Geometric Morphometrics for Mathematica (Ver. 9.0)

This Mathematica add-on package performs common geometric morphometric functions. Includes Procrustes superimposition, thin-plate spline graphics, Centroid Size calculation, Procrustes distance calculation, Mantel tests, Ancestral Node reconstruction, Eclidean Distance Matrix Analysis (EDMA), and import function for TPS files. Installation: The file is a ".m" file, which can be imported into Mathematica 6.0 and later (functions do not work in earlier versions of Mathematica). Install using the "Install" item on the "File" menu. Once installed, you must load the package like any other with the line "<<PollyMorphometrics", using either this suggested name or another. If some functions do not work, load the MultivariateStatistics and Combinatorica packages

Modularity for Mathematica

Morphological integration is correlation of parts, the integration of morphological traits or features that must function, grow, or be passed to offspring on as working units. Individual integrated units are modules, a group of traits that are highly correlated among themselves but only loosely correlated with traits in other modules. The study of integration and modularity was first developed by Olson and Miller (1958) and expanded on by Cheverud (1982), Zelditch (1988), Wagner (1995), Raff (1996), Klingenberg (2000), Mitteroecker (2007) and many others. The basic component of studying modularity and integration is identifying packages of intercorrelated traits that behave independently of other such packages, whether through ontogeny, across individuals within a population, or during the course of evolution. This package performs a simple analysis of modularity on geometric morphometric landmark data. This package accompanies the review by Goswami and Polly (2010). Users are referred to that paper for a discussion of the methods embedded in this package, including their strengths and weaknesses, and for elaboration of other methods that address broader problems

Modelling of quasi-optical arrays

A model for analyzing quasi-optical grid amplifiers based on a finite-element electromagnetic simulator is presented. This model is deduced from the simulation of the whole unit cell and takes into account mutual coupling effects. By using this model, the gain of a 10×10 grid amplifier has been accurately predicted. To further test the validity of the model three passive structures with different loads have been fabricated and tested using a new focused-beam network analyzer that we developed

The implications of autoantibodies to a single islet antigen in relatives with normal glucose tolerance:development of other autoantibodies and progression to type 1 diabetes

AIMS/HYPOTHESIS: Autoantibodies directed at single islet autoantigens are associated with lower overall risk of type 1 diabetes than multiple autoantibodies, but individuals with one autoantibody may progress to higher risk categories. We examined the characteristics of this progression in relatives followed prospectively in the TrialNet Pathway to Prevention. METHODS: The study population comprised 983 relatives who were single autoantibody positive with normal baseline glucose tolerance (median age 16.2 years). Samples were screened for antibodies to GAD, insulinoma-associated antigen 2 (IA-2) and insulin, and all positive samples tested for antibodies to zinc transporter 8 and islet cell antibodies. RESULTS: Antibodies to at least one additional islet autoantigen appeared in 118 of 983 relatives (overall 5 year risk 22%, 95% CI [17.9, 26.1]). At baseline, antibodies to GAD alone (68%) were more frequent than antibodies to insulin (26%) or IA-2 (6%), but all were associated with a similar risk of developing additional autoantibodies. Risk was associated with younger age (p = 0.002) and HLA class II genotype, but was similar in high and intermediate genetic risk groups (p = 0.65). Relatives who became multiple autoantibody positive during the follow-up had increased risk of developing diabetes comparable with the risk in relatives with multiple autoantibodies at study entry. CONCLUSIONS/INTERPRETATION: Progression of islet autoimmunity in single autoantibody positive relatives in late childhood/adult life is associated with a predominance of autoantibodies to GAD and a distinct HLA risk profile. This heterogeneity in type 1 diabetes autoimmunity has potentially important implications for disease prevention. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s00125-015-3830-2) contains peer-reviewed but unedited supplementary material, which is available to authorised users

Trophically Integrated Ecometric Models as Tools for Demonstrating Spatial and Temporal Functional Changes in Mammal Communities

