Biomedical subjects

V Ducrocq

Publications and source records attributed to V Ducrocq.

At least 19 recordsLinked to original sources

PubMed2006

Genetic and environmental correlations between longevity and litter size in rabbits.

An estimation of the genetic and environmental correlations between prolificacy (kits born alive and number of kits at weaning) and functional longevity in a population selected for litter size at weaning since 1992 was carried out. The method is only an approximation, but suggests that genetically longevity and litter size are not antagonistic objectives in breeding programmes, because the estimated genetic correlations are not significantly different from zero.

Animals↗

PubMed2006

Survival analysis in two lines of rabbits selected for reproductive traits.

The objective of the study was to analyze the reproductive longevity of 2 selected lines of rabbits. The first one was the Prat line, a line selected in Spain on litter size at weaning, and raised in overlapping generations. The second one was a French line, the A1077 line, selected on litter size at birth and individual weight at 63 d of age, managed in batches, and artificially inseminated with discrete generations. Reproductive longevity was measured beginning at the first successful mating, assessed by a pregnancy diagnosis in the Prat line, and at the first kindling in the A1077 line. In the A1077 line, culling for infertility occurred after 3 unsuccessful artificial inseminations. The trait analyzed, defined as the doe length of productive life (LPL), was the time in days between date of the first positive pregnancy diagnosis and date of culling or death in the Prat line. In the A1077 line, the trait was the number of AI after the first kindling. Effects included in the model were year-season, litter size at birth, reproductive cycle or physiological status x cycle interaction, age at first mating, batch (only for the A1077 line), and additive genetic value of the animal as a random effect. Survival analyses were carried out with a Cox model for the Prat line and a discrete model for the A1077 line. The estimated heritability values for LPL were around 0.16 in the Prat and A1077 lines with a model including physiological status x cycle interaction effect. Removing this effect from the model led to an increase in estimated genetic variance with h2 = 0.24 and 0.19 in the Prat and A1077 lines, respectively. Including the traits LPL and number of AI from first fertile mating or AI in selection programs could increase reproductive longevity and decrease the replacement rate.

Animals↗

PubMed2006

Analysis of longevity and exterior traits on Large White sows in Switzerland.

Records of length of productive life, from first farrowing to culling, of 16,464 Large White purebred sows from SUISAG were studied using survival analysis. The major aims of the study were to model the risk of culling within parity and to assess the influence of exterior traits, such as the number of teats or feet and leg scores, on culling. Culling was concentrated at the first day after each farrowing or at the first day after weaning. Weaning itself was mostly between 21 and 49 d after farrowing, with an average weaning age of 35 d. Because of the definition of culling date used, there was practically no risk of culling from these periods. The culling rates at different periods suggested a modeling of the baseline hazard function within parity instead of over the entire productive life of the animals. A piecewise Weibull function and a simple graphical method to validate its adequacy were proposed for sow longevity analysis. The risk of culling increased with older parities (P < 0.001) and with decreasing litter size at weaning (P < 0.001). The exterior traits analyzed (number of teats, and feet and leg scores, on a scale from 1 to 7) had a moderate effect on the risk of culling compared with other factors but were still influential on survival, productive life expectancy, and annual replacement rate. Sows with less than 13 good teats had 1.35 times greater risk of being culled than sows with more good teats (P < 0.05). Sows with an X-O rear leg score of 2 had 1.4 times greater risk of being culled than sows with an intermediate score of 4 (P < 0.05). Sows at the optimum score of 4 for the size of inner claws of the rear leg had 0.83 times less risk of being culled (P < 0.01) than sows with scores of 2 and 3. Furthermore, when a phenotypic index for feet and legs was used to group these variables, the effect was highly significant (P < 0.001). Therefore, a means to improve longevity is through phenotypic selection of replacement gilts based on exterior traits: gilts with 13 or less good teats or with extreme feet and leg scores should be culled. From a genetic point of view, sows with the best value in the current index for exterior traits had a lower risk of culling (P < 0.01), and therefore, it is possible to obtain a response for sow longevity via indirect selection for exterior traits. From 1999 to 2003, the trend has been to eliminate extreme animals on exterior traits. This may partly explain the improvement of sow length of productive life longevity from 560 d in 2000 to nearly 710 d in 2003 observed in the data set.

