Differences in 3D vs. 2D analysis in lumbar spinal fusion simulations

Lumbar interbody fusion is currently the gold standard in treating patients with disc degeneration or segmental instability. Despite it having been used for several decades, the non-union rate remains high. A failed fusion is frequently attributed to an inadequate mechanical environment after instrumentation. Finite element (FE) models can provide insights into the mechanics of the fusion process. Previous fusion simulations using FE models showed that the geometries and material of the cage can greatly influence the fusion outcome. However, these studies used axisymmetric models which lacked realistic spinal geometries. Therefore, different modeling approaches were evaluated to understand the bone-formation process.Three FE models of the lumbar motion segment (L4–L5) were developed: 2D, Sym-3D and Nonsym-3D. The fusion process based on existing mechano-regulation algorithms using the FE simulations to evaluate the mechanical environment was then integrated into these models. In addition, the influence of different lordotic angles (5, 10 and 15°) was investigated. The volume of newly formed bone, the axial stiffness of the whole segment and bone distribution inside and surrounding the cage were evaluated.In contrast to the Nonsym-3D, the 2D and Sym-3D models predicted excessive bone formation prior to bridging (peak values with 36 and 9% higher than in equilibrium, respectively). The 3D models predicted a more uniform bone distribution compared to the 2D model.The current results demonstrate the crucial role of the realistic 3D geometry of the lumbar motion segment in predicting bone formation after lumbar spinal fusion.     

Comparative performance analysis of 2D and 3D gamma metrics for patient specific QA in VMAT using Octavius 4D with 2D-Array 1500

IntroductionGamma pass percentage (GPP) is the predominant metric used for Patient Specific Quality Assurance (PSQA) in radiation therapy. The dimensionality of the measurement geometry in PSQA has evolved from 2D planar to 3D planar, and presently to state-of-the-art 3D volumetric geometry. We aim to critically examine the performance of the three-dimensional gammas vis-à-vis the older gamma metrics of lower dimensionality to determine their mutual fungibility in PSQA, using clinically approved Volumetric Arc Therapy (VMAT) plans.Methods and materialsGamma pass percentages derived from PSQA for VMAT plans using Octavius 4D phantom with 2D-Array 1500 and its proprietary software were recorded. 2D planar, 3D planar, and 3D volumetric gamma pass percentages were retrospectively extracted for multiple treatment plans at three sites, using three acceptance limits, and for two modes of normalization. The differences in mean pass percentages, and the pairwise correlation between geometries were calculated within limits of statistical significance.ResultsA significant increase in mean pass rates was observed from 2D planar to 3D planar geometries. The difference was less pronounced from 3D planar to 3D volumetric. 2D planar v/s 3D planar showed a significant degree of correlation among themselves, which was not seen against most of the 3D volumetric pass rates.ConclusionThe mean gamma pass rates show conclusive evidence of the benefits of shifting from 2D planar to higher dimensions measurement geometries, but the benefits of using 3D volumetric compared to 3D planar is not always unequivocal. The correlations show mixed results regarding the interdependence of pass percentages at different geometries.     

Rayleigh-Taylor instability in quantum magnetized viscous plasma

Quantum effects on Rayleigh-Taylor instability of stratified viscous plasmas layer under the influence of vertical magnetic field are investigated. By linearly solving the viscous QMHD equations into normal mode, a forth-order ordinary differential equation is obtained to describe the velocity perturbation. Then the growth rate is derived for the case where a plasma with exponential density distribution is confined between two rigid planes. The results show that, the presence of vertical magnetic field beside the quantum effect will bring about more stability on the growth rate of unstable configuration for viscous plasma, which is greater than that of inviscous plasma.     

Construction of 3D human distal femoral surface models using a 3D statistical deformable model

Construction of 3D geometric surface models of human knee joint is always a challenge in biomedical engineering. This study introduced an improved statistical shape model (SSM) method that only uses 2D images of a joint to predict the 3D joint surface model. The SSM was constructed using 40 distal femur models of human knees. In this paper, a series validation and parametric analysis suggested that more than 25 distal femur models are needed to construct the SSM; each distal femur should be described using at least 3000 nodes in space; and two 2D fluoroscopic images taken in 45° directions should be used for the 3D surface shape prediction. Using this SSM method, ten independent distal femurs from 10 independent living subjects were predicted using their 2D plane fluoroscopic images. The predicted models were compared to their native 3D distal femur models constructed using their 3D MR images. The results demonstrated that using two fluoroscopic images of the knee, the overall difference between the predicted distal femur surface and the MR image-based surface was 0.16±1.16 mm. These data indicated that the SSM method could be a powerful method for construction of 3D surface geometries of the distal femur.     

