bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of single nucleotide polymorphisms in the bovine CCL2, IL8, CCR2 and IL8RA genes and their association with health and production in Canadian Holsteins
Authors: Leyva‐Baca I. , Schenkel F. , Sharma B. S. , Jansen G. B. , Karrow N. A. 
Published: April 2007

SummaryThe aim of this study was to identify the presence of SNPs in the chemokine genes CCL2 and IL8 and the chemokine receptor genes IL8RA and CCR2, and assess their potential contribution to variation in estimated breeding values (EBVs) for somatic cell score (SCS) and four other traits in Canadian Holstein bulls. Pools of DNA for bulls with high (H) and low (L) EBVs for SCS were used for identification of 11 SNPs. Two unreported SNPs were found in the CCL2 gene and one SNP was found in the CCR2 gene. Previously reported SNPs (three in the IL8 gene and five in the IL8RA chemokine receptor) were also identified. Two SNPs in CCL2, three in IL8, one in IL8RA and one in CCR2 were genotyped in Canadian Holstein bulls (n = 338) using tetra primer ARMS‐PCR. We investigated associations of these seven polymorphisms with three production traits (milk yield, fat yield and protein yield) and one conformation trait related to mastitis (udder depth). The allele substitution effect for the CCL2 rs41255713:T>C SNP was significant at an experimental‐wise level for milk yield (247.5 ± 79.9 kg) and protein yield (7.4 ± 2.3 kg) EBVs (P ≤ 0.05). The associations of the SNPs with SCS EBVs were not significant at an experimental‐wise level. However, the allele substitution effect of the CCR2 rs41257559:C>T SNP on SCS was significant at the comparison‐wise level (−0.04 ± 0.02, P = 0.05), which might indicate a possible association in support of other published studies. Lastly, we assigned CCR2 to BTA22q24, where a previously QTL for SCS was identified.
The locus for bovine dilated cardiomyopathy maps to chromosome 18
Authors: Guziewicz K. E. , Owczarek‐Lipska M. , Küffer J. , Schelling C. , Tontis A. , Denis C. , Eggen A. , Leeb T. , Dolf G. , Braunschweig M. H. 
Published: April 2007

SummaryBovine dilated cardiomyopathy (BDCMP) is a severe and terminal disease of the heart muscle observed in Holstein–Friesian cattle over the last 30 years. There is strong evidence for an autosomal recessive mode of inheritance for BDCMP. The objective of this study was to genetically map BDCMP, with the ultimate goal of identifying the causative mutation. A whole‐genome scan using 199 microsatellite markers and one SNP revealed an assignment of BDCMP to BTA18. Fine‐mapping on BTA18 refined the candidate region to the MSBDCMP06–BMS2785 interval. The interval containing the BDCMP locus was confirmed by multipoint linkage analysis using the software loki. The interval is about 6.7 Mb on the bovine genome sequence (Btau 3.1). The corresponding region of HSA19 is very gene‐rich and contains roughly 200 genes. Although telomeric of the marker interval, TNNI3 is a possible positional and a functional candidate for BDCMP given its involvement in a human form of dilated cardiomyopathy. Sequence analysis of TNNI3 in cattle revealed no mutation in the coding sequence, but there was a G‐to‐A transition in intron 6 (AJ842179:c.378+315G>A). The analysis of this SNP using the study's BDCMP pedigree did not conclusively exclude TNNI3 as a candidate gene for BDCMP. Considering the high density of genes on the homologous region of HSA19, further refinement of the interval on BTA18 containing the BDCMP locus is needed.
The stress dependent elastic properties of thermally induced microfractures in aeolian Rotliegend sandstone
Authors: MacBeth Colin , Schuett Hartmut 
Published: April 2007

