal  , Shaw
Published: March 2003

Euler's homogeneity equation has been used to develop a new technique to interpret the gravity anomalies over some simple geometrical sources, namely a finite horizontal line/vertical line, a finite vertical ribbon, a semicircular dome/basin and an isosceles triangle approximating an anticline/syncline. A linear over‐determined system of equations has been solved to compute the depth, the horizontal location and the structural index, all treated as free parameters. The concept of a variable structural index provides better depth estimates and helps to identify the source geometry. Nomograms have been prepared to compute an additional model parameter, namely the horizontal/vertical extent of a line, the vertical extent of a ribbon and the radius of a dome/basin. The efficacy of the proposed method has been evaluated using two real field examples.
Automatic cross‐well tomography by semblance and differential semblance optimization: theory and gradient computation
Authors: Plessix R.‐E. , Mulder W.A. , Kroode A.P.E. ten
Published: March 2003

A technique for automatic cross‐well tomography based on semblance and differential semblance optimization is presented. Given a background velocity, the recorded seismic data traces are back‐propagated towards the source, i.e. shifted towards time zero using the modelled traveltime between the source and the receiver and corrected for the geometrical spreading. Therefore each back‐propagated trace should be a pulse, close to time zero. The mismatches between the back‐propagated traces indicate an error in the velocity model. This error can be measured by stacking the back‐propagated traces (semblance optimization) or by computing the norm of the difference between adjacent traces (differential semblance optimization).

It is known from surface seismic reflection tomography that both the semblance and differential semblance functional have good convexity properties, although the differential semblance functional is believed to have a larger basin of attraction (region of convergence) around the true velocity model. In the case of the cross‐well transmission tomography described in this paper, similar properties are found for these functionals.

The implementation of this automatic method for cross‐well tomography is based on the high‐frequency approximation to wave propagation. The wavefronts are constructed using a ray‐tracing algorithm. The gradient of the cost function is computed by the adjoint‐state technique, which has the same complexity as the computation of the functional. This provides an efficient algorithm to invert cross‐well data. The method is applied to a synthetic data set to demonstrate its efficacy.
Detection of potential fields source boundaries by enhanced horizontal derivative method
Authors: Fedi M. , Florio G.
Published: March 2003

A high‐resolution method to image the horizontal boundaries of gravity and magnetic sources is presented (the enhanced horizontal derivative (EHD) method). The EHD is formed by taking the horizontal derivative of a sum of vertical derivatives of increasing order. The location of EHD maxima is used to outline the source boundaries. While for gravity anomalies the method can be applied immediately, magnetic anomalies should be previously reduced to the pole. We found that working on reduced‐to‐the‐pole magnetic anomalies leads to better results than those obtainable by working on magnetic anomalies in dipolar form, even when the magnetization direction parameters are not well estimated. This is confirmed also for other popular methods used to estimate the horizontal location of potential fields source boundaries.

The EHD method is highly flexible, and different conditions of signal‐to‐noise ratios and depths‐to‐source can be treated by an appropriate selection of the terms of the summation. A strategy to perform high‐order vertical derivatives is also suggested. This involves both frequency‐ and space‐domain transformations and gives more stable results than the usual Fourier method.

The high resolution of the EHD method is demonstrated on a number of synthetic gravity and magnetic fields due to isolated as well as to interfering deep‐seated prismatic sources. The resolving power of this method was tested also by comparing the results with those obtained by another high‐resolution method based on the analytic signal. The success of the EHD method in the definition of the source boundary is due to the fact that it conveys efficiently all the different boundary information contained in any single term of the sum.

Application to a magnetic data set of a volcanic area in southern Italy helped to define the probable boundaries of a calderic collapse, marked by a number of magmatic intrusions. Previous interpretations of gravity and magnetic fields suggested a subcircular shape for this caldera, the boundaries of which are imaged with better detail using the EHD method.
The AVA (amplitude‐versus‐angle) signature of small‐scale reflector topography
Authors: Quinn Rosemary K. , Clark Roger A. , Neuberg Jürgen W.
Published: March 2003

