bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunogenicity of recombinant hepatitis B vaccine (rHBV) in recipients of unrelated or related allogeneic hematopoietic cell (HC) transplants
Authors: Jaffe Dana , Papadopoulos Esperanza B. , Young James W. , O'Reilly Richard J. , Prockop Susan , Kernan Nancy A. , Jakubowski Ann , Boulad Farid , Perales Miguel-Angel , Castro-Malaspina Hugo , Small Trudy N.
Published: June 2006

Current European and US guidelines for recombinant hepatitis B vaccine (rHBV) after hematopoietic-cell transplantation (HCT) vary. The European Group for Blood and Marrow Transplantation (EBMT) recommends rHBV starting 6 to 12 months after HCT. Immunization is optional in the Centers for Disease Control and Prevention (CDC) guidelines. Nevertheless, rHBV is required for re-entry to school and certain workplaces. To determine the immunogenicity of rHBV following HCT, the prevaccine and postvaccine titers of 292 allogeneic transplant recipients who were immunized with rHBV were analyzed. Immunization was initiated in patients off immunosuppression who achieved specific minimal milestones of immune competence. Overall, 64% of patients seroconverted. In multivariate analyses, response was adversely affected by age older than 18 years (P < .01) and history of prior chronic graft-versus-host disease (GVHD; P < .001) but not by donor type or by use of T-cell depletion, adoptive immunotherapy, or rituximab. By comparison, 89% of rHBV nonresponders mounted a 3-fold or greater rise in polio titers following 3 doses of inactivated poliovirus. These data demonstrate that the rate of seroconversion following rHBV is lower in allogeneic HC transplant recipients compared with age-matched healthy controls. The data emphasize the need to document prevaccine and postvaccine titers to ensure response and suggest that immunization guidelines based on time interval from HCT, irrespective of immune competence, may not ensure adequate protection against certain vaccine-preventable diseases.
MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics
Authors: Spasić Irena , Dunn Warwick B , Velarde Giles , Tseng Andy , Jenkins Helen , Hardy Nigel , Oliver Stephen G , Kell Douglas B
Published: June 2006

Background

The genome sequencing projects have shown our limited knowledge regarding gene function, e.g. S. cerevisiae has 5–6,000 genes of which nearly 1,000 have an uncertain function. Their gross influence on the behaviour of the cell can be observed using large-scale metabolomic studies. The metabolomic data produced need to be structured and annotated in a machine-usable form to facilitate the exploration of the hidden links between the genes and their functions.

Description

MeMo is a formal model for representing metabolomic data and the associated metadata. Two predominant platforms (SQL and XML) are used to encode the model. MeMo has been implemented as a relational database using a hybrid approach combining the advantages of the two technologies. It represents a practical solution for handling the sheer volume and complexity of the metabolomic data effectively and efficiently. The MeMo model and the associated software are available at http://dbkgroup.org/memo/.

Conclusion

The maturity of relational database technology is used to support efficient data processing. The scalability and self-descriptiveness of XML are used to simplify the relational schema and facilitate the extensibility of the model necessitated by the creation of new experimental techniques. Special consideration is given to data integration issues as part of the systems biology agenda. MeMo has been physically integrated and cross-linked to related metabolomic and genomic databases. Semantic integration with other relevant databases has been supported through ontological annotation. Compatibility with other data formats is supported by automatic conversion.
Automated in-silico detection of cell populations in flow cytometry readouts and its application to leukemia disease monitoring
Authors: Toedling Joern , Rhein Peter , Ratei Richard , Karawajew Leonid , Spang Rainer
Published: June 2006

Background

Identification of minor cell populations, e.g. leukemic blasts within blood samples, has become increasingly important in therapeutic disease monitoring. Modern flow cytometers enable researchers to reliably measure six and more variables, describing cellular size, granularity and expression of cell-surface and intracellular proteins, for thousands of cells per second. Currently, analysis of cytometry readouts relies on visual inspection and manual gating of one- or two-dimensional projections of the data. This procedure, however, is labor-intensive and misses potential characteristic patterns in higher dimensions.

Results

Leukemic samples from patients with acute lymphoblastic leukemia at initial diagnosis and during induction therapy have been investigated by 4-color flow cytometry. We have utilized multivariate classification techniques, Support Vector Machines (SVM), to automate leukemic cell detection in cytometry. Classifiers were built on conventionally diagnosed training data. We assessed the detection accuracy on independent test data and analyzed marker expression of incongruently classified cells. SVM classification can recover manually gated leukemic cells with 99.78% sensitivity and 98.87% specificity.

Conclusion

Multivariate classification techniques allow for automating cell population detection in cytometry readouts for diagnostic purposes. They potentially reduce time, costs and arbitrariness associated with these procedures. Due to their multivariate classification rules, they also allow for the reliable detection of small cell populations.
Quantify single nucleotide polymorphism (SNP) ratio in pooled DNA based on normalized fluorescence real-time PCR
Authors: Yu Airong , Geng Haifeng , Zhou Xuerui
Published: June 2006

Background

Conventional real-time PCR to quantify the allele ratio in pooled DNA mainly depends on PCR amplification efficiency determination and Ct value, which is defined as the PCR cycle number at which the fluorescence emission exceeds the fixed threshold. Because of the nature of exponential calculation, slight errors are multiplied and the variations of the results seem too large. We have developed a new PCR data point analysis strategy for allele ratio quantification based on normalized fluorescence ratio.

