bluuebunny/crossref_metadata_2025 huggingface dataset:
Impaired Behavior Regulation Under Conditions of Concurrent Variable Schedules of Reinforcement in Children With ADHD
Authors: Taylor David , Lincoln Alan J. , Foster Sharon L.
Published: June 2009

Objective: To bridge theory of response inhibition and learning in children with ADHD. Method: Thirty ADHD and 30 non-ADHD children (ages 9-12) were compared under concurrent variable interval (VI-15 sec., VI-30 sec. and VI- 45 sec.) reinforcement schedules that required the child to switch between the three schedules under conditions of experimentally controlled inhibition (change over delay [COD] vs. No COD). Classical matching law was used to evaluate children’s success in maximizing reinforcement opportunities. Results: Children with ADHD showed normal matching only when immediate reinforcement for responding was blocked by the presence of a 3-s COD. Without a COD, ADHD children failed to conform to the normal matching law. Non-ADHD children’s behavior fit the matching law (i.e., rate of response was proportional to rate of reinforcement) whether a COD was present or absent. Conclusions: Results supported other findings that response inhibition is a key mechanism in responses to reinforcement schedules by children with ADHD and that the absence of contingencies that inhibit impulsive responding might impair complex learning in which the child must choose between many different behavioral options, each with associated reinforcement schedules. (J. of Att. Dis. 2010; 13(4) 358-368)
Immigration, Economic Disadvantage, and Homicide
Authors: Akins Scott , Rumbaut Rubén G. , Stansfield Richard
Published: June 2009

In this article, the effect of recent immigration on homicide rates across city of Austin, Texas census tracts is examined. Since 1980, Austin's recent immigrant population increased by more than 580% across the metropolitan area and it is now considered a “pre-emerging” immigrant gateway city to the United States. Therefore the changing population dynamics in Austin provide an excellent opportunity to study the effect of recent immigration on homicide. After controlling for structural predictors of homicide and correcting for spatial autocorrelation, our findings indicate that recent immigration is not associated with homicide.
Understanding anthropological understanding
Authors: Zeitlyn David
Published: June 2009

In this article I argue for a merological anthropology in which ideas of `partiality' and `practical adequacy' provide a way out of the impasse of relativism which is implied by postmodernism and the related abandonment of a concern with `truth'. Ideas such as `aptness' and `faithfulness' enable us to re-establish empirical foundations without having to espouse a simple realism which has been rightly criticized. Ideas taken from ethnomethodology, particularly the way we bootstrap from `practical adequacy' to `warrants for confidence', point to a merological anthropology in which we recognize that we do not and cannot know everything, but that we can have reasons for being confident in the little we know.
Contesting secularism/s
Authors: Bangstad Sindre
Published: June 2009

This essay deals with the influential anthropological work of Prof. Talal Asad on Islam, secularism and the secular. I argue that the binary `Western—non-Western' which is constitutive for Asad, the relative absence of ethnography in Asad's work, and the state-centred nature of Asad's approach to secularism and the secular has contributed to an anthropological impasse whereby the complex engagement of Muslims living in secular and liberal `Western' contexts with the secular has become difficult to conceptualize. I argue in favour of the conceptualizations in a nascent body of works which transcend some of these binaries, most notably those of Marsden and Soares and Otayek, and in favour of investigating the secular as a vernacular practice.
Promoting Lifestyle Change Among Cancer Survivors: When Is the Teachable Moment?
Authors: Rabin Carolyn
Published: June 2009

There is mounting evidence that cancer survivors who adopt a healthy lifestyle—for example, by exercising, consuming a healthy diet, and not smoking—reap physical and emotional benefits. Depending on the behavior targeted, these benefits may include reduced fatigue, improved physical functioning, improved quality of life, and greater likelihood of disease-free survival. Given the advantages, cancer survivors should be urged to address any unhealthy behaviors. It remains unclear, however, when cancer survivors will be most receptive to advice from health care providers and others about their lifestyle behaviors. In other words, it is unclear if a “teachable moment” occurs shortly after the cancer diagnosis, during cancer treatment, or sometime after treatment has been completed. This review describes the reasons it has been difficult to identify the optimal time within the cancer trajectory to promote healthy lifestyle behaviors. Some strategies for clarifying the optimal timing are discussed. The review concludes by summarizing health behavior recommendations for cancer survivors outlined by an American Cancer Society expert panel.
Double-Calcaneal Osteotomy With a Unilateral Rail External Fixator for Correction of Pes Planus
Authors: Penney Nathan T. , Viselli Sarah J. , Holmes Timothy R. , Weiner Richard D.
Published: June 2009

