An expanded Fermi solution for microbial risk assessment

'Fermi solution' refers to an estimate of a quantity of interest derived from a sequence of guesses about factors of which detailed knowledge is unavailable. When one makes such guesses, it is unlikely that the large majority of them will be either too high or too low. Most probably, some of the overestimates will be offset by some of the underestimates, and the final result will be often close to the correct value. The method has been popularized as recreational physics but it has also been applied in risk assessment, where the factors involved, but not their exact magnitudes, are known. The concept has potential application in certain types of food poisoning risk assessments, and in estimating the number victims of a bioterrorist attack on the food or water supply, where some guessing is inevitable because of the absence of accurate relevant data. We consider a version of the method in which ranges instead of single values are entered as the factors' estimates. For simplicity, the risk to be assessed is taken to be the product of the factors, and their true values are regarded as being uniformly distributed over their respective ranges. The risk itself is therefore construed as a random variable with a probability distribution whose parameters are explicitly determined by the individual factors' ranges and which can often be approximated by a lognormal distribution. The mode of this lognormal distribution is taken to be the "best guess" of the risk, and a credible interval is constructed with a specified level of "confidence". The best guess and credible interval are shown to be robust against small perturbations of the ranges. Thus, even if the ranges are misspecified to some degree, assessments based on the best guess or credible interval will not be substantially altered. This can help to achieve consensus among assessors in situations where very little hard knowledge exists. The calculation procedure has been automated in software that has been made freely available over the Internet. The concept is demonstrated with two hypothetical problems: predicting the number of persons who would come down with acute food poisoning after consuming a contaminated dish, and estimating the number of daily salmonellosis cases in a large metropolitan area.     

Prediction of consumer acceptability of potato chips with various moisture contents using survival analysis

Consumer acceptability of potato chips with different moisture contents (MC) was evaluated using survival analysis. Nine different humidity conditions (30–70%) at 25°C were used. MC values of samples ranged from 2.2–9.2% after treatment. Panelists (50) were asked to rate chip acceptability. The chip MC was predicted using non-linear models. Panelist-generated data were categorized as left, interval, and right censored. A total of 18 panelists were left censored and 30 were interval censored. Weibull and lognormal distributions were used to fit the censored data. The mean MC of chips rejected by 50% of consumers were 3.54% (95% confidence interval, 3.14–3.99%) and 3.60% (CI 3.23–4.01%) for the Weibull and lognormal distribution, respectively. These values corresponded to 5.7 and 5.6 overall consumer liking values (Weibull and lognormal distributions, respectively). MC of 3.5–3.6% was necessary to attain consumer acceptability values of 5.6 and product acceptance by 50% of consumers.     

Least equivalent allowable differences in equivalence testing

This paper aims at an extension and refinement of some recent work on equivalence testing in sensory science. The performance of the two-one-sided-tests (TOST) approach using the t-test statistic for normally distributed data is briefly compared from a practical point of view to alternatives found in the literature. Based on the TOST and on several other methods like, e.g., the Binomial test for 2- and 3-AFC methods, it is shown how a least equivalent allowable difference (LEAD) can be determined. This is related to an appropriate confidence interval, while typically only the absolutely larger bound is taken into account. The LEAD gives valuable information to the investigator and is particularly independent from the analyst’s choice of a maximum allowable difference. Re-visiting some examples from the literature illustrates this concept.     

艾拉姆咖分布的统计推断

为了对艾拉姆咖分布参数进行参数估计,利用数学归纳法和卷积公式,给出艾拉姆咖分布参数的充分统计量,在此基础上得出分布参数的一致最小方差无偏估计和置信区间的计算公式.经计算机模拟,利用Matlab产生的随机数验证所给点估计公式和区间估计方法的有效性.结果表明所给估计量准确性高,区间估计方法正确可用.     

