bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic analysis of genetic markers associated with inherited cardiomyopathy (round heart disease) in the turkey (Meleagris gallopavo)
Authors: Reed K. M. , Mendoza K. M. , Hu G. R. , Sullivan L. R. , Grace M. W. , Chaves L. D. , Kooyman D. L. 
Published: April 2007

SummaryIn turkeys, spontaneous cardiomyopathy or round heart (RH) disease is characterised by dilated ventricles and cardiac muscle hypertrophy. Although the aetiology of RH is still unknown, the disease can have a significant economic impact on turkey producers. In an initial attempt to identify genomic regions associated with RH, we utilised the chicken genome sequence to target short DNA sequences (sequence‐characterised amplified regions, SCARs) identified in previous studies that had significant differences in frequency distribution between RH+ and RH− turkeys. SCARs were comparatively aligned with the chicken whole‐genome sequence to identify flanking regions for primer design. Primers from 32 alignments were tested and target sequences were successfully amplified for 30 loci (94%). Comparative re‐sequencing identified putative SNPs in 20 of the 30 loci (67%). Genetically informative SNPs at 16 loci were genotyped in the UMN/NTBF turkey mapping population. As a result of this study, 34 markers were placed on the turkey/chicken comparative map and 15 markers were added to the turkey genetic linkage map. The position of these markers relative to cardiac‐related genes is presented. In addition, analysis of genotypes at 109 microsatellite loci presumed to flank the SCAR sequences in the turkey genome identified four significant associations with RH.
A polymorphism within the equine CRISP3 gene is associated with stallion fertility in Hanoverian warmblood horses
Authors: Hamann H. , Jude R. , Sieme H. , Mertens U. , Töpfer‐Petersen E. , Distl O. , Leeb T. 
Published: April 2007

SummaryFertility of stallions is of high economic importance, especially for large breeding organisations and studs. Breeding schemes with respect to fertility traits and selection of stallions at an early stage may be improved by including molecular genetic markers associated with traits. The genes coding for equine cysteine‐rich secretory proteins (CRISPs) are promising candidate genes because previous studies have shown that CRISPs play a role in the fertilising ability of male animals. We have previously characterised the three equine CRISP genes and identified a non‐synonymous polymorphism in the CRISP1 gene. In this study, we report one non‐synonymous polymorphism in the CRISP2 gene and four non‐synonymous polymorphisms in the CRISP3 gene. All six CRISP polymorphisms were genotyped in 107 Hanoverian breeding stallions. Insemination records of stallions were used to analyse the association between CRISP polymorphisms and fertility traits. Three statistical models were used to evaluate the influence of single mutations, genotypes and haplotypes of the polymorphisms. The CRISP3 AJ459965:c.+622G>A SNP leading to the amino acid substitution E208K was significantly associated with the fertility of stallions. Stallions heterozygous for the CRISP3 c.+622G>A SNP had lower fertility than homozygous stallions (P = 0.0234). The pregnancy rate per cycle in these stallions was estimated to be ∼7% lower than in stallions homozygous at this position.
A QTL study of growth and body shape in the inter‐species hybrid of Père David's deer (Elaphurus davidianus) and red deer (Cervus elaphus)
Authors: Maqbool N. J. , Tate M. L. , Dodds K. G. , Anderson R. M. , McEwan K. M. , Mathias H. C. , McEwan J. C. , Hall R. J. 
Published: April 2007

SummaryAn interspecies deer hybrid resource population developed from a cross of Père David's and red deer was used to detect QTL that account for species differences. A genome scan, coupled with composite interval mapping, was conducted to search for QTL controlling body measurements at pre‐pubescent age (6 months of age) and puberty (15 months of age) in this interspecies hybrid. Five linkage groups that harbour QTL affecting morphology were identified. A joint‐traits analysis was used to search for putative pleiotropic QTL on four of these linkage groups, and three were significantly associated with pleiotropic QTL for nose width and foot length (metacarpal and phalanges), which collectively accounted for 29–58% of the phenotypic difference between the two deer species. This study suggests that a few loci with large pleiotropic effects may be responsible for species‐specific differences in growth and structure‐related traits.
An advanced sheep (Ovis aries, 2n = 54) cytogenetic map and assignment of 88 new autosomal loci by fluorescence in situ hybridization and R‐banding
Authors: Di Meo G. P. , Perucatti A. , Floriot S. , Hayes H. , Schibler L. , Rullo R. , Incarnato D. , Ferretti L. , Cockett N. , Cribiu E. , Williams J. L. , Eggen A. , Iannuzzi L. 
Published: April 2007

