5,137 research outputs found
Testing Foundations of Biological Scaling Theory Using Automated Measurements of Vascular Networks
Scientists have long sought to understand how vascular networks supply blood
and oxygen to cells throughout the body. Recent work focuses on principles that
constrain how vessel size changes through branching generations from the aorta
to capillaries and uses scaling exponents to quantify these changes. Prominent
scaling theories predict that combinations of these exponents explain how
metabolic, growth, and other biological rates vary with body size.
Nevertheless, direct measurements of individual vessel segments have been
limited because existing techniques for measuring vasculature are invasive,
time consuming, and technically difficult. We developed software that extracts
the length, radius, and connectivity of in vivo vessels from contrast-enhanced
3D Magnetic Resonance Angiography. Using data from 20 human subjects, we
calculated scaling exponents by four methods--two derived from local properties
of branching junctions and two from whole-network properties. Although these
methods are often used interchangeably in the literature, we do not find
general agreement between these methods, particularly for vessel lengths.
Measurements for length of vessels also diverge from theoretical values, but
those for radius show stronger agreement. Our results demonstrate that vascular
network models cannot ignore certain complexities of real vascular systems and
indicate the need to discover new principles regarding vessel lengths
Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates
The study of cerebral anatomy in developing neonates is of great importance for
the understanding of brain development during the early period of life. This
dissertation therefore focuses on three challenges in the modelling of cerebral
anatomy in neonates during brain development. The methods that have been
developed all use Magnetic Resonance Images (MRI) as source data.
To facilitate study of vascular development in the neonatal period, a set of image
analysis algorithms are developed to automatically extract and model cerebral
vessel trees. The whole process consists of cerebral vessel tracking from
automatically placed seed points, vessel tree generation, and vasculature
registration and matching. These algorithms have been tested on clinical Time-of-
Flight (TOF) MR angiographic datasets.
To facilitate study of the neonatal cortex a complete cerebral cortex segmentation
and reconstruction pipeline has been developed. Segmentation of the neonatal
cortex is not effectively done by existing algorithms designed for the adult brain
because the contrast between grey and white matter is reversed. This causes pixels
containing tissue mixtures to be incorrectly labelled by conventional methods. The
neonatal cortical segmentation method that has been developed is based on a novel
expectation-maximization (EM) method with explicit correction for mislabelled
partial volume voxels. Based on the resulting cortical segmentation, an implicit
surface evolution technique is adopted for the reconstruction of the cortex in
neonates. The performance of the method is investigated by performing a detailed
landmark study.
To facilitate study of cortical development, a cortical surface registration algorithm
for aligning the cortical surface is developed. The method first inflates extracted
cortical surfaces and then performs a non-rigid surface registration using free-form
deformations (FFDs) to remove residual alignment. Validation experiments using
data labelled by an expert observer demonstrate that the method can capture local
changes and follow the growth of specific sulcus
Simulated annealing approach to vascular structure with application to the coronary arteries
Do the complex processes of angiogenesis during organism development ultimately lead to a near optimal coronary vasculature in the organs of adult mammals? We examine this hypothesis using a powerful and universal method, built on physical and physiological principles, for the determination of globally energetically optimal arterial trees. The method is based on simulated annealing, and can be used to examine arteries in hollow organs with arbitrary tissue geometries. We demonstrate that the approach can generate in silico vasculatures which closely match porcine anatomical data for the coronary arteries on all length scales, and that the optimized arterial trees improve systematically as computational time increases. The method presented here is general, and could in principle be used to examine the arteries of other organs. Potential applications include improvement of medical imaging analysis and the design of vascular trees for artificial organs
Shape minimization of the dissipated energy in dyadic trees
In this paper, we study the role of boundary conditions on the optimal shape
of a dyadic tree in which flows a Newtonian fluid. Our optimization problem
consists in finding the shape of the tree that minimizes the viscous energy
dissipated by the fluid with a constrained volume, under the assumption that
the total flow of the fluid is conserved throughout the structure. These
hypotheses model situations where a fluid is transported from a source towards
a 3D domain into which the transport network also spans. Such situations could
be encountered in organs like for instance the lungs and the vascular networks.
