Detection and prediction of tooth mobility during the periodontitis healing process

The focus of the article is on a generic approach to prediction of a healing process based on automatic measurement and modelling of mechanical disease indicators. As a specific example the healing process after treatment of advanced periodontitis is characterised and predicted based on measurement of tooth mobility (TM). For the measurement a new mechatronic instrument was developed that includes a pneumatically driven probe with incorporated sensors of tooth displacement and loading force. TM is measured by a computer controlled data acquisition system and predicted by a non-parametric regression. Similarly as in the characterisation of technical processes, a measured sample is described by TM time series detected on a particular patient, while the regression is determined by a set of samples obtained from a group of patients following periodontal therapy. The influence of surgical access therapy and systemic administration of metronidazole as an adjunct to the mechanical treatment is demonstrated. For this purpose the average changes of tooth mobility are determined on variously treated subgroups. A new method of healing process prediction is demonstrated and its performance is described by a prediction quality.     

A test of the model to predict unusually stable RNA hairpin loop stability

To investigate the accuracy of a model [Giese et al., 1998, Biochemistry37:1094-1100 and Mathews et al., 1999, JMol Biol 288:911-940] that predicts the stability of RNA hairpin loops, optical melting studies were conducted on sets of hairpins previously determined to have unusually stable thermodynamic parameters. Included were the tetraloops GNRA and UNCG (where N is any nucleotide and R is a purine), hexaloops with UU first mismatches, and the hairpin loop of the iron responsive element, CAGUGC. The experimental values for the GNRA loops are in excellent agreement (deltaG degrees 37 within 0.2 kcal/mol and melting temperature (TM) within 4 degrees C) with the values predicted by the model. When the UNCG hairpin loops are treated as tetraloops, and a bonus of 0.8 kcal/mol included in the prediction to account for the extra stable first mismatch (UG), the measured and predicted values are also in good agreement (deltaG degrees 37 within 0.7 kcal/mol and TM within 3 degrees C). Six hairpins with unusually stable UU first mismatches also gave good agreement with the predictions (deltaG degrees 37 within 0.5 kcal/mol and TM within 8 degrees C), except for hairpins closed by wobble base pairs. For these hairpins, exclusion of the additional stabilization term for UU first mismatches improved the prediction (AG degrees 37 within 0.1 kcal/mol and TM within 3 degrees C). Hairpins with the iron-responsive element loop were not predicted well by the model, as measured deltaG degrees 37 values were at least 1 kcal/mol greater than predicted.     

Development of a novel intraoral measurement device to determine the biomechanical characteristics of the human periodontal ligament

Periodontal diseases like gingivitis and periodontitis have damaging effects on the periodontium and commonly affect the mechanical properties of the periodontal ligament (PDL), which in the end might lead to loss of teeth. Monitoring tooth mobility and changes of the material properties of the PDL might help in early diagnosis of periodontal diseases and improve their prognosis. It was the aim of this study to develop a novel intraoral device to determine the biomechanical characteristics of the periodontal ligament. This includes the measurement of applied forces and resulting tooth displacement in order to investigate the biomechanical behaviour of the periodontium with varying loading protocols with respect to velocity and tooth displacement. The developed device uses a piezoelectric actuator to apply a displacement to a tooth's crown, and the resulting force is measured by an integrated force sensor. To measure the tooth displacement independently and non-invasively, two magnets are fixed on the teeth. The change in the magnetic field caused by the movement of the magnets is measured by a total of 16 Hall sensors. The displacement of the tooth is calculated from the movement of the magnets. The device was tested in vitro on premolars of four porcine mandibular segments and in vivo on two volunteers. The teeth were loaded with varying activation curves. Comparing the force progression of different activation velocities, the forces decreased with decreasing velocity. Intensive testing demonstrated that the device fulfils all requirements. After acceptance of the ethical committee, further testing in clinical measurements is planned.     

A numerical model of the fracture healing process that describes tissue development and revascularisation

A dynamic model was developed to simulate complex interactions of mechanical stability, revascularisation and tissue differentiation in secondary fracture healing. Unlike previous models, blood perfusion was included as a spatio-temporal state variable to simulate the revascularisation process. A 2D, axisymmetrical finite element model described fracture callus mechanics. Fuzzy logic rules described the following biological processes: angiogenesis, intramembranous ossification, chondrogenesis, cartilage calcification and endochondral ossification, all of which depended on local strain state and local blood perfusion. In order to evaluate how the predicted revascularisation depended on the mechanical environment, we simulated two different healing cases according to two groups of transverse metatarsal osteotomies in sheep with different axial stability. The model predicted slower revascularisation and delayed bony bridging for the less stable case, which corresponded well to the experimental observations. A revascularisation sensitivity analysis demonstrated the potential of the model to account for different conditions regarding the blood supply.     

