Visualising muscle anatomy using three-dimensional computer models - an example using the head and neck muscles of Sphenodon

We demonstrate how the computer-based technique of multi-body dynamics analysis (MDA) can be used to create schematic, but informative three-dimensional (3D) representations of complex muscle anatomy. As an example we provide an overview of the head and neck muscles present in Sphenodon (Diapsida: Lepidosauria: Rhynchocephalia). First a computer model based on micro-computed tomography datasets provides a detailed and anatomically correct three-dimensional (3D) framework to work from. Secondly, muscles are represented by groups of cylinders that can be colour coded as desired. This allows muscle positions, attachment areas, and 3D orientation to be visualised clearly. This method has advantages over imaging techniques such as two-dimensional drawings and permits the form and function of the muscles to be understood in a way that is not always possible with more classical visualisation techniques. Copyright: Palaeontological Association December 2009

The head and neck muscles associated with feeding in sphenodon (Reptilia: Lepidosauria: Rhynchocephalia)

Feeding in Sphenodon, the tuatara of New Zealand, is of interest for several rea-sons. First, the modern animal is threatened by extinction, and some populations are in competition for food with Pacific rats. Second, Sphenodon demonstrates a feeding apparatus that is unique to living amniotes: an enlarged palatine tooth row, acrodont dentition, enlarged incisor-like teeth on the premaxilla, a posterior extension of the dentary and an elongate articular surtace that permits prooral shearing. Third, Spheno-don has a skull with two complete lateral temporal bars and is therefore structurally analogous to the configuration hypothesised for the ancestral diapsid reptile. Further-more, the fossil relatives of Sphenodon demonstrate considerable variation in terms of feeding apparatus and skull shape. Lastly, as Sphenodon is the only extant rhyn-chocephalian it represents a potentially useful reference taxon for both muscle recon-struction in extinct reptile taxa and determination of muscle homology in extant taxa. Here we provide an up-to-date consensus view of osteology and musculature in Sphenodon that is relevant to feeding. Discrepancies within previous descriptions are evaluated and synthesised with new observations. This paper displays the complex muscle arrangement using a range of different imaging techniques and a variety of different angles. This includes photographs, illustrations, schematic diagrams, and microcomputed tomography (micro-CT) slice images. © Palaeontological Association August 2009

Challenges of achieving good environmental status in the Northeast Atlantic

The sustainable exploitation of marine ecosystem services is dependent on achieving and maintaining an adequate ecosystem state to prevent undue deterioration. Within the European Union, the Marine Strategy Framework Directive (MSFD) requires member states to achieve Good Environmental Status (GEnS), specified in terms of 11 descriptors. We analyzed the complexity of social-ecological factors to identify common critical issues that are likely to influence the achievement of GEnS in the Northeast Atlantic (NEA) more broadly, using three case studies. A conceptual model developed using a soft systems approach highlights the complexity of social and ecological phenomena that influence, and are likely to continue to influence, the state of ecosystems in the NEA. The development of the conceptual model raised four issues that complicate the implementation of the MSFD, the majority of which arose in the Pressures and State sections of the model: variability in the system, cumulative effects, ecosystem resilience, and conflicting policy targets. The achievement of GEnS targets for the marine environment requires the recognition and negotiation of trade-offs across a broad policy landscape involving a wide variety of stakeholders in the public and private sectors. Furthermore, potential cumulative effects may introduce uncertainty, particularly in selecting appropriate management measures. There also are endogenous pressures that society cannot control. This uncertainty is even more obvious when variability within the system, e.g., climate change, is accounted for. Also, questions related to the resilience of the affected ecosystem to specific pressures must be raised, despite a lack of current knowledge. Achieving good management and reaching GEnS require multidisciplinary assessments. The soft systems approach provides one mechanism for bringing multidisciplinary information together to look at the problems in a different light

Exploring motion using geometric morphometrics in microscopic aquatic invertebrates: ‘modes’ and movement patterns during feeding in a bdelloid rotifer model species

Background: Movement is a defining aspect of animals, but it is rarely studied using quantitative methods in microscopic invertebrates. Bdelloid rotifers are a cosmopolitan class of aquatic invertebrates of great scientific interest because of their ability to survive in very harsh environment and also because they represent a rare example of an ancient lineage that only includes asexually reproducing species. In this class, Adineta ricciae has become a model species as it is unusually easy to culture. Yet, relatively little is known of its ethology and almost nothing on how it behaves during feeding. Methods: To explore feeding behaviour in A. ricciae, as well as to provide an example of application of computational ethology in a microscopic invertebrate, we apply Procrustes motion analysis in combination with ordination and clustering methods to a laboratory bred sample of individuals recorded during feeding. Results: We demonstrate that movement during feeding can be accurately described in a simple two-dimensional shape space with three main ‘modes’ of motion. Foot telescoping, with the body kept straight, is the most frequent ‘mode’, but it is accompanied by periodic rotations of the foot together with bending while the foot is mostly retracted. Conclusions: Procrustes motion analysis is a relatively simple but effective tool for describing motion during feeding in A. ricciae. The application of this method generates quantitative data that could be analysed in relation to genetic and ecological differences in a variety of experimental settings. The study provides an example that is easy to replicate in other invertebrates, including other microscopic animals whose behavioural ecology is often poorly known

Pooled analysis of prognostic impact of urokinase-type plasminogen activator and its inhibitor PAI-1 in 8377 breast cancer patients