We are in a modern biodiversity crisis that will restructure community compositions and ecological functions globally. Large mammals, important contributors to ecosystem function, have been affected directly by purposeful extermination and indirectly by climate and land-use changes, yet functional turnover is rarely assessed on a global scale using metrics based on functional traits. Using ecometrics, the study of functional trait distributions and functional turnover, we examine the relationship between vegetation cover and locomotor traits for artiodactyl and carnivoran communities. We show that the ability to detect a functional relationship is strengthened when locomotor traits of both primary consumers (artiodactyls, n = 157 species) and secondary consumers (carnivorans, n = 138 species) are combined into one trophically integrated ecometric model. Overall, locomotor traits of 81% of communities accurately estimate vegeta-tion cover, establishing the advantage of trophically integrated ecometric models over single-group models (58 to 65% correct). We develop an innovative approach within the ecometrics framework, using ecometric anomalies to evaluate mismatches in model estimates and observed values and provide more nuance for understanding relationships between functional traits and vegetation cover. We apply our integrated model to five paleontological sites to illustrate mismatches in the past and today and to demonstrate the utility of the model for paleovegetation interpretations. Observed changes in com-munity traits and their associated vegetations across space and over time demonstrate the strong, rapid effect of environmental filtering on community traits. Ultimately, our trophically integrated ecometric model captures the cascading interactions between taxa, traits, and changing environment

Evaluating Children’s Advocacy Centers’ Response to Child Sexual Abuse

Children’s Advocacy Centers (CACs) play an increasingly significant role in the response to child sexual abuse and other child maltreatment in the United States. First developed in the 1980s, CACs were designed to reduce the stress on child abuse victims and families created by traditional child abuse investigation and prosecution procedures and to improve the effectiveness of the response. According to several experts (Fontana, 1984; Pence and Wilson, 1992; Whitcomb, 1992), child victims were subjected to multiple, redundant interviews about their abuse by different agencies, and were questioned by professionals who had no knowledge of children’s developmental limitations or experience working with children. Child interviews would take place in settings like police stations that would further stress already frightened children. Moreover, the response was hampered because the multiple agencies involved did not coordinate their investigations, and children’s need for services could be neglected

Combining geometric morphometrics and finite element analysis with evolutionary modeling:towards a synthesis

<p>Geometric morphometrics (GM) and finite element analysis (FEA) are increasingly common techniques for the study of form and function. We show how principles of quantitative evolution in continuous phenotypic traits can link the two techniques, allowing hypotheses about the relative importance of different functions to be tested in a phylogenetic and evolutionary framework. Finite element analysis is used to derive quantitative surfaces that describe the comparative performance of different morphologies in a morphospace derived from GM. The combination of two or more performance surfaces describes a quantitative adaptive landscape that can be used to predict the direction morphological evolution would take if a combination of functions was selected for. Predicted paths of evolution also can be derived for hypotheses about the relative importance of multiple functions, which can be tested against evolutionary pathways that are documented by phylogenies or fossil sequences. Magnitudes of evolutionary trade-offs between functions can be estimated using maximum likelihood. We apply these methods to an earlier study of carapace strength and hydrodynamic efficiency in emydid turtles. We find that strength and hydrodynamic efficiency explain about 45% of the variance in shell shape; drift and other unidentified functional factors are necessary to explain the remaining variance. Measurement of the proportional trade-off between shell strength and hydrodynamic efficiency shows that throughout the Cenozoic aquatic turtles generally sacrificed strength for streamlining and terrestrial species favored stronger shells; this suggests that the selective regime operating on small to mid-sized emydids has remained relatively static.</p> <p>SUPPLEMENTAL DATA—Supplemental materials are available for this article for free at <a href="http://www.tandfonline.com/UJVP" target="_blank">www.tandfonline.com/UJVP</a></p> <p>Citation for this article: Polly, P. D., C. T. Stayton, E. R. Dumont, S. E. Pierce, E. J. Rayfield, and K. D. Angielczyk. 2016. Combining geometric morphometrics and finite element analysis with evolutionary modeling: towards a synthesis. Journal of Vertebrate Paleontology. DOI: 10.1080/02724634.2016.1111225.</p