Development and validation of a new set-up simulator dedicated to ocular proton therapy at CNAO

An Eye Tracking System (ETS) is used at CNAO for providing a stable and reproducible ocular proton therapy (OPT) set-up, featuring a fixation light (FL) and monitoring stereo-cameras embedded in a rigid case. The aim of this work is to propose an ETS set-up simulation algorithm, that automatically provides the FL positioning in space, according to patient-specific gaze direction and avoiding interferences with patient, beam and collimator.Two configurations are provided: one in the CT room for acquiring images required for treatment planning with the patient lying on a couch, and one related to the treatment room with the patient sitting in front of the beam. Algorithm validation was performed reproducing ETS simulation (CT) and treatment (room) set-up for 30 patients previously treated at CNAO. The positioning accuracy of the device was quantified through a set of 14 control points applied to the ETS case and localizable both in the CT volume and in room X-ray images.Differences between the position of ETS reference points estimated by the algorithm and those measured by imaging systems are reported. The corresponding gaze direction deviation is on average 0.2° polar and 0.3° azimuth for positioning in CT room and 0.1° polar and 0.4° azimuth in the treatment room.The simulation algorithm was embedded in a clinically usable software application, which we assessed as capable of ensuring ETS positioning with an average accuracy of 2 mm in CT room and 1.5 mm in treatment room, corresponding to gaze direction deviations consistently lower than 1°.     

Development of a robotic walking simulator for gait rehabilitation]

Restoration of gait is a major concern of rehabilitation after stroke or spinal cord injury. Modern concepts of motor learning favour a task-specific repetitive approach, i.e. "whoever wants to learn to walk again must walk." However, the physical demands this places on the therapist, is a limiting factor in the clinical routine setting. This article describes a robotic walking simulator for gait training that enables wheelchair-bound subjects to freely carry out repetitive practicing of an individually adapted gait pattern under simulation of the manual guidance of an experienced therapist. The technical principle applied makes use of programmable footplates with permanent foot/machine contact in combination with compliance control. The solution chosen comprises a planar parallel-serial hybrid kinematic system with three degrees of freedom that moves the feet in the sagittal plane. Gait analysis while floor walking and stair climbing, clinical practicability and safety aspects were the basis for the design. A variable compliance control enables man-machine interaction, ranging from purely position controlled movement to full compliance during swing phase above a virtual ground profile. In full compliance mode the robotic walking simulator behaves like a haptic device. The concept presented offers new prospects for individualized gait rehabilitation.     

Development of a practical small-scale circulation bioreactor and application to a drug metabolism simulator

We developed an easy-to-use, small-scale circulation-type bioreactor system that enables the simultaneous evaluation of many specimens. Medium flow was generated by a magnetic stirrer in this system. Primary rat hepatocytes formed a monolayer, and there were no morphological differences between cells in circulation and stationary cultures. The mitochondrial activity of hepatocytes in the circulation culture was 23% lower than that in the stationary culture after 2 days of culture. On the other hand, albumin production activity in the circulation culture after 2 days of culture was 1.4 times higher than that in the stationary culture. Albumin production activity per cell in the circulation culture was 1.9 times higher than that in the stationary culture after 2 days of culture. In addition, lidocaine metabolism rate per cell in the circulation culture was 1.3 times higher than that in the stationary culture. The lidocaine clearance of the circulation culture in our circulation-type bioreactor was 1.3 times higher than that of the stationary culture. It was shown that this bioreactor is suitable for the expression of the liver-specific functions of primary rat hepatocytes. Therefore, we can expect that this circulation-type bioreactor system will be a practical drug metabolism simulator.     

Development and validation of a model for radiofrequency ablation]

Since 1986, cardiac arrhythmias have been successfully treated by destroying the underlying arrhythmogenic substrate with radiofrequency energy (radiofrequency ablation). The aim of this study was to develop a model for radiofrequency ablation enabling evaluation of the temperature distribution within cardiac tissue and the influence of electrode tissue contact. The model describes a 7F electrode, 4 mm in length and positioned perpendicular to the tissue. Heat convection within the tissue and heat lost via the blood was taken into account. Simulation of constant tissue exposure to 4 W resulted in a temperature increase of 35 degrees C after 10 sec. The temperature increase in the depths was less steep, but constant, and exceeded the electrode temperature at depths of 1 mm after 40 sec, 2 mm after 100 sec, and 3 mm after 200 sec. Electrode tissue contact proved to have a great influence on tissue temperature. Poor contact resulted in a temperature rise of only 0.68 degree C with a maximum of 50 W, whereas with ideal contact, 4 W sufficed to achieve a chosen setpoint of 70 degrees C. The model was validated in an in vitro setup using ventricular tissue from the pig. A strong correlation was found between simulated heating efficiency during temperature-controlled ablations under different contact conditions, and the respective measured values in the in vitro setup with a correlation coefficient of 0.97.     

