Three-dimensional joint kinematics of swimming using body-worn inertial and magnetic sensors

Wearable inertial and magnetic measurements units (IMMU) are an important tool for underwater motion analysis because they are swimmer-centric, they require only simple measurement set-up and they provide the performance results very quickly. In order to estimate 3D joint kinematics during motion, protocols were developed to transpose the IMMU orientation estimation to a biomechanical model. The aim of the thesis was to validate a protocol originally propositioned to estimate the joint angles of the upper limbs during one-degree-of-freedom movements in dry settings and herein modified to perform 3D kinematics analysis of shoulders, elbows and wrists during swimming. Eight high-level swimmers were assessed in the laboratory by means of an IMMU while simulating the front crawl and breaststroke movements. A stereo-photogrammetric system (SPS) was used as reference. The joint angles (in degrees) of the shoulders (flexion-extension, abduction-adduction and internal-external rotation), the elbows (flexion-extension and pronation-supination), and the wrists (flexion-extension and radial-ulnar deviation) were estimated with the two systems and compared by means of root mean square errors (RMSE), relative RMSE, Pearson’s product-moment coefficient correlation (R) and coefficient of multiple correlation (CMC). Subsequently, the athletes were assessed during pool swimming trials through the IMMU. Considering both swim styles and all joint degrees of freedom modeled, the comparison between the IMMU and the SPS showed median values of RMSE lower than 8°, representing 10% of overall joint range of motion, high median values of CMC (0.97) and R (0.96). These findings suggest that the protocol accurately estimated the 3D orientation of the shoulders, elbows and wrists joint during swimming with accuracy adequate for the purposes of research. In conclusion, the proposed method to evaluate the 3D joint kinematics through IMMU was revealed to be a useful tool for both sport and clinical contexts.

Interacting bosons and fermions in three-dimensional optical lattice potentials

This thesis reports on the realization, characterization and analysis of ultracold bosonic and fermionic atoms in three-dimensional optical lattice potentials. Ultracold quantum gases in optical lattices can be regarded as ideal model systems to investigate quantum many-body physics. In this work interacting ensembles of bosonic 87Rb and fermionic 40K atoms are employed to study equilibrium phases and nonequilibrium dynamics. The investigations are enabled by a versatile experimental setup, whose core feature is a blue-detuned optical lattice that is combined with Feshbach resonances and a red-detuned dipole trap to allow for independent control of tunneling, interactions and external confinement. The Fermi-Hubbard model, which plays a central role in the theoretical description of strongly correlated electrons, is experimentally realized by loading interacting fermionic spin mixtures into the optical lattice. Using phase-contrast imaging the in-situ size of the atomic density distribution is measured, which allows to extract the global compressibility of the many-body state as a function of interaction and external confinement. Thereby, metallic and insulating phases are clearly identified. At strongly repulsive interaction, a vanishing compressibility and suppression of doubly occupied lattice sites signal the emergence of a fermionic Mott insulator. In a second series of experiments interaction effects in bosonic lattice quantum gases are analyzed. Typically, interactions between microscopic particles are described as two-body interactions. As such they are also contained in the single-band Bose-Hubbard model. However, our measurements demonstrate the presence of multi-body interactions that effectively emerge via virtual transitions of atoms to higher lattice bands. These findings are enabled by the development of a novel atom optical measurement technique: In quantum phase revival spectroscopy periodic collapse and revival dynamics of the bosonic matter wave field are induced. The frequencies of the dynamics are directly related to the on-site interaction energies of atomic Fock states and can be read out with high precision. The third part of this work deals with mixtures of bosons and fermions in optical lattices, in which the interspecies interactions are accurately controlled by means of a Feshbach resonance. Studies of the equilibrium phases show that the bosonic superfluid to Mott insulator transition is shifted towards lower lattice depths when bosons and fermions interact attractively. This observation is further analyzed by applying quantum phase revival spectroscopy to few-body systems consisting of a single fermion and a coherent bosonic field on individual lattice sites. In addition to the direct measurement of Bose-Fermi interaction energies, Bose-Bose interactions are proven to be modified by the presence of a fermion. This renormalization of bosonic interaction energies can explain the shift of the Mott insulator transition. The experiments of this thesis lay important foundations for future studies of quantum magnetism with fermionic spin mixtures as well as for the realization of complex quantum phases with Bose-Fermi mixtures. They furthermore point towards physics that reaches beyond the single-band Hubbard model.