Animal Husbandry↗

PubMed2006

Estimation of genetic correlations among countries in international dairy sire evaluations with structural models.

The increase in the number of participating countries and the lack of genetic ties between some countries has lead to statistical and computational difficulties in estimating the genetic (co)variance matrix needed for international sire evaluation of milk yield and other traits. Structural models have been proposed to reduce the number of parameters to estimate by exploiting patterns in the genetic correlation matrix. Genetic correlations between countries are described as a simple function of unspecified country characteristics that can be mapped in a space of limited dimensions. Two link functions equal to the exponential of minus the Euclidian distance between the coordinates of two countries and the exponential of minus the square of this Euclidian distance were used for the study on international simulated and field data. On simulated data, it was shown that structural models might allow an easier estimation of genetic correlations close to the border of the parameter space. This is not always possible with an unstructured model. On milk yield data, genetic correlations obtained from 22 countries for structural models based on 2 and 7 dimensions, respectively, were analyzed. Only a structural model with a large number of axes gave reasonable estimates of genetic correlations compared with correlations obtained for an unstructured model: 76.7% of correlations deviated by less than 0.030. Such a model reduces the number of parameters from 231 genetic correlations to 126 coordinates. On foot angle data, large deviations were observed between genetic correlations estimated with an unstructured model and correlations estimated with a structural model, regardless of the number of axes taken into account.

Algorithms↗

PubMed2006

Development of a survival model with piecewise Weibull baselines for the analysis of length of productive life of Holstein cows in Japan.

A total of 100,000 records of Holstein dairy cows in Hokkaido, Japan, were used to study the current characteristics of their length of productive life, to build up a suitable model for genetic survival analysis, and to apply the piecewise Weibull baseline model. The data for this analysis only included records of cows belonging to herds in which more than 60% of cows had type score. Compared with other studies, the proportions of cows with only 1 or 2 calvings were low (24 and 46%, respectively), indicating a very low culling rate in first or second parity in Hokkaido. The median length of productive life was about 1,250 d (3 yr and 5 mo). Four different definitions of stages of lactation were studied. The best fit of the data was obtained when stages of lactation were chosen with cutpoints at 0, 60, 250, and 350 d after calving. Whatever the definition of stages of lactation, the piecewise Weibull baseline model was better than a unique baseline model. The estimated shape Weibull parameters rho for the different parity x stage of lactation combinations varied greatly (1.0 to 5.0). The estimated hazard functions based on the piecewise Weibull baseline model were smooth and reflected the important changes in observed hazard within lactation. The results of this study are expected to contribute to the development of a genetic model for sire evaluation and to genetic improvement of length of productive life of Holstein cattle in Hokkaido, Japan.

Animals↗

PubMed2006

Short communication: genetic evaluation of the interval from first to last insemination with survival analysis and linear models.

Sire breeding values for the interval between the first and last insemination were predicted using 4 proportional hazards models (survival analyses) and 2 linear mixed models to determine which would result in a more accurate genetic evaluation. A stochastic simulation describing the reproductive cycle of first-parity cows was conducted, in which true breeding values for conception rate were created. The model included the effects of sire and herd. The highest correlations between true breeding values for conception rate and breeding values for the interval between first and last insemination predicted by the survival analysis model and the linear model were 0.803 and 0.744, respectively. The results showed that when pregnancy status was known, survival models were more accurate than linear models to predict breeding values for conception rate when using observations on the interval between first and last insemination.

Animals↗

PubMed2005

Interval mapping methods for detecting QTL affecting survival and time-to-event phenotypes.

