Recommended Practice Regarding Selection of Sensitivity Analysis Methods Applied to Microbial Food Safety Process Risk Models

A guideline is presented for selection of sensitivity analysis methods applied to microbial food safety process risk (MFSPR) models. The guideline provides useful boundaries and principles for selecting sensitivity analysis methods for MSFPR models. Although the guideline is predicated on a specific branch of risk assessment models related to food-borne diseases, the principles and recommendations provided are typically generally applicable to other types of risk models. Applicable situations include: prioritizing potential critical control points; identifying key sources of variability and uncertainty; and refinement, verification, and validation of a model. Based on the objective of the analysis, characteristics of the model under study, amount of detail expected from sensitivity analysis, and characteristics of the sensitivity analysis method, recommendations for selection of sensitivity analysis methods are provided. A decision framework for method selection is introduced. The decision framework can substantially facilitate the process of selecting a sensitivity analysis method.     

Analysis of Counts involving Random Effects with Applications in Experimental Biology

This paper is concerned with the analysis of count data with special reference to experimental biology and agricultural research. The model considered in this paper is obtained by extending a generalized linear model by introducing random effects with associated variance components on the scale of the linear predictor. Maximum likelihood estimation is discussed and compared with a method which uses a simplified version of the likelihood equations. Two practical applications are used to illustrate the methods.     

Models for Estimating Abundance from Repeated Counts of an Open Metapopulation

Summary Using only spatially and temporally replicated point counts, Royle (2004b, Biometrics 60, 108–115) developed an N ‐mixture model to estimate the abundance of an animal population when individual animal detection probability is unknown. One assumption inherent in this model is that the animal populations at each sampled location are closed with respect to migration, births, and deaths throughout the study. In the past this has been verified solely by biological arguments related to the study design as no statistical verification was available. In this article, we propose a generalization of the N ‐mixture model that can be used to formally test the closure assumption. Additionally, when applied to an open metapopulation, the generalized model provides estimates of population dynamics parameters and yields abundance estimates that account for imperfect detection probability and do not require the closure assumption. A simulation study shows these abundance estimates are less biased than the abundance estimate obtained from the original N ‐mixture model. The proposed model is then applied to two data sets of avian point counts. The first example demonstrates the closure test on a single‐season study of Mallards (Anas platyrhynchos), and the second uses the proposed model to estimate the population dynamics parameters and yearly abundance of American robins (Turdus migratorius) from a multi‐year study.     

A comparison of different ways of including baseline counts in negative binomial models for data from falls prevention trials

A common design for a falls prevention trial is to assess falling at baseline, randomize participants into an intervention or control group, and ask them to record the number of falls they experience during a follow‐up period of time. This paper addresses how best to include the baseline count in the analysis of the follow‐up count of falls in negative binomial (NB) regression. We examine the performance of various approaches in simulated datasets where both counts are generated from a mixed Poisson distribution with shared random subject effect. Including the baseline count after log‐transformation as a regressor in NB regression (NB‐logged) or as an offset (NB‐offset) resulted in greater power than including the untransformed baseline count (NB‐unlogged). Cook and Wei's conditional negative binomial (CNB) model replicates the underlying process generating the data. In our motivating dataset, a statistically significant intervention effect resulted from the NB‐logged, NB‐offset, and CNB models, but not from NB‐unlogged, and large, outlying baseline counts were overly influential in NB‐unlogged but not in NB‐logged. We conclude that there is little to lose by including the log‐transformed baseline count in standard NB regression compared to CNB for moderate to larger sized datasets.     

微生物物种多样性的保护与其资源保藏

从微生物物种多样性的保护以及微生物物种资源的保藏等方面较全面地阐述了微生物物种资源保护与保藏的重要性及其相互关系 ,阐明了微生物菌种保藏的原理及方法 ,同时介绍了保藏技术领域的研究动向和保藏机构或组织在微生物资源的保藏、开发和交流等方面所起的重要作用     