Three-dimensional electron microscopy of myriapod hemocyanin, planorbid snail acetylcholine-binding protein and cyanobacterial Vipp1

Three-dimensional electron microscopy (3-D EM) provides a framework for the analysis of large protein quaternary structures. The advantage over the generally higher resolving meth- od of X-ray crystallography is the embedding of the proteins in their physiological environ- ment. However, results of the two methods can be combined to obtain superior structural information. In this work, three different protein types – (i) Myriapod hemocyanin, (ii) vesi- cle-inducing protein in plastids 1 (Vipp1) and (iii) acetylcholine-binding protein (AChBP) – were structurally analyzed by 2-D and 3-D EM and, where possible, functionally interpreted.rnMyriapod hemocyanins have been previously shown to be 6x6-meric assemblies that, in case of Scutigera coleoptrata hemocyanin (ScoHc), show two 3x6-mer planes whith a stag- gering angle of approximately 60°. Here, previously observed structural differences between oxy- and deoxy-ScoHc could be substantiated. A 4° rotation between hexamers of two dif- ferent 3x6-mer planes was measured, which originates at the most central inter-hexamer in- terface. Further information about allosteric behaviour in myriapod hemocyanin was gained by analyzing Polydesmus angustus hemocyanin (PanHc), which shows a stable 3x6-mer and divergent histidine patterns in the inter-hexamer interfaces when compared to ScoHc. Both findings would conclusively explain the very different oxygen binding properties of chilopod and diplopod hemocyanin.rnVipp1 is a protein found in cyanobacteria and higher plants which is essential for thyla- koid membrane function and forms highly variable ring-shaped structures. In the course of this study, the first 3-D analysis of Vipp1 was conducted and yielded reconstructions of six differently sized Vipp1 rings from negatively stained images at resolutions between 20 to 30 Å. Furthermore, mutational analyses identified specific N-terminal amino acids that are essential for ring formation. On the basis of these analyses and previously published results, a hypothetical model of the Vipp1 tertiary and quaternary structure was generated.rnAChBP is a water-soluble protein in the hemolymph of mollusks. It is a structural and functional homologue of the ligand-binding domain of nicotinic acetylcholine receptors. For the freshwater snail Biomphalaria glabrata, we previously described two types of AChBP (BgAChBP1 and BgAChBP2). In this work, a 6 Å 3-D reconstruction of native BgAChBP is presented, which shows a dodecahedral assembly that is unprecedented for an AChBP. Single particle analysis of recombinantely expressed BgAChBP types led to preliminary results show- ing a dodecahedral assembly of BgAChBP1 and a dipentameric assembly of BgAChBP2. This indicates divergent biological functions of the two types.

Three dimensional finite element simulation of polymer melting and flow in a single-screw extruder : optimization of screw channel geometry

