Heterogeneity‐constrained random resampling of phytosociological databases

Aim: Phytosociological databases often contain unbalanced samples of real vegetation, which should be carefully resampled before any analyses. We propose a new resampling method based on species composition, called heterogeneity‐constrained random (HCR) resampling. Method: Many subsets of the source vegetation database are selected randomly. These subsets are sorted by decreasing mean dissimilarity between pairs of the vegetation plots, and then sorted again by increasing variance of these dissimilarities. Ranks from both sortings are summed for each subset, and the subset with the lowest summed rank is considered as the most representative. The performance of this method was tested using simulated point patterns that represented different levels of aggregation of vegetation plots within a database. The distributions of points in the subsets resulting from different resampling methods, both with and without database stratification, were compared using Ripley's K function. The mean of random selections from an unbiased sample was used as a reference in these comparisons. The efficiency of the method was also demonstrated with real phytosociological data. Results: Both stratified and HCR resampling yielded selection patterns more similar to the reference than resampling without these tools. Outcomes from the resampling that combined these two methods were the most similar to the reference. The efficiency of the HCR resampling method varied with different levels of aggregation in the database. Conclusions: This new method is efficient for resampling phytosociological databases. As it only uses information on species occurrences/abundances, it does not require the definition of strata, thereby avoiding the effect of subjective decisions on the selection outcome. Nevertheless, this method can also be applied to stratified databases.     

Comparison between Colony Morphology and Molecular Phylogeny in the Caribbean Scleractinian Coral Genus Madracis

A major challenge in coral biology is to find the most adequate and phylogenetically informative characters that allow for distinction of closely related coral species. Therefore, data on corallite morphology and genetic data are often combined to increase phylogenetic resolution. In this study, we address the question to which degree genetic data and quantitative information on overall coral colony morphologies identify similar groupings within closely related morphospecies of the Caribbean coral genus Madracis. Such comparison of phylogenies based on colony morphology and genetic data will also provide insight into the degree to which genotype and phenotype overlap. We have measured morphological features of three closely related Caribbean coral species of the genus Madracis (M. formosa, M. decactis and M. carmabi). Morphological differences were then compared with phylogenies of the same species based on two nuclear DNA markers, i.e. ATPSα and SRP54. Our analysis showed that phylogenetic trees based on (macroscopical) morphological properties and phylogenetic trees based on DNA markers ATPSα and SRP54 are partially similar indicating that morphological characteristics at the colony level provide another axis, in addition to commonly used features such as corallite morphology and ecological information, to delineate genetically different coral species. We discuss this new method that allows systematic quantitative comparison between morphological characteristics of entire colonies and genetic data.     

Fast Census of Moth Diversity in the Neotropics: A Comparison of Field-Assigned Morphospecies and DNA Barcoding in Tiger Moths

The morphological species delimitations (i.e. morphospecies) have long been the best way to avoid the taxonomic impediment and compare insect taxa biodiversity in highly diverse tropical and subtropical regions. The development of DNA barcoding, however, has shown great potential to replace (or at least complement) the morphospecies approach, with the advantage of relying on automated methods implemented in computer programs or even online rather than in often subjective morphological features. We sampled moths extensively for two years using light traps in a patch of the highly endangered Atlantic Forest of Brazil to produce a nearly complete census of arctiines (Noctuoidea: Erebidae), whose species richness was compared using different morphological and molecular approaches (DNA barcoding). A total of 1,075 barcode sequences of 286 morphospecies were analyzed. Based on the clustering method Barcode Index Number (BIN) we found a taxonomic bias of approximately 30% in our initial morphological assessment. However, a morphological reassessment revealed that the correspondence between morphospecies and molecular operational taxonomic units (MOTUs) can be up to 94% if differences in genitalia morphology are evaluated in individuals of different MOTUs originated from the same morphospecies (putative cases of cryptic species), and by recording if individuals of different genders in different morphospecies merge together in the same MOTU (putative cases of sexual dimorphism). The results of two other clustering methods (i.e. Automatic Barcode Gap Discovery and 2% threshold) were very similar to those of the BIN approach. Using empirical data we have shown that DNA barcoding performed substantially better than the morphospecies approach, based on superficial morphology, to delimit species of a highly diverse moth taxon, and thus should be used in species inventories.     