Quantitative trait loci (QTL) are usually searched for using classical interval mapping methods which assume that the trait of interest follows a normal distribution. However, these methods cannot take into account features of most survival data such as a non-normal distribution and the presence of censored data. We propose two new QTL detection approaches which allow the consideration of censored data. One interval mapping method uses a Weibull model (W), which is popular in parametrical modelling of survival traits, and the other uses a Cox model (C), which avoids making any assumption on the trait distribution. Data were simulated following the structure of a published experiment. Using simulated data, we compare W, C and a classical interval mapping method using a Gaussian model on uncensored data (G) or on all data (G'=censored data analysed as though records were uncensored). An adequate mathematical transformation was used for all parametric methods (G, G' and W). When data were not censored, the four methods gave similar results. However, when some data were censored, the power of QTL detection and accuracy of QTL location and of estimation of QTL effects for G decreased considerably with censoring, particularly when censoring was at a fixed date. This decrease with censoring was observed also with G', but it was less severe. Censoring had a negligible effect on results obtained with the W and C methods.

Animals↗

PubMed2005

Genetic analysis of herd life in Canadian dairy cattle on a lactation basis using a Weibull proportional hazards model.

The objectives of this study were to identify the most important factors that influence functional survival and to estimate the genetic parameters of functional survival for Canadian dairy cattle. Data were obtained from lactation records extracted for the May 2002 genetic evaluation of Holstein, Jersey, and Ayrshire breeds that calved between July 1, 1985 and April 5, 2002. Analysis was performed using a Weibull proportional hazard model, and the baseline hazard function was defined on a lactation basis instead of the traditional analysis of the whole length of life. The statistical model included the effects of stage of lactation; season of production; the annual change in herd size; type of milk recording supervision; age at first calving; effects of milk, fat, and protein yields calculated within herd-year-parity deviations; and the random effects of herd-year-season of calving and sire. All effects fitted in the model had a significant effect on functional survival of cows in all breeds. Milk yield was by far the most important factor influencing survival, and the hazard increased as the milk production of the cows decreased. The hazard also increased as the fat content increased compared with the average group. Heifers that were older at calving were at higher risk of being culled, and expanding herds were at lower risk of being culled compared with stable herds. More culling was found in unsupervised herds than in supervised herds. The heritability values obtained were 0.14, 0.10, and 0.09 for Holstein, Jersey, and Ayrshire, respectively. Rank correlation between estimated breeding values (EBV) obtained from the current national genetic evaluation of direct herd life and the survival kit used in this study ranged from 0.65 to 0.87, depending on the number of daughters per sire. Estimated genetic trend obtained using the survival kit was overestimated.

Animals↗

PubMed2005

Survival analysis applied to genetic evaluation for female fertility in dairy cattle.

The objective of this research was to study whether survival analysis results in a more accurate genetic evaluation for female fertility traits compared with the usual methodology based on linear models. The fertility trait studied was interval between calving and last insemination. A stochastic simulation describing the reproductive cycle of first-parity cows was done, in which true breeding values for conception rate were created. A model containing effects of sire and herd was used both with survival analysis and with mixed linear model analysis to predict sire breeding values. Correlations between true breeding values for conception rate and breeding values for calving to last insemination predicted by the best survival analysis model or the best linear model were 0.77 and 0.68, respectively. The results showed that when pregnancy status is known, survival analysis is a better method than linear models for genetic evaluation of conception rate when using observations on the interval between calving and last insemination.

Animals↗

PubMed2005

Principal components and factorial approaches for estimating genetic correlations in international sire evaluation.

The increasing number of participating countries and the lack of genetic links among some of them lead to statistical and computational difficulties in estimating the genetic (co)variance matrix needed for international sire evaluation of milk yield. Reparameterization using principal components or factorial approaches is proposed to exploit patterns in the genetic correlation matrix in order to reduce the number of parameters to be estimated without much loss of information. A 2-step approach was used. First, the genetic matrix between 8 or 9 "base" countries was used to determine a reduced number of principal components or factors. Then, the contributions of the remaining countries to these principal components or factors were computed. The resulting genetic correlations for the 18 countries were compared with the "reference" genetic correlations obtained with a classical model. The impact of using reparameterized genetic correlation matrices on breeding value prediction was investigated for both approaches. A better agreement between predicted breeding values and stability of their rankings was found when an approximate factor analysis was used, whatever the number of factors considered. The estimation of genetic correlations among 18 countries using an approximate factorial approach with 5 factors taken into account led to a reduction of the number of parameters to estimate from 171 to 80. The average absolute deviation of the correlations estimated with an approximate factorial approach from the "reference" genetic correlations was 0.014, which is considered very satisfactory in light of the computational ease.