SummaryPresented herein is an updated sheep cytogenetic map that contains 452 loci (291 type I and 161 type II) assigned to specific chromosome bands or regions on standard R‐banded ideograms. This map, which significantly extends our knowledge of the physical organization of the ovine genome, includes new assignments for 88 autosomal loci, including 74 type I loci (known genes) and 14 type II loci (SSRs/microsatellite marker/STSs), by FISH‐mapping and R‐banding. Comparison of the ovine map to the cattle and goat cytogenetic maps showed that common loci were located within homologous chromosomes and chromosome bands, confirming the high level of conservation of autosomes among ruminant species. Eleven loci that were FISH‐mapped in sheep (B3GAT2, ASCC3, RARSL, BRD2, POLR1C, PPP2R5D, TNRC5, BAT2, BAT4, CDC5L and OLA‐DRA) are unassigned in cattle and goat. Eleven other loci (D3S32, D1S86, BMS2621, SFXN5, D5S3, D5S68, CSKB1, D7S49, D9S15, D9S55 and D29S35) were assigned to specific ovine chromosome (OAR) bands but have only been assigned to chromosomes in cattle and goat.
Low‐dose lenograstim is as effective as standard dose in shortening neutrophil engraftment time following myeloablative chemotherapy and peripheral blood progenitor cell rescue
Authors: Nolan L. , Lorigan P. , Chilton S. , Newman J. , Else R. , Smith P. , Linch D. , Sweetenham J. W. , Johnson P. W. 
Published: April 2007

SummaryGranulocyte colony‐stimulating factor (G‐CSF) is widely used following myeloablative chemotherapy (high‐dose therapy; HDT) and peripheral blood progenitor cell rescue (PBPCR) to reduce neutrophil engraftment time. The dose and duration required to gain maximum clinical and economic benefit has not been fully investigated. This double blind placebo‐controlled randomised trial was performed to determine whether short course low‐dose or standard‐dose Lenograstim (L) would influence recovery of haematopoiesis following HDT and PBPCR. Sixty‐one patients were randomised between May 1999 and November 2004, to receive standard‐dose lenograstim (263 μg/d), low‐dose lenograstim (105 μg/d) or placebo injections. These commenced on day +5 following PBPCR and continued until neutrophil engraftment [absolute neutrophil count (ANC)] ≥ 0·5 × 109/l. Patients received standard supportive care until haemopoietic recovery. Both standard‐ and low‐dose lenograstim resulted in a significantly shorter median time to neutrophil recovery (ANC ≥ 0·1 × 109/l:10·0 vs. 11·0 d, P = 0·025; ANC ≥ 0·5 × 109/l:11·0 vs. 14·0 d, P = 0·0002) compared with placebo. There was no significant difference in blood product support, antibiotic usage, documented infection, overall survival or relapse‐free survival between the groups. Short course low‐dose lenograstim is as effective as standard‐dose in reducing neutrophil engraftment time following HDT and PBPCR.
Hybrid genetic algorithms in view of the evolution theories with application for the electrical sounding method
Authors: Başokur Ahmet T. , Akça Irfan , Siyam Nedal W.A. 
Published: April 2007