High resolution ECG analysis by an improved signal averaging method and comparison with a beat-to-beat approach

The aim of this paper is to describe the analysis of a high resolution ECG recorded from the body surface. Standard signal averaging techniques are improved by using a new time delay estimation method which leads to a better alignment accuracy of P and T waves. A second method uses adaptive identification to achieve a beat by beat fine ECG estimation. Information provided by the two methods allows a better interpretation of low and very low level signals.     

Assessing reliability of gene clusters from gene expression data

The rapid development of microarray technologies has raised many challenging problems in experiment design and data analysis. Although many numerical algorithms have been successfully applied to analyze gene expression data, the effects of variations and uncertainties in measured gene expression levels across samples and experiments have been largely ignored in the literature. In this article, in the context of hierarchical clustering algorithms, we introduce a statistical resampling method to assess the reliability of gene clusters identified from any hierarchical clustering method. Using the clustering trees constructed from the resampled data, we can evaluate the confidence value for each node in the observed clustering tree. A majority-rule consensus tree can be obtained, showing clusters that only occur in a majority of the resampled trees. We illustrate our proposed methods with applications to two published data sets. Although the methods are discussed in the context of hierarchical clustering methods, they can be applied with other cluster-identification methods for gene expression data to assess the reliability of any gene cluster of interest. Electronic Publication     

Isolation of Fetal ECG Signals from Abdominal ECG Using Wavelet Analysis

ObjectiveMonitoring the heartbeat of the fetus during pregnancy is a vital part in determining their health. Current fetal heart monitoring techniques lack the accuracy in fetal heart rate monitoring and features acquisition, resulting in diagnostic medical issues. The demand for a reliable method of non-invasive fetal heart monitoring is of high importance.MethodElectrocardiogram (ECG) is a method of monitoring the electrical activity produced by the heart. The extraction of the fetal ECG (FECG) from the abdominal ECG (AECG) is challenging since both ECGs of the mother and the baby share similar frequency components, adding to the fact that the signals are corrupted by white noise. This paper presents a method of FECG extraction by eliminating all other signals using AECG. The algorithm is based on attenuating the maternal ECG (MECG) by filtering and wavelet analysis to find the locations of the FECG, and thus isolating them based on their locations. Two signals of AECG collected at different locations on the abdomens are used. The ECG data used contains MECG of a power of five to ten times that of the FECG.ResultsThe FECG signals were successfully isolated from the AECG using the proposed method through which the QRS complex of the heartbeat was conserved, and heart rate was calculated. The fetal heart rate was 135 bpm and the instantaneous heart rate was 131.58 bpm. The heart rate of the mother was at 90 bpm with an instantaneous heart rate of 81.9 bpm.ConclusionThe proposed method is promising for FECG extraction since it relies on filtering and wavelet analysis of two abdominal signals for the algorithm. The method implemented is easily adjusted based on the power levels of signals, giving it great ease of adaptation to changing signals in different biosignals applications.     

A resampling approach and implications for estimating the phalangeal index from unassociated hand bones in fossil primates

Primate fossil assemblages often have metacarpals and phalanges from which functional/behavioral interpretations may be inferred. For example, intrinsic hand proportions can indicate hand function and substrate use. But, estimates of intrinsic hand proportions from unassociated hand elements can be imperfect due to digit misattribution. Although isolated metacarpals can be identified to a specific digit, phalanges are difficult to assign to a specific ray. We used a resampling approach to evaluate how estimates of intrinsic hand proportions are affected by such uncertainty. First, the phalangeal index—intermediate phalanx length plus proximal phalanx length divided by metacarpal length—for the third digit was calculated for associated specimens of terrestrial, semiterrestrial, and arboreal taxa. We then used resampling procedures to generate distributions of “composite digits” based on resampled ratios in which phalanges from the second, fourth, and fifth rays, and from different individuals, were chosen randomly. Results confirm that the phalangeal index for associated third digits significantly discriminates groups. We also found that resampled ratios had significantly lower means, indicating that using composite digits is prone to systematic underestimation. Resampled ratios also generated distributions with greater variance around the means that obscured distinctions between groups, although significant differences between the most arboreal and terrestrial taxa are maintained. We conclude that using unassociated phalanges to calculate a phalangeal index is prone to sampling bias. Nevertheless, a resampling approach has the potential to inform estimates of hand proportions for fossil taxa, provided that the comparative sample is constrained to mimic the fossil composition. Am J Phys Anthropol 151:280–289, 2013. © 2013 Wiley Periodicals, Inc.     