Analysis of Variance↗

PubMed2003

The distinctive isotopic signature of plant-derived chloromethane: possible application in constraining the atmospheric chloromethane budget.

Chloromethane (CH(3)Cl) is the most abundant halocarbon in the atmosphere. Although largely of natural origin it is responsible for around 17% of chlorine-catalysed ozone destruction. Sources identified to date include biomass burning, oceanic emissions, wood-rotting fungi, higher plants and most recently tropical ferns. Current estimates reveal a shortfall of around 2 million ty(-1) in sources versus sinks for the halocarbon. It is possible that emissions from green plants have been substantially underestimated. A potentially valuable tool for validating emission flux estimates is comparison of the delta13C value of atmospheric CH(3)Cl with those of CH(3)Cl from the various sources. Here we report delta13C values for CH(3)Cl released by two species of tropical ferns and show that the isotopic signature of CH(3)Cl from pteridophytes like that of CH(3)Cl from higher plants is quite different from that of CH(3)Cl produced by biomass burning, fungi and industry. delta13C values for CH(3)Cl produced by Cyathea smithii and Angiopteris evecta were respectively -72.7 per thousand and -69.3 per thousand representing depletions relative to plant biomass of 42.3 per thousand and 43.4 per thousand. The characteristic isotopic signature of CH(3)Cl released by green plants should help constrain their contribution to the atmospheric burden when reliable delta13C values for all other major sources of CH(3)Cl are obtained and a globally averaged delta13C value for atmospheric CH(3)Cl is available.

Air Pollutants↗

PubMed2003

Mortality of Creole kids during infection with gastrointestinal strongyles: a survival analysis.

Mortality due to strongyles infection in small ruminants is a critical component of flock productivity in a tropical climate. In goat production, few experiments have been conducted to estimate the variability of this trait. A survival analysis study was carried out in the Creole experimental flock of INRA-Gardel (Moule, Guadeloupe) to identify management and genetic factors influencing mortality of kids reared at pasture and infected with gastrointestinal strongyles, predominantly Haemonchus contortus and Trichostrongylus colubriformis. Survival curves from 3 and 11 mo of age were analyzed for 837 kids sired by 48 bucks and 250 does. The causes of death were recorded. Mortality due to gastrointestinal strongyles was the variable considered. The flock management included drenchings with levamisole every 8 wk. Fecal egg counts and packed cell volume were regularly measured after 7 wk of natural infection. All but 6.7% of the records were uncensored, with an average failure time of 165 d. The probability of death following gastrointestinal infection was more than three times greater in males than in females. Kids raised by their mother before weaning had a lower (P < 0.05) relative risk of dying than those reared in nursery (0.40 vs. 1). Parity of the dam and litter size effects were not significant. The risk of death was reduced by approximately 80% during the 3 wk that followed a drenching (P < 0.01). Risk decreased by about 25% for each additional kilogram of body weight at weaning. Live weight, fecal egg counts, and packed cell volume all had significant effects on risk of death when introduced as time-dependent covariates in the model (P < 0.0001 for live weight and packed cell volume, and P < 0.01 for fecal egg counts). The estimated genetic variability was small and inaccurate. These results demonstrated that risk of death from gastrointestinal infection could be reduced with appropriate flock management. High infection levels increased the risk of death, but they were not the direct cause. The important mediation of reduced body weight and anemia in likelihood of death is highlighted. More data are needed to better assess the possibility for genetic improvement of viability in Creole kids during gastrointestinal strongyle infection.

Animals↗

PubMed2003

Modeling lactation curves and estimation of genetic parameters for first lactation test-day records of French Holstein cows.

