21 research outputs found

    Robust estimation of bacterial cell count from optical density

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    Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

    Sea-Land Clutter Classification Based on Graph Spectrum Features

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    In this paper, an approach for radar clutter, especially sea and land clutter classification, is considered under the following conditions: the average amplitude levels of the clutter are close to each other, and the distributions of the clutter are unknown. The proposed approach divides the dataset into two parts. The first data sequence from sea and land is used to train the model to compute the parameters of the classifier, and the second data sequence from sea and land under the same conditions is used to test the performance of the algorithm. In order to find the essential structure of the data, a new data representation method based on the graph spectrum is utilized. The method reveals the nondominant correlation implied in the data, and it is quite different from the traditional method. Furthermore, this representation is combined with the support vector machine (SVM) artificial intelligence algorithm to solve the problem of sea and land clutter classification. We compare the proposed graph feature set with nine exciting valid features that have been used to classify sea clutter from the radar in other works, especially when the average amplitude levels of the two types of clutter are very close. The experimental results prove that the proposed extraction can represent the characteristics of the raw data efficiently in this application

    (Colour online) Results of the evolutionary model.

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    <p>With respect to the empirical data, we set the initial state of the simulation same with the data applied in this study, i.e. <i>M</i> = 61, 184, <i>N</i> = 366, 715 and we use the empirical social structure as the pre-defined network among users. Furthermore, each simulation continues for 1,569,264 steps (same with the empirical data). <b>a,</b> Distributions of the simulated global popularity. The simulations with different parameters <i>μ</i> can all reproduce the power-law global popularity distribution with slope same to the empirical observation. <b>b,</b> Distributions of the real-time local popularity with different parameters <i>μ</i>. Each distribution exhibits a linear pattern in the log-log plot. <b>c,</b> The slope <i>γ</i> of the linear pattern for local popularity distributions with different parameter <i>μ</i>. For each parameter <i>μ</i>, the result is calculated based on 100 independent simulations. For each simulation, the fitting is based on a linear regression after taking logarithm for the simulated local popularity <i>LP</i>(<i>c</i>) and the frequency (p.d.f.) of it <i>p</i>(<i>LP</i>(<i>c</i>)) (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175761#pone.0175761.s001" target="_blank">S1 File</a>). The inset in the subplot (c) shows the coefficient of determination <i>R</i><sup>2</sup> of corresponding fittings. The <i>R</i><sup>2</sup> of the fittings are generally larger than 0.98 which indicates that the fittings can be considered good for all the experiments with different parameters <i>μ</i>. The red dashed line is the slope <i>γ</i> of the empirical local popularity distribution shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0175761#pone.0175761.g001" target="_blank">Fig 1(d)</a>, i.e. <i>γ</i><sub><i>em</i></sub> = −2.7. The green boxes are those which agree with the empirical result.</p

    Social influence on selection behaviour: Distinguishing local- and global-driven preferential attachment - Fig 1

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    <p>(Color online) <b>a,</b> An example of user-business bipartite network with social structure to illustrate the Yelp data set and the research scenario. On the user layer, each user may establish friendships with others and those friends are the target user’s local neighbourhood. On the other hand, the whole user layer is the global environment for each user. The interactions between the user and business layer represented by the bipartite links, are the comment behaviours. Although it is impossible to know exactly each user’s real-world consumption for those businesses, we assume the online comment behaviour could largely reflect what those users have selected (consumed). <b>b,</b> The distribution of the businesses’ final global popularity, i.e. popularity at the end <i>t</i> = <i>T</i> of the Yelp data set, <i>GP</i>(<i>T</i>). As what have been observed from most networks, the global popularity distribution displays a power-law form with slope of −1.7. <b>c,</b> Local popularity of selection behaviours <i>LP</i>(<i>c</i>) versus the expected local popularity <i>LP</i><sup><i>exp</i></sup>. The red dashed line shows the condition that <i>LP</i>(<i>c</i>) = <i>LP</i><sup><i>exp</i></sup>. While the local popularity of the random experiments and global-driven preferential attachment (GPA) model are very similar to the expected value, the empirical local popularity is significantly higher which suggests that the users tend to select locally popular businesses. <b>d,</b> The distribution of real-time local popularity <i>LP</i>(<i>c</i>). For the empirical data, the local popularity follows the power-law distribution with slope of −2.7. On the other hand, the local popularity of the GPA model being very similar to the random experiment, cannot reproduce the empirical observation.</p
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