High resolution Synchrotron-based X-ray Phase Contrast Tomography (XPCT) allows the simultaneous detection of three dimensional neuronal and vascular networks without using contrast agents or invasive casting preparation. We show and discuss the different features observed in reconstructed XPCT volumes of the ex vivo mouse spinal cord in the lumbo-sacral region, including motor neurons and blood vessels. We report the application of an intensity-based segmentation method to detect and quantitatively characterize the modification in the vascular networks in terms of reduction in experimental visibility. In particular, we apply our approach to the case of the experimental autoimmune encephalomyelitis (EAE), i.e. human multiple sclerosis animal model. 相似文献
Segmentation of the 3D human body is a very challenging problem in applications exploiting volume capture data. Direct clustering in the Euclidean space is usually complex or even unsolvable. This paper presents an original method based on the Isomap (isometric feature mapping) transform of the volume data-set. The 3D articulated posture is mapped by Isomap in the pose of Da Vinci's Vitruvian man. The limbs are unrolled from each other and separated from the trunk and pelvis, and the topology of the human body shape is recovered. In such a configuration, Hoshen–Kopelman clustering applied to concentric spherical shells is used to automatically group points into the labelled principal curves. Shepard interpolation is utilised to back-map points of the principal curves into the original volume space. The experimental results performed on many different postures have proved the validity of the proposed method. Reliability of less than 2 cm and 3° in the location of the joint centres and direction axes of rotations has been obtained, respectively, which qualifies this procedure as a potential tool for markerless motion analysis. 相似文献
A software system for interactive manipulation of three-dimensional data has been developed, based on the Open Inventor tool kit. The primary use of this software system is in the segmentation of tomographic reconstructions of subcellular structures. To this end, the reconstruction is represented by volume rendering and displayed in stereo. A three-dimensional cursor with adjustable shape and size is used to define and isolate regions of interest inside the volume, based on the user's expert knowledge. Once isolated, the region of interest can be conveniently analyzed and displayed. 相似文献
Tissue vascularization is critical to enable oxygen and nutrient supply. Therefore, establishing expedient vasculature is necessary for the survival of tissue after transplantation. The use of biomechanical forces, such as cell-induced traction forces, may be a promising method to encourage growth of the vascular network. Three-dimensional (3D) bioprinting, which offers unprecedented versatility through precise control over spatial distribution and structure of tissue constructs, can be used to generate capillary-like structures in vitro that would mimic microvessels. This study aimed to develop an in vitro, 3D bioprinted tissue model to study the effect of cellular forces on the spatial organization of vascular structures and tissue maturation. The developed in vitro model consists of a 3D bioprinted polycaprolactone (PCL) frame with a gelatin spacer hydrogel layer and a gelatin–fibrin–hyaluronic acid hydrogel layer containing normal human dermal fibroblasts and human umbilical vein endothelial cells printed as vessel lines on top. The formation of vessel-like networks and vessel lumens in the 3D bioprinted in vitro model was assessed at different fibrinogen concentrations with and without inhibitors of cell-mediated traction forces. Constructs containing 5 mg/ml fibrinogen had longer vessels compared to the other concentrations of fibrinogen used. Also, for all concentrations of fibrinogen used, most of the vessel-like structures grew parallel to the direction the PCL frame-mediated tensile forces, with very few branching structures observed. Treatment of the 3D bioprinted constructs with traction inhibitors resulted in a significant reduction in length of vessel-like networks. The 3D bioprinted constructs also had better lumen formation, increased collagen deposition, more elaborate actin networks, and well-aligned matrix fibers due to the increased cell-mediated traction forces present compared to the non-anchored, floating control constructs. This study showed that cell traction forces from the actomyosin complex are critical for vascular network assembly in 3D bioprinted tissue. Strategies involving the use of cell-mediated traction forces may be promising for the development of bioprinting approaches for fabrication of vascularized tissue constructs. 相似文献
Abstract The water transport and storage system of palms is adapted to maintain the primary stem xylem functional over the life of the shoot, and in spite of severe drought. However, our structural information far exceeds our knowledge of vascular function, and these functional considerations bring more questions than answers. The tendency to generalize from limited data on a few species begs the question of how the hydraulic parameters discussed vary between palms with different growth forms and ecologies. 相似文献
Selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) is a facile technique for quantitative analysis of RNA secondary structure. In general, low SHAPE signal values indicate Watson-Crick base-pairing, and high values indicate positions that are single-stranded within the RNA structure. However, the relationship of SHAPE signals to structural properties such as non-Watson-Crick base-pairing or stacking has thus far not been thoroughly investigated. Here, we present results of SHAPE experiments performed on several RNAs with published three-dimensional structures. This strategy allows us to analyze the results in terms of correlations between chemical reactivities and structural properties of the respective nucleotide, such as different types of base-pairing, stacking, and phosphate-backbone interactions. We find that the RNA SHAPE signal is strongly correlated with cis-Watson-Crick/Watson-Crick base-pairing and is to a remarkable degree not dependent on other structural properties with the exception of stacking. We subsequently generated probabilistic models that estimate the likelihood that a residue with a given SHAPE score participates in base-pairing. We show that several models that take SHAPE scores of adjacent residues into account perform better in predicting base-pairing compared with individual SHAPE scores. This underscores the context sensitivity of SHAPE and provides a framework for an improved interpretation of the response of RNA to chemical modification. 相似文献
A reliable and fast numerical scheme is crucial for the 1D simulation of blood flow in compliant vessels. In this paper, a 1D blood flow model is incorporated with a Kelvin–Voigt viscoelastic arterial wall. This leads to a nonlinear hyperbolic–parabolic system, which is then solved with four numerical schemes, namely: MacCormack, Taylor–Galerkin, monotonic upwind scheme for conservation law and local discontinuous Galerkin. The numerical schemes are tested on a single vessel, a simple bifurcation and a network with 55 arteries. The numerical solutions are checked favorably against analytical, semi-analytical solutions or clinical observations. Among the numerical schemes, comparisons are made in four important aspects: accuracy, ability to capture shock-like phenomena, computational speed and implementation complexity. The suitable conditions for the application of each scheme are discussed. 相似文献
The study purpose is to optimize modeling parameters, specifically segmentation spacing and centerline extraction, to efficiently construct accurate 3D aortic models. Models are constructed by centerline extraction and orthogonal 2D segmentations. We examine the effect of segmentation interval spacing (2, 1, 0.5, 0.25 cm) and orthogonal segmentation and centerline extraction iteration (one, two, three iterations) for constructing models of Healthy, Tortuous, Aneurysmal, and Dissected human thoracic aortas. Aortic arclength, curvature, and cross-sectional axis ratio were computed to compare variations in modeling parameters. Centerline arclength is precisely characterized for all aortas with a single iteration of centerline extraction (≤1% deviation), however, complex anatomies required 1 cm segmentation intervals whereas the Healthy aorta only required 2 cm intervals. Centerline curvature is more sensitive to modeling methods, requiring 1 cm intervals for ≤5% deviation in peak curvature for the three diseased anatomies, and two iterations of segmentation and centerline extraction for the Aneurysmal and Dissected aortas. Accurate lumen cross-sectional characterization required 1 or 0.5 cm segmentation intervals, and two or three segmentation and centerline iterations, with greater refinement needed for more complex geometries. Depending on the geometric characteristic and complexity of anatomy and pathology, different levels of segmentation interval refinement and iterations of segmentation and centerline extraction are required. 相似文献
Third harmonic generation (THG) microscopy is a label‐free imaging technique that shows great potential for rapid pathology of brain tissue during brain tumor surgery. However, the interpretation of THG brain images should be quantitatively linked to images of more standard imaging techniques, which so far has been done qualitatively only. We establish here such a quantitative link between THG images of mouse brain tissue and all‐nuclei‐highlighted fluorescence images, acquired simultaneously from the same tissue area. For quantitative comparison of a substantial pair of images, we present here a segmentation workflow that is applicable for both THG and fluorescence images, with a precision of 91.3 % and 95.8 % achieved respectively. We find that the correspondence between the main features of the two imaging modalities amounts to 88.9 %, providing quantitative evidence of the interpretation of dark holes as brain cells. Moreover, 80 % bright objects in THG images overlap with nuclei highlighted in the fluorescence images, and they are 2 times smaller than the dark holes, showing that cells of different morphologies can be recognized in THG images. We expect that the described quantitative comparison is applicable to other types of brain tissue and with more specific staining experiments for cell type identification.
