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At least 523 records · Page 29Linked to original sources

arXiv2017

Abdominal aortic aneurysms and endovascular sealing: deformation and dynamic response

Endovascular sealing is a new technique for the repair of abdominal aortic aneurysms. Commercially available in Europe since~2013, it takes a revolutionary approach to aneurysm repair through minimally invasive techniques. Although aneurysm sealing may be thought as more stable than conventional endovascular stent graft repairs, post-implantation movement of the endoprosthesis has been described, potentially leading to late complications. The paper presents for the first time a model, which explains the nature of forces, in static and dynamic regimes, acting on sealed abdominal aortic aneurysms, with references to real case studies. It is shown that elastic deformation of the aorta and of the endoprosthesis induced by static forces and vibrations during daily activities can potentially promote undesired movements of the endovascular sealing structure.

physics.med-ph↗

arXiv2017

Dynamics of Motile Populations in Heterogeneous Environments

Movement behavior of biological entities plays a crucial role in their destiny through regulating their intraspecific and interspecific interactions as well as their interaction with surrounding environment. In spite of various models for population dynamics, the effect of movement behavior and heterogeneity of environment on population dynamics has remained poorly understood. We introduced an extended version of Kolmogorov equation which captures movement behavior and translated our model to a biased random walk on percolation lattice. Then we explored the effect of mentioned topic on population dynamics, especially for intratumor heterogeneity, metastasis and immune surveillance. In the case of tumor, our result reveals that communication between cell colons and the structure of host tissue together regulate the intratumor heterogeneity. For metastasis, our model predicts that the interplay between the structure of metastatic niche and interactions between metastatic cells arrived from different colons determines that which kind of seeds, polyclonal or monoclonal, can successfully metastasized there. Finally, studying the immune cells-tumor cells interaction in this context reveals the negative effect of the heterogeneous structure of host tissue on immune surveillance. These findings deepen our understanding of cancer biology and may have applications in Immunotherapy.

q-bio.TO↗

arXiv2017

Universal statistics of epithelial tissue topology

Cells forming various epithelial tissues have a strikingly universal distribution for the number of their edges. It is generally assumed that this topological feature is predefined by the statistics of individual cell divisions in growing tissue but existing theoretical models are unable to predict the observed distribution. Here we show experimentally, as well as in simulations, that the probability of cellular division increases exponentially with the number of edges of the dividing cell and show analytically that this is responsible for the observed shape of cell-edge distribution.

q-bio.TO↗

arXiv2017

Fast PET Scan Tumor Segmentation using Superpixels, Principal Component Analysis and K-means Clustering

Positron Emission Tomography scan images are extensively used in radiotherapy planning, clinical diagnosis, assessment of growth and treatment of a tumor. These all rely on fidelity and speed of detection and delineation algorithm. Despite intensive research, segmentation remained a challenging problem due to the diverse image content, resolution, shape, and noise. This paper presents a fast positron emission tomography tumor segmentation method in which superpixels are extracted first from the input image. Principal component analysis is then applied on the superpixels and also on their average. Distance vector of each superpixel from the average is computed in principal components coordinate system. Finally, k-means clustering is applied on distance vector to recognize tumor and non-tumor superpixels. The proposed approach is implemented in MATLAB 2016 which resulted in an average Dice similarity of 84.2% on the dataset. Additionally, a very fast execution time was achieved as the number of superpixels and the size of distance vector on which clustering was done was very small compared to the number of raw pixels in dataset images.

physics.med-ph↗

arXiv2017

Hydrodynamics of shape-driven rigidity transitions in motile tissues

In biological tissues, it is now well-understood that mechanical cues are a powerful mechanism for pattern regulation. While much work has focused on interactions between cells and external substrates, recent experiments suggest that cell polarization and motility might be governed by the internal shear stiffness of nearby tissue, deemed "plithotaxis". Meanwhile, other work has demonstrated that there is a direct relationship between cell shapes and tissue shear modulus in confluent tissues. Joining these two ideas, we develop a hydrodynamic model that couples cell shape, and therefore tissue stiffness, to cell motility and polarization. Using linear stability analysis and numerical simulations, we find that tissue behavior can be tuned between largely homogeneous states and patterned states such as asters, controlled by a composite "morphotaxis" parameter that encapsulates the nature of the coupling between shape and polarization. The control parameter is in principle experimentally accessible, and depends both on whether a cell tends to move in the direction of lower or higher shear modulus, and whether sinks or sources of polarization tend to fluidize the system.