A combination of the medial displacement calcaneal osteotomy with the Evans lateral column-lengthening osteotomy has been suggested when hindfoot valgus, forefoot abduction, and midtarsal joint instability are significant. However, the deforming forces must be flexible. The goal of this procedure is to restore alignment, stabilize the foot, and improve overall function. This double-calcaneal osteotomy addresses all components of the pes planus deformity. This article reports the use of a unilateral external fixator to callus distract the Evans calcaneal osteotomy while compressing the posterior medial calcaneal displacement osteotomy, which to the authors' knowledge has not been performed or reported in the literature. At the final post-operative visit of this clinical patient, the foot was rectus, and X-rays demonstrated an increased calcaneal inclination angle from 10° preoperatively to 15° postoperatively, a decreased talar declination angle from 39° preoperatively to 26° postoperatively, and the cuboid abduction angle decreased from 32° preoperatively to 9° postoperatively. The patient was pain free and extremely satisfied with the surgery, especially with the use of the external fixator.
Plasma polymerisation of siloxanes at atmospheric pressure
Authors: De Geyter N , Morent R , Van Vlierberghe S , Dubruel P , Leys C , Schacht E
Published: June 2009

This work deals with the plasma polymerisation of two siloxane precursors, [hexamethyldisiloxane (HMDSO) and tetramethyldisiloxane (TMDSO)] with an atmospheric pressure pseudoglow dielectric barrier discharge operated in argon and an argon–air mixture. The influence of gas composition and precursor type on the physical and chemical properties of the deposited films is examined in detail using contact angle measurements, Fourier transform infrared spectroscopy (FTIR) and atomic force microscopy (AFM). Results clearly show that precursor type as well as gas composition has an profound impact on film growth rate and chemical composition of the deposited films. Plasma polymerisation of both siloxane precursors in argon leads to the formation of hydrophobic polymers consisting of a Si–O–Si backbone, while for deposition in an argon–air mixture, hydrophilic inorganic silica-like coatings are obtained.
Effect of heat treatment on microstructure and residual stress of wire arc sprayed high carbon steel coating
Authors: Chen Y. X. , Liang X. B. , Liu Y. , Wei S. C. , Xu B. S.
Published: June 2009

The 0·8% carbon steel wire was used to deposit coating, and the coated samples were annealed at 550, 650 and 800°C respectively, which were then quenched in water. The microstructure, phase composition and residual stress of the heat treated coatings were studied and compared with that of the coating without any post-treatment. Results show that the heat treatment processes have significant influences on coating oxide, steel alloy grains and residual stresses. The high carbon steel coating expressed tensile stress after spraying, but when the special quenching process was applied, martensite and bainite were formed in the coating, resulting in expansion of material volume, which made the residual stress of the coating change from tension to compression. The correlation between the microstructure and residual stress strongly informed that phase transformation in the coating should be carefully controlled if spray forming thick coating is aimed.
Effect of thermal spray processes on anatase–rutile phase transformation in nano-structured TiO2 photo-catalyst coatings
Authors: Bozorgtabar M. , Rahimipour M. , Salehi M.
Published: June 2009

TiO2 photo-catalytic coatings were deposited using three different thermal spray techniques, namely, flame, plasma and high velocity oxy-fuel (HVOF). TiO2 nanopowders were used as feedstock. X-ray diffraction analysis and scanning electron microscopy were used to study the deposited TiO2 coating. It was concluded that a high anatase content of 80 vol.% can be achieved for the coating deposited by HVOF if kerosene is used as fuel. On the contrary, the anatase contents in the coating deposited by the flame and plasma spray processes were reduced to 29 and 5 vol.% respectively due to their structural transformation of anatase to rutile. Microstructure shows that the as sprayed HVOF TiO2 coating had nanostructure characteristics with smaller grain size than feedstock powder. It was found that the structural transformation of anatase to rutile is significantly influenced by the thermal spray processes. Liquid fuelled HVOF technique can prevent this transformation.
Processing and microstructure of NiRuAl diffusion barrier coating on Ni-based superalloy
Authors: Wang Y , Guo H-B , Peng L-Q , Gong S-K
Published: June 2009

Thermal barrier coatings (TBCs), consisting of ceramic topcoat and metallic bond coat, are applied onto Ni-based superalloy hot components in turbine engines to protect the components from high temperature gas. Detrimental phases in the superalloy substrate such as topologically close-packed phase (TCP) and secondary reaction zone (SRZ), resulting from interdiffusion between the bond coat and the substrate, significantly deteriorate the desired mechanical properties of the superalloy substrate. In this paper, a NiRuAl coating was produced onto Ni-based superalloy to inhibit the interdiffusion between the coating and substrate. During the processing, a dense and continuous Ru film of around 4 μm thickness was first electrodeposited onto a K3 superalloy at 70°C using a current density of 1·2 A dm−2. The NiRuAl coating was formed by pack aluminisation of the Ru coated specimen in argon atmosphere at 900°C. The coating shows a two-layered structure: the top layer NiAl and the bottom layer NiRuAl, with the potential functions of diffusion barrier and high temperature oxidation resistance.
Role of sialic acid for platelet life span: exposure of β-galactose results in the rapid clearance of platelets from the circulation by asialoglycoprotein receptor–expressing liver macrophages and hepatocytes
Authors: Sørensen Anne Louise , Rumjantseva Viktoria , Nayeb-Hashemi Sara , Clausen Henrik , Hartwig John H. , Wandall Hans H. , Hoffmeister Karin M.
Published: June 2009

