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PubMedDate not supplied

Methods of implementation of the MUMPS global data-base.

Recent standardization of the MUMPS language (ANSI X11.1-1977) has resulted in increased investigations into its efficient implementation. Of particular concern is the method of implementation of the MUMPS hierarchical data file, or global. Two implementation techniques have found substantial support: a traditional technique utilizing linked physical blocks, and a more recent, self-indexing method based on the theory of balanced trees. Comparison of these methods shows that the balanced-tree implementation offers significant advantages in most MUMPS environments.

Computers↗

PubMedDate not supplied

Variables processing in expert system building: application to the aetiological diagnosis of infantile meningitis.

We describe a method for the analysis and quantitative synthesis of information in a clinical data file using as an example the aetiological diagnosis of infantile meningitis. The results obtained together with the qualitative knowledge of experts in the field have enabled an experimental system to be constructed. This is performing sufficiently well to be introduced into a hospital environment to assist young doctors facing an emergency situation.

Acute Disease↗

PubMedDate not supplied

A pathology database system for autopsy diagnoses using free-text method.

Using natural language a computerized indexing and retrieval system was developed on a commercial database program, DATATRIEVE (Digital Equipment Corporation, Japan). Summarized anatomical diagnoses of nearly 4000 autopsy cases have been registered over a 13-year period at Tokyo Metropolitan Geriatric Hospital. There were 187,367 words in the pathological diagnoses with 4689 distinct words excluding articles, prepositions and conjunctions. 'Atrophy', 'congestion' and 'metastasis' were the most frequent words with frequencies of 4335, 3377, and 3373, respectively. Distinct clinical diagnoses were 2497, among which 'pneumonia', 'hypertension' and 'DIC' predominated. Each step of retrieval by character strings from the sequential data file requires less than a minute.

Aged↗

PubMed2003

Predicting average feed intake of lactating Holstein cows fed totally mixed rations.

A dry matter intake (DMI) prediction equation was estimated by using a data file that contained 124 treatment means collected from published studies. Animal factors considered for inclusion in the prediction model were body weight (BW) and its natural logarithm, BW(0.75), milk yield (MY) and its natural logarithm, milk fat and protein yields, month of lactation and its square, as well as its natural logarithm. The dietary factors considered were the percentages of neutral detergent fiber, acid detergent fiber, crude protein and hemicellulose in the ration dry matter together with the square of all these predictors. The multiple regression model selected by using the maximum R2 method include both animal and dietary factors as independent variables. The accuracy of this DMI prediction equation was evaluated and compared with that of five other equations previously published by using three independent datasets also containing treatment means collected from literature. Even though the latest NRC equation was slightly more accurate than the equation proposed in this study with the three evaluation datasets, the latter can be used for some applications for which the NRC equation is not appropriate.

Animal Feed↗

PubMed2004

Economic value of female fertility and its relationship with profit in Spanish dairy cattle.

A data file of 225,085 inseminations and 120,713 lactations from 63,160 Holstein cows was analyzed to obtain female fertility economic value according to number of inseminations per service period (INS). Fertility cost (FCOST) was included in a bioeconomic model, taking into account number of doses of semen, hormonal treatments, fertility culling cost, and delayed milk and calf sales. A profit equation was elaborated to estimate fertility cost and profit according to INS. Fertility in Spanish dairy cattle has worsened >10% over the last 14 yr. Days open have increased by about 15 d, and INS has increased from 1.7 to 2.0. A quadratic relationship was found between FCOST and INS. Similar profitability was estimated for cows who needed one or 2 INS, but when >3 INS were needed, profit decreased by >205 (US dollars)/yr per cow. Cows that needed more INS had higher milk yield per lactation, but also had a higher culling risk and lower productive life and lifetime production, therefore, lower profit. Calving interval (CI) and INS economic values were, respectively, -4.90 and -67.32 (US dollars)/yr per cow and per one unit of change. The economic values of productive traits were 4.04, 1.02, and 1.19 (US dollars)/yr per cow and per one unit of change for kg protein, kg fat, and days in milk, respectively. A mature body weight economic value of -0.67 (US dollars)/yr per cow and per kg was estimated. The relative importance of fertility traits with respect to protein was 64% for CI and 24% for INS, although the CI economic value is highly influenced by phenotypic standard deviation considered.