Results

In our method, initial reaction background fluorescence was determined based upon fitting of raw fluorescence data to four-parametric sigmoid function. After that, each fluorescence data point was first subtracted by respective background fluorescence and then each subtracted fluorescence data point was divided by the specific background fluorescence to get normalized fluorescence. By relating the normalized fluorescence ratio to the premixed known allele ratio of two alleles in standard samples, standard linear regression equation was generated, from which unknown specimens allele ratios were extrapolated using the measured normalized fluorescence ratio. In this article, we have compared the results of the proposed method with those of baseline subtracted fluorescence ratio method and conventional Ct method.

Conclusion

Results demonstrated that the proposed method could improve the reliability, precision, and repeatability for quantifying allele ratios. At the same time, it has the potential of fully automatic allelic ratio quantification.
Genome-wide transcriptional analysis of temperature shift in L. interrogans serovar lai strain 56601
Authors: Qin Jin-Hong , Sheng Yue-Ying , Zhang Zhi-Ming , Shi Yao-Zhou , He Ping , Hu Bao-Yu , Yang Yang , Liu Shi-Gui , Zhao Guo-Ping , Guo Xiao-Kui
Published: June 2006

Background

Leptospira interrogans is an important mammalian pathogen. Transmission from an environmental source requires adaptation to a range of new environmental conditions in the organs and tissues of the infected host. Several studies have shown that a shift in culture temperature from 28°C to 37°C, similar to that encountered during infection of a host from an environmental source, is associated with differential synthesis of several proteins of the outer membrane, periplasm and cytoplasm. The whole genome of the Leptospira interrogans serogroup Icterohaemorrhagiae serovar lai type strain #56601 was sequenced in 2003 and microarrays were constructed to compare differential transcription of the whole genome at 37°C and 28°C.

Results

DNA microarray analyses were used to investigate the influence of temperature on global gene expression in L. interrogans grown to mid-exponential phase at 28°C and 37°C. Expression of 106 genes differed significantly at the two temperatures. The differentially expressed genes belonged to nine functional categories: Cell wall/membrane biogenesis genes, hemolysin genes, heat shock proteins genes, intracellular trafficking and secretion genes, two-component system and transcriptional regulator genes, information storage and processing genes, chemotaxis and flagellar genes, metabolism genes and genes with no known homologue. Real-time reverse transcription-PCR assays confirmed the microarray data.

Conclusion

Microarray analyses demonstrated that L. interrogans responds globally to temperature alteration. The data delineate the spectrum of temperature-regulated gene expression in an important human pathogen and provide many new insights into its pathogenesis.
Soluble egg antigen of Schistosoma Haematobiuminduces HCV replication in PBMC from patients with chronic HCV infection
Authors: El-Awady Mostafa K , Youssef Samar S , Omran Moataza H , Tabll Ashraf A , El Garf Wael T , Salem Ahmed M
Published: June 2006

Background

This study was conducted to examine, in vitro , the effect of soluble egg antigen (SEA) of
S. haematobium
on intracellular HCV RNA load in peripheral mononuclear cells (PBMC) as well as on cell proliferation in patients with chronic HCV infection.

Methods

PBMC from 26 patients with chronic HCV infection were cultured for 72 hours in presence and absence of 50 μg SEA/ml medium. Intracellular HCV RNA quantification of plus and minus strands was assessed before and after stimulation. PBMC from five healthy subjects were cultured for 7 days, flow cytometric analysis of DNA content was used to assess the mitogenic effect of SEA on PBMC proliferation compared to phytoheamaglutinine (PHA).

Results

Quantification of the intracellular viral load showed increased copy number/cell of both or either viral strands after induction with SEA in 18 of 26 patients (69.2%) thus indicating stimulation of viral replication. Flow cytometric analysis showed that mean ± S.D. of percent values of cell proliferation was induced from 3.2 ± 1.5% in un-stimulated cells to 16.7 ± 2.5 % and 16.84 ± 1.7 % in cells stimulated with PHA and SEA respectively.

Conclusion

the present study supports earlier reports on SEA proliferative activity on PBMC and provides a strong evidence that the higher morbidity observed in patients co-infected with schistosomiasis and HCV is related, at least in part, to direct stimulation of viral replication by SEA.
Is the NEI-VFQ-25 a useful tool in identifying visual impairment in an elderly population?
Authors: Owen Christopher G , Rudnicka Alicja R , Smeeth Liam , Evans Jennifer R , Wormald Richard PL , Fletcher Astrid E
Published: June 2006

Background

The use of self-report questionnaires to substitute for visual acuity measurement has been limited. We examined the association between visual impairment and self reported visual function in a population sample of older people in the UK.

Methods

Cross sectional study of people aged more than 75 years who initially participated in a trial of health screening. The association between 25-item National Eye Institute Visual Function Questionnaire (NEI-VFQ) scores and visual impairment (defined as an acuity of less than 6/18 in the better eye) was examined using logistic regression.

