The use of Markov chain Monte Carlo for analysis of correlated binary data: patterns of somatic cells in milk and the risk of clinical mastitis in dairy cows

Two analytical approaches were used to investigate the relationship between somatic cell concentrations in monthly quarter milk samples and subsequent, naturally occurring clinical mastitis in three dairy herds. Firstly, cows with clinical mastitis were selected and a conventional matched analysis was used to compare affected and unaffected quarters of the same cow. The second analysis included all cows, and in order to overcome potential bias associated with the correlation structure, a hierarchical Bayesian generalised linear mixed model was specified. A Markov chain Monte Carlo (MCMC) approach, that is Gibbs sampling, was used to estimate parameters.

The results of both the matched analysis and the hierarchical modelling suggested that quarters with a somatic cell count (SCC) in the range 41,000–100,000 cells/ml had a lower risk of clinical mastitis during the next month than quarters <41,000 cell/ml. Quarters with an SCC >200,000 cells/ml were at the greatest risk of clinical mastitis in the next month. There was a reduced risk of clinical mastitis between 1 and 2 months later in quarters with an SCC of 81,000–150,000 cells/ml compared with quarters below this level. The hierarchical modelling analysis identified a further reduced risk of clinical mastitis between 2 and 3 months later in quarters with an SCC 61,000–150,000 cells/ml, compared to other quarters.

We conclude that low concentrations of somatic cells in milk are associated with increased risk of clinical mastitis, and that high concentrations are indicative of pre-existing immunological mobilisation against infection. The variation in risk between quarters of affected cows suggests that local quarter immunological events, rather than solely whole cow factors, have an important influence on the risk of clinical mastitis. MCMC proved a useful tool for estimating parameters in a hierarchical Bernoulli model. Model construction and an approach to assessing goodness of model fit are described.     

Fire-driven dynamic mosaics in the Great Victoria Desert,Australia – II. A spatial and temporal landscape model

An explicitly spatial, large scale, high resolution model of fire driven landscape dynamics in the Great Victoria Desert is constructed and parameterized to simulate frequency distributions of fire size and shape obtained from previous analyses of satellite chronosequences. We conclude that probabilities of fire spread cannot be constant over time, and that realistic distributions of fire size and plausible rates of fire spread can be obtained by assuming that fire spread is conditional on observed durations of windy conditions. Landscapes subject to this form of disturbance show large scale correlation structure many times greater than the average dimensions of single fires, and exhibit low frequency quasi-periodic stochastically driven oscillations in proportions of the landscape at different successional states over spatial scales exceeding 100,000 km². Average fire return intervals are 30 yrs. Analysis of patch structure suggests that this landscape is composed of few large younger patches, embedded in a mature sea of surrounding habitat. Intermediate and late successional habitat must exist in more abundant patches somewhat smaller than young habitat. Numerous small patches of mature habitat are likely to be scattered throughout this younger habitat. The model predicts that fire size frequency distributions are relatively insensitive to changes of as much as ±50% of observed fire ignition frequency.     

Disease Progression by Active Mycelial Growth and Biocontrol of Pythium ultimum var. ultimum Studied Using a Rhizobox System

ABSTRACT This study demonstrates that outward growth of mycelium from primary foci through bulk potting mix to roots of adjoining plants can be an important means of spread of damping-off and root rot caused by Pythium ultimum. The use of a rhizobox system, which confines plant roots, enabled us to study the spread of actively growing mycelium between root systems placed at precise distances from each other. In steamed potting mix, hyphae of P. ultimum on average grew 9.6 cm from diseased root tissue compared to 5.3 cm in raw potting mix. The density of mycelium was highest within the first 2 cm from the infected root tissue, decreasing with increasing distances from the roots. Accordingly, the disease on adjacent plants decreased as the distance from infected roots increased. The time required for damping-off of adjacent plants was 3 days slower in raw as compared to steamed potting mix and increased by 2 days for each additional centimeter between the rhizoboxes. The presence of Trichoderma harzianum diminished the production of secondary inoculum and reduced the ability of P. ultimum hyphae to extend through bulk potting mix. In conclusion, the concentration of the primary inoculum, the plant density, the distance separating diseased from healthy roots, the resident microflora, and the presence of an antagonist were shown to be important factors affecting disease spread by mycelial growth.     

The importance of comprehensive agricultural education in land-grant institutions: a historical perspective

Any thorough examination of the present and future of agricultural education must certainly begin with a look into its past. Since the creation of the United States, many leading American philosophers have viewed a strong agrarian culture as the bedrock of American vigor. These same philosophers repeatedly noted the significance of comprehensive agricultural education to a nation rich in agricultural wealth. The signing of the Agricultural Colleges Act legitimized the concept of formal education in the agricultural sciences and provided funding for such education. The Act, which came to be known as the Morrill Act, after one of its primary authors, stressed the importance of comprehensive education. In fact, the inclusion of liberal studies was specifically mentioned in the Morrill Act and was defended repeatedly by Morrill himself. Comprehensive education prevented graduating technically trained students who were lacking in the basic outcomes of education--critical, comprehensive problem solving, cohesive thought, and effective communication. However, throughout history, the demands of a growing population coupled with rapid advancements in scientific knowledge led to a gradual move away from comprehensive education in agricultural sciences toward increasing specialization, resulting in more narrowly trained students. Today's agricultural students are technically well versed but often lack the skill and knowledge required for cohesive thought and critical problem solving. Addressing the multitude of challenges facing leaders in the future of agriculture requires much more than technical skill. These challenges require quick, yet careful thinkers and communicators who can respond to changing market structure and consumer demand in a dynamic way. Students who are a product of a conscious move toward amalgamation of burgeoning scientific knowledge and technical prowess with an integrative education emphasizing relationships between disciplines would better serve tomorrow's agriculture.     

