scholarly journals Centric Allometry: Studying Growth Using Landmark Data

Author(s):  
Fred L. Bookstein

AbstractThe geometric morphometric (GMM) construction of Procrustes shape coordinates from a data set of homologous landmark configurations puts exact algebraic constraints on position, orientation, and geometric scale. While position as digitized is not ordinarily a biologically meaningful quantity, and orientation is relevant mainly when some organismal function interacts with a Cartesian positional gradient such as horizontality, size per se is a crucially important biometric concept, especially in contexts like growth, biomechanics, or bioenergetics. “Normalizing” or “standardizing” size (usually by dividing the square root of the summed squared distances from the centroid out of all the Cartesian coordinates specimen by specimen), while associated with the elegant symmetries of the Mardia–Dryden distribution in shape space, nevertheless can substantially impeach the validity of any organismal inferences that ensue. This paper adapts two variants of standard morphometric least-squares, principal components and uniform strains, to circumvent size standardization while still accommodating an analytic toolkit for studies of differential growth that supports landmark-by-landmark graphics and thin-plate splines. Standardization of position and orientation but not size yields the coordinates Franz Boas first discussed in 1905. In studies of growth, a first principal component of these coordinates often appears to involve most landmarks shifting almost directly away from their centroid, hence the proposed model’s name, “centric allometry.” There is also a joint standardization of shear and dilation resulting in a variant of standard GMM’s “nonaffine shape coordinates” where scale information is subsumed in the affine term. Studies of growth allometry should go better in the Boas system than in the Procrustes shape space that is the current conventional workbench for GMM analyses. I demonstrate two examples of this revised approach (one developmental, one phylogenetic) that retrieve all the findings of a conventional shape-space-based approach while focusing much more closely on the phenomenon of allometric growth per se. A three-part Appendix provides an overview of the algebra, highlighting both similarities to the Procrustes approach and contrasts with it.

2020 ◽  
Author(s):  
F. Robin O’Keefe

AbstractThe study of modularity in geometric morphometric landmark data has focused attention on an underlying question, that of whole-shape modularity, or the pattern and strength of covariation among all landmarks. Measuring whole-shape modularity allows measurement of the dimensionality of the shape, but current methods used to measure this dimensionality are limited in application. This paper proposes a metric for measuring the “effective dimensionality”, De, of geometric morphometric landmark data based on the Shannon entropy of the eigenvalue vector of the covariance matrix of GPA landmark data. A permutation test to establish null rank deficiency is developed to allow standardization for comparing dimensionality metrics between data sets, and a bootstrap test is employed for measures of dispersion. These novel methods are applied to a data set of 14 landmarks taken from 119 dire wolf jaws from Rancho La Brea. Comparison with the current test based on eigenvalue dispersion demonstrates that the new metric is more sensitive to detecting population differences in whole-shape modularity. The effective dimensionality metric is extended, in the dense semilandmark case, to a measure of “latent dimensionality”, Dl. Latent dimensionality should be comparable among landmark spaces, whether they are homologous or not.


Paleobiology ◽  
10.1666/13042 ◽  
2014 ◽  
Vol 40 (4) ◽  
pp. 640-658 ◽  
Author(s):  
Holly A. Schreiber ◽  
Peter D. Roopnarine ◽  
Sandra J. Carlson