利用不确定度比对乳粉中叶酸含量的快速检测方法

目的 利用不确定度比对乳粉中叶酸含量的快速检测方法。方法 分别用进口和国产的微生物法和酶联免疫法的试剂盒对代表性乳粉样品进行3 d 3平行检测, 对检测数据做正态分布分析及不确定度计算。结果 各方法检测结果正态分布检验值(anderson-darling, AD)均小于临界值0.725(95%置信区间), 服从正态分布; 微生物快速检测方法不确定度范围为13.3%~27.4%; 酶联免疫方法不确定度范围为9.6%~ 31.3%。结论 微生物试剂盒快速检测方法, 具有稳定性较好, 品牌差异较小的特点, 适合质控品的长期监测, 质控图的建立。酶联免疫检测方法, 具有简单、快速的特点, 适合样品中叶酸的快速检测。     

Effect of iron supplementation during pregnancy on birthweight: evidence from Zimbabwe

BACKGROUND: Iron deficiency in pregnant women has been shown to reduce the oxygen supply to the fetus, cause intrauterine growth retardation, and increase the risk of premature delivery and reduced birthweight. Yet the effects of iron supplementation programs on pregnancy outcomes are not well documented for developing countries. OBJECTIVE: To examine the relation between iron supplementation of mothers during pregnancy and children's birthweight using data from a national population-based survey in Zimbabwe. METHODS: The analysis uses information on 3559 births during the five years preceding the 1999 Zimbabwe Demographic and Health Survey. The effect of iron supplementation during pregnancy on birthweight was estimated by multiple regression, controlling for potential confounding effects of prenatal care, child's sex and birth order, mother's education and nutritional status (measured by body-mass index), household living standard, smoke exposure, and other variables. RESULTS: Babies born to mothers who received iron supplementation during pregnancy were 103 g heavier (95% confidence interval, 42-164; p = .001), on average, than babies born to mothers who did not receive iron supplementation during pregnancy. The difference was 64 g (95% confidence interval, 2-125; p = .043) for children whose birthweights were taken from health cards and 163 g (95% confidence interval, 44-281; p = .008) for children whose birthweights were reported by their mothers. CONCLUSIONS: Iron supplementation during pregnancy is associated with significantly higher birthweight, independent of other pregnancy care factors, mother's nutritional status, smoke exposure, and a number of demographic and socioeconomic factors. Prenatal iron supplementation programs can improve pregnancy outcomes and promote child survival in developing countries.     

自适应逐步混合截尾MOEE分布的统计分析

在自适应逐步混合截尾恒加试验模型下,研究Marshall-Olkin扩展指数分布的可靠性指标。基于失效数据,建立似然函数,获得了参数的极大似然估计,并利用自助模拟的百分位Bootstrap方法构建了参数的置信区间。利用蒙特卡洛模拟方法对自适应逐步混合截尾恒加试验模型进行仿真。数值模拟结果表明:随着样本容量的增大,参数极大似然估计值越接近真值,Bootstrap区间的效果更优。     

Detection of Mycobacterium avium subspecies paratuberculosis in naturally exposed dairy heifers and associated risk factors

An observational prospective study was conducted to identify risk factors associated with fecal shedding of Mycobacterium avium ssp. paratuberculosis (MAP) in naturally exposed dairy heifers. The study population consisted of heifers from 8 dairy herds in Michigan participating in a MAP control demonstration project. Ten heifers from 4 age groups (0 to 3, 4 to 6, 7 to 14, and 15 to 24 mo) were selected from each herd every 4 mo for 28 mo and tested for the presence of MAP by fecal culture (FC). Heifers from dams testing positive for MAP by serum ELISA or FC were preferentially selected, with the remainder of the age cohort filled with randomly selected heifers. Logistic regression using generalized estimating equations to account for clustering of data within herds and repeated measures across heifers was used to evaluate the relationship between MAP FC status of heifers and herd risk factors. In total, 1,842 fecal samples were collected from 1,202 heifers. Thirty-six (2%) fecal samples, representing 27 individual heifers, cultured positive for MAP. Heifers shedding MAP were more likely to occur in herds with adult-cow MAP ELISA prevalence >10% (odds ratio = 4.7; 95% confidence interval: 2.0-11.1) and herds milking >300 cows (odds ratio = 5.7; 95% confidence interval: 2.4-13.4). Mycobacterium avium ssp. paratuberculosis can be cultured from the feces of naturally infected dairy heifers. The future performance of these MAP FC-positive heifers is unknown and needs to be explored.     