Hysteresis and Statistical Errors in Free Energy Perturbation L to D Amino Acid Conversion

Abstract

A theory based on a Langevin equation along the reaction coordinate is developed to explain and calculate systematic and statistical errors in free energy perturbation simulations. The errors are calculated exactly when both the perturbation potential and the mean potential from the surrounding degrees of freedom are harmonic in the reaction coordinate. The effect of the mean potential is small as long as the force constant is small compared to the force constant of the perturbation potential. This indicates that the results obtained with zero mean force may still be valid as long as the second derivate of the mean potential is small compared to that of the perturbation potential. The theory is applied to conversion between L and D amino acids by changing the position of the minimum of the harmonic improper dihedral potential between ±35.264 degrees. For phenylalanine bound in the active site of a protein (thermolysin) we find from 20 psec. simulations statistical errors and hysteresis that both are about 2.5 kJ/mol in agreement with what is obtained from the theoretical predictions. The statistical errors are proportional to the square root of the coupling to the heat bath and inversely proportional to the square root of integration time while the (positive) hysteresis due to that the reaction coordinate lags behind is linear in the same quantities. This shows that the systematic errors will dominate in short simulations while the statistical ones will dominate for long simulations. The treatment is based on that the systematic influence of the surroundings can be represented by a mean force upon the reaction coordinate. If the relaxation processes of the environment are slow this may not be true. Then additional errors have to be considered.     

Mitochondrial reactive oxygen species-mediated genomic instability in low-dose irradiated human cells through nuclear retention of cyclin D1

Mitochondria are associated with various radiation responses, including adaptive responses, mitophagy, the bystander effect, genomic instability, and apoptosis. We recently identified a unique radiation response in the mitochondria of human cells exposed to low-dose long-term fractionated radiation (FR). Such repeated radiation exposure inflicts chronic oxidative stresses on irradiated cells via the continuous release of mitochondrial reactive oxygen species (ROS) and decrease in cellular levels of the antioxidant glutathione. ROS-induced oxidative mitochondrial DNA (mtDNA) damage generates mutations upon DNA replication. Therefore, mtDNA mutation and dysfunction can be used as markers to assess the effects of low-dose radiation. In this study, we present an overview of the link between mitochondrial ROS and cell cycle perturbation associated with the genomic instability of low-dose irradiated cells. Excess mitochondrial ROS perturb AKT/cyclin D1 cell cycle signaling via oxidative inactivation of protein phosphatase 2A after low-dose long-term FR. The resulting abnormal nuclear accumulation of cyclin D1 induces genomic instability in low-dose irradiated cells.     

A model of effective diffusion and tortuosity in the extracellular space of the brain

Tortuosity of the extracellular space describes hindrance posed to the diffusion process by a geometrically complex medium in comparison to an environment free of any obstacles. Calculating tortuosity in biologically relevant geometries is difficult. Yet this parameter has proved very important for many processes in the brain, ranging from ischemia and osmotic stress to delivery of nutrients and drugs. It is also significant for interpretation of the diffusion-weighted magnetic resonance data. We use a volume-averaging procedure to obtain a general expression for tortuosity in a complex environment. A simple approximation then leads to tortuosity estimates in a number of two-dimensional (2D) and three-dimensional (3D) geometries characterized by narrow pathways between the cellular elements. It also explains the counterintuitive fact of lower diffusion hindrance in a 3D environment. Comparison with Monte Carlo numerical simulations shows that the model gives reasonable tortuosity estimates for a number of regular and randomized 2D and 3D geometries. Importantly, it is shown that addition of dead-end pores increases tortuosity in proportion to the square root of enlarged total extracellular volume fraction. This conclusion is further supported by the previously described tortuosity decrease in ischemic brain slices where dead-end pores were partially occluded by large macromolecules introduced into the extracellular space.     

