Modelling complex and partially identified engineering problems- Application to the individualised multiscale simulation of the musculoskeletal system

Lead Research Organisation: University of Sheffield
Department Name: Chemical & Biological Engineering

Abstract

Traditionally, engineering design relies on scale separation. Virtually every physical process involves complex interactions across several space-time scales. For most engineering problems it is assumed that processes at different scales can be represented at the larger scale through some averaged property. However, when such assumptions of scale separation cannot be made, as in the modelling of biological systems where scales overlap, the inherent complexity of multi-scale interaction cannot be avoided. This proposal focuses on the establishment of a currently non-existent but essential computational platform for the treatment of musculoskeletal disorders. A multi-scale process in human physiology can be modelled as a collection of single scale models acting on a specific level of biological organisation coupled together across scales using appropriate scale bridging methods. Several unresolved challenges in the biomedical field have inhibited the development of predictive models needed in personalised medicine including (i) How to link mixed multiphysics models across several space-time scales. (ii) How to replace unobservable (possibly invasive and hence expensive) variables and states using proxy measurements (non invasive) reconstructed from the observable variables. (iii) How to use population data across patient classes or animal proxies to accommodate missing data. (iv) How to model uncertainty and the propagation of this across the simulations. (v) How to achieve these objectives within a framework that can be mapped to other engineering problems.
This proposal will tackle each of these challenges with:
- the development of a multi-scale model of the musculoskeletal system that describes the mechanobiological processes from the whole body (neuromuscular control and body dynamics) down to the cellular level (bone remodelling and mechanosensing);
- the creation of a multi-scale model from a partially identified input obtained by fusing a generic atlas of the anatomy, physiology, biology, and biomechanics for each individual.
This framework will be integrated in an efficient hypermodelling approach, numerically optimised at each scale level. Once fully realised, such a multi-scale framework will enable (i) deployment of specialised implementations as decision-support systems for diagnosis, prognosis, and treatment planning and monitoring for specific skeletal diseases such as lower back pain, osteoporosis, bone tumours and secondary metastases and osteoarthritis; (ii) implementation of in silico clinical trials for new orthopaedic and tissue engineering implants, modelling the variability of populations, providing a more accurate pre-clinical assessment for musculoskeletal devices and predicting the clinical outcome of these new devices; (iii) optimised interventions with respect to high socioeconomic impact conditions such as obesity, ageing population, disabilities, and chronic diseases in relation to physical activity, and assistive and rehabilitative technologies for neuromuscular deficits.

Planned Impact

The underlying modelling framework, developed to address multi-scale modelling with unobservable states and uncertainty, is increasingly required for nationally important research disciplines and societal problems such as: healthcare, environmental engineering, energy networks and advanced manufacturing. The focus on the musculoskeletal system addresses the economic burden of musculoskeletal diseases, which according to the WHO is 1%-2.5% of GDP of western nations, i.e. £30 billion p.a. in UK. The need for such a platform is essential considering that total healthcare expenditure in the UK has doubled from 2000-2010 to a staggering 10% of GDP. During this period about half of the annual cost increase has been attributed to the use of new technologies or the intensified use of old ones, such as the increased use of CT scans. To control the spiralling cost, models are required so that patient specific diagnosis and treatment procedures can be pre-assessed to predict the benefits, quality of life, and costs and hence aid decision making in each case. As well as the economic cost, musculoskeletal disorders cause poor quality-of-life, notably pain.
In addition to overcoming the above burden, the UK has industrial strength in the supply of orthopaedic devices, including the world's largest supplier outside the USA, namely Smith & Nephew, and innovative SMEs such as JRI Orthopaedics (each of whom are Partners of Frontier Multi-Scale). The modelling capabilities and the supply of skilled engineers enable their economic growth and anchors their presence in the UK.

Once fully realised, such a multi-scale framework will enable (i) deployment of specialised implementations as decision-support systems for diagnosis, prognosis, and treatment planning and monitoring for specific skeletal diseases such as lower back pain, osteoporosis, bone tumours and secondary metastases and osteoarthritis; (ii) implementation of in silico clinical trials for new orthopaedic and tissue engineering implants, modelling the variability of populations, providing a more accurate pre-clinical assessment for musculoskeletal devices and predicting the clinical outcome of these new devices; (iii) optimised interventions with respect to high socioeconomic impact conditions such as obesity, ageing population, disabilities, and chronic diseases in relation to physical activity, and assistive and rehabilitative technologies for neuromuscular deficits.

Publications

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Angelini L (2021) A Multifactorial Model of Multiple Sclerosis Gait and Its Changes Across Different Disability Levels. in IEEE transactions on bio-medical engineering

 
Description We are developing a new healthcare technology that can account for the fact that biological tissues span a number of scales in terms of space and time. For example, the human body will respond to its environment by adapting to it and reducing (e.g. astronauts) or increasing (e.g. athletes) its bone mass. This process involves molecular, cell, tissue response over a time scale that differs for each space scale. In this grant, we are developing a framework that can simulate tissue adaptation for a number of cases. For example, we are now able to predict the risk of femoral bone fracture in osteoporotic patients with more accuracy than conventional clinical practice. We have developed a novel computational and experimental approach to test the effect of a new drug or medical device on bone response in a in vivo mouse pre-clinical testing context.
Exploitation Route We have developed a number of online services available through a web portal to any clinician or researcher. For example, we have developed the CT2S service which enables to predict the risk of bone fracture in a patient-specific manner for osteoporotic patient once the user uploads CT data from the patient.
We are also developing an online service based on High Resolution peripheral Quantitative Computed Tomography (HRpQCT) to calculate the bone stiffness and regions of bone weakening. We have now also completed the definition of a methodology for combining medical images and gait analysis data, which allows us to understand how much force each muscle is producing to allow a person to walk. This has been fully described in a published paper and a step-by-step guide has been shared on FigShare, together with relevant datasets to allow other researchers to replicate our results. We have also launched a new type of event called 'Modelathon' in which PhD students and Research Associates can participate during 3 days to solve a multiscale problem defined by our team. This enables the participants to get acquainted to multiscale modelling and develop further technologies later on for their own challenges.
Sectors Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology

URL https://www.sheffield.ac.uk/multisim-insigneo
 
Description Public Outreach: We have disseminated our gait biomechanics research and multiscale modelling capability to the public through the Sheffield Science Festival in 2017. During 4 sessions of 1 hour each a lay audience mixed of adults and children were able to understand how research in bone biomechanics can improve the diagnostics and treatment of diseases in elderly people. The outputs of the MultiSim project (EP/K03877X/1) were taken forward with the Progression Award MultiSim2 (EP/S032940/1). The following statement covers the impact of the combined projects. Webservices: We have developed a number of online services available through a web portal to any clinician or researcher. For example: 1) We have developed the CT2S service which enables to predict the risk of bone fracture in a patient-specific manner for osteoporotic patient once the user uploads CT data from the patient. This service is open to any clinician or company and we are currently in discussion with some for its use. 2) We have developed the BoneDVC web-application has been used by other groups including the University of Bologna (Italy), Vienna University of Technology (Austria), Western University Canada (Canada), and Flinders University Adelaide (Australia). Clinical Workflow: Musculoskeletal models to aid in clinical decision-making in children with Cerebral Palsy The use of musculoskeletal models in clinical settings is limited although they have shown potential for augmenting evidence for surgical intervention decisions. By showing that our musculoskeletal modelling approach can perform at par with the current method used to quantify outcomes after surgery [1], we are together with partners at the Sheffield Children's Hospital Gait Laboratory looking into using these models to identify biomarkers for predicting outcomes after surgery [2]. Based on this information, surgeons can identify and select candidates for surgery who would most likely benefit from the intervention. References [1] C. F. Hayford, E. Pratt, J. P. Cashman, O. G. Evans, and C. Mazzà, "Effectiveness of Global Optimisation and Direct Kinematics in Predicting Surgical Outcome in Children with Cerebral Palsy," Life, vol. 11, no. 12, p. 1306, 2021. [Online]. Available: https://www.mdpi.com/2075-1729/11/12/1306. [2] C. F. Hayford, E. Pratt, J. P. Cashman, O. G. Evans, and C. Mazzà, "Role of Pre-surgery Muscle-tendon lengths on the outcome of Femoral Derotation Osteotomy". In preparation.
First Year Of Impact 2022
Sector Digital/Communication/Information Technologies (including Software),Healthcare,Pharmaceuticals and Medical Biotechnology
Impact Types Societal

 
Description BBSRC Research Grant (Dall Ara)
Amount £261,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 01/2018 
End 12/2019
 
Description Biomedical Research Centre Competition
Amount £4,049,681 (GBP)
Organisation University of Leicester 
Department NIHR Biomedical Research Centre
Sector Hospitals
Country United Kingdom
Start 03/2017 
End 05/2027
 
Description Dassault Systems La Foundation Grant
Amount £85,000 (GBP)
Organisation La Fondation Dassault Systèmes 
Sector Charity/Non Profit
Country France
Start 09/2016 
End 09/2017
 
Description First Grant Scheme (Dall Ara)
Amount £100,578 (GBP)
Funding ID EP/P015778/1 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 10/2018
 
Description H2020 Research Grant - CompBioMed
Amount € 4,938,215 (EUR)
Funding ID 675451 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 09/2016 
End 09/2019
 
Description H2020-WIDESPREAD-04-2017-TeamingPhase1
Amount € 399,963 (EUR)
Funding ID 763734 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 08/2017 
End 08/2018
 
Description Insigneo Bursary for Clinical Translation
Amount £7,720 (GBP)
Organisation Sheffield Hospitals Charity 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2014 
End 12/2014
 
Description MSCA-ITN-EID - European Industrial Doctorates
Amount € 1,588,449 (EUR)
Funding ID 766012 
Organisation European Commission H2020 
Sector Public
Country Belgium
Start 01/2018 
End 12/2021
 
Description NC3Rs Research Grant (Dall Ara)
Amount £357,401 (GBP)
Funding ID NC/R001073/1 
Organisation National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs) 
Sector Charity/Non Profit
Country United Kingdom
Start 12/2017 
End 08/2020
 
Description Network on Computational Statistics and Machine Learning (NCSML)
Amount £1,000 (GBP)
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 08/2014 
End 09/2016
 
Description Newton Mobility Grants
Amount £3,000 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 07/2017 
End 11/2017
 
Description Research grants
Amount £16,615 (GBP)
Organisation Sheffield Hospitals Charity 
Sector Charity/Non Profit
Country United Kingdom
Start 04/2016 
End 10/2016
 
Description Research grants
Amount £9,896 (GBP)
Organisation White Rose University Consortium 
Sector Academic/University
Country United Kingdom
Start 03/2015 
End 03/2016
 
Description Research grants
Amount £15,000 (GBP)
Organisation The Royal Society 
Sector Charity/Non Profit
Country United Kingdom
Start 08/2015 
End 08/2016
 
Description Research grants
Amount £8,058 (GBP)
Organisation Sheffield Hospitals Charity 
Sector Charity/Non Profit
Country United Kingdom
Start 11/2013 
End 04/2014
 
Title BoneDVC: Digital Volume Correlation (DVC) 
Description BoneDVC: this is services for biomechanics research. It exposes as an on-line service the Digital Volume Correlation (DVC) algorithm described here (Dall'Ara E et al., 2014). This tool allows researchers who have multiple microCT taken to a specimen of bone tissue in its unloaded and loaded configurations to compute with high accuracy the displacement field induced by such compression, which once differentiated provides a full-field quantification of the mechanical strains at the tissue spatial resolution. 
Type Of Material Computer model/algorithm 
Year Produced 2020 
Provided To Others? Yes  
Impact the BoneDVC web-application has been used by other groups but in academic collaboration, including: -) University of Bologna for biomechanics of bone with metastases (pending publications) -) Vienna University of Technology for validating nonlinear microFE models of trabecular bone (pending publications) -) Western University Canada for assessment of biomechanics of humerus and scapula (5 publications) -) Flinders University Adelaide for fracture behaviour of proximal femur (1 publication) 
URL https://bonedvc.insigneo.org/dvc/
 
Title CT2S: Stochastic Finite element Analysis of subject-specific model generated from CT data 
Description CT2S: Stochastic Finite element Analysis of subject-specific model generated from CT data, to predict the femoral strength under side-fall conditions. The minimum side-fall strength was found to be an excellent predictor of the risk of hip fracture in fragile elders, significantly better than the current standard of care. For a recent review of this and other clinical services please see (Viceconti M et al., 2018). 
Type Of Material Computer model/algorithm 
Year Produced 2020 
Provided To Others? Yes  
Impact Service available to research community. We are at early preliminary stage interactions with two clinicians. We think our pipeline can help answer some of their questions, but no work has been done yet. 1. Dr Craig Jones from the STAMPEDE project, who is looking to use our pipeline to investigate bone mineral density (potential bone strength) changes in the cohort of patients they collected undergoing prostate cancer treatment. He is particularly interested in the phantomless calibration techniques. 2. Dr Shankar Thiagarajah from Doncaster, who is interested in using the pipeline to address challenges with hip dysplasia treatment in children and young adults. 
URL https://ct2s.insigneo.org/ct2s/
 