Results

Visual acuity and NEI-VFQ scores were obtained from 1807 participants (aged 77 to 101 years, 36% male), from 20 general practices throughout the UK. After adjustment for age, gender, practice and NEI-VFQ sub-scale scores, those complaining of poor vision in general were 4.77 times (95% CI 3.03 to 7.53) more likely to be visually impaired compared to those who did not report difficulty. Self-reported limitations with social functioning and dependency on others due to poor vision were also associated with visual impairment (odds ratios, 2.52, 95% CI 1.55 to 4.11; 1.73, 95% CI 1.05 to 2.86 respectively). Those reporting difficulties with near vision and colour vision were more likely to be visually impaired (odds ratios, 2.32, 95% CI 1.30 to 4.15; 2.25, 95% CI 1.35 to 3.73 respectively). Other NEI-VFQ sub-scale scores were unrelated to measures of acuity. Similar but weaker odds ratios were found with reduced visual acuity (defined as less than 6/12 in the better eye). Although differences in NEI-VFQ scores were small, scores were strongly associated with visual acuity, binocular status, and difference in acuity between eyes.

Conclusion

NEI-VFQ questions regarding the quality of general vision, social functioning, visual dependency, near vision and colour vision are strongly and independently associated with an objective measure of visual impairment in an elderly population.
Block modeling and segmentally iterative ray tracing in complex 3D media
Authors: Xu Tao , Xu Guoming , Gao Ergen , Li Yingchun , Jiang Xianyi , Luo Kaiyun
Published: June 2006

We propose using a set of blocks to approximate geologically complex media that cannot be well described by layered models. Interfaces between blocks are triangulated to prevent overlaps or gaps often produced by other techniques, such as B-splines, and to speed up the calculation of intersection points between a ray and block interfaces. We also use a smoothing algorithm to make the normal vector of each triangle continuous at the boundary, so that ray tracing can be performed with stability and accuracy. Based on Fermat’s principle, we perturb an initial raypath between two points, generally obtained by shooting, with a segmentally iterative ray-tracing (SIRT) method. Intersection points on a ray are updated in sequence, instead of simultaneously, because the number of new intersection points may be increased or decreased during the iteration process. To improve convergence speed, we update the intersection points by a first-order explicit formula instead of traditional iterative methods. Only transmitted and reflected waves are considered. Numerical tests demonstrate that the combination of block modeling and segmentally iterative ray tracing is effective in implementing kinematic two-point ray tracing in complex 3D media.
A new formula to compute apparent resistivities from marine magnetometric resistivity data
Authors: Chen Jiuping , Oldenburg Douglas W.
Published: June 2006

Magnetometric resistivity (MMR) is an electromagnetic (EM) exploration method that has been used successfully to investigate electrical-resistivity structures below the sea-floor. Apparent resistivity, derived from the observed azimuthal component of the magnetic field, often is used as an approximation to the resistivity of a layered earth. Two commonly used formulas to compute the apparent resistivity have their own limitations and are invalid for a deep-sea experiment. In this paper, we derive an apparent-resistivity formula based upon the magnetic field resulting from a semi-infinite electrode buried in a 1D layered earth. This new formula can be applied to both shallow and deep marine MMR surveys. In addition, we address the effects that arise from the transmitter-receiver (Tx-Rx) depth difference and the choice of the normalized range (the radial distance between transmitter and receiver, divided by the thickness of seawater) on data interpretation and survey design. The performance of the new formula is shown by processing synthetic and field data.
Waveform inversion using a logarithmic wavefield
Authors: Shin Changsoo , Min Dong-Joo
Published: June 2006

Although waveform inversion has been studied extensively since its beginning [Formula: see text] ago, applications to seismic field data have been limited, and most of those applications have been for global-seismology- or engineering-seismology-scale problems, not for exploration-scale data. As an alternative to classical waveform inversion, we propose the use of a new, objective function constructed by taking the logarithm of wavefields, allowing consideration of three types of objective function, namely, amplitude only, phase only, or both. In our wave form inversion, we estimate the source signature as well as the velocity structure by including functions of amplitudes and phases of the source signature in the objective function. We compute the steepest-descent directions by using a matrix formalism derived from a frequency-domain, finite-element/finite-difference modeling technique. Our numerical algorithms are similar to those of reverse-time migration and waveform inversion based on the adjoint state of the wave equation. In order to demonstrate the practical applicability of our algorithm, we use a synthetic data set from the Marmousi model and seismic data collected from the Korean continental shelf. For noise-free synthetic data, the velocity structure produced by our inversion algorithm is closer to the true velocity structure than that obtained with conventional waveform inversion. When random noise is added, the inverted velocity model is also close to the true Marmousi model, but when frequencies below [Formula: see text] are removed from the data, the velocity structure is not as good as those for the noise-free and noisy data. For field data, we compare the time-domain synthetic seismograms generated for the velocity model inverted by our algorithm with real seismograms and find that the results show that our inversion algorithm reveals short-period features of the subsurface. Although we use wrapped phases in our examples, we still obtain reasonable results. We expect that if we were to use correctly unwrapped phases in the inversion algorithm, we would obtain better results.
CRP-based seismic migration velocity analysis
Authors: Fei Weihong , McMechan George A.
Published: June 2006