Crura, the calcareous support structures of the lophophore in rhynchonellide brachiopods, have historically been used to justify higher-level rhynchonellide classification and reveal major evolutionary lineages within rhynchonellides. Seventeen crural types have been described and categorized into four groups based on variation in overall structure and cross-sectional shape, but not evaluated in a quantitative or comprehensive manner. Heterochrony has been hypothesized to play a role in the evolutionary transitions among some types, but the structural, developmental, and phylogenetic context for testing these hypotheses has not yet been established. In this study, we use three-dimensional geometric morphometric techniques to quantify morphological disparity among all six crural morphs in Recent adult rhynchonellides, with the goal of delineating more objective criteria for identifying and comparing crural morphs, ultimately to test hypotheses explaining morphological transformations in ontogeny and phylogeny. We imaged the crura of seven Recent rhynchonellide species, using X-ray computed microtomography. We used landmarks and semi-landmarks to define the dimensions and curvature of the crura and the surrounding hinge area. Procrustes-standardized landmark coordinates were analyzed using a principal component analysis to test the discreteness of the individual crural morphs and named groups of morphs, and to identify features that vary most among the crural configurations.Our results demonstrate that microCT imaging techniques provide novel ways to investigate the morphology of small features that may be otherwise impossible to quantify using more conventional imaging techniques. Although we predicted overlap among crural morphs in the 3-D shape space, the principal component analyses suggest that five of the six crural morphs differ distinctly from one another. Some but not all previously designated crural groups appear to exhibit morphological cohesion. This study establishes a quantitative morphological foundation necessary to begin an investigation of the phylogenetic significance of ontogenetic changes in crura, which will allow hypotheses of heterochrony to be tested.


Diversity ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 8
Author(s):  
Sebastian Hüllen ◽  
Chiara Mandl ◽  
Matthias Geiger ◽  
Renny Hadiaty ◽  
Gema Wahyudewantoro ◽  
...  

Within the subfamily Danioninae, rasborine cyprinids are known as a ‘catch-all’ group, diagnosed by only a few characteristics. Most species closely resemble each other in morphology. Species identification is therefore often challenging. In this study, we attempted to determine the number of rasborine species occurring in samples from the Mesangat wetlands in East Kalimantan, Indonesia, by using different approaches. Morphological identification resulted in the distinction of five species (Trigonopoma sp., Rasbora cf. hubbsi Brittan, 1954, R. rutteni Weber and de Beaufort, 1916, R. trilineata Steindachner, 1870, and R. vaillantii, Popta 1905). However, genetic species delimitation methods (Poisson tree processes (PTP) and multi-rate PTP (mPTP)) based on DNA barcodes and principal component analysis (PCA) based on homologous geometric morphometric landmarks, revealed a single cluster for Trigonopoma sp. and R. trilineata, respectively, whereas the remaining traditionally identified species were distinguished neither by DNA barcodes nor by the morphometry approach. A k-mean clustering based on the homologous landmarks divided the sample into 13 clusters and was thus found to be inappropriate for landmark data from species extremely resembling each other in morphology. Due to inconsistent results between the applied methods we refer to the traditional identifications and distinguish five rasborine species for the Mesangat wetlands.


2015 ◽  
Vol 14 (4) ◽  
pp. 165-181 ◽  
Author(s):  
Sarah Dudenhöffer ◽  
Christian Dormann

Abstract. The purpose of this study was to replicate the dimensions of the customer-related social stressors (CSS) concept across service jobs, to investigate their consequences for service providers’ well-being, and to examine emotional dissonance as mediator. Data of 20 studies comprising of different service jobs (N = 4,199) were integrated into a single data set and meta-analyzed. Confirmatory factor analyses and explorative principal component analysis confirmed four CSS scales: disproportionate expectations, verbal aggression, ambiguous expectations, disliked customers. These CSS scales were associated with burnout and job satisfaction. Most of the effects were partially mediated by emotional dissonance. Further analyses revealed that differences among jobs exist with regard to the factor solution. However, associations between CSS and outcomes are mainly invariant across service jobs.


2018 ◽  
Author(s):  
Peter De Wolf ◽  
Zhuangqun Huang ◽  
Bede Pittenger

Abstract Methods are available to measure conductivity, charge, surface potential, carrier density, piezo-electric and other electrical properties with nanometer scale resolution. One of these methods, scanning microwave impedance microscopy (sMIM), has gained interest due to its capability to measure the full impedance (capacitance and resistive part) with high sensitivity and high spatial resolution. This paper introduces a novel data-cube approach that combines sMIM imaging and sMIM point spectroscopy, producing an integrated and complete 3D data set. This approach replaces the subjective approach of guessing locations of interest (for single point spectroscopy) with a big data approach resulting in higher dimensional data that can be sliced along any axis or plane and is conducive to principal component analysis or other machine learning approaches to data reduction. The data-cube approach is also applicable to other AFM-based electrical characterization modes.