结核分枝杆菌培养物不同组份蛋白质组研究

将结核分枝杆菌H37RV株在苏通培养基内,37℃培养21d,然后将培养物分成上清液(A)、细胞浆(B)和细胞膜?蛋白质样品。以pH3.0～10.0的IPG预制胶条等电聚焦电泳为第一向,SDSPAGE为第二向进行双向电泳(2DE)、银染。经扫描、计算机处理。A组份的部分蛋白质斑点采用质谱仪进行蛋白质鉴定。A、B和C 3个组份蛋白质斑点总数分别为907、884和681;3个组份蛋白质分子量分布基本相似,约70.5%～74.4%在10～49kD之间;蛋白质等电点(pH)A、B两组份分布基本相似,约80.9%～83.5%在pH3.0～6.4之间,而C组份pH7.6～10.0之间的蛋白质斑点数比A和B两组分略多;A、B和C 3个组份表达丰度较高的蛋白质斑点数占各组蛋白质斑点总数的比例分别为7.8%、27.4%和2.8%,蛋白质等电点90.0%均分布在pH3.0～6.4范围内。B组份蛋白质分子质量73.1%分布在10～49kD之间,比A、B两组份略高。A组份14个蛋白质斑点经肽质量指纹谱分析,其中,9个点有同源性的或推测的蛋白质功能,5个蛋白质功能不清楚。总之,初步获得了结核分枝杆菌H37RV株在上述体外培养条件下收获的培养物的上清液、细胞浆、细胞膜蛋白质组2DE图谱及其特点,为该菌功能基因组研究提供蛋白质组信息。     

利用污泥提取液制备微生物絮凝剂

以污水厂剩余污泥作为培养基原料,经过一系列处理,探索微生物絮凝剂产生菌的最适发酵培养基配方,结果表明,污泥预处理条件以pH 12碱解条件最优,碳氮源产出量最大,补加8 g/L葡萄糖后灭菌,微生物絮凝剂产生菌LLin6可正常产絮,絮凝率达91.55%。该结果为降低微生物絮凝剂的制备成本,并实现污泥的减量化和污泥资源化利用提供了基础。     

Evaluation of Sampling-Based Methods for Sensitivity Analysis: Case Study for the E. coli Food Safety Process Risk Model

This article evaluates selected sensitivity analysis methods applicable to risk assessment models with two-dimensional probabilistic frameworks, using a microbial food safety process risk model as a test-bed. Six sampling-based sensitivity analysis methods were evaluated including Pearson and Spearman correlation, sample and rank linear regression, and sample and rank stepwise regression. In a two-dimensional risk model, the identification of key controllable inputs that can be priorities for risk management can be confounded by uncertainty. However, despite uncertainty, results show that key inputs can be distinguished from those that are unimportant, and inputs can be grouped into categories of similar levels of importance. All selected methods are capable of identifying unimportant inputs, which is helpful in that efforts to collect data to improve the assessment or to focus risk management strategies can be prioritized elsewhere. Rank-based methods provided more robust insights with respect to the key sources of variability in that they produced narrower ranges of uncertainty for sensitivity results and more clear distinctions when comparing the importance of inputs or groups of inputs. Regression-based methods have advantages over correlation approaches because they can be configured to provide insight regarding interactions and nonlinearities in the model.     

A Probabilistic Analysis of Regional Mercury Impacts on Wildlife

We investigate the uncertainties associated with modeling the potential health effects on piscivorous animals of mercury released to the atmosphere. The multimedia modeling system combines an atmospheric fate and transport model, an aquatic cycling model, and a terrestrial food web model. First, the modeling system is used to calculate point values of the animals' hazard quotients (i.e., measures of toxic dose). Next, we use a simplified version of the modeling system to conduct a probabilistic analysis for the Great Lakes region that takes into account input uncertainty, variability, and uncertainty and variability combined. The use of two different software packages for the combined uncertainty/variability analysis led to similar results except for high values (>90th percentile) where some differences were evident. A sensitivity study was performed on the combined uncertainty and variability analysis. Regional variability caused more than 70% of the variance in the results, with the fish bioaccumulation factor accounting for the majority of the variability. The major sources of uncertainty were the speciation of the mercury emissions, the lake pH, and the sediment burial rate.     

A likelihood ratio test for equality of deviations from randomness

The use of the sample variance-to-mean ratio as a measure of deviation from randomness in spatial pattern is reviewed. The likelihood ratio method of constructing a statistical test for the equality of several population variance-to-mean ratios is described, and details are provided for the special case where counts are modelled as arising from a negative binomial distribution. This test is illustrated by application to example data sets in ecology. Likelihood ratio tests represent a general methodology whereby relationships among several indices of aggregation can be systematically investigated, provided one is able to specify a suitable parametric form for the underlying distributions.     