ABSTRACTThe impact of thermally induced microfractures on the stress‐sensitive elastic wave properties of aeolian Rotliegend sandstone samples is analysed. It is found that to identify the effects of the microfracture contribution accurately, a correction must first be made to account for water loss (representing a mass loss of 4–6%) from the pore throats and clays due to the heating process, despite care being taken to ensure that the thermally fractured samples re‐adsorb room moisture. Both the original and thermally fractured rocks are stress‐sensitive at the ultrasonic wave frequencies of the laboratory. However, a distinct shift in the estimated distribution of internal rock compliance indicates that the population of thermal microfractures differs in nature from that caused solely by core‐plug extraction damage. In particular, the ratio of normal to tangential compliance is observed to be higher for the thermally generated microfractures than for the broken grain‐grain contacts created by extraction unloading. This can be explained by the intragranular thermal‐fracture surfaces being smoother when compared to the intergranular boundaries. Mechanical hysteresis is observed between the up‐ and downgoing test cycles for both the original and, to a greater extent, the thermally fractured rock. This indicates that there is compaction‐induced movement of the fractures in the samples during application of stress in the laboratory.
Converted‐wave imaging in anisotropic media: theory and case studies
Authors: Li Xiang‐Yang , Dai Hengchang , Mancini Fabio 
Published: April 2007

ABSTRACTCommon‐conversion‐point binning associated with converted‐wave (C‐wave) processing complicates the task of parameter estimation, especially in anisotropic media. To overcome this problem, we derive new expressions for converted‐wave prestack time migration (PSTM) in anisotropic media and illustrate their applications using both 2D and 3D data examples.The converted‐wave kinematic response in inhomogeneous media with vertical transverse isotropy is separated into two parts: the response in horizontally layered vertical transverse isotrophy media and the response from a point‐scatterer. The former controls the stacking process and the latter controls the process of PSTM. The C‐wave traveltime in horizontally layered vertical transverse isotrophy media is determined by four parameters: the C‐wave stacking velocity VC2, the vertical and effective velocity ratios γ0 and γeff, and the C‐wave anisotropic parameter χeff. These four parameters are referred to as the C‐wave stacking velocity model. In contrast, the C‐wave diffraction time from a point‐scatterer is determined by five parameters: γ0, VP2, VS2, ηeff and ζeff, where ηeff and ζeff are, respectively, the P‐ and S‐wave anisotropic parameters, and VP2 and VS2 are the corresponding stacking velocities. VP2, VS2, ηeff and ζeff are referred to as the C‐wave PSTM velocity model. There is a one‐to‐one analytical link between the stacking velocity model and the PSTM velocity model. There is also a simple analytical link between the C‐wave stacking velocities VC2 and the migration velocity VCmig, which is in turn linked to VP2 and VS2.Based on the above, we have developed an interactive processing scheme to build the stacking and PSTM velocity models and to perform 2D and 3D C‐wave anisotropic PSTM. Real data applications show that the PSTM scheme substantially improves the quality of C‐wave imaging compared with the dip‐moveout scheme, and these improvements have been confirmed by drilling.
Mitochondrial phylogeography of New Zealand freshwater crayfishes, Paranephrops spp.
Authors: APTE S. , SMITH P. J. , WALLIS G. P. 
Published: April 2007

AbstractTectonic movement at the boundary of the Indo‐Australian and Pacific Plates during the Miocene and Pliocene is recognized as a driving force for invertebrate speciation in New Zealand. Two endemic freshwater crayfish (koura) species, Paranephrops planifrons White 1842 and Paranephrops zealandicus White 1842, represent good model taxa to test geological hypotheses because, due to their low dispersal capacity and life history, geographical restriction of populations may be caused by vicariant processes. Analysis of a mitochondrial DNA marker (cytochrome oxidase subunit I) reveals not two, but three major koura lineages. Contrary to expectation, the cryptic West Coast group appears to be more closely related to P. zealandicus than to P. planifrons and has diverged earlier than the final development (Late Pleistocene) of Cook Strait. Our date estimates suggest that koura lineage diversification probably coincided with early to mid‐Alpine orogeny in the mid‐Pliocene. Estimates of node ages and the phylogenies are inconsistent with both ancient Oligocene and recent postglacial Pleistocene range expansion, but suggest central to north colonization of North Island and west to east movement in South Island during mid‐ to late Pliocene. Crypsis and paraphyly of the West Coast group suggest that morphological characters presently used to classify koura species could be misleading.
Finding the relevant scale: clonality and genetic structure in a marine invertebrate (Crambe crambe, Porifera)
Authors: CALDERÓN ISABEL , ORTEGA NATALIA , DURAN SANDRA , BECERRO MIKEL , PASCUAL MARTA , TURON XAVIER 
Published: April 2007

