Trypanosoma cruzi mitochondrial maxicircles display species- and strain-specific variation and a conserved element in the non-coding region

Abstract Background The mitochondrial DNA of kinetoplastid flagellates is distinctive in the eukaryotic world due to its massive size, complex form and large sequence content. Comprised of catenated maxicircles that contain rRNA and protein-coding genes and thousands of heterogeneous minicircles encoding small guide RNAs, the kinetoplast network has evolved along with an extreme form of mRNA processing in the form of uridine insertion and deletion RNA editing. Many maxicircle-encoded mRNAs cannot be translated without this post-transcriptional sequence modification. Results We present the complete sequence and annotation of the Trypanosoma cruzi maxicircles for the CL Brener and Esmeraldo strains. Gene order is syntenic with Trypanosoma brucei and Leishmania tarentolae maxicircles. The non-coding components have strain-specific repetitive regions and a variable region that is unique for each strain with the exception of a conserved sequence element that may serve as an origin of replication, but shows no sequence identity with L. tarentolae or T. brucei. Alternative assemblies of the variable region demonstrate intra-strain heterogeneity of the maxicircle population. The extent of mRNA editing required for particular genes approximates that seen in T. brucei. Extensively edited genes were more divergent among the genera than non-edited and rRNA genes. Esmeraldo contains a unique 236-bp deletion that removes the 5'-ends of ND4 and CR4 and the intergenic region. Esmeraldo shows additional insertions and deletions outside of areas edited in other species in ND5, MURF1, and MURF2, while CL Brener has a distinct insertion in MURF2. Conclusion The CL Brener and Esmeraldo maxicircles represent two of three previously defined maxicircle clades and promise utility as taxonomic markers. Restoration of the disrupted reading frames might be accomplished by strain-specific RNA editing. Elements in the non-coding region may be important for replication, transcription, and anchoring of the maxicircle within the kinetoplast network.

Nonlinear / electromagnetic co-simulation and co-design of microwave links in highly polluted and / or strongly inhomogeneous environments

The objective of the Ph.D. thesis is to put the basis of an all-embracing link analysis procedure that may form a general reference scheme for the future state-of-the-art of RF/microwave link design: it is basically meant as a circuit-level simulation of an entire radio link, with – generally multiple – transmitting and receiving antennas examined by EM analysis. In this way the influence of mutual couplings on the frequency-dependent near-field and far-field performance of each element is fully accounted for. The set of transmitters is treated as a unique nonlinear system loaded by the multiport antenna, and is analyzed by nonlinear circuit techniques. In order to establish the connection between transmitters and receivers, the far-fields incident onto the receivers are evaluated by EM analysis and are combined by extending an available Ray Tracing technique to the link study. EM theory is used to describe the receiving array as a linear active multiport network. Link performances in terms of bit error rate (BER) are eventually verified a posteriori by a fast system-level algorithm. In order to validate the proposed approach, four heterogeneous application contexts are provided. A complete MIMO link design in a realistic propagation scenario is meant to constitute the reference case study. The second one regards the design, optimization and testing of various typologies of rectennas for power generation by common RF sources. Finally, the project and implementation of two typologies of radio identification tags, at X-band and V-band respectively. In all the cases the importance of an exhaustive nonlinear/electromagnetic co-simulation and co-design is demonstrated to be essential for any accurate system performance prediction.

Fiber beam-columns models with flexure-shear interaction for nonlinear analysis of reinforced concrete structures

