共查询到20条相似文献,搜索用时 15 毫秒
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Sellers WI Hepworth-Bell J Falkingham PL Bates KT Brassey CA Egerton VM Manning PL 《Biology letters》2012,8(5):842-845
Body mass is a critical parameter used to constrain biomechanical and physiological traits of organisms. Volumetric methods are becoming more common as techniques for estimating the body masses of fossil vertebrates. However, they are often accused of excessive subjective input when estimating the thickness of missing soft tissue. Here, we demonstrate an alternative approach where a minimum convex hull is derived mathematically from the point cloud generated by laser-scanning mounted skeletons. This has the advantage of requiring minimal user intervention and is thus more objective and far quicker. We test this method on 14 relatively large-bodied mammalian skeletons and demonstrate that it consistently underestimates body mass by 21 per cent with minimal scatter around the regression line. We therefore suggest that it is a robust method of estimating body mass where a mounted skeletal reconstruction is available and demonstrate its usage to predict the body mass of one of the largest, relatively complete sauropod dinosaurs: Giraffatitan brancai (previously Brachiosaurus) as 23200 kg. 相似文献
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Declines in populations of Palearctic migrants wintering in the Sahel of Africa have been linked to the impacts of climate change and habitat degradation in the region. Despite this, there is an almost complete lack of data on the density and distribution of Palearctic migrants wintering in the Sahel and whether they have the same habitat requirements as similar, resident Afrotropical species. We measured the density of five species of Palearctic warblers (Sylviidae) and 10 species of Afrotropical gleaning passerines (Sylviidae, Nectariniidae, Malaconotidae and Ploceidae) at 16 sites in the Sahel of northern Nigeria between October and April during two winters. Two species of Afrotropical gleaner (Hippolais pallida and Ploceus luteolus) showed seasonal variation in abundance, but this variation was unlikely to have decreased Afrotropical densities sufficiently to change the degree of competition experienced by Palearctic migrants. This observation, combined with a positive correlation between abundances of Afrotropical and Palearctic species, suggests that these two groups occur together and have similar spatial and temporal habitat requirements, and therefore possibly similar responses to habitat degradation. Sylvia communis appears to be the principal species utilising the region during spring migration, presumably for fattening prior to the trans-Saharan crossing, and is thus perhaps the most vulnerable species to habitat loss in the region. 相似文献
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Joel Monárrez-Espino José Antonio Enciso-Moreno Lucie Laflamme Carmen J Serrano 《Memórias do Instituto Oswaldo Cruz》2014,109(7):863-870
A cohort of 123 adult contacts was followed for 18‐24 months (86 completed the
follow-up) to compare conversion and reversion rates based on two serial measures of
QuantiFERON (QFT) and tuberculin skin test (TST) (PPD from TUBERSOL, Aventis Pasteur,
Canada) for diagnosing latent tuberculosis (TB) in household contacts of TB patients
using conventional (C) and borderline zone (BZ) definitions. Questionnaires were used
to obtain information regarding TB exposure, TB risk factors and socio-demographic
data. QFT (IU/mL) conversion was defined as <0.35 to ≥0.35 (C) or <0.35 to
>0.70 (BZ) and reversion was defined as ≥0.35 to <0.35 (C) or ≥0.35 to <0.20
(BZ); TST (mm) conversion was defined as <5 to ≥5 (C) or <5 to >10 (BZ) and
reversion was defined as ≥5 to <5 (C). The QFT conversion and reversion rates were
10.5% and 7% with C and 8.1% and 4.7% with the BZ definitions, respectively. The TST
rates were higher compared with QFT, especially with the C definitions (conversion
23.3%, reversion 9.3%). The QFT conversion and reversion rates were higher for TST
≥5; for TST, both rates were lower for QFT <0.35. No risk factors were associated
with the probability of converting or reverting. The inconsistency and apparent
randomness of serial testing is confusing and adds to the limitations of these tests
and definitions to follow-up close TB contacts. 相似文献
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In this work we extend approximate aggregation methods to deal with a very general linear time discrete model. Approximate aggregation consists in describing some features of the dynamics of a general system in terms of the dynamics of a reduced system governed by a few global variables. We present a time discrete model for a structured population (i.e., the population is subdivided in subpopulations) in which we can distinguish two processes of a general nature and whose corresponding time scales are very different from each other. We transform the general system to make the global variables appear and obtain the reduced system. These global variables are, for each subpopulation, a certain linear combination of the corresponding state variables. We show that, under quite general conditions, the asymptotic behavior of the reduced system can be known in terms of the corresponding behavior for the reduced system. The general method is applied to aggregate a multiregional Leslie model in which the demographic process is supposed to be fast with respect to migration. 相似文献