Several functions were used to model the fixed part of the lactation curve and genetic parameters of milk test-day records to estimate using French Holstein data. Parametric curves (Legendre polynomials, Ali-Schaeffer curve, Wilmink curve), fixed classes curves (5-d classes), and regression splines were tested. The latter were appealing because they adjusted the data well, were relatively insensitive to outliers, were flexible, and resulted in smooth curves without requiring the estimation of a large number of parameters. Genetic parameters were estimated with an Average Information REML algorithm where the average information matrix and the first derivatives of the likelihood functions were pooled over 10 samples. This approach made it possible to handle larger data sets. The residual variance was modeled as a quadratic function of days in milk. Quartic Legendre polynomials were used to estimate (co)variances of random effects. The estimates were within the range of most other studies. The greatest genetic variance was in the middle of the lactation while residual and permanent environmental variances mostly decreased during the lactation. The resulting heritability ranged from 0.15 to 0.40. The genetic correlation between the extreme parts of the lactation was 0.35 but genetic correlations were higher than 0.90 for a large part of the lactation. The use of the pooling approach resulted in smaller standard errors for the genetic parameters when compared to those obtained with a single sample.

Animals↗

PubMed2002

Heritability, reliability of genetic evaluations and response to selection in proportional hazard models.

The purposes of this study were 1) to investigate the heritability, reliability, and selection response for survival traits following a Weibull frailty proportional hazard model; and 2) to examine the relationship between genetic parameters from a Weibull model, a discrete proportional hazard model, and a binary data analysis using a linear model. Both analytical methods and Monte Carlo simulations were used to achieve these aims. Data were simulated using the Weibull frailty model with two different shapes of the Weibull distribution. Breeding values of 100 unrelated sires with 50 to 100 progeny (with different levels of censoring) were generated from a normal distribution and two different sire variances. For analysis of longevity data on the discrete scale, simulated data were transformed to a discrete scale using arbitrary ends of discrete intervals of 400, 800, or 1200 d. For binary data analysis, an individual's longevity was either 0 (when longevity was less than the end of interval) or 1 (when longevity was equal or greater than the end of interval). Three different statistical models were investigated in this study: a Weibull model, a discrete-time model (a proportional hazard model assuming that the survival data are measured on a discrete scale with few classes), and a linear model based upon binary data. An alternative derivation using basic expressions of reliabilities in sire models suggests a simple equation for the heritability on the original scale (effective heritability) that is not dependent on the Weibull parameters. The predictions of reliabilities using the proposed formulae in this study are in very good agreement with reliabilities observed from simulations. In general, the estimates of reliability from either the discrete model or the binary data analysis were close to estimates from the Weibull model for a given number of uncensored records in this simplified case of a balanced design. Although selection response from the binary data analysis depends on the end of interval point, there is a relatively good agreement between selection responses in the Weibull model and the binary data analysis. In general, when the underlying survival data is from a Weibull distribution, it appears that the method of analyzing data does not greatly affect the results in terms of sire ranking or response to selection, at least for the simplified context considered in this study.

Animals↗

PubMed2002

[Acute respiratory failure in obesity].

Obstructive sleep apnea, obesity-related hypoventilation - a hypoventilation which is independent of apneas and increased by sleep -, and hypoxemia related to local ventilation-perfusion disorders are the main mechanisms of respiratory failure occurring during acute respiratory decompensation following an often minimal triggering event. Non-invasive ventilation has been found to be an effective treatment, particularly with a ventilator capable of maintaining positive expiratory and pressure. The level of the expiratory positive airway pressure must be adapted to cure episodes of obstructive apnea or hypopnea. The level of the inspiratory positive airway pressure (pressure support ventilator), or the tidal volume (volume-controlled ventilator) must be adapted to correct the residual hypoventilation. These adaptations can be made by proper assessment of nocturnal SaO(2) recordings. In particularly severe cases, use of endotracheal ventilation may be necessary to control a state of shock or consciousness disorders incompatible with the patient cooperation necessary for non-invasive ventilation.

