Optimal sampling in retrospective logistic regression via two-stage method

Case-control sampling is popular in epidemiological research because of its cost and time saving. In a logistic regression model, with limited knowledge on the covariance matrix of the point estimator of the regression coefficients a priori, there exists no fixed sample size analysis. In this study, we propose a two-stage sequential analysis, in which the optimal sample fraction and the required sample size to achieve a predetermined volume of a joint confidence set are estimated in an interim analysis. Additionally required observations are collected in the second stage according to the estimated optimal sample fraction. At the end of the experiment, data from these two stages are combined and analyzed for statistical inference. Simulation studies are conducted to justify the proposed two-stage procedure and an example is presented for illustration. It is found that the proposed two-stage procedure performs adequately in the sense that the resultant joint confidence set has a well-controlled volume and achieves the required coverage probability. Furthermore, the optimal sample fractions among all the selected scenarios are close to one. Hence, the proposed procedure can be simplified by always considering a balance design.     

Preference for structured environment in zebrafish (Danio rerio) and checker barbs (Puntius oligolepis)

Information about the welfare and husbandry of pet and laboratory fish is scarce although millions of fish are sold in pet shops and used in laboratory research every year. Inadequate housing conditions can cause behavioural problems also in fish since they are complex animals with sophisticated behaviour. In this study, we investigated the influence of environmental complexity on compartment preference and behaviour in zebrafish (Danio rerio) and checker barbs (Puntius oligolepis). For the preference test, large aquaria were divided by two semi-transparent walls of Plexiglas into an empty compartment, a structured compartment enriched with plants and clay pots, and a smaller compartment in-between, where food was provided. For observation, the empty and structured compartments were divided into six zones of similar size by defining three vertical layers and two horizontal areas (back vs. front area). Seven groups of six to nine zebrafish and seven groups of seven or eight checker barbs were observed on four days each (within a time period of ten days) to assess compartment use and activity, and to assess behavioural diversity and use of zones within compartments. Both zebrafish and checker barbs showed a significant preference for the structured compartment. Nevertheless, in neither species did behavioural diversity differ between the empty and structured compartment. Zebrafish used all zones in both compartments to the same extent. Checker barbs, however, used the structured compartment more evenly than the empty compartment, where they mainly used the lower and middle zones. These results suggest that zebrafish and checker barbs have a preference for complex environments. Furthermore, they indicate that the behavioural and ecological needs of fish may vary depending on species, and recommendations for husbandry should be specified at species level.     

Optimized enrichment for the detection of Escherichia coli O26 in French raw milk cheeses

Aims: Our main objective was to optimize the enrichment of Escherichia coli O26 in raw milk cheeses for their subsequent detection with a new automated immunological method. Methods and Results: Ten enrichment broths were tested for the detection of E. coli O26. Two categories of experimentally inoculated raw milk cheeses, semi‐hard uncooked cheese and ‘Camembert’ type cheese, were initially used to investigate the relative efficacy of the different enrichments. The enrichments that were considered optimal for the growth of E. coli O26 in these cheeses were then challenged with other types of raw milk cheeses. Buffered peptone water supplemented with cefixim–tellurite and acriflavin was shown to optimize the growth of E. coli O26 artificially inoculated in the cheeses tested. Despite the low inoculum level (1–10 CFU per 25 g) in the cheeses, E. coli O26 counts reached at least 5·10⁴ CFU ml^?1 after 24‐h incubation at 41·5°C in this medium. Conclusions: All the experimentally inoculated cheeses were found positive by the immunological method in the enrichment broth selected. Significance and Impact of the Study: Optimized E. coli O26 enrichment and rapid detection constitute the first steps of a complete procedure that could be used in routine to detect E. coli O26 in raw milk cheeses.     