cond-mat.soft↗

arXiv2018

Deep Multi-Modal Classification of Intraductal Papillary Mucinous Neoplasms (IPMN) with Canonical Correlation Analysis

Pancreatic cancer has the poorest prognosis among all cancer types. Intraductal Papillary Mucinous Neoplasms (IPMNs) are radiographically identifiable precursors to pancreatic cancer; hence, early detection and precise risk assessment of IPMN are vital. In this work, we propose a Convolutional Neural Network (CNN) based computer aided diagnosis (CAD) system to perform IPMN diagnosis and risk assessment by utilizing multi-modal MRI. In our proposed approach, we use minimum and maximum intensity projections to ease the annotation variations among different slices and type of MRIs. Then, we present a CNN to obtain deep feature representation corresponding to each MRI modality (T1-weighted and T2-weighted). At the final step, we employ canonical correlation analysis (CCA) to perform a fusion operation at the feature level, leading to discriminative canonical correlation features. Extracted features are used for classification. Our results indicate significant improvements over other potential approaches to solve this important problem. The proposed approach doesn't require explicit sample balancing in cases of imbalance between positive and negative examples. To the best of our knowledge, our study is the first to automatically diagnose IPMN using multi-modal MRI.

cs.CV↗

arXiv2017

High-Resolution, Three-Dimensional Reconstruction of the Outflow Tract Demonstrates Segmental Differences in Cleared Eyes

Purpose: The rate of conventional aqueous humor outflow is the highest nasally. We hypothesized that this is reflected in regionally different outflow structures and analyzed the entire limbus by high-resolution, full-thickness ribbon-scanning confocal microscopy (RSCM). Methods: We perfused pig eyes by anterior chamber cannulation with eight lectin-fluorophore conjugates, followed by optical clearance with benzyl alcohol benzyl benzoate (BABB). RSCM and an advanced analysis software (Imaris) were used to reconstruct a three-dimensional, whole-specimen rendering of the perilimbal outflow structures. We performed morphometric analyses of the outflow tract from the level of the trabecular meshwork (TM) to the scleral vascular plexus (SVP). Results: Except for pigmented structures, BABB cleared the entire eye. Rhodamine-conjugated Glycine max agglutinin (soybean, SBA) labeled the outflow tract evenly and retained fluorescence for months. RSCM produced terabyte-sized files allowing for in silico dissection of outflow tract vessel at a high resolution and in 3D. Networks of interconnected lumina were traced from the TM to downstream drainage structures. The collector channel (CC) volumes were ten times smaller than the receiving SVP vessels, the largest of which were in the inferior limbus. Proximal CC diameters were up to four times the size of distal diameters and more elliptical at their proximal ends. The largest CCs were found in the superonasal and inferonasal quadrants where the highest outflow occurs. Conclusions: RSCM of cleared eyes enabled high-resolution, volumetric analysis of the outflow tract. The proximal structures had greater diameters nasally while the SVP was larger in the inferior limbus.

q-bio.TO↗

arXiv2017

The phenomenon of growing surface interference explains the rosette pattern of jaguar

One possible mechanism to explain how animals got their coat patterns was proposed by Alan Turing. He assumed that two kinds of morphogens diffuse on a surface and interact with each other, generating a reaction-diffusion mechanism. We developed a new framework for pattern generation incorporating a non-diffusing transcription factor in the system. The diffusion factors (one inhibitor and one activator) acting on cell surface receptors modulate the activity of a transcription factor. The difference in the local concentration of diffusion factors is translated into the degree of activation of transcription factors. The speed of this process determines then pattern formation velocity, i.e. the elapsed time from an initial noisy situation to a final developed pattern. If the pattern formation velocity slows down compared to the growth of the surface, the phenomenon of "growing surface interference" occurs. We find that this phenomenon might explain the rosette pattern observed on different types of felids and the pale stripes found between the regular black stripes of zebras. We also investigate the dynamics between pattern formation velocity and growth and to what extent a pattern may freeze on growing domains.