Microbial Communities and Exopolysaccharides from Polynesian Mats

Microbial mats present in two shallow atolls of French Polynesia were characterized by high amounts of exopolysaccharides associated with cyanobacteria as the predominating species. Cyanobacteria were found in the first centimeters of the gelatinous mats, whereas deeper layers showing the occurrence of the sulfate reducers Desulfovibrio and Desulfobacter species as determined by the presence of specific biomarkers. Exopolysaccharides were extracted from these mats and partially characterized. All fractions contained both neutral sugars and uronic acids with a predominance of the former. The large diversity in monosaccharides can be interpreted as the result of exopolymer biosynthesis by either different or unidentified cyanobacterial species. Received July 25, 2000; accepted October 21, 2000     

Antigenic Makeup of Subcellular Fractions of Trypanosoma cruzi

Trypanosoma cruzi epimastigotes from cultures were separated into nuclear, mitochondrial, lysosomal, microsomal, and cell-sap fractions. Enzymic and ultrastructutal controls served to determine the cleanness of separation. The bulk of the DNA was in the nuclear (78%) and mitochondrial (12%) fractions. RNA was found in microsomal (74%) and cell-sap (14%) fractions. Marker enzyme distribution (succinic dehydrogenase, acid phosphatase, and glucose-6-phosphatase) was compared with their distribution in mammalian tissues. Subcellular localization of antigens by Ouchterlony tests revealed 2 specific precipitin lines in cell sap and 1 in the microsomal fraction. These antigens may prove diagnostically and immunoprotectively valuable.     

New Chromosome Counts of Some Dicots in the Sino-Japanese Region and Their Systematics and Evolutionary Significance

