bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a novel transcription factor, ELYS, expressed predominantly in mouse foetal haematopoietic tissues
Authors: Kimura Naoki , Takizawa Makiko , Okita Keisuke , Natori Osamu , Igarashi Katsuhide , Ueno Masaya , Nakashima Kin‐ichi , Nobuhisa Ikuo , Taga Tetsuya 
Published: March 2003

AbstractBackground:  The precise mechanism governing the generation of haematopoietic stem cells still remains to be understood, partly because the molecules required for early haematopoiesis have not fully been identified.Results:  We have identified a novel gene expressed in embryonic haematopoietic tissues, designated ELYS (for embryonic large molecule derived from yolk sac), which has no significant homology with any other known molecules. Based on the cDNA sequence, mouse ELYS protein is composed of 2243 amino acid residues and contains an AT‐hook DNA‐binding domain, eight nuclear localization signals (NLSs) at the C‐terminal region, three nuclear export signals (NESs) and two WD repeats at the N‐terminal region. ELYS has a potential to shuttle between the cytoplasm and nucleus. When in the nucleus, ELYS is present in the nuclear matrix. Fusions of the yeast GAL4 DNA‐binding domain and various ELYS mutants reveal the presence of transcriptional activation and inhibitory domains. The ELYS gene is predominantly expressed in embryonic haematopoietic tissues, i.e. foetal liver, spleen, and thymus, whereas the expression is down‐regulated in the adult. In the aorta‐gonad‐mesonephros (AGM) region of an 11.5 dpc mouse embryo, ELYS is expressed in the endothelium lining the dorsal aorta. In the adult bone marrow, ELYS is notably expressed in the Lin−/c‐kit+/Sca‐1+ population.Conclusions:  We have reported the isolation and characterization of a novel molecule, ELYS. ELYS seems to be a nuclear transcription factor associated with both early and mature haematopoietic events.
Role of nectin in organization of tight junctions in epithelial cells
Authors: Fukuhara Atsunori , Irie Kenji , Yamada Akio , Katata Tatsuo , Honda Tomoyuki , Shimizu Kazuya , Nakanishi Hiroyuki , Takai Yoshimi 
Published: March 2003

AbstractBackground In polarized epithelial cells, cell‐cell adhesion forms specialized membrane structures comprised of claudin‐based tight junctions (TJs) and of E‐cadherin‐based adherens junctions (AJs). These structures are aligned from the apical to the basal side of the lateral membrane, but the mechanism of this organization remains unknown. Nectin is a Ca2+ independent immunoglobulin‐like cell‐cell adhesion molecule which localizes at AJs. Nectin is associated with E‐cadherin through their respective cytoplasmic tail‐binding proteins, afadin and catenins, and involved in the formation of AJs in cooperation with E‐cadherin. We show here that nectin is also involved in the formation of TJs.Results: During the formation of the junctional complex consisting of AJs and TJs in Madin‐Darby canine kidney (MDCK) cells, claudin and occludin accumulated at the apical sites of the nectin‐based cell‐cell adhesion sites. This accumulation of claudin and occludin was inhibited by inhibitors acting on the trans interaction of nectin. The barrier function of TJs was also impaired by the nectin inhibitors. It has been shown that a phorbol ester promotes the formation of a TJ‐like structure in an E‐cadherin‐independent manner. This phorbol ester‐induced formation of the TJ‐like structure was also inhibited by the nectin inhibitors.Conclusions: These results suggest a role of the nectin‐afadin system in the organization of TJs as well as AJs in epithelial cells.
Zebrafish CRY represses transcription mediated by CLOCK‐BMAL heterodimer without inhibiting its binding to DNA
Authors: Ishikawa Tomoko , Hirayama Jun , Kobayashi Yuri , Todo Takeshi 
Published: March 2003