Although surface sialic acid is considered a key determinant for the survival of circulating blood cells and glycoproteins, its role in platelet circulation lifetime is not fully clarified. We show that thrombocytopenia in mice deficient in the St3gal4 sialyltransferase gene (St3Gal-IV−/− mice) is caused by the recognition of terminal galactose residues exposed on the platelet surface in the absence of sialylation. This results in accelerated platelet clearance by asialoglycoprotein receptor-expressing scavenger cells, a mechanism that was recently shown to induce thrombocytopenia during Streptococcus pneumoniae sepsis. We now identify platelet GPIbα as a major counterreceptor on ST3Gal-IV−/− platelets for asialoglycoprotein receptors. Moreover, we report data that establish the importance of sialylation of the von Willebrand factor in its function.
Exposure of human megakaryocytes to high shear rates accelerates platelet production
Authors: Dunois-Lardé Claire , Capron Claude , Fichelson Serge , Bauer Thomas , Cramer-Bordé Elisabeth , Baruch Dominique
Published: June 2009

Platelets originate from megakaryocytes (MKs) by cytoplasmic elongation into proplatelets. Direct platelet release is not seen in bone marrow hematopoietic islands. It was suggested that proplatelet fragmentation into platelets can occur intravascularly, yet evidence of its dependence on hydrodynamic forces is missing. Therefore, we investigated whether platelet production from MKs could be up-regulated by circulatory forces. Human mature MKs were perfused at a high shear rate on von Willebrand factor. Cells were observed in real time by videomicroscopy, and by confocal and electron microscopy after fixation. Dramatic cellular modifications followed exposure to high shear rates: 30% to 45% adherent MKs were converted into proplatelets and released platelets within 20 minutes, contrary to static conditions that required several hours, often without platelet release. Tubulin was present in elongated proplatelets and platelets, thus ruling out membrane tethers. By using inhibitors, we demonstrated the fundamental roles of microtubule assembly and MK receptor GPIb. Secretory granules were present along the proplatelet shafts and in shed platelets, as shown by P-selectin labeling. Platelets generated in vitro were functional since they responded to thrombin by P-selectin expression and cytoskeletal reorganization. In conclusion, MK exposure to high shear rates promotes platelet production via GPIb, depending on microtubule assembly and elongation.
Identification of ZNF366 and PTPRD as novel determinants of plasma homocysteine in a family-based genome-wide association study
Authors: Mälarstig Anders , Buil Alfonso , Souto Juan Carolos , Clarke Robert , Blanco-Vaca Francisco , Fontcuberta Jordi , Peden John , Andersen Malin , Silveira Angela , Barlera Simona , Seedorf Udo , Watkins Hugh , Almasy Laura , Hamsten Anders , Soria José Manuel
Published: June 2009

Total plasma homocysteine concentration (tHcy) is a biomarker for atherothrombotic disease, but causality remains uncertain. Polymorphisms in the genes involved in methionine metabolism explain only a small fraction of the heritability of tHcy levels. In a genome-wide association study, we examined the genetic determinants of tHcy using a 2-stage design. First, 283 437 single nucleotide polymorphisms (SNPs) were tested for association with tHcy in 387 persons recruited from 21 large Spanish families. Of those, 17 SNPs showed equal or stronger association with tHcy level compared with the MTHFR 677C>T SNP (β = 0.10, P = .0001). Second, a replication analysis of these 17 SNPs was performed in patients with premature myocardial infarction (n = 1238). Novel associations were found for SNPs near the ZNF366 gene (lead SNP rs7445013; discovery stage: adjusted β = −0.12, P = 5.30 × 10−6, replication stage: adjusted β = −0.13, P = .004) and the PTPRD gene (lead SNP rs973117; discovery stage: adjusted β = 0.11, P = 5.5 × 10−6, replication stage: adjusted β = 0.10, P = .005). These associations were independent of known confounders, including creatinine clearance and plasma fibrinogen concentration. Our findings implicate novel pathways in homocysteine metabolism, and highlight the need for investigation of the associated genes in the etiology of vascular diseases.
A bivariate quantitative genetic model for a linear Gaussian trait and a survival trait
Authors: Damgaard Lars Holm , Korsgaard Inge Riis
Published: June 2009

With the increasing use of survival models in animal breeding to address the genetic aspects of mainly longevity of livestock but also disease traits, the need for methods to infer genetic correlations and to do multivariate evaluations of survival traits and other types of traits has become increasingly important. In this study we derived and implemented a bivariate quantitative genetic model for a linear Gaussian and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted. Model parameters were inferred from their marginal posterior distributions. The required fully conditional posterior distributions were derived and issues on implementation are discussed. The twoWeibull baseline parameters were updated jointly using a Metropolis-Hastingstep. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. Simulation results showed that the estimated marginal posterior distributions covered well and placed high density to the true parameter values used in the simulation of data. In conclusion, the proposed method allows inferring additive genetic and environmental correlations, and doing multivariate genetic evaluation of a linear Gaussian trait and a survival trait.
Optimum allocation of conservation funds and choice of conservation programs for a set of African cattle breeds
Authors: Reist-Marti Sabine B. , Abdulai Awudu , Simianer Henner
Published: June 2009