A new migration velocity analysis is developed by combining the speed of parsimonious prestack depth migration with velocity adjustments estimated within and across common-reflection-point (CRP) gathers. The proposed approach is much more efficient than conventional tomographic velocity analysis because only the traces that contribute to a series of CRP gathers are depth migrated at each iteration. The local interval-velocity adjustments for each CRP are obtained by maximizing the stack amplitude over the predicted (nonhyperbolic) moveout in each CRP gather; this does not involve retracing rays. At every iteration, the velocity in each pixel is updated by averaging over all the predicted velocity updates. Finally, CRP positions and orientations are updated by parsimonious migration, and rays are retraced to define new CRP gathers for the next iteration; this ensures internal consistency between the updated velocity model and the CRP gather. Because the algorithm has a gridded-model parameterization, no explicit representation or fitting of reflectors is involved. Strong lateral-velocity variations, such as those found at salt flanks, can be handled. Application to synthetic and field data sets show that the proposed algorithm works effectively and efficiently.
Ultrasonic borehole velocity imaging
Authors: Winkler Kenneth W. , D’Angelo Ralph
Published: June 2006

We describe a new technique for making high-resolution velocity images of rocks using refracted ultrasonic waves. The use of refracted waves makes this technique potentially suitable for imaging borehole walls. In the laboratory, we use a single-transmitter, two-receiver, first-arrival method for making velocity measurements, with a spatial resolution on the order of [Formula: see text]. Our acoustic pulses are centered near [Formula: see text]. Scans of a borehole wall reveal dipping thin layers and fractures. When external stress is applied perpendicular to the borehole, stress concentrations appear on our images as axial bands of high and low velocities. Breakouts created by high stress also can be imaged. On a planar sample, a velocity image reveals shale laminations and carbonate stringers. For field applications, this technique offers the potential for imaging in both conductive and nonconductive muds and provides images based on a physical property (velocity) that currently is not used for fine-scale borehole imaging.
Exponential asymptotically bounded velocity model: Part II — Ray tracing
Authors: Ravve Igor , Koren Zvi
Published: June 2006

A ray-tracing procedure is derived for the new exponential asymptotically bounded (EAB) velocity model introduced in Part I of this paper. The model inherits the properties of a medium with linear-velocity variation in depth in the shallow zone and of a medium with constant velocity in the deep zone. Two types of rays departing from the source point on the earth’s surface exist in this model, depending on the takeoff angles. The rays of the first kind are symmetric arcs that return up to the earth’s surface and have a limited maximum depth of propagation. The rays of the second kind propagate down to infinite depth. In the shallow region, they are curved lines, but at large depth they become asymptotically straight. The form of the ray is governed by the takeoff angle at the source point, where a critical angle splits the two kinds of rays. This critical angle depends only on the ratio between the velocity at the source point and the asymptotic velocity of the EAB model. We derive the formulae required to calculate the two kinds of rays and solve the inverse problem of two-point ray tracing. Finally, we construct the 2D- and 3D-isochron surfaces for a finite offset.
Nonhyperbolic moveout analysis in VTI media using rational interpolation
Authors: Douma Huub , Calvert Alexander
Published: June 2006

Anisotropic velocity analysis using qP-waves in transversely isotropic media with a vertical symmetry axis (VTI) usually is done by inferring the anellipticity parameter [Formula: see text] and the normal moveout velocity [Formula: see text] from the nonhyperbolic character of the moveout. Several approximations explicit in these parameters exist with varying degrees of accuracy. Here, we present a rational interpolation approach to nonhyperbolic moveout analysis in the [Formula: see text] domain. This method has no additional computational overhead compared to using expressions explicit in [Formula: see text] and [Formula: see text]. The lack of such overhead stems from the observation that, for fixed [Formula: see text] and zero-offset two-way traveltime [Formula: see text], the moveout curve for different values of [Formula: see text] can be calculated by simple stretching of the offset axis. This observation is based on the assumptions that the traveltimes of qP-waves in transversely isotropic media mainly depend on [Formula: see text] and [Formula: see text], and that the shear-wave velocity along the symmetry axis has a negligibleinfluence on these traveltimes. The accuracy of the rational interpolation method is as good as that of these approximations. The method can be tuned accurately to any offset range of interest by increasing the order of the interpolation. We test the method using both synthetic and field data and compare it with the nonhyperbolic moveout equation of Alkhalifah and Tsvankin (1995) and the shifted hyperbola equation of Fomel (2004). Both data types confirm that for [Formula: see text], our method significantly outperforms the nonhyperbolic moveout equation in terms of combined unbiased parameter estimation with accurate moveout correction. Comparison with the shifted hyperbola equation of Fomel for Greenhorn-shale anisotropy establishes almost identical accuracy of the rational interpolation method and his equation. Even though the proposed method currently deals with homogeneous media only, results from application to synthetic and field data confirm the applicability of the proposed method to horizontally layered VTI media.
Elastic impedance in weakly anisotropic media
Authors: Martins Jorge L.
Published: June 2006