Calculating bootstrap probabilities of phylogeny using multilocus sequence data

Phylogeny estimation is extremely crucial in the study of molecular evolution. The increase in the amount of available genomic data facilitates phylogeny estimation from multilocus sequence data. Although maximum likelihood and Bayesian methods are available for phylogeny reconstruction using multilocus sequence data, these methods require heavy computation, and their application is limited to the analysis of a moderate number of genes and taxa. Distance matrix methods present suitable alternatives for analyzing huge amounts of sequence data. However, the manner in which distance methods can be applied to multilocus sequence data remains unknown. Here, we suggest new procedures to estimate molecular phylogeny using multilocus sequence data and evaluate its significance in the framework of the distance method. We found that concatenation of the multilocus sequence data may result in incorrect phylogeny estimation with an extremely high bootstrap probability (BP), which is due to incorrect estimation of the distances and intentional ignorance of the intergene variations. Therefore, we suggest that the distance matrices for multilocus sequence data be estimated separately and these matrices be subsequently combined to reconstruct phylogeny instead of phylogeny reconstruction using concatenated sequence data. To calculate the BPs of the reconstructed phylogeny, we suggest that 2-stage bootstrap procedures be adopted; in this, genes are resampled followed by resampling of the sequence columns within the resampled genes. By resampling the genes during calculation of BPs, intergene variations are properly considered. Via simulation studies and empirical data analysis, we demonstrate that our 2-stage bootstrap procedures are more suitable than the conventional bootstrap procedure that is adopted after sequence concatenation.     

基于小波变换的混合二维ECG数据压缩方法

提出了一种新的基于小波变换的混合二维心电(electrocardiogram,ECG)数据压缩方法。基于ECG数据的两种相关性,该方法首先将一维ECG信号转化为二维信号序列。然后对二维序列进行了小波变换,并利用改进的编码方法对变换后的系数进行了压缩编码:即先根据不同系数子带的各自特点和系数子带之间的相似性,改进了等级树集合分裂(setpartitioninghierarchicaltrees,SPIHT)算法和矢量量化(vectorquantization,VQ)算法;再利用改进后的SPIHT与VQ相混合的算法对小波变换后的系数进行了编码。利用所提算法与已有具有代表性的基于小波变换的压缩算法和其他二维ECG信号的压缩算法,对MIT/BIH数据库中的心律不齐数据进行了对比压缩实验。结果表明:所提算法适用于各种波形特征的ECG信号,并且在保证压缩质量的前提下,可以获得较大的压缩比。     

Offshore cultivation methods affects blade features of the edible seaweed <Emphasis Type="Italic">Saccharina latissima</Emphasis> in a bay of Galicia,Northwest Spain

Variation in blade morphology of Saccharina latissima may be of importance for its commercial cultivation. Blade features were compared between offshore cultivation on horizontal ropes versus hanging ropes during its reproduction period (early autumn and early spring of the following year). Cultivation experiments were conducted in February 2002 in a sheltered coastal area of a bay of Galicia (Northwest Spain). Significant differences were found between methods in blade area, which in turn affected blade biomass. However, the differences were only significant during the reproduction period in early spring. The cultivation method also significantly affected the “substantiality value”, which is an index that expresses the blade quality for human consumption. The observed variations in morphological features of S. latissima blades likely were caused by the different hydrodynamics of the two cultivation methods.     

Impact de la méthode de segmentation dans la caractérisation des adénocarcinomes pulmonaires en TEP-TDM au 18FDG