The development,calibration and validation of a numerical total knee replacement kinematics simulator considering laxity and unconstrained flexion motions

Kinematics testing is essential during the development of total knee replacement (TKR) designs. Although computational analysis cannot replace physical testing, it offers repeatability and consistency at a much lower cost and shorter time, making it an excellent complement to experiments. Previous numerical models have been limited by several factors: the validity of the models is usually only considered for a single TKR design, friction models are typically overly simplified and the determination of simulation parameters is often inadequate, or tedious and expensive. The objective of this study is to develop, calibrate and validate a TKR kinematics simulation considering multiple TKR geometries, an accurate friction model and simulation parameters determined using a systematic optimisation method. The calibrated model was able to predict TKR kinematics for different TKR geometries, and is ideal for screening new implant designs, reducing the number of experiments required at the design stage.     

The development, calibration and validation of a numerical total knee replacement kinematics simulator considering laxity and unconstrained flexion motions

Kinematics testing is essential during the development of total knee replacement (TKR) designs. Although computational analysis cannot replace physical testing, it offers repeatability and consistency at a much lower cost and shorter time, making it an excellent complement to experiments. Previous numerical models have been limited by several factors: the validity of the models is usually only considered for a single TKR design, friction models are typically overly simplified and the determination of simulation parameters is often inadequate, or tedious and expensive. The objective of this study is to develop, calibrate and validate a TKR kinematics simulation considering multiple TKR geometries, an accurate friction model and simulation parameters determined using a systematic optimisation method. The calibrated model was able to predict TKR kinematics for different TKR geometries, and is ideal for screening new implant designs, reducing the number of experiments required at the design stage.     

Development and validation of a diagnostic microbial microarray for methanotrophs

The potential of DNA microarray technology in high-throughput detection of bacteria and quantitative assessment of their community structures is widely acknowledged but has not been fully realised yet. A generally applicable set of techniques, based on readily available technologies and materials, was developed for the design, production and application of diagnostic microbial microarrays. A microarray targeting the particulate methane monooxygenase (pmoA) gene was developed for the detection and quantification of methanotrophs and functionally related bacteria. A microarray consisting of a set of 59 probes that covers the whole known diversity of these bacteria was validated with a representative set of extant strains and environmental clones. The potential of the pmoA microarray was tested with environmental samples. The results were in good agreement with those of clone library sequence analyses. The approach can currently detect less dominant bacteria down to 5% of the total community targeted. Initial tests assessing the quantification potential of this system with artificial PCR mixtures showed very good correlation with the expected results with standard deviations in the range of 0.4-17.2%. Quantification of environmental samples with this method requires the design of a reference mixture consisting of very close relatives of the strains within the sample and is currently limited by biases inherent in environmental DNA extraction and universal PCR amplification.     

Development and validation of a correction equation for Corvis tonometry

Primary objective: This study uses numerical analysis and validation against clinical data to develop a method to correct intraocular pressure (IOP) measurements obtained using the Corvis Tonometer for the effects of central corneal thickness (CCT), and age. Materials and Methods: Finite element analysis was conducted to simulate the effect of tonometric air pressure on the intact eye globe. The analyses considered eyes with wide variations in IOP (10–30 mm Hg), CCT (445–645 microns), R (7.2–8.4 mm), shape factor, P (0.6–1) and age (30–90 years). In each case, corneal deformation was predicted and used to estimate the IOP measurement by Corvis (CVS-IOP). Analysis of the results led to an algorithm relating estimates of true IOP as a function of CVS-IOP, CCT and age. All other parameters had negligible effect on CVS-IOP and have therefore been omitted from the algorithm. Predictions of corrected CVS-IOP, as obtained by applying the algorithm to a clinical data-set involving 634 eyes, were assessed for their association with the cornea stiffness parameters; CCT and age. Results: Analysis of CVS-IOP measurements within the 634-large clinical data-set showed strong correlation with CCT (3.06 mm Hg/100 microns, r² = 0.204) and weaker correlation with age (0.24 mm Hg/decade, r² = 0.009). Applying the algorithm to IOP measurements resulted in IOP estimations that became less correlated with both CCT (0.04 mm Hg/100 microns, r² = 0.005) and age (0.09 mm Hg/decade, r² = 0.002). Conclusions: The IOP correction process developed in this study was successful in reducing reliance of IOP measurements on both corneal thickness and age in a healthy European population.     

Development and validation of a subject-specific finite element model of a human clavicle

This study aimed to develop and validate a finite element (FE) model of a human clavicle which can predict the structural response and bone fractures under both axial compression and anterior–posterior three-point bending loads. Quasi-static non-injurious axial compression and three-point bending tests were first conducted on a male clavicle followed by a dynamic three-point bending test to fracture. Then, two types of FE models of the clavicle were developed using bone material properties which were set to vary with the computed tomography image density of the bone. A volumetric solid FE model comprised solely of hexahedral elements was first developed. A solid-shell FE model was then created which modelled the trabecular bone as hexahedral elements and the cortical bone as quadrilateral shell elements. Finally, simulations were carried out using these models to evaluate the influence of variations in cortical thickness, mesh density, bone material properties and modelling approach on the biomechanical responses of the clavicle, compared with experimental data. The FE results indicate that the inclusion of density-based bone material properties can provide a more accurate reproduction of the force–displacement response and bone fracture timing than a model with uniform bone material properties. Inclusion of a variable cortical thickness distribution also slightly improves the ability of the model to predict the experimental response. The methods developed in this study will be useful for creating subject-specific FE models to better understand the biomechanics and injury mechanism of the clavicle.     