2020 ◽  
Vol 16 (8) ◽  
pp. 1088-1105
Author(s):  
Nafiseh Vahedi ◽  
Majid Mohammadhosseini ◽  
Mehdi Nekoei

Background: The poly(ADP-ribose) polymerases (PARP) is a nuclear enzyme superfamily present in eukaryotes. Methods: In the present report, some efficient linear and non-linear methods including multiple linear regression (MLR), support vector machine (SVM) and artificial neural networks (ANN) were successfully used to develop and establish quantitative structure-activity relationship (QSAR) models capable of predicting pEC50 values of tetrahydropyridopyridazinone derivatives as effective PARP inhibitors. Principal component analysis (PCA) was used to a rational division of the whole data set and selection of the training and test sets. A genetic algorithm (GA) variable selection method was employed to select the optimal subset of descriptors that have the most significant contributions to the overall inhibitory activity from the large pool of calculated descriptors. Results: The accuracy and predictability of the proposed models were further confirmed using crossvalidation, validation through an external test set and Y-randomization (chance correlations) approaches. Moreover, an exhaustive statistical comparison was performed on the outputs of the proposed models. The results revealed that non-linear modeling approaches, including SVM and ANN could provide much more prediction capabilities. Conclusion: Among the constructed models and in terms of root mean square error of predictions (RMSEP), cross-validation coefficients (Q2 LOO and Q2 LGO), as well as R2 and F-statistical value for the training set, the predictive power of the GA-SVM approach was better. However, compared with MLR and SVM, the statistical parameters for the test set were more proper using the GA-ANN model.


2017 ◽  
Vol 727 ◽  
pp. 447-449 ◽  
Author(s):  
Jun Dai ◽  
Hua Yan ◽  
Jian Jian Yang ◽  
Jun Jun Guo

To evaluate the aging behavior of high density polyethylene (HDPE) under an artificial accelerated environment, principal component analysis (PCA) was used to establish a non-dimensional expression Z from a data set of multiple degradation parameters of HDPE. In this study, HDPE samples were exposed to the accelerated thermal oxidative environment for different time intervals up to 64 days. The results showed that the combined evaluating parameter Z was characterized by three-stage changes. The combined evaluating parameter Z increased quickly in the first 16 days of exposure and then leveled off. After 40 days, it began to increase again. Among the 10 degradation parameters, branching degree, carbonyl index and hydroxyl index are strongly associated. The tensile modulus is highly correlated with the impact strength. The tensile strength, tensile modulus and impact strength are negatively correlated with the crystallinity.


2021 ◽  
Vol 11 (7) ◽  
pp. 3208
Author(s):  
Andrea De Montis ◽  
Vittorio Serra ◽  
Giovanna Calia ◽  
Daniele Trogu ◽  
Antonio Ledda

Composite indicators (CIs), i.e., combinations of many indicators in a unique synthetizing measure, are useful for disentangling multisector phenomena. Prominent questions concern indicators’ weighting, which implies time-consuming activities and should be properly justified. Landscape fragmentation (LF), the subdivision of habitats in smaller and more isolated patches, has been studied through the composite index of landscape fragmentation (CILF). It was originally proposed by us as an unweighted combination of three LF indicators for the study of the phenomenon in Sardinia, Italy. In this paper, we aim at presenting a weighted release of the CILF and at developing the Hamletian question of whether weighting is worthwhile or not. We focus on the sensitivity of the composite to different algorithms combining three weighting patterns (equalization, extraction by principal component analysis, and expert judgment) and three indicators aggregation rules (weighted average mean, weighted geometric mean, and weighted generalized geometric mean). The exercise provides the reader with meaningful results. Higher sensitivity values signal that the effort of weighting leads to more informative composites. Otherwise, high robustness does not mean that weighting was not worthwhile. Weighting per se can be beneficial for more acceptable and viable decisional processes.