Title Code used in the study "A new method to monitor bone geometry changes at different spatial scales in the longitudinal in vivo µCT studies of mice bones" 
Description Link to the code used in: Yang Z, Dall'Ara E, Viceconti M, Kadirkamanathan V (2019) An approach to split bone growth and remodelling from longitudinal in vivo microCT imaging of the mouse tibia; Plos One 2019. The folder includes the codes used to process the images. A "readme.docx" file is added to describe how to run the analyses. The whole dataset is stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP6/YangZhang For further information please contact Dr Enrico Dall'Ara: e.dallara@sheffield.ac.uk 
Type Of Material Computer model/algorithm 
Year Produced 2019 
Provided To Others? Yes  
Impact Code available to research community 
URL https://doi.org/10.15131/shef.data.8397989
 
Title Data for "Changes in cell mechanical properties at different stages of bone cell differentiation" 
Description Pre-processed data obtained by AFM nano-indentation of MC3T3 pre-osteoblast cells, MLO-A5 pre-osteocyte cells, IDG-SW3 osteoblast/osteocyte cells. The data pre-processing consisted in contact point fitting, tip-sample separation correction and drift correction of raw data, all performed in MATLAB (v2016a). The experimental methodology and data processing are described in the author's thesis (Chapter 5). Methods * AFM cantilever preparation Tip-less cantilevers (Windsor Scientific) with nominal spring constant of 0.2 N/m were customised by glueing a silica bead (D = 6 µm, Bangs Laboratories) at the tip extremity. * AFM set-up A NanoWizard 3 atomic force microscope (JPK Instruments AG) coupled to an Eclipse Ti-S optical inverted microscope (Nikon Instruments) was used for all the experiments. The cells were washed in phosphate buffer solution (PBS) and fresh medium was added. Samples were positioned on the heated sample holder to allow for testing at 37?C. Single cells were located through the coupled optical microscope and images of cell shape were recorded for morphological analysis. The cantilever was centred over the location of interest and a grid of 5 points spaced 3 µm within each other was set. Force spectroscopy measurements were obtained on the 5-point grid for 3 times to collect a total of 15 data on each location. The relative set point and the approach velocity were set to 10 nN and 4 µm/s respectively. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Dataset available to research community 
URL https://doi.org/10.15131/shef.data.5632777.v1
 
Title Data for "Heterogeneity in The Mechanical Properties of Integrins Determines Mechanotransduction Dynamics in Bone Osteoblasts" 
Description Data for: Shuaib, A., Motan, D., Bhattacharya, P., McNabb, A., Skerry, T. M., Lacroix, D. (2019), "Heterogeneity in The Mechanical Properties of Integrins Determines Mechanotransduction Dynamics in Bone Osteoblasts", Scientific Reports, 9, Article number: 13113, URL: https://doi.org/10.1038/s41598-019-47958-z This includes: Heterogeneity in The Mechanical Properties of Integrins: Mech-ABM Codes and Algorithm The file contains the codes and algorithms for the Mech-ABM. These include the descriptions of the algorithm to execute the mechanical model (Mech-), which deals with the biomechanics of the bone tissue; and the agent-based model (-ABM) which simulates the intercellular events of mechanotransduction after the activation of integrins (the predominant mechanoreceptors). The mechanical model is the .cpp with its application compute. The ABM files are file transition function code (.c), the agent-memory parameters (.xml) and 0.xml which include the initial state at t0. 0.xml include those for the homogeneous sensitive and ultrasensitive models and the heterogeneous models (10%-HM and 1%-HM). The files necessary for coupling the Mech- and the ABM models were included in the file "Essential Files to run hybrid model" Heterogeneity in The Mechanical Properties of Integrins: essential files to run hybrid Mech-ABM Files and description of coupling the tissue scale mechanical model with the ABM Files and description of coupling the tissue scale mechanical model with the ABM This folder includes figures illustrating the rules implemented in a hybrid multiscale model (Mech-ABM) which simulates mechanotransduction and mechanobiology of an osteoblast. These figures shows the state-transitions of every agent in the agent-based model (ABM) and a diagram demonstrating the interaction between the ABM and a mathematical model Heterogeneity in The Mechanical Properties of Integrins: Mech-ABM figures Additional supplementary figures which were not included within the manuscript or the supplementary materials of the manuscript Mech-ABM Raw and Processed Data This file includes the primary data generated from the Mech-ABM which was mostly used in the paper titled "Heterogeneity in The Mechanical Properties of Integrins Determines Mechanotransduction Dynamics in Bone Osteoblasts". These include data in the following formats: CSV XML .PZFX (summaries of the raw data and processed data) As the full Mech-ABM generates a high magnitude of data (in terabytes), thus only samples have been uploaded. For additional raw data contact the authors of the published paper 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://figshare.shef.ac.uk/projects/Heterogeneity_in_The_Mechanical_Properties_of_Integrins/67427
 
Title Data for "Personalised 3D knee compliance from clinically viable knee laxity measurements: A proof of concept ex vivo experiment" 
Description Data pertaining to: Lamberto, G., Amin, D., Solomon, B., Reynolds, K., Mazzà, C., Martelli, S. (In Submission), "Personalized 3D knee compliance from clinically viable knee laxity measurements: a proof of ex vivo experiment", Medical Engineering & Physics 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Data available to research community 
URL https://doi.org/10.15131/shef.data.7442645.v1
 
Title Data for "Single molecule force spectroscopy of Hyaluronic Acid" 
Description Pre-processed data obtained by AFM single molecule force spectroscopy on MC3T3 pre-osteoblast cells targeting hyaluronic acid. The data pre-processing consisted in contact point fitting, tip-sample separation correction and drift correction of raw data, all performed in MATLAB (v2016a). The experimental methodology and data processing are described in the author's thesis (Chapter 6). The thesis has been deposited in White Rose eTheses Online (see link in References). Methods * Samples Hyaluronic Acid Binding Protein (HABP) was used to specifically bind Hyaluronic Acid (HA) on the cell surface. Four different samples were employed for experiments, designed as follows: 1. HABP/HA: cantilever functionalised with HABP, untreated cell sample; 2. BSA/HA: cantilever functionalised with bovine serum albumin (BSA), untreated cell sample; 3. untreated/HA: non functionalised cantilever, untreated cell sample; 4. HABP/HAase: cantilever functionalised with HABP, cell sample treated with hyaluronidase (HAase). * Cantilever functionalisation Low spring constant cantilevers with pyramidal tip (Olympus) were used for all the experiments (nominal spring constant 0:02 N=m, tip radius 15 nm). The steps of cantilever functionalisation are listed below and were the same for Sample 1 (HABP/HA, functionalisation molecule: HABP), Sample 2 (BSA/HA, functionalisation molecule: BSA) and Sample 4 (HABP/HAase, functionalisation molecule: HABP). The cantilevers used to test cells in Sample 3 (untreated/HA) were not treated, but washed in ultra-pure water prior to experiments. The following activation steps were performed just before the experiments: • deposition of (-SH) groups: cantilevers were oxidised using an ozone cleaner and submerged in 2% (3-Aminopropyl)triethoxysilane (APTES)/ultra-pure water for 15 minutes to depose (-SH) groups on the probe surface; • attachment of intermediate linker molecules: after washing, the cantilevers were submerged in 6 mM Maleimide-PEG-NHS ester/Tris for 30 minutes. This compound bound to the (-SH) groups and exposed NHS esters for subsequent binding to the carboxyl groups of the functionalisation molecules; • functionalisation: after washing, the functionalisation molecule was bound to the exposed NHS ester groups by submerging the cantilever in 100 nM HABP/Tris solution (Sample 1 HABP/HA and Sample 4 HABP/HAase) or 1% BSA/ultra-pure water (Sample 2 BSA/HA) for 1 hour; • blocking: the excess maleimide was quenched with 50 mM 2-mercaptoethanol/ ultra-pure water by submerging the cantilevers for 1 minute; • washing: after a final washing, the functionalised cantilevers were kept submerged in ultra-pure water until mounting on the AFM holder. * AFM set-up A NanoWizard 3 Atomic Force Microscope (JPK Instruments AG) coupled to a IX series optical inverted microscope (Olympus) enclosed in a metal box to reduce environmental noise was used for all the experiments. Cells were located through the optical microscope and tested within an area of 10 x 10 µm2. A 16-point grid was drawn and force spectroscopy measurements were obtained on the grid for 3 times to collect a total of 48 data on each cell. The relative set point and the approach velocity were set to 0.5 nN and 2 µm/s respectively. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Dataset available for research community 
URL https://doi.org/10.15131/shef.data.5632783.v1
 
Title Data for MicroCT-based MicroFE of human vertebrae 
Description This file contains the results collected in the study: "Effect of size and location of simulated lytic lesions on the structural properties of human vertebral bodies, a micro-finite element study" by "M.C. Costa, L.B. Bresani Campello, M. Ryan, J. Rochester, M. Viceconti, E. Dall'Ara" published in Bone Reports: https://doi.org/10.1016/j.bonr.2020.100257. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Dataset available for research community. 
URL https://doi.org/10.15131/shef.data.11958954.v1
 
Title Data for Revealing hidden information in osteoblast's mechanotransduction through analysis of time patterns of critical events 
Description Data for the paper: Ascolani, G., Skerry, T. M., Lacroix, D., Dal'Ara, E., Shuaib, A. (2020), "Revealing hidden information in osteoblast's mechanotransduction through analysis of time patterns of critical events", BMC Bioinformatics, 21 (114), URL: https://doi.org/10.1186/s12859-020-3394-0 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Dataset and code available to research community 
URL https://drive.google.com/drive/folders/1Q0HFuvmv6NTxpBXfKQerR93I-4_t9LAu?usp=sharing
 
Title Data for Tagliapietra, L., Modenese, L., Reggiani, M., Ceseracciu, E., Mazzà, C., Validation of a model-based inverse kinematics approach based on wearable inertial sensors Computer Methods in Biomechanics and Biomedical Engineering 
Description Data for Tagliapietra, L., Modenese, L., Reggiani, M., Ceseracciu, E., Mazzà, C., Validation of a model-based inverse kinematics approach based on wearable inertial sensors Computer Methods in Biomechanics and Biomedical Engineering https://doi.org/10.1080/10255842.2018.1522532 This dataset contains all the results presented in the linked paper. Data are organized as follow: - Framework_01 - out_data - ob-ik: contains the joint angles (in degrees) estimated from the orientation based inverse kinematics using the imu's orientations - robot: contains the joint angles recorded from the robot encorders, thus they can be considered the ground of truth - Framework_02 - out_data - ob-ik: contains the joint angles (in degrees) estimated from the orientation based inverse kinematics using the imu's orientations - mb-ik: contains the joint angles (in degrees) estimated from the marker based inverse kinematics, the gold-standard in human motion analysis. Therefore, they are used as reference values. - Framework_03 : same as Framework 02. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset is available for the research community. 
URL https://doi.org/10.15131/shef.data.7097744.v1
 
Title Data for manuscript titled "A systematic approach to the scale separation problem in the development of multiscale models" 
Description The following files are included: Patient60y.vtk, an anonymised data file (in VTK unstructured grid format) for a proximal femur, which is used as input to the multiscale model illustrated in §2.3 of the main manuscript The proximal femur data corresponds to a subject aged 60 years at the time of clinical presentationThe data file contains the proximal femur geometry, discretised using tetrahedral elements possessing heterogeneous element-wise volumetric bone mineral density (vBMD)Units for the fields in the data file are given in the Readme.txt file Figs1and4.pvsm, a state file in the open-source viewer Paraview format. It contains the image manipulations needed to convert the data in Patient60y.vtk to that in Fig 1 of the main manuscriptIt also contains the code to convert the vBMD data to that corresponding to age 70 y, as shown in Fig 4 of the main manuscriptThis dataset contains data in only processed and anonymised form. It is derived from an original dataset that was collected under the project UK MRC grant G0601272. Ethics approval was obtained for this project from the relevant local ethics committee in Sheffield. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Dataset made available for research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_manuscript_titled_A_systematic_approach_to_the...
 
Title Data for manuscript titled "A systematic approach to the scale separation problem in the development of multiscale models" 
Description The following files are included: Patient60y.vtk, an anonymised data file (in VTK unstructured grid format) for a proximal femur, which is used as input to the multiscale model illustrated in §2.3 of the main manuscript The proximal femur data corresponds to a subject aged 60 years at the time of clinical presentationThe data file contains the proximal femur geometry, discretised using tetrahedral elements possessing heterogeneous element-wise volumetric bone mineral density (vBMD)Units for the fields in the data file are given in the Readme.txt file Figs1and4.pvsm, a state file in the open-source viewer Paraview format. It contains the image manipulations needed to convert the data in Patient60y.vtk to that in Fig 1 of the main manuscriptIt also contains the code to convert the vBMD data to that corresponding to age 70 y, as shown in Fig 4 of the main manuscriptThis dataset contains data in only processed and anonymised form. It is derived from an original dataset that was collected under the project UK MRC grant G0601272. Ethics approval was obtained for this project from the relevant local ethics committee in Sheffield. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Dataset made available to the research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_manuscript_titled_A_systematic_approach_to_the...
 