A numerical model of the fracture healing process that describes tissue development and revascularisation

A dynamic model was developed to simulate complex interactions of mechanical stability, revascularisation and tissue differentiation in secondary fracture healing. Unlike previous models, blood perfusion was included as a spatio-temporal state variable to simulate the revascularisation process. A 2D, axisymmetrical finite element model described fracture callus mechanics. Fuzzy logic rules described the following biological processes: angiogenesis, intramembranous ossification, chondrogenesis, cartilage calcification and endochondral ossification, all of which depended on local strain state and local blood perfusion. In order to evaluate how the predicted revascularisation depended on the mechanical environment, we simulated two different healing cases according to two groups of transverse metatarsal osteotomies in sheep with different axial stability. The model predicted slower revascularisation and delayed bony bridging for the less stable case, which corresponded well to the experimental observations. A revascularisation sensitivity analysis demonstrated the potential of the model to account for different conditions regarding the blood supply.     

Age assessment of fallow deer (Dama dama): from a scoring scheme based on radiographs of developing permanent molariform teeth

The stages of permanent tooth development observed in radiographs of the mandible were described for known-aged fallow deer Dama dama . Ten stages were defined and, by allocating scores for these stages, the scores that may be expected for a particular age have been identified. Lastly, the predicted age was given for total molariform scores. These were obtained, with 95% prediction intervals, from a regression of age on total molariform scores. An age assessment from tooth development stages can be made up to three years, after which, no further development takes place.     

Simulation of the nutrient supply in fracture healing

The healing process for bone fractures is sensitive to mechanical stability and blood supply at the fracture site. Most currently available mechanobiological algorithms of bone healing are based solely on mechanical stimuli, while the explicit analysis of revascularization and its influences on the healing process have not been thoroughly investigated in the literature. In this paper, revascularization was described by two separate processes: angiogenesis and nutrition supply. The mathematical models for angiogenesis and nutrition supply have been proposed and integrated into an existing fuzzy algorithm of fracture healing. The computational algorithm of fracture healing, consisting of stress analysis, analyses of angiogenesis and nutrient supply, and tissue differentiation, has been tested on and compared with animal experimental results published previously. The simulation results showed that, for a small and medium-sized fracture gap, the nutrient supply is sufficient for bone healing, for a large fracture gap, non-union may be induced either by deficient nutrient supply or inadequate mechanical conditions. The comparisons with experimental results demonstrated that the improved computational algorithm is able to simulate a broad spectrum of fracture healing cases and to predict and explain delayed unions and non-union induced by large gap sizes and different mechanical conditions. The new algorithm will allow the simulation of more realistic clinical fracture healing cases with various fracture gaps and geometries and may be helpful to optimise implants and methods for fracture fixation.     

Effect of temperature on the nanomechanics of lipid bilayers studied by force spectroscopy

The effect of temperature on the nanomechanical response of supported lipid bilayers has been studied by force spectroscopy with atomic force microscopy. We have experimentally proved that the force needed to puncture the lipid bilayer (Fy) is temperature dependent. The quantitative measurement of the evolution of Fy with temperature has been related to the structural changes that the surface undergoes as observed through atomic force microscopy images. These studies were carried out with three different phosphatidylcholine bilayers with different main phase transition temperature (TM), namely, 1,2-dimyristoyl-sn-glycero-3-phosphocholine, 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, and 2-dilauroyl-sn-glycero-3-phosphocholine. The solid-like phase shows a much higher Fy than the liquid-like phase, which also exhibits a jump in the force curve. Within the solid-like phase, Fy decreases as temperature is increased and suddenly drops as it approaches TM. Interestingly, a "well" in the Fy versus temperature plot occurs around TM, thus proving an "anomalous mechanical softening" around TM. Such mechanical softening has been predicted by experimental techniques and also by molecular dynamics simulations and interpreted in terms of water ordering around the phospholipid headgroups. Ion binding has been demonstrated to increase Fy, and its influence on both solid and liquid phases has also been discussed.     