ABSTRACTThe classical genetic algorithm is a stochastic process which operates by natural selection. Although the algorithm may localize a point around the global minimum of the misfit function, it is not efficient at finding the precise solution. This paper suggests some hybrid genetic algorithms, derived from evolution theories, to overcome this problem. Firstly, sexual selection has been incorporated in the classical genetic algorithm to obtain a full representation of the Darwinist evolution concept. The simulation of sexual selection is performed by assigning a higher probability of surviving to some parameters that satisfy some algebraic relationships. This method is called the ‘marked constraints’ algorithm since it permits us to insert geological and geophysical constraints into the problem. The algorithm implementation is realized by progressively shrinking the parameter search space through successive generations. In this way, the genetic algorithm gains some degree of determinism. Secondly, since the evolution theory of Lamarck postulates that the acquired traits are passed on to the next generation, a hybrid use of the damped least‐squares method and the genetic algorithm is called Lamarckian inversion. Lamarckian inversion involves some improvement procedures that simulate the reduction of the misfit with the help of a derivative‐based method between two generations. Finally, although there is no correspondence in nature, Lamarckian and Darwinist evolution concepts are combined to strengthen the deterministic part of the solution algorithm. This is called the Lamarckian‐marked‐constraint algorithm. The merits and behaviours of the suggested algorithms are discussed using two examples. The first is a hypothetical example affected by a multiminima problem. The second examines the equivalence problem using vertical electrical sounding data.
Fluid‐dependent shear‐wave splitting in a poroelastic medium with conjugate fracture sets
Authors: Galvin Robert J. , Gurevich Boris , Sayers Colin M. 
Published: April 2007

ABSTRACTThe dependence of shear‐wave splitting in fractured reservoirs on the properties of the filling fluid may provide a useful attribute for identifying reservoir fluids. If the direction of wave propagation is not perpendicular or parallel to the plane of fracturing, the wave polarized in the plane perpendicular to the fractures is a quasi‐shear mode, and therefore the shear‐wave splitting will be sensitive to the fluid bulk modulus. The magnitude of this sensitivity depends upon the extent to which fluid pressure can equilibrate between pores and fractures during the period of the deformation. In this paper, we use the anisotropic Gassmann equations and existing formulations for the excess compliance due to fracturing to estimate the splitting of vertically propagating shear waves as a function of the fluid modulus for a porous medium with a single set of dipping fractures and with two conjugate fracture sets, dipping with opposite dips to the vertical. This is achieved using two alternative approaches. In the first approach, it is assumed that the deformation taking place is quasi‐static: that is, the frequency of the elastic disturbance is low enough to allow enough time for fluid to flow between both the fractures and the pore space throughout the medium. In the second approach, we assume that the frequency is low enough to allow fluid flow between a fracture set and the surrounding pore space, but high enough so that there is not enough time during the period of the elastic disturbance for fluid flow between different fracture sets to occur. It is found that the second approach yields a much stronger dependence of shear‐wave splitting on the fluid modulus than the first approach. This is a consequence of the fact that at higher wave frequencies there is not enough time for fluid pressure to equilibrate and therefore the elastic properties of the fluid have a greater effect on the magnitude of the shear‐wave splitting.
Elastic‐impedance analysis constrained by rock‐physics bounds†
Authors: Tsuneyama Futoshi , Mavko Gary 
Published: April 2007

ABSTRACTBy applying seismic inversion, we can derive rock impedance from seismic data. Since it is an interval property, impedance is valuable for reservoir characterization. Furthermore, the decomposition of the impedance into two fundamental properties, i.e. velocity and density, provides a link to the currently available rock‐physics applications to derive quantitative reservoir properties. However, the decomposition is a challenging task due to the strong influence of noise, especially for seismic data with a maximum offset angle of less than 30°. We present a method of impedance decomposition using three elastic impedance data derived from the seismic inversion of angle stacks, where the far‐stack angle is 23.5°. We discuss the effect of noise on the analysis as being the most significant cause of making the decomposition difficult. As the result, the offset‐consistent component of noise mostly affects the determination of density but not the velocities (P‐ and S‐wave), whereas the effect of the random component of noise occurs equally in the determination of the velocities and density. The effect is controlled by the noise enhancement factor 1/A, which is determined by a combination of stack angles. Based on the results of the analysis, we show an innovative method of decomposition incorporating rock‐physics bounds as constraints for the analysis. The method is applied to an actual data set from an offshore oilfield; we demonstrate the result of analysis for sandbody detection.
Overburden complexity and repeatability of seismic data: Impacts of positioning errors at the Oseberg field, North Sea
Authors: Misaghi Ali , Landrø Martin , Petersen Steen A. 
Published: April 2007