PROTMAP2D: visualization, comparison and analysis of 2D maps of protein structure

MOTIVATION: Protein structure comparison is a fundamental problem in structural biology and bioinformatics. Two-dimensional maps of distances between residues in the structure contain sufficient information to restore the 3D representation, while maps of contacts reveal characteristic patterns of interactions between secondary and super-secondary structures and are very attractive for visual analysis. The overlap of 2D maps of two structures can be easily calculated, providing a sensitive measure of protein structure similarity. PROTMAP2D is a software tool for calculation of contact and distance maps based on user-defined criteria, quantitative comparison of pairs or series of contact maps (e.g. alternative models of the same protein, model versus native structure, different trajectories from molecular dynamics simulations, etc.) and visualization of the results. AVAILABILITY: PROTMAP2D for Windows / Linux / MacOSX is freely available for academic users from http://genesilico.pl/protmap2d.htm     

Linking 3D and 2D binding kinetics of membrane proteins by multiscale simulations

Membrane proteins are among the most functionally important proteins in cells. Unlike soluble proteins, they only possess two translational degrees of freedom on cell surfaces, and experience significant constraints on their rotations. As a result, it is currently challenging to characterize the in situ binding of membrane proteins. Using the membrane receptors CD2 and CD58 as a testing system, we developed a multiscale simulation framework to study the differences of protein binding kinetics between 3D and 2D environments. The association and dissociation processes were implemented by a coarse‐grained Monte‐Carlo algorithm, while the dynamic properties of proteins diffusing on lipid bilayer were captured from all‐atom molecular dynamic simulations. Our simulations show that molecular diffusion, linker flexibility and membrane fluctuations are important factors in adjusting binding kinetics. Moreover, by calibrating simulation parameters to the measurements of 3D binding, we derived the 2D binding constant which is quantitatively consistent with the experimental data, indicating that the method is able to capture the difference between 3D and 2D binding environments. Finally, we found that the 2D dissociation between CD2 and CD58 is about 100‐fold slower than the 3D dissociation. In summary, our simulation framework offered a generic approach to study binding mechanisms of membrane proteins.     

The Dopamine D3 Receptor Knockout Mouse Mimics Aging-Related Changes in Autonomic Function and Cardiac Fibrosis

Blood pressure increases with age, and dysfunction of the dopamine D3 receptor has been implicated in the pathogenesis of hypertension. To evaluate the role of the D3 receptor in aging-related hypertension, we assessed cardiac structure and function in differently aged (2 mo, 1 yr, 2 yr) wild type (WT) and young (2 mo) D3 receptor knockout mice (D3KO). In WT, systolic and diastolic blood pressures and rate-pressure product (RPP) significantly increased with age, while heart rate significantly decreased. Blood pressure values, heart rate and RPP of young D3KO were significantly elevated over age-matched WT, but similar to those of the 2 yr old WT. Echocardiography revealed that the functional measurements of ejection fraction and fractional shortening decreased significantly with age in WT and that they were significantly smaller in D3KO compared to young WT. Despite this functional change however, cardiac morphology remained similar between the age-matched WT and D3KO. Additional morphometric analyses confirmed an aging-related increase in left ventricle (LV) and myocyte cross-sectional areas in WT, but found no difference between age-matched young WT and D3KO. In contrast, interstitial fibrosis, which increased with age in WT, was significantly elevated in the D3KO over age-matched WT, and similar to 2 yr old WT. Western analyses of myocardial homogenates revealed significantly increased levels of pro- and mature collagen type I in young D3KO. Column zymography revealed that activities of myocardial MMP-2 and MMP-9 increased with age in WTs, but in D3KO, only MMP-9 activity was significantly increased over age-matched WTs. Our data provide evidence that the dopamine D3 receptor has a critical role in the emergence of aging-related cardiac fibrosis, remodeling, and dysfunction.     

A 3D Freehand Ultrasound System for Multi-view Reconstructions from Sparse 2D Scanning Planes

Background  

A significant limitation of existing 3D ultrasound systems comes from the fact that the majority of them work with fixed acquisition geometries. As a result, the users have very limited control over the geometry of the 2D scanning planes.     