The aim of this study was to develop a model capable to capture the different contributions which characterize the nonlinear behaviour of reinforced concrete structures. In particular, especially for non slender structures, the contribution to the nonlinear deformation due to bending may be not sufficient to determine the structural response. Two different models characterized by a fibre beam-column element are here proposed. These models can reproduce the flexure-shear interaction in the nonlinear range, with the purpose to improve the analysis in shear-critical structures. The first element discussed is based on flexibility formulation which is associated with the Modified Compression Field Theory as material constitutive law. The other model described in this thesis is based on a three-field variational formulation which is associated with a 3D generalized plastic-damage model as constitutive relationship. The first model proposed in this thesis was developed trying to combine a fibre beamcolumn element based on the flexibility formulation with the MCFT theory as constitutive relationship. The flexibility formulation, in fact, seems to be particularly effective for analysis in the nonlinear field. Just the coupling between the fibre element to model the structure and the shear panel to model the individual fibres allows to describe the nonlinear response associated to flexure and shear, and especially their interaction in the nonlinear field. The model was implemented in an original matlab® computer code, for describing the response of generic structures. The simulations carried out allowed to verify the field of working of the model. Comparisons with available experimental results related to reinforced concrete shears wall were performed in order to validate the model. These results are characterized by the peculiarity of distinguishing the different contributions due to flexure and shear separately. The presented simulations were carried out, in particular, for monotonic loading. The model was tested also through numerical comparisons with other computer programs. Finally it was applied for performing a numerical study on the influence of the nonlinear shear response for non slender reinforced concrete (RC) members. Another approach to the problem has been studied during a period of research at the University of California Berkeley. The beam formulation follows the assumptions of the Timoshenko shear beam theory for the displacement field, and uses a three-field variational formulation in the derivation of the element response. A generalized plasticity model is implemented for structural steel and a 3D plastic-damage model is used for the simulation of concrete. The transverse normal stress is used to satisfy the transverse equilibrium equations of at each control section, this criterion is also used for the condensation of degrees of freedom from the 3D constitutive material to a beam element. In this thesis is presented the beam formulation and the constitutive relationships, different analysis and comparisons are still carrying out between the two model presented.

The long-term mechanical integrity of non-reinforced PEEK-OPTIMA polymer for demanding spinal applications: experimental and finite-element analysis

Polyetheretherketone (PEEK) is a novel polymer with potential advantages for its use in demanding orthopaedic applications (e.g. intervertebral cages). However, the influence of a physiological environment on the mechanical stability of PEEK has not been reported. Furthermore, the suitability of the polymer for use in highly stressed spinal implants such as intervertebral cages has not been investigated. Therefore, a combined experimental and analytical study was performed to address these open questions. A quasi-static mechanical compression test was performed to compare the initial mechanical properties of PEEK-OPTIMA polymer in a dry, room-temperature and in an aqueous, 37 degrees C environment (n=10 per group). The creep behaviour of cylindrical PEEK polymer specimens (n=6) was measured in a simulated physiological environment at an applied stress level of 10 MPa for a loading duration of 2000 hours (12 weeks). To compare the biomechanical performance of different intervertebral cage types made from PEEK and titanium under complex loading conditions, a three-dimensional finite element model of a functional spinal unit was created. The elastic modulus of PEEK polymer specimens in a physiological environment was 1.8% lower than that of specimens tested at dry, room temperature conditions (P<0.001). The results from the creep test showed an average creep strain of less than 0.1% after 2000 hours of loading. The finite element analysis demonstrated high strain and stress concentrations at the bone/implant interface, emphasizing the importance of cage geometry for load distribution. The stress and strain maxima in the implants were well below the material strength limits of PEEK. In summary, the experimental results verified the mechanical stability of the PEEK-OPTIMA polymer in a simulated physiological environment, and over extended loading periods. Finite element analysis supported the use of PEEK-OPTIMA for load-bearing intervertebral implants.

Analytical investigation of squeeze film dampers

Squeeze film damping effects naturally occur if structures are subjected to loading situations such that a very thin film of fluid is trapped within structural joints, interfaces, etc. An accurate estimate of squeeze film effects is important to predict the performance of dynamic structures. Starting from linear Reynolds equation which governs the fluid behavior coupled with structure domain which is modeled by Kirchhoff plate equation, the effects of nondimensional parameters on the damped natural frequencies are presented using boundary characteristic orthogonal functions. For this purpose, the nondimensional coupled partial differential equations are obtained using Rayleigh-Ritz method and the weak formulation, are solved using polynomial and sinusoidal boundary characteristic orthogonal functions for structure and fluid domain respectively. In order to implement present approach to the complex geometries, a two dimensional isoparametric coupled finite element is developed based on Reissner-Mindlin plate theory and linearized Reynolds equation. The coupling between fluid and structure is handled by considering the pressure forces and structural surface velocities on the boundaries. The effects of the driving parameters on the frequency response functions are investigated. As the next logical step, an analytical method for solution of squeeze film damping based upon Green’s function to the nonlinear Reynolds equation considering elastic plate is studied. This allows calculating modal damping and stiffness force rapidly for various boundary conditions. The nonlinear Reynolds equation is divided into multiple linear non-homogeneous Helmholtz equations, which then can be solvable using the presented approach. Approximate mode shapes of a rectangular elastic plate are used, enabling calculation of damping ratio and frequency shift as well as complex resistant pressure. Moreover, the theoretical results are correlated and compared with experimental results both in the literature and in-house experimental procedures including comparison against viscoelastic dampers.