Detection of pleiotropic effects of quantitative trait loci in outbred populations using regression analysis

In this paper a method is presented to determine pleiotropic quantitative trait loci (QTL) or closely linked QTL in an outbred population. The method is based on results from single-trait analyses for different traits and is derived for a granddaughter design. The covariance between estimated contrasts of grandsires obtained in single-trait regression analysis is computed. When there is no pleiotropic QTL, the covariance between contrasts depends on the heritabilities of the traits involved, the polygenic and environmental correlation between the traits, the phenotypic standard deviations, the number of sires per grandsire, and the number of daughters per sire. A pleiotropic QTL results in a covariance that deviates from this expected covariance. The deviation depends on the size of the effects on both traits and on the fraction of grandsires heterozygous for the QTL. When analyzing experimental data, the expected covariance and the confidence interval for the expected covariance can be determined by permutation of the data. A covariance outside the confidence interval suggests the presence of a pleiotropic QTL or a closely linked QTL. The method is verified by simulation and illustrated by analyzing an experimental data set on chromosome 6 in dairy cattle.     

Evaluation of confidence limit estimates of cluster analysis on molecular marker data

BACKGROUND: Diversity studies employ cluster analysis as a statistical tool, whereby relationships between individuals are shown in a dendrogram, mostly accompanied by bootstrap support for merging branches to indicate confidence limits. The objective of this study was to evaluate the reliability of the currently applied method of obtaining confidence limit estimates in cluster analysis and to propose an improved alternative bootstrap method. RESULTS: It was illustrated via a simulation study that conventional bootstrap support for cluster analysis was affected by the sample size. The reliability of merging branches decreased with increasing number of individuals in the sample. Unlike the current bootstrap support for cluster analysis, the proposed method provides confidence intervals for the similarity coefficients between individuals. To facilitate the interpretation of similarity coefficients and confidence intervals, alternative graphical presentations are proposed for both ‘similarity coefficients’ and ‘confidence interval range’. CONCLUSION: The proposed bootstrap method is not affected by the number of individuals in the sample. Copyright © 2011 Society of Chemical Industry     

Calf and replacement heifer mortality from birth until weaning in pasture-based dairy herds in New Zealand

The aims of this study were to (1) estimate the perinatal (birth to 24 h) and postnatal (～24 h to the mean weaning age of 13 wk) mortality risk in pasture-based dairy calves until weaning, and (2) identify associated risk factors in the 2015 calving season. A prospective survey of 32 seasonal calving dairy farms was undertaken. Farmers recorded (daily) the number and sex of the calves alive or dead in the paddocks where cows calved. All daily animal movements in and out of the calf rearing facilities, including death and euthanasia, and the identification of the animals (if applicable) were recorded, and a survey of the farm management practices was undertaken. Individual and farm-level risk factors for perinatal mortality were modeled separately using generalized logistic mixed models with a random effect fitted for herd. Postnatal mortality incidence risk was calculated using time at risk for each calf from 24 h of age, collapsed into weeks, and multiplying the incidence risk by the mean weaning age of the study population. Farm-level risk factors contributing to postnatal mortality in the first week of life were assessed using a multivariable logistic mixed regression model. The mean perinatal mortality risk was 5.7% (95% confidence interval 5.4 to 6.1%) with a range from 2.2 to 8.6% (18,437 calves, 30 farms). Perinatal calf mortality was greater for male relative to female calves (odds ratio 1.39; 95% confidence interval 1.22 to 1.59), calves born in the first week of the calving period in comparison to wk 2 to 11 (odds ratio 0.32 to 0.66), and those born on days with greater rainfall (odds ratio 1.01 per 1 mm increase; 95% confidence interval 1.00 to 1.02). At the farm level, perinatal mortality increased for every extra week of calving period length (odds ratio 1.12; 95% confidence interval 1.06 to 1.17). The mean postnatal mortality risk was 4.1% (95% confidence interval 3.6 to 4.6%) with a range of 0 to 11% between farms. Farm-level risk factors contributing to mortality in the first week of life included farmer-reported disease problems in calves (odds ratio 2.2; 95% confidence interval 1.62 to 2.96), or calves hand-fed colostrum in the first 12 h of life (odds ratio 1.66; 95% confidence interval 1.26 to 2.19), which was assumed to be associated with poor colostrum quality and bacterial contamination. Regional differences were also observed in both perinatal and postnatal mortality risks, indicating that weather conditions, herd size, and management variations contribute to mortality incidence. In summary, the mortality risk of perinatal calves and postnatal calves until weaning on pasture-based farms is comparable with data published from other dairying systems despite the notable management differences. Several risk factors were identified that could be managed to reduce mortality incidence of dairy calves.     