Although funds for livestock conservation are limited there is little known about the optimal allocation of conservation funds. A new algorithm was used to allocate Mio US$ 1, 2, 3, 5 or unlimited funds, discounted over 50 years, on 23 African cattle breeds conserved with four different possible conservation programs. Additionally, Mio US$ 1 was preferably allocated to breeds with special traits. The conceptional in situ conservation programs strongly involve breeders and give them part of the responsibility for the conservation of the breed. Therefore, the pure in situ conservation was more efficient than cryoconservation or combined in situ and cryoconservation. The average annual discounted conservation cost for a breed can be as low as US$ 1000 to US$ 4400 depending on the design of the conservation program and the economic situation of the country of conservation. The choice of the breeds and the optimal conservation program and the amount of money allocated to each breed depend on many factors such as the amount of funds available, the conservation potential of each breed, the effects of the conservation program as well as its cost. With Mio US$ 1, 64% of the present diversity could be maintained over 50 years, which is 13% more than would be maintained if no conservation measures were implemented. Special traits could be conserved with a rather small amount of the total funds. Diversity can not be conserved completely, not even with unlimited funds. A maximum of 92% of the present diversity could be conserved with Mio US$ 10, leaving 8% of the diversity to unpredictable happenings. The suggested algorithm proved to be useful for optimal allocation of conservation funds. It allocated the funds optimally among breeds by identifying the most suited conservation program for each breed, also accounting for differences in currency exchange rates between the different countries.
The efficiency of mapping of quantitative trait loci using cofactor analysis in half-sib design
Authors: Sahana Goutam , de Koning Dirk Jan , Guldbrandtsen Bernt , Sørensen Peter , Lund Mogens Sandø
Published: June 2009

This simulation study was designed to study the power and type I error rate in QTL mapping using cofactor analysis in half-sib designs. A number of scenarios were simulated with different power to identify QTL by varying family size, heritability, QTL effect and map density, and three threshold levels for cofactor were considered. Generally cofactor analysis did not increase the power of QTL mapping in a half-sib design, but increased the type I error rate. The exception was with small family size where the number of correctly identified QTL increased by 13% when heritability was high and 21% when heritability was low. However, in the same scenarios the number of false positives increased by 49% and 45% respectively. With a liberal threshold level of 10% for cofactor combined with a low heritability, the number of correctly identified QTL increased by 14% but there was a 41% increase in the number of false positives. Also, the power of QTL mapping did not increase with cofactor analysis in scenarios with unequal QTL effect, sparse marker density and large QTL effect (25% of the genetic variance), but the type I error rate tended to increase. A priori, cofactor analysis was expected to have higher power than individual chromosome analysis especially in experiments with lower power to detect QTL. Our study shows that cofactor analysis increased the number of false positives in all scenarios with low heritability and the increase was up to 50% in low power experiments and with lower thresholds for cofactors.
Estimation of breed contributions to present and future genetic diversity of 44 North Eurasian cattle breeds using core set diversity measures
Authors: Bennewitz Jörn , Kantanen Juha , Tapio Ilma , Li Meng Hua , Kalm Ernst , Vilkki Johanna , Ammosov Innokentyi , Ivanova Zoya , Kiselyova Tatyana , Popov Ruslan , Meuwissen Theo HE
Published: June 2009

Extinction of breeds threatens genetic diversity of livestock species. The need to conserve genetic diversity is widely accepted but involves in general two questions: (i) is the expected loss of diversity in a set of breeds within a defined future time horizon large enough to establish a conservation plan, and if so (ii) which breeds should be prioritised for such a conservation plan? The present study uses a marker assisted methodology to address these questions. The methodology combines core set diversity measures with a stochastic method for the estimation of expected future diversity and breed marginal diversities. The latter is defined as the change in the total diversity of all breeds caused by a one unit decrease in extinction probability of a particular breed. The stochastic method was validated by means of simulations. A large field data set consisting of 44 North Eurasian cattle breeds was analysed using simplified determined extinction probabilities. The results show that the expected loss of diversity in this set within the next 20 to 50 years is between 1 and 3% of the actual diversity, provided that the extinction probabilities which were used are approximately valid. If this loss is to be reduced, it is sufficient to include those three to five breeds with the highest marginal diversity in a conservation scheme.
Prediction of IBD based on population history for fine gene mapping
Authors: Hernández-Sánchez Jules , Haley Chris S. , Woolliams John A.
Published: June 2009

A novel multiple regression method (RM) is developed to predict identity-by-descent probabilities at a locus L (IBD

L
), among individuals without pedigree, given information on surrounding markers and population history. These IBD

L
probabilities are a function of the increase in linkage disequilibrium (LD) generated by drift in a homogeneous population over generations. Three parameters are sufficient to describe population history: effective population size (Ne), number of generations since foundation (T), and marker allele frequencies among founders (p). IBD