Title Data for manuscript titled "Personalised 3D assessment of trochanteric soft tissues improves hip fracture classification accuracy" 
Description This dataset contain the three-dimensional characterisation of soft tissue thickness (STT) in the near hip region. The data is for 94 British postmenopausal subjects. Of these subjects, 47 had suffered a hip fracture, and the remaining 47 were age, height and weight matched controls. STT was measured from proximal femur CT images, and is defined as the distance between the femur surface and the skin layer along a specific fall impact direction with origin at the femur head centre. For each subject, STT was measured along 33 impact orientations.For more information, see the preprint of the manuscript at: https://doi.org/10.17605/OSF.IO/DZMKHThe dataset is presented in Microsoft Excel format, named STTdata.xlsx. Columns in the table refer to an individual subject, and rows contains the following data fields:- patients label- fracture status- BMI (in kg/m2)- soft-tissue thickness (in mm) as estimated using BMI at the point of the greater trochanter- soft-tissue thickness as measured using CT for the various impact orientations considered in the manuscriptA README.txt file is also provided and contains the above information. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Dataset shared with research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_manuscript_titled_Personalised_3D_assessment_o...
 
Title Data for paper "A novel approach to evaluate the effects of artificial bone focal lesion on the threedimensional strain distributions within the vertebral body" 
Description Data used in the paper : "A novel approach to evaluate the effects of artificial bone focal lesion on the threedimensionalstrain distributions within the vertebral body"byMarco Palanca, Giulia de Donno, Enrico Dall'Araaccepted for publication in PlosOne, 2021.We share here an example of microCT images collected for porcine vertebrae in the undeformed and deformed state, before and after having induced a mechanical lesion in the anterior side of the bone:Specimen1_Intact_Scan1_unloaded_4241.dcmSpecimen1_Intact_Scan2_loaded_4245.dcmSpecimen1_Lesion_Scan1_unloaded_4369.dcmSpecimen1_Lesion_Scan2_loaded_4370.dcmThe images are used to run Digital Volume Correlation with BoneDVC (https://bonedvc.insigneo.org/dvc/). Example of results from the DVC are reported in:DVC_Intact_results_xyz.txtDVC_Intact_output_map_xyz.txtDVC_Lesion_results_xyz.txtDVC_Lesion_output_map_xyz.txtIn each DVC folder the following data are reported:_output_map.txt (displacement components)_results_xyz.txt (strain components)The whole dataset is stored at:https://web-unidrive.sheffield.ac.uk/shared/bone_biomechanics1/Projects/19_METASPINE_EU_ED/In case the reader is interested in the whole database they should contact Dr Enrico Dall'Ara (e.dallara@sheffield.ac.uk) and/or Dr Marco Palanca (m.palanca@sheffield.ac.uk). 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Dataset available for research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_paper_A_novel_approach_to_evaluate_the_effects...
 
Title Data for paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis" 
Description This deposit contains data for reproducing the results reported in the paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis". The folder "Repeatability Study" contains two sub folders: 1. "Fitting3x3" with data relative to three subjects (P1,P2,P3). For each subject, the foot bone geometries are in "Geometries", the surfaces used for fitting and the output of fitting are in "Fitting results", where nine repetitions are available (3x3operators). 2. "RepeatabilityKinematicsP3" containing "Inputdata" for the subject with worst repeatability results with c3d and trc files for a standing and a walking trial; "OpemsimModels3x3" with nine repetitions (3x3operators) of the opensim model of that subject. The folder "Models for analysis" contains forty sub folders, relative to the two limbs of the twenty enrolled subjects. Each folder contains the opensim model of the foot and ankle and a sub folder with the full lower limb model, geometries, trc data, and results of IK simulations in opernsim. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset available to research community 
URL https://doi.org/10.15131/shef.data.5863443
 
Title Data for paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis" 
Description This deposit contains data for reproducing the results reported in the paper "An image-based kinematic model of the tibiotalar and subtalar joints and its application to gait analysis in children with Juvenile Idiopathic Arthritis".The folder "Repeatability Study" contains two sub folders:1. "Fitting3x3" with data relative to three subjects (P1,P2,P3). For each subject, the foot bone geometries are in "Geometries", the surfaces used for fitting and the output of fitting are in "Fitting results", where nine repetitions are available (3x3operators).2. "RepeatabilityKinematicsP3" containing "Inputdata" for the subject with worst repeatability results with c3d and trc files for a standing and a walking trial; "OpemsimModels3x3" with nine repetitions (3x3operators) of the opensim model of that subject.The folder "Models for analysis" contains forty sub folders, relative to the two limbs of the twenty enrolled subjects. Each folder contains the opensim model of the foot and ankle and a sub folder with the full lower limb model, geometries, trc data, and results of IK simulations in opernsim. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset made available to research community. 
URL https://figshare.shef.ac.uk/articles/Data_for_paper_An_image-based_kinematic_model_of_the_tibiotalar...
 
Title Data for paper "Free-living and laboratory gait characteristics in patients with multiple sclerosis" 
Description This space has been created to support the paper "Free-living and laboratory gait characteristics in patients with multiple sclerosis", where all the information about the data collection can be recovered. (Paper doi: https://doi.org/10.1371/journal.pone.0196463) The .xlsx file includes information about the participants. The .csv file contains the participant's mean and SD values for each investigated gait parameter. 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact This dataset has been made open access (CC BY 4.0) to the research community. 
URL https://doi.org/10.15131/shef.data.5478460
 
Title Data for paper "Investigation of the dependence of joint contact forces on musculotendon parameters using a codified workflow for image-based modelling" 
Description This folder contains data and material used in the paper "Investigation of the dependence of joint contact forces on musculotendon parameters using a codified workflow for image-based modelling".A complementary figshare is available with Matlab code. The content of this figshare is:1. PDF document with guidelines: "Step-by-step_modelling_guide.pdf" contains step-by-step operations for building subject-specific anatomical model of the lower-limb from gait data and MR Images.2. Modelling_materiala. Modelling Folder Structure: this folder structure helps in the organisation of the modelling data and files and is required to correctly use the Matlab scripts. Reference to the structure and how to populate it can be find in in the "Step-by-step_modelling_guide.pdf".b. NMSBuilder model structure template: this template is used in NMSBuilder to build the subject-specific anatomical model of the lower-limb according to the pipeline described in "Step-by-step_modelling_guide.pdf".c. NMSBuilder dictionaries: these dictionaries can be imported in NMSBuilder to perform virtual palpation of anatomical landmarks and visible gait markers. A description of the anatomical landmarks is also available as excel file.d. Muscle attachments atlas: this in contained in the folder "NMSBuilder_gait2392_muscle_attachments (mm)" where muscle attachments and their 3d coordinates (derived from the Opensim model gait2392) are listed within the respective body segment as txt files.3. Simulations results (see README.txt): this folder contains the results published in the paper. It is organised in subfolders depending on the different approach to calculate musculotendon parameters, with the same identifiers as in the paper. For each approach, twenty-two folders contain each patient's OpenSim model (vtp files for geometries are not included due to sharing policies) and a Mat_summary with the results of the dynamic simulations run in OpenSim (as .mat files). 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Sharing of data to the research community. 
URL https://figshare.shef.ac.uk/articles/Data_for_paper_Investigation_of_the_dependence_of_joint_contact...
 
Title Data for paper "Is a wearable sensor based characterisation of gait robust enough to overcome differences between measurement protocols? A multi-centric pragmatic study in patients with Multiple Sclerosis" 
Description This repository has been created to support the paper "Is a wearable sensor based characterisation of gait robust enough to overcome differences between measurement protocols? A multi-centric pragmatic study in patients with Multiple Sclerosis". The excel file includes both demographic and clinical information of each participant (1st worksheet) and the gait outcomes extracted from the wearable sensors for each participant (mean and SD values, 2nd worksheet). For details email l.angelini@sheffield.ac.uk 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Dataset available to research community 
URL https://doi.org/10.15131/shef.data.11395641.v1
 
Title Data for paper "Linking joint impairment and gait biomechanics in patients with Juvenile Idiopathic Arthritis" 
Description This Figshare contains the data used to produce the results reported in the paper "Linking joint impairment and gait biomechanics in patients with Juvenile Idiopathic Arthritis". The folder "Data analysis" contains: 1. the folder "ExampeModel" with the single-limb OpenSim models (left and right) for a representative subject. 2. the folders "IK", "ID", "JP", "SO", and "JCF" contain the kinematic and kinetic data (as .mat files) for all the subjects in the BI (bilateral), MI (monolateral), and (NI) non-impaired groups, used for the time-dependent statistical analysis. 3. the "Parameters for analysis" file including the final values used for the statistical analysis. The folder "Repeatability" contains: 1. the file "Joint_cent_Orient" including the intra- and inter-operator repetitions in the identification of the joint locations and orientations for the datasets (P1, P2, P3). 2. the file "Mus_points" including the intra- and inter-operator repetitions in the identification of the muscle coordinates for the datasets (P1, P2, P3). 3. the folders "Intra" and "Inter" contain the kinematic and kinetic data used for the repeatability analysis. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset available to the research community 
URL https://doi.org/10.15131/shef.data.6237146
 
Title Data for paper "MRI-based anatomical characterisation of lower-limb muscles in older women" 
Description This Figshare contains:1. additional material.docx, including supplementary information associated with the paper "MRI-based anatomical characterisation of lower-limb muscles in older women";2. Segmentations for the eleven subjects in the study labelled as MC17, MC18, MC19, MC20, MC22, MC24, MC25, MC26, MC27, MC28, MC29 (corresponding to Subject 1 to 11, respectively, see additional material for details):a. bone and soft tissue (skin) segmentations as stl files;b. muscle segmentations as stl files;3. Muscle centrelines as vtk files. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_paper_MRI-based_anatomical_characterisation_of...
 
Title Data for paper "Modeling Musculoskeletal Dynamics During Gait: Evaluating the Best Personalization Strategy Through Model Anatomical Consistency" 
Description This repository contains the data and models used to generate the results reported in the paper "Modeling Musculoskeletal Dynamics During Gait: Evaluating the Best Personalization Strategy Through Model Anatomical Consistency".Ethical approval for the studies was obtained from the local ethical comittees.The 'Data_for_paper' folder contains 10 folders, one for each participant of the study (Subject1, ..., Subject10). Please, note that for some participants bi-lateral data are available, while for others only one body side was collected. Body sides are denoted by "_R/L" in the name of folders and models.Within each of these folders, two sets of models are available: Model1 contains the models generated under the scenario referred to as M1 in the paper; Model2 contains the models where ligament and cartilage forces were accounted for while simulating gait. Input data are available as well in folders "Data_L/R".A .doc file containing all the additional results mentioned in the paper is made available as well. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Data made available for research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_paper_Modeling_Musculoskeletal_Dynamics_During...
 
Title Data for paper: A multiscale model to predict current absolute risk of femoral fracture in a postmenopausal population 
Description Complete results set of the study reported in "A multiscale model to predict current absolute risk of femoral fracture in a postmenopausal population" by Pinaki Bhattacharya, Zainab Altai, Muhammad Qasim, and Marco Viceconti (preprint: https://doi.org/10.17605/OSF.IO/549UM) 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Recently published, too soon to say. 
URL https://doi.org/10.15131/shef.data.5882554
 
Title Data for paper: An objective functional characterisation of head movement impairment in individuals with neck muscle weakness due to Amyotrophic lateral sclerosis 
Description Please refer to the Readme.docx file for information about the dataset. These data were collected for a research project entitled "An objective functional characterisation of head movement impairment in individuals with neck muscle weakness due to Amyotrophic lateral sclerosis" published in PLOS ONE https://doi.org/10.1371/journal.pone.0169019. Methods involved in generating the data are described in the paper. Data are also included in the PhD thesis entitled "Assessing residual neck mobility when wearing a cervical orthosis: an application in patients with Motor Neurone Disease" which is available online through WREO http://etheses.whiterose.ac.uk/id/eprint/16179. REFERENCES https://doi.org/10.1371/journal.pone.0169019 http://eprints.whiterose.ac.uk/109783/ http://etheses.whiterose.ac.uk/id/eprint/16179 FUNDING EPSRC Frontier Engineering Awards, Grant Reference No. EP/K03877X/1 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: "An objective functional characterisation of head movement impairment in individuals with neck muscle weakness due to Amyotrophic lateral sclerosis" published in PLOS ONE https://doi.org/10.1371/journal.pone.0169019. 
URL https://doi.org/10.15131/shef.data.4476734
 
Title Data for paper: Extended discrete element method can evaluate the effect of time dependency and translation of the talus on the estimation of cartilage pressure at the ankle joint 
Description Data for paper "Extended discrete element method can evaluate the effect of time dependency and translation of the talus on the estimation of cartilage pressure at the ankle joint" 15.02.2018, 11:49 by Ivan Benemerito Luca Modenese Erica Montefiori Claudia Mazza Marco Viceconti Damien Lacroix Lingzhong Guo Input kinematics and ankle forces are included as MATLAB file. The Extended Discrete Element Method has been used to compute the ankle joint contact pressure distribution. For details email ibenemerito1@sheffield.ac.uk 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Recently published, too soon to report. 
URL https://doi.org/10.15131/shef.data.5829120
 