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This note presents a general time-dependent study of linear stochastic compartmental models in discrete time. The transient
distribution of the state of the system is obtained by adapting methods used in the continuous time analysis. Covariance functions
with and without a time lag are then deduced by a simple probabilistic argument. Results are derived in the Markov case and
are partly extended to the semi-Markov case. 相似文献
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Inference regarding the inclusion or exclusion of random effects in linear mixed models is challenging because the variance components are located on the boundary of their parameter space under the usual null hypothesis. As a result, the asymptotic null distribution of the Wald, score, and likelihood ratio tests will not have the typical χ(2) distribution. Although it has been proved that the correct asymptotic distribution is a mixture of χ(2) distributions, the appropriate mixture distribution is rather cumbersome and nonintuitive when the null and alternative hypotheses differ by more than one random effect. As alternatives, we present two permutation tests, one that is based on the best linear unbiased predictors and one that is based on the restricted likelihood ratio test statistic. Both methods involve weighted residuals, with the weights determined by the among- and within-subject variance components. The null permutation distributions of our statistics are computed by permuting the residuals both within and among subjects and are valid both asymptotically and in small samples. We examine the size and power of our tests via simulation under a variety of settings and apply our test to a published data set of chronic myelogenous leukemia patients. 相似文献
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Summary Microarray gene expression studies over ordered categories are routinely conducted to gain insights into biological functions of genes and the underlying biological processes. Some common experiments are time‐course/dose‐response experiments where a tissue or cell line is exposed to different doses and/or durations of time to a chemical. A goal of such studies is to identify gene expression patterns/profiles over the ordered categories. This problem can be formulated as a multiple testing problem where for each gene the null hypothesis of no difference between the successive mean gene expressions is tested and further directional decisions are made if it is rejected. Much of the existing multiple testing procedures are devised for controlling the usual false discovery rate (FDR) rather than the mixed directional FDR (mdFDR), the expected proportion of Type I and directional errors among all rejections. Benjamini and Yekutieli (2005, Journal of the American Statistical Association 100, 71–93) proved that an augmentation of the usual Benjamini–Hochberg (BH) procedure can control the mdFDR while testing simple null hypotheses against two‐sided alternatives in terms of one‐dimensional parameters. In this article, we consider the problem of controlling the mdFDR involving multidimensional parameters. To deal with this problem, we develop a procedure extending that of Benjamini and Yekutieli based on the Bonferroni test for each gene. A proof is given for its mdFDR control when the underlying test statistics are independent across the genes. The results of a simulation study evaluating its performance under independence as well as under dependence of the underlying test statistics across the genes relative to other relevant procedures are reported. Finally, the proposed methodology is applied to a time‐course microarray data obtained by Lobenhofer et al. (2002, Molecular Endocrinology 16, 1215–1229). We identified several important cell‐cycle genes, such as DNA replication/repair gene MCM4 and replication factor subunit C2, which were not identified by the previous analyses of the same data by Lobenhofer et al. (2002) and Peddada et al. (2003, Bioinformatics 19, 834–841). Although some of our findings overlap with previous findings, we identify several other genes that complement the results of Lobenhofer et al. (2002) . 相似文献
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Background