Animals↗

PubMed2005

Genetic and phenotypic parameter estimates of total and partial lifetime traits for dairy ewes.

A data file with 11,547 lactations for 2602 Spanish Churra ewes, daughters of 100 sires and 2179 dams, was used to estimate genetic and phenotypic parameters of total and partial lifetime traits with a multiple-trait animal model using REML. These ewes first lambed between 1992 and 1998 and belonged to 27 flocks enrolled in the nucleus scheme of the breed. The study took into account 4 life span traits, 2 productive traits, and 2 reproductive traits. Lifetime revenues from milk and lambs were calculated. Daily traits for both milk and revenues of lifetime, productive life, and useful life were also calculated. Partial lifetime traits were considered for the first 3 parities. The model included flock and birth year within flock as fixed effects and animal as a random effect. Both fixed effects contributed significantly to variation of all total lifetime traits. Milk production level was included in the model as a covariable to adjust life span traits. Heritability estimates for life span traits were low (0.02 to 0.06), indicating few possibilities for direct genetic selection. Genetic and phenotypic correlations among life span traits averaged 0.90 and 0.87, respectively. Heritabilities for daily milk and revenue traits were always higher than those for their corresponding lifetime traits. Heritability for milk yield per day of useful life was 0.25 (+/-0.04). Heritability estimates for partial lifetime performance traits increased notably when more parities were included (from the first parity to the first 3 parities). Their genetic and phenotypic correlations with total lifetime traits also increased gradually when more information was considered. These results indicate that possibilities for early genetic selection for some lifetime traits are not totally excluded.

Animals↗

PubMed2006

Effects of breed and region on longevity traits through five years of age in Brown Swiss, Holstein, and Jersey cows in the United States.

The objective of this study was to assess breed, and breed x region interactions for several longevity-related traits, measured up to 5 yr of age in Brown Swiss, Holstein, and Jersey cows in 7 regions of the United States. Data were analyzed using logistic, poisson, and linear models, and survival analyses. The traits were stayability (yes/no survived to 5 yr of age), number of completed lactations, days lived, herd-life, and days in milk (DIM) to 5 yr of age. Probable lifetime DIM were also estimated using data from the first 5 yr of age of the cows. Herd-life was defined as the days lived up to 5 yr of age minus the age at first calving. Days in milk consisted of herd-life up to 5 yr of age minus the dry periods. Three data files were analyzed: herds with one breed of cows, herds with Holstein and Brown Swiss, and herds with Holstein and Jersey cows. Breed x region interaction was usually significant, with larger effects for the southern regions. Jerseys obtained largest values for the ratio of DIM to days lived, and for the number of completed lactations to 5 yr of age. Brown Swiss had the largest probabilities of surviving to 5 yr of age (stayabilities) in all regions. For the other traits, the results for Brown Swiss were inconsistent, but usually the cows of this breed had shorter herd-life and DIM to 5 yr of age than Holsteins. Brown Swiss cows were expected to have more total DIM in their lifetime in the Southeast than Holsteins. Survival analysis gave the most readily interpretable information, although the linear, poisson, and logistic analyses answered slightly different questions. Adjustment for herd size did not modify the results.

Animals↗

PubMed1985

Prediction of transmitting ability of heifers from genetic evaluations of dams when dams and herdmates are required to have a first record.

Estimated transmitting ability for milk production calculated from only first lactation records was regressed on milk proofs of the sire and maternal grandsire and either estimated transmitting ability of the dam calculated from only first lactations or estimated transmitting ability of the dam calculated from all lactations of a data set in which all cows were required to have milk records of first lactation. Records of 222,576 Holstein heifers in the northeastern United States were analyzed. Partial regression coefficients were similar to those from reports in which all records in the data file were used to estimate transmitting abilities. The partial regression coefficient for estimated transmitting ability of the dam from all lactation records (.17) was smaller than the approximate theoretical regression coefficient (.70). The partial regression coefficient for estimated transmitting ability of the dam calculated from first records (.72) was similar to the approximate theoretical regression coefficient (.80).