Variation in nutrient limitation and seagrass nutrient content in Bahamian tidal creek ecosystems

The traditional model of nutrient availability in coastal estuarine ecosystems is based on predictable inputs of nitrogen (N) and phosphorus (P) via riverine and oceanic sources, respectively. But coastlines with low nutrient input from these sources may not fit into this simple framework. Here we use observational (seagrass nutrient content) and experimental (nutrient enrichment assays) data for assessing nutrient availability and limitation for primary producers along a spatial transect extending from the mouth (nearest to the ocean) to the terminal portion (boundary with the terrestrial ecosystem) of three coastal mangrove-lined tidal creeks in The Bahamas. Compiling seagrass nutrient content from all sites showed a negative relationship between seagrass nutrient limitation (either N or P) and distance from mouth, but this pattern differed across sites with respect to which nutrient was more limiting. Our experimental results demonstrated patterns of decreased response by microalgae to dual nutrient enrichment in one site with distance from the creek mouth, and increased response to single nutrient enrichment in another, with the third showing no trend along this gradient. Our findings show that Bahamian mangrove wetlands are extremely nutrient-limited ecosystems, and that the most limiting nutrient varied among sites. In general, these ecosystems deviate from the typical paradigm of spatial nutrient limitation patterns in estuaries. We suggest that various site-specific biological and physical factors may be more important than large-scale hydrologic factors in driving trends of nutrient availability in coastal ecosystems under strong nutrient constraints, such as in The Bahamas. Our findings suggest that even minor changes in nutrient loading rates can have significant implications for primary production in subtropical oligotrophic systems.     

Age class differences in the feeding behavior of captive Japanese macaques (Macaca fuscataia) in the forested and nonvegetated enclosure groups

Age class differences in feeding behavior of primates are affected by many factors, including feeding competition, foraging skills, habitat type, food abundance and distribution, body mass, and food types. Two captive groups of Japanese macaques (Macaca fuscata), one housed in a forested enclosure and the other in a nonvegetated enclosure, were studied to examine the effect of environmental enrichment on age class differences in feeding behavior. Although there was no significant age class difference in time spent feeding on provisioned foods in either enclosure, the feeding rate (intake of unit food/minute) of adults consuming provisioned monkey chow was significantly higher than that of immatures in both enclosures, and was faster for both age groups in the nonvegetated than in the forested enclosure. Overall, feeding time was greatly extended for individuals of both age classes in the forested enclosure compared with their counterparts in the nonvegetated enclosure. Immatures in the forested enclosure utilized a significantly greater number of plant species and food items, exploiting many food items available among the terminal branches, and spent significantly more time feeding than adults. Perhaps constrained by larger body size, adults fed more often on the ground or middle height of the trees, likely reducing competition over plant food resources between adults and immatures. The natural vegetation played an important role in extending feeding time and segregating substrate use during feeding by adults and immatures. This study revealed the benefits concerning environmental enrichment of a naturally forested enclosure, which provides captive primates the opportunity to exhibit age class and species-typical feeding behaviors of importance for their dietary maintenance and general health.     

磷酸化蛋白质组学的新进展及其在肝脏生理和病理机制中的应用

蛋白质磷酸化是最常见的蛋白质翻译后修饰形式。由于蛋白质的磷酸化形式可以被磷酸酶和磷酸激酶进行可逆的调控,所以在众多的生命活动过程中蛋白质的磷酸化修饰起着重要的调控作用,因此对生物体内蛋白质磷酸化修饰的系统研究对于揭示生命科学的奥秘显得十分重要。近年来,随着质谱技术和生物信息学软件以及磷酸化肽段富集方法的发展,利用质谱对生物体内蛋白质磷酸化修饰研究的技术逐渐成熟。肝脏作为人体最重要的代谢和免疫器官,深入研究肝脏细胞内蛋白质磷酸化修饰形式对于理解其功能具有重要指导意义。目前,迅速发展的磷酸化蛋白质组学技术已经被广泛应用到肝脏功能的生物学研究中。这些研究加深了人们对肝脏的生理及病理状态的分子生物学机制的了解。本文综述了当前磷酸化蛋白质组学的研究进展和磷酸化蛋白质组学在肝脏中的研究。     