Development and validation of a consistency based multiple structure alignment algorithm

SUMMARY: We introduce an algorithm that uses the information gained from simultaneous consideration of an entire group of related proteins to create multiple structure alignments (MSTAs). Consistency-based alignment (CBA) first harnesses the information contained within regions that are consistently aligned among a set of pairwise superpositions in order to realign pairs of proteins through both global and local refinement methods. It then constructs a multiple alignment that is maximally consistent with the improved pairwise alignments. We validate CBA's alignments by assessing their accuracy in regions where at least two of the aligned structures contain the same conserved sequence motif. RESULTS: CBA correctly aligns well over 90% of motif residues in superpositions of proteins belonging to the same family or superfamily, and it outperforms a number of previously reported MSTA algorithms.     

Development and validation of a prognostic gene-expression signature for lung adenocarcinoma

Although several prognostic signatures have been developed in lung cancer, their application in clinical practice has been limited because they have not been validated in multiple independent data sets. Moreover, the lack of common genes between the signatures makes it difficult to know what biological process may be reflected or measured by the signature. By using classical data exploration approach with gene expression data from patients with lung adenocarcinoma (n = 186), we uncovered two distinct subgroups of lung adenocarcinoma and identified prognostic 193-gene gene expression signature associated with two subgroups. The signature was validated in 4 independent lung adenocarcinoma cohorts, including 556 patients. In multivariate analysis, the signature was an independent predictor of overall survival (hazard ratio, 2.4; 95% confidence interval, 1.2 to 4.8; p = 0.01). An integrated analysis of the signature revealed that E2F1 plays key roles in regulating genes in the signature. Subset analysis demonstrated that the gene signature could identify high-risk patients in early stage (stage I disease), and patients who would have benefit of adjuvant chemotherapy. Thus, our study provided evidence for molecular basis of clinically relevant two distinct two subtypes of lung adenocarcinoma.     

Development and validation of a bioenergetics model for juvenile and adult burbot

Oxygen consumption of juvenile and adult burbot Lota lota was measured in an intermittent-flow respirometer to determine the effect of temperature and fish body mass on metabolic rate. These results were combined with data from earlier experiments and the 'Wisconsin bioenergetics' model was constructed. The model was validated under laboratory conditions by comparing observed and predicted food consumption and growth of burbot fed on dead vendace Coregonus albula . There was a good correspondence between observed and estimated growth and food consumption under experimental conditions: the mean absolute per cent errors of growth and food consumption were 4·8 and 24·0%. Estimated values with the new model were an improvement over the Atlantic cod Gadus morhua model previously used for burbot. In the field, the reliability of food consumption estimates was verified by using polychlorinated biphenyls (PCB) accumulation as an indirect indicator of the food consumption rate. The total PCB concentration of nine out of 13 burbot was estimated accurately. Thus, the burbot model produced good estimates of food consumption, even under field conditions.     

Development and validation of a bioreactor for physical stimulation of engineered cartilage

A bioreactor has been developed to apply different regimes of physical stimulation to tissue specimens under highly controlled conditions. The computer-controlled device exposes specimens to compressive deformation at various strains and frequencies, measures the load applied to each sample and allows simultaneous medium stirring at different velocities. Validation tests confirmed the accuracy of the system in (i) its displacement (errors averaged 0.072+/-0.051 microm), and in (ii) setting the contact with the samples utilizing micrometer screws coupled to plungers (errors averaged 1.74+/-0.36% for samples of 1.60-3.18 mm thickness), thus ensuring accurate compressive deformation. The developed bioreactor, which represents an advance in the technology for physical stimulation of tissue specimens, is currently used to apply compressive deformation and hydrodynamic forces to human chondrocytes cultured in biodegradable polymer scaffolds, with the goals of (i) engineering functional grafts for the repair of cartilage defects (ii).     

Development and validation of a simulation model for blowfly strike of sheep

A comprehensive simulation model for sheep blowfly strike due to Lucilia sericata (Meigen) (Diptera: Calliphoridae), which builds on previously published versions but also incorporates important new empirical data, is used to explain patterns of lamb and ewe strike recorded on 370 farms in south-west, south-east and central England and Wales. The model is able to explain a significant percentage of the variance in lamb strike incidence in all four regions, and ewe strike in three of the four regions. The model is able to predict the start of seasonal blowfly strike within one week in three of the four regions for both ewes and lambs, and within 3 weeks in the fourth region. It is concluded that the accuracy of the model will allow it to be used to assess the likely efficacy of new control techniques and the effects of changes in existing husbandry practices on strike incidence. The model could also be used to give sheep farmers advance warning of approaching strike problems. However, the ability to forecast future strike patterns is dependent on the accuracy of the weather projections; the more long-term the forecast, the more approximate the prediction is likely to be. When applied on a regional basis, model forecasts indicate expected average patterns of strike incidence and may not therefore be appropriate for individual farmers whose husbandry practices differ substantially from the average.