L
are used in a simulation study to map a quantitative trait locus (QTL) via variance component estimation. RM is compared to a coalescent method (CM) in terms of power and robustness of QTL detection. Differences between RM and CM are small but significant. For example, RM is more powerful than CM in dioecious populations, but not in monoecious populations. Moreover, RM is more robust than CM when marker phases are unknown or when there is complete LD among founders or Ne is wrong, and less robust when p is wrong. CM utilises all marker haplotype information, whereas RM utilises information contained in each individual marker and all possible marker pairs but not in higher order interactions. RM consists of a family of models encompassing four different population structures, and two ways of using marker information, which contrasts with the single model that must cater for all possible evolutionary scenarios in CM.
Efficient computation of the inverse of gametic relationship matrix for a marked QTL
Authors: Sargolzaei Mehdi , Iwaisaki Hiroaki , Colleau Jean-Jacques
Published: June 2009

Best linear unbiased prediction of genetic merits for a marked quantitative trait locus (QTL) using mixed model methodology includes the inverse of conditional gametic relationship matrix (G
-1) for a marked QTL. When accounting for inbreeding, the conditional gametic relationships between two parents of individuals for a marked QTL are necessary to build G
-1 directly. Up to now, the tabular method and its adaptations have been used to compute these relationships. In the present paper, an indirect method was implemented at the gametic level to compute these few relationships. Simulation results showed that the indirect method can perform faster with significantly less storage requirements than adaptation of the tabular method. The efficiency of the indirect method was mainly due to the use of the sparseness of G
-1. The indirect method can also be applied to construct an approximate G
-1 for populations with incomplete marker data, providing approximate probabilities of descent for QTL alleles for individuals with incomplete marker data.
Parallel computations on pedigree data through mapping to configurable computing devices
Authors: Henshall John M. , Little Bryce Alvin
Published: June 2009

Pedigree data structures have a number of applications in genetics, including the estimation of allelic or haplotype probabilities in humans and agricultural species, and the estimation of breeding values in agricultural species. Sequential algorithms for general purpose CPU-based computers are commonly used, but are inadequate for some tasks on large data sets. We show that pedigree data can be directly represented on Field Programmable Gate Arrays (FPGA), allowing highly efficient massively parallel simulation of the flow of genes. Operating on the whole pedigree in parallel, the transmission of genes can occur for all individuals in a single clock cycle. By using FPGA, the algorithms to estimate inbreeding coefficients and allelic probabilities are shown to operate hundreds to thousands of times faster than the corresponding sequentially based algorithms. Where problems can be largely represented in an integer form, FPGA provide an efficient platform for computations on pedigree data.
Analysis of rabbit doe longevity using a semiparametric log-Normal animal frailty model with time-dependent covariates
Authors: Sánchez Juan Pablo , Korsgaard Inge Riis , Damgaard Lars Holm , Baselga Manuel
Published: June 2009

Data on doe longevity in a rabbit population were analysed using a semiparametric log-Normal animal frailty model. Longevity was defined as the time from the first positive pregnancy test to death or culling due to pathological problems. Does culled for other reasons had right censored records of longevity. The model included time dependent covariates associated with year by season, the interaction between physiological state and the number of young born alive, and between order of positive pregnancy test and physiological state. The model also included an additive genetic effect and a residual in log frailty. Properties of marginal posterior distributions of specific parameters were inferred from a full Bayesian analysis using Gibbs sampling. All of the fully conditional posterior distributions defining a Gibbs sampler were easy to sample from, either directly or using adaptive rejection sampling. The marginal posterior mean estimates of the additive genetic variance and of the residual variance in log frailty were 0.247 and 0.690.
A 7-bp insertion in the 3' untranslated region suggests the duplication and concerted evolution of the rabbit SRY gene
Authors: Geraldes Armando , Ferrand Nuno
Published: June 2009

In this work we report the genetic polymorphism of a 7-bp insertion in the 3' untranslated region of the rabbit SRY gene. The polymorphic GAATTAA motif was found exclusively in one of the two divergent rabbit Y-chromosomal lineages, suggesting that its origin is more recent than the separation of the O. c. algirus and O. c. cuniculus Y-chromosomes. In addition, the remarkable observation of haplotypes exhibiting 0, 1 and 2 7-bp inserts in essentially all algirus populations suggests that the rabbit SRY gene is duplicated and evolving under concerted evolution.
Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome
Authors: MacEachern Sean , McEwan John , Mather Andrew , McCulloch Alan , Sunnucks Paul , Goddard Mike
Published: June 2009

Despite growing evidence of rapid evolution in protein coding genes, the contribution of positive selection to intra- and interspecific differences in protein coding regions of the genome is unclear. We attempted to see if genes coding for secreted proteins and genes with narrow expression, specifically those preferentially expressed in the mammary gland, have diverged at a faster rate between domestic cattle (Bos taurus) and humans (Homo sapiens) than other genes and whether positive selection is responsible. Using a large data set, we identified groups of genes based on secretion and expression patterns and compared them for the rate of nonsynonymous (dN) and synonymous (dS) substitutions per site and the number of radical (Dr) and conservative (Dc) amino acid substitutions. We found evidence of rapid evolution in genes with narrow expression, especially for those expressed in the liver and mammary gland and for genes coding for secreted proteins. We compared common human polymorphism data with human-cattle divergence and found that genes with high evolutionary rates in human-cattle divergence also had a large number of common human polymorphisms. This argues against positive selection causing rapid divergence in these groups of genes. In most cases dN/dS ratios were lower in human-cattle divergence than in common human polymorphism presumably due to differences in the effectiveness of purifying selection between long-term divergence and short-term polymorphism.
Estimation of non-linear growth models by linearization: a simulation study using a Gompertz function
Authors: Vuori Kaarina , Strandén Ismo , Sevón-Aimonen Marja-Liisa , Mäntysaari Esa A.
Published: June 2009