Neuroblastoma Tumor (NT) is one of the most aggressive types of infant cancer. Essential to accurate diagnosis and prognosis is cellular quantitative analysis of the tumor. Counting enormous numbers of cells under an optical microscope is error-prone. There is therefore an urgent demand from pathologists for robust and automated cell counting systems. However, the main challenge in developing these systems is the inability of them to distinguish between overlapping cells and single cells, and to split the overlapping cells. We address this challenge in two stages by: 1) distinguishing overlapping cells from single cells using the morphological differences between them such as area, uniformity of diameters and cell concavity; and 2) splitting overlapping cells into single cells. We propose a novel approach by using the dominant concave regions of cells as markers to identify the overlap region. We then find the initial splitting points at the critical points of the concave regions by decomposing the concave regions into their components such as arcs, chords and edges, and the distance between the components is analyzed using the developed seed growing technique. Lastly, a shortest path determination approach is developed to determine the optimum splitting route between two candidate initial splitting points.Results
We compare the cell counting results of our system with those of a pathologist as the ground-truth. We also compare the system with three state-of-the-art methods, and the results of statistical tests show a significant improvement in the performance of our system compared to state-of-the-art methods. The F-measure obtained by our system is 88.70%. To evaluate the generalizability of our algorithm, we apply it to images of follicular lymphoma, which has similar histological regions to NT. Of the algorithms tested, our algorithm obtains the highest F-measure of 92.79%.Conclusion
We develop a novel overlapping cell splitting algorithm to enhance the cellular quantitative analysis of infant neuroblastoma. The performance of the proposed algorithm promises a reliable automated cell counting system for pathology laboratories. Moreover, the high performance obtained by our algorithm for images of follicular lymphoma demonstrates the generalization of the proposed algorithm for cancers with similar histological regions and histological structures. 相似文献11.
Lin D Shkedy Z Burzykowski T Ion R Göhlmann HW Bondt AD Perer T Geerts T Van den Wyngaert I Bijnens L 《Biometrical journal. Biometrische Zeitschrift》2008,50(5):801-823
One of multiple testing problems in drug finding experiments is the comparison of several treatments with one control. In this paper we discuss a particular situation of such an experiment, i.e., a microarray setting, where the many-to-one comparisons need to be addressed for thousands of genes simultaneously. For a gene-specific analysis, Dunnett's single step procedure is considered within gene tests, while the FDR controlling procedures such as Significance Analysis of Microarrays (SAM) and Benjamini and Hochberg (BH) False Discovery Rate (FDR) adjustment are applied to control the error rate across genes. The method is applied to a microarray experiment with four treatment groups (three microarrays in each group) and 16,998 genes. Simulation studies are conducted to investigate the performance of the SAM method and the BH-FDR procedure with regard to controlling the FDR, and to investigate the effect of small-variance genes on the FDR in the SAM procedure. 相似文献
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Pizzi C Rastas P Ukkonen E 《IEEE/ACM transactions on computational biology and bioinformatics / IEEE, ACM》2011,8(1):69-79
Position weight matrices are an important method for modeling signals or motifs in biological sequences, both in DNA and protein contexts. In this paper, we present fast algorithms for the problem of finding significant matches of such matrices. Our algorithms are of the online type, and they generalize classical multipattern matching, filtering, and superalphabet techniques of combinatorial string matching to the problem of weight matrix matching. Several variants of the algorithms are developed, including multiple matrix extensions that perform the search for several matrices in one scan through the sequence database. Experimental performance evaluation is provided to compare the new techniques against each other as well as against some other online and index-based algorithms proposed in the literature. Compared to the brute-force O(mn) approach, our solutions can be faster by a factor that is proportional to the matrix length m. Our multiple-matrix filtration algorithm had the best performance in the experiments. On a current PC, this algorithm finds significant matches (p = 0.0001) of the 123 JASPAR matrices in the human genome in about 18 minutes. 相似文献
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Marius Thomas Björn Bornkamp Martin Posch Franz König 《Biometrical journal. Biometrische Zeitschrift》2020,62(1):53-68