Title Data for paper: Sensitivity of a juvenile subject -specific musculoskeletal model of the ankle joint to the variability of operator dependent input 
Description MultiSim (Grant No. EP/K03877X/1) Data for paper 'Sensitivity of a juvenile subject -specific musculoskeletal model of the ankle joint to the variability of operator dependent input' 25.07.2017, 15:52 by Iain Hannah Erica Montefiori Luca Modenese Marco Viceconti Claudia Mazza These files represent the data used for the study reported in the paper: Hannah, I. et al. (2017) Sensitivity of a juvenile subject-specific musculoskeletal model of the ankle joint to the variability of operator dependent input. Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine. ISSN 0954-4119. https://doi.org/10.1177/0954411917701167 The Statistics folder contains the raw data for the inter- and intra-operator analysis, for each subject, for the three considered procedures: muscles attachments adjustment; virtual palpation, reference systesms definition. Three folders represent the subjects' data used for the simulations: Subject A, Subject B, Subject C. Inside each subject's folder there is a folder with the input data (static motion data), and the musculoskeletal simulations for each operator (i.e. Mod A.1 contains the simulations for subject A done by operator 1 ). Inside these folders there are the results for each simulated walking trial and the final OpenSim model of the subject, done by the respective operator. REFERENCES https://doi.org/10.1177/0954411917701167 http://multisim-insigneo.org/ FUNDING EPSRC: EP/K03877X/1 and EUROPEAN COMMISSION - FP6/FP7: MDPAEDIGREE - 600932 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: Hannah, I. et al. (2017) Sensitivity of a juvenile subject-specific musculoskeletal model of the ankle joint to the variability of operator dependent input. Proceedings of the Institution of Mechanical Engineers, Part H: Journal of Engineering in Medicine. ISSN 0954-4119. https://doi.org/10.1177/0954411917701167 
URL https://doi.org/10.15131/shef.data.4286519
 
Title Data for the article "Effectiveness of global optimisation and direct kinematics in predicting surgical outcome in children with cerebral palsy." 
Description This Figshare contains data for reproducing results reported in the paper titled "Effectiveness of Global Optimisation and Direct Kinematics in Predicting Surgical Outcome in Children with Cerebral Palsy".The folder contains:1. kinematic data for Cerebral Palsy (CP) and Typically Developing (TD) groups. Each file has data for both mGen and PiG kinematics2. pre and post-surgery ages for CP group for selecting appropriate age-matched control group.2. excel file with specification of limbs that received the FDO and the non-3D data judgement of outcome. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Dataset shared with research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_the_article_Effectiveness_of_global_optimisati...
 
Title Data for the article "Effectiveness of global optimisation and direct kinematics in predicting surgical outcome in children with cerebral palsy." 
Description This Figshare contains data for reproducing results reported in the paper titled "Effectiveness of Global Optimisation and Direct Kinematics in Predicting Surgical Outcome in Children with Cerebral Palsy".The folder contains:1. kinematic data for Cerebral Palsy (CP) and Typically Developing (TD) groups. Each file has data for both mGen and PiG kinematics2. pre and post-surgery ages for CP group for selecting appropriate age-matched control group.2. excel file with specification of limbs that received the FDO and the non-3D data judgement of outcome. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Dataset made available to research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_the_article_Effectiveness_of_global_optimisati...
 
Title Data for the assessment of the effect of repositioning in in vivo loading studies with Digital Volume Correlation 
Description Data for the assessment of the effect of repositioning in in vivo loading studies with Digital Volume Correlation Fileset modified on 10.09.2018, 10:59 by Enrico Dall'Ara Mario Giorgi Link to the data used in: Giorgi, M., Dall'Ara, E. (2018) Variability in strain distribution in the mice tibia loading model: preliminary study using digital volume correlation. Medical Engineering and Physics 2018 The images and data are too large to be uploaded in ORDA, so please contact e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if you are interested in working on the files. Only an example of a dataset has been uploaded. In the B-03-a folder the preloaded image (Scan1_crop.dcm) has been registered with three different files "Scan2_cop.dcm" that represent: 01_Scan2_preload_REGwith_Scan1_load: registration between the second preloaded image and the first loaded image 01_Scan2_preload_REGwith_Scan2: registration between the second preloaded image and the repeated image in the loaded configuration 01_Scan2_preload_REGwith_Repositioning: registration between the second preloaded image and the image of the loaded specimen taken after repositioning In the folder C-03-a-02-Nodes the results from the deformable registration are reported for each registration for Node Spacing of 50. Registrations have been done with ShIRT followed by the voxel detection algorithms as described in the paper. "output_map.txt" reports the coordinates of the nodes of the grid and the computed displacements "results.txt" reports the principal strains in each node The whole dataset is stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/Mario_Giorgi/DVC_Tibia_Precision_Study/ 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact This data has been made available to the research community (CC BY 4.0) 
URL https://doi.org/10.15131/shef.data.7058078
 
Title Data for the paper "Humeral Fractures in Non-Ambulant Infants: CT-Based Finite Element Investigation Indicates an Unlikely Mechanism " 
Description Complete results set of the study reported in "Humeral Fractures in Non-Ambulant Infants: CT-Based Finite Element Investigation Indicates an Unlikely Mechanism" by Zainab Altai, Marco Viceconti, Xinshan Li, and Amaka C. Offiah, which was published as: Altai, Z., Viceconti, M., Li, X., Offiah, A. C. (2020), "Investigating Rolling as Mechanism for Humeral Fractures in Non-Ambulant Infants: A Preliminary Finite Element Study", Clinical Radiology, 75 (1), 78.e9-78.e16, URL: https://doi.org/10.1016/j.crad.2019.08.026 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Dataset is a available for the research commuity. 
URL https://doi.org/10.15131/shef.data.7301591.v1
 
Title Data for the paper "The effect of boundary constraints on patient classification using finite element predicted risk of fracture " 
Description Complete results set of the study reported in Altai, Z., Qasim, M., Li, X., Viceconti, M. (2019), "The Effect of Boundary and Loading Conditions on Patient Classification Using Finite Element Predicted Risk of Fracture", Clinical Biomechanics, 68, pp 137-143, URL: https://doi.org/10.1016/j.clinbiomech.2019.06.004 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Dataset available for research community. 
URL https://doi.org/10.15131/shef.data.5901364.v1
 
Title Data for the paper: "Bone remodelling in the mouse tibia is spatio-temporally modulated by oestrogen deficiency and external mechanical loading: a combined in vivo/ in silico study" 
Description Data used in the paper : "Bone remodelling in the mouse tibia is spatio-temporally modulated by oestrogen deficiency and external mechanical loading: a combined in vivo/ in silico study"byVee San Cheong, Bryant Roberts, Visakan Kadirkamanathan, Enrico Dall'Arapublished in Acta BiomaterialiaWe share here an example of in vivo microCT images collected for a mouse that underwent ovariectomy at week 14 of age and mechanical loading at week 19 and 21 of age. In vivo 3D microCT images of the mouse tibia have been acquired at week 14, 18, 20, and 22 of age. The registered and cropped images are reported here.In case the reader is interested in the whole database they should contact Dr Enrico Dall'Ara (e.dallara@sheffield.ac.uk). 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_the_paper_Bone_remodelling_in_the_mouse_tibia_...
 
Title Data for the paper: "Development of subject-specific finite element models of the mouse knee joint for preclinical applications" 
Description Data for the paper: "Development of subject-specific finite element models of the mouse knee joint for preclinical applications"by:Sahnd Zanjani-Pour, Mario Giorgi, Enrico Dall'Arapublished in:Frontiers in Bioengineering and Biotechnology (Biomechanics) https://www.frontiersin.org/articles/10.3389/fbioe.2020.558815/abstractMicroCT images of the native bones and PTA stained bones have been reported after registrations. These images were used to create the finite element models of the mouse knee joint including bone, cartilage, and idealised meniscus as described in the paper. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Sharing of data to research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_the_paper_Development_of_subject-specific_fini...
 
Title Data for the paper: "Non-invasive prediction of the mouse tibia mechanical properties from microCT images: comparison between different finite element models" 
Description Data used in the paper: "Non-invasive prediction of the mouse tibia mechanical properties from microCT images: comparison between different finite element models"Oliviero, Owen, Reilly, Bellantuono, Dall'Arapublished in BMMBWe share here an example of ex vivo microCT image used for the assessment, and the results obtained from the different analyses.Short description of the files included:-microFE_results.xlsx includes:Stiffness estimated for each specimen with microFE models, and correlations with experimental data.Failure load estimated with microFE models, and correlations with experimental data, for each model type:Hexahedral Homogeneous modelsHexahedral models with subject-specific modulusTedrahedral Homogenous modelsTetrahedral models with subject-specific modulusHexahedral Heterogeneous modelsTetrahedral Homogeneous models -microCT data:Example of a segmented microCT image used as input for the microFE model (Specimen1, C57BL/6J, wild type, 16 weeks of age, right tibia).In case the reader is interested in the whole database they should contact Dr Enrico Dall'Ara (e.dallara@sheffield.ac.uk). 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_the_paper_Non-invasive_prediction_of_the_mouse...
 
Title Data for the paper: "Optimization of the failure criterion in micro-Finite Element models of the mouse tibia for the non-invasive prediction of its failure load in preclinical applications" 
Description Data used in the paper: "Optimization of the failure criterion in micro-Finite Element models of the mouse tibia for the non-invasive prediction of its failure load in preclinical applications"Oliviero, Owen, Reilly, Bellantuono, Dall'Arapublished in JMBBMWe share here an example of ex vivo microCT image used for the assessment, and the results obtained from the different analyses.Short description of the files included:Densitometric_and_morphometric_parameters.xlsx includes:-Densitometric parameters, and correlations with experimental mechanical data, calculated for each specimen and each region of interestTotal = total volume of interest (80% of tibia length)10 Longitudinal sections: section 1 corresponds to proximal tibia, section 10 corresponds to distal tibiaSectors: anterior (A), posterior (P), medial (M) and lateral (L)-Morphometric parameters calculated for each specimen, and correlations with experimental mechanical data. -microFE_results.xlsx includes:Stiffness estimated for each specimen with microFE models, and correlations with experimental data.Failure load estimated with microFE models, and correlations with experimental data, for each failure criterion:Pistoia methodCompression: tibia fails when a portion of the nodes (failure volume) reaches a critical compressive (third principal) strain levelTension: tibia fails when a portion of the nodes reaches a critical tensile (first principal) strain levelCompression&Tension: tibia fails when a portion of the nodes reaches a critical strain, either in tension or in compressionSections: tibia fails when the median first principal strain or third principal strain in one section (tibia divided into ten portions) or in one sector (tibia divided into ten sections and each section divided into anterior and posterior partitions; 20 portions in total) reaches a critical strain level -microCT data:Example of a segmented microCT image used as input for the microFE model (Specimen1, C57BL/6J, wild type, 16 weeks of age, right tibia).In case the reader is interested in the whole database they should contact Dr Enrico Dall'Ara (e.dallara@sheffield.ac.uk). 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_the_paper_Optimization_of_the_failure_criterio...
 
Title Data for the paper: "PTH(1-34) treatment and/or mechanical loading have different osteogenic effects on the trabecular and cortical bone in the ovariectomized C57BL/6 mouse" 
Description Link to the data used in:Roberts, Arredondo Carrera, Zanjani-pour, Boudiff, Wang, Gartland and Dall'AraPTH(1-34) treatment and/or mechanical loading have different osteogenic effects on the trabecular and cortical bone in the ovariectomized C57BL/6 mouseScientific Reports 10, 8889 (2020).All the procedures were performed under a British Home Office licence (PF61050A3) and in compliance with the Animal (Scientific Procedures) Act 1986.The images and data are too large to be uploaded in ORDA. The whole dataset can be assessed at: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/PTH_Loading/. Please contact the senior author at: e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if you are interested in working on the files.In this repository we have uploaded only the result file obtained from assessment of the microCT images. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_the_paper_PTH_1-34_treatment_and_or_mechanical...
 
Title Data for the paper: "Patient-specific finite element models of posterior pedicle screw fixation: effect of screw's size and geometry" 
Description Data used in the paper: "Patient-specific finite element models of posterior pedicle screw fixation: effect of screw's size and geometry"Sensale, Vendeuvre, Schilling, Grupp, Rochette and Dall'Ara published in Frontiers Bioengineering and BiotechnologyWe share here the results and one example of FE models for the implanted vertebrae.Short description of the files included:-) the results of the paper are reported in "Results_file.xlsx". In this file, there are different sheets:.NumElements_CompTime - this contains the number of elements and computational time to solve the FE models, reported in Table 2 and 3;.MeshConvergenceStudy - this contains the results of the Mesh convergence study reported in Figure 3..Sensitivity Deflection - Stress AND Sensitivity Strain - these contain the results of the sensitivity analysis reported in Table 4, 5 and 6;.Correlation - this contains the results of the correlation analysis reported in Figure 6;-) In the "Frequency_plot_files" folder, the result files for the frequency plots reported in Figure 7 are reported:.MinStrainMeshPoints(...).txt - these files contains the values of minimum principal strain used in the frequency plots in Figure 7.-) The "Example_Model" folder contains an example of the models used in the sensitivity analysis for Patient #3 with simplified pedicle screw with diamter D6.5mm and length L45mmThe folder contains:- the Ansys workbench 2020R2 project file corresponding to the model in the name of the folder;- the corresponding geometry SpaceClaim file;- the Ansys cdb mesh file exported from Bonemat;- the calibration xml file used in Bonemat;- the Ansys apdl command snippet used in Mechanical to build an heterogeneous model of the bone.In case the reader is interested in the whole database they should contact Dr Enrico Dall'Ara (e.dallara@sheffield.ac.uk). 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Dataset shared with research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_the_paper_Patient-specific_finite_element_mode...
 
