A periodic analysis of longitudinal binary responses: a case study of clinical mastitis in Norwegian Red cows

A Bayesian procedure for analyzing longitudinal binary responses using a periodic cosine function was developed. It was assumed that, after adjustment for "seasonal" effects, the oscillation of the underlying latent variables for longitudinal binary responses was a stationary series. Based on this assumption, a single dimension sinusoidal analysis of longitudinal binary responses using the Gibbs sampling and Metropolis algorithms was implemented in a study of clinical mastitis records of Norwegian Red cows taken over five lactations.     

A model to predict transformations and losses of nitrogen in UK pastures grazed by beef cattle

The model simulates the cycling of N in grassland systems grazed by beef cattle and predicts the annual amount of N in liveweight gain, and the amounts lost through ammonia volatilization, denitrification and leaching, on the basis of fertilizer application and soil and site characteristics. It aims to provide a better understanding of the way in which these various factors interact in their influence on N transformations. The model has been programmed to run on IBM-compatible personal computers and responds rapidly to changes in input parameters. The model has been constructed from the average annual amounts of N passing through various components of the N cycle in ten field systems grazed by beef cattle. The amounts were either measured directly or were calculated from empirical sub-models, assuming a balance between inputs to, and outputs from the soil inorganic N pool. The model is given wide applicability through the inclusion of a mineralization sub-model which is sensitive to soil texture, sward age, previous cropping history, and climatic zone. Another important sub-model determines the partitioning of soil inorganic N to either plant uptake or the processes of loss: the proportion partitioned to plant uptake decreases as the total amount of soil inorganic N increases. Outputs from the model indicate that fertilizer N has a strong influence on ammonia volatilization, denitrification and leaching at a given site but that, over a range of sites with a given rate of fertilizer N, total loss and the proportions lost by the three processes are greatly influenced by the amount of N mineralized by the soil. The model indicates how fertilizer N should be matched with mineralization to limit gaseous and leaching losses and to achieve optimum efficiency of N use in grazing systems.     

Effect of a deep uterine insemination on spermatozoal accessibility to the ovum in cattle: a competitive insemination study

A competitive insemination study was conducted to determine the effect of a deep uterine insemination on accessory sperm number per embryo in cattle. Cryopreserved semen of a fertile bull characterized by spermatozoa with a semi-flattened region of the anterior sperm head (marked bull) was matched with cryopreserved semen from an unmarked bull having spermatozoa with a conventional head shape. Using 0.25-mL French straws and a side delivery embryo transfer device, deep uterine insemination (0.125 mL deposited in each horn) was performed 2 cm from the uterotubal junction. Immediately after, the uterine body was artificially inseminated using semen (0.25 mL) from an alternate bull and a conventional insemination device. The complete dose (both inseminations) was 50x10(6) total sperm cells consisting of an equal number of spermatozoa from each bull. Single ovulating cows (n = 95) were inseminated at random with either the unmarked semen in the uterine body and marked semen in the uterine horn, or the unmarked semen in the uterine horn and marked semen in the uterine body. Sixty-one embryos(ova) were recovered nonsurgically 6 d post insemination, of which 40 were fertilized and contained accessory spermatozoa. The ratio and total number of accessory spermatozoa recovered was different among treatments: 62:38 (326) for the unmarked semen in the uterine body and marked semen in the uterine horn, and 72:28 (454) for the unmarked semen in the uterine horn and marked semen in the uterine body (P<0.05). Deep uterine insemination using this semen in a split dose and a side delivery device favors accessibility of spermatozoa to the ovum compared with conventional uterine body insemination.     

A meta-analytic assessment of a Thyroglobulin marker for marbling in beef cattle

A meta-analysis was undertaken reporting on the association between a polymorphism in the Thyroglobulin gene (TG5) and marbling in beef cattle. A Bayesian hierarchical model was adopted, with alternative representations assessed through sensitivity analysis. Based on the overall posterior means and posterior probabilities, there is substantial support for an additive association between the TG5 marker and marbling. The marker effect was also assessed across various breed groups, with each group displaying a high probability of positive association between the T allele and marbling. The WinBUGS program code used to simulate the model is included as an Appendix available online at http://www.edpsciences.org/gse.     