Stiffness characterization of anisotropic trabecular meshwork

Elevation of intraocular pressure has been correlated to changes in stiffness of trabecular meshwork (TM) in glaucomatous eyes although mechanical properties of the TM remain to be quantitatively determined. Data in the literature suggest that the TM cannot be considered mechanically as a uniform layer of isotropic elastic material, because the value of its Young’s modulus depends on the methods of measurements and can vary up to five orders of magnitude. To this end, we proposed a new theoretical framework for mechanical analysis of the TM, in which the inner wall of Schlemm’s canal and the juxtacanalicular tissue in the TM were treated as a uniform layer of isotropic elastic material, and the rest of the TM, i.e., the uveal and corneoscleral meshworks, were modeled as a uniform layer of transversely isotropic material. Using the model, we demonstrated that the large discrepancy in the apparent Young’s modulus reported in the literature could be caused by the anisotropy of the meshwork that was significantly stiffer in the longitudinal direction than in the transverse direction. The theoretical framework could be used to integrate existing data of the stiffness, investigate anisotropic behaviors of the tissues, and develop new methods to measure mechanical properties of the TM.     

COMSAT: Residue contact prediction of transmembrane proteins based on support vector machines and mixed integer linear programming

In this article, we present COMSAT, a hybrid framework for residue contact prediction of transmembrane (TM) proteins, integrating a support vector machine (SVM) method and a mixed integer linear programming (MILP) method. COMSAT consists of two modules: COMSAT_SVM which is trained mainly on position–specific scoring matrix features, and COMSAT_MILP which is an ab initio method based on optimization models. Contacts predicted by the SVM model are ranked by SVM confidence scores, and a threshold is trained to improve the reliability of the predicted contacts. For TM proteins with no contacts above the threshold, COMSAT_MILP is used. The proposed hybrid contact prediction scheme was tested on two independent TM protein sets based on the contact definition of 14 Å between Cα‐Cα atoms. First, using a rigorous leave‐one‐protein‐out cross validation on the training set of 90 TM proteins, an accuracy of 66.8%, a coverage of 12.3%, a specificity of 99.3% and a Matthews' correlation coefficient (MCC) of 0.184 were obtained for residue pairs that are at least six amino acids apart. Second, when tested on a test set of 87 TM proteins, the proposed method showed a prediction accuracy of 64.5%, a coverage of 5.3%, a specificity of 99.4% and a MCC of 0.106. COMSAT shows satisfactory results when compared with 12 other state‐of‐the‐art predictors, and is more robust in terms of prediction accuracy as the length and complexity of TM protein increase. COMSAT is freely accessible at http://hpcc.siat.ac.cn/COMSAT/ . Proteins 2016; 84:332–348. © 2016 Wiley Periodicals, Inc.     

Three-dimensional load measurements in an external fixator

On the basis of a six-degree-of-freedom adjustable fracture reduction hexapod external fixator, a system which can be used for measuring axial and shear forces as well as torsion and bending moments in the fixator in vivo was developed. In a pilot study on 9 patients (7 fresh fractures and 2 osteotomies of the tibia), the load in the fixator during the healing process was measured after 2, 4, 8 and 12 weeks and at fixator removal. The measured values enabled both the type of fracture to be determined as well as the monitoring of the healing process. In well-reduced type A3 fractures small axial (direction of the bone axis) forces were found in the fixator. A2, B2 and C3 fractures showed distinct axial forces, which decreased during the healing process, according to an increasing load transfer over the bone. Bending moments in the fixator showed good correspondence with the clinical healing process, except in the case of a C3 fracture. A combination of bending moment and axial force proved to be particularly suitable to assess fracture healing. In transverse fractures, the well-known resorption phenomenon of bone in the fracture gap at approximately 4 weeks was detected by the system. Compared with other external fixator load measurements in vivo, the hexapod offers the advantage of being able to measure all forces and moments in the fixator separately and with a relatively simple mechanical arrangement. In our opinion, it will be possible to control fracture healing using this system, thereby minimizing radiation exposure from radiographs. Furthermore, the measurement system is a step towards the development of external fixator systems that enable automatic adjustments of the callus mechanical situation ("automatic dynamization") and inform the patients about the optimal weight bearing of their extremity ("intelligent fixator").     