Title Data for the paper: "Positive interactions of mechanical loading and PTH treatments on spatio-temporal bone remodelling" 
Description Data used in the paper : "Bone remodelling in the mouse tibia is spatio-temporally modulated by oestrogen deficiency and external mechanical loading: a combined in vivo/ in silico study"byVS Cheong, BC Roberts, V Kadirkamanathan, E Dall'Ara (2021)published in Acta BiomaterialiaWe share here an example of in vivo microCT images collected for a mouse that underwent the following interventions:-ovariectomy at week 14 of age - mechanical loading at week 19 and 21 of age.- injections of Parathyroid hormone (PTH; 5 days per week) between weeks 18 and 22 of ageIn vivo 3D microCT images of the mouse tibia have been acquired at week 14, 18, 20, and 22 of age.The registered and cropped images are reported here.In case the reader is interested in the whole database they should contact Dr Enrico Dall'Ara (e.dallara@sheffield.ac.uk). 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Data made available to the research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Data_for_the_paper_Positive_interactions_of_mechanical_...
 
Title Data for the paper: "The longitudinal effects of ovariectomy on the morphometric, densitometric and mechanical properties in the murine tibia: a comparison between two mouse strains" 
Description Link to the data used in: Roberts, Giorgi, Oliviero, Wang, Boudiffa, Dall'Ara The longitudinal effects of ovariectomy on the morphometric, densitometric and mechanical properties in the murine tibia: a comparison between two mouse strains Bone 2019. The images and data are too large to be uploaded in ORDA, so please contact the senior author at: e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if you are interested in working on the files. The whole dataset can be assessed at: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/Mario_Giorgi/OVX_Study/ In this repository we have uploaded only the result file obtained from assessment of the microCT images. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset available to the research community 
URL https://doi.org/10.15131/shef.data.8313254
 
Title Data for the paper: "Uncertainties of Synchrotron microCT-based Digital Volume Correlation bone strain measurements under simulated deformation" 
Description Link to the data used in: Comini F, Palanca M, Cristofolini L, Dall'Ara E. (2019) Uncertainties of Synchrotron microCT-based Digital Volume Correlation bone strain measurements under simulated deformation. Journal of Biomechanics 2019. The images and data are too large to be uploaded in ORDA, so please contact the corresponding author at: e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if you are interested in working on the files. In this repository we have uploaded only the result file obtained from the Digital Volume Correlation analyses post-processed with Matlab. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact This data has been made available to the research community (CC BY 4.0) 
URL https://doi.org/10.15131/shef.data.7624958.v1
 
Title Data for the paper: A new proxy measurement algorithm with applications to estimation of vertical ground reaction forces using wearable sensors 
Description Data for the paper "A new proxy measurement algorithm with applications to estimation of vertical ground reaction forces using wearable sensors" 06.12.2017, 12:49 by Yuzhu Guo Fabio Storm Yifan Zhao Stephen Billings Alex Pavic Claudia Mazza Lingzhong Guo Guo, Y., Storm, F., Zhao, Y. et al. (2017) A new proxy measurement algorithm with application to the estimation of vertical ground reaction forces using wearable sensors. Sensors, 17 (10). 2181. ISSN 1424-8220. DOI:10.3390/s17102181 Measurement of the ground reaction forces (GRF) during walking is typically limited to laboratory settings and only short observations using wearable pressure insoles have been reported so far. In this study, a new proxy measurement method is proposed to estimate the vertical component of the GRF (vGRF) from wearable accelerometer signals. The accelerations are used as the proxy variable. An orthogonal forward regression algorithm (OFR) is employed to identify the dynamic relationships between the proxy variables and the measured vGRF using pressure-sensing insoles. The obtained model, which represents the connection between the proxy variable and the vGRF, is then used to predict the latter. The results have been validated using pressure insoles data collected from nine healthy individuals under two outdoor walking tasks in non-laboratory settings. Results show that the vGRFs can be reconstructed with high accuracy (with an average prediction error of less than 6%) using only one wearable sensor mounted at forehead level. Proxy measures with different sensor positions are also discussed. Results show that the forehead accelerations based proxy measurement is more stable with less inter-task and inter-subject variability than the proxy measures using cervical and low back level accelerations. The proposed proxy measure provides a promising low-cost method for monitoring ground reaction forces in real life settings and introduces a novel generic approach for replacing the direct determination of difficult to measure variables in many applications. REFERENCES https://doi.org/10.3390/s17102181 http://eprints.whiterose.ac.uk/121805/ FUNDING The research was funded by the UK Engineering and Physical Sciences Research Council (EP/K03877X/1). 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: Guo, Y., Storm, F., Zhao, Y. et al. (2017) A new proxy measurement algorithm with application to the estimation of vertical ground reaction forces using wearable sensors. Sensors, 17 (10). 2181. ISSN 1424-8220. DOI:10.3390/s17102181 
URL https://doi.org/10.15131/shef.data.5341309
 
Title Data for the paper: Gait event detection in laboratory and real life settings: accuracy of ankle and waist sensor based methods 
Description Data for the paper 'Gait event detection in laboratory and real life settings: accuracy of ankle and waist sensor based methods' 28.09.2017, 17:13 by Fabio Storm Chris Buckley Claudia Mazza The aim of this study was to evaluate the accuracy of two algorithms for the detection of gait events and temporal parameters during free-living walking, one based on two shank-worn inertial sensors, and the other based on one waist-worn sensor. The algorithms were applied to gait data of ten healthy subjects walking both indoor and outdoor, and completing protocols that entailed both straight supervised and free walking in an urban environment. REFERENCES http://dx.doi.org/10.1016/j.gaitpost.2016.08.012 http://eprints.whiterose.ac.uk/103798/ FUNDING This study was supported by the EPSRC Frontier Engineering Awards, Grant Reference No. EP/K03877X/1 and by the MRC and Arthritis Research UK as part of the MRC - Arthritis Research UK Centre for Integrated research into Musculoskeletal Ageing (CIMA). 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: Gait event detection in laboratory and real life settings: Accuracy of ankle and waist sensor based methods Storm, Fabio A. et al. Gait & Posture , Volume 50 , 42 - 46 http://dx.doi.org/10.1016/j.gaitpost.2016.08.012 
URL https://doi.org/10.15131/shef.data.3503180
 
Title Data used in the study "A new method to monitor bone geometry changes at different spatial scales in the longitudinal in vivo µCT studies of mice bones" 
Description Link to the data used in: Yang Z, Dall'Ara E, Viceconti M, Kadirkamanathan V (2019) An approach to split bone growth and remodelling from longitudinal in vivo microCT imaging of the mouse tibia; Plos One 2019. The folder includes examples of microCT images cropped for the analyses that are used as input of the computational frameworks. In the folder there are dicom files of: 1x Wild Type Mouse scanned at week 16 of age (WildM5W2N1228cropped) 1x Wild Type Mouse scanned at week 14 of age (WildM5W20N1228cropped) The "Code" used to process the images can be found in: https://doi.org/10.15131/shef.data.8397989 The whole dataset is stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP6/YangZhang For further information please contact Dr Enrico Dall'Ara: e.dallara@sheffield.ac.uk 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset available to the research community 
URL https://doi.org/10.15131/shef.data.8319956
 
Title Data used in the study "A novel algorithm to predict bone changes in the mouse tibia properties under physiological conditions" 
Description Link to the data used in: Cheong VS, Campos Marin A, Lacroix D, Dall'Ara E (2019) A novel algorithm to predict bone changes in the mouse tibia properties under physiological conditions; Biomechanics and Modeling in Mechanobiology, 2019. DOI: 10.1007/s10237-019-01266-7 The zip folder includes examples of microCT images used in the methodology (.dcm) and the data processed in this study in ASCII format(.csv). Zip file structure: source_images |_M1W0 : scan at week 14 of age of mouse M1 |_M1W2 : scan at week 16 of age of mouse M1 |_M1W6 : scan at week 20 of age of mouse M1 |_M1W8 : scan at week 22 of age of mouse M1 results |_fig3 |_fig5 |_fig8 The naming conventions of the files are as follow: sed: strain energy density maxstrain: maximum principal strain ssp14_lz0: subject-specific parameters from week 14, without lazy zone ssp20_lz0: subject-specific parameters from week 20, without lazy zone The source_images folder contain the aligned and cropped images for the right tibia of mouse 1 microCT scanned at weeks 0, 2, 6 and 8 of the experiment (weeks 14, 16, 20, 22 of age). The full dataset is stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP4/boneremod/physiological_loading For further information please contact Dr Enrico Dall'Ara: e.dallara@sheffield.ac.uk 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset available to research community 
URL https://doi.org/10.15131/shef.data.10756928
 
Title Data used in the study "ChronoMID - cross-modal neural networks for 3-D temporal medical imaging data" 
Description Link to the data used in: Alexander G. Rakowski, Petar Velickovic, Enrico Dall'Ara, Pietro Liò from: -) Computer Laboratory, University of Cambridge, Cambridge, Cambs, United Kingdom -) Insigneo Institute for in silico medicine, University of Sheffield, Sheffield, South Yorkshire, United Kingdom ChronoMID - cross-modal neural networks for 3-D temporal medical imaging data; Plos One 2020. Provided here are a selection of images from the study. The images have been resized to have consistent dimensions, but otherwise have not undergone any of the preprocessing steps listed in the ChronoMID paper. Input images for both the control (WildType) and treated (Anabolic) groups have been uploaded at three different time points: at the start of the experiment (W0), at the beginning of the treatment (W5), and at the end of the experiment (W8). Within each mouse-week, the stack of cross-sections ranges from the proximal epiphysis (e.g. 0100.dcm) and extend toward the distal epiphysis (e.g. 1300.dcm). The whole dataset is stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/ The code used in this study can be found in the following link: https://doi.org/10.15131/shef.data.11798595 For further information please contact Dr Enrico Dall'Ara: e.dallara@sheffield.ac.uk 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Data available to research community 
URL https://doi.org/10.15131/shef.data.11764446.v1
 
Title Data used in the study "Effect of repeated in vivo microCT imaging on the properties of the mouse tibia" 
Description Link to the data used in: Oliviero S, Giorgi M, Laud P, Dall'Ara E (2019) Effect of repeated in vivo microCT imaging on the properties of the mouse tibia; Plos One 2019. The zip folder includes examples of microCT images used for the analyses and a spreadsheet with all the data processed in the study. File with data: Results_radiation_effects.xlsx The file reports all the data for every specimen calculated from the morphometric, densitometric and finite element analyses. We have reported the DICOM files of the reconstructed microCT images (left control and right irradiated) for one animal for each group: Black6_WT_Sample5 BLack6_OVX_Sample6 BalbC_WT_Sample2 BalbC_OVX_Sample1 With Black6: C57Bl6 OVX: Ovariecomised WT: WIld Type The whole dataset is stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/Mario_Giorgi/OVX_Study/B_ImageProcessing For further information please contact Dr Enrico Dall'Ara: e.dallara@sheffield.ac.uk 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset is available to research community 
URL https://doi.org/10.15131/shef.data.10247816.v1
 
Title Data used in the study "Prenatal growth map of the mouse knee joint by means of deformable registration technique" 
Description Link to the data used in: Giorgi, Sotiriou, Fanchini, Conigliaro, Bignardi, Nowlan, Dall'Ara (2018) Prenatal growth map of the mouse knee joint by mean of deformable registration technique. Plos One 2018. The shared files within each subfolder are arranged as following: "B02_..." includes the cropped images of the joints for each anatomical site "C01b_..." includes the result file of the deformable registration "C03_..." includes the results for the Modified Hausdorff Distance (MDH) "C04_..." includes the average of the differences of the displacements between control and average maps "G_..." includes the scripts used to compute the results 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Dataset available to research community 
URL https://doi.org/10.15131/shef.data.7447406.v2
 
Title Data used in the study "Regional nanoindentation properties in different locations on the mouse tibia from two different mouse strains" 
Description Link to the data used in: Regional nanoindentation properties in different locations on the mouse tibia from two different mouse strains V. Pepe, S. Oliviero, L. Cristofolini, E. Dall'Ara The indentation parameters are reported for each indentation (rows) and each specimen (sheets) as described in the paper. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset available to research community 
URL https://doi.org/10.15131/shef.data.11309678
 
Title Dataset SRACC: Synchrotron microCT for testing accuracy of Digital Volume Correlation (DVC) methods 
Description Database of the results obtained in: Palanca et al. Local Displacement and Strain Uncertainties in different Bone Types by Digital Volume Correlation of Synchrotron Microtomograms JBiomech 2017 http://doi.org/10.1016/j.jbiomech.2017.04.007 The images are too large to be uploaded in figshare so please contact the corresponding author at: e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if interested in working on the files. REFERENCES http://doi.org/10.1016/j.jbiomech.2017.04.007 FUNDING EPSRC Frontier Grant (MultiSim project code EP/K03877X/1), FP7 European program MAMBO (PIEF-GA-2012-327357), Diamond Light Source (MT10315), 'Marco Polo' travel grant awarded by University of Bologna 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: Palanca et al. Local Displacement and Strain Uncertainties in different Bone Types by Digital Volume Correlation of Synchrotron Microtomograms JBiomech 2017 http://doi.org/10.1016/j.jbiomech.2017.04.007 
URL https://doi.org/10.15131/shef.data.4865300
 
Title Dataset behind the results of: Automatic methods of hoof-on and -off detection in horses using wearable inertial sensors during walk and trot on asphalt, sand and grass 
Description This dataset contains the data behind the results of the associated paper. It includes the timing of gait events as detected by the different methods explored in the paper, for a group of horses at walk and trot. A ReadMe file explains fully the layout of the data and naming conventions used. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Data made available to the research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Dataset_behind_the_results_of_Automatic_methods_of_hoof...
 