Mapping quantitative trait loci for binary trait in the F2:3 design

In the analysis of inheritance of quantitative traits with low heritability, an F_2:3 design that genotypes plants in F₂ and phenotypes plants in F_2:3 progeny is often used in plant genetics. Although statistical approaches for mapping quantitative trait loci (QTL) in the F_2:3 design have been well developed, those for binary traits of biological interest and economic importance are seldom addressed. In this study, an attempt was made to map binary trait loci (BTL) in the F_2:3 design. The fundamental idea was: the F₂ plants were genotyped, all phenotypic values of each F_2:3 progeny were measured for binary trait, and these binary trait values and the marker genotype informations were used to detect BTL under the penetrance and liability models. The proposed method was verified by a series of Monte-Carlo simulation experiments. These results showed that maximum likelihood approaches under the penetrance and liability models provide accurate estimates for the effects and the locations of BTL with high statistical power, even under of low heritability. Moreover, the penetrance model is as efficient as the liability model, and the F_2:3 design is more efficient than classical F₂ design, even though only a single progeny is collected from each F_2:3 family. With the maximum likelihood approaches under the penetrance and the liability models developed in this study, we can map binary traits as we can do for quantitative trait in the F_2:3 design.     

Efficiency considerations in the analysis of inter-observer agreement

The reliability of binary assessments is often measured by the proportion of agreement above chance, as estimated by the kappa statistic. In this paper, we develop a model to estimate inter-rater and intra-rater reliability when each of the two observers has the opportunity to obtain a pair of replicate measurements on each subject. The model is analogous to the nested beta-binomial model proposed by Rosner (1989, 1992). We show that the gain in precision obtained from increasing the number of measurements per rater from one to two may allow fewer subjects to be included in the study with no net loss in efficiency for estimating the inter-rater reliability.     

Energy flow and the persistence of a human population: A simulation analysis

A human ecosystem model, NUÑOA, simulates the yearly energy balance of individuals, families, and extended families in a hypothetical farming and herding community of Quechua Indians in the high Andes. The yearly energy demand of each family, based on the caloric requirements of its members, is computed by simulation of agricultural and herding activities in response to stochastic environmental conditions. The family energy balance is used in determining births, deaths, marriages, and resource sharing. The model user has the opportunity to investigate the effect of changes in marriage patterns, resource sharing patterns, or subsistence activities on the ability of the human population to survive in the harsh Andean environment. Results from the model suggest that the substructuring of a population into extended families provides a mechanism for sheltering the population from control by exogenous influences. A population without substructures for resource sharing is shown to be unstable in such an unpredictable environment.Research supported by the National Science Foundation's Ecosystem Studies Program under Interagency Agreement No. DEB-77-25781 with the U.S. Department of Energy under contract W-7405-eng-26 with Union Carbide Corporation.Publication No. 1966, Environmental Science Division, ORNL.     

Population dynamics of the West Indian sweetpotato weevil Euscepes postfasciatus (Fairmaire): a simulation analysis

The West Indian sweetpotato weevil Euscepes postfasciatus (Fairmaire) is a major pest of the sweet potato Ipomoea batatas (L.) Lam. and this weevil is a target of an eradication program using the Sterile Insect Technique in Okinawa Prefecture, Japan. Understanding the population ecology is essential in the planning of an eradication program; hence, a host‐plant infestation survey and light trap survey have been conducted to monitor the population dynamics of the weevil on Kume Island (Okinawa Prefecture), which is the target area of the trial weevil eradication project. Seasonal tendencies of weevil density were found in these field surveys, but the tendency found in the host‐plant infestation survey was not seen every year, and the effectiveness of the light trap is somewhat suspect. To confirm the reliability of the tendency observed in these field surveys, the present study attempted to explain the tendency by a seasonal temperature change using a temperature‐based model of weevil population dynamics. The seasonal changes of weevil density differed according to host plants and host‐plant fields. The seasonal changes of weevil density inside the host plant Ipomoea indica and outside the host plants in I. indica fields were consistent with those predicted by the model. However, those inside the host plant Ipomoea pes‐caprae in the host‐plant infestation survey were contrary to the predicted ones, and those observed outside host plants in I. pes‐caprae fields by the light trap survey were not in good agreement with the predicted ones. It was concluded that the seasonal change of the weevil density observed in I. indica and I. indica fields can be explained by a seasonal temperature change, but factors other than seasonal temperature change are needed to explain those in I. pes‐caprae and I. pes‐caprae fields.     

Application of a simulation model of hydrobiological survey in complex analysis of in situ data

The model realizes the algorithm simulating the motions of a group of organisms with mutually independent, stochastic paths in a homogeneous medium, which results in the random distribution of the organisms in local areas in space (sampling units). Substitution of the mean abundance values of individual species found in the actual hydrobiological samples into the sample as one of its parameters produces a given set of artificial samples similar to the in situ sample with its elements possessing complete stochastic independence. They are further used to test the reliability of results obtained by statistical methods of data analysis and computations of threshold values for some indices and coefficients employed in ecology.     