A method based on Taylor series expansion for estimation of location parameters and variance components of non-linear mixed effects models was considered. An attractive property of the method is the opportunity for an easily implemented algorithm. Estimation of non-linear mixed effects models can be done by common methods for linear mixed effects models, and thus existing programs can be used after small modifications. The applicability of this algorithm in animal breeding was studied with simulation using a Gompertz function growth model in pigs. Two growth data sets were analyzed: a full set containing observations from the entire growing period, and a truncated time trajectory set containing animals slaughtered prematurely, which is common in pig breeding. The results from the 50 simulation replicates with full data set indicate that the linearization approach was capable of estimating the original parameters satisfactorily. However, estimation of the parameters related to adult weight becomes unstable in the case of a truncated data set.
Recording strategies and selection potential of feed intake measured using the X-ray method in rainbow trout
Authors: Kause Antti , Tobin Declan , Dobly Alexandre , Houlihan Dominic , Martin Sam , Mäntysaari Esa A. , Ritola Ossi , Ruohonen Kari
Published: June 2009

This study examines the way long-term feed intake should be recorded accurately for selective breeding purposes, and estimates selection potential in feed intake using the X-ray method to record individual daily feed intake in rainbow trout (Oncorhynchus mykiss). The analysis showed that the point estimates of daily feed intake displayed low repeatabilities (r = 0.09–0.32). This indicates that a minimum of three repeated records were needed to accurately record average feed intake at a fixed age. To effectively breed for feed intake over the whole growing period, it is necessary to determine average feed intake at different ages, since there were only moderate phenotypic and genetic correlations between average daily feed intake recorded at 140 g, 750 g and 2000 g wet mass. Heritability for average daily feed intake was low (average h
2 = 0.10), indicating that modest genetic changes can be obtained in response to selection. It was concluded that selection to genetically change long-term feed intake can be successful, yet repeated observations at several life stages are needed to ensure the accuracy of feed intake estimates and the efficiency of selection.
Phylogeographic study of brown trout from Serbia, based on mitochondrial DNA control region analysis
Authors: Marić Saša , Sušnik Simona , Simonović Predrag , Snoj Aleš
Published: June 2009

In order to illuminate the phylogeography of brown trout (Salmo trutta) populations in the Balkan state of Serbia, the 561 bp 5'-end of mtDNA control region of 101 individuals originating from upland tributaries of the Danubian, Aegean and Adriatic drainages were sequenced and compared to corresponding brown trout sequences obtained in previous studies. Among 15 haplotypes found, 14 were considered native, representing the Danubian and Adriatic lineages of the brown trout, while one haplotype (ATcs1), found only in two individuals originating from two stocked rivers, corresponded to the Atlantic lineage and was considered introduced. Native haplotypes exhibited a strong geographic pattern of distribution: the Danubian haplotypes were strictly confined to the Danubian drainage, while the Adriatic haplotypes dominated in the Aegean and Adriatic drainages; most of the total molecular variance (69%) was attributed to differences among the drainages. Phylogenetic reconstruction, supplemented with seven haplotypes newly described in this study, suggested a sister position of the Atlantic-Danubian and Adriatic-Mediterranean-marmoratus ("southern") phylogenetic group, and pointed to the existence of a distinct clade, detected within the "southern" group. The data obtained confirmed our expectation of the existence of high genetic diversity in Balkan trout populations, and we recommend more widespread surveys covering trout stocks from the region.
The effects of selective breeding against scrapie susceptibility on the genetic variability of the Latxa Black-Faced sheep breed
Authors: Alfonso Leopoldo , Parada Analia , Legarra Andrés , Ugarte Eva , Arana Ana
Published: June 2009

Breeding sheep populations for scrapie resistance could result in a loss of genetic variability. In this study, the effect on genetic variability of selection for increasing the ARR allele frequency was estimated in the Latxa breed. Two sources of information were used, pedigree and genetic polymorphisms (fifteen microsatellites). The results based on the genealogical information were conditioned by a low pedigree completeness level that revealed the interest of also using the information provided by the molecular markers. The overall results suggest that no great negative effect on genetic variability can be expected in the short time in the population analysed by selection of only ARR/ARR males. The estimated average relationship of ARR/ARR males with reproductive females was similar to that of all available males whatever its genotype: 0.010 vs. 0.012 for a genealogical relationship and 0.257 vs. 0.296 for molecular coancestry, respectively. However, selection of only ARR/ARR males implied important losses in founder animals (87 percent) and low frequency alleles (30 percent) in the ram population. The evaluation of mild selection strategies against scrapie susceptibility based on the use of some ARR heterozygous males was difficult because the genetic relationships estimated among animals differed when pedigree or molecular information was used, and the use of more molecular markers should be evaluated.
Polymorphisms of two Y chromosome microsatellites in Chinese cattle
Authors: Cai Xin , Chen Hong , Wang Shan , Xue Kai , Lei Chuzhao
Published: June 2009