In a previous paper we introduced a method called augmented sparse reconstruction (ASR) that identifies links among nodes of ordinary differential equation networks, given a small set of observed trajectories with various initial conditions. The main purpose of that technique was to reconstruct intracellular protein signaling networks.In this paper we show that a recursive augmented sparse reconstruction generates artificial networks that are homologous to a large, reference network, in the sense that kinase inhibition of several reactions in the network alters the trajectories of a sizable number of proteins in comparable ways for reference and reconstructed networks. We show this result using a large in-silico model of the epidermal growth factor receptor (EGF-R) driven signaling cascade to generate the data used in the reconstruction algorithm.The most significant consequence of this observed homology is that a nearly optimal combinatorial dosage of kinase inhibitors can be inferred, for many nodes, from the reconstructed network, a result potentially useful for a variety of applications in personalized medicine. 相似文献
Translation of eukaryotic mRNAs is often regulated by nucleotides around the start codon. A purine at position −3 and a guanine at position +4 contribute significantly to enhance the translation efficiency. Algorithms to predict the translation initiation site often fail to predict the start site if the sequence context is not present. We have developed a neural network method to predict the initiation site of mRNA sequences that lack the preferred nucleotides at the positions −3 and +4 surrounding the translation initiation site. Neural networks of various architectures comprising different number of hidden layers were designed and tested for various sizes of windows of nucleotides surrounding translation initiation sites. We found that the neural network with two hidden layers showed a sensitivity of 83% and specificity of 73% indicating a vastly improved performance in successfully predicting the translation initiation site of mRNA sequences with weak Kozak context. WeakAUG server is freely available at http://bioinfo.iitk.ac.in/AUGPred/. 相似文献
Many studies have been conducted about the information contained in the anatomy of the mammalian middle ear. Most of these only use a few specimens. Thus we aim to provide a quantitative analysis of the intraspecific and interspecific variations of the middle ear, focusing on the auditory bulla. For that purpose, we focused on the mustelids, as a quite generalist taxon and, more specifically, on the European badger, Meles meles. Our study includes two types of statistical methods. We first compared the mean of a subjectively chosen measure between individuals of the same species and between individuals of different species. We then used a multidimensional scaling procedure to cluster individuals according to different measures. We conclude that the middle ear varies effectively less intraspecifically than interspecifically. However, we think that the few anatomical parameters to measure in the auditory bulla involve using more specimens or focusing on geometric morphometrics in studies focusing on middle ear. 相似文献
The role of mechanics is known to be of primary order in many arterial diseases; however, determining mechanical properties of arteries remains a challenge. This paper discusses the identifiability of the passive mechanical properties of a mouse carotid artery, taking into account the orientation of collagen fibres in the medial and adventitial layers. On the basis of 3D digital image correlation measurements of the surface strain during an inflation/extension test, an inverse identification method is set up. It involves a 3D finite element mechanical model of the mechanical test and an optimisation algorithm. A two-layer constitutive model derived from the Holzapfel model is used, with five and then seven parameters. The five-parameter model is successfully identified providing layer-specific fibre angles. The seven-parameter model is over parameterised, yet it is shown that additional data from a simple tension test make the identification of refined layer-specific data reliable. 相似文献
The U.S. Environmental Protection Agency (USEPA) is developing the Multimedia, Multipathway, Multireceptor Risk Assessment (3MRA) model to evaluate potential human and ecological risks associated with the disposal of solid wastes designated as hazardous wastes in nonhazardous waste management units. USEPA intends to use the 3MRA model to determine national exit levels that will allow solid wastes that theoretically pose acceptable human and ecological risks to be safely managed in Subtitle D nonhazardous waste management units. We critically evaluated the 3MRA model to determine whether the methodology, interim modules, and input parameters are appropriate and scientifically defensible. Overall, our review of the 3MRA model indicates that it contains many conservative assumptions that may limit the validity of the model results and its use as a national model adequate for making regulatory decisions. Many of the assumptions and data inputs used to model the pathways involved in the transport of chemicals from a waste management unit are flawed. Other specific concerns include the lack of model validation, incompatibility of data between modules, and overestimation of potential human and ecological exposures. Before using the 3MRA model, we recommend that USEPA consider whether the 3MRA model is either an appropriate or accurate tool for evaluating the disposal of hazardous wastes nationwide. 相似文献