q-bio.TO↗

arXiv2017

A phase field approach to trabecular bone remodeling

We introduce a continuous modeling approach which combines elastic responds of the trabecular bone structure, the concentration of signaling molecules within the bone and a mechanism how this concentration at the bone surface is used for local bone formation and resorption. In an abstract setting bone can be considered as a shape changing structure. For similar problems in materials science phase field approximations have been established as an efficient computational tool. We adapt such an approach for trabecular bone remodeling. It allows for a smooth representation of the trabecular bone structure and drastically reduces computational costs if compared with traditional micro finite element approaches. We demonstrate the advantage of the approach within a minimal model. We quantitatively compare the results with established micro finite element approaches on simple geometries and consider the bone morphology within a bone segment obtained from $μ$CT data of a sheep vertebra with realistic parameters.

q-bio.TO↗

arXiv2017

Assessing Mortality of Blunt Trauma with Co-morbidity

Objectives: To obtain a better estimate of the mortality of individuals suffering from blunt force trauma, including co-morbidity. Methodology: The Injury severity Score (ISS) is the default world standard for assessing the severity of multiple injuries. ISS is a mathematical fit to empirical field data. It is demonstrated that ISS is proportional to the Gibbs/Shannon Entropy. A new Entropy measure of morbidity from blunt force trauma including co-morbidity is derived based on the von Neumann Entropy, called the Abbreviated Morbidity Scale (AMS). Results: The ISS trauma measure has been applied to a previously published database, and good correlation has been achieved. Here the existing trauma measure is extended to include the co-morbidity of disease by calculating an Abbreviated Morbidity Score (AMS), which encapsulates the disease co-morbidity in a manner analogous to AIS, and on a consistent Entropy base. Applying Entropy measures to multiple injuries, highlights the role of co-morbidity and that the elderly die at much lower levels of injury than the general population, as a consequence of co-morbidity. These considerations lead to questions regarding current new car assessment protocols, and how well they protect the most vulnerable road users. Keywords: Blunt Force Trauma, Injury Severity Score, Co-morbidity, Entropy.

q-bio.TO↗

arXiv2017

Effect of sodium chloride (NaCl) on the growth of six Acacia species

Background: Salinity is one of the major abiotic stresses affecting plant production in arid and semi-arid regions. It causes reduction of cultivable area and combined with other factors, presents a serious threat to food stability in these areas. Context: In front of this problem, the selection of salt tolerant species and varieties remains the best economic approach for exploitation and rehabilitation of salt-affected regions. Objective: The purpose of this study was to assess and compare the seed germination response of six Acacia species under different NaCl concentrations in order to explore opportunities for selection and breeding salt tolerant genotypes. Methods: The salinity effect was examined by measuring some agro-morphological parameters in controlled growth environment using five treatment levels: 0, 100, 200, 300 and 400 mM of NaCl. Results: The analyzed data revealed significant variability in salt response within and between species. All growth parameters were progressively reduced by increased NaCl concentrations. Growth in height, leaf number and total plant dry weight were considered as the most sensitive parameters. However, the growth reduction varied among species in accordance with their tolerance level. It is important to note that all species survived at the highest salinity (400 mM). Whereas A. horrida and A. raddiana were proved to be often the best tolerant, they recorded the lowest reduction percentage at this stage. Conclusion: The genetic variability found in the studied species at seedling stage may be used to select genotypes particularly suitable for rehabilitation and exploitation of lands affected by salinity.

q-bio.TO↗

arXiv2017

Estimated Incidence of Ophthalmic Conditions Associated with Optic Nerve Disease in Middle Tennessee