基于Meta分析的大豆磷效率相关QTL的整合

在搜集已经报道大豆磷效率相关的96个QTL基础上,利用BioMercator2.1软件和公共标记将这些QTL映射整合到大豆公共遗传图谱soymap2上,并利用Meta分析在16个连锁群上提取29个＂真实＂QTL区间,其中16个位点由控制1个性状的QTL组成,另13个位点由控制多个性状的QTL组成。经Meta分析后QTL置信区间缩小,平均置信区间由原来的9.95cM降到7.62cM,其中有4个＂真实＂QTL的置信区间小于1cM,另有8个＂真实＂QTL的置信区间在1～5 cM之间。这些＂真实＂QTL区间中,D1b-2和G-2与大豆磷吸收效率、磷利用效率和多个干重性状相关,D2-1与大豆磷含量和多个干重性状相关。这些QTL两侧标记可用于大豆磷效率的分子标记辅助选择。     

Influence of mercury and chlorine content of coal on mercury emissions from coal-fired power plants in China

China is the largest mercury emitter in the world and coal combustion is the most important mercury source in China. This paper updates the coal quality database of China and evaluates the mercury removal efficiency of air pollution control devices (APCDs) based on 112 on-site measurements. A submodel was developed to address the relationship of mercury emission factor to the chlorine content of coal. The mercury emissions from coal-fired power plants (CFPPs) in China were estimated using deterministic mercury emission factor model, nonchlorine-based and chlorine-based probabilistic emission factor models, respectively. The national mercury emission from CFPPs in 2008 was calculated to be 113.3 t using the deterministic model. The nonchlorine-based probabilistic emission factor model, which addresses the log-normal distribution of the mercury content of coal, estimates that the mercury emission from CFPPs is 96.5 t (P50), with a confidence interval of 57.3 t (P10) to 183.0 t (P90). The best estimate by the chlorine-based probabilistic emission factor model is 102.5 t, with a confidence interval of 71.7 to 162.1 t. The chlorine-based model addresses the influence of chlorine and reduces the uncertainties of mercury emission estimates.     

Survival Analysis Applied to Sensory Shelf Life of Foods

ABSTRACT: Survival analysis concepts to be used in sensory shelf life studies were introduced, together with the equations necessary for calculations. The survival function was defined as the probability of consumers accepting a product beyond a certain storage time. Censoring phenomena, a key concept in survival analysis, was defined and has been shown to occur in sensory shelf‐life data. Concepts and calculations were applied to a data set obtained from 50 consumers who each tasted seven yogurt samples with different storage times, answering “yes” or “no” to whether they would consume the samples. From this censored data set, nonparametric and parametric models were obtained that allowed shelf‐life estimations.     

A novel approach for calculating shelf life of minimally processed vegetables

Shelf life of minimally processed vegetables is often calculated by using the kinetic parameters of Gompertz equation as modified by Zwietering et al. [Zwietering, M.H., Jongenburger, F.M., Roumbouts, M., van't Riet, K., 1990. Modelling of the bacterial growth curve. Applied and Environmental Microbiology 56, 1875-1881.] taking 5x10(7) CFU/g as the maximum acceptable contamination value consistent with acceptable quality of these products. As this method does not allow estimation of the standard errors of the shelf life, in this paper the modified Gompertz equation was re-parameterized to directly include the shelf life as a fitting parameter among the Gompertz parameters. Being the shelf life a fitting parameter is possible to determine its confidence interval by fitting the proposed equation to the experimental data. The goodness-of-fit of this new equation was tested by using mesophilic bacteria cell loads from different minimally processed vegetables (packaged fresh-cut lettuce, fennel and shredded carrots) that differed for some process operations or for package atmosphere. The new equation was able to describe the data well and to estimate the shelf life. The results obtained emphasize the importance of using the standard errors for the shelf life value to show significant differences among the samples.     