Identifying subgroups of patients with an enhanced response to a new treatment has become an area of increased interest in the last few years. When there is knowledge about possible subpopulations with an enhanced treatment effect before the start of a trial it might be beneficial to set up a testing strategy, which tests for a significant treatment effect not only in the full population, but also in these prespecified subpopulations. In this paper, we present a parametric multiple testing approach for tests in multiple populations for dose-finding trials. Our approach is based on the MCP-Mod methodology, which uses multiple comparison procedures (MCPs) to test for a dose–response signal, while considering multiple possible candidate dose–response shapes. Our proposed methods allow for heteroscedastic error variances between populations and control the family-wise error rate over tests in multiple populations and for multiple candidate models. We show in simulations that the proposed multipopulation testing approaches can increase the power to detect a significant dose–response signal over the standard single-population MCP-Mod, when the specified subpopulation has an enhanced treatment effect. 相似文献
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Determining a portfolio of linear time series models 总被引:1,自引:0,他引:1
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Angela M. Sibbald Hans W. Erhard James E. McLeod Russell J. Hooper 《Behavioural processes》2009,82(3):319-326
Impacts of individual personality on group distribution were investigated using sheep (Ovis aries) as a model. In an indoor exploration test, individuals who visited <4 (out of 6) objects in a novel environment were classified as ‘shy’ (n = 10), and those who visited 5 or 6 objects were classified as ‘bold’ (n = 10). Nine weeks later, using a series of groups (n = 40) of either 5 shy or 5 bold sheep, we measured distribution at pasture and responses to disturbance and the approach of a human handler. When grazing undisturbed, the mean nearest neighbour distance and spread (minimum convex hull area) of shy groups were less than those of bold groups, with shy individuals moving towards one another more often. Shy groups explored a smaller area than bold groups. When disturbed, shy sheep were more likely to stop grazing and move closer together. Shy sheep kept further away from the handler and moved faster when driven. The results demonstrate a link between personality and group distribution, suggesting that our ‘shy’ and ‘bold’ individuals may occupy different positions on the shy-bold continuum documented for other species. We discuss implications for diet composition and impacts on vegetation grazed by animals with different personalities. 相似文献
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Xiongzhi Chen R. W. Doerge Sanat K. Sarkar 《Biometrical journal. Biometrische Zeitschrift》2020,62(6):1544-1563
Multiple testing (MT) with false discovery rate (FDR) control has been widely conducted in the “discrete paradigm” where p-values have discrete and heterogeneous null distributions. However, in this scenario existing FDR procedures often lose some power and may yield unreliable inference, and for this scenario there does not seem to be an FDR procedure that partitions hypotheses into groups, employs data-adaptive weights and is nonasymptotically conservative. We propose a weighted p-value-based FDR procedure, “weighted FDR (wFDR) procedure” for short, for MT in the discrete paradigm that efficiently adapts to both heterogeneity and discreteness of p-value distributions. We theoretically justify the nonasymptotic conservativeness of the wFDR procedure under independence, and show via simulation studies that, for MT based on p-values of binomial test or Fisher's exact test, it is more powerful than six other procedures. The wFDR procedure is applied to two examples based on discrete data, a drug safety study, and a differential methylation study, where it makes more discoveries than two existing methods. 相似文献
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Estimates of utilization distributions (UDs) are used in analyses of home-range area, habitat and resource selection, and social interactions. We simulated data from 12 parent UDs, representing 3 series of increasingly intense space-use patterns (clustering of points around a home site, restriction of locations to a network of nodes and corridors, and dominance of a central hole in the UD) and compared the ability of kernel density estimation (KDE) and local convex hull (LCH) construction to reconstruct known UDs from samples of 10, 50, 250, and 1,000 location points. For KDE, we considered 4 bandwidth selectors: the reference bandwidth, least-squares cross-validation (LSCV), direct plug-in (DPI), and solve-the-equation (STE). For the sample sizes and UD patterns tested here, KDE achieved significantly higher volume-of-intersection (VI) scores with known parent UDs than did LCH; KDE also provided less biased home-range area estimates under many conditions. However, LCH minimized the UD volume that occurred outside the true home range boundary (Vout). Among the KDE bandwidth estimators, relative performance depended on the type and intensity of space use patterns, sample size, and the metric used to evaluate performance. Biologists should use KDE for UD and home range estimation within a probabilistic context, unless their objective is to exclude potentially unused areas by defining the area delimited by data. © 2011 The Wildlife Society. 相似文献
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