A nonlinear QCT-based finite element model validation study for the human femur tested in two configurations in vitro

Purpose Femoral fracture is a common medical problem in osteoporotic individuals. Bone mineral density (BMD) is the gold standard measure to evaluate fracture risk in vivo. Quantitative computed tomography (QCT)-based homogenized voxel finite element (hvFE) models have been proved to be more accurate predictors of femoral strength than BMD by adding geometrical and material properties. The aim of this study was to evaluate the ability of hvFE models in predicting femoral stiffness, strength and failure location for a large number of pairs of human femora tested in two different loading scenarios. Methods Thirty-six pairs of femora were scanned with QCT and total proximal BMD and BMC were evaluated. For each pair, one femur was positioned in one-legged stance configuration (STANCE) and the other in a sideways configuration (SIDE). Nonlinear hvFE models were generated from QCT images by reproducing the same loading configurations imposed in the experiments. For experiments and models, the structural properties (stiffness and ultimate load), the failure location and the motion of the femoral head were computed and compared. Results In both configurations, hvFE models predicted both stiffness (R2=0.82 for STANCE and R2=0.74 for SIDE) and femoral ultimate load (R2=0.80 for STANCE and R2=0.85 for SIDE) better than BMD and BMC. Moreover, the models predicted qualitatively well the failure location (66% of cases) and the motion of the femoral head. Conclusions The subject specific QCT-based nonlinear hvFE model cannot only predict femoral apparent mechanical properties better than densitometric measures, but can additionally provide useful qualitative information about failure location.

Finite Element Based Nonlinear Normalization of Human Lumbar Intervertebral Disc Stiffness to Account for Its Morphology

Disc degeneration, usually associated with low back pain and changes of intervertebral stiffness, represents a major health issue. As the intervertebral disc (IVD) morphology influences its stiffness, the link between mechanical properties and degenerative grade is partially lost without an efficient normalization of the stiffness with respect to the morphology. Moreover, although the behavior of soft tissues is highly nonlinear, only linear normalization protocols have been defined so far for the disc stiffness. Thus, the aim of this work is to propose a nonlinear normalization based on finite elements (FE) simulations and evaluate its impact on the stiffness of human anatomical specimens of lumbar IVD. First, a parameter study involving simulations of biomechanical tests (compression, flexion/extension, bilateral torsion and bending) on 20 FE models of IVDs with various dimensions was carried out to evaluate the effect of the disc's geometry on its compliance and establish stiffness/morphology relations necessary to the nonlinear normalization. The computed stiffness was then normalized by height (H), cross-sectional area (CSA), polar moment of inertia (J) or moments of inertia (Ixx, Iyy) to quantify the effect of both linear and nonlinear normalizations. In the second part of the study, T1-weighted MRI images were acquired to determine H, CSA, J, Ixx and Iyy of 14 human lumbar IVDs. Based on the measured morphology and pre-established relation with stiffness, linear and nonlinear normalization routines were then applied to the compliance of the specimens for each quasi-static biomechanical test. The variability of the stiffness prior to and after normalization was assessed via coefficient of variation (CV). The FE study confirmed that larger and thinner IVDs were stiffer while the normalization strongly attenuated the effect of the disc geometry on its stiffness. Yet, notwithstanding the results of the FE study, the experimental stiffness showed consistently higher CV after normalization. Assuming that geometry and material properties affect the mechanical response, they can also compensate for one another. Therefore, the larger CV after normalization can be interpreted as a strong variability of the material properties, previously hidden by the geometry's own influence. In conclusion, a new normalization protocol for the intervertebral disc stiffness in compression, flexion, extension, bilateral torsion and bending was proposed, with the possible use of MRI and FE to acquire the discs' anatomy and determine the nonlinear relations between stiffness and morphology. Such protocol may be useful to relate the disc's mechanical properties to its degree of degeneration.