Two fluid regimes are studied: (i) low flow regime (Poiseuille) in trees with
an arbitrary number of generations using a matricial approach and (ii) non
linear flow regime (Navier-Stokes, moderate regime with a Reynolds number 100)
in trees of two generations using shape derivatives in an augmented Lagrangian
algorithm coupled with a 2D/3D finite elements code to solve Navier-Stokes
equations. It relies on the study of a finite dimensional optimization problem
in the case (i) and on a standard shape optimization problem in the case (ii).
We show that the behaviours of both regimes are very similar and that the
optimal shape is highly dependent on the boundary conditions of the fluid
applied at the leaves of the tree.Comment: \`a para\^itre dans Discrete Contin. Dyn. Syst. (B
Pulmonary CT and MRI phenotypes that help explain chronic pulmonary obstruction disease pathophysiology and outcomes
Pulmonary x-ray computed tomographic (CT) and magnetic resonance imaging (MRI) research and development has been motivated, in part, by the quest to subphenotype common chronic lung diseases such as chronic obstructive pulmonary disease (COPD). For thoracic CT and MRI, the main COPD research tools, disease biomarkers are being validated that go beyond anatomy and structure to include pulmonary functional measurements such as regional ventilation, perfusion, and inflammation. In addition, there has also been a drive to improve spatial and contrast resolution while at the same time reducing or eliminating radiation exposure. Therefore, this review focuses on our evolving understanding of patient-relevant and clinically important COPD endpoints and how current and emerging MRI and CT tools and measurements may be exploited for their identification, quantification, and utilization. Since reviews of the imaging physics of pulmonary CT and MRI and reviews of other COPD imaging methods were previously published and well-summarized, we focus on the current clinical challenges in COPD and the potential of newly emerging MR and CT imaging measurements to address them. Here we summarize MRI and CT imaging methods and their clinical translation for generating reproducible and sensitive measurements of COPD related to pulmonary ventilation and perfusion as well as parenchyma morphology. The key clinical problems in COPD provide an important framework in which pulmonary imaging needs to rapidly move in order to address the staggering burden, costs, as well as the mortality and morbidity associated with COPD
Structural Adaptation and Heterogeneity of Normal and Tumor Microvascular Networks
Relative to normal tissues, tumor microcirculation exhibits high structural and functional heterogeneity leading to hypoxic regions and impairing treatment efficacy. Here, computational simulations of blood vessel structural adaptation are used to explore the hypothesis that abnormal adaptive responses to local hemodynamic and metabolic stimuli contribute to aberrant morphological and hemodynamic characteristics of tumor microcirculation. Topology, vascular diameter, length, and red blood cell velocity of normal mesenteric and tumor vascular networks were recorded by intravital microscopy. Computational models were used to estimate hemodynamics and oxygen distribution and to simulate vascular diameter adaptation in response to hemodynamic, metabolic and conducted stimuli. The assumed sensitivity to hemodynamic and conducted signals, the vascular growth tendency, and the random variability of vascular responses were altered to simulate ‘normal’ and ‘tumor’ adaptation modes. The heterogeneous properties of vascular networks were characterized by diameter mismatch at vascular branch points (d3var) and deficit of oxygen delivery relative to demand (O2def). In the tumor, d3var and O2def were higher (0.404 and 0.182) than in normal networks (0.278 and 0.099). Simulated remodeling of the tumor network with ‘normal’ parameters gave low values (0.288 and 0.099). Conversely, normal networks attained tumor-like characteristics (0.41 and 0.179) upon adaptation with ‘tumor’ parameters, including low conducted sensitivity, increased growth tendency, and elevated random biological variability. It is concluded that the deviant properties of tumor microcirculation may result largely from defective structural adaptation, including strongly reduced responses to conducted stimuli
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Think tank: water relations of Bromeliaceae in their evolutionary context