The original formulation for the P-wave elastic impedance (EI) equation ignores seismic anisotropy. Incorporation of anisotropy effects into the EI formula requires a suitable approximation for reflection coefficients. In order to derive an anisotropic EI equation, this paper uses an approximation for PP-wave reflection [Formula: see text] coefficients which holds for weak-contrast interfaces separating weakly anisotropic media of arbitrary symmetry. Inserting the chosen [Formula: see text] coefficient approximation into the original formalism provides an anisotropic EI formula, which is written as a product of two terms: a modified version for the isotropic EI equation and a correction because of weak anisotropy. The latter term shows dependence of the anisotropic EI formula on the so-called weak anisotropy (WA) parameters, on a reference isotropic medium, and on the azimuthal and incident phase angles. Numerical tests show the performance of the EI formula in calculating anisotropic [Formula: see text] coefficients and in constructing azimuthal far-offset EI logs. Since EI allows applying poststack algorithms without modification, an inversion methodology can be designed for investigating anisotropy in sedimentary formations.
Straight-rays redatuming: A fast and robust alternative to wave-equation-based datuming
Authors: Alkhalifah Tariq , Bagaini Claudio
Published: June 2006

Wave-equation-based redatuming is expensive and requires a detailed knowledge of the shallow velocity field. We derive the analytical expression of a new prestack wavefield extrapolation operator, the Topographic Datuming Operator (TDO), which applies redatuming based on straight-rays approximation above and below a chosen datum. This redatuming operator is directly applied to common-source gathers to downward continue the source and the receivers, simultaneously, to the datum level without resorting to common-receiver gathers. As a result, the method is far more efficient and robust than the conventional wave-equation-based redatuming and does not require an accurate depth-domain interval velocity model. In addition, TDO, unlike wave-equation-based redatuming, requires effective velocities above datum, and thus can be applied using attributes valid for static correction methods. Effective velocities beneath the datum permit us to replace the surface integral, which is needed for wave-equation redatuming with a line integral. In the particular case of infinite (in practice, very high with respect to the shallow layers) velocity beneath the datum, the TDO impulse response collapses to a point, and TDO redatuming is equivalent to conventional static correction, which may, therefore, be regarded as a special case of the newly derived operator. The computational cost of applying TDO is slightly larger than static corrections, yet provides higher quality results partially attributable to the ability of TDO to suppress diffractions emanating from anomalies above datum. Since TDO is an operation based on geometrical optics approximation, velocity after TDO is not biased by the vertical shift correction associated with conventional static correction. Application to a synthetic data set demonstrates the features of the method.
Induced-polarization detection and mapping of contaminant plumes
Authors: Sogade John A. , Scira-Scappuzzo Francesca , Vichabian Yervant , Shi Weiqun , Rodi William , Lesmes David P. , Morgan Frank Dale
Published: June 2006

Several laboratory and scaled model investigations suggest that organic contaminants affect the surface electrical properties of exposed soils/rocks and therefore produce measurable induced polarization (IP) signatures. However, there is little field evidence of an IP methodology for contaminant mapping. A 2D time-domain IP method is developed for mapping the FS-12 contaminant plume at the Massachusetts Military Reservation (MMR) located in Cape Cod, Massachusetts. The FS-12 plume consists of approximately [Formula: see text] of fuel that erupted from a broken underground pipeline in the early 1970s. Benzene and ethylene dibromide (EDB) are the primary contaminants at FS-12, with concentrations exceeding the allowed maximum concentration levels (MCL), while other constituents of the plume did not exceed their MCL. Therefore, the contaminants of interest are benzene and EDB, partly because of their health risk and partly because they present the highest concentrations (2400 and [Formula: see text], respectively) among the plume constituents and are therefore more likely to be related to the polarization source. IP data were acquired along a survey line that partially transects the plume extending over contaminated and uncontaminated zones and were inverted to give 2D resistivity and chargeability plots to [Formula: see text] depth and a horizontal extent of [Formula: see text]. By separately inverting IP data derived from time windows located at short and long decay times, a time-domain gross (spectral) chargeability difference is produced. Both the chargeability and gross spectral chargeability difference show good agreement with the known location of the plume from monitoring wells, with the IP chargeability section suggesting contaminant distribution detail that cannot otherwise be inferred from the sparse borehole distribution.
Structural inversion of gravity data using linear programming
Authors: van Zon Tim , Roy-Chowdhury Kabir
Published: June 2006

Structural inversion of gravity data — deriving robust images of the subsurface by delineating lithotype boundaries using density anomalies — is an important goal in a range of exploration settings (e.g., ore bodies, salt flanks). Application of conventional inversion techniques in such cases, using [Formula: see text]-norms and regularization, produces smooth results and is thus suboptimal. We investigate an [Formula: see text]-norm-based approach which yields structural images without the need for explicit regularization. The density distribution of the subsurface is modeled with a uniform grid of cells. The density of each cell is inverted by minimizing the [Formula: see text]-norm of the data misfit using linear programming (LP) while satisfying a priori density constraints. The estimate of the noise level in a given data set is used to qualitatively determine an appropriate parameterization. The 2.5D and 3D synthetic tests adequately reconstruct the structure of the test models. The quality of the inversion depends upon a good prior estimation of the minimum depth of the anomalous body. A comparison of our results with one using truncated singular value decomposition (TSVD) on a noisy synthetic data set favors the LP-based method.