Finite element analysis predicts experimental failure patterns in vertebral bodies loaded via intervertebral discs up to large deformation

Vertebral compression fracture is a common medical problem in osteoporotic individuals. The quantitative computed tomography (QCT)-based finite element (FE) method may be used to predict vertebral strength in vivo, but needs to be validated with experimental tests. The aim of this study was to validate a nonlinear anatomy specific QCT-based FE model by using a novel testing setup. Thirty-seven human thoracolumbar vertebral bone slices were prepared by removing cortical endplates and posterior elements. The slices were scanned with QCT and the volumetric bone mineral density (vBMD) was computed with the standard clinical approach. A novel experimental setup was designed to induce a realistic failure in the vertebral slices in vitro. Rotation of the loading plate was allowed by means of a ball joint. To minimize device compliance, the specimen deformation was measured directly on the loading plate with three sensors. A nonlinear FE model was generated from the calibrated QCT images and computed vertebral stiffness and strength were compared to those measured during the experiments. In agreement with clinical observations, most of the vertebrae underwent an anterior wedge-shape fracture. As expected, the FE method predicted both stiffness and strength better than vBMD (R2 improved from 0.27 to 0.49 and from 0.34 to 0.79, respectively). Despite the lack of fitting parameters, the linear regression of the FE prediction for strength was close to the 1:1 relation (slope and intercept close to one (0.86 kN) and to zero (0.72 kN), respectively). In conclusion, a nonlinear FE model was successfully validated through a novel experimental technique for generating wedge-shape fractures in human thoracolumbar vertebrae.

Morphological ripening of fluid inclusions and coupled zone-refining in quartz crystals revealed by cathodoluminescence imaging: Implications for CL-petrography, fluid inclusion analysis and trace-element geothermometry

Cathodoluminescence (CL) studies have previously shown that some secondary fluid inclusions in luminescent quartz are surrounded by dark, non-luminescent patches, resulting from fracture-sealing by late, trace-element-poor quartz. This finding has led to the tacit generalization that all dark CL patches indicate influx of low temperature, late-stage fluids. In this study we have examined natural and synthetic hydrothermal quartz crystals using CL imaging supplemented by in-situ elemental analysis. The results lead us to propose that all natural, liquid-water-bearing inclusions in quartz, whether trapped on former crystal growth surfaces (i.e., of primary origin) or in healed fractures (i.e., of pseudosecondary or secondary origin), are surrounded by three-dimensional, non-luminescent patches. Cross-cutting relations show that the patches form after entrapment of the fluid inclusions and therefore they are not diagnostic of the timing of fluid entrapment. Instead, the dark patches reveal the mechanism by which fluid inclusions spontaneously approach morphological equilibrium and purify their host quartz over geological time. Fluid inclusions that contain solvent water perpetually dissolve and reprecipitate their walls, gradually adopting low-energy euhedral and equant shapes. Defects in the host quartz constitute solubility gradients that drive physical migration of the inclusions over distances of tens of μm (commonly) up to several mm (rarely). Inclusions thus sequester from their walls any trace elements (e.g., Li, Al, Na, Ti) present in excess of equilibrium concentrations, thereby chemically purifying their host crystals in a process analogous to industrial zone refining. Non-luminescent patches of quartz are left in their wake. Fluid inclusions that contain no liquid water as solvent (e.g., inclusions of low-density H2O vapor or other non-aqueous volatiles) do not undergo this process and therefore do not migrate, do not modify their shapes with time, and are not associated with dark-CL zone-refined patches. This new understanding has implications for the interpretation of solids within fluid inclusions (e.g., Ti- and Al-minerals) and for the elemental analysis of hydrothermal and metamorphic quartz and its fluid inclusions by microbeam methods such as LA-ICPMS and SIMS. As Ti is a common trace element in quartz, its sequestration by fluid inclusions and its depletion in zone-refined patches impacts on applications of the Ti-in-quartz geothermometer.

Experimental validation of a nonlinear μ FE model based on cohesive-frictional plasticity for trabecular bone

Trabecular bone is a porous mineralized tissue playing a major load bearing role in the human body. Prediction of age-related and disease-related fractures and the behavior of bone implant systems needs a thorough understanding of its structure-mechanical property relationships, which can be obtained using microcomputed tomography-based finite element modeling. In this study, a nonlinear model for trabecular bone as a cohesive-frictional material was implemented in a large-scale computational framework and validated by comparison of μFE simulations with experimental tests in uniaxial tension and compression. A good correspondence of stiffness and yield points between simulations and experiments was found for a wide range of bone volume fraction and degree of anisotropy in both tension and compression using a non-calibrated, average set of material parameters. These results demonstrate the ability of the model to capture the effects leading to failure of bone for three anatomical sites and several donors, which may be used to determine the apparent behavior of trabecular bone and its evolution with age, disease, and treatment in the future.