91例主动脉夹层动脉瘤的临床治疗体会

目的:依据临床经验,熟练运用开放手术、腔内修复术及杂交手术方法治疗各类主动脉夹层动脉瘤。方法:收集2009年7月~2013年1月在我院手术治疗的主动脉夹层动脉瘤患者共91例,StanfordB型夹层动脉瘤36例(其中21例降主动脉瘤、9例腹主动脉及双髂动脉瘤行腔内覆膜支架隔绝术,6例行腹主动脉人工血管置换术),StanfordA型夹层动脉瘤55例(其中单纯Sun,s手术12例伴Bentall术6例,Bentall术伴部分主动脉弓人工血管置换36例,1例行Ⅱ型的主干与分支动脉人工血管转流+介入腔内隔绝降主动脉及左半弓杂交术),分别以不同的手术方法给予治疗。结果:顺利治愈出院85例,死亡6例,4例因全弓置换术后出现难以控制的大出血、肠坏死、肾功能不全、少尿等并发症而死亡,2例死于Bentall术后严重多功能脏器急性衰竭,1例杂交手术术后出现高血压伴神经系统并发症,1例伴肺部感染及低心排综合征,给予对症治疗后效果不佳,有2例出现肾功能不全,经过透析治愈。腔内修复术后有神经系统的并发症2例,下肢的功能障碍2例,少量内漏4例,以上并发症均经对症治疗后痊愈。术后随访76例,时间3~12个月,除2例于术后第9个月死亡、1例因脑梗塞、脑血管意外等与手术无关的疾病而死亡,2例因吻合口动脉瘤或动脉瘤破裂大出血死亡外,余患者生活状态良好,心功能在I~Ⅱ级。结论:根据主动脉瘤疾病的临床特点和定位诊断,合理选择和运用治疗方法使手术操作变得更为迅速、安全和方便,同时能够取得良好的临床治疗效果。     

Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment

Chemical mutagenesis is routinely used to create large numbers of rare mutations in plant and animal populations, which can be subsequently subjected to selection for beneficial traits and phenotypes that enable the characterization of gene functions. Several next‐generation sequencing (NGS)‐based target enrichment methods have been developed for the detection of mutations in target DNA regions. However, most of these methods aim to sequence a large number of target regions from a small number of individuals. Here, we demonstrate an effective and affordable strategy for the discovery of rare mutations in a large sodium azide‐induced mutant rice population (F₂). The integration of multiplex, semi‐nested PCR combined with NGS library construction allowed for the amplification of multiple target DNA fragments for sequencing. The 8 × 8 × 8 tridimensional DNA sample pooling strategy enabled us to obtain DNA sequences of 512 individuals while only sequencing 24 samples. A stepwise filtering procedure was then elaborated to eliminate most of the false positives expected to arise through sequencing error, and the application of a simple Student's t‐test against position‐prone error allowed for the discovery of 16 mutations from 36 enriched targeted DNA fragments of 1024 mutagenized rice plants, all without any false calls.     

Genetic assessment of safflower (Carthamus tinctorius L.) collection with microsatellite markers acquired via pyrosequencing method

A genetic evaluation of safflower germplasm collections derived from different geographical regions and countries will provide useful information for sustainable conservation and the utilization of genetic diversity. However, the molecular marker information is limited for evaluation of genetic diversity of safflower germplasm. In this study, we acquired 509 putative genomic SSR markers for sufficient genome coverage using next‐generation sequencing methods and characterized thirty polymorphic SSRs in safflower collection composed of 100 diverse accessions. The average allele number and expected heterozygosity were 2.8 and 0.386, respectively. Analysis of population structure and phylogeny based on thirty SSR profiles revealed genetic admixture between geographical regions contrary to genetic clustering. However, the accessions from Korea were genetically conserved in distinctive groups in contrast to other safflower gene pool. In conclusion, these new genomic SSRs will facilitate valuable studies to clarify genetic relationships as well as conduct population structure analyses, genetic map construction and association analysis for safflower.