There are two advantages in using LP for structural inversion of gravity data. First, it offers a natural way to incorporate a priori information regarding the model parameters. Second, it produces subsurface images with sharp boundaries (structure).
MMT forward modeling for a layered earth with arbitrary anisotropy
Authors: Yin Changchun
Published: June 2006

The standard model of a layered isotropic earth is a good approximation to geophysical reality in geoelectromagnetic mapping. In regions with distinct dipping stratification, however, it is difficult to model these fine structures because of large storage and time requirements. In this case, we may approximately replace the isotropic conductors with a preferential electrical direction by macro-scale anisotropy. The marine-magnetotelluric (MMT) forward problem is formulated for a layered earth with arbitrary anisotropy. For a given layer beneath the ocean, the two horizontal components of the electric field are projected onto the principal anisotropic directions and continued from layer to layer using continuity conditions.

The formulation is used to derive the impedance tensor and apparent resistivities for a uniform anisotropic half-space, which clearly distinguish the effect of electrical anisotropy on MMT responses. The principal anisotropic orientations are clearly identified in the polar plots, which show the azimuthal variation of the apparent resistivity. The resolvability analysis of a resistive intermediate layer indicates that the depth of exploration for the MMT method depends strongly on the anomaly threshold associated with system sensitivity and environmental noise level but less on the resistivity contrast between the target and surrounding media. For an anisotropic target, to obtain a larger depth of exploration the electric field should be measured in the direction of higher target-host resistivity contrast.

The simulation of reservoir characterization using marine MT shows that the current MMT technique cannot be an effective tool yet for direct offshore reservoir characterization, but it can be a good complementary tool for controlled-source electromagnetic (EM) technologies emerging for offshore hydrocarbon exploration.
Peroxisome Proliferator-Activated Receptor α Deficiency Increases the Risk of Maternal Abortion and Neonatal Mortality in Murine Pregnancy with or without Diabetes Mellitus: Modulation of T Cell Differentiation
Authors: Yessoufou Akadiri , Hichami Aziz , Besnard Philippe , Moutairou Kabirou , Khan Naim A.
Published: June 2006

We assessed the implication of peroxisome proliferator-activated receptor (PPAR) α deficiency in pregnancy outcome and neonatal survival and in the modulation of T cell differentiation in murine diabetic pregnancy and their offspring. Pregnant wild-type (WT) and PPARα-null mice of C57BL/6J genetic background were rendered diabetic by five low doses of streptozotocin. We observed that, in the absence of diabetes, PPARα deficiency resulted in an increase in abortion rate, i.e. 0% in WT mice vs. 20% in PPARα-null mice [odds ratio (OR) = 14.33; P = 0.013]. Under diabetic conditions, the abortion rate was enhanced, i.e. 8.3% in WT mice vs. 50% in PPARα-null mice (OR = 4.28; P = 0.011). In the pups born to diabetic dams, the offspring mortality, due to the absence of PPARα, was enhanced, i.e. 27.7% in WT mice vs. 78.9% in PPARα-null animals (OR = 11.48; P < 0.001). Moreover, we observed that T helper (Th) 1/Th2 balance was shifted to a pregnancy protecting Th2 phenotype in WT diabetic dams and to a noxious Th1 phenotype in PPARα-null mice with diabetic pregnancy. Furthermore, offspring born to diabetic WT dams were hyperinsulinemic and hyperglycemic, and they exhibited up-regulated profile of Th2 cytokines, whereas those born to diabetic PPARα-null dams were hypoinsulinemic and hyperglycemic, and they showed down-regulated profile of Th2 cytokines. However, IFN-γ, a Th1 cytokine, was up-regulated in the offspring of both diabetic WT and PPARα-null dams. Altogether, our results suggest that PPARα deficiency in mice may be implicated in the increase in maternal abortion, neonatal mortality, and T cell differentiation.
Insulin-Like Growth Factor Binding Protein-3 in Extracellular Matrix Stimulates Adhesion of Breast Epithelial Cells and Activation of p44/42 Mitogen-Activated Protein Kinase
Authors: Martin Janet L. , Jambazov Stan
Published: June 2006

IGF-binding protein-3 (IGFBP-3) is a multifunctional protein that regulates the potent mitogenic and antiapoptotic effects of IGF-I and IGF-II and exerts bioactivity independent of modulating IGF receptor activation. Previous studies have shown that in solution, IGFBP-3 binds constituent proteins of the extracellular matrix (ECM) such as fibronectin and collagen and is present in ECM deposited by fibroblasts in vitro; however, binding of IGFBP-3 to matrix has not been characterized, nor has its function in this environment been investigated. In this study, we show that IGFBP-3 binds to ECM deposited by human breast epithelial and cancer cells and neonatal human fibroblasts. IGF-I and heparin blocked binding of IGFBP-3 to matrix when added with the binding protein but were unable to displace IGFBP-3 already bound to the matrix. IGF-I bound to matrix-immobilized IGFBP-3 with approximately 25-fold reduced affinity compared with IGFBP-3 in solution. Mutation of the C-terminal basic domain of IGFBP-3 (228KGRKR→MDGEA) resulted in markedly reduced binding to matrix compared with wild-type IGFBP-3, whereas mutation of the adjacent consensus heparin-binding domain (220KKK→HSR) had relatively little effect. In the presence of matrix-bound IGFBP-3, adhesion of breast epithelial cells was increased by approximately 25%, and activation of the signaling pathway intermediate p44/42 MAPK was enhanced greater than 3-fold. These results indicate a previously unrecognized and potentially important role for IGFBP-3 in the extracellular matrix.
Akt1 Suppresses Radiation-Induced Germ Cell Apoptosis in Vivo
Authors: Rasoulpour Teresa , DiPalma Kathryn , Kolvek Branko , Hixon Mary
Published: June 2006