Single-screw extrusion is one of the widely used processing methods in plastics industry, which was the third largest manufacturing industry in the United States in 2007 [5]. In order to optimize the single-screw extrusion process, tremendous efforts have been devoted for development of accurate models in the last fifty years, especially for polymer melting in screw extruders. This has led to a good qualitative understanding of the melting process; however, quantitative predictions of melting from various models often have a large error in comparison to the experimental data. Thus, even nowadays, process parameters and the geometry of the extruder channel for the single-screw extrusion are determined by trial and error. Since new polymers are developed frequently, finding the optimum parameters to extrude these polymers by trial and error is costly and time consuming. In order to reduce the time and experimental work required for optimizing the process parameters and the geometry of the extruder channel for a given polymer, the main goal of this research was to perform a coordinated experimental and numerical investigation of melting in screw extrusion. In this work, a full three-dimensional finite element simulation of the two-phase flow in the melting and metering zones of a single-screw extruder was performed by solving the conservation equations for mass, momentum, and energy. The only attempt for such a three-dimensional simulation of melting in screw extruder was more than twenty years back. However, that work had only a limited success because of the capability of computers and mathematical algorithms available at that time. The dramatic improvement of computational power and mathematical knowledge now make it possible to run full 3-D simulations of two-phase flow in single-screw extruders on a desktop PC. In order to verify the numerical predictions from the full 3-D simulations of two-phase flow in single-screw extruders, a detailed experimental study was performed. This experimental study included Maddock screw-freezing experiments, Screw Simulator experiments and material characterization experiments. Maddock screw-freezing experiments were performed in order to visualize the melting profile along the single-screw extruder channel with different screw geometry configurations. These melting profiles were compared with the simulation results. Screw Simulator experiments were performed to collect the shear stress and melting flux data for various polymers. Cone and plate viscometer experiments were performed to obtain the shear viscosity data which is needed in the simulations. An optimization code was developed to optimize two screw geometry parameters, namely, screw lead (pitch) and depth in the metering section of a single-screw extruder, such that the output rate of the extruder was maximized without exceeding the maximum temperature value specified at the exit of the extruder. This optimization code used a mesh partitioning technique in order to obtain the flow domain. The simulations in this flow domain was performed using the code developed to simulate the two-phase flow in single-screw extruders.

Modeling spontaneous three-dimensional polymerization

For human beings, the origin of life has always been an interesting and mysterious matter, particularly how life arose from inorganic matter through natural processes. Polymerization is always involved in such processes. In this paper we built what we refer to as ideal and physical models to simulate spontaneous polymerization based on certain physical principles. As the modeling confirms, without taking external energy, small and simple inorganic molecules formed bigger and more complicated molecules, which are necessary ingredients of all living organisms. In our simulations, we utilized actual ranges of parameters according to their experimentally observed values. The results from the simulations led to a good agreement with the nature of polymerization. After sorting out through all the models that were built, we arrived at a final model that, it is hoped, can be used to simply and efficiently describe spontaneous polymerization using only three parameters: the dipole moment, the distance between molecules, and the temperature.

THE THREE DIMENSIONAL SHAPE AND ROUGHNESS OF MINERAL DUST

Mineral dust shape and roughness are important for a multitude of processes; it is known for aspherical shape but the true measurements in three dimensions are rare. Atomic Force Microscope was used for determine both 3D shape and roughness for two dust which are commonly used in laboratory experiments – Arizona Test Dust (ATD) and Kaolinite. We determined both of them are rather flat and round; an oblate spheroid would be a good model. Loess Filter was used to smooth the particles' surface and correlation analysis was used to examine the surfaces' properties of the dust; we found no features under 100nm scales. Also, our particles' surface area result is very similar to BET surface area.

Three-dimensional magnetic resonance observation of cartilage repair tissue (MOCART) score assessed with an isotropic three-dimensional true fast imaging with steady-state precession sequence at 3.0 Tesla