Routine amplitude‐versus‐offset or amplitude‐versus‐angle (AVA) analysis is founded on the predicted reflectivity of a planar boundary between isotropic homogeneous half‐spaces, yet many real boundaries of interest to hydrocarbon exploration may violate these assumptions. Here, we evaluate consequences of boundary roughness, i.e. small‐scale, sub‐resolution topography, on the reflecting boundary, to find whether sub‐resolution topography can deceive routine AVA analysis and produce misleading hydrocarbon indicators. We use noise‐free synthetic CMP and stacked‐section seismograms, generated with a Kirchhoff‐integral method, for offsets up to 4000 m. The reflecting boundary was at 2000 m depth below a single overburden layer, and comprised isolated mounds or channels (sinusoidal cross‐section, 5–40 m high and 100–750 m wide), and more complex roughness (simulated with seven 1.5–2 km long bathymetric profiles across modern‐day river‐beds, with dune and bar features up to approximately 20 m or 20 ms TWT vertical relief, and 10–100 m or more lateral extent). Flat‐boundary responses were taken as the ‘reference’ against which to compare waveforms and amplitudes through semblance analysis, AVA intercept A and slope B cross‐plots, and inferred Poisson's ratios. Physical properties of the media were based on shales and brine‐ or oil‐sands from an offshore UK oilfield.

For the CMP centred on the topographic feature, isolated mounds and channels produced correlated excursions of A and B from the flat‐boundary response (by approximately 35–200%), simulating the familiar ‘background trend’ but sometimes oblique to it. Inferred Poisson's ratios were around 0.3, but for some channels often fell as low as 0.2, potentially interpretable as gas sand. For complex boundary topographies on a shale/brine‐sand model, AVA parameters were extracted for 29 CMPs, 100 m apart along each of seven profiles. On a cross‐plot, they spanned the flat‐boundary response on a linear trend B = (0.01 ± 0.02) – (1.72 ± 0.09)A, similar to reported real data and a realistic ‘mudrock trend’ but with outliers both above and below it that could be interpreted as ‘real’ weak anomalies. Poisson's ratios were 0.30 ± 0.01, between the expected values for brine‐ and oil‐sand. This suggests that boundary roughness may contribute to observed trends on cross‐plots and possibly small, but potentially laterally extensive, false AVA anomalies may also be induced.
Implementing the fast marching eikonal solver: spherical versus Cartesian coordinates
Authors: Alkhalifah Tariq , Fomel Sergey
Published: March 2003

Spherical coordinates are a natural orthogonal system for describing wavefronts emanating from a point source. A regular grid distribution in the Cartesian‐coordinate system tends to undersample the wavefront description near the source (at the highest wavefront curvature) and oversample it away from the source. Spherical coordinates, in general, provide a more balanced grid distribution for characterizing point‐source wavefronts. Our numerical implementation confirms that the recently introduced fast marching algorithm is both a highly efficient and an unconditionally stable eikonal solver. However, its first‐order approximation of traveltime derivatives can induce relatively large traveltime errors for waves propagating in a diagonal direction with respect to the coordinate system. Examples, including the IFP Marmousi and the SEG/EAGE 3D salt‐dome models, show that a spherical‐coordinate implementation of the method results in far fewer errors in traveltime calculation than the conventional Cartesian‐coordinate implementation, and with practically no loss in computational advantages.
Using refracted shear waves for velocity estimation
Authors: Pautet L. , Kuperman W.A. , Dorman L.
Published: March 2003

The most difficult part of multicomponent processing is the estimation of the shear‐wave velocity map for migration. We used refracted shear waves and a simple iterative method called wavefield continuation (WFC) to evaluate the shallow shear‐wave velocity profile on a real data example. The WFC was developed in 1981 by Clayton and McMechan to determine compressional‐wave velocity profiles from refracted compressional waves. The application to refracted shear waves is straightforward. The real data example shows that shear structure can be easily determined independently of the compressional structure.
Finding the strike direction of fractures using GPR
Authors: Seol Soon Jee , Kim Jung‐Ho , Song Yoonho , Chung Seung‐Hwan
Published: March 2003

GPR reflection energy varies with antenna orientation relative to the strike and dip of the reflector. This directional dependence of GPR responses was investigated through numerical experiments and was used to estimate the azimuth of fractures and joints. Three antenna configurations were considered in this study: perpendicular‐broadside (YY mode), parallel‐broadside (XX mode) and cross‐polarization (YX mode). The reflection energy in the cross‐polarization mode shows a shape characteristic similar to the strike, regardless of the dip angle. Those in the other two modes show quite different amplitudes from the strike, depending on the dip angle. We have developed a strike‐direction‐finding scheme using data obtained from the three different modes for the same survey line. The azimuth angle of each reflector was displayed in colour on the GPR profile. This scheme was applied to a field survey at a granite quarry in southern Korea. The GPR profiles showed different images of the reflectors depending on the antenna configuration. The estimated azimuths of reflectors obtained using our scheme matched fairly well with those of known fractures and joints.
The seismic transmission volume
Authors: Hagedoorn J.G. , Diephuis G.
Published: March 2003