BACKGROUND: Urokinase-type plasminogen activator (uPA) and its inhibitor (PAI-1) play essential roles in tumor invasion and metastasis. High levels of both uPA and PAI-1 are associated with poor prognosis in breast cancer patients. To confirm the prognostic value of uPA and PAI-1 in primary breast cancer, we reanalyzed individual patient data provided by members of the European Organization for Research and Treatment of Cancer-Receptor and Biomarker Group (EORTC-RBG). METHODS: The study included 18 datasets involving 8377 breast cancer patients. During follow-up (median 79 months), 35% of the patients relapsed and 27% died. Levels of uPA and PAI-1 in tumor tissue extracts were determined by different immunoassays; values were ranked within each dataset and divided by the number of patients in that dataset to produce fractional ranks that could be compared directly across datasets. Associations of ranks of uPA and PAI-1 levels with relapse-free survival (RFS) and overall survival (OS) were analyzed by Cox multivariable regression analysis stratified by dataset, including the following traditional prognostic variables: age, menopausal status, lymph node status, tumor size, histologic grade, and steroid hormone-receptor status. All P values were two-sided. RESULTS: Apart from lymph node status, high levels of uPA and PAI-1 were the strongest predictors of both poor RFS and poor OS in the analyses of all patients. Moreover, in both lymph node-positive and lymph node-negative patients, higher uPA and PAI-1 values were independently associated with poor RFS and poor OS. For (untreated) lymph node-negative patients in particular, uPA and PAI-1 included together showed strong prognostic ability (all P<.001). CONCLUSIONS: This pooled analysis of the EORTC-RBG datasets confirmed the strong and independent prognostic value of uPA and PAI-1 in primary breast cancer. For patients with lymph node-negative breast cancer, uPA and PAI-1 measurements in primary tumors may be especially useful for designing individualized treatment strategies

Morphometric maps of bilateral asymmetry in the human humerus: An implementation in the R package morphomap

In biological anthropology, parameters relating to cross-sectional geometry are calculated in paired long bones to evaluate the degree of lateralization of anatomy and, by inference, function. Here, we describe a novel approach, newly added to the morphomap R package, to assess the lateralization of the distribution of cortical bone along the entire diaphysis. The sample comprises paired long bones belonging to 51 individuals (10 females and 41 males) from The New Mexico Decedent Image Database with known biological profile, occupational and loading histories. Both males and females show a pattern of right lateralization. In addition, males are more lateralized than females, whereas there is not a significant association between lateralization with occupation and loading history. Body weight, height and long-bone length are the major factors driving the emergence of asymmetry in the humerus, while interestingly, the degree of lateralization decreases in the oldest individuals

Pooled Analysis of Prognostic Impact of Urokinase-Type Plasminogen Activator and Its Inhibitor PAI-1 in 8377 Breast Cancer Patients

Background: Urokinase-type plasminogen activator (uPA) and its inhibitor (PAI-1) play essential roles in tumor invasion and metastasis. High levels of both uPA and PAI-1 are associated with poor prognosis in breast cancer patients. To confirm the prognostic value of uPA and PAI-1 in primary breast cancer, we reanalyzed individual patient data provided by members of the European Organization for Research and Treatment of Cancer-Receptor and Biomarker Group (EORTC-RBG). Methods: The study included 18 datasets involving 8377 breast cancer patients. During follow-up (median 79 months), 35% of the patients relapsed and 27% died. Levels of uPA and PAI-1 in tumor tissue extracts were determined by different immunoassays; values were ranked within each dataset and divided by the number of patients in that dataset to produce fractional ranks that could be compared directly across datasets. Associations of ranks of uPA and PAI-1 levels with relapse-free survival (RFS) and overall survival (OS) were analyzed by Cox multivariable regression analysis stratified by dataset, including the following traditional prognostic variables: age, menopausal status, lymph node status, tumor size, histologic grade, and steroid hormone-receptor status. All P values were two-sided. Results: Apart from lymph node status, high levels of uPA and PAI-1 were the strongest predictors of both poor RFS and poor OS in the analyses of all patients. Moreover, in both lymph node-positive and lymph node-negative patients, higher uPA and PAI-1 values were independently associated with poor RFS and poor OS. For (untreated) lymph node-negative patients in particular, uPA and PAI-1 included together showed strong prognostic ability (all P<.001). Conclusions: This pooled analysis of the EORTC-RBG datasets confirmed the strong and independent prognostic value of uPA and PAI-1 in primary breast cancer. For patients with lymph node-negative breast cancer, uPA and PAI-1 measurements in primary tumors may be especially useful for designing individualized treatment strategie

Ecomorphology of Carnivora challenges convergent evolution

Convergent evolution is often reported in the mammalian order Carnivora. Their adaptations to particularly demanding feeding habits such as hypercarnivory and durophagy (consumption of tough food) appear to favour morphological similarities between distantly related species, especially in the skull. However, phylogenetic effect in phenotypic data might obscure such a pattern. We first validated the hypotheses that extant hypercarnivorous and durophagous large carnivorans converge in mandibular shape and form (size and shape). Hypercarnivores generally exhibit smaller volumes of the multidimensional shape and form space than their sister taxa, but this pattern is significantly different from random expectation only when hunting behaviour categorisations are taken into account. Durophages share areas of the morphospace, but this seems to be due to factors of contingency. Carnivorans that hunt in pack exhibit incomplete convergence while even stronger similarities occur in the mandible shape of solitary hunters due to the high functional demands in killing the prey. We identified a stronger phylogenetic signal in mandibular shape than in size. The quantification of evolutionary rates of changes suggests that mandible shape of solitary hunters evolved slowly when compared with other carnivorans. These results consistently indicate that the need for a strong bite force and robust mandible override sheer phylogenetic effect in solitary hunters