AbstractImportant changes in genetic relatedness may occur at extremely small scales in benthic invertebrates, providing key information about structuring processes in populations of these organisms. We performed a small‐scale study of the population structure of the sponge Crambe crambe, in which 177 individuals from the same rocky wall (interindividual distances from 0 to 7 m) were genotyped using six microsatellite markers. 101 sponges had unique genotypes and the remaining 76 individuals formed 24 groups of sponges sharing genotypes (clones). Mean intraclone distances were found to be c. 20 cm. Spatial autocorrelation analyses showed a drastic decrease in genetic relatedness over the first 100 cm of distance. If the contribution of clonality to this pattern was eliminated, the trend was attenuated, but remained a marked one and was still significant within the first distance classes (30–40 cm). Estimated mean dispersal distances per generation were c. 35 cm, and neighbourhood sizes were estimated at c. 33 sponges. Genetic similarities with sponges of the same locality, or from other Mediterranean localities, were within the same range as those found in sponges 2–7 m apart. It is concluded that asexual reproduction plays an important role in structuring populations in this species. However, over and above the effects of clonality, a strong fine‐scale genetic structure was present at distances in the range of tens of centimetres, probably as a result of short dispersal of larvae. This fine‐scale genetic structure may be common in invertebrates with lecitotrophic larvae.
Limitation of nocturnal import of ATP into Arabidopsis chloroplasts leads to photooxidative damage†
Authors: Reinhold Thomas , Alawady Ali , Grimm Bernhard , Beran Karl Christian , Jahns Peter , Conrath Uwe , Bauer Jenny , Reiser Jens , Melzer Michael , Jeblick Wolfgang , Neuhaus H. Ekkehard 
Published: April 2007

SummaryWhen grown in short day conditions and at low light, leaves of Arabidopsis plants with mutations in the genes encoding two plastidial ATP/ADP transporters (so‐called null mutants) spontaneously develop necrotic lesions. Under these conditions, the mutants also display light‐induced accumulation of H2O2 and constitutive expression of genes for copper/zinc superoxide dismutase 2 and ascorbate peroxidase 1. In the light phase, null mutants accumulate high levels of phototoxic protoporphyrin IX but have only slightly reduced levels of Mg protoporphyrin IX. The physiological changes are associated with reduced magnesium–chelatase activity. Since the expression of genes encoding any of the three subunits of magnesium–chelatase is similar in wild type and null mutants, decreased enzyme activity is probably due to post‐translational modification which might be due to limited availability of ATP in plastids during the night. Surprisingly, the formation of necrotic lesions was absent when null mutants were grown either in long days and low light intensity or in short days and high light intensity. We ascribe the lack of lesion phenotype to increased nocturnal ATP supply due to glycolytic degradation of starch which may lead to additional substrate‐level phosphorylation in the stroma. Thus, nocturnal import of ATP into chloroplasts represents a crucial, previously unknown process that is required for controlled chlorophyll biosynthesis and for preventing photooxidative damage.
Elevated calcium phosphate product after renal transplantation is a risk factor for graft failure
Authors: Egbuna Ogo I. , Taylor Jeremy G. , Bushinsky David A. , Zand Martin S. 
Published: April 2007

