Commentary on the Integration of Model Sharing and Reproducibility Analysis to Scholarly Publishing Workflow in Computational Biomechanics

© 1964-2012 IEEE.Objective: The overall goal of this paper is to demonstrate that dissemination of models and analyses for assessing the reproducibility of simulation results can be incorporated in the scientific review process in biomechanics. Methods: As part of a special issue on model sharing and reproducibility in the IEEE Transactions on Biomedical Engineering, two manuscripts on computational biomechanics were submitted: Rajagopal et al., IEEE Trans. Biomed. Eng., 2016 and Schmitz and Piovesan, IEEE Trans. Biomed. Eng., 2016. Models used in these studies were shared with the scientific reviewers and the public. In addition to the standard review of the manuscripts, the reviewers downloaded the models and performed simulations that reproduced results reported in the studies. Results: There was general agreement between simulation results of the authors and those of the reviewers. Discrepancies were resolved during the necessary revisions. The manuscripts and instructions for download and simulation were updated in response to the reviewers' feedback; changes that may otherwise have been missed if explicit model sharing and simulation reproducibility analysis was not conducted in the review process. Increased burden on the authors and the reviewers, to facilitate model sharing and to repeat simulations, were noted. Conclusion: When the authors of computational biomechanics studies provide access to models and data, the scientific reviewers can download and thoroughly explore the model, perform simulations, and evaluate simulation reproducibility beyond the traditional manuscript-only review process. Significance: Model sharing and reproducibility analysis in scholarly publishing will result in a more rigorous review process, which will enhance the quality of modeling and simulation studies and inform future users of computational models

A review of spatial causal inference methods for environmental and epidemiological applications

The scientific rigor and computational methods of causal inference have had great impacts on many disciplines, but have only recently begun to take hold in spatial applications. Spatial casual inference poses analytic challenges due to complex correlation structures and interference between the treatment at one location and the outcomes at others. In this paper, we review the current literature on spatial causal inference and identify areas of future work. We first discuss methods that exploit spatial structure to account for unmeasured confounding variables. We then discuss causal analysis in the presence of spatial interference including several common assumptions used to reduce the complexity of the interference patterns under consideration. These methods are extended to the spatiotemporal case where we compare and contrast the potential outcomes framework with Granger causality, and to geostatistical analyses involving spatial random fields of treatments and responses. The methods are introduced in the context of observational environmental and epidemiological studies, and are compared using both a simulation study and analysis of the effect of ambient air pollution on COVID-19 mortality rate. Code to implement many of the methods using the popular Bayesian software OpenBUGS is provided

Modeling of the condyle elements within a biomechanical knee model

The development of a computational multibody knee model able to capture some of the fundamental properties of the human knee articulation is presented. This desideratum is reached by including the kinetics of the real knee articulation. The research question is whether an accurate modeling of the condyle contact in the knee will lead to reproduction of the complex combination of flexion/extension, abduction/adduction and tibial rotation ob-served in the real knee? The model is composed by two anatomic segments, the tibia and the femur, whose characteristics are functions of the geometric and anatomic properties of the real bones. The biomechanical model characterization is developed under the framework of multibody systems methodologies using Cartesian coordinates. The type of approach used in the proposed knee model is the joint surface contact conditions between ellipsoids, represent-ing the two femoral condyles, and points, representing the tibial plateau and the menisci. These elements are closely fitted to the actual knee geometry. This task is undertaken by con-sidering a parameter optimization process to replicate experimental data published in the lit-erature, namely that by Lafortune and his co-workers in 1992. Then, kinematic data in the form of flexion/extension patterns are imposed on the model corresponding to the stance phase of the human gait. From the results obtained, by performing several computational simulations, it can be observed that the knee model approximates the average secondary mo-tion patterns observed in the literature. Because the literature reports considerable inter-individual differences in the secondary motion patterns, the knee model presented here is also used to check whether it is possible to reproduce the observed differences with reasonable variations of bone shape parameters. This task is accomplished by a parameter study, in which the main variables that define the geometry of condyles are taken into account. It was observed that the data reveal a difference in secondary kinematics of the knee in flexion ver-sus extension. The likely explanation for this fact is the elastic component of the secondary motions created by the combination of joint forces and soft tissue deformations. The proposed knee model is, therefore, used to investigate whether this observed behavior can be explained by reasonable elastic deformations of the points representing the menisci in the model.Fundação para a Ciência e a Tecnologia (FCT) - PROPAFE – Design and Development of a Patello-Femoral Prosthesis (PTDC/EME-PME/67687/2006), DACHOR - Multibody Dynamics and Control of Hybrid Active Orthoses MIT-Pt/BSHHMS/0042/2008, BIOJOINTS - Development of advanced biological joint models for human locomotion biomechanics (PTDC/EME-PME/099764/2008)