Parallels are drawn between phenomena observed in optics and typical characteristics in exploration seismology. Considerations are also made in the context of major physical theories throughout the centuries. It is concluded that the one key similarity between optics and seismics is the transmission volume, which has ‘fuzzy’ characteristics. Distribution of energy in this volume determines the achievable resolution and might give an insight into spatial inhomogeneities in the subsurface.
J.H. Hagedoorn – inventing the Hapa: A review of a geophysicist's ‘other’ work and how it inspired others
Authors: Schmidt Theodor
Published: March 2003

This paper describes J.G. Hagedoorn's work on ‘ultimate sailing’– the combination of a manned kite and a water kite called a Hapa, constituting a minimal sailing system – and the way others have taken up his challenge to sail while suspended from a kite. Hagedoorn's goal has not been entirely achieved, but ‘near’ and partial solutions have been reached. Kite‐Hapa‐sailing continues to pose a ‘Holy Grail’ type challenge to many kite‐sailors.
Detection and analysis of LNAPL using the instantaneous amplitude and frequency of ground‐penetrating radar data
Authors: Orlando Luciana
Published: March 2003

This paper reports the results of using the ground‐penetrating radar (GPR) method to detect light non‐aqueous phase liquids (LNAPL) floating on the water table in an area where the thickness of LNAPL present ranges from a few centimetres to several decimetres. To understand the GPR response in this context, GPR theoretical models are calculated using information from the literature and hydrogeological field data. The study revealed that in the case of LNAPL floating on the water table in a static condition, there is an increase in the reflection amplitude from the water table due to the decrease in the capillary fringe. Nevertheless the amplitude of reflection from the water table can discriminate the contaminated from the non‐contaminated zone. Apart from an analysis of the real traces, the analysis of some attributes of the complex trace, instantaneous amplitude, phase and frequency, are also good tools to detect hydrocarbons floating on the water table. Such attributes, depending on both the signal frequency and the hydrocarbon thickness, can also give information about the thickness of the hydrocarbon layer. It is concluded that analysing the lateral variations in signal amplitude of the real trace and in the amplitude, phase and instantaneous frequency of the complex signal permits the delimiting of the area polluted by the hydrocarbon.
Rough seas and time‐lapse seismic
Authors: Laws Robert , Kragh Ed
Published: March 2003

Time‐lapse seismic surveying has become an accepted tool for reservoir monitoring applications, thus placing a high premium on data repeatability. One factor affecting data repeatability is the influence of the rough sea‐surface on the ghost reflection and the resulting seismic wavelets of the sources and receivers. During data analysis, the sea‐surface is normally assumed to be stationary and, indeed, to be flat. The non‐flatness of the sea‐surface introduces amplitude and phase perturbations to the source and receiver responses and these can affect the time‐lapse image.

We simulated the influence of rough sea‐surfaces on seismic data acquisition. For a typical seismic line with a 48‐fold stack, a 2‐m significant‐wave‐height sea introduces RMS errors of about 5–10% into the stacked data. This level of error is probably not important for structural imaging but could be significant for time‐lapse surveying when the expected difference anomaly is small. The errors are distributed differently for sources and receivers because of the different ways they are towed. Furthermore, the source wavelet is determined by the sea shape at the moment the shot is fired, whereas the receiver wavelet is time‐varying because the sea moves significantly during the seismic record.
Committee neural networks for porosity and permeability prediction from well logs
Authors: Bhatt Alpana , Helle Hans B.
Published: March 2003

Neural computing has moved beyond simple demonstration to more significant applications. Encouraged by recent developments in artificial neural network (ANN) modelling techniques, we have developed committee machine (CM) networks for converting well logs to porosity and permeability, and have applied the networks to real well data from the North Sea.

Simple three‐layer back‐propagation ANNs constitute the blocks of a modular system where the porosity ANN uses sonic, density and resistivity logs for input. The permeability ANN is slightly more complex, with four inputs (density, gamma ray, neutron porosity and sonic). The optimum size of the hidden layer, the number of training data required, and alternative training techniques have been investigated using synthetic logs. For both networks an optimal number of neurons in the hidden layer is in the range 8–10. With a lower number of hidden units the network fails to represent the problem, and for higher complexity overfitting becomes a problem when data are noisy. A sufficient number of training samples for the porosity ANN is around 150, while the permeability ANN requires twice as many in order to keep network errors well below the errors in core data. For the porosity ANN the overtraining strategy is the suitable technique for bias reduction and an unconstrained optimal linear combination (OLC) is the best method of combining the CM output. For permeability, on the other hand, the combination of overtraining and OLC does not work. Error reduction by validation, simple averaging combined with range‐splitting provides the required accuracy. The accuracy of the resulting CM is restricted only by the accuracy of the real data. The ANN approach is shown to be superior to multiple linear regression techniques even with minor non‐linearity in the background model.
Optimum pilot sweep
Authors: Tyapkin Yuriy K. , Robinson Enders A.
Published: March 2003