A comparative study of the adsorption of water and methanol in zeolite BEA: a molecular simulation study

Grand canonical Monte Carlo simulations were carried out to study the equilibrium adsorption concentration of methanol and water in all-silica BEA zeolite and HBEA zeolites with different Si/Al ratios over a wide range of temperatures and loadings. These zeolites have oval-shaped channels with one side longer than the other. Water sorption into the hydrophobic BEA zeolite had a sharp transition with its sorption going from zero to near full capacity over a very small pressure range. Methanol sorption was much more gradual with respect to pressure. With the addition of hydrophilic sites for the HBEA zeolites by decreasing the Si/Al ratio, adsorption at lower pressures increased significantly for water and methanol. At higher loadings, water and methanol adsorption were found to behave in fundamentally different ways. Water structures in the zeolite channels formed hydrogen-bonded chains while maximising contact with the surfaces on the longer edges of the zeolite channels. Methanol molecules, in contrast, formed very few hydrogen bonds between themselves, with their hydroxyl groups primarily binding with surface of the shorter edge of the zeolite channels and their methyl groups located near the middle of the zeolite channels. The addition of hydrophilic groups in the HBEA zeolites strongly influenced positions of the methanol hydroxyl groups at high loadings, but did not have a significant effect on water structure.     

A description of the findings from bull breeding soundness evaluations and their association with pregnancy outcomes in a study of western Canadian beef herds

The primary objectives were to describe beef bulls considered for use and those reported as used in 205 beef herds in western Canada, and to determine whether factors typically assessed during breeding soundness evaluations were associated with reproductive success. More than 100 veterinary clinics reported 2990 breeding soundness evaluations for bulls considered for natural service in client's herds. Differences among clinics explained 5.2% of the variation in scrotal circumference (SC) and 6.9% of the variation in percentage of morphologically normal sperm of all bulls considered for use (after accounting for age, breed, body condition, significant physical abnormalities, month, and year). The percentage of morphologically normal sperm was lower in bulls with an SC ≤34 versus >34 cm (P < 0.006). This study included data from 1384 and 1370 bulls used for breeding in 2001 and 2002, respectively. Most (80%) of the bulls used were Simmental, Black Angus, Charolais, Red Angus, or Hereford, and 80% were ≤4 y of age. Before the breeding season, a veterinarian evaluated 89.5% of all bulls used in these herds. Of the bulls subjected to a breeding soundness evaluation and subsequently used, 93.1% were satisfactory. In 2001 and 2002, injuries were reported in 2.5 and 2.1% of bulls and in 16.6 and 11.4% of herds, and necrobacillosis of the foot was reported in 2.5 and 1.2% of bulls and 11.2 and 6.5% of the herds. The average number of cows exposed to each bull was 26 (both years). Cows exposed to bulls with a smaller SC were less likely to be diagnosed pregnant (P < 0.047) and had a longer median interval from first bull exposure to calving (P < 0.016) than bulls with a larger SC. In conclusion, our findings emphasized the value of breeding soundness evaluations, including measurements of SC, in fertility management of beef cattle.     

A degree-day simulation model for the population dynamics of the rice bug, Leptocorisa acuta (Thunb.)

The rice bug, Leptocorisa acuta (Thunb.) is a major pest of the rice crop in India. A computer simulation model of the bug's population dynamics was formulated using the information generated on the thermal requirements of development stages. It is a mechanistic model which follows the state variable–rate variable approach. The model works based on the accumulation of heat units over stage-specific thresholds of development. Validation using light trap catches has shown that the model has satisfactory predictive value. Simulated population dynamics over the years were compared and the influence of global warming on bug population dynamics was predicted. The model can forecast the pest population in the field and help in timely adoption of management practices.     

Effects of obesity on occupant responses in frontal crashes: a simulation analysis using human body models

The objective of this study is to investigate the effects of obesity on occupant responses in frontal crashes using whole-body human finite element (FE) models representing occupants with different obesity levels. In this study, the geometry of THUMS 4 midsize male model was varied using mesh morphing techniques with target geometries defined by statistical models of external body contour and exterior ribcage geometry. Models with different body mass indices (BMIs) were calibrated against cadaver test data under high-speed abdomen loading and frontal crash conditions. A parametric analysis was performed to investigate the effects of BMI on occupant injuries in frontal crashes based on the Taguchi method while controlling for several vehicle design parameters. Simulations of obese occupants predicted significantly higher risks of injuries to the thorax and lower extremities in frontal crashes compared with non-obese occupants, which is consistent with previous field data analyses. These higher injury risks are mainly due to the increased body mass and relatively poor belt fit caused by soft tissues for obese occupants. This study demonstrated the feasibility of using a parametric human FE model to investigate the obesity effects on occupant responses in frontal crashes.     