Abstract:  Background:  Abnormal mineral metabolism is not uncommon after renal transplant (TXP). In dialysis patients, elevated serum phosphorous (P), calcium (Ca), CaP product, and parathyroid hormone (PTH) are associated with increased morbidity and mortality. The effect of these abnormalities on recipient and graft survival after renal transplantation is unknown.Methods:  We retrospectively analyzed 422 kidney‐only transplants performed between June 1996 and June 2003. Cases with graft or recipient survival less than three months, pre‐TXP parathyroidectomy (PTX), cinacalcet therapy and incomplete records were excluded, leaving 303 cases for analysis using Cox models that included post‐TXP PTX, levels of albumin‐adjusted Ca(Caadj), P, CaadjP product and PTH.Results:  There was an 11–25% prevalence of abnormal serum Caadj, P or CaadjP product within the first year post‐TXP. At least 24% of recipients not undergoing PTX with an equation estimated GFR of 40–60 mL/min had PTH levels >130 pg/mL at one yr post‐TXP. This is above levels recommended by the U.S National Kidney Foundation kidney disease quality initiative for patients with stages I–IV chronic kidney disease. Adjusted Ca > 10.5 mg/dL at three months post‐TXP was an independent risk for recipient death (OR 3.0; 95% CI: 1.2–7.4). A CaadjP product >35 mg2/dL2 at six months (OR 4.0; 95% CI: 1.2–13.1), and Ca >10.5 mg/dL at 12 months post‐TXP (OR 4.0; 95% CI: 1.2–14) were independent risks for death‐censored graft loss. Twenty‐two recipients underwent PTX for severe hyperparathyroidism.Conclusion:  Abnormalities of mineral metabolism are common early after renal TXP. An elevated serum Caadj at three months post‐TXP increases the risk for recipient death, while an elevated CaadjP and Caadj later in the first post‐TXP year increases the risk of long‐term death‐censored graft loss.
Population samples and genotyping technology
Authors: Mack S. J. , Sanchez‐Mazas A. , Single R. M. , Meyer D. , Hill J. , Dron H. A. , Jani A. J. , Thomson G. , Erlich H. A. 
Published: April 2007

AbstractThe 14th International HLA (human leukocyte antigen) Immunogenetics Workshop (14th‐IHIWS) Biostatistics and Anthropology/Human Genetic Diversity project continues the population sampling, genotype data generation, and biostatistic analyses of the 13th International Histocompatibility Workshop Anthropology/Human Genetic Diversity Component, with the overall goal of further characterizing global HLA allele and haplotype diversity and better describing the relationships between major histocompatibility complex diversity, geography, linguistics, and population history. Since the 13th Workshop, new investigators have and continue to be recruited to the project and new high‐resolution class I and class II genotype data are being generated for 112 population samples from around the world.
Nomenclature for HLA microsatellites
Authors: Gourraud P. A. , Cambon‐Thomsen A. , Dauber E. M. , Feolo M. , Hansen J. , Mickelson E. , Single R. M. , Thomsen M. , Mayr W. R. 
Published: April 2007

AbstractA proposal for a standardized nomenclature for human leukocyte antigen (HLA) microsatellites is presented. It provides recommendations for Microsatellites as regards to locus name, primer names, and denominations for alleles.
14th International HLA and Immunogenetics Workshop: Report on the immunogenetics of aging
Authors: Naumova E. , Pawelec G. , Ivanova M. , Constantinescu I. , Bogunia‐Kubik K. , Lange A. , Qguz F. , Carin M. 
Published: April 2007

AbstractThe ‘Immunogenetics of Aging’ is a newly included component within the 14th International HLA and Immunogenetics Workshop. The aim of this component was to determine the contribution of human leukocyte antigen (HLA), cytokine genes and other major histocompatibility complex‐encoded loci to successful aging and to determine an increased capacity to reach the extreme limits of life span. Two main data sets from four European populations were included in this study: unrelated healthy elderly individuals and ethnically matched young controls, and families with longevity members. Analysis was focused on HLA class I and II and cytokine gene polymorphisms. Preliminary results showed increased frequencies of DRB1*11‐ and DRB*16‐associated haplotypes that were found to be protective for autoimmune diseases in some populations. Additionally, in families with longevity members, alleles and haplotypes positively associated with autoimmunity were not observed. Analysis of cytokine gene polymorphisms showed prevalence of anti‐inflammatory profiles in healthy elderly individuals. Inheritance of extended haplotypes in families with longevity members allowed the identification of immunogenetic profiles that could be predictive for longevity. These preliminary studies indicate the relevance of genes regulating immune functions in human longevity and the importance of clarifying further their impact in successful aging.
Overview of registries, HLA typing and diversity, and search algorithms
Authors: Hurley C. K. , Maiers M. , Marsh S. G. E. , Oudshoorn M. 
Published: April 2007

AbstractOver 10 million volunteer donors and cord blood units are typed for human leukocyte antigen (HLA) within hematopoietic stem cell registries and cord blood banks. Identification of matched donors in countries different from that of the searching patient is facilitated by Bone Marrow Donors Worldwide and the World Marrow Donor Association (WMDA). A survey of new volunteer donor typing among WMDA member registries has identified the methods and resolution of HLA testing and the level of quality control used to evaluate the accuracy of typing results. The diversity of HLA assignments within registries has generated a number of informatics challenges. Registries are using population genetics to enhance registry diversity and to facilitate the identification of matched donors.
Strategies for typing new volunteer donors
Authors: Setterholm M. , Morishima Y. , Pepperall J. , Schmidt A. 
Published: April 2007