ObjectiveThe treatment of lung adenocarcinomas is conditioned by the presence of certain genetic abnormalities. Certain quantitative parameters obtained from FDG PET-CT, at the voxel scale, provide tumour shape and texture characteristics and might predict their mutational status. Our objective was to determine the impact of the segmentation method in the characterization of lung adenocarcinomas in FDG PET-CT.MethodsForty-nine patients with pulmonary adenocarcinomas were retrospectively included, with their initial FDG PET-CT image. The studied tumours were big, heterogeneous and difficult to segment automatically. The automatic FLAB algorithm was used with and without manual adjustment. The parameters were extracted and compared to the ALK, PDL1, and KRAS status, in order to compare the performances of the two segmentation methods. Their performance was determined by the ROC curve method.ResultsSeveral parameters were significant to predict genetic status (AUC > 0.65). The best performing parameters were different according to the genes studied and according to the resampling methods used. The results were less dependent on resampling in automatic segmentation without manual adjustment. The best performing parameters were volume dependent parameters for segmentation with manual adjustment, and texture parameters for automatic segmentation without adjustment.ConclusionThe study of texture parameters is more efficient in automatic segmentation that is not manually adjusted, and it is advantageous to use a manual adjustment when studying volume-dependent parameters in the case of very heterogeneous tumors.     

Allometry, sexual dimorphism, and phylogeny: A cladistic analysis of extant African papionins using craniodental data

This study conducts a phylogenetic analysis of extant African papionin craniodental morphology, including both quantitative and qualitative characters. We use two different methods to control for allometry: the previously described narrow allometric coding method, and the general allometric coding method, introduced herein. The results of this study strongly suggest that African papionin phylogeny based on molecular systematics, and that based on morphology, are congruent and support a Cercocebus/Mandrillus clade as well as a Papio/Lophocebus/Theropithecus clade. In contrast to previous claims regarding papionin and, more broadly, primate craniodental data, this study finds that such data are a source of valuable phylogenetic information and removes the basis for considering hard tissue anatomy “unreliable” in phylogeny reconstruction. Among highly sexually dimorphic primates such as papionins, male morphologies appear to be particularly good sources of phylogenetic information. In addition, we argue that the male and female morphotypes should be analyzed separately and then added together in a concatenated matrix in future studies of sexually dimorphic taxa. Character transformation analyses identify a series of synapomorphies uniting the various papionin clades that, given a sufficient sample size, should potentially be useful in future morphological analyses, especially those involving fossil taxa.     

Respiratory sinus arrhythmia from two coupled pacemakers.

We reproduce global features of respiratory sinus arrhythmia (RSA), a prominent source of heart rate variability, from two signals coupled in alternate fashion so dominance periodically switches back and forth between them. We consider two different possibilities for this coupling and illustrate our method with numerical simulations that we contrast with the corresponding results from real data. We interpret our findings within the context of the two-pacemaker model of the heartbeat, an alternative to the single-pacemaker mechanism of pulse generation in the orthodox conduction model.     

Tree-based delimitation of morphologically ambiguous taxa: a study of the lizard malaria parasites on the Caribbean island of Hispaniola

Malaria parasites in the genus Plasmodium have been classified primarily on the basis of differences in morphology. These single-celled organisms often lack distinguishing morphological features, and this can encumber both species delimitation and identification. Six saurian malaria parasites have been described from the Caribbean island of Hispaniola. All six infect lizards in the genus Anolis, but only two of these parasites can be distinguished using morphology. The remaining four species overlap in morphology and geography, and cannot be consistently identified using traditional methods. We compared a morphological approach with a molecular phylogenetic approach for assessing the taxonomy of these parasites. We surveyed for blood parasites from 677 Anolis lizards, representing 26 Anolis spp. from a total of 52 sites across Hispaniola. Fifty-five of these lizards were infected with Plasmodium spp., representing several new host records, but only 24 of these infections could be matched to previously described species using traditional morphological criteria. We then estimated the phylogeny of these parasites using both mitochondrial (cytb and coxI) and nuclear (EF2) genes, and included carefully selected GenBank sequences to confirm identities for certain species. Our molecular results unambiguously corroborated our morphology-based species identifications for only the two species previously judged to be morphologically distinctive. The remaining infections fell into two well-supported and reciprocally monophyletic clades, which contained the morphological variation previously reported for all four of the morphologically ambiguous species. One of these clades was identified as Plasmodium floridense and the other as Plasmodium fairchildi hispaniolae. We elevate the latter to Plasmodium hispaniolae comb. nov. because it is polyphyletic with the mainland species Plasmodium fairchildifairchildi and we contribute additional morphological and molecular characters for future species delimitation. Our phylogenetic hypotheses indicate that two currently recognised taxa, Plasmodium minasense anolisi and Plasmodium tropiduri caribbense, are not valid on Hispaniola. These results illustrate that molecular data can improve taxonomic hypotheses in Plasmodium when reliable morphological characters are lacking.     