Radiation exposure is a well-characterized germ cell injury model leading to cell cycle arrest or apoptosis. The serine-threonine kinase, Akt1, has been implicated in inhibiting cell death induced by different stimuli including growth factor withdrawal, cell cycle discordance, DNA damage, and loss of cell adhesion. However, the in vivo relevance of this prosurvival pathway has not been explored in the testis. To evaluate a protective role for Akt1 in the testis in vivo, we examined the incidence of apoptosis in Akt1-deficient mice after radiation-induced germ cell injury. We found that Akt kinase activity increases in the testes of wild-type mice after ionizing radiation, and that loss of Akt1 results in an earlier onset of germ cell apoptosis and enhanced sensitivity of mitotic spermatogonia to ionizing radiation. At both the mRNA and protein level, neither Akt2 nor Akt3 expression were induced in the absence of Akt1. These data demonstrate an important survival function governed by Akt1 and, to a lesser extent, Akt2 in the survival of germ cells after radiation-induced testicular injury. In addition, the results point to a role for Fas ligand in the regulation of this response.
Bone Re/Modeling Is More Dynamic in the Endothelial Nitric Oxide Synthase(−/−) Mouse
Authors: Grassi F. , Fan X. , Rahnert J. , Weitzmann M. N. , Pacifici R. , Nanes M. S. , Rubin J.
Published: June 2006

Nitric oxide is a ubiquitous estrogen-regulated signaling molecule that has been implicated in the regulation of bone maturation and remodeling. To better understand the role that bone-cell-secreted nitric oxide plays in ovariectomy-induced modifications of bone turnover, we examined the expression of endothelial NO synthase (eNOS) in bone cells and bone progenitor cells at regular intervals up to 10 wk after acute estrogen deprivation. Ovariectomy led to an anticipated initial decline in bone cell eNOS production, but surprisingly, 17 d after ovariectomy, eNOS expression by bone and marrow stromal cells dramatically rebounded and was maintained at high levels for at least 10 wk after surgery. We examined the long-term consequences of eNOS in the process of ovariectomy-induced bone loss by prospectively analyzing bone mineral density in wild-type and eNOS(−/−) mice for 10 wk after ovariectomy. Ovariectomized eNOS(−/−) mice were observed to undergo an exaggerated state of estrogen-deficiency-induced bone remodeling compared with wild-type controls, suggesting that eNOS may act to mitigate this process. Furthermore, we found that whereas bone formation in estrogen-replete wild-type mice slowed between 14 and 20 wk of age, eNOS knockout mice continued to accrue basal bone mass at a high rate and showed no sign of entering a remodeling stage. Our data suggest that eNOS may play an important role in limiting ovariectomy-induced bone remodeling as well as regulating the transition from basal modeling to remodeling.
Intraovarian Tumor Necrosis Factor-Related Weak Inducer of Apoptosis/Fibroblast Growth Factor-Inducible-14 Ligand-Receptor System Limits Ovarian Preovulatory Follicles from Excessive Luteinization
Authors: De Ananya , Park Jae-Il , Kawamura Kazuhiro , Chen Ruby , Klein Cynthia , Rauch Rami , Mulders Sabine M. , Sollewijn Gelpke Maarten D. , Hsueh Aaron J. W.
Published: June 2006

In addition to gonadotropins, many ovarian paracrine factors are crucial for optimal follicle rupture, oocyte maturation, and luteinization. Based on DNA microarray analyses, we found that transcripts for the fibroblast growth factor-inducible-14 (Fn14) receptor are increased after LH/human chorionic gonadotropin (hCG) treatment of gonadotropin-primed immature mice or rats. Fn14 is the cognate receptor for TNF-related weak inducer of apoptosis (TWEAK), a TNF superfamily member. TWEAK transcripts also were detected in the ovary; however, their levels were not regulated by gonadotropins. In situ hybridization analyses indicated that the Fn14 receptor is expressed in the granulosa and cumulus cells of preovulatory follicles and, to a lesser extent, in theca cells. In contrast, in situ hybridization analyses revealed that TWEAK is primarily expressed in theca cells. In cultured granulosa cells pretreated with hCG to induce Fn14 receptor expression, treatment with TWEAK suppressed progesterone synthesis without accompanying changes in cAMP production. Furthermore, intrabursal injection of TWEAK suppressed ovarian progesterone content in gonadotropin-primed rats. In contrast, preovulatory follicles cultured in the presence of the Fn14 decoy, a recombinant protein containing the ligand-binding domain of Fn14, led to increases in progesterone production, presumably by antagonizing the actions of endogenous TWEAK. Likewise, ip injection of the Fn14 decoy enhanced serum progesterone levels with accompanying increases in transcript levels for several key steroidogenic enzymes. The present findings demonstrate a suppressive role of the TWEAK/Fn14 signaling system in the ovary. Following gonadotropin induction of ovulation, Fn14 is induced and could protect preovulatory follicles from excessive luteinization.
The Human Growth Hormone Gene Contains a Silencer Embedded within an Alu Repeat in the 3′-Flanking Region
Authors: Trujillo Miguel A. , Sakagashira Michiko , Eberhardt Norman L.
Published: June 2006