Author(s):  
Fred L. Bookstein

AbstractA matrix manipulation new to the quantitative study of develomental stability reveals unexpected morphometric patterns in a classic data set of landmark-based calvarial growth. There are implications for evolutionary studies. Among organismal biology’s fundamental postulates is the assumption that most aspects of any higher animal’s growth trajectories are dynamically stable, resilient against the types of small but functionally pertinent transient perturbations that may have originated in genotype, morphogenesis, or ecophenotypy. We need an operationalization of this axiom for landmark data sets arising from longitudinal data designs. The present paper introduces a multivariate approach toward that goal: a method for identification and interpretation of patterns of dynamical stability in longitudinally collected landmark data. The new method is based in an application of eigenanalysis unfamiliar to most organismal biologists: analysis of a covariance matrix of Boas coordinates (Procrustes coordinates without the size standardization) against their changes over time. These eigenanalyses may yield complex eigenvalues and eigenvectors (terms involving $$i=\sqrt{-1}$$ i = - 1 ); the paper carefully explains how these are to be scattered, gridded, and interpreted by their real and imaginary canonical vectors. For the Vilmann neurocranial octagons, the classic morphometric data set used as the running example here, there result new empirical findings that offer a pattern analysis of the ways perturbations of growth are attenuated or otherwise modified over the course of developmental time. The main finding, dominance of a generalized version of dynamical stability (negative autoregressions, as announced by the negative real parts of their eigenvalues, often combined with shearing and rotation in a helpful canonical plane), is surprising in its strength and consistency. A closing discussion explores some implications of this novel pattern analysis of growth regulation. It differs in many respects from the usual way covariance matrices are wielded in geometric morphometrics, differences relevant to a variety of study designs for comparisons of development across species.


Author(s):  
Daniel Rojas-Valverde ◽  
José Pino-Ortega ◽  
Rafael Timón ◽  
Randall Gutiérrez-Vargas ◽  
Braulio Sánchez-Ureña ◽  
...  

The extensive use of wearable sensors in sport medicine, exercise medicine, and health has increased the interest in their study. That is why it is necessary to test these technologies’ efficiency, effectiveness, agreement, and reliability in different settings. Consequently, the purpose of this article was to analyze the magnetic, angular rate, and gravity (MARG) sensor’s test-retest agreement and reliability when assessing multiple body segments’ external loads during off-road running. A total of 18 off-road runners (38.78 ± 10.38 years, 73.24 ± 12.6 kg, 172.17 ± 9.48 cm) ran two laps (1st and 2nd Lap) of a 12 km circuit wearing six MARG sensors. The sensors were attached to six different body segments: left (MPLeft) and right (MPRight) malleolus peroneus, left (VLLeft) and right (VLRight) vastus lateralis, lumbar (L1-L3), and thorax (T2-T4) using a special neoprene suit. After a principal component analysis (PCA) was performed, the total data set variance of all body segments was represented by 44.08%–70.64% for the 1st PCA factor considering two variables, Player LoadRT and Impacts, on L1-L3, respectively. These two variables were chosen among three total accelerometry-based external load indicators (ABELIs) to perform the agreement and reliability tests due to their relevance based on PCAs for each body segment. There were no significant differences between laps in the Player LoadRT or Impacts ( p > 0.05, trivial). The intraclass correlation and lineal correlation showed a substantial to almost perfect over-time test consistency assessed via reliability in both Player LoadRT and Impacts. Bias and t-test assessments showed good agreement between Laps. It can be concluded that MARGs sensors offer significant test re-test reliability and good agreement when assessing off-road kinematics in the six different body segments.


Sign in / Sign up

Export Citation Format

Share Document