Simultaneous small-sample multivariate Bernoulli confidence intervals

A technique based on the bootstrap is presented for assessing the simultaneous confidence level of k small-sample confidence intervals for multivariate Bernoulli marginal frequencies. The small-sample intervals used are those of Clopper and Pearson (1934, Biometrika 26, 404-413) and require iterative computation. To estimate the simultaneous confidence level, the multivariate Bernoulli vectors are resampled via the bootstrap and the Clopper-Pearson intervals recomputed on each pseudosample. The bootstrap estimate is then the proportion of times (computed via Monte Carlo) that all the k intervals computed by resampling contain the original sample frequencies. The technique is applied to single-sample HLA data.     

Morphological variation in the cosmopolitan fish parasite Neobenedenia girellae (Capsalidae: Monogenea)

Intra-species morphological variation presents a considerable problem for species identification and can result in taxonomic confusion. This is particularly pertinent for species of Neobenedenia which are harmful agents in captive fish populations and have historically been identified almost entirely based on morphological characters. This study aimed to understand how the morphology of Neobenedenia girellae varies with host fish species and the environment. Standard morphological features of genetically indistinct parasites from various host fish species were measured under controlled temperatures and salinities. An initial field-based investigation found that parasite morphology significantly differed between genetically indistinct parasites infecting various host fish species. The majority of the morphological variation observed (60%) was attributed to features that assist in parasite attachment to the host (i.e. the posterior and anterior attachment organs and their accessory hooks) which are important characters in monogenean taxonomy. We then experimentally examined the effects of the interaction between host fish species and environmental factors (temperature and salinity) on the morphology of isogenic parasites derived from a single, isolated hermaphroditic N. girellae infecting barramundi, Lates calcarifer. Experimental infection of L. calcarifer and cobia, Rachycentron canadum, under controlled laboratory conditions did not confer host-mediated phenotypic plasticity in N. girellae, suggesting that measured morphological differences could be adaptive and only occur over multiple parasite generations. Subsequent experimental infection of a single host species, L. calcarifer, at various temperatures (22, 30 and 32?°C) and salinities (35 and 40‰) showed that in the cooler environments (22?°C) N. girellae body proportions were significantly smaller compared with warmer temperatures (30 and 32?°C; P?<?0.0001), whereas salinity had no effect. This is evidence that temperature can drive phenotypic plasticity in key taxonomic characters of N. girellae under certain environmental conditions.     

Fasciola hepatica: ultrastructure and histochemistry of the glycocalyx of the tegument.

The morphology and histochemistry of the glycocalyx of the tegument was investigated by electron microscopy. The results showed that both the morphology and histochemistry of the glycocalyx varied depending on the environment immediately prior to fixation and also on postfixation treatments. Conventional electron microscope fixation appeared to preserve only about half the total thickness of the glycocalyx, and only histochemical tests applied en bloc gave a true morphological and histochemical picture. The glycocalyx, therefore, consists of two parts, an inner continuous layer which is tightly bound to the apical plasma membrane and is always preserved, and an outer fibrillar layer, which is not always preserved by conventional fixation. Both layers are anionic and carbohydrate-rich and therefore contain glycoproteins and sialic acids. The surface of Fasciola hepatica, therefore, has morphological and chemical features very like those proposed for the “greater membrane” by Lehninger.     

Evaluating the stability of the classification of community data

We propose a method for a posteriori evaluation of classification stability which compares the classification of sites in the original data set (a matrix of species by sites) with classifications of subsets of its sites created by without‐replacement bootstrap resampling. Site assignments to clusters of the original classification and to clusters of the classification of each subset are compared using Goodman‐Kruskal's lambda index. Many resampled subsets are classified and the mean of lambda values calculated for the classifications of these subsets is used as an estimation of classification stability. Furthermore, the mean of the lambda values based on different resampled subsets, calculated for each site of the data set separately, can be used as a measure of the influence of particular sites on classification stability. This method was tested on several artificial data sets classified by commonly used clustering methods and on a real data set of forest vegetation plots. Its strength lies in the ability to distinguish classifications which reflect robust patterns of community differentiation from unstable classifications of more continuous patterns. In addition, it can identify sites within each cluster which have a transitional species composition with respect to other clusters.