On the influence of mechanical conditions in osteochondral defect healing

Despite the introduction of new surgical techniques, the treatment of cartilage defects remains challenging. Delay or complete failure of cartilage healing is associated with problems in biological regeneration. The influence of mechanical conditions on this process, however, remains unevaluated. Osteochondral defects were generated on the left femoral condyle in 18 Yucatan minipigs. After 4, 6 and 12 weeks the defect filling, trabecular orientation and bone density were compared to the intact contralateral side. The mechanical straining during this period was then analyzed using an adaptive finite element technique. Histologically, the osteochondral defects showed bone resorption at the base and bone formation from the circumference. At 12 weeks, the macroscopically healed specimens showed fibrous cartilage formation, a minimally organized trabecular structure and increased trabecular volume fraction compared to the controls (p < 0.002). The amount of cancellous, cartilagineous, and fibrous tissue and the defect size as measured in histomorphometric analysis for the three time points (4, 6 and 12 weeks) was comparable in magnitude to that predicted by finite element analysis. The simulated osteochondral healing process was not fully capable of re-establishing a hyaline-like cartilage layer. The correlation between simulation and histology allows identification of mechanical factors that appear to have a larger impact on the healing of osteochondral defects than previously considered.     

Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction

Reported performance of existing transmembrane (TM) topology prediction methods were often based on evaluations which neglected the risk of signal peptides (SP) being predicted as putative TM as well. Here, we evaluated 12 selected TM topology prediction methods (TMpred, TopPred II, DAS, TMAP, MEMSAT 2, SOSUI, PRED-TMR2, TMHMM 2.0, HMMTOP 2.0, SPLIT 3.5, TM Finder, and MPEx) for the effect of SP in prediction performance considering three SP treatments, namely: "remain" (untreated), "removed first", and "removed later". The results showed that the presence of SP significantly affected the prediction performance of the 12 selected TM topology prediction methods for all three predicted attributes (the number of transmembrane segments (TMSs), the number of TMSs plus position, and the N-tail location) and for the predicted topology (combined predictions of three attributes) by causing a reduction in prediction accuracy. In particular, lower prediction accuracies were obtained if SP is left untreated (remain) while significant increases were observed if SP is removed either first or later. However, between "removed first" and "removed later" SP treatments, the difference was statistically insignificant. In addition, we found that machine learning-based prediction methods were less affected by the presence of SP than hydropathy-based methods, but still the potential risk of degrading the prediction performance is there however to a lesser degree. Thus, when performing genome-wide analysis, the SP issue should be addressed during TM topology prediction.     

Structural modeling of dual-affinity purified Pho84 phosphate transporter

The phosphate transporter Pho84 of Saccharomyces cerevisiae is predicted to contain 12 transmembrane (TM) regions, divided into two partially duplicated parts of 6 TM segments. The three-dimensional (3D) organization of the Pho84 protein has not yet been determined. However, the 3D crystal structure of the Escherichia coli MFS glycerol-3-phosphate/phosphate antiporter, GlpT, and lactose transporter, LacY, has recently been determined. On the basis of extensive prediction and fold recognition analyses (at the MetaServer), GlpT was proposed as the best structural template on which the arrangement of TM segments of the Pho84 transporter was fit, using the comparative structural modeling program MODELLER. To initiate an evaluation of the appropriateness of the Pho84 model, we have performed two direct tests by targeting spin labels to putative TM segments 8 and 12. Electron paramagnetic resonance spectroscopy was then applied on purified and spin labeled Pho84. The line shape from labels located at both positions is consistent with the structural environment predicted by the template-generated model, thus supporting the model.     

Computational simulation of fracture healing: influence of interfragmentary movement on the callus growth

Bone fractures heal through a complex process involving several cellular events. This healing process can serve to study factors that control tissue growth and differentiation from mesenchymal stem cells. The mechanical environment at the fracture site is one of the factors influencing the healing process and controls size and differentiation patterns in the newly formed tissue. Mathematical models can be useful to unravel the complex relation between mechanical environment and tissue formation. In this study, we present a mathematical model that predicts tissue growth and differentiation patterns from local mechanical signals. Our aim was to investigate whether mechanical stimuli, through their influence on stem cell proliferation and chondrocyte hypertrophy, predict characteristic features of callus size and geometry. We found that the model predicted several geometric features of fracture calluses. For instance, callus size was predicted to increase with increasing movement. Also, increases in size were predicted to occur through increase in callus diameter but not callus length. These features agree with experimental observations. In addition, spatial and temporal tissue differentiation patterns were in qualitative agreement with well-known experimental results. We therefore conclude that local mechanical signals can probably explain the shape and size of fracture calluses.     