Aims. The objective of this paper is to determine the incidence of ophthalmic disease potentially leading to optic nerve disease in Middle Tennessee. Methods. We use a retrospective population-based incidence study design focusing on the population of middle Tennessee and its nearby suburbs (N=3 397 515). The electronic medical records for all patients evaluated or treated at a large tertiary care hospital and clinics with an initial diagnosis of a disease either affecting the optic nerve, or potentially associated with optic nerve disease, between 2007 and 2014 were retrieved and analyzed. Results. 18 291 patients (10 808 F) with 18 779 incidence events were identified with an age range of 0-101 years from the query of the Vanderbilt BioVU. Estimated age-adjusted incidence per 100 000 population per year was 198.4/145.1 (glaucoma F/M), 14.4/11.4 (intrinsic optic nerve disease F/M), 10.6/5.8 (optic nerve edema F/M), 6.1/6.6 (orbital inflammation F/M), and 23.7/6.7 (thyroid disease F/M). Glaucoma incidence was strongly correlated with age with the incidence sharply increasing after age 40. Optic nerve edema incidence peaked in the 25-34 old females. African American population has increased likelihood of glaucoma, orbital inflammation, and thyroid disease. Conclusions. Mapping the incidence of pathologies of the optic nerve is essential to the understanding of the relative likelihood of these conditions and impacts upon public health. We find incidence of optic nerve diseases strongly varies by gender, age, and race which have not been previously studied using a unified framework or within a single metropolitan population

q-bio.TO↗

arXiv2018

Hemodynamic assessment of pulmonary hypertension in mice: a model based analysis of the disease mechanism

This study uses a one dimensional fluid dynamics arterial network model to infer changes in hemodynamic quantities associated with pulmonary hypertension in mice. Data for this study include blood flow and pressure measurements from the main pulmonary artery for 7 control mice with normal pulmonary function and 5 hypertensive mice with hypoxia induced pulmonary hypertension. Arterial dimensions for a 21 vessel network are extracted from micro-CT images of lungs from a representative control and hypertensive mouse. Each vessel is represented by its length and radius. Fluid dynamic computations are done assuming that the flow is Newtonian, viscous, laminar, and has no swirl. The system of equations is closed by a constitutive equation relating pressure and area, using a linear model derived from stress-strain deformation in the circumferential direction assuming that the arterial walls are thin, and also an empirical nonlinear model. For each dataset, an inflow waveform is extracted from the data, and nominal parameters specifying the outflow boundary conditions are computed from mean values and characteristic time scales extracted from the data. The model is calibrated for each mouse by estimating parameters that minimize the least squares error between measured and computed waveforms. Optimized parameters are compared across the control and the hypertensive groups to characterize vascular remodeling with disease. Results show that pulmonary hypertension is associated with stiffer and less compliant proximal and distal vasculature with augmented wave reflections, and that elastic nonlinearities are insignificant in the hypertensive animal.

physics.flu-dyn↗

arXiv2017

Modeling mammalian gastrulation with embryonic stem cells

Understanding cell fate patterning and morphogenesis in the mammalian embryo remains a formidable challenge. Recently, in vivo models based on embryonic stem cells (ESCs) have emerged as complementary methods to quantitatively dissect the physical and molecular processes that shape the embryo. Here we review recent developments in using embryonic stem cells to create both two and three-dimensional culture models that shed light on mammalian gastrulation.

q-bio.TO↗

arXiv2017

A Two-Parameter Model for Ultrasonic Tissue Characterization with Harmonic Imaging

Over the past few decades, researchers have developed several approaches such as the Reference Phantom Method (RPM) to estimate ultrasound attenuation coefficient (AC) and backscatter coefficient (BSC). AC and BSC can help to discriminate pathology from normal tissue during in-vivo imaging. In this paper, we propose a new RPM model to simultaneously compute AC and BSC for harmonic imaging and a normalized score that combines the two parameters as a measure of disease progression. The model utilizes the spectral difference between two regions of interest, the first, a proximal, close to the probe and second, a distal, away from the probe. We have implemented an algorithm based on the model and shown that it provides accurate and stable estimates to within 5% of AC and BSC for simulated received echo from post-focal depths of a homogeneous liver-like medium. For practical applications with time gain and time frequency compensated in-phase and quadrature (IQ) data from ultrasound scanner, the method has been approximated and generalized to estimate AC and BSC for tissue layer underlying a more attenuative subcutaneous layer. The angular spectrum approach for ultrasound propagation in biological tissue is employed as a virtual Reference Phantom (VRP). The VRP is calibrated with a fixed probe and scanning protocol for application to liver tissue. In a feasibility study with 16 subjects, the method is able to separate 9/11 cases of progressive non-alcoholic fatty liver disease from 5 normal. In particular, it is able to separate 4/5 cases of non-alcoholic steato-hepatitis and early fibrosis (F<=2) from normal tissue. More extensive clinical studies are needed to assess the full capability of this model for screening and monitoring disease progression in liver and other tissues.