Vitamin D and 1,25-dihydroxyvitamin D3 as modulators in the immune system

Treatment from weaning until old age with 1,25-dihydroxyvitamin D (1,25(OH)(2)D(3)) prevents diabetes in NOD mice. It is mainly through its actions on dendritic cells (DCs), that 1,25(OH)(2)D(3) changes the function of potentially autoreactive T lymphocytes. In contrast, early life treatment (from 3 to 70 days of age) of NOD mice with vitamin D or 1,25(OH)(2)D(3) did not influence final diabetes incidence at 200 days of age. Also in spontaneous diabetic BB rats, diabetes could not be prevented by early life treatment (from 3 to 50 days of age) with vitamin D (1000 IU per day) or 1,25(OH)(2)D(3) (0.2 microg/kg per day or 1 microg/kg per 2 days). However, when NOD mice were made vitamin D deficient in early life (until 100 days of age), diabetes onset occurred earlier and final incidence was increased. These data further support a role for vitamin D and its metabolites in the pathogenesis of type 1 diabetes in NOD mice.     

Constructing complex 3D biological environments from medical imaging using high performance computing

Extracting information about the structure of biological tissue from static image data is a complex task requiring computationally intensive operations. Here, we present how multicore CPUs and GPUs have been utilized to extract information about the shape, size, and path followed by the mammalian oviduct, called the fallopian tube in humans, from histology images, to create a unique but realistic 3D virtual organ. Histology images were processed to identify the individual cross sections and determine the 3D path that the tube follows through the tissue. This information was then related back to the histology images, linking the 2D cross sections with their corresponding 3D position along the oviduct. A series of linear 2D spline cross sections, which were computationally generated for the length of the oviduct, were bound to the 3D path of the tube using a novel particle system technique that provides smooth resolution of self-intersections. This results in a unique 3D model of the oviduct, which is grounded in reality. The GPU is used for the processor intensive operations of image processing and particle physics based simulations, significantly reducing the time required to generate a complete model.     

Finite Element Model of Oxygen Transport for the Design of Geometrically Complex Microfluidic Devices Used in Biological Studies

Red blood cells play a crucial role in the local regulation of oxygen supply in the microcirculation through the oxygen dependent release of ATP. Since red blood cells serve as an oxygen sensor for the circulatory system, the dynamics of ATP release determine the effectiveness of red blood cells to relate the oxygen levels to the vessels. Previous work has focused on the feasibility of developing a microfluidic system to measure the dynamics of ATP release. The objective was to determine if a steep oxygen gradient could be developed in the channel to cause a rapid decrease in hemoglobin oxygen saturation in order to measure the corresponding levels of ATP released from the red blood cells. In the present study, oxygen transport simulations were used to optimize the geometric design parameters for a similar system which is easier to fabricate. The system is composed of a microfluidic device stacked on top of a large, gas impermeable flow channel with a hole to allow gas exchange. The microfluidic device is fabricated using soft lithography in polydimethyl-siloxane, an oxygen permeable material. Our objective is twofold: (1) optimize the parameters of our system and (2) develop a method to assess the oxygen distribution in complex 3D microfluidic device geometries. 3D simulations of oxygen transport were performed to simulate oxygen distribution throughout the device. The simulations demonstrate that microfluidic device geometry plays a critical role in molecule exchange, for instance, changing the orientation of the short wide microfluidic channel results in a 97.17% increase in oxygen exchange. Since microfluidic devices have become a more prominent tool in biological studies, understanding the transport of oxygen and other biological molecules in microfluidic devices is critical for maintaining a physiologically relevant environment. We have also demonstrated a method to assess oxygen levels in geometrically complex microfluidic devices.     