Animals↗

PubMed1992

Genetic analysis of fertility traits in Israeli Holsteins by linear and threshold models.

Conception rates of Israeli Holstein cows and heifers were analyzed separately by linear and threshold models. Fixed effects for both data files were insemination number, AI institute, geographical region, and calendar month. Analysis of cows also included the fixed effects of parity, calving status, and DIM at insemination. Random effects included in the models were herd-year-season, insemination technician, sire of cow, and service sire. Fixed effect solutions for heifers and cows were not similar. For cows, insemination month had the greatest effect on conception rate. Heritability of conception rate ranged from 2 to 3.5% for heifers and from 1 to 2% for cows. Correlations between corresponding threshold and linear model random effect solutions were all greater than or equal to .99. Correlations between heifer and cow analyses for sire and service sire solutions were less than .4. Analysis with an incorrect herd-year-season variance component affected only the technician solutions.

Animals↗

PubMed1993

Absence of quadratic relationships between genetic evaluations for somatic cell scores and udder linear traits.

Sire genetic evaluations for lactation average somatic cell scores from first and second lactation daughters were regressed in separate models on genetic evaluations for udder linear traits. Somatic cell scores were from Pennsylvania DHIA, and udder linear scores were from the Holstein Association of America classifications of first lactation cows in the northeastern US excluding Pennsylvania. The independent data files for calculation of genetic evaluations included 108,632 cows from 301 sires with udder linear scores and 58,235 cows from the same 301 sires with somatic cell scores. Sire genetic evaluations for higher udders, stronger fore udder attachments, closer teat placement, and shorter teats were associated with lower somatic cell scores. Quadratic relationships between genetic evaluations for the udder traits and somatic cell scores were not important. Quadratic components were significant only for somatic cell scores and teat length. Evaluations for intermediate teat length tended to be associated with higher somatic cell score evaluations. Selection and mating for intermediate udder depth, fore udder attachment, and front teat placement scores are not as effective in reducing somatic cell scores as selection for higher udders, stronger fore udders, and closer front teats.

Animals↗

PubMed1995

Estimates using an animal model of (co)variances for yields of milk, fat, and protein for the first lactation of Holstein cows in California and New York.

First lactation yields of milk, fat, and protein from Holstein cows in New York and California were used to obtain REML estimates of (co)variances for yield traits using a multitrait animal model. Data from each state were split randomly into 10 samples, averaging 5504 cows per sample from California and 5078 from New York. Mean heritability estimates for milk, fat, and protein yields were .30 +/- .02, .31 +/- .01, and .29 +/- .01 for California data and .33 +/- .01, .35 +/- .01, and .30 +/- .01 for New York data. Averages of genetic correlation estimates for California and New York were .63 +/- .01 and .52 +/- .02 between milk and fat, .84 +/- .01 and .83 +/- .01 between milk and protein, and .73 +/- .01 and .68 +/- .01 between fat and protein. Estimates of environmental correlations were larger than estimates of genetic correlations. Mean estimates of phenotypic correlations for California and New York were .75 +/- .01 and .72 +/- .01 between milk and fat, .92 +/- .01 and .91 +/- .01 between milk and protein, and .81 +/- .01 and .79 +/- .01 between fat and protein yields. On average, these estimates agree with those obtained from animal models with limited rounds of iteration for small data files.

Animals↗

PubMed1995

The effect of alternative economic and genetic covariation structures on the relative economic gain from selection using stayability traits.