Acute Disease↗

PubMed2001

Analysis of survival in dairy cows with supplementary data on type scores and housing systems from a region of northwest Germany.

In survival analysis, type traits can be included as covariates to evaluate their use as predictors for survival. One problem in such an analysis is the availability of suitable data. Whereas data on the length of productive life (LPL) of individual cows can be retrieved from milk recording data, for type traits, all cows in the population must be scored for type at least once. In the present analysis, a dataset from the Osnabruck region in northwestern Germany, which fulfilled this requirement in recent years, was used. Data consisted of 169,733 cows with information on LPL for calving years 1980 to 1996 (dataset I) and of 39,233 cows with information on LPL and type for calving years 1990 to 1996 (dataset II). A further dataset (III) contained 43,116 cows from calving years 1987 to 1996 and included information on the housing system for each herd. The basic model included stage of lactation, relative production within herd, change of herd size, and year-season as time dependent effects; age at calving as a time-independent effect; and herd-year-season and sire as random effects. Other effects (information on type, housing system) were included additionally. For data-set II, the scores for 15 linear type traits were also included as corrected phenotypic values, estimated breeding values, and residuals from a previous BLUP analysis. The package Survival Kit 3.0 was used for all analyses. The results indicate a moderate heritability of 0.17 and 0.18 for true and functional LPL (dataset I). Almost all type traits analyzed (dataset II) exceeded a 0.001 level of significance in their effect on survival. The strongest relationships between survival and type were found for udder depth, fore udder attachment, and front teat placement. The main result from the comparison of housing systems (dataset III) was that bedding has a positive effect on survival.

Age Factors↗

PubMed1999

Genetic susceptibility and transmission factors in scrapie: detailed analysis of an epidemic in a closed flock of Romanov.

Information from a scrapie epidemic in a closed INRA Romanov flock is presented. Performances, pedigree, histopathological diagnoses and PrP genotypes were recorded from the beginning of the outbreak (in 1993). Between 1st of April, 1993 and 1st of May, 1997, 1015 animals were exposed to scrapie, and 304 died from this disease. A major influence of the polymorphisms at codons 136, 154 and 171 is shown, A136H154Q171 allele carriers proving to be nearly as resistant as A136R154R171 carriers. A possible relationship between gastrointestinal parasitism and scrapie is discussed. There is evidence of maternal transmission, with a risk ratio for artificially fed lambs of 67 percent of the risk of lambs fed by their mother. Our results strongly suggest that resistant animals were not healthy carriers or at least were less infectious when comparing risk for lambs born to healthy dams either of resistant (risk = 0.431) or of susceptible (risk = 1.000) genotype.

Animals↗

PubMed1999

Cloning and characterization of the genes encoding a cytochrome P450 (PipA) involved in piperidine and pyrrolidine utilization and its regulatory protein (PipR) in Mycobacterium smegmatis mc2155.

Transposon mutagenesis of Mycobacterium smegmatis mc2155 enabled the isolation of a mutant strain (called LGM1) altered in the regulation of piperidine and pyrrolidine utilization. The complete nucleotide sequence of the gene inactivated in mutant LGM1 was determined from the wild-type strain. This gene (pipR) encoded a member of the GntR family of bacterial regulatory proteins. An insertion element (IS1096), previously described for M. smegmatis, was detected downstream of the gene pipR. Three additional open reading frames were found downstream of IS1096. The first open reading frame (pipA) appeared to encode a protein identified as a cytochrome P450 enzyme. This gene is the first member of a new family, CYP151. By a gene replacement experiment, it was demonstrated that the cytochrome P450 pipA gene is required for piperidine and pyrrolidine utilization in M. smegmatis mc2155. Genes homologous to pipA were detected by hybridization in several, previously isolated, morpholine-degrading mycobacterial strains. A gene encoding a putative [3Fe-4S] ferredoxin (orf1) and a truncated gene encoding a putative glutamine synthetase (orf2') were found downstream of pipA.

Amino Acid Sequence↗