AbstractBackground CLOCK and BMAL1 proteins, members of the basic helix‐loop‐helix PAS (PER‐ARNT‐SIM) superfamily of transcription factors which bind to the E‐box DNA motif, are required for the high‐level expression of the circadian clock genes period (per) and cryptochrome (cry). CRY inhibits transcriptional activity of the CLOCK‐BMAL1 heterodimer, generating a negative‐feedback loop that is the core element of the circadian oscillator.Results: We show that zebrafish CRY (zCRY1a) neither disrupts the association between zfCLOCK and zfBMAL nor inhibits binding of the zfCLOCK‐zfBMAL heterodimer to an E‐box‐bearing DNA fragment. Instead it binds to the heterodimer to form a stable zCRY1a‐zfCLOCK‐zfBMAL‐E‐box complex. Another zebrafish CRY protein, zCRY4, does not have transcriptional inhibitor activity, whereas zCRY1a has strong activity. zCRY4 does not associate with zfCLOCK and zfBMAL. We also show that the presence of a chemical reductant in the reaction mixture is crucial for efficient binding of the CLOCK‐BMAL heterodimer to E‐box bearing DNA, which is indicative of the reduction/oxidation (redox)‐sensitive character of the heterodimer.Conclusions: Our findings suggest that CRY represses CLOCK‐BMAL‐mediated transcription by interacting directly with the zfCLOCK‐zfBMAL–E‐box complex.
Two conserved structural components, A‐rich bulge and P4 XJ6/7 base‐triples, in activating the group I ribozymes
Authors: Ikawa Yoshiya , Yoshimura Takeshi , Hara Hidemi , Shiraishi Hideaki , Inoue Tan 
Published: March 2003

AbstractBackground: The A‐rich bulge of the group I intron ribozyme, a highly conserved structural element in its P5 peripheral region, plays a significant role in activating the ribozyme. The bulge has been known to interact with the P4 stem forming P4 XJ6/7 base‐triples in the conserved core. The base‐triples by themselves have also been identified as a distinctive element responsible for enhancing the activity of the ribozyme.Results: A weakly active variant of the Tetrahymena ribozyme lacking the P5 extension was dramatically activated by the addition of an A‐rich bulge at the peripheral region, or by replacement of the original P4 XJ6/7 base‐triples in the core structure with more stabilized isosteric ones. Biochemical analyses showed that the two methods of activation affect the ribozyme differently.Conclusions: The long‐range interaction between the A‐rich bulge and P4 or additionally stabilized P4 XJ6/7 base‐triples can contribute dramatically to activation of the Tetrahymena ribozyme. Both improve the kcat value, which represents the rate of the limiting step of the ribozyme reaction when its binding site is saturated with GTP. However, the bulge or the modified base‐triples gave a moderate reduction or considerable increase, respectively, to the Km(GTP) value.
Instability of sensory histidine kinase mRNAs in Escherichia coli
Authors: Aiso Toshiko , Ohki Reiko 
Published: March 2003

AbstractBackground: Regulating mRNA stability is one of the essential mechanisms in gene expression. In order to identify genes from Escherichia coli whole genome whose expression is effectively modulated during the process of mRNA decay, we previously performed differential display‐PCR as the first step. In the screening, it was suggested that two mRNAs from the histidine kinase genes, narX and yojN, in a two‐component signal transduction system, were extremely unstable. In this study we analysed the stability of sensory kinase mRNAs, e.g. arcB, barA, rcsC, narQ, narX and evgS mRNA.Results: The cellular level of the histidine kinase mRNAs was very low and the mRNAs were rapidly degraded in wild‐type cells cultured at 37 °C in LB medium. Additional experiments using RNase E deficient cells indicated that the mRNAs existed abundantly and expressed a prolonged half‐life in the cells. Monocistronic transcripts of the cognate response regulator genes, arcA, rcsB, narP and narL have a half‐life of 1.5–3.4 min.Conclusions: mRNAs of the six histidine kinase genes in E. coli are synthesized efficiently, but rapidly degraded in wild‐type cells.
Comparative analysis of the self‐incompatibility (S‐) locus region of Prunus mume: identification of a pollen‐expressed F‐box gene with allelic diversity
Authors: Entani Tetsuyuki , Iwano Megumi , Shiba Hiroshi , Che Fang‐Sik , Isogai Akira , Takayama Seiji 
Published: March 2003