INTRODUCTION: Cartilage defects are common pathologies and surgical cartilage repair shows promising results. In its postoperative evaluation, the magnetic resonance observation of cartilage repair tissue (MOCART) score, using different variables to describe the constitution of the cartilage repair tissue and the surrounding structures, is widely used. High-field magnetic resonance imaging (MRI) and 3-dimensional (3D) isotropic sequences may combine ideal preconditions to enhance the diagnostic performance of cartilage imaging.Aim of this study was to introduce an improved 3D MOCART score using the possibilities of an isotropic 3D true fast imaging with steady-state precession (True-FISP) sequence in the postoperative evaluation of patients after matrix-associated autologous chondrocyte transplantation (MACT) as well as to compare the results to the conventional 2D MOCART score using standard MR sequences. MATERIAL AND METHODS: The study had approval by the local ethics commission. One hundred consecutive MR scans in 60 patients at standard follow-up intervals of 1, 3, 6, 12, 24, and 60 months after MACT of the knee joint were prospectively included. The mean follow-up interval of this cross-sectional evaluation was 21.4 +/- 20.6 months; the mean age of the patients was 35.8 +/- 9.4 years. MRI was performed at a 3.0 Tesla unit. All variables of the standard 2D MOCART score where part of the new 3D MOCART score. Furthermore, additional variables and options were included with the aims to use the capabilities of isotropic MRI, to include the results of recent studies, and to adapt to the needs of patients and physician in a clinical routine examination. A proton-density turbo spin-echo sequence, a T2-weighted dual fast spin-echo (dual-FSE) sequence, and a T1-weighted turbo inversion recovery magnitude (TIRM) sequence were used to assess the standard 2D MOCART score; an isotropic 3D-TrueFISP sequence was prepared to evaluate the new 3D MOCART score. All 9 variables of the 2D MOCART score were compared with the corresponding variables obtained by the 3D MOCART score using the Pearson correlation coefficient; additionally the subjective quality and possible artifacts of the MR sequences were analyzed. RESULTS: The correlation between the standard 2D MOCART score and the new 3D MOCART showed for the 8 variables "defect fill," "cartilage interface," "surface," "adhesions," "structure," "signal intensity," "subchondral lamina," and "effusion"-a highly significant (P < 0.001) correlation with a Pearson coefficient between 0.566 and 0.932. The variable "bone marrow edema" correlated significantly (P < 0.05; Pearson coefficient: 0.257). The subjective quality of the 3 standard MR sequences was comparable to the isotropic 3D-TrueFISP sequence. Artifacts were more frequently visible within the 3D-TrueFISP sequence. CONCLUSION: In the clinical routine follow-up after cartilage repair, the 3D MOCART score, assessed by only 1 high-resolution isotropic MR sequence, provides comparable information than the standard 2D MOCART score. Hence, the new 3D MOCART score has the potential to combine the information of the standard 2D MOCART score with the possible advantages of isotropic 3D MRI at high-field. A clear limitation of the 3D-TrueFISP sequence was the high number of artifacts. Future studies have to prove the clinical benefits of a 3D MOCART score.

A comparison between two-dimensional and three-dimensional cephalometry on frontal radiographs and on cone beam computed tomography scans of human skulls

The aim of this study was to evaluate whether measurements performed on conventional frontal radiographs are comparable to measurements performed on three-dimensional (3D) models of human skulls derived from cone beam computed tomography (CBCT) scans and if the latter can be used in longitudinal studies. Cone beam computed tomography scans and conventional frontal cephalometric radiographs were made of 40 dry human skulls. From the CBCT scan a 3D model was constructed. Standard cephalometric software was used to identify landmarks and to calculate ratios and angles. The same operator identified 10 landmarks on both types of cephalometric radiographs, and on all images, five times with a time interval of 1 wk. Intra-observer reliability was acceptable for all measurements. There was a statistically significant and clinically relevant difference between measurements performed on conventional frontal radiographs and on 3D CBCT-derived models of the same skull. There was a clinically relevant difference between angular measurements performed on conventional frontal cephalometric radiographs, compared with measurements performed on 3D models constructed from CBCT scans. We therefore recommend that 3D models should not be used for longitudinal research in cases where there are only two-dimensional (2D) records from the past.

Three-dimensional electron beam dose calculations

The MDAH pencil-beam algorithm developed by Hogstrom et al (1981) has been widely used in clinics for electron beam dose calculations for radiotherapy treatment planning. The primary objective of this research was to address several deficiencies of that algorithm and to develop an enhanced version. Two enhancements have been incorporated into the pencil-beam algorithm; one models fluence rather than planar fluence, and the other models the bremsstrahlung dose using measured beam data. Comparisons of the resulting calculated dose distributions with measured dose distributions for several test phantoms have been made. From these results it is concluded (1) that the fluence-based algorithm is more accurate to use for the dose calculation in an inhomogeneous slab phantom, and (2) the fluence-based calculation provides only a limited improvement to the accuracy the calculated dose in the region just downstream of the lateral edge of an inhomogeneity. The source of the latter inaccuracy is believed primarily due to assumptions made in the pencil beam's modeling of the complex phantom or patient geometry.^ A pencil-beam redefinition model was developed for the calculation of electron beam dose distributions in three dimensions. The primary aim of this redefinition model was to solve the dosimetry problem presented by deep inhomogeneities, which was the major deficiency of the enhanced version of the MDAH pencil-beam algorithm. The pencil-beam redefinition model is based on the theory of electron transport by redefining the pencil beams at each layer of the medium. The unique approach of this model is that all the physical parameters of a given pencil beam are characterized for multiple energy bins. Comparisons of the calculated dose distributions with measured dose distributions for a homogeneous water phantom and for phantoms with deep inhomogeneities have been made. From these results it is concluded that the redefinition algorithm is superior to the conventional, fluence-based, pencil-beam algorithm, especially in predicting the dose distribution downstream of a local inhomogeneity. The accuracy of this algorithm appears sufficient for clinical use, and the algorithm is structured for future expansion of the physical model if required for site specific treatment planning problems. ^