Development of a planar multi-body model of the human knee joint

The aim of this work is to develop a dynamic model for the biological human knee joint. The model is formulated in the framework of multibody systems methodologies, as a system of two bodies, the femur and the tibia. For the purpose of describing the formulation, the relative motion of the tibia with respect to the femur is considered. Due to their higher stiffness compared to that of the articular cartilages, the femur and tibia are considered as rigid bodies. The femur and tibia cartilages are considered to be deformable structures with specific material characteristics. The rotation and gliding motions of the tibia relative to the femur can not be modeled with any conventional kinematic joint, but rather in terms of the action of the knee ligaments and potential contact between the bones. Based on medical imaging techniques, the femur and tibia profiles in the sagittal plane are extracted and used to define the interface geometric conditions for contact. When a contact is detected, a continuous non-linear contact force law is applied which calculates the contact forces developed at the interface as a function of the relative indentation between the two bodies. The four basic cruciate and collateral ligaments present in the knee are also taken into account in the proposed knee joint model, which are modeled as non-linear elastic springs. The forces produced in the ligaments, together with the contact forces, are introduced into the system’s equations of motion as external forces. In addition, an external force is applied on the center of mass of the tibia, in order to actuate the system mimicking a normal gait motion. Finally, numerical results obtained from computational simulations are used to address the assumptions and procedures adopted in this study.Fundação para a Ciência e a Tecnologia (FCT

Cuestiones reglamentarias, ambientales y de inocuidad, relacionadas con la cría y el comercio internacional de insectos comestibles en África

Insect breeding or farming for food and feed is an emerging enterprise that can address the ever-growing demand for protein and curb high unemployment rates in Africa and beyond. However, for the sector to prosper, its value chain needs to be regulated to ensure sustainability and safety for consumers and the environment. Although a few African countries, such as Kenya, Uganda and Rwanda, have promulgated standards on the use of insects as food and feed, greater efforts are needed in other countries, and relevant policies governing the sector need to be formulated. All over the globe, attention to the regulation of the edible insect sector is increasing, and more investment in the in- dustry is foreseen. Safety issues such as identifying which species should be reared, substrate quality and traceability imposed by importing countries will be critical for expansion of the sector. This paper analyses safety, regulatory and environmental issues related to breeding and international trade of edible insects in Africa and provides case studies and recommendations for sustainable use of insects for food and feed.La cría o producción de insectos con fines de alimentación humana o animal es una actividad incipiente que puede ayudar a responder a la siempre creciente demanda de proteínas y a contener las elevadas tasas de desempleo de África y otras regiones. Para que el sector prospere, no obstante, es preciso reglamentar su cadena de valor a fin de asegurar su sostenibilidad y su inocuidad para el consumidor y el medio ambiente. Aunque unos pocos países africanos, como Kenia, Uganda o Ruanda, tienen promulgadas normas sobre el uso de insectos para la alimentación humana o la producción de piensos, aún hay que redoblar esfuerzos en otros países y formular políticas que ordenen el sector. En todo el planeta se presta hoy una atención sin precedentes a la regulación del sector de los insectos comestibles, un sector que previsiblemente va a recibir cada vez más inversiones. Las cuestiones ligadas a la inocuidad, como la identidad de los insectos que se van a producir, la calidad del substrato o la rastreabilidad impuesta por los países importadores, serán fundamentales para el desarrollo del sector. Los autores analizan las cuestiones reglamentarias, ambientales y de inocuidad que se plantean en relación con la cría y el comercio internacional de insectos comesti- bles en África, presentan ejemplos concretos y formulan recomendaciones para un uso sostenible de los insectos con fines de alimentación humana o animal.Les élevages et les fermes d’insectes destinés à l’alimentation humaine et animale sont de nouvelles entreprises qui pourraient répondre à la hausse continue de la demande en protéines tout en réduisant les taux élevés du chômage en Afrique et ailleurs. Néanmoins, pour que ce secteur puisse prospérer, sa chaîne de création de valeur doit être réglementée afin de garantir sa durabilité et son innocuité pour les consommateurs et l’environnement. Si un petit nombre de pays africains dont le Kenya, l’Ouganda et le Rwanda ont élaboré des normes applicables à l’utilisation des insectes pour l’alimentation humaine et animale, dans d’autres pays les efforts doivent se poursuivre et des politiques appropriées doivent être mises en place pour régir ce secteur. Partout dans le monde, la réglementation du secteur des insectes comestibles fait désormais l’objet d’une attention considérable et des investissements accrus dans la filière sont attendus. Les questions de sécurité telles que l’identi- fication des insectes à élever, la qualité du substrat et la traçabilité exigée par les pays importateurs seront cruciales pour le développement du secteur. Les auteurs analysent les questions de sécurité et les enjeux réglementaires et environnementaux liés à l’élevage et au commerce international d’insectes comestibles en Afrique et présentent des études de cas et des recommandations pour une utilisation durable des insectes destinés à l’alimentation humaine et animale.Denmark’s development cooperation DANIDA through the project Healthynsect and the icipe core fund- ing provided by the Swedish International Development Cooperation Agency (SIDA); the Swiss Agency for Development and Cooperation (SDC); the Federal Ministry for Economic Cooperation and Development (BMZ), Germany; the Federal Democratic Republic of Ethiopia; the South African National Research Foundation; and the Government of the Republic of Kenya.https://www.woah.org/en/what-we-do/publications/scientific-and-technical-reviewhj2023Zoology and Entomolog