This is the final version of the article. It first appeared from Wiley via https://doi.org/10.1111/boj.12423Water relations represent a pivotal nexus in plant biology due to the multiplicity of functions affected by water status. Hydraulic properties of plant parts are therefore likely to be relevant to evolutionary trends in many taxa. Bromeliaceae encompass a wealth of morphological, physiological and ecological variations and the geographical and bioclimatic range of the family is also extensive. The diversification of bromeliad lineages is known to be correlated with the origins of a suite of key innovations, many of which relate directly or indirectly to water relations. However, little information is known regarding the role of change in morphoanatomical and hydraulic traits in the evolutionary origins of the classical ecophysiological functional types in Bromeliaceae or how this role relates to the diversification of specific lineages. In this paper, I present a synthesis of the current knowledge on bromeliad water relations and a qualitative model of the evolution of relevant traits in the context of the functional types. I use this model to introduce a manifesto for a new research programme on the integrative biology and evolution of bromeliad water-use strategies. The need for a wide-ranging survey of morphoanatomical and hydraulic traits across Bromeliaceae is stressed, as this would provide extensive insight into structure–function relationships of relevance to the evolutionary history of bromeliads and, more generally, to the evolutionary physiology of flowering plants.Natural Environment Research Counci
Machine intelligence for nerve conduit design and production
Nerve guidance conduits (NGCs) have emerged from recent advances within tissue engineering as a promising alternative to autografts for peripheral nerve repair. NGCs are tubular structures with engineered biomaterials, which guide axonal regeneration from the injured proximal nerve to the distal stump. NGC design can synergistically combine multiple properties to enhance proliferation of stem and neuronal cells, improve nerve migration, attenuate inflammation and reduce scar tissue formation. The aim of most laboratories fabricating NGCs is the development of an automated process that incorporates patient-specific features and complex tissue blueprints (e.g. neurovascular conduit) that serve as the basis for more complicated muscular and skin grafts. One of the major limitations for tissue engineering is lack of guidance for generating tissue blueprints and the absence of streamlined manufacturing processes. With the rapid expansion of machine intelligence, high dimensional image analysis, and computational scaffold design, optimized tissue templates for 3D bioprinting (3DBP) are feasible. In this review, we examine the translational challenges to peripheral nerve regeneration and where machine intelligence can innovate bottlenecks in neural tissue engineering
Comparison of Image Registration Based Measures of Regional Lung Ventilation from Dynamic Spiral CT with Xe-CT
Purpose: Regional lung volume change as a function of lung inflation serves
as an index of parenchymal and airway status as well as an index of regional
ventilation and can be used to detect pathologic changes over time. In this
article, we propose a new regional measure of lung mechanics --- the specific
air volume change by corrected Jacobian.
Methods: 4DCT and Xe-CT data sets from four adult sheep are used in this
study. Nonlinear, 3D image registration is applied to register an image
acquired near end inspiration to an image acquired near end expiration.
Approximately 200 annotated anatomical points are used as landmarks to evaluate
registration accuracy. Three different registration-based measures of regional
lung mechanics are derived and compared: the specific air volume change
calculated from the Jacobian (SAJ); the specific air volume change calculated
by the corrected Jacobian (SACJ); and the specific air volume change by
intensity change (SAI).
Results: After registration, the mean registration error is on the order of 1
mm. For cubical ROIs in cubes with size 20 mm 20 mm 20 mm,
the SAJ and SACJ measures show significantly higher correlation (linear
regression, average and ) with the Xe-CT based measure of
specific ventilation (sV) than the SAI measure. For ROIs in slabs along the
ventral-dorsal vertical direction with size of 150 mm 8 mm 40
mm, the SAJ, SACJ, and SAI all show high correlation (linear regression,
average , and ) with the Xe-CT based sV without
significant differences when comparing between the three methods.
Conclusion: Given a deformation field by an image registration algorithm,
significant differences between the SAJ, SACJ, and SAI measures were found at a
regional level compared to the Xe-CT sV in four sheep that were studied
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