基于低场核磁共振横向弛豫谱的注水肉检测模型建立

用直接注射的方式,将猪背最长肌制备成注水比例分别为0、2%、6%、10%和14%的肉样本。利用低场核磁共振（field nuclear magnetic resonance,LF-NMR）技术测量肉样本产生的NMR信号,并将反演后得到的横向弛豫谱参数作为自变量,通过判别分析（Discriminant analysis,DA）和偏最小二乘回归（partial least square regression,PLSR）分析,分别建立注水肉检测模型,并尝试多种可能性的PLSR建模,评估分析模型对较低注水比例的注水肉的检测性能。结果表明,对DA模型进行回代验证和留一交叉验证,模型对注水肉分类的总正确率分别为89.4%和88.2%。采用将杠杆值和学生化残差相结合的方式判别和删除异常数据,用变量投影重要性分析法筛选出6个横向弛豫谱参数作为自变量建立的优化PLSR模型的检测性能最优,校准集决定系数（R_c2）和标准误差（SEV）分别为0.9603和1.0033%,交叉验证的决定系数（R_cv2）和标准误差（SECV）分别为0.9508和1.1169%,预测集决定系数（R_p2）和标准误差（SEP）分别为0.9518和1.1280%。在95%的置信概率下,优化PLSR模型能够预测未知样本中注水百分比的置信区间的最好估计值约为2.256%。表明基于LF-NMR横向弛豫谱建立的DA模型和PLSR模型可以对注水肉进行有效的定性和定量检测。     

Invited review: Effectiveness of precalving treatment on postcalving udder health in nulliparous dairy heifers: A systematic review and meta-analysis

Clinical mastitis affects 3% of primiparous dairy cattle (heifers) in the first month after calving. Additionally, the prevalence of intramammary infection (IMI) in the months before first calving is high, resulting in a high prevalence of heifers calving with IMI. Precalving therapy is an accepted recommendation for reducing mastitis in multiparous cows, but prophylactic treatment for heifers is uncommon in North America. Objectives of this study were to (1) quantify changes in postcalving udder health in heifers following application of a precalving treatment; (2) compare effectiveness among various types of treatments; and (3) compare effectiveness of various types of treatments against specific pathogens. A systematic review was conducted comparing interventions aimed at improving udder health in heifers. Of 62 included studies, 48 clinical trials were used in a meta-analysis. Data were synthesized using a random effects model for meta-analysis, followed by sub-group analyses comparing treatment types, and specific pathogens with statistical testing using meta-regression. Occurrence of mastitis (defined as elevated somatic cell count, clinical mastitis, and IMI) was reduced in treated heifers compared with untreated controls with a pooled risk ratio of treated to untreated heifers of 0.56 (95% confidence interval: 0.47 to 0.67). Upon stratification by treatment types, teat sealants and combination therapies (vaccines and antimicrobials; antimicrobials and teat sealants; and all 3) were most effective at improving udder health with pooled risk ratios of 0.40 (95% confidence interval: 0.30 to 0.52) and 0.34 (95% confidence interval: 0.25 to 0.45), respectively. Antimicrobials and vaccines also reduced occurrence of IMI and subclinical and clinical mastitis when compared with untreated heifers. Although variation was observed in the pathogen-specific effectiveness of treatments at reducing rates of disease, antimicrobials, teat sealants, and combinations of vaccines or teat sealants with antimicrobials were consistently effective, whereas vaccines were only effective for contagious pathogens. Recommendations for use of antibiotics should consider their relative benefit while also considering potential for increasing antimicrobial resistance.     