AbstractUnrelated donor registries use a variety of strategies for human leukocyte antigen typing newly recruited volunteers and for prospective typing and file maintenance projects. The approaches change over time with respect to the level of resolution and loci tested based on costs, advances in technologies and emerging clinical outcome data from matching studies.
14th International HLA and Immunogenetics Workshop: Report on hematopoietic cell transplantation
Authors: Petersdorf E. , Bardy P. , Cambon‐Thomsen A. , Goulmy E. , Hansen J. , Schwarer A. , Velardi A. ,   The IHWG HCT
Published: April 2007

AbstractDeciphering the role of human leukocyte antigen (HLA), killer immunoglobulin like receptor, and immune response genes in a model as complex as unrelated donor hematopoietic cell transplantation is a challenge. The allelic diversity of these genes is shaped by the race and ethnicity of transplant donors and recipients. Coupled with the genetic polymorphism is the complexity of clinical phenotypes of transplant populations: donor and recipient demographic characteristics and the regimens used by transplant physicians to prepare patients for transplantation and to prevent and treat graft‐vs‐host disease (GVHD). Furthermore, GVHD is itself a complex disease shaped by both genes and ‘environment’. How does one begin to deconstruct the genetic barrier to understand risk factors important to transplant outcome? To begin with, population‐based studies, particularly retrospective ones, benefit from adequate sample sizes to measure genetic effects. The more homogeneous the population for variables that influence clinical endpoints, the higher the likelihood that a real genetic effect can be uncovered. Even so, the feasibility of studies can be hampered if genotype and clinical data are not both complete and precise. For studies of HLA, diversity of alleles and antigens contributed by ethnically different transplant populations is an asset, because not only can a broader range of HLA mismatches be studied but they provide the opportunity for side‐by‐side analyses that may yield clues as to why transplant outcomes differ between populations.
Effect of HLA‐A2 allele disparity on clinical outcome in hematopoietic cell transplantation from unrelated donors
Authors: Morishima Y. , Kawase T. , Malkki M. , Petersdorf E. W. ,   International Histocompatibility Working Group in Hematopoietic Cell Transplantation Component
Published: April 2007

AbstractPopulation‐based differences in clinical outcome after unrelated donor hematopoietic cell transplantation suggest that the significance of human leukocyte antigen (HLA) mismatching may be related to locus‐specific and allele‐specific differences that distinguish ethnically diverse transplant donors and recipients. We studied the risks associated with HLA‐A locus mismatching in two large transplant populations from the International Histocompatibility Working Group in hematopoietic cell transplantation data set to better understand permissible and nonpermissible HLA‐A mismatches.
MHC class I, II, and III microsatellite marker matching and survival in unrelated donor hematopoietic cell transplantation
Authors: Malkki M. , Gooley T. , Horowitz M. , Petersdorf E. W. ,   on behalf of the IHWG HCT Component
Published: April 2007

AbstractMicrosatellites (Msats) are effective markers for disease association mapping. The International Histocompatibility Working Group in hematopoietic cell transplantation applied Msats to determine whether potential new transplantation determinants are encoded within the major histocompatibility complex. Retrospective analysis of human leukocyte antigen‐identical unrelated donor transplants provided a homogeneous population to measure Msat‐associated risks of mortality.
The identification and characterisation of a novel null HLA‐DRB1 allele
Authors: Fidler S. J. , Smith L. K. , Christiansen F. T. 
Published: April 2007

AbstractSince the introduction of DNA‐based human leukocyte antigen (HLA) typing a number of discrepancies with serological typing have been documented. At the time of submission of this abstract (July 2005 ImMunoGeneTics project (IMGT) project database release) 42 HLA class I and II null alleles had been described characterised by a lack of expression of cell surface antigen. These null alleles can be accounted for by a number of demonstrated molecular mechanisms including insertion, deletion and point mutation and may lead to a nonsense codon, splicing defect or premature stop codon.