Two Y chromosome specific microsatellites UMN2404 and UMN0103 were genotyped and assessed for polymorphisms in a total of 423 unrelated males from 25 indigenous Chinese cattle breeds. Consistently, both microsatellites displayed specific indicine and taurine alleles in each bull examined. The indicine and taurine alleles were detected in 248 males (58.6%), and 175 males (41.4%), respectively, although these frequencies varied amongst different breeds examined. The indicine alleles dominated in the southern group (92.4%), while the taurine alleles dominated in the northern group (95.5%). Hainan Island was possibly the site for the origin of Chinese zebu, and Tibetan cattle were probably independently domesticated from another strain of Bos primigenius. The geographical distribution of these frequencies reveals a pattern of male indicine introgression and a hybrid zone of indicine and taurine cattle in China. The declining south-to-north and east-to-west gradient of male indicine introgression in China could be explained by historical data, geographical segregation and temperature and weather conditions.
Sequence heterogeneity and phylogenetic relationships between the copia retrotransposon in Drosophila species of the repleta and melanogaster groups
Authors: De Almeida Luciane M. , Carareto Claudia M.A.
Published: June 2009

Although the retrotransposon copia has been studied in the melanogaster group of Drosophila species, very little is known about copia dynamism and evolution in other groups. We analyzed the occurrence and heterogeneity of the copia 5'LTR-ULR partial sequence and their phylogenetic relationships in 24 species of the repleta group of Drosophila. PCR showed that copia occurs in 18 out of the 24 species evaluated. Sequencing was possible in only eight species. The sequences showed a low nucleotide diversity, which suggests selective constraints maintaining this regulatory region over evolutionary time. On the contrary, the low nucleotide divergence and the phylogenetic relationships between the D. willistoni/Zaprionus tuberculatus/melanogaster species subgroup suggest horizontal transfer. Sixteen transcription factor binding sites were identified in the LTR-ULR repleta and melanogaster consensus sequences. However, these motifs are not homologous, neither according to their position in the LTR-ULR sequences, nor according to their sequences. Taken together, the low motif homologies, the phylogenetic relationship and the great nucleotide divergence between the melanogaster and repleta copia sequences reinforce the hypothesis that there are two copia families.
Comparative analysis of vertebrate EIF2AK2 (PKR) genes and assignment of the equine gene to ECA15q24–q25 and the bovine gene to BTA11q12–q15
Authors: Perelygin Andrey A. , Lear Teri L. , Zharkikh Andrey A. , Brinton Margo A.
Published: June 2009

The structures of the canine, rabbit, bovine and equine EIF2AK2 genes were determined. Each of these genes has a 5' non-coding exon as well as 15 coding exons. All of the canine, bovine and equine EIF2AK2 introns have consensus donor and acceptor splice sites. In the equine EIF2AK2 gene, a unique single nucleotide polymorphism that encoded a Tyr329Cys substitution was detected. Regulatory elements predicted in the promoter region were conserved in ungulates, primates, rodents, Afrotheria (elephant) and Insectifora (shrew). Western clawed frog and fugu EIF2AK2 gene sequences were detected in the USCS Genome Browser and compared to those of other vertebrate EIF2AK2 genes. A comparison of EIF2AK2 protein domains in vertebrates indicates that the kinase catalytic domains were evolutionarily more conserved than the nucleic acid-binding motifs. Nucleotide substitution rates were uniform among the vertebrate sequences with the exception of the zebrafish and goldfish EIF2AK2 genes, which showed substitution rates about 20% higher than those of other vertebrates. FISH was used to physically assign the horse and cattle genes to chromosome locations, ECA15q24–q25 and BTA11q12–15, respectively. Comparative mapping data confirmed conservation of synteny between ungulates, humans and rodents.
Genetic analysis of growth curves using the SAEM algorithm
Authors: Jaffrézic Florence , Meza Cristian , Lavielle Marc , Foulley Jean-Louis
Published: June 2009

The analysis of nonlinear function-valued characters is very important in genetic studies, especially for growth traits of agricultural and laboratory species. Inference in nonlinear mixed effects models is, however, quite complex and is usually based on likelihood approximations or Bayesian methods. The aim of this paper was to present an efficient stochastic EM procedure, namely the SAEM algorithm, which is much faster to converge than the classical Monte Carlo EM algorithm and Bayesian estimation procedures, does not require specification of prior distributions and is quite robust to the choice of starting values. The key idea is to recycle the simulated values from one iteration to the next in the EM algorithm, which considerably accelerates the convergence. A simulation study is presented which confirms the advantages of this estimation procedure in the case of a genetic analysis. The SAEM algorithm was applied to real data sets on growth measurements in beef cattle and in chickens. The proposed estimation procedure, as the classical Monte Carlo EM algorithm, provides significance tests on the parameters and likelihood based model comparison criteria to compare the nonlinear models with other longitudinal methods.
Genetic heterogeneity of residual variance in broiler chickens
Authors: Rowe Suzanne J , White Ian MS , Avendaño Santiago , Hill William G
Published: June 2009