AbstractBackground: Self‐incompatibility (SI) in the Solanaceae, Rosaceae and Scrophulariaceae is gametophytically controlled by a single polymorphic locus, termed the S‐locus. To date, the only known S‐locus product is a polymorphic ribonuclease, termed S‐RNase, which is secreted by stylar tissue and thought to act as a cytotoxin that degrades the RNA of incompatible pollen tubes. However, understanding how S‐RNase causes S‐haplotype specific inhibition of pollen tubes has been hampered by the lack of a cloned pollen S‐determinant gene.Results: To identify the pollen S‐determinant gene, we investigated the genomic structure of the S‐locus region of the S1‐ and S7‐haplotypes of Prunus mume (Japanese apricot), and identified 13 genes around the S‐RNase gene. Among them, only one F‐box gene, termed SLF (S‐locus F‐box), fulfilled the conditions for a pollen S‐determinant gene: (i) together with the S‐RNase gene, it is located within the highly divergent genomic region of the S‐locus, (ii) it exhibits S‐haplotype specific diversity among three analysed S‐haplotypes, and (iii) it is specifically expressed in pollen, but not in the styles or leaves.Conclusion: The results indicate that SLF is a prime candidate for the pollen S‐determinant gene of SI.
A Bayesian criterion for simplicity in inverse problem parametrization
Authors: Malinverno Alberto 
Published: March 2003

Summary
To solve a geophysical inverse problem in practice means using noisy measurements to estimate a finite number of parameters. These parameters in turn describe a continuous spatial distribution of physical properties. (For example, the continuous solution may be expressed as the linear combination of a number of orthogonal functions; the parameters are the coefficients multiplying each of these functions.) As the solution is non-unique, estimating the parameters of interest also requires a measure of their uncertainty for the given data. In a Bayesian approach, this uncertainty is quantified by the posterior probability density function (pdf) of the parameters. This ‘parameter estimation’, however, can only be carried out for a given way of parametrizing the problem; choosing a parametrization is the ‘model selection’ problem.
The purpose of this paper is to illustrate a Bayesian model selection criterion that ranks different parametrizations from their posterior probability for the given set of geophysical measurements. This posterior probability is computed using Bayes’ rule and is higher for parametrizations that better fit the data, which are simple in that they have fewer free parameters, and which result in a posterior pdf that departs the least from what is expected a priori. Bayesian model selection is illustrated for a gravitational edge effect inverse problem, where the variation of density contrast with depth is to be inferred from gravity gradient measurements at the surface. Two parametrizations of the density contrast are examined, where the parameters are the coefficients of an orthogonal function expansion or the values at the nodes of a cubic spline interpolation. Bayesian model selection allows one to decide how many free parameters should be used in either parametrization and which of the two parametrizations is preferred given the data. While the illustration used here is for a simple linear problem, the proposed Bayesian criterion can be extended to the general non-linear case.
Nanoscale haematite–ilmenite lamellae in massive ilmenite rock: an example of ‘lamellar magnetism’ with implications for planetary magnetic anomalies
Authors: McEnroe S. A. , Harrison R. J. , Robinson Peter , Langenhorst Falko 
Published: March 2003

Summary
Massive, nearly ‘pure’, haemo-ilmenite layers from historic ore deposits in Rogaland, Norway contain very few silicates or other oxides and typically produce remanence-dominated magnetic anomalies. These rocks are ideal for evaluating the magnetic properties of fine exsolution intergrowths and the larger titanohaematite lamellae in the host ilmenite grains. A typical bulk composition, Ilm 84, exsolved at high temperature to produce host ilmenite Ilm 94 and micron-sized haematite lamellae Ilm 23 as measured by electron microprobe (EMP). Subsequent undercooling of the ilmenite and the micron-scale haematite lamellae led to metastable nucleation of nanoscale lamellae down to unit-cell scale, leaving depleted hosts between lamellae with compositions of Ilm 98 and Ilm 15–13 as measured by TEM–EDX. Samples have high coercivities, and average NRM values of 25 A m−1, which typically show ∼2 per cent saturation in the NRM state. The amount of magnetization in these samples is too high to be solely accounted for by a spin-canted AF moment in the haematite. Based on Monte Carlo simulations of haematite–ilmenite interfaces at the atomic scale and on measured rock-magnetic properties, we predict that the magnetization is carried by a ferrimagnetic substructure produced at the contacts of the very fine-scale titanohaematite and ilmenite exsolution lamellae.
Some unintended features of elastic finite‐difference models
Authors: Wild A.J. , Singh S.C. 
Published: March 2003

