PhysiomeSpace: digital library service for biomedical data

Efficient Health Information Management Based on Patient-Generated Digital Data

Technology has been a growing part of healthcare for decades. The patient experience is going digital, and consumers are leading the way by accessing EHRs and using digital tools, such as wearables and apps, to manage their health. Patient-generated health data (PGHD) are health-related data created, recorded, or gathered by or from patients (or family members or other caregivers) to help address a health concern. PGHD may have several reported patient engagement and empowerment benefits, but lingering issues may prohibit providers from actually using patients' data. In this paper we review the main recent PGHD uses, challenges and opportunities.

Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data

C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop an open-source and multi-platform framework to read, write, modify and visualize data from any motion analysis systems using standard (C3D) and proprietary file formats (used by many companies producing motion capture systems). The Biomechanical ToolKit (BTK) was developed to provide cost-effective and efficient tools for the biomechanical community to easily deal with motion analysis data. A large panel of operations is available to read, modify and process data through C++ API, bindings for high-level languages (Matlab, Octave, and Python), and standalone application (Mokka). All these tools are open-source and cross-platform and run on all major operating systems (Windows, Linux, MacOS X).

Patient-specific fibre-based models of muscle wrapping

In many biomechanical problems, the availability of a suitable model for the wrapping of muscles when undergoing movement is essential for the estimation of forces produced on and by the body during motion. This is an important factor in the Osteoporotic Virtual Physiological Human project which is investigating the likelihood of fracture for osteoporotic patients undertaking a variety of movements. The weakening of their skeletons makes them particularly vulnerable to bone fracture caused by excessive loading being placed on the bones, even in simple everyday tasks. This paper provides an overview of a novel volumetric model that describes muscle wrapping around bones and other muscles during movement, and which includes a consideration of how the orientations of the muscle fibres change during the motion. The method can calculate the form of wrapping of a muscle of medium size and visualize the outcome within tenths of seconds on commodity hardware, while conserving muscle volume. This makes the method suitable not only for educational biomedical software, but also for clinical applications used to identify weak muscles that should be strengthened during rehabilitation or to identify bone stresses in order to estimate the risk of fractures.

A vision and strategy for the virtual physiological human: 2012 update

European funding under Framework 7 (FP7) for the virtual physiological human (VPH) project has been in place now for 5 years. The VPH Network of Excellence (NoE) has been set up to help develop common standards, open source software, freely accessible data and model repositories, and various training and dissemination activities for the project. It is also working to coordinate the many clinically targeted projects that have been funded under the FP7 calls. An initial vision for the VPH was defined by the FP6 STEP project in 2006. In 2010, we wrote an assessment of the accomplishments of the first two years of the VPH in which we considered the biomedical science, healthcare and information and communications technology challenges facing the project (Hunter et al. 2010 Phil. Trans. R. Soc. A 368, 2595-2614 (doi:10.1098/rsta.2010.0048)). We proposed that a not-for-profit professional umbrella organization, the VPH Institute, should be established as a means of sustaining the VPH vision beyond the time-frame of the NoE. Here, we update and extend this assessment and in particular address the following issues raised in response to Hunter et al.: (i) a vision for the VPH updated in the light of progress made so far, (ii) biomedical science and healthcare challenges that the VPH initiative can address while also providing innovation opportunities for the European industry, and (iii) external changes needed in regulatory policy and business models to realize the full potential that the VPH has to offer to industry, clinics and society generally.

Femoral loads during gait in a patient with massive skeletal reconstruction

BACKGROUND

Biological massive skeletal reconstructions in tumours adopt a long rehabilitation protocol aimed at minimising the fracture risk. To improve rehabilitation and surgical procedures it is important to fully understand the biomechanics of the reconstructed limb. The aim of the present study was to develop a subject-specific musculoskeletal model of a patient with a massive biological skeletal reconstruction, to investigate the loads acting on the femur during gait, once the rehabilitation protocol was completed.

METHODS

A personalised musculoskeletal model of the patient's lower limbs was built from a CT exam and registered with the kinematics recorded in a gait analysis session. Predicted activations for major muscles were compared to EMG signals to assess the model's predictive accuracy.