Aims were to estimate the extent of genetic heterogeneity in environmental variance. Data comprised 99 535 records of 35-day body weights from broiler chickens reared in a controlled environment. Residual variance within dam families was estimated using ASREML, after fitting fixed effects such as genetic groups and hatches, for each of 377 genetically contemporary sires with a large number of progeny (> 100 males or females each). Residual variance was computed separately for male and female offspring, and after correction for sampling, strong evidence for heterogeneity was found, the standard deviation between sires in within variance amounting to 15–18% of its mean. Reanalysis using log-transformed data gave similar results, and elimination of 2–3% of outlier data reduced the heterogeneity but it was still over 10%. The correlation between estimates for males and females was low, however. The correlation between sire effects on progeny mean and residual variance for body weight was small and negative (-0.1). Using a data set bigger than any yet presented and on a trait measurable in both sexes, this study has shown evidence for heterogeneity in the residual variance, which could not be explained by segregation of major genes unless very few determined the trait.
Comparison of methods for analysis of selective genotyping survival data
Authors: McElroy Joseph P , Zhang Wuyan , Koehler Kenneth J , Lamont Susan J , Dekkers Jack CM
Published: June 2009

Survival traits and selective genotyping datasets are typically not normally distributed, thus common models used to identify QTL may not be statistically appropriate for their analysis. The objective of the present study was to compare models for identification of QTL associated with survival traits, in particular when combined with selective genotyping. Data were simulated to model the survival distribution of a population of chickens challenged with Marek disease virus. Cox proportional hazards (CPH), linear regression (LR), and Weibull models were compared for their appropriateness to analyze the data, ability to identify associations of marker alleles with survival, and estimation of effects when all individuals were genotyped (full genotyping) and when selective genotyping was used. Little difference in power was found between the CPH and the LR model for low censoring cases for both full and selective genotyping. The simulated data were not transformed to follow a Weibull distribution and, as a result, the Weibull model generally resulted in less power than the other two models and overestimated effects. Effect estimates from LR and CPH were unbiased when all individuals were genotyped, but overestimated when selective genotyping was used. Thus, LR is preferred for analyzing survival data when the amount of censoring is low because of ease of implementation and interpretation. Including phenotypic data of non-genotyped individuals in selective genotyping analysis increased power, but resulted in LR having an inflated false positive rate, and therefore the CPH model is preferred for this scenario, although transformation of the data may also make the Weibull model appropriate for this case. The results from the research presented herein are directly applicable to interval mapping analyses.
Sox genes in grass carp (Ctenopharyngodon idella) with their implications for genome duplication and evolution
Authors: Zhong Lei , Yu Xiaomu , Tong Jingou
Published: June 2009

The Sox gene family is found in a broad range of animal taxa and encodes important gene regulatory proteins involved in a variety of developmental processes. We have obtained clones representing the HMG boxes of twelve Sox genes from grass carp (Ctenopharyngodon idella), one of the four major domestic carps in China. The cloned Sox genes belong to group B1, B2 and C. Our analyses show that whereas the human genome contains a single copy of Sox4, Sox11 and Sox14, each of these genes has two co-orthologs in grass carp, and the duplication of Sox4 and Sox11 occurred before the divergence of grass carp and zebrafish, which support the "fish-specific whole-genome duplication" theory. An estimation for the origin of grass carp based on the molecular clock using Sox1, Sox3 and Sox11 genes as markers indicates that grass carp (subfamily Leuciscinae) and zebrafish (subfamily Danioninae) diverged approximately 60 million years ago. The potential uses of Sox genes as markers in revealing the evolutionary history of grass carp are discussed.
Character process model for semen volume in AI rams: evaluation of correlation structures for long and short-term environmental effects
Authors: David Ingrid , Bodin Loys , Lagriffoul Gilles , Manfredi Eduardo , Robert-Granié Christèle
Published: June 2009

The objective of this study was to build a character process model taking into account serial correlations for the analysis of repeated measurements of semen volume in AI rams. For each ram, measurements were repeated within and across years. Therefore, we considered a model including three environmental effects: the long-term environmental effect, which is a random year* subject effect, the short-term environmental effect, which is a random within year subject* collection effect, and the classical measurement error. We used a four-step approach to build the model. The first step explored graphically the serial correlations. The second step compared four models with different correlation structures for the short-term environmental effect. We selected fixed effects in the third step. In the fourth step, we compared four correlation structures for the long-term environmental effect. The model, which fitted best the data, used a spatial power correlation structure for the short-term environmental effect and a first order autoregressive process for the long-term environmental effect. The heritability estimate was 0.27 (0.04), the within year repeatability decreased from 0.56 to 0.44 and the repeatability across years decreased from 0.43 to 0.37.