The relationship between reaction to sudden, intermittent movements and sounds and temperament

Casual observations indicated that some cattle are more sensitive to sudden movement or intermittent sound than other cattle. Six commercial livestock auctions in two states and a total of 1,636 cattle were observed to assess the relationship between breed, sex, and temperament score on the response to sudden, intermittent visual and sound stimuli, such as the ringman swinging his arm for a bid and the sound of him briefly yelling a bid. A 4-point temperament score was used to score each animal while it was in the ring. The scores used were 1) walks and(or) stands still, with slow, smooth body movements; 2) continuously walks or trots, and vigilant; 3) gait is faster than a trot (runs even a couple of steps), with fast, abrupt, jerky movements, and very vigilant; and 4) hits the ring fence, walls, partitions, or people with its head. Animals were observed for flinches, startle responses, or orientation toward sudden, intermittent sounds, motions, and tactile stimulation, such as being touched with a cane or plastic paddle. The cattle observed were mostly Bos taurus beef breeds and Holstein dairy cattle. Holsteins were more sound-sensitive (P = .02) and touch-sensitive (P < .01) than beef cattle. Sensitivity to sudden, intermittent stimuli (e.g., sound, motion, and touch) increased as temperament score (excitability) increased. Cattle with a temperament score of 1 were the least sensitive to sudden, intermittent movement and sound and those with a temperament score of 4 were the most sensitive (P < .01). This same relationship was sometimes observed for touch but was not statistically significant. Motion-sensitive cattle were more likely than nonsensitive cattle to score a temperament rating of 3 or 4 (P < .01). Steers and heifers were more motion-sensitive than the older bulls and cows (P = .03). Beef cattle urinated (P < .01, n = 1,581) and defecated (P < .01, n = 1,582) more often in the ring than did dairy cattle. Cattle that became agitated during handling in an auction ring were the individuals that were most likely to be startled by sudden, intermittent sounds and movements. Reactivity to sudden, intermittent stimuli may be an indicator of an excitable temperament.     

ADAPT模型在不同尺度土壤数据库中的预报精度--以美国俄亥俄州Darby Creek流域为例

在俄亥俄州的中部Darby Creek 流域,用ADAPT模型预测1991～1995年每日的径流数量和质量.ADAPT模型的主要输入参数来源于MUUF(Map Unit Use File), 其它参数来源于ADAPT的辅助模型.辅助模型的输入数据和参数来源于公开出版物和历史气象资料等.研究目的之一是基于两种不同尺度的土壤数据库STATSGO和MUIR,比较ADAPT模型在预报一个水流域的水、泥沙、养分负载的流失精度.研究结果表明,水和泥沙的流失预报结果没有显著的差异,而养分流失有微小差异(＜5%).因MUIR数据库的分辨率远远高于STATSGO,如果在研究一个流域范围内,预报结果几乎没有区别或仅有极小的差异,使用STATSGO土壤数据将比使用MUIR节约大量的时间和资源.     

Changes in Hemocyte Counts in Litopenaeus stylirostris Subjected to Sublethal Infection and to Vaccination

Abstract.— A study was conducted with juvenile Litopenaeus stylirostris to evaluate the impact on total hemocyte counts of the injection of (1) formalin-killed Vibrio penueicida cells (vaccine) and (2) a sublethal infection with a moderately pathogenic strain of Vibrio alginolyticus . After an initial decrease in hemocyte counts, both the vaccination and the sublethal infection induced higher hemocyte counts than controls. In order to investigate the possibility of increasing the number of circulating hemocytes in pond-reared juvenile shrimp, the vaccine was added to the diet. No effect on the hemocyte counts was observed over a 20-d feeding period.     

Composition of Proteins Extracted from Two Species of Leguminous Bauhinia Grains

There is a growing demand for alternative protein sources for industrial applications. Bauhinia are underutilized protein‐rich oilseed legumes primarily grown as ornamental plants. In this study, the composition and structure of proteins extracted from two Bauhinia species, B. galpinii and B. petersiana, were determined in comparison with soya bean. Albumin and globulin (75%) were the major storage proteins of Bauhinia. Albumin content of B. galpinii was substantially high (28%), about twice those of soya and B. petersiana. Bauhinia grains were good sources of lysine (approximately 4 g/100 g of protein). By SDS‐PAGE, Bauhinia proteins showed three major protein bands ranging from 17,000 to 76,000 for both species. Only one subunit (17,000) of the basic glycinin (11S) seemed to be present in Bauhinia compared with soya. Bauhinia proteins had more β‐sheet conformation (42%) than α‐helix (22%). Bauhinia grains may provide a new opportunity of protein for industrial applications.