Three-dimensional printing for perioperative planning of complex aortic arch surgery

Purpose In this study, we show the use of three-dimensional printing models for preoperative planning of surgery for patients with complex aortic arch anomalies. Description A 70-year-old man with an extensively arteriosclerotic aneurysm reaching from the ascending aorta to the descending aorta was referred to our center for complete aortic arch replacement. We visualized and reconstructed computed tomography data of the patient and fabricated a flexible three-dimensional model of the aortic arch including the aneurysm. Evaluation This model was very helpful for the preoperative decision making and planning of the frozen elephant trunk procedure owing to the exact and lifelike illustration of the native aortic arch. Conclusions Three-dimensional models are helpful in preoperative planning and postoperative evaluation of frozen elephant trunk procedures in patients with complex aortic anatomy.

The Utilization of Classical Spin Monte Carlo Methods to Simulate the Magnetic Behavior of Extended Three-Dimensional Cubic Networks Incorporating M(II) Ions with an S = 5/2 Ground State Spin

The numerical simulations of the magnetic properties of extended three-dimensional networks containing M(II) ions with an S = 5/2 ground-state spin have been carried out within the framework of the isotropic Heisenberg model. Analytical expressions fitting the numerical simulations for the primitive cubic, diamond, together with (10−3) cubic networks have all been derived. With these empirical formulas in hands, we can now extract the interaction between the magnetic ions from the experimental data for these networks. In the case of the primitive cubic network, these expressions are directly compared with those from the high-temperature expansions of the partition function. A fit of the experimental data for three complexes, namely [(N(CH3)4][Mn(N3)] 1, [Mn(CN4)]n 2, and [FeII(bipy)3][MnII2(ox)3] 3, has been carried out. The best fits were those obtained using the following parameters, J = −3.5 cm-1, g = 2.01 (1); J = −8.3 cm-1, g = 1.95 (2); and J = −2.0 cm-1, g = 1.95 (3).

Luminescence and Energy Transfer of [Ru(bpy) 3 ] 2+ , [Cr(ox) 3 ] 3- , and [Os(bpy) 3 ] 2+ in Three-Dimensional Oxalato-Networks

Luminescence and energy transfer in [Zn1-xRux(bpy)3][NaAl1-yCry(ox)3] (x ≈ 0.01, y = 0.006 − 0.22; bpy = 2,2‘-bipyridine, ox = C2O42-) and [Zn1-x-yRuxOsy(bpy)3][NaAl(ox)3] (x ≈ 0.01, y = 0.012) are presented and discussed. Surprisingly, the luminescence of the isolated luminophores [Ru(bpy)3]2+ and [Os(bpy)3]2+ in [Zn(bpy)3][NaAl(ox)3] is hardly quenched at room temperature. Steady-state luminescence spectra and decay curves show that energy transfer occurs between [Ru(bpy)3]2+ and [Cr(ox)3]3- and between [Ru(bpy)3]2+ and [Os(bpy)3]2+ in [Zn1-xRux(bpy)3][NaAl1-yCry(ox)3] and [Zn1-x-yRuxOsy(bpy)3] [NaAl(ox)3], respectively. For a quantitative investigation of the energy transfer, a shell type model is developed, using a Monte Carlo procedure and the structural parameters of the systems. A good description of the experimental data is obtained assuming electric dipole−electric dipole interaction between donors and acceptors, with a critical distance Rc for [Ru(bpy)3]2+ to [Cr(ox)3]3- energy transfer of 15 Å and for [Ru(bpy)3]2+ to [Os(bpy)3]2+ energy transfer of 33 Å. These values are in good agreement with those derived using the Förster−Dexter theory.