ABSTRACTRepeatability of seismic data plays a crucial role in time‐lapse seismic analysis. There are several factors that can decrease the repeatability, such as positioning errors, varying tide, source variations, velocity changes in the water layer (marine data) and undesired effects of various processing steps. In this work, the complexity of overburden structure, as an inherent parameter that can affect the repeatability, is studied. A multi‐azimuth three‐dimensional vertical‐seismic‐profiling data set with 10 000 shots is used to study the relationship between overburden structure and repeatability of seismic data. In most repeatability studies, two data sets are compared, but here a single data set has been used because a significant proportion of the 10 000 shots are so close to each other that a repeatability versus positioning error is possible. We find that the repeatability decreases by a factor of approximately 2 under an overburden lens. Furthermore, we find that the X‐ and Y‐components have approximately the same sensitivity to positioning errors as the Z‐component (for the same events) in this three‐dimensional vertical‐seismic‐profiling experiment. This indicates that in an area with complex overburden, positioning errors between monitor and base seismic surveys are significantly more critical than outside such an area. This study is based on a three‐dimensional three‐component vertical‐seismic‐profiling data set from a North Sea reservoir and care should be taken when extrapolating these observations into a general four‐dimensional framework.
Elastic behaviour of North Sea chalk: A well‐log study
Authors: Gommesen L. , Fabricius I.L. , Mukerji T. , Mavko G. , Pedersen J.M. 
Published: April 2007

ABSTRACTWe present two different elastic models for, respectively, cemented and uncemented North Sea chalk well‐log data. We find that low Biot coefficients correlate with anomalously low cementation factors from resistivity measurements at low porosity and we interpret this as an indication of cementation. In contrast, higher Biot coefficients and correspondingly higher cementation factors characterize uncemented chalk for the same (low) porosity. Accordingly, the Poisson's ratio–porosity relationship for cemented chalk is different from that of uncemented chalk.We have tested the application of the self‐consistent approximation, which here represents the unrelaxed scenario where the pore spaces of the rock are assumed to be isolated, and the Gassmann theory, which assumes that pore spaces are connected, as tools for predicting the effect of hydrocarbons from the elastic properties of brine‐saturated North Sea reservoir chalk. In the acoustic impedance–Poisson's ratio plane, we forecast variations in porosity and hydrocarbon saturation from their influence on the elastic behaviour of the chalk. The Gassmann model and the self‐consistent approximation give roughly similar predictions of the effect of fluid on acoustic impedance and Poisson's ratio, but we find that the high‐frequency self‐consistent approach gives a somewhat smaller predicted fluid‐saturation effect on Poisson's ratio than the low‐frequency Gassmann model. The Gassmann prediction for the near and potentially invaded zone corresponds more closely to logging data than the Gassmann prediction for the far, virgin zone. We thus conclude that the Gassmann approach predicts hydrocarbons accurately in chalk in the sonic‐frequency domain, but the fluid effects as recorded by the acoustic tool are significantly affected by invasion of mud filtrate.The amplitude‐versus‐angle (AVA) response for the general North Sea sequence of shale overlying chalk is predicted as a function of porosity and pore‐fill. The AVA response of both cemented and uncemented chalk generally shows a declining reflectivity coefficient versus offset and a decreasing normal‐incidence reflectivity with increasing porosity. However, for the uncemented model, a phase reversal will appear at a relatively lower porosity compared to the cemented model.
On the retrieval of moment tensors from borehole data
Authors: Vavryčuk Václav 
Published: April 2007