A longitudinal study of remodeling in a revised peripheral artery bypass graft using 3D ultrasound imaging and computational hemodynamics

We report a study of the role of hemodynamic shear stress in the remodeling and failure of a peripheral artery bypass graft. Three separate scans of a femoral to popliteal above-knee bypass graft were taken over the course of a 16 month period following a revision of the graft. The morphology of the lumen is reconstructed from data obtained by a custom 3D ultrasound system. Numerical simulations are performed with the patient-specific geometries and physiologically realistic flow rates. The ultrasound reconstructions reveal two significant areas of remodeling: a stenosis with over 85% reduction in area, which ultimately caused graft failure, and a poststenotic dilatation or widening of the lumen. Likewise, the simulations reveal a complicated hemodynamic environment within the graft. Preliminary comparisons with in vivo velocimetry also showed qualitative agreement with the flow dynamics observed in the simulations. Two distinct flow features are discerned and are hypothesized to directly initiate the observed in vivo remodeling. First, a flow separation occurs at the stenosis. A low shear recirculation region subsequently develops distal to the stenosis. The low shear region is thought to be conducive to smooth muscle cell proliferation and intimal growth. A poststenotic jet issues from the stenosis and subsequently impinges onto the lumen wall. The lumen dilation is thought to be a direct result of the high shear stress and high frequency pressure fluctuations associated with the jet impingement.     

2D与3D景观指数测定山区植被景观格局变化对比分析

植被和土地覆盖变化是环境变化的一个重要因素,同时也是引起景观和生态系统变化的重要原因。景观指数是定量分析植被和土地覆盖变化的重要研究方法之一。以滇西北高山峡谷区为案例区,比较分析传统2D景观指数和3D景观指数进行植被变化定量测定的差异。研究主要选取了基于斑块面积和周长几个常用指数来进行比较分析。研究结果表明在斑块层次上,除了分维数指数,其他指数的三维方法计算值显著地高于二维方法计算值;在类型层次上,三维的类型面积指数、平均斑块面积指数、平均最小邻近距离指数测定的变化值显著大于二维的相应指数测定变化值,但是二维和三维平均形状指数和分维指数测定的植被斑块的平均形状变化结果没有显著差异;在景观层次,只有三维的平均斑块面积和最小邻近距离指数测定的变化结果显著高于二维的平均面积和最小邻近距离指数测定的变化结果,其它指数如形状指数、分维指数、多样性指数和均一度指数等测定出两个不同时期的植被图格局变化结果均无显著差异,主要由于这些指数是采用面积和周长的对数或者比值计算得出,从而缩小了斑块表面面积与平面面积,表面周长与平面周长之间的差异。总体而言,利用二维景观指数在进行定量分析山区植被格局变化时,往往低估了其类型面积、平均斑块面积、斑块邻近距离等指数变化量,而三维景观指数得到相对较精确的变化值。     

Spontaneously Self‐Assembly of a 2D/3D Heterostructure Enhances the Efficiency and Stability in Printed Perovskite Solar Cells

As perovskite solar cells (PSCs) are highly efficient, demonstration of high‐performance printed devices becomes important. 2D/3D heterostructures have recently emerged as an attractive way to relieving the film inhomogeneity and instability in perovskite devices. In this work, a 2D/3D ensemble with 2D perovskites self‐assembled atop 3D methylammonium lead triiodide (MAPbI₃) via a one‐step printing process is shown. A clean and flat interface is observed in the 2D/3D bilayer heterostructure for the first time. The 2D perovskite capping layer significantly suppresses nonradiative charge recombination, resulting in a marked increase in open‐circuit voltage (V_OC) of the devices by up to 100 mV. An ultrahigh V_OC of 1.20 V is achieved for MAPbI₃ PSCs, corresponding to 91% of the Shockley–Queisser limit. Moreover, notable enhancement in light, thermal, and moisture stability is obtained as a result of the protective barrier of the 2D perovskites. These results suggest a viable approach for scalable fabrication of highly efficient perovskite solar cells with enhanced environmental stability.     