While finite‐difference methods have been used extensively for many years to model wave propagation in elastic media, some of the more subtle effects observable in such models are very inadequately documented in the geophysical literature, especially in regard to their practical numerical consequences.In addition to the intended travelling waves, and the undesirable exponential instability revealed by the von Neumann test, typical second‐order‐time finite‐difference equations also support drifting linear solutions, as can be verified, both theoretically and by numerical experiment. The necessity of these solutions, and their relationship to the incompleteness of the set of travelling‐wave eigenfunctions of the finite‐difference operator, can be exposed by a matrix‐based analysis, and exact expressions for them can be obtained by using standard algebraic techniques.A further peculiarity of the finite‐difference formulation is numerical anisotropy, which emerges in a grid of more than one spatial dimension, even when the modelled medium is intended to be isotropic. This anisotropy can be explained and quantified in terms of the exact eigenfunction solutions to the finite‐difference equation, which, it is found, can be obtained in a simple, closed form, for a typical modern 3D staggered scheme.
Magnetotelluric survey for exploration of a volcanic‐rock reservoir in the Yurihara oil and gas field, Japan*
Authors: Mitsuhata Yuji , Matsuo Koichi , Minegishi Masato 
Published: March 2003

The Yurihara oil and gas field is located on the southern edge of Akita Prefecture, northeastern Japan. In this area, drilling, surface geological surveys and many seismic surveys have been used to investigate the geological structure. Wells drilled into the Nishikurosawa Basalt Group (NBG) of Miocene age found oil and gas reservoirs at depths of 1.5–2 km. Oil and gas are now being produced commercially and further exploration is required in the surrounding areas. However, since the neighbouring areas are covered with young volcanic products from the Chokai volcano, and have a rough topography, the subsurface distribution of the NBG must be investigated using other methods in addition to seismic reflection. According to the well data, the resistivity of the NBG is comparatively higher than that of the overlying sedimentary formations, and therefore the magnetotelluric (MT) method is expected to be useful for the estimation of the distribution of the NBG.An MT survey was conducted along three survey lines in this area. Each line trended east–west, perpendicular to the regional geological strike, and was composed of about 25 measurement sites. Induction vectors evaluated from the magnetic field show that this area has a two‐dimensional structure. The evaluated resistivity sections are in agreement with the log data. In conclusion, we were able to detect resistive layers (the NBG) below conductive layers. The results indicate that the NBG becomes gradually less resistive from north to south. In the centre of the northern line, an uplifted resistive area is interpreted as corresponding to the reservoir. By comparison with a seismic section, we prove the effectiveness of the integration of seismic and MT surveys for the investigation of the morphology and internal structure of the NBG. On other survey lines, the resistive uplifted zones are interpreted as possible prospective areas.
Sharp boundary inversion of 2D magnetotelluric data
Authors: Smith Torquil , Hoversten Michael , Gasperikova Erika , Morrison Frank 
Published: March 2003

We consider 2D earth models consisting of laterally variable layers. Boundaries between layers are described by their depths at a set of nodes and interpolated laterally between nodes. Conductivity within each layer is described by values at a set of nodes fixed within each layer, and is interpolated laterally within each layer. Within the set of possible models of this sort, we iteratively invert magnetotelluric data for models minimizing the lateral roughness of the layer boundaries, and the lateral roughness of conductivities within layers, for a given level of data misfit. This stabilizes the inverse problem and avoids superfluous detail. This approach allows the determination of boundary positions between geological units with sharp discontinuities in properties across boundaries, while sharing the stability features of recent smooth conductivity distribution inversions.We compare sharp boundary inversion results with smooth conductivity distribution inversion results on a numerical example, and on inversion of field data from the Columbia River flood basalts of Washington State. In the synthetic example, where true positions and resistivities are known, sharp boundary inversion results determine both layer boundary locations and layer resistivities accurately. In inversion of Columbia flood basalt data, sharp boundary inversion recovers a model with substantially less internal variation within units, and less ambiguity in both the depth to base of the basalts and depth to resistive basement.
Effective velocities in fractured media: a numerical study using the rotated staggered finite‐difference grid
Authors: Saenger Erik H. , Shapiro Serge A. 
Published: March 2003