Three alternative cost ratios and the ratio of annual fixed cost for cows to net replacement cost for three populations that differed in genetic (co)variances were investigated. We studied their effect on the value of longevity records to supplement production records to achieve genetic gains for reducing the nonfeed cost of producing a unit of milk. Data files were constructed from stochastically generated production records and culling variant records; the later records represented the relative value for cow survival of all nonproduction traits. The use of one stayability trait instead of none increased gain by 1 to 9% across the populations and cost ratios. Only 2% additional gain occurred with two stayability traits instead of one. Populations that differed in genetic correlation between production and the survival value of nonproduction traits and in survival heritabilities contributed 2 to 5% toward the greater gains. The different cost ratios contributed 1 to 3%. The effect of increasing the length of herd life independent of production is inherently secondary to the effect of increasing the production during lactation. If genetic antagonism between production and the survival of nonproduction traits is found and if the net replacement costs are high, the use of production and longevity records for selection can enhance gain by up to 10%.

Animals↗

PubMed1995

The prediction of methane production of Holstein cows by several equations.

Ruminants are one of many sources contributing to atmospheric methane. The accuracy of seven published equations for methane prediction was evaluated using a data file consisting of 16 experiments (602 observations). Methane energy emissions ranged from .89 to 7.21 Mcal/d for Holstein cows. The DMI ranged from 9.7 to 28.7 kg/d for lactating cows and 4.0 to 12.9 kg/d for nonlactating cows. Mean dietary concentrations of ADF, CP, and ether extract were similar for lactating and nonlactating cows (20.9, 16.5, and 3.0% for lactating cows versus 21.2, 15.7, and 2.9% for nonlactating cows, respectively). Milk production ranged from 2.7 to 55.9 kg/d. Prediction equations were ranked by correlation coefficients and error of prediction. Prediction of methane energy loss from lactating and nonlactating Holstein cows with equations based on the daily total intake or intake of digested cellulose, hemicellulose, and nonfiber carbohydrates (OM - NDF - CP - ether extract) provided the highest correlation coefficients for reproducibility and the lowest errors of prediction. Predictions were poor for lactating cows when a quadratic function of DMI was used. In general, equations estimated methane production more accurately and precisely for nonlactating than for lactating cows.

Animals↗

PubMed1996

Impacts of cytoplasmic inheritance on genetic evaluations.

Simulation was used to examine the consequences of ignoring cytoplasmic effects on genetic evaluations. Effects on variance component estimation, accuracy of selection, genetic trend, and selection of bull-dams were considered. Comparisons were made for sire and animal models, several levels of cytoplasmic variance, and definition of cytoplasmic effects as either fixed or random. Ten replications with approximately 9000 cows and 20,000 records were simulated for each model and level of cytoplasmic variance. Derivative-free REML was used for estimation of variance components. Ignoring cytoplasmic effects caused overestimation of heritability with an animal model. Permanent environmental variance was underestimated with an animal model and overestimated with a sire model. Results were used for simulation of large (approximately 200,000 cow) data files for analysis of effects on accuracy of selection. Accuracy of selection increased when cytoplasmic effects were accounted for properly. Improvement of predicted breeding values was greater for cows than for sires and increased as cytoplasmic variance increased. Genetic trend also increased slightly, primarily as a function of increased accuracy of bull-dam selection. Little practical difference was detected when cytoplasmic effects were considered to be fixed rather than random.

Animals↗

PubMed1996

Genetic parameters and trends for milk production of blond-faced Latxa sheep using Bayesian analysis.

The genetic progress attained with the breeding scheme of the blond-faced Latxa dairy sheep in the Spanish Basque Country was assessed by a Bayesian approach based on the marginal posterior distributions of parameters achieved via Gibbs sampling. The data file included 49,056 milk yield records of 22,363 ewes. Normal distributions were assumed for EBV and fixed effects, and scaled inverted chi-square distributions were assumed for variance components or additive, permanent environment, and residual effects. Under vague priors for variance components, the posterior means (SD) for heritability and permanent environment coefficient for milk yield at 120 d were 0.22(0.01) and 0.20(0.01). An important effect on the milk yield (41.6% of the mean) was evident for a genetic group of imported rams. Selection was effective for sheep that were bred by AI and that had known parents. The robustness of results for effect of genetic group and genetic trends was validated using a mildly informative prior constructed from variance components estimated with the related black-faced Latxa breed.

