bluuebunny/crossref_metadata_2025_split huggingface dataset:
Subsurface Jets in the Northwestern Gulf of Mexico
Authors: Hamilton Peter , Badan Antoine 
Published: June 2009

Abstract
Subsurface jets, defined as having velocity maxima &gt;40 cm s−1 at depths between 100 and 350 m, and being surrounded by much weaker near-surface currents, have been observed over the northwestern Gulf of Mexico continental slope. The observations were from an array of 14 moorings equipped with upward-looking 75-kHz ADCPs deployed at 450–500 m. A total of 10 jet events were observed in 18 ADCP years of velocity profile data, where these events were clearly not the result of downward-propagating inertial internal waves. The jets had durations from about 1 to 8 days and were usually associated with interactions between similarly sized cyclones and anticyclones over the slope or with the interaction of an eddy with upper-slope topography. The jets are associated with potential vorticity anomalies and their inferred length scales indicate that the dynamics depart from simple geostrophic balances. Observed anomalous density gradients present during the jets seem to involve the tilting of the vertical axis of the center of rotation of one or more of the interacting eddies.
Intercomparison of Spatial Forecast Verification Methods
Authors: Gilleland Eric , Ahijevych David , Brown Barbara G. , Casati Barbara , Ebert Elizabeth E. 
Published: June 2009

Abstract
Advancements in weather forecast models and their enhanced resolution have led to substantially improved and more realistic-appearing forecasts for some variables. However, traditional verification scores often indicate poor performance because of the increased small-scale variability so that the true quality of the forecasts is not always characterized well. As a result, numerous new methods for verifying these forecasts have been proposed. These new methods can mostly be classified into two overall categories: filtering methods and displacement methods. The filtering methods can be further delineated into neighborhood and scale separation, and the displacement methods can be divided into features based and field deformation. Each method gives considerably more information than the traditional scores, but it is not clear which method(s) should be used for which purpose.
A verification methods intercomparison project has been established in order to glean a better understanding of the proposed methods in terms of their various characteristics and to determine what verification questions each method addresses. The study is ongoing, and preliminary qualitative results for the different approaches applied to different situations are described here. In particular, the various methods and their basic characteristics, similarities, and differences are described. In addition, several questions are addressed regarding the application of the methods and the information that they provide. These questions include (i) how the method(s) inform performance at different scales; (ii) how the methods provide information on location errors; (iii) whether the methods provide information on intensity errors and distributions; (iv) whether the methods provide information on structure errors; (v) whether the approaches have the ability to provide information about hits, misses, and false alarms; (vi) whether the methods do anything that is counterintuitive; (vii) whether the methods have selectable parameters and how sensitive the results are to parameter selection; (viii) whether the results can be easily aggregated across multiple cases; (ix) whether the methods can identify timing errors; and (x) whether confidence intervals and hypothesis tests can be readily computed.
Repair of Chronic Rupture of the Achilles Tendon using 2 Intratendinous Flaps from the Proximal Gastrocnemius-Soleus Complex
Authors: El Shewy Mohamed Taha , El Barbary Hassan Magdy , Abdel-Ghani Hisham 
Published: June 2009

Background Chronic rupture of the Achilles tendon is a surgical challenge, owing to the presence of a gap between the retracted ends, which renders direct repair almost impossible. Purpose In this study, 2 intratendinous distally based flaps fashioned from the proximal gastrocnemius-soleus complex are used to bridge the gap between the retracted edges of the ruptured Achilles tendon. The flaps are placed in the same line of pull of the ruptured tendon, in an effort to make the graft mimic the original biomechanics as much as possible. Study Design Case series; Level of evidence, 4. Methods Eleven patients (9 male and 2 female) with neglected ruptures of the Achilles tendon with retracted ends were included in this study. Two flaps fashioned from the proximal gastrocnemius-soleus complex were rotated over themselves, passed through the proximal stump, and then securely inserted into a previously prepared bed in the distal stump. Results The patients were followed up for a period of 6 to 9 years. At the final follow-up, all patients were able to return to their preinjury level of activity within a period of 6 to 9 months. The mean preoperative American Orthopedic Foot and Ankle Society score was 42.27, whereas it was 98.91 at the final follow-up, with a range of 88 (in 1 patient) to 100 points (in 10 patients). All 11 patients showed statistically significant improvement according to the Holz rating system. Conclusion This technique allows for a bridging of the defect present in chronic ruptures of Achilles tendons, with a minimum of complications and a good final outcome.
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

AbstractAlthough 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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.