New somatic chromosome numbers for nine species eight families and eight gen era in the Sino-Japanese Region are reported here as shown in Table 1. Data of six genera are previously unknown cytologically. The bearings of these new data on the systematics and evolution of the related species, genera or families are discussed as follows: (1) Platycarya strobilacea Sieb. et Zucc. (Juglandaceae). The chromosome number of this species is 2n=24, with a basic number of x=12, which deviates from 2n=32 occurred in Juglans, Carya, Pterocarya and Engelhardtia with the basic number x= 16. The Juglandaceae appears to be fundamentally paleotetraploid, with an original basic number of x = 6 in Platycarya and x-8 in the other four genera, although secondary polyploidy occurs in Carya. Based on the remarkable morphological differences between Platycarya and the rest seven genera of the family, Manning (1978) established two subfamilies: Platycaryoideae for Platycarya and Juglandoideae for the other genera. Iljinskaya (1990), however, recently established a new subfamily: Engelhardioideae for Engelhardtia. Lu (1982) points out that because of a great number of primitive characters occurring in Platycarya, the genus could not be derived from any other extant juglandaceous taxa but probably originated with the other groups from a common extinct ancestor. The present cytological data gives support to Manning′s treatment. We are also in favor of Lu′s supposition and suggest that basic aneuploid changes, both ascending and descending, from a common ancestor with the original basic number x=7, took place during the course of early evolution of the Juglandaceae and led to the origin of taxa with x=6 and 8. Subsequent polyploidy based on these diploids occurred and brought forth polyploids of relic nature today, whereas their diploid progenitors apparently have become extinct. (2) Nanocnide pilosa Migo (Urticaceae). The chromosome number of this Chinese endemic is 2n-24, with a basic number of x=12. An aneuploid series occurs in the Urticaceae, with x--13, 12, I1, 10, 9, 8, 7, etc. According to Ehrendorfer (1976), x = 14, itself being of tetraploid origin, is the original basic number of the whole Urticales, and descending aneuploid changes took place in the early stage of evolution of the Urticaceae and Cannabinaceae. In addition to Nanocnide, x= 12 also occurs in Australina, Hesperonide and Lecanthus, and partly in Chamabainia, Elatostema, Girardinia, Pouzolzia and Urtica. (3--4) Sedum sarmentosum Bunge and S. angustifolium Z. B. Hu et X. L. Huang (Crassulaceae). The former is a member of the Sino-Japanese Region, while the latter is only confined to eastern China. The chromosome number of Sedum is remarkably complex with n=4-12, 14-16…74, etc. S. angustifolium with 2n=72 of the present report is evidently a polyploid with a basic number of x =18 (9^?) Previous and present counts of S. sarmentosum show infraspecific aneupolyploidy: n = c. 36 (Uhl at al. 1972) and 2n=58 (the present report). These two species are sympatric in eastern China and are morphologically very similar, yet distinguishable from each other (Hsu et al. 1983) S. sarmentosum escaped from cultivation in the United States gardens exhibited high irregularity in meiosis (Uhl et al. 1972). Uhl (pets. comm. ) suspected strongly that it is a highly sterile hybrid. R. T. Clausen (pets. comm.) found that plants of S. sarmentosum naturalized in the American Gardens propagated by means of their long stolons and broken stem tips, and could not yield viable seeds. Hsu et al. (1983) found that some of the plants of S. sarmentosum and S. angustifolium did yield a few seeds, but other did not. These species are, therefore, by the large vegetatively apomictic. (5) Glochidion puberum (L. ) Hutch. (Euphorbiaceae). The genus Glochidion includes about 300 species, but only eigth species from the Himalayas have been studied cytologically, with n= 36 and 2n= 52, having a basic number of x= 13. The present count for the Chinese endemic G. puberum establishes the tetraploid chromosome number 2n= 64, and adds a new basic number x= 16 to the genus. (6) Orixa japonica Thunb. (Rutaceae). Orixa is a disjunct Sino-Japanese monotypic genus. Out of the 158 genera of the Rutaceae, chromosome numbers of 65 genera have hitherto been investigated, of which 42 genera are with x=9 (66.61%), some with x=7, 8 and 10, and rarely with x=13, 15, 17 and 19. The present count of 2n=34 for O. japonica may have resulted from a dibasic tetraploidy of n=8+9. (7) Rhamnella franguloides (Maxim.) Weberb. (Rhamnaceae). The chromosome number of this member of the Sino-Japanese Region is 2n= 24. with a basic number of x= 12. The basic number x= 12 also occurs in Hovenia, Paliurus, Sageretia, Ceanothus and Berchemia. Hong (1990) suggested that x= 12 in Rhamnaceae may be derived from descending aneuploidy of a paleotetraploid ancestor. (8) Sinojackia xylocarpa Hu (Styracaceae). The chromosome number of this rare Chinese endemic is 2n= 24, with a basic number of x =12, which is identical with that in Halesia and Pterostyrax, but deviates from that in Styrax (x=8). The basic number x=8 in the Styracaceae may be derived from the original basic number x=7 by ascending aneuploidy in the early stage of evolution of the family, and x=12 may be derived from polyploidy. (9) Thyrocarpus glochidiatus Maxim. (Boraginaceae). The chromosome number of this Chinese endemic species is 2n=24, with a basic number of x=12. An extensive aneuploid sequence of x = 4-12 occurs in the Boraginaceae, of which x = 8, 7 and 6 are the most common. The basic number x=12 also occurs in Cynoglossum and Mertensia. It is evident that aneuploid changes, both descending and ascending, from an ancestor with x = 7, have taken place in the primary phase of evolutionary diversification of the Boraginaceae, and subsequent polyploidy has given rise to x=15, 17 and 19 in a few genera (e. g. Amsinskia and Heliotropium). The origin of x=12 is not certain. Either it be a result of ascending aneuploidy, or a product of polyploidy on the basis of x = 6. The present authors are in favorof the latter.     