Animals↗

PubMed1997

Predicting optimal time of insemination in cows that show visual signs of estrus by estimating onset of estrus with pedometers.

An experiment was designed to estimate the optimal interval from the beginning of estrus to artificial insemination (AI). The data were analyzed by means of a mathematical model. The analysis was based on pedometer readings and results of rectal palpation at 42 to 49 d post-AI of 171 breedings in 121 cows. The chance of conception was highest between 6 and 17 h after increased pedometer activity; the estimated optimum was at 11.8 h. In this data file, the effects of disease, inseminator, time of AI (a.m. or p.m.), and bull did not contribute to the improvement of the model. The effects of disease were not significant because of the low incidence of any specific disease. Activity measurements can be used as a tool for AI strategy to improve conception in groups of healthy cows and heifers already showing visual signs of estrus.

Animals↗

PubMed1998

Design and validation of a dynamic discrete event stochastic simulation model of mastitis control in dairy herds.

A dynamic stochastic simulation model for discrete events, SIMMAST, was developed to simulate the effect of mastitis on the composition of the bulk tank milk of dairy herds. Intramammary infections caused by Streptococcus agalactiae, Streptococcus spp. other than Strep. agalactiae, Staphylococcus aureus, and coagulase-negative staphylococci were modeled as were the milk, fat, and protein test day solutions for individual cows, which accounted for the fixed effects of days in milk, age at calving, season of calving, somatic cell count (SCC), and random effects of test day, cow yield differences from herdmates, and autocorrelated errors. Probabilities for the transitions among various states of udder health (uninfected or subclinically or clinically infected) were calculated to account for exposure, heifer infection, spontaneous recovery, lactation cure, infection or cure during the dry period, month of lactation, parity, within-herd yields, and the number of quarters with clinical intramammary infection in the previous and current lactations. The stochastic simulation model was constructed using estimates from the literature and also using data from 164 herds enrolled with Quality Milk Promotion Services that each had bulk tank SCC between 500,000 and 750,000/ml. Model parameters and outputs were validated against a separate data file of 69 herds from the Northeast Dairy Herd Improvement Association, each with a bulk tank SCC that was > or = 500,000/ml. Sensitivity analysis was performed on all input parameters for control herds. Using the validated stochastic simulation model, the control herds had a stable time average bulk tank SCC between 500,000 and 750,000/ml.

Animals↗

PubMed1998

Genetic and phenotypic parameters for 305-day yield, fertility, and survival in Holsteins.

A data file containing 122,715 lactation records of Holstein cows distributed across 11,374 herd-year-season groups was analyzed to obtain (co)variance estimates for yield, fertility and cow survival. Milk, fat, and protein yields were adjusted to 305 d. Days open was truncated to 305 d, and the number of services was truncated to 9. Survival of a cow during a full lactation (305 d) was recorded as 0 (died) or 1 (alive). Variance components for the six traits were estimated using a multiple-trait animal model and the REML procedure. The model included herd-year-season, parity (three groups), age (three groups nested within parity), sex of calf (1 = male, 2 = female), and dystocia score (1 = no problem,..., 5 = extreme difficulty) as fixed effects and animal and permanent environment as random effects. Heritabilities for milk, fat, and protein yields, days open, number of services and cow survival were 0.2, 0.18, 0.18, 0.04, 0.03, and 0.002, respectively. The corresponding repeatabilities were 0.42, 0.41, 0.41, 0.12, 0.08, and 0.009, respectively. Genetic and phenotypic correlations between yield traits were high and positive, and correlations between yields and reproduction traits were high and antagonistic. Phenotypic correlations between survival and yields were about 0.1, and their genetic counterparts were slightly negative. Thus, management practices seem to keep mortality rates of high producing cows lower even though those cows have lower genetic potential for survival than do the low producers. Fertility traits showed a slightly undesirable (e.g., 0.1 to 0.3) genetic relationship with survival, but phenotypic correlations were essentially 0. For heifers, yields increased significantly with age. For cows in other parities, the significant changes with age were reduced fertility and reduced survival.

Aging↗