Title FE-based Femoral strength of 100 osteoporotic women 
Description FE-based Femoral strength of 100 osteoporotic women 11.10.2017, 15:39 by Marco Viceconti Complete results set of the study reported in "Patient-Specific Finite Element Estimated Femur Strength as a Predictor of the Risk of Hip Fracture: The Effect of Methodological Determinants" by Muhammad Qasim, Giovanna Farinella, Ju Zhang, Xinshan Li, Lang Yang, Richard Eastell, and Marco Viceconti, Osteoporosis International, 2016. DOI: 10.1007/s00198-016-3597-4. Open access full text: http://link.springer.com/article/10.1007/s00198-016-3597-4 REFERENCES http://dx.doi.org/10.1007/s00198-016-3597-4 FUNDING EP/K03877X/1 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: "Patient-Specific Finite Element Estimated Femur Strength as a Predictor of the Risk of Hip Fracture: The Effect of Methodological Determinants" by Muhammad Qasim, Giovanna Farinella, Ju Zhang, Xinshan Li, Lang Yang, Richard Eastell, and Marco Viceconti, Osteoporosis International, 2016. DOI: 10.1007/s00198-016-3597-4. 
URL https://doi.org/10.15131/shef.data.3124108
 
Title Failure strength of infant femurs under 4 point bending of 15 cases 
Description Failure strength of infant femurs under 4 point bending of 15 cases 28.10.2016, 13:52 by Xinshan Li Complete results set of the study reported in " X. Li, M. Viceconti, M. C. Cohen, G. C. Reilly, M. J. Carre, A. C. Offiah 2015. "Developing CT Based Computational Models of Pediatric Femurs", in Journal of Biomechanics, 48, 2034-40" REFERENCES http://dx.doi.org/10.1016/j.jbiomech.2015.03.027 FUNDING EP/K03877X/1 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact See: Complete results set of the study reported in " X. Li, M. Viceconti, M. C. Cohen, G. C. Reilly, M. J. Carre, A. C. Offiah 2015. "Developing CT Based Computational Models of Pediatric Femurs", in Journal of Biomechanics, 48, 2034-40" http://dx.doi.org/10.1016/j.jbiomech.2015.03.027 
URL https://doi.org/10.15131/shef.data.3969285
 
Title Femoral neck strain prediction during level walking using a combined musculoskeletal and finite element model approach 
Description The full of set of data contains; peak first and third principal strains at the femoral neck as predicted by the FE model, hip and knee joint contact forces personolised by the body weight, and Gluteus Medius muscle forces as calculated by the musculoskeletal model. Those are reported for the five cases and along the 100% of one gait cycle.The study was approved by the Health Research Authority of East of England (Cambridgeshire and Hertfordshire Research Ethics Committee, reference 16/EE/0049). 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://figshare.shef.ac.uk/articles/dataset/Femoral_neck_strain_prediction_during_level_walking_usi...
 
Title Figures for the review article: In Vitro Bone Cell Models: Impact of Fluid Shear Stress on Bone formation 
Description Figures for the review article: 'In Vitro Bone Cell Models: Impact of Fluid Shear Stress on Bone formation' 28.09.2017, 17:16 by Claudia Wittkowske Cecile Perrault Damien Lacroix Gwendolen Reilly This folder contains the figures which were included in the review article "In Vitro Bone Cell Models: Impact of Fluid Shear Stress on Bone formation" (Frontiers in Bioengineering and Biotechnology 4:87. doi: 10.3389/fbioe.2016.00087). This review describes the role of bone cells and their surrounding matrix in maintaining bone strength through the process of bone remodeling. Subsequently, this work focusses on how bone formation is guided by mechanical forces and fluid shear stress in particular. In vitro, it has been reported that bone cells respond to fluid shear stress by releasing osteogenic signaling factors, such as nitric oxide, and prostaglandins. This work focusses on the application of in vitro models to study the effects of fluid flow on bone cell signaling, collagen deposition, and matrix mineralization. REFERENCES http://dx.doi.org/10.3389/fbioe.2016.00087 http://eprints.whiterose.ac.uk/109118/ FUNDING MultiSim, an EPSRC Frontier Engineering Award, Grant Reference No. EP/K03877X/1 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: 'In Vitro Bone Cell Models: Impact of Fluid Shear Stress on Bone formation' 28.09.2017, 17:16 by Claudia Wittkowske Cecile Perrault Damien Lacroix Gwendolen Reilly http://dx.doi.org/10.3389/fbioe.2016.00087 http://eprints.whiterose.ac.uk/109118/ 
URL https://doi.org/10.15131/shef.data.4203153
 
Title Kinematic data for the Concurrent repeatability and reproducibility analysis of four gait models for foot-ankle complex 
Description Multi-segment models of the foot have been proposed in the past years to overcome limitations imposed by oversimplified traditional approaches used to describe foot kinematics, but they have been only partially validated and never compared. This paper presents a unique comparative assessment of the four most widely adopted foot kinematic models and aims to provide a guidance for the clinical interpretation of their results. Sensitivity of the models to differences between treadmill and overground walking was tested in nine young healthy adults using a 1D paired t-test. Repeatability was assessed by investigating the joint kinematics obtained when the same operator placed the markers on thirteen young healthy adults in two occasions. Reproducibility was then assessed using data from three randomly selected participants, asking three operators to repeat the marker placement three times. The analyses were performed on sagittal kinematics using curve similarity and correlation indices (Linear Fit Method) and absolute differences between selected points. Differences between treadmill and overground gait were highlighted by all the investigated models. The two most repeatable and reproducible investigated models had average correlations higher than 0.70, with the lowest values (0.56) obtained for the midfoot. Averaged correlations were always higher than 0.74 for the former and 0.70 for the latter, with the lowest obtained for the midfoot (0.64 and 0.51). For all investigated models, foot kinematics generally showed low repeatability: normative bands must be adopted with caution when used for comparison with patient data. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact Dataset available for research community 
URL https://doi.org/10.15131/shef.data.3502712.v1
 
Title MAMBO_IND sub-project: Indentation data for cortical bone (Depth-sensing Micro-Indentation and RPI), database and statistics 
Description MultiSim (Grant No. EP/K03877X/1) MAMBO_IND sub-project: Indentation data for cortical bone (Depth-sensing Micro-Indentation and RPI), database and statistics 11.10.2017, 14:54 by Enrico Dall'Ara The data are reported in a spreadsheet. Each sheet reports the data from microindentation tests (along the three directions axial A, circumferential C and radial R) and reference point indentation (RPI) tests. Details are reported in the manuscript: Estimation of local anisotropy of plexiform bone: Comparison between depth sensing micro-indentation and Reference Point Indentation. Dall'Ara E, Grabowski P, Zioupos P, Viceconti M. J Biomech. 2015 Nov 26;48(15):4073-80. doi: 10.1016/j.jbiomech.2015.10.001. Epub 2015 Oct 9. For any questions the reader can contact Dr Enrico Dall'Ara e.dallara@sheffield.ac.uk REFERENCES http://www.sciencedirect.com/science/article/pii/S0021929015005473 FUNDING EPSRC (MultiSim project EP/K03877X/1 and Point-of-Care High Accuracy Fracture Risk Prediction EP/K020196) and FP7 European Program (PIEF-GA-2012-327357) 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: Estimation of local anisotropy of plexiform bone: Comparison between depth sensing micro-indentation and Reference Point Indentation. Dall'Ara E, Grabowski P, Zioupos P, Viceconti M. J Biomech. 2015 Nov 26;48(15):4073-80. doi: 10.1016/j.jbiomech.2015.10.001. Epub 2015 Oct 9. 
URL https://doi.org/10.15131/shef.data.3827046
 
Title METVERT_Validation_Results: Micro Finite Element models of the vertebral body: Validation of local displacement predictions 
Description This file contains the results collected in the study: "Micro Finite Element models of the vertebral body: Validation of local displacement predictions" by "Costa, Tozzi, Cristofolini, Danesi, Viceconti, Dall'Ara" published in PLoS ONE 12(7): e0180151. https://doi.org/10.1371/journal.pone.0180151. In order to access the original raw files the reader can contact the the corresponding author (Dr Enrico Dall'Ara, e.dallara@sheffield.ac.uk). The files are stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/METVERT_Validation/ REFERENCES https://doi.org/10.1371/journal.pone.0180151 FUNDING The project was partially funded by the Sheffield Hospitals Charity (141515-1), the Engineering and Physical Sciences Research Council (EP/K03877X/1) and the Royal Society (RG130831 and RG150012) 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: "Micro Finite Element models of the vertebral body: Validation of local displacement predictions" by "Costa, Tozzi, Cristofolini, Danesi, Viceconti, Dall'Ara" published in PLoS ONE 12(7): e0180151. https://doi.org/10.1371/journal.pone.0180151. 
URL https://doi.org/10.15131/shef.data.5121871
 
Title Mechanoregulation of bone remodelling in mice under physiological loading 
Description Mechanoregulation of bone remodelling in mice under physiological loading 11.10.2017, 15:39 by Marco Viceconti Enrico Dall'Ara Maya Boudiffa These are the raw data analysed and reported in the manuscript entitled "EVALUATION OF DIFFERENT BONE REMODELLING THEORIES ON THE CHANGES IN BONE MINERAL DENSITY OF MICE TIBIAE UNDER PHYSIOLOGICAL LOADING" by Yongtao Lu, Enrico Dall'Ara, Maya Boudiffa, and Marco Viceconti, submitted for publication to the Journal of the Royal Society Interface. FUNDING This work was funded by the UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs), grant number:NC/K000780/1, the Engineering and Physical Sciences Research Council - MultiSim project, grant number: EP/K03877X/1 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: "EVALUATION OF DIFFERENT BONE REMODELLING THEORIES ON THE CHANGES IN BONE MINERAL DENSITY OF MICE TIBIAE UNDER PHYSIOLOGICAL LOADING" by Yongtao Lu, Enrico Dall'Ara, Maya Boudiffa, and Marco Viceconti, submitted for publication to the Journal of the Royal Society Interface. 
URL https://doi.org/10.15131/shef.data.3814701
 
Title MicroCT Dataset of mouse tibiae for DVC precision analyses (repeated scans ex vivo and in vivo) 
Description Database of the images (repeated scans of mouse tibiae obtained in vivo and ex vivo) used in: Precision of DVC approaches for strain analysis in bone imaged with µCT at different dimensional levels. by: Enrico Dall'ara, Marta Peña-Fernández, Marco Palanca, Mario Giorgi, Luca Cristofolini, Gianluca Tozzi Original Research, Front. Mater. - Mechanics of Materials, 2017 The images related to the precision of DVC applied to the mouse tibiae are too large to be uploaded in figshare so please contact the corresponding author at: e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if interested in working on the files. The files are stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/Mario_Giorgi/DVC_Tibia_Precision_Study 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: Dall'Ara Enrico, Peña-Fernández Marta, Palanca Marco, Giorgi Mario, Cristofolini Luca, Tozzi Gianluca Precision of Digital Volume Correlation Approaches for Strain Analysis in Bone Imaged with Micro-Computed Tomography at Different Dimensional Levels Frontiers in Materials (2017) 4, 31 https://www.frontiersin.org/articles/10.3389/fmats.2017.00031/abstract https://doi.org/10.3389/fmats.2017.00031 
URL https://doi.org/10.15131/shef.data.5528104
 
Title MicroCT Dataset of mouse tibiae for evaluating the effect of the integration time on output parameters 
Description Database of the results obtained from the images (repeated scans of mouse tibiae obtained ex vivo with different scanning parameters) used in: Oliviero, S., Lu, Y., Viceconti, M. et al. (2017) Effect of integration time on the morphometric, densitometric and mechanical properties of the mouse tibia. Journal of Biomechanics , 65. https://doi.org/10.1016/j.jbiomech.2017.10.026 The images are too large to be uploaded in figshare so please contact the corresponding author at: e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if interested in working on the files. The files are stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/In_vivo_imaging_procedure/ REFERENCES https://doi.org/10.1016/j.jbiomech.2017.10.026 FUNDING UK National Centre for the Replacement, Refinement and Reduction of Animals in Research (NC3Rs, Grant number: NC/K000780/1) and by the Engineering and Physical Sciences Research Council (EPSRC, MultiSim project, Grant number: EP/K03877X/1) 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: Oliviero, S., Lu, Y., Viceconti, M. et al. (2017) Effect of integration time on the morphometric, densitometric and mechanical properties of the mouse tibia. Journal of Biomechanics , 65. https://doi.org/10.1016/j.jbiomech.2017.10.026 
URL https://doi.org/10.15131/shef.data.5562529
 