微生物传感器及其在氨基酸分析中的应用

介绍了微生物传感器的发展状况、制作方法,综述了微生物传感器在氨基酸分析中的应用,引文献４２篇。     

早期宫颈癌患者围手术期外周血淋巴细胞数与其预后的关系

目的:探讨早期宫颈癌患者围手术期外周血淋巴细胞数与其预后之间的关系。方法:回顾性分析2006年1月至2012年12年就诊于解放军总医院,根据2009年最新宫颈癌FIGO指南诊断为Ⅰb~ⅡA期宫颈癌进行阴式宫颈癌根治术患者的临床病历资料。分析患者的围手术期淋巴细胞数和其无瘤生存期、总生存期间的关系。结果:共143例阴式早期宫颈癌根治术患者纳入研究,随访时间为6~87个月,中位随访时间为53个月。术后,宫颈癌患者外周血淋巴细胞数显著下降。术前外周血淋巴细胞数较高的患者无瘤生存期及总生存期均较外周血淋巴细胞数低于平均水平的患者显著延长(P0.05);术后第三天淋巴细胞数恢复或高于术前水平的患者无瘤生存期较术后第三天淋巴细胞数低于术前水平的患者显著延长(P0.05),但总生存期无明显差异(P0.05)。COX回归分析显示术前淋巴细胞数高于平均水平及术后第三天淋巴细胞数高于或等于术前水平的宫颈癌患者的预后相对较好。结论:术前淋巴细胞数和术后第三天淋巴细胞数的变化均可作为评估宫颈癌术后患者预后的重要参考指标。     

Multivariate study of different beef quality traits from local Spanish cattle breeds

Different raw beef quality traits from four local Spanish cattle breeds were studied using correlation, factorial, discriminant and multiple regression analysis. The following variables were studied after 0, 5, 10 and 15 days of storage under 60% O₂, 30% CO₂ and 10% N₂ modified atmosphere packaging (MAP): colour physical variables, meat pigments, sensory degradation of odour and colour, microbial counts, thiobarbituric acid (TBA), pH, drip loss, lipid composition and volatile compounds. The degradation of raw beef quality was related to the increase in 2,3,3-trimethylpentane, 2,2,5-trimethylhexane, 3-methyl-2-heptene, 2-octene, 3-octene, 2-propanone, Enterobacteriaceae and aerobial plate counts (APC), metmyoglobin (MMb), lightness (L*), yellowness (b*), drip loss and TBA. Among these variables, TBA, b* and MMb may be useful in evaluating raw beef quality. No variables related to fat, except for TBA, including pH were limiting factors of the colour and odour shelf-life of raw beef under MAP. Each breed had some characteristics that were unique and these differences may influence the stability of meat to oxidation depending on myoglobin concentration and the polyunsaturated fatty acid (PUFA)/saturated fatty acid (SFA) ratio.     

Microbial production of specialty organic acids from renewable and waste materials

Microbial production of organic acids has become a fast-moving field due to the increasing role of these compounds as platform chemicals. In recent years, the portfolio of specialty fermentation-derived carboxylic acids has increased considerably, including the production of glyceric, glucaric, succinic, butyric, xylonic, fumaric, malic, itaconic, lactobionic, propionic and adipic acid through innovative fermentation strategies. This review summarizes recent trends in the use of novel microbial platforms as well as renewable and waste materials for efficient and cost-effective bio-based production of emerging high-value organic acids. Advances in the development of robust and efficient microbial bioprocesses for producing carboxylic acids from low-cost feedstocks are also discussed. The industrial market scenario is also reviewed, including the latest information on the stage of development for producing these emerging bio-products via large-scale fermentation.     

红树林人工修复区根际微生物群落结构分析

目的:通过比较不同年份红树林修复区的根际微生物结构,建立微生物区系与修复质量的相关性,为红树林修复提供理论借鉴。方法:采集4年、8年、10年红树林修复区以及原生红树林的根际微生物,利用末端限制性片段长度多态性技术(Terminal Restriction Fragment Length Polymorphism,T-RFLP)、聚类分析(Cluster Analysis,CA)、主成分分析法(Principal Component Analysis,PCA)、α多样性分析法、文氏图、稀释性曲线等分析方法,研究不同样本间根际微生物的群落组成并进行差异性对比。结果:通过分析不同修复年限间根际微生物的短片段重复序列(Short Tandem Repeat,STR)测序结果,发现三个不同修复时间的红树林修复区和原生红树林根际微生物间均存在差异,10年修复区更加接近原生红树林,4年和8年修复区享有更加相似的微生物群落,且同原生红树林间存在较大差异。结论:修复区红树林的根际微生物群落结构会逐步向着原生红树林根际微生物群落结构演替,但这一过程并非简单的加和式线性变化,而是存在复杂性和年份突变性的可能。     

专利微生物菌种的保藏与发放统计分析

对WIPO公开的"国际保藏机构2001～2010年专利微生物保藏与发放"数据进行了统计分析。结果表明:全世界的专利菌种保藏量与发放量处于快速增长中;美国是专利菌种保藏与发放量最多的国家;近年中国的专利菌种年保藏量实现三连冠,但专利菌种的发放率处于极低水平。