CompuCell3D Simulations Reproduce Mesenchymal Cell Migration on Flat Substrates

Mesenchymal cell crawling is a critical process in normal development, in tissue function, and in many diseases. Quantitatively predictive numerical simulations of cell crawling thus have multiple scientific, medical, and technological applications. However, we still lack a low-computational-cost approach to simulate mesenchymal three-dimensional (3D) cell crawling. Here, we develop a computationally tractable 3D model (implemented as a simulation in the CompuCell3D simulation environment) of mesenchymal cells crawling on a two-dimensional substrate. The Fürth equation, the usual characterization of mean-squared displacement (MSD) curves for migrating cells, describes a motion in which, for increasing time intervals, cell movement transitions from a ballistic to a diffusive regime. Recent experiments have shown that for very short time intervals, cells exhibit an additional fast diffusive regime. Our simulations’ MSD curves reproduce the three experimentally observed temporal regimes, with fast diffusion for short time intervals, slow diffusion for long time intervals, and intermediate time -interval-ballistic motion. The resulting parameterization of the trajectories for both experiments and simulations allows the definition of time- and length scales that translate between computational and laboratory units. Rescaling by these scales allows direct quantitative comparisons among MSD curves and between velocity autocorrelation functions from experiments and simulations. Although our simulations replicate experimentally observed spontaneous symmetry breaking, short-timescale diffusive motion, and spontaneous cell-motion reorientation, their computational cost is low, allowing their use in multiscale virtual-tissue simulations. Comparisons between experimental and simulated cell motion support the hypothesis that short-time actomyosin dynamics affects longer-time cell motility. The success of the base cell-migration simulation model suggests its future application in more complex situations, including chemotaxis, migration through complex 3D matrices, and collective cell motion.     

Dopamine D1 receptor agonist and D2 receptor antagonist effects of the natural product (-)-stepholidine: molecular modeling and dynamics simulations

(-)-Stepholidine (SPD), an active ingredient of the Chinese herb Stephania, is the first compound found to have dual function as a dopamine receptor D1 agonist and D2 antagonist. Insights into dynamical behaviors of D1 and D2 receptors and their interaction modes with SPD are crucial in understanding the structural and functional characteristics of dopamine receptors. In this study a computational approach, integrating protein structure prediction, automated molecular docking, and molecular dynamics simulations were employed to investigate the dual action mechanism of SPD on the D1 and D2 receptors, with the eventual aim to develop new drugs for treating diseases affecting the central nervous system such as schizophrenia. The dynamics simulations revealed the surface features of the electrostatic potentials and the conformational "open-closed" process of the binding entrances of two dopamine receptors. Potential binding conformations of D1 and D2 receptors were obtained, and the D1-SPD and D2-SPD complexes were generated, which are in good agreement with most of experimental data. The D1-SPD structure shows that the K-167_EL-2-E-302_EL-3 (EL-2: extracellular loop 2; EL-3: extracellular loop 3) salt bridge plays an important role for both the conformational change of the extracellular domain and the binding of SPD. Based on our modeling and simulations, we proposed a mechanism of the dual action of SPD and a subsequent signal transduction model. Further mutagenesis and biophysical experiments are needed to test and improve our proposed dual action mechanism of SPD and signal transduction model.     

A phase-contrast microscopy-based method for modeling the mechanical behavior of mesenchymal stem cells

We present three-dimensional (3D) finite element (FE) models of single, mesenchymal stem cells (MSCs), generated from images obtained by optical phase-contrast microscopy and used to quantify the structural responses of the studied cells to externally applied mechanical loads. Mechanical loading has been shown to affect cell morphology and structure, phenotype, motility and other biological functions. Cells experience mechanical loads naturally, yet under prolonged or sizable loading, damage and cell death may occur, which motivates research regarding the structural behavior of loaded cells. For example, near the weight-bearing boney prominences of the buttocks of immobile persons, tissues may become highly loaded, eventually leading to massive cell death that manifests as pressure ulcers. Cell-specific computational models have previously been developed by our group, allowing simulations of cell deformations under compressive or stretching loads. These models were obtained by reconstructing specific cell structures from series of 2D fluorescence, confocal image-slices, requiring cell-specific fluorescent-staining protocols and costly (confocal) microscopy equipment. Alternative modeling approaches represent cells simply as half-spheres or half-ellipsoids (i.e. idealized geometries), which neglects the curvature details of the cell surfaces associated with changes in concentrations of strains and stresses. Thus, we introduce here for the first time an optical image-based FE modeling, where loads are simulated on reconstructed 3D geometrical cell models from a single 2D, phase-contrast image. Our novel modeling method eliminates the need for confocal imaging and fluorescent staining preparations (both expensive), and makes cell-specific FE modeling affordable and accessible to the biomechanics community. We demonstrate the utility of this cost-effective modeling method by performing simulations of compression of MSCs embedded in a gel.