Title MicroCT, DVC and MicroFE datasets for the validation for finite element models of the Mouse Tibia 
Description Link to the data used in: Oliviero, S., Giorgi, M., Dall'Ara, E. (2018) Validation of Finite Element models of the Mouse Tibia using Digital Volume Correlation. Journal of Mechanical Behaviour of Biomedical Materials 2018. https://doi.org/10.1016/j.jmbbm.2018.06.022 The images and data are too large to be uploaded in ORDA, so please contact the corresponding author at: e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if you are interested in working on the files. The files are stored in the University of Sheffield file-store at the link: https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/Validation/Oliviero_JMBBM_2018/ 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact This data has been made available to the research community (CC BY 4.0) 
URL https://doi.org/10.15131/shef.data.6635561
 
Title MicroCT, DVC and MicroFE datasets for the validation for finite element models of the Mouse Tibia 
Description Link to the data used in:Oliviero, S., Giorgi, M., Dall'Ara, E. (2018) Validation of Finite Element models of the Mouse Tibia using Digital Volume Correlation. Journal of Mechanical Behaviour of Biomedical Materials 2018. https://doi.org/10.1016/j.jmbbm.2018.06.022The images and data are too large to be uploaded in ORDA, so please contact the corresponding author at: e.dallara@sheffield.ac.uk or the Project Management Office at: pmo@insigneo.org if you are interested in working on the files.The files are stored in the University of Sheffield file-store at the link:https://web-unidrive.sheffield.ac.uk/shared/multisim2/WP7/Validation/Oliviero_JMBBM_2018/ 
Type Of Material Database/Collection of data 
Year Produced 2018 
Provided To Others? Yes  
Impact Dataset available to research community. 
URL https://figshare.shef.ac.uk/articles/online_resource/MicroCT_DVC_and_MicroFE_datasets_for_the_valida...
 
Title Models and data for the paper: To what extent is joint and muscle mechanics predicted by musculoskeletal models sensitive to soft tissue artefacts? 
Description MultiSim (Grant No. EP/K03877X/1) Models and data for the paper "To what extent is joint and muscle mechanics predicted by musculoskeletal models sensitive to soft tissue artefacts?" 28.09.2017, 15:55 by Giuliano Lamberto Saulo Martelli Aurelio Cappozzo Claudia Mazzà Model and data used in the study "To what extent is joint and muscle mechanics predicted by musculoskeletal models sensitive to soft tissue artefacts?" by Giuliano Lamberto, Saulo Martelli, Aurelio Cappozzo, and Claudia Mazzà, Journal of Biomechanics. Please, consider the READ ME document to understand the structure and names of the dataset included in this repository. REFERENCES http://dx.doi.org/10.1016/j.jbiomech.2016.07.042 http://eprints.whiterose.ac.uk/103365/ FUNDING EP/K03877X/1; European Commission, 7th FP, "MD- Paedigree", ICT Programme (Contract Number 600932); the Australian Research Council (DE140101530) 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: "To what extent is joint and muscle mechanics predicted by musculoskeletal models sensitive to soft tissue artefacts?" by Giuliano Lamberto, Saulo Martelli, Aurelio Cappozzo, and Claudia Mazzà, Journal of Biomechanics. http://dx.doi.org/10.1016/j.jbiomech.2016.07.042 
URL https://doi.org/10.15131/shef.data.3502652
 
Title Models, data and supplementary material for 'Muscle recruitment strategies can reduce joint loading during level walking' 
Description This repository contains the model, data and supplementary material for the paper 'Muscle recruitment strategies can reduce joint loading during level walking' by van Veen, Montefiori, Modenese, Mazzà and Viceconti. README files that explain the file contents are provided. Ethical approval p01: Ethical approval for the data collection was provided by the University Research Ethics Committee at the University of Sheffield. p02: The original dataset was provided through the Knee Grand Challenge (Fregly et al., 2012). p03: The data were previously collected as part of the MD-Paedigree project (EC 7th FP, ICT Programme, Ref. No. 600932). p04: The data were provided as part of the MultiSim project (EPSRC Frontier Engineering Awards, Ref. No. EP/K03877X/1) for which the data collection was approved by the NHS research ethics committee. 
Type Of Material Database/Collection of data 
Year Produced 2019 
Provided To Others? Yes  
Impact Dataset available for research community 
URL https://doi.org/10.15131/shef.data.5288311
 
Title Moving from laboratory to real life conditions: Influence on the assessment of variability and stability of gait 
Description Data for the paper: Tamburini, Paola; Storm, Fabio; Buckley, Christopher; Cristina Bisi, Maria; Stagni, Rita; Mazza, Claudia (2017): Moving from laboratory to real life conditions: Influence on the assessment of variability and stability of gait. Gait & Posture, 2018, 59, 248-252 REFERENCES http://www.sciencedirect.com/science/article/pii/S0966636217309815 
Type Of Material Database/Collection of data 
Year Produced 2017 
Provided To Others? Yes  
Impact See: Tamburini, Paola; Storm, Fabio; Buckley, Christopher; Cristina Bisi, Maria; Stagni, Rita; Mazza, Claudia (2017): Moving from laboratory to real life conditions: Influence on the assessment of variability and stability of gait. Gait & Posture, 2018, 59, 248-252 REFERENCES http://www.sciencedirect.com/science/article/pii/S0966636217309815 
URL https://doi.org/10.15131/shef.data.5519680
 
Title Reliability of Inertial Sensors in the Assessment of Patients with Vestibular Disorders - a feasibility study 
Description The data set contains values of parameters from 27 participants and falls data collected from TUG and Sway test. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact Data available to the research community 
URL https://doi.org/10.6084/m9.figshare.4276376.v2
 
Title Resistance training combined with stretching increases tendon stiffness and is more effective than stretching alone in children with cerebral palsy: A randomised controlled trial 
Description Raw data of fascicle lengths and tendon stiffness corresponding to the paper: Resistance training combined with stretching increases tendon stiffness and is more effective than stretching alone in children with cerebral palsy: A randomised controlled trial. From the paper: Kalkman, B. M., Holmes, G., Bar-On, L., Maganaris, C. N., Barton, G. J., Bass, A., Wright, D. M., Walton, R., O'Brien, T. D. (2019), "Resistance Training Combined With Stretching Increases Tendon Stiffness and Is More Effective Than Stretching Alone in Children With Cerebral Palsy: A Randomized Controlled Trial", Frontiers in Pediatrics, 7, 333, URL: https://doi.org/10.3389/fped.2019.00333 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Dataset available to the research community. 
URL https://figshare.shef.ac.uk/s/1f6a6d565083e49cab1e
 
Title Supplementary Fig. 1 from Analysis of mechanotransduction dynamics during combined mechanical stimulation and modulation of the extracellular-regulated kinase cascade uncovers hidden information within the signalling noise 
Description Osteoporosis is a bone disease characterized by brittle bone and increased fracture incidence. With ageing societies worldwide, the disease presents a high burden on health systems. Furthermore, there are limited treatments for osteoporosis with just two anabolic pharmacological agents approved by the US Food and Drug Administration. Healthy bones are believed to be maintained via an intricate relationship between dual biochemical and mechanical (bio-mechanical) stimulations. It is widely considered that osteoporosis emerges as a result of disturbances to said relationship. The mechanotransduction process is key to this balance, and disruption of its dynamics in bone cells plays a role in osteoporosis development. Nonetheless, the exact details and mechanisms that drive and secure the health of bones are still elusive at the cellular and molecular scales. This study examined the dual modulation of mechanical stimulation and mechanotransduction activation dynamics in an osteoblast (OB). The aim was to find patterns of mechanotransduction dynamics demonstrating a significant change that can be mapped to alterations in the OB responses, specifically at the level of gene expression and osteogenic markers such as alkaline phosphatase. This was achieved using a three-dimensional hybrid multiscale computational model simulating mechanotransduction in the OB and its interaction with the extracellular matrix, combined with a numerical analytical technique. The model and the analysis method predict that within the noise of mechanotransduction, owing to modulation of the bio-mechanical stimulus and consequent gene expression, there are unique events that provide signatures for a shift in the system's dynamics. Furthermore, the study uncovered molecular interactions that can be potential drug targets. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Figure shared with research community. 
URL https://rs.figshare.com/articles/figure/Supplementary_Fig_1_from_Analysis_of_mechanotransduction_dyn...
 
Title Supplementary Material: A Quality Control Check to Ensure Comparability of Stereophotogrammetric Data between Sessions and Systems 
Description OVERVIEW:This is a stereophotogrammetric quality control check developed by K.Scott and shared to assist in the adoption of the methods of the associated paper: https://doi.org/10.3390/s21248223. This function in the "matlab code" folder compiles the processing required to complete the quality control check as explained in the material and methods of the paper.To ensure easy adoption to different labs and calibration objects, the functions have been refined to allow for easy adaption. Please read the accompanying commented notes in the script first.This function has been created for adaption and therefore editing is allowed based on the MIT License agreement. DISCLAIMER:The current function relies on the open-source C3D reader, Biomechanical ToolKit (BTK). Reference: https://doi.org/10.1016/j.cmpb.2014.01.012.PLEASE ENSURE TO DOWNLOAD THIS TOOLKIT PRIOR TO USE OR AMEND CODE TO FIT PREFFERED C3D READER. Link to BTK download: https://code.google.com/archive/p/b-tk/Version: 1.1Date completed: 09/12/2021 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Dataset shared with research community. 
URL https://figshare.shef.ac.uk/articles/software/Supplementary_Material_A_Quality_Control_Check_to_Ensu...
 
Title Supplementary material for 'The uncontrolled manifold theory can explain only part of the inter-trial variability of knee contact force during level walking' 
Description This repository contains the supplementary material for the paper 'The uncontrolled manifold theory can explain only part of the inter-trial variability of knee contact force during level walking' by van Veen, Mazzà and Viceconti. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://figshare.shef.ac.uk/articles/figure/Supplementary_material_for_The_uncontrolled_manifold_the...
 
Title Supplementary material from "Analysis of mechanotransduction dynamics during combined mechanical stimulation and modulation of the extracellular-regulated kinase cascade uncovers hidden information within the signalling noise" 
Description Osteoporosis is a bone disease characterized by brittle bone and increased fracture incidence. With ageing societies worldwide, the disease presents a high burden on health systems. Furthermore, there are limited treatments for osteoporosis with just two anabolic pharmacological agents approved by the US Food and Drug Administration. Healthy bones are believed to be maintained via an intricate relationship between dual biochemical and mechanical (bio-mechanical) stimulations. It is widely considered that osteoporosis emerges as a result of disturbances to said relationship. The mechanotransduction process is key to this balance, and disruption of its dynamics in bone cells plays a role in osteoporosis development. Nonetheless, the exact details and mechanisms that drive and secure the health of bones are still elusive at the cellular and molecular scales. This study examined the dual modulation of mechanical stimulation and mechanotransduction activation dynamics in an osteoblast (OB). The aim was to find patterns of mechanotransduction dynamics demonstrating a significant change that can be mapped to alterations in the OB responses, specifically at the level of gene expression and osteogenic markers such as alkaline phosphatase. This was achieved using a three-dimensional hybrid multiscale computational model simulating mechanotransduction in the OB and its interaction with the extracellular matrix, combined with a numerical analytical technique. The model and the analysis method predict that within the noise of mechanotransduction, owing to modulation of the bio-mechanical stimulus and consequent gene expression, there are unique events that provide signatures for a shift in the system's dynamics. Furthermore, the study uncovered molecular interactions that can be potential drug targets. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://rs.figshare.com/collections/Supplementary_material_from_Analysis_of_mechanotransduction_dyna...
 