Significance of electrophoretic mobility distribution to bacterial transport in granular porous media

A method is developed to obtain the electrophoretic mobility distribution of colloidal particles by microelectrophoresis. The results demonstrate that for small particles (< 1 microm), the experimental mobility distribution must be deconvoluted to remove the effect of the random Brownian motion so that the electrophoretic mobility distribution can be obtained. For bacteria-sized particles (on the order of 1 microm or larger), the random Brownian motion is not significant, and the experimental mobility distribution represents the electrophoretic mobility distribution. The significance of the electrophoretic mobility distribution to bacterial transport is demonstrated through comparison between experimental and theoretical values of collision efficiency. Using the extended Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, the electrophoretic mobility distribution of bacteria is transformed to the distribution of collision efficiencies. For strain Comamonas sp. DA001, the predicted collision efficiency values span orders of magnitude, indicating that variation of surface charge density in a monoclonal bacterial population is a cause for the orders of magnitude variation of experimentally determined collision efficiencies. However, despite the fact that the predicted and experimental alpha distributions overlap, the match is not adequate. This inadequacy is ascribed to inability to probe heterogeneity of bacterial surface hydrophobicity, and the inability of the DLVO theory to quantitatively model particle deposition.     

Optimizing the Prediction Process: From Statistical Concepts to the Case Study of Soccer

We present a systematic approach for prediction purposes based on panel data, involving information about different interacting subjects and different times (here: two). The corresponding bivariate regression problem can be solved analytically for the final statistical estimation error. Furthermore, this expression is simplified for the special case that the subjects do not change their properties between the last measurement and the prediction period. This statistical framework is applied to the prediction of soccer matches, based on information from the previous and the present season. It is determined how well the outcome of soccer matches can be predicted theoretically. This optimum limit is compared with the actual quality of the prediction, taking the German premier league as an example. As a key step for the actual prediction process one has to identify appropriate observables which reflect the strength of the individual teams as close as possible. A criterion to distinguish different observables is presented. Surprisingly, chances for goals turn out to be much better suited than the goals themselves to characterize the strength of a team. Routes towards further improvement of the prediction are indicated. Finally, two specific applications are discussed.     

Quantitative measures for fracture healing: an in-vitro biomechanical study

A method is presented to assess the functional capabilities of plated osteotomized canine femora as load bearing structures and to quantify their healing status. In this method the osteotomized bones and their intact contralateral controls are tested in nondestructive bending, in twenty-four planes of loading at 15 degree angular increments. Flexural rigidity (EI), in each of the planes, is determined by using classical beam theory. It has been found that the EI values have the expected elliptical distribution. The 24 EI values, obtained for each bone, are curve fitted by regression analysis and the characteristics of each bone are described by the three parameters defining its ellipse. The parameters of the ellipses of the osteotomized bone and of its contralateral control are used to define four new parameters that may serve as measures for the healing efficiency. One of these serves as an indicator for the fragility of the healed bone and the other three add quantitative information on its mechanical state.     

Comparison of biophysical stimuli for mechano-regulation of tissue differentiation during fracture healing

Most long-bone fractures heal through indirect or secondary fracture healing, a complex process in which endochondral ossification is an essential part and bone is regenerated by tissue differentiation. This process is sensitive to the mechanical environment, and several authors have proposed mechano-regulation algorithms to describe it using strain, pore pressure and/or interstitial fluid velocity as biofeedback variables. The aim of this study was to compare various mechano-regulation algorithms' abilities to describe normal fracture healing in one computational model. Additionally, we hypothesized that tissue differentiation during normal fracture healing could be equally well regulated by the individual mechanical stimuli, e.g. deviatoric strain, pore pressure or fluid velocity. A biphasic finite element model of an ovine tibia with a 3mm fracture gap and callus was used to simulate the course of tissue differentiation during normal fracture healing. The load applied was regulated in a biofeedback loop, where the load magnitude was determined by the interfragmentary movement in the fracture gap. All the previously published mechano-regulation algorithms studied, simulated the course of normal fracture healing correctly. They predicted (1) intramembranous bone formation along the periosteum and callus tip, (2) endochondral ossification within the external callus and cortical gap, and (3) creeping substitution of bone towards the gap from the initial lateral osseous bridge. Some differences between the effects of the algorithms were seen, but they were not significant. None of the volumetric components, i.e. pore pressure or fluid velocity, alone were able to correctly predict spatial or temporal tissue distribution during fracture healing. However, simulation as a function of only deviatoric strain accurately predicted the course of normal fracture healing. This suggests that the deviatoric component may be the most significant mechanical parameter to guide tissue differentiation during indirect fracture healing.