Alu family sequences are middle repetitive short interspersed elements (SINEs) dispersed throughout vertebrate genomes that can modulate gene transcription. The human (h) GH locus contains 44 complete and four partial Alu elements. An Sx Alu repeat lies in close proximity to the hGH-1 and hGH-2 genes in the 3′-flanking region. Deletion of the Sx Alu repeat in reporter constructs containing hGH-1 3′-flanking sequences increased reporter activity in transfected pituitary GC cells, suggesting this region contained a repressor element. Analysis of multiple deletion fragments from the 3′-flanking region of the hGH-1 gene revealed a strong orientation- and position-independent silencing activity mapping between nucleotides 2158 and 2572 encompassing the Sx Alu repeat. Refined mapping revealed that the silencer was a complex element comprising four discrete entities, including a core repressor domain (CRD), an antisilencer domain (ASE) that contains elements mediating the orientation-independent silencer activity, and two domains flanking the CRD/ASE that modulate silencer activity in a CRD-dependent manner. The upstream modulator domain is also required for orientation-independent silencer function. EMSA with DNA fragments representing all of the silencer domains yielded a complex pattern of DNA-protein interactions indicating that numerous GC cell nuclear proteins bind specifically to the CRD, ASE, and modulator domains. The silencer is GH promoter dependent and, in turn, its presence decreases the rate of promoter-associated histone acetylation resulting in a significant decrease of RNA polymerase II recruitment to the promoter. The silencer may provide for complex regulatory control of hGH gene expression in pituitary cells.
One-Pot Coupling of Two Alkynes and One Alkene for Formation of Cyclohexene Derivatives via Zirconacyclopentadienes
Authors: Zhou Lishan , Xi Chanjuan , Wang Hui , Kong Fanzhi , Takahashi Tamotsu
Published: June 2006

One-pot synthesis of cyclohexene derivatives from two alkynes and one maleic acid derivative could be achieved. Two alkynes were treated with [Cp2ZrBu2] to give zirconacyclopentadienes. Addition of 2 equiv of H2O followed by the reaction with maleic anhydride at 100 °C in toluene for 12 h afforded the cyclohexene derivatives in high yields. The corresponding titanacyclopentadiene did not give the desired product under the same conditions. In the case of Hf, only 8% of the product was obtained. Dienylzirconocene, which could be prepared by the addition of one equiv of EtOH or t-BuOH to the zirconacyclopentadiene, also reacted with maleic anhydride to give the cyclohexene derivative in 82 and 62% yield, respectively.
Effects of Calcitonin and Parathyroid Hormone on Calcification of Primary Cultures of Chicken Growth Plate Chondrocytes
Authors: Ishikawa Yoshinori , Wu Licia N. Y. , Genge Brian R. , Mwale Fackson , Dr. Wuthier Roy E.
Published: June 2006

Few studies have been directed toward elucidating the action of calcitonin (CT) and parathyroid hormone (PTH) on growth plate chondrocytes, cells directly involved in longitudinal bone growth and provisional calcification. In this study, primary cultures of avian growth plate chondrocytes that calcify without the supplement of β-glycerophosphate were used to investigate the effects of synthetic human CT and 1–34 bovine PTH on (1) cell division and growth; (2) the deposition of Ca2+ and inorganic phosphate (Pi); (3) the activity of alkaline phosphatase (AP), an enzyme long associated with the mineralization process; (4) the levels of proteoglycans; and (5) the synthesis of collagens. Added continually to preconfluent cultures from day 6 until harvest, CT (1–30 nM) and PTH (0.1–1.0 nM) increased mineral deposition; the maximal increase was seen between days 18–21 at 10 nM CT (175–260%) and 0.5 nM PTH (∼170–280%), both p < 0.001. CT had no significant effect on cellular protein, or AP-specific activity, whereas PTH increased cellular protein, DNA, proteoglycan, and collagen content of the cultures in a dosage-dependent manner. AP activity and levels of Type II and X collagens and fibronectin in the culture medium showed a biphasic response to PTH; maximal increases were seen at 0.5 nM between days 15–18. Longer exposure (days 21–27) to PTH at higher levels (5–10 nM) caused a marked decrease in AP activity but a lesser decrease in the collagens. These results indicate that CT and PTH can act directly on chondrocytes to stimulate mineralization, but that PTH specifically stimulated cell division and synthesis of cellular and extracellular proteins by growth plate chondrocytes. The implications of these findings with regard to Ca2+ homeostasis and bone formation are discussed.