Title Supplementary materials for: Damage tolerance and toughness of elderly human femora 
Description Supplementary materials: Martelli, S., Giorgi, M., Dall'Ara, E., Perilli, E (2021), "Damage tolerance and toughness of elderly human femora", Acta Biomaterialia, 123, pp 167-177, URL: https://doi.org/10.1016/j.actbio.2021.01.011 Figure. S1 - Analysis of the DVC strain error with varying grid size and image resolution. The standard deviation of the error (SDER) is reported for the low (pixel size = 0.12 mm) and high image resolution (pixel size = 0.03 mm) used in the present study. Figure S2 - Cortical instability. The entire proximal epiphysis (right) is displayed as reference. The femoral head surface before loading, before fracture and after fracture displayed cortical depressions distributed over the most highly compressed region growing as the load increases (left). Figure S3 - The internal bone collapse occurring in two separate regions in two subsequent load steps for specimen #2. A single region reaching 3% compression (top) is visible under load step 3 (2134 N) while under load step 4 (1993 N), a second larger region reaching 9% compression (middle) is visible deeper inside the head. The difference between load step 4 and 3 (bottom) showed that the second internal collapse largely occurred separately in time and independently from the first internal collapse visible under load step 3 (top). Supplementary animations 1. Setup.avi: The animation displays the proximal femur in the imaging chamber, including the pressure socked and the soaked fabric maintaining bone moisture throughout the experiment. 2. S1.avi: The fracture sequence for specimen #1 displayed for a 1.5 mm slice. 3. S2.avi: The fracture sequence for specimen #2 displayed for a 1.5 mm slice. 4. S3.avi: The fracture sequence for specimen #3 displayed for a 1.5 mm slice. 5. S4.avi: The fracture sequence for specimen #4 displayed for a 1.5 mm slice. 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? Yes  
Impact Diagrams and animations shared with the research community. 
URL https://ars.els-cdn.com/content/image/1-s2.0-S1742706121000295-mmc1.zip
 
Title Supplementary tables from Analysis of mechanotransduction dynamics during combined mechanical stimulation and modulation of the extracellular-regulated kinase cascade uncovers hidden information within the signalling noise 
Description Osteoporosis is a bone disease characterized by brittle bone and increased fracture incidence. With ageing societies worldwide, the disease presents a high burden on health systems. Furthermore, there are limited treatments for osteoporosis with just two anabolic pharmacological agents approved by the US Food and Drug Administration. Healthy bones are believed to be maintained via an intricate relationship between dual biochemical and mechanical (bio-mechanical) stimulations. It is widely considered that osteoporosis emerges as a result of disturbances to said relationship. The mechanotransduction process is key to this balance, and disruption of its dynamics in bone cells plays a role in osteoporosis development. Nonetheless, the exact details and mechanisms that drive and secure the health of bones are still elusive at the cellular and molecular scales. This study examined the dual modulation of mechanical stimulation and mechanotransduction activation dynamics in an osteoblast (OB). The aim was to find patterns of mechanotransduction dynamics demonstrating a significant change that can be mapped to alterations in the OB responses, specifically at the level of gene expression and osteogenic markers such as alkaline phosphatase. This was achieved using a three-dimensional hybrid multiscale computational model simulating mechanotransduction in the OB and its interaction with the extracellular matrix, combined with a numerical analytical technique. The model and the analysis method predict that within the noise of mechanotransduction, owing to modulation of the bio-mechanical stimulus and consequent gene expression, there are unique events that provide signatures for a shift in the system's dynamics. Furthermore, the study uncovered molecular interactions that can be potential drug targets. 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Data shared with research community. 
URL https://rs.figshare.com/articles/journal_contribution/Supplementary_tables_from_Analysis_of_mechanot...
 
Title XCT2FE: Computes the stiffness and strength of a small portion of distal radius or distal tibia examined with High-Resolution peripheral Quantitative Computed Tomography (HRpQCT) 
Description XCT2FE: this service computes the stiffness and strength of a small portion of distal radius or distal tibia examined with High-Resolution peripheral Quantitative Computed Tomography (HRpQCT). It can be used in clinical research to derive more reliable functional endpoints from HRpQCT images. 
Type Of Material Computer model/algorithm 
Year Produced 2019 
Provided To Others? Yes  
Impact Modeal Available to research community 
URL https://xct2fe.insigneo.org/hrpqct/
 
Title code, data and appropriate materials associated with: "Analysis of mechanotransduction dynamics during combined mechanical stimulation and modulation of the extracellular-regulated kinase cascade uncovers hidden information within the signalling noise" 
Description Code, data and appropriate materials are available under the Creative Commons Attribution License. Associated with paper: Ascolani, G., Skerry, T. M., Lacroix, D., Dal'Ara, E., Shuaib, A. (2020), "Analysis of mechanotransduction dynamics during combined mechanical stimulation and modulation of the extracellular-regulated kinase cascade uncovers hidden information within the signalling noise", Interface Focus, 11(1): 20190136, URL: https://doi.org/10.1098/rsfs.2019.0136 
Type Of Material Database/Collection of data 
Year Produced 2020 
Provided To Others? Yes  
Impact Code and Data shared with research community. 
URL https://drive.google.com/drive/folders/0AEwfzIdJmd_BUk9PVA
 
Title microCT scans of bone and cement-bone microstructures 
Description Repeated scans of: VOI1 - the largest possible area that could be inscribed in all vertebrae (300x300x432 voxels); VOI2 - regions of fully cement-augmented trabecular bone (152x152x432 voxels); VOI3 - regions of interface between augmented and non-augmented trabecular bone (152x152x432 voxels); VOI4 - regions containing both trabecular and cortical bone (152x152x432 voxels); VOI5 - regions containing both trabecular and cortical bone with surrounding saline solution (152x152x432 voxels). The spatial resolution of each scan is of 39 micrometers. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact Data available to the research community 
URL https://doi.org/10.6084/m9.figshare.4308926.v2
 
Title microCT scans of natural and augmented vertebrae 
Description Repeated scans of natural and augmented vertebrae in zero-strain conditions. Each tomograms have a spatial resolution of 39 micrometers. 
Type Of Material Database/Collection of data 
Year Produced 2016 
Provided To Others? Yes  
Impact Data available to research community 
URL https://doi.org/10.6084/m9.figshare.4062351.v1
 
Description FP7 PIPER (Xinshan Li) 
Organisation European Commission
Country European Union (EU) 
Sector Public 
PI Contribution We are currently investigating the difference in mechanical response by comparing the 3-yr-old PIPER model and our personalised model. The PIPER model is generated by scaling down from an adult femur. This research will shine some light on the validity of scaling adult models for paediatric applications, and could be a game changer if the adult model is proven to be inaccurate.
Collaborator Contribution There has been 2 teleconference. And we have received some help from the consortia regarding the running of 3-yr-old PIPER model. The PIPER consortia provided some additional material in terms of the validation of their organ-scale model for the 3-yr-old femur, which was not previously made public, as part of the open source code released by the consortia.
Impact Not yet. The final year project student is wrapping up the work. There could be a potential publication.
Start Year 2017
 
Description Great Ormond Street Hospital (Xinshan Li) 
Organisation Great Ormond Street Hospital (GOSH)
Country United Kingdom 
Sector Hospitals 
PI Contribution The Sheffield team developed a new pipeline to create personalised paediatric long bone models from paired MRI-CT scans. This is the first in the field as the combination of mineralising bone and mineralised bone in infant bone modelling has never been attempted before.
Collaborator Contribution We received 4 sets of paired MRI-CT scans from GOSH. We have also visited the GOSH team in the past for 4 face to face meetings. The GOSH team has also provided valuable clinical opinion on the topic of personalised modelling for children.
Impact There is a publication being submitted to CMBBE. No specific agreements, as it only involved a small number of dataset which has already got research ethics approval on the GOSH side.
Start Year 2016
 
Description Making things through movement, Leeds, Mazza 
Organisation University of Leeds
Country United Kingdom 
Sector Academic/University 
PI Contribution Access and expert support in the use of motion capture technology, provided by the Insigneo Gait Laboratory, associated with MultiSim WP2.
Collaborator Contribution Dancers and choreography to create a performance and video of performance.
Impact This is a collaboration between Mechanical Engineering - Biomechanics, providing motion capture technology and the creative arts providing creative dance and choreography. A collaborative performance 'Making things through movement' working across disabled and able communities, recorded under engagement. Further funding and opportunities are being explored to extend this collaboration and produce further performances.
Start Year 2017
 
Description Making things through movement, Leeds, Mazza 
Organisation University of Sheffield
Department Department of Infection, Immunity and Cardiovascular Disease
Country United Kingdom 
Sector Academic/University 
PI Contribution Access and expert support in the use of motion capture technology, provided by the Insigneo Gait Laboratory, associated with MultiSim WP2.
Collaborator Contribution Dancers and choreography to create a performance and video of performance.
Impact This is a collaboration between Mechanical Engineering - Biomechanics, providing motion capture technology and the creative arts providing creative dance and choreography. A collaborative performance 'Making things through movement' working across disabled and able communities, recorded under engagement. Further funding and opportunities are being explored to extend this collaboration and produce further performances.
Start Year 2017
 
Description Dem Bones are Gonna Walk About, Sheffield Festival of Science 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Dem Bones Gonna Walk Around: An overview of our session
This session briefly explains how the musculoskeletal system is made up of bones, muscles and joints that help us take part in everyday physical activities such as sitting, standing and walking. It then demonstrates how these movements can be captured and used to predict the forces created in our joints between the muscles and bones. Find out how computer models of physical activities can be developed to predict the risk of bone fracture!
Members of the public were invited to the Insigneo Gait Laboratory, for an hour long workshop, including presentations and interactive demonstrations of motion capture and computer simulations. This workshop was ran four times over Sheffield Festival of Science to groups of 20 people, across a wide range of ages.
Year(s) Of Engagement Activity 2017
URL http://multisim-insigneo.org/events/fun-inspiring-free-events-sheffield-festival-science-engineering...
 
Description Exploring STEM for Girls 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Schools
Results and Impact MultiSim will hold a stand at an Engineering Faculty organised outreach event aimed at Year 9-11, providing interactive activities, and a videos explaining our research.
Year(s) Of Engagement Activity 2020
URL https://www.sheffield.ac.uk/faculty/science/stem
 
Description Ideas Bazaar 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Media (as a channel to the public)
Results and Impact MultiSim held a stand at the University's Ideas Bazaar.
The Ideas Bazaar is an opportunity for Sheffield academics to meet with local artists and media practitioners, to form collaborations for the next Sheffield Festival of the Mind, in September 2020, a high profile public engagement activity.
MultiSim interacted with a number of local artists and practitioners explaining our research and exploring possible collaborations.
From this event three collaborations were established, linking artists with Insigneo projects:
* A dancer/choreographer with MultiSim
* A Ceramicist with Spinner-EID
* A Sculpture with VPM2 - In silico approaches for preclinical assessment of bone changes in osteoporosis and osteoarthritis studies
Each of these were converted into a proposal for a Festival of the Mind project.
The dancer/choreographer collaboration with MultiSim:

Women's Movement 100: a performance and exhibition resulting from an exploration of the women's suffrage movement, emancipation and health related through dance and installation involving both academia and the wider community.

was successful and will progress to be part of Festival of the Mind.
Year(s) Of Engagement Activity 2019
URL https://www.sheffield.ac.uk/ideasbazaar
 
Description Making things through movement, Leeds, Mazza 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Making things through movement explored the creative, socially beneficial and therapeutic benefits of working with and through movement across disabled and abled communities. On this project, supported, by the Faculty of Engineering as part of their outreach events, we worked with cultural theorist and choreographer, Nicolas Salazar Sutil (University of Leeds). The project brought together disabled participants with different levels of paralysis and previous exposure to dance, collaborating with a dancer and choreographer to explore and extend the experience of embodiment, through movement, narration and music. Motion capture technology was used to produce a visualisation of the processes through which movement was collaboratively explored. The topic that organically emerged from the participants' interactions is pain, and this video shows a performance that developed from the collaboration. It was, however, the process of working across arts and humanities and engineering, with active input from our participants, that made this project particularly rewarding for everyone involved. We aim to extend it further to explore how motion capture technology can augment the experience of movement for people who have limited movement.
Year(s) Of Engagement Activity 2017
URL http://mhs.group.shef.ac.uk/moving-bodies-humanitiesengingeering-pilot-projects/
 
Description Modelathon 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Aim of Modelathon: To engage researchers in the field of musculoskeletal and cardiovascular research with the principles and practice of multiscale modelling through addressing an authentic research challenge using both industrial and open source research tools and frameworks. To raise the profile of the project amongst the academic community and industry.

The MultiSim Modelathon brings together PhD and PostDoc researchers in the field of Multi-Scale Modelling and Biomechanical Engineering, from around the world, to compete in teams against one another to solve a complex multi-scale modelling problem. This three-day event is based on the concept of a hackathon event where different teams work on a challenging problem to 'hack' a computer code. Here there is no 'hacking' but 'modelling'. The teams competed to solve a challenging multi-scale biomechanical problem within the musculoskeletal system using state-of-the-art techniques and software.

Industry members and multi-scale experts supported the event, including software providers and Ansys, Simpleware, Materialise and Simulia. They supported the Modelathon by providing licences for the academic developers preparing and testing the challenges before the event, and the Modelathon participants during the event. They provided expertise and technical support during the event to encourage participants to make the most of the software available and sponsored the events to subsidise the costs to the participants.

In 2017, a scene-setting one-day symposium was added to the Modelathon.

The 2018 and 2020 offerings of the Modelathon were co-sponsored and supported by OATech+, and focused on the clinical problem of osteoarthritis in the hip and knee joints respectively.

Each year the Modelathon attracts approximately 25 researchers.
Year(s) Of Engagement Activity 2015,2016,2017,2018,2020
URL http://multisim-insigneo.org/modelathon/
 
Description SoleLincs 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact Three researchers from MultiSim WP2, Body Model, were invited to a CPD (Career and Professional Development) day workshop by Sole Lincs, a practice network in for Foot Health professionals based in Lincolnshire. The researchers presented their work on the biomechanics of the gait cycle in the morning, with demonstrations of the sensors and motion capture equipment. In the afternoon, participants then reflected on how this knowledge may influenced their practice in the context of case studies that they brought to the session.
Year(s) Of Engagement Activity 2018