FINDINGS

Gait kinematics showed only minor discrepancies between the two legs and was compatible with normality data. External moments showed slightly higher differences and were almost always lower on the operated leg exhibiting a lower variability. In the beginning of the stance phase, the joint moments were, conversely, higher on the operated side and showed a higher variability. This pattern was reflected and amplified on the femoral forces where the differences became important: on the hip, a maximum difference of 1.6 BW was predicted. The variability of the forces seemed, generally, lower on the operated leg than on the contralateral one.

INTERPRETATION

Small asymmetries in kinematic patterns might be associated, in massive skeletal reconstruction, to significant difference in the skeletal loads (up to 1.6 BW for the hip joint reaction) during gait.

The development of lower limb musculoskeletal models with clinical relevance is dependent upon the fidelity of the mathematical description of the lower limb. Part 2: patient-specific geometry

Musculoskeletal models have the potential to evolve into sensitive clinical tools that provide relevant therapeutic guidance. A key impediment to this is the lack of understanding as to the function of such models. In order to improve this it is useful to recognise that musculoskeletal modelling is the mathematical description of musculoskeletal movement – a process that involves the construction and solution of equations of motion. These equations are derived from standard mechanical considerations and the mathematical representation of anatomy. The fidelity of musculoskeletal models is highly dependent on the assumption that such representations also describe the function of the musculoskeletal geometry. In addition, it is important to understand the sensitivity of such representations to patient-specific variations in anatomy. The exploration of these twin considerations will be fundamental to the creation of musculoskeletal modelling tools with clinical relevance and a systematic enquiry of these key parameters is recommended.

Are spontaneous fractures possible? An example of clinical application for personalised, multiscale neuro-musculo-skeletal modelling

Elderly frequently present variable degrees of osteopenia, sarcopenia, and neuromotor control degradation. Severely osteoporotic patients sometime fracture their femoral neck when falling. Is it possible that such fractures might occur without any fall, but rather spontaneously while the patient is performing normal movements such as level walking? The aim of this study was to verify if such spontaneous fractures are biomechanically possible, and in such case, which conditions of osteoporosis, sarcopenia, and neuromotor degradation could produce them. To the purpose, a probabilistic multiscale body-organ model validated against controlled experiments was used to predict the risk of spontaneous fractures in a population of 80-years old women, with normal weight and musculoskeletal anatomy, and variable degree of osteopenia, sarcopenia, and neuromotor control degradation. A multi-body inverse dynamics sub-model, coupled to a probabilistic neuromuscular sub-model, and to a femur finite element sub-model, formed the multiscale model, which was run within a Monte Carlo stochastic scheme, where the various parameters were varied randomly according to well defined distributions. The model predicted that neither extreme osteoporosis, nor extreme neuromotor degradation alone are sufficient to predict spontaneous fractures. However, when the two factors are combined an incidence of 0.4% of spontaneous fractures is predicted for the simulated population, which is consistent with clinical reports. When the model represented only severely osteoporotic patients, the incidence of spontaneous fractures increased to 29%. Thus, is biomechanically possible that spontaneous femoral neck fractures occur during level walking, due to a combination of severe osteoporosis and severe neuromotor degradation.

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions

Background

The practice and research of medicine generates considerable quantities of data and model resources (DMRs). Although in principle biomedical resources are re-usable, in practice few can currently be shared. In particular, the clinical communities in physiology and pharmacology research, as well as medical education, (i.e. PPME communities) are facing considerable operational and technical obstacles in sharing data and models.

Findings

We outline the efforts of the PPME communities to achieve automated semantic interoperability for clinical resource documentation in collaboration with the RICORDO project. Current community practices in resource documentation and knowledge management are overviewed. Furthermore, requirements and improvements sought by the PPME communities to current documentation practices are discussed. The RICORDO plan and effort in creating a representational framework and associated open software toolkit for the automated management of PPME metadata resources is also described.

Conclusions

RICORDO is providing the PPME community with tools to effect, share and reason over clinical resource annotations. This work is contributing to the semantic interoperability of DMRs through ontology-based annotation by (i) supporting more effective navigation and re-use of clinical DMRs, as well as (ii) sustaining interoperability operations based on the criterion of biological similarity. Operations facilitated by RICORDO will range from automated dataset matching to model merging and managing complex simulation workflows. In effect, RICORDO is contributing to community standards for resource sharing and interoperability.