A kernel method for incorporating information on disease progression in the analysis of survival

This paper considers incorporating information on disease progressionin the analysis of survival. A three-state model is assumed,with the distribution of each transition estimated separately.The distribution of survival following progression can dependon the time of progression. Kernel methods are used to giveconsistent estimators under general forms of dependence. Theestimators for the individual transitions are then combinedinto an overall estimator of the survival distribution. A teststatistic for equality of survival between treatment groupsis proposed based on the tests of Pepe & Fleming (1989,1991). In simulations the kernel method successfully incorporateddependence on the time of progression in some reasonable settings,but under extreme forms of dependence the tests had substantialbias. If survival beyond progression can be predicted fairlyaccurately, then gains in power over standard methods that ignoreprogression can be substantial, but the gains are smaller whensurvival beyond progression is more variable. The methodologyis illustrated with an application to a breast cancer clinicaltrial.     

A Fuzzy Logic Model to Describe the Cyanobacteria Nodularia spumigena Blooms in the Gulf of Finland, Baltic Sea

A fuzzy logic model to describe the seasonal evolution of Nodularia spumigena blooms in the Gulf of Finland was built and calibrated on the basis of monitoring data. The model includes three phosphate sources: excess phosphate after the annual spring bloom and parameterised phosphate transport to the upper mixed layer by turbulent mixing and upwelling events. Surface layer temperature and wind mixing form the physical conditions controlling the growth of N. spumigena. Model simulations revealed that phosphate input caused by turbulent mixing and upwelling have to be taken into account to achieve the best fit with observed data. Testing the fuzzy model for early prediction of maximum N. spumigena biomass about a month before the usual occurrence of blooms, gave good results. The potential use of the model for prediction of bloom risk at a certain location along the Estonian or Finnish coast was tested. The bloom transport velocities used in the fuzzy model were pre-calculated by a 3D numerical circulation model for different wind regimes.     

Bayes factor for testing between different structures of random genetic groups: A case study using weaning weight in Bruna dels Pirineus beef cattle

The implementation of genetic groups in BLUP evaluations accounts for different expectations of breeding values in base animals. Notwithstanding, many feasible structures of genetic groups exist and there are no analytical tools described to compare them easily. In this sense, the recent development of a simple and stable procedure to calculate the Bayes factor between nested competing models allowed us to develop a new approach of that method focused on compared models with different structures of random genetic groups. The procedure is based on a reparameterization of the model in terms of intraclass correlation of genetic groups. The Bayes factor can be easily calculated from the output of a Markov chain Monte Carlo sampling by averaging conditional densities at the null intraclass correlation. It compares two nested models, a model with a given structure of genetic groups against a model without genetic groups. The calculation of the Bayes factor between different structures of genetic groups can be quickly and easily obtained from the Bayes factor between the nested models. We applied this approach to a weaning weight data set of the Bruna dels Pirineus beef cattle, comparing several structures of genetic groups, and the final results showed that the preferable structure was an only group for unknown dams and different groups for unknown sires for each year of calving.     

A simulation study of the effects of architectural constraints and resource translocation on population structure and competition in clonal plants

(1) Spatially explicit simulation of clonal plant growth is used to determine how ramet-level traits affect ramet density, spatial pattern of ramets and competitive ability of a clonal plant. The simulation model used combines elements of (i) an individual-based model of plant interactions, (ii) an architectural model of clonal plant growth, and (iii) a model of resource translocation within a set of physiologically integrated plant individuals. (2) The effects of two groups of parameters were studied: growth and resource acquisition parameters (resource accumulation, density-dependence of resource accumulation, resource translocation between ramets) and architectural rules (branching angle and probability of branching, internode length). The model was parameterised by values approximating those of clonally growing grasses as closely as possible. The basic parameter values were chosen from a short-turf grassland. Sensitivity analysis was carried out on relevant parameters around three basic points in the parameter space. Both single-species and two-species systems were studied. (3) It is shown that increasing resource acquisition and growth parameters increase ramet density, genet number and competitive ability. Translocation parameters and architectural parameters modify the effects of resource acquisition and growth, but their effect in single-species stands was smaller. (4) The simulations of species with fixed ramet sizes showed that ramet density in single-species stands cannot be used for predicting competitive ability. Increase in resource acquisition and growth parameters was correlated with an increase in equilibrium ramet density and competitive ability. Increasing branching angle, branching probability or internode length lead to an increased competitive ability, but did not affect equilibrium ramet density. Change of architectural parameters could therefore affect competitive ability independently of their effect on the final ramet density. (5) Spatial pattern both in single-species and two-species stands was also highly parameter-dependent. Changes in architectural parameters and in translocation usually lead to pronounced change in the spatial pattern; change in growth and resource acquisition parameters generally had little effect on spatial pattern.