ABSTRACTThe modelling of elastic waves in fractured media with an explicit finite‐difference scheme causes instability problems on a staggered grid when the medium possesses high‐contrast discontinuities (strong heterogeneities). For the present study we apply the rotated staggered grid. Using this modified grid it is possible to simulate the propagation of elastic waves in a 2D or 3D medium containing cracks, pores or free surfaces without hard‐coded boundary conditions. Therefore it allows an efficient and precise numerical study of effective velocities in fractured structures. We model the propagation of plane waves through a set of different, randomly cracked media. In these numerical experiments we vary the wavelength of the plane waves, the crack porosity and the crack density. The synthetic results are compared with several static theories that predict the effective P‐ and S‐wave velocities in fractured materials in the long wavelength limit. For randomly distributed and randomly orientated, rectilinear, non‐intersecting, thin, dry cracks, the numerical simulations of velocities of P‐, SV‐ and SH‐waves are in excellent agreement with the results of the modified (or differential) self‐consistent theory. On the other hand for intersecting cracks, the critical crack‐density (porosity) concept must be taken into account. To describe the wave velocities in media with intersecting cracks, we propose introducing the critical crack‐density concept into the modified self‐consistent theory. Numerical simulations show that this new formulation predicts effective elastic properties accurately for such a case.
Improved NMO correction with a specific application to shallow‐seismic data
Authors: Brouwer Jan H. 
Published: March 2003

ABSTRACTThe application of traditional NMO‐correction techniques in the processing of seismic data may result in severe distortion. This distortion is observed as a decrease in frequency content (NMO stretch) or even a total loss of data for steep velocity gradients. It is shown that the specific nature of the observed distortion is introduced by the particular implementation of the traditional NMO‐correction technique. It is also shown that other techniques that have been proposed in the literature suffer from similar artefacts. An alternative approach is suggested, based on the correction of tapered blocks of seismic data, followed by a coherence filter to compensate for the specific artefacts thus introduced. Correction of seismic amplitudes (e.g. geometrical spreading and attenuation) is implemented as an integral part of the NMO‐correction method thus allowing for both dynamic and kinematic reconstruction of interfering events. From the application of this method to synthetic and field data, it is concluded that the proposed technique may be particularly useful in the processing of shallow seismic (shear‐wave) data. Although not illustrated in this paper, it is emphasized that application of the proposed method is by no means restricted to shear waves; application to P‐wave data will prove equally useful, although the stretch effects involved may not be as severe as in the examples given in this paper.
Velocity anisotropy and attenuation of shale in under‐ and overpressured conditions
Authors: Domnesteanu Patricia , McCann Clive , Sothcott Jeremy 
Published: March 2003

The seismic velocity and attenuation of fully saturated shales were measured for the first time under overpressured conditions, using the ultrasonic reflection technique. Shale cores from naturally overpressured horizons in the North Sea were tested in the laboratory, at confining and pore pressures relevant to in situ conditions.A single‐frequency tone‐burst pulse wave was used to determine the seismic wave velocities and quality factors of the shale samples, with errors less than 0.3% and 0.1 dB/cm, respectively, at a frequency of 0.75 MHz. Sample length changes with varying confining and pore pressure were measured and the pore pressure equilibration time was monitored for each sample.The anisotropy of the seismic attributes (Vp, Vs, Qp and Qs) was determined over a range of differential pressures from 5 to 60 MPa, with respect to the predominant foliation. The ultrasonic velocity data followed a transversely isotropic pattern depending on the direction of wave propagation with respect to the laminations. The Poisson's ratio was found to rise by 5% as the shale material progressed from a normally pressured to an overpressured state. The quality factor (Q) characteristics were interpreted in terms of pore geometry and connectivity as well as the directional permeability of the transversely isotropic shale material. The results were converted to bulk and shear loss modulus defects, and a positive bulk loss was observed for waves propagating perpendicular to the lamination plane even above differential pressures of 20 MPa. This indicates different levels of Biot‐flow and squirt‐flow attenuation mechanisms acting within the shale structure, depending on the wave propagation and vibration directions.
Towards high‐resolution 3D marine seismic surveying using Boomer sources
Authors: Müller Christof , Milkereit Bernd , Bohlen Thomas , Theilen Friedrich 
Published: March 2003

The use of Boomer sources for 3D seismic imaging of shallow marine structures was investigated in a feasibility study. Boomers show sufficient stability to be used in multichannel seismic surveys. The acquisition of a high‐frequency, densely sampled seismic data volume was successfully performed in the Baltic Sea. A Pleistocene fluvial channel system and shallow gas accumulations were revealed beneath the unconsolidated sediments which constitute the sea‐floor in the southern Kiel Bay.