Achieving a more realistic assessment of rockfall hazards by coupling three-dimensional process models and field-based tree-ring data

Sound knowledge of the spatial and temporal patterns of rockfalls is fundamental for the management of this very common hazard in mountain environments. Process-based, three-dimensional simulation models are nowadays capable of reproducing the spatial distribution of rockfall occurrences with reasonable accuracy through the simulation of numerous individual trajectories on highly-resolved digital terrain models. At the same time, however, simulation models typically fail to quantify the ‘real’ frequency of rockfalls (in terms of return intervals). The analysis of impact scars on trees, in contrast, yields real rockfall frequencies, but trees may not be present at the location of interest and rare trajectories may not necessarily be captured due to the limited age of forest stands. In this article, we demonstrate that the coupling of modeling with tree-ring techniques may overcome the limitations inherent to both approaches. Based on the analysis of 64 cells (40 m × 40 m) of a rockfall slope located above a 1631-m long road section in the Swiss Alps, we illustrate results from 488 rockfalls detected in 1260 trees. We illustrate that tree impact data cannot only be used (i) to reconstruct the real frequency of rockfalls for individual cells, but that they also serve (ii) the calibration of the rockfall model Rockyfor3D, as well as (iii) the transformation of simulated trajectories into real frequencies. Calibrated simulation results are in good agreement with real rockfall frequencies and exhibit significant differences in rockfall activity between the cells (zones) along the road section. Real frequencies, expressed as rock passages per meter road section, also enable quantification and direct comparison of the hazard potential between the zones. The contribution provides an approach for hazard zoning procedures that complements traditional methods with a quantification of rockfall frequencies in terms of return intervals through a systematic inclusion of impact records in trees.

Morphological Functions to Quantify Three-Dimensional Tomograms of Macropore Structure in a Vineyard Soil with Two Different Management Regimes

Soil tomography and morphological functions built over Minkowski functionals were used to describe the impact on pore structure of two soil management practices in a Mediterranean vineyard. Soil structure controls important physical and biological processes in soil–plant–microbial systems. Those processes are dominated by the geometry of soil pore structure, and a correct model of this geometry is critical for understanding them. Soil tomography has been shown to provide rich three-dimensional digital information on soil pore geometry. Recently, mathematical morphological techniques have been proposed as powerful tools to analyze and quantify the geometrical features of porous media. Minkowski functionals and morphological functions built over Minkowski functionals provide computationally efficient means to measure four fundamental geometrical features of three-dimensional geometrical objects, that is, volume, boundary surface, mean boundary surface curvature, and connectivity. We used the threshold and the dilation and erosion of three-dimensional images to generate morphological functions and explore the evolution of Minkowski functionals as the threshold and as the degree of dilation and erosion changes. We analyzed the three-dimensional geometry of soil pore space with X-ray computed tomography (CT) of intact soil columns from a Spanish Mediterranean vineyard by using two different management practices (conventional tillage versus permanent cover crop of resident vegetation). Our results suggested that morphological functions built over Minkowski functionals provide promising tools to characterize soil macropore structure and that the evolution of morphological features with dilation and erosion is more informative as an indicator of structure than moving threshold for both soil managements studied.

Three-dimensional spatial distribution of synapses in the neocortex: A dual-beam electron microscopy study

In the cerebral cortex, most synapses are found in the neuropil, but relatively little is known about their 3-dimensional organization. Using an automated dual-beam electron microscope that combines focused ion beam milling and scanning electron microscopy, we have been able to obtain 10 three-dimensional samples with an average volume of 180 µm(3) from the neuropil of layer III of the young rat somatosensory cortex (hindlimb representation). We have used specific software tools to fully reconstruct 1695 synaptic junctions present in these samples and to accurately quantify the number of synapses per unit volume. These tools also allowed us to determine synapse position and to analyze their spatial distribution using spatial statistical methods. Our results indicate that the distribution of synaptic junctions in the neuropil is nearly random, only constrained by the fact that synapses cannot overlap in space. A theoretical model based on random sequential absorption, which closely reproduces the actual distribution of synapses, is also presented.