ABSTRACTThe complete moment tensors of seismic sources in homogeneous or vertically inhomogeneous isotropic structures cannot be retrieved using receivers deployed in one vertical borehole. The complete moment tensors can be retrieved from amplitudes of P‐waves, provided that receivers are deployed in at least three boreholes. Using amplitudes of P‐ and S‐waves, two boreholes are, in principle, sufficient. Similar rules also apply to transversely isotropic media with a vertical axis of symmetry.In the case of limited observations, the inversion can be stabilized by imposing the zero‐trace constraint on the moment tensors. However, this constraint is valid only if applied to observations of shear faulting on planar faults in isotropic media, which produces double‐couple mechanisms. For shear faulting on non‐planar faults, for tensile faulting, and for shear faulting in anisotropic media, the zero‐trace constraint is no longer valid and can distort the retrieved moment tensor and bias the fault‐plane solution.Numerical modelling simulating the inversion of the double‐couple mechanism from real data reveals that the errors in the double‐couple and non‐double‐couple percentages of the moment tensors rapidly decrease with increase in the number of boreholes used. For noisy P‐ and S‐wave amplitudes with noise of 15% of the top amplitude at each channel and for a velocity model biased by 10%, the errors in the double‐couple percentage attain 25, 13 and 6% when inverting for the double‐couple mechanism from one, two and three boreholes.
Disruption of Rxra gene in thymocytes and T lymphocytes modestly alters lymphocyte frequencies, proliferation, survival and T helper type 1/type 2 balance
Authors: Stephensen Charles B. , Borowsky Alexander D. , Lloyd Kevin C. Kent 
Published: April 2007

SummaryRetinoid X receptor (RXR) agonists, including the vitamin A metabolite 9‐cis retinoic acid, decrease T‐lymphocyte apoptosis and promote T helper type 2 (Th2) development ex vivo. To examine the in vivo role of RXR‐α in T‐lymphocyte development and function, we disrupted the Rxra gene in thymocytes and T lymphocytes using cyclization recombinase (Cre)‐loxP‐mediated excision of Rxra exon 4. Expression of Cre was targeted to these cells using the Lck promoter. Successful disruption of exon 4 was seen in thymus and T lymphocytes. Mice were healthy and the thymus, spleen and lymph nodes appeared normal. However, knockout mice had a lower percentage of double‐positive (CD4+ CD8+) and a higher percentage of double‐negative thymocytes than wild‐type mice. The percentage of splenic B lymphocytes was lower in unimmunized and ovalbumin‐immunized knockout mice and the percentage of T lymphocytes was lower in immunized knockout mice. Ex vivo proliferation was decreased and apoptosis was increased in T lymphocytes from knockout mice. Memory CD4+ T lymphocytes from knockout mice produced more interferon‐γ and interleukin‐2 (IL‐2) and less IL‐5 and IL‐10 than memory cells from wild‐type mice, indicating a Th1 bias in vivo. However, Rxra disruption did not similarly bias ex vivo differentiation of naive CD4+ T lymphocytes, nor did Rxra disruption alter the serum immunoglobulin G1/immunoglobulin G2a response to immunization. In summary, disruption of Rxra altered the percentages of T and B lymphocytes, produced a Th1 bias in vivo, and altered T‐lymphocyte proliferation and apoptosis ex vivo. These differences were modest in magnitude and their impact on disease resistance is yet to be examined.
Genetic diversity, but not hatching success, is jointly affected by postglacial colonization and isolation in the threatened frog, Rana latastei
Authors: FICETOLA GENTILE FRANCESCO , GARNER TRENTON W. J. , DE BERNARDI FIORENZA 
Published: April 2007

AbstractBoth postglacial colonization and habitat fragmentation can reduce the genetic diversity of populations, which in turn can affect fitness. However, since these processes occur at different spatial and temporal scales, the consequences of either process may differ. To disentangle the relative role of isolation and postglacial colonization in determining genetic diversity and fitness, we studied microsatellite diversity of 295 individuals from 10 populations and measured the hatch rate of 218 clutches from eight populations of a threatened frog, R. latastei. The populations that were affected by fragmentation to a greater extent suffered higher embryo mortality and reduced hatch rate, while no effects of distance from glacial refugium on hatch rate were detected. Altogether, distance from glacial refugium and isolation explained > 90% of variation in genetic diversity. We found that the genetic diversity was lowest in populations both isolated and far from the glacial refugium, and that distance from refugium seems to have the primary role in determining genetic diversity. The relationship between genetic diversity and hatch rate was not significant. However, the proportion of genetic diversity lost through recent isolation had a significant, negative effect on fitness. It is possible that selection at least partially purged the negative effects of the ancestral loss of genetic diversity.