The successful application of high‐resolution seismic methods requires evaluating each element in the seismic system and ensuring that each part of the system contributes optimally to the success of the method. Unfortunately, unlike data processing, seismic signal generation is not carefully optimized. The purpose of our study was to optimize the source signal in order to better coordinate field operations with subsequent data processing to achieve their common objective. We developed an iterative method for a rational frequency distribution of the energy of a seismic source. The method allows the optimum amplitude spectrum of a source signal to be calculated, thus providing the best data quality at the end of the processing. We assume that the source signal is affected by a total transfer function, by the reflectivity function of a target interval, and by ambient noise, whose characteristics, if not known, can be estimated or measured in practice. The transfer function includes data processing other than the correlation stage and the final trace‐optimizing filter. The variance of a reflectivity estimate is considered to be a measure of the data quality and improvement of the characteristic corresponds to a decrease in the variance. For this reason, a constrained Wiener deconvolution filter is used as the final trace‐optimizing filter. It not only minimizes the variance of a reflectivity estimate but also ensures a specific signal‐to‐noise ratio. The method is made feasible by following the Vibroseis technique, primarily because of the versatility of the technique in controlling the signal spectrum. With the optimum amplitude spectrum obtained, the corresponding optimum pilot sweep can be readily calculated. Examples using synthetic data are presented to illustrate the method.
The effects of increasing CO2 and temperature on oak leaf palatability and the implications for herbivorous insects
Authors: Dury S. J. , Good J. E. G. , Perrins C. M. , Buse A. , Kaye T.
Published: March 2003

Rising levels of atmospheric CO2 are expected to perturb forest ecosystems, although the extent to which specific ecological interactions will be modified is unclear. This research evaluates the effects of elevated CO2 and temperature, alone and in combination, on the leaf nutritional quality of Pendunculate oak (Quercus robur L.), and the implications for herbiverous insect defoliators are discussed. A 3 °C temperature rise reduced leaf nutritional quality, by reducing foliar nitrogen concentration and increasing condensed tannin content. Doubling atmospheric CO2 temporarily increased total phenolics, but also reduced leaf toughness. The nutritional quality of the second leaf flush (lammas growth) was considerably reduced at elevated CO2. It is concluded that larval development of spring‐feeding defoliators and hence adult fecundity may be adversely affected by increased temperatures.
Net primary and ecosystem production and carbon stocks of terrestrial ecosystems and their responses to climate change
Authors: Cao Mingkui , Woodward F. IaN.
Published: March 2003

Evaluating the role of terrestrial ecosystems in the global carbon cycle requires a detailed understanding of carbon exchange between vegetation, soil, and the atmosphere. Global climatic change may modify the net carbon balance of terrestrial ecosystems, causing feedbacks on atmospheric CO2 and climate. We describe a model for investigating terrestrial carbon exchange and its response to climatic variation based on the processes of plant photosynthesis, carbon allocation, litter production, and soil organic carbon decomposition. The model is used to produce geographical patterns of net primary production (NPP), carbon stocks in vegetation and soils, and the seasonal variations in net ecosystem production (NEP) under both contemporary and future climates. For contemporary climate, the estimated global NPP is 57.0 Gt C y–1, carbon stocks in vegetation and soils are 640 Gt C and 1358 Gt C, respectively, and NEP varies from –0.5 Gt C in October to 1.6 Gt C in July. For a doubled atmospheric CO2 concentration and the corresponding climate, we predict that global NPP will rise to 69.6 Gt C y–1, carbon stocks in vegetation and soils will increase by, respectively, 133 Gt C and 160 Gt C, and the seasonal amplitude of NEP will increase by 76%. A doubling of atmospheric CO2 without climate change may enhance NPP by 25% and result in a substantial increase in carbon stocks in vegetation and soils. Climate change without CO2 elevation will reduce the global NPP and soil carbon stocks, but leads to an increase in vegetation carbon because of a forest extension and NPP enhancement in the north. By combining the effects of CO2 doubling, climate change, and the consequent redistribution of vegetation, we predict a strong enhancement in NPP and carbon stocks of terrestrial ecosystems. This study simulates the possible variation in the carbon exchange at equilibrium state. We anticipate to investigate the dynamic responses in the carbon exchange to atmospheric CO2 elevation and climate change in the past and future.