Prevalence and risk factors for Salmonella and Campylobacter spp. carcass contamination in broiler chickens slaughtered in Quebec, Canada

An observational study was conducted to estimate prevalence and risk factors for Salmonella and Campylobacter spp. carcass contamination in broiler chickens. Eighty-two lots were sampled in four slaughterhouses located in the province of Québec, Canada, over a 10-month period. Carcass contamination was evaluated by the carcass rinse technique for about 30 birds per lot. Exposure to potential risk factors was evaluated based on data from questionnaires, meteorology, and cecal cultures. Multivariable binomial negative regression models were used for risk factor analysis at the lot level. The prevalence of Salmonella-positive carcasses was 21.2% (95% confidence interval: 15.7 to 26.7%). Significant risk factors (P < 0.05) associated with a higher proportion of positive carcasses within lots were Salmonella-positive cecal culture, low rainfall during transportation to the slaughterhouse, temperature of > or = 0 degree C during transportation to the slaughterhouse, and a > or = 4-h waiting period in shipping crates before slaughtering. The prevalence of Campylobacter-positive carcasses was 35.8% (95% confidence interval: 27.1 to 44.5%). Lots containing birds with Campylobacter-positive cecal culture results, lots of birds that were slaughtered at the end of the week, and lots with at least 20% of birds with digestive contents detected in the jejunum at time of slaughtering had a significantly higher proportion (P < 0.05) of contaminated carcasses. These results support the importance of preharvest control measures implemented during rearing to reduce contamination of the final product. Weather during transportation to slaughter and the day of the week that birds were slaughtered also were associated with carcass contamination; further studies are needed to determine the underlying mechanisms by which these factors influence carcass contamination.     

Occurrence and sorption behavior of sulfonamides, macrolides, and trimethoprim in activated sludge treatment

The occurrence of sulfonamide and macrolide antimicrobials, as well as trimethoprim, was investigated in conventional activated sludge treatment. Average daily loads in untreated wastewater correlated well with those estimated from annual consumption data and pharmacokinetic behavior. Considerable variations were found during a day, and seasonal differences seem to occur for the macrolides, probably caused by a higher consumption of these substances in winter. The most predominant macrolide and sulfonamide antimicrobials were clarithromycin and sulfamethoxazole, respectively. In the case of sulfamethoxazole, the main human metabolite, N4-acetylsulfamethoxazole, was included as an analyte, accounting for up to 86% of the total load in untreated wastewater. The results obtained illustrate the importance of considering retransformable substances, for example human metabolites, when investigating the behavior and fate of pharmaceuticals. Average concentrations of sulfapyridine, sulfamethoxazole, trimethoprim, azithromycin, and clarithromycin in activated sludge ranged between 28 and 68 microg/kg of dry weight. Overall the sorption to activated sludge was shown to be low for the investigated antimicrobials, with estimated sorption constants for activated sludge below 500 L/kg. Elimination in activated sludge treatment was found to be incomplete for all investigated compounds. In final effluents, the median concentrations for sulfamethoxazole and clarithromycin were 290 and 240 ng/L, respectively.     

Does importance influence confidence in organic food attributes?

Previous studies have established that consumers have a significantly higher willingness to pay (WTP) for organic foods over their conventional counterparts. Not fully understood is how consumers view the importance of the required attributes of organic, how confident they are that the organic label reflects these attributes, and how these two factors interact and influence WTP. This study used non-hypothetical auction experiments to examine these issues with a sample of 128 consumers from the general population. Participants first entered their WTP for conventional and organic versions of four different foods selected in different categories (dairy, meat, vegetable) to cover the different possible organic attributes. They were then asked to rate their importance level in, and confidence of, seven required attributes of USDA organic (e.g. no synthetic pesticides, non-GM). The specific goals were to examine the relationship between importance and confidence ratings, and to determine if confidence ratings can be predicted by importance and how confidence in turn influences WTP. For the former, importance ratings for all organic attributes were found to be significantly higher than corresponding confidence ratings. Results from a simultaneous equation system then showed that higher importance ratings significantly increased confidence ratings, while higher confidence increased marginal WTP for all four organic food products. These findings suggest WTP for organic foods is more complex than typically perceived, with it relying heavily on how important consumers see each attribute and their confidence that they are really getting those attributes with their purchases.