physics.med-ph↗

arXiv2017

Interdependence Theory of Tissue Failure: Bulk and Boundary Effects

The mortality rate of many complex multicellular organisms increase with age, which suggests that net aging damage is accumulative, despite remodeling processes. But how exactly do little mishaps in the cellular level accumulate and spread to become a systemic catastrophe? To address this question we present experiments with synthetic tissues, an analytical model consistent with experiments, and a number of implications that follow the analytical model. Our theoretical framework describes how shape, curvature and density influences the propagation of failure in a tissue subject to oxidative damage. We propose that aging is an emergent property governed by interaction between cells, and that intercellular processes play a role that are at least as important as intracellular ones.

q-bio.TO↗

arXiv2017

Late stages of mineralisation and their signature on the bone mineral density distribution

Purpose: Experimental measurements of bone mineral density distributions (BMDDs) enable a determination of secondary mineralisation kinetics in bone, but the maximum degree of mineralisation and how this maximum is approached remain uncertain. We thus test computationally different hypotheses on late stages of bone mineralisation by simulating BMDDs in low turnover conditions. Materials and Methods: An established computational model of the BMDD that accounts for mineralisation and remodelling processes was extended to limit mineralisation to various maximum calcium capacities of bone. Simulated BMDDs obtained by reducing turnover rate from the reference trabecular BMDD under different assumptions on late stage mineralisation kinetics were compared with experimental BMDDs of low-turnover bone. Results: Simulations show that an abrupt stopping of mineralisation near a maximum calcium capacity induces a pile-up of minerals in the BMDD statistics that is not observed experimentally. With a smooth decrease of mineralisation rate, imposing low maximum calcium capacities helps to match peak location and width of simulated low turnover BMDDs with peak location and width of experimental BMDDs, but results in a distinctive asymmetric peak shape. No tuning of turnover rate and maximum calcium capacity was able to explain the differences found in experimental BMDDs between trabecular bone (high turnover) and femoral cortical bone (low turnover). Conclusions: Secondary mineralisation in human bone does not stop abruptly, but continues slowly up to a calcium content greater than 30 wt% Ca. The similar mineral heterogeneity seen in trabecular and femoral cortical bones at different peak locations was unexplained by turnover differences tested.

q-bio.CB↗

arXiv2017

Optical study of stress hormone-induced nanoscale structural alteration in brain using partial wave spectroscopic (PWS) microscopy

Chronic stress affects nano to microscale structures of the brain cells/tissues due the suppression of neural growths and reconnections, hence the neuronal activities. This results in depression, memory loss and even the death of the brain cells. Our recently developed novel optical technique, partial wave spectroscopic (PWS) microscopy has nanoscale sensitivity, and hence, can detect nanoscale changes in brain tissues due to stress. In this study, we applied this technique to quantify the stress related structural changes in the corticosterone-treated mouse model of stress. Our results show that brains from corticosterone-treated mice showed higher nanoscale structural disorder in the hippocampal region as compared to the brain from normal (vehicle) mice. The increase in structural alteration correlates with the duration of the stress. We further quantified the relative changes and the spatial localization of these changes in this mouse model and found out that the maximum changes occurred nearly symmetrically in both regions of the hippocampus. The mRNA for stress-related genes, BDNF and TrkB were also significantly reduced in the hippocampus of corticosterone-treated mice compared to that in control mice. These results indicate that chronic corticosterone treatment induces nanoscale structural alterations in mouse brain that corresponds to the changes in stress-related gene expression.

physics.bio-ph↗