1,021,937 research outputs found

    Software for full-color 3D reconstruction of the biological tissues internal structure

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    A software for processing sets of full-color images of biological tissue histological sections is developed. We used histological sections obtained by the method of high-precision layer-by-layer grinding of frozen biological tissues. The software allows restoring the image of the tissue for an arbitrary cross-section of the tissue sample. Thus, our method is designed to create a full-color 3D reconstruction of the biological tissue structure. The resolution of 3D reconstruction is determined by the quality of the initial histological sections. The newly developed technology available to us provides a resolution of up to 5 - 10 {\mu}m in three dimensions.Comment: 11 pages, 8 figure

    Gene expression for simulation of biological tissue

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    BioDynaMo is a biological processes simulator developed by an international community of researchers and software engineers working closely with neuroscientists. The authors have been working on gene expression, i.e. the process by which the heritable information in a gene - the sequence of DNA base pairs - is made into a functional gene product, such as protein or RNA. Typically, gene regulatory models employ either statistical or analytical approaches, being the former already well understood and broadly used. In this paper, we utilize analytical approaches representing the regulatory networks by means of differential equations, such as Euler and Runge-Kutta methods. The two solutions are implemented and have been submitted for inclusion in the BioDynaMo project and are compared for accuracy and performance

    Method Of Applying Acoustic Energy Effective To Alter Transport Or Cell Viability

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    A method for reversibly, or irreversibly, altering the permeability of cells, tissues or other biological barriers, to molecules to be transported into or through these materials, through the application of acoustic energy, is enhanced by applying the ultrasound in combination with devices for monitoring and/or implementing feedback controls. The acoustic energy is applied directly or indirectly to the cells or tissue whose permeability is to be altered, at a frequency and intensity appropriate to alter the permeability to achieve the desired effect, such as the transport of endogenous or exogenous molecules and/or fluid, for drug delivery, measurement of analyte, removal of fluid, alteration of cell or tissue viability or alteration of structure of materials such as kidney or gall bladder stones. In the preferred embodiment, the method includes measuring the strength of the acoustic field applied to the cell or tissue at the applied frequency or other frequencies, and using the acoustic measurement to modify continued or subsequent application of acoustic energy to the cell or tissue. In another preferred embodiment, the method further includes simultaneously, previously, or subsequently exposing the cell or tissue to the chemical or biological agent to be transported into or across the cell or tissue. In another preferred application, the method includes removing biological fluid or molecules from the cells or tissue simultaneously, previously or subsequently to the application of acoustic energy and, optionally, assaying the biological fluid or molecules.Georgia Tech Research Corporatio

    Plum pudding random medium model of biological tissue toward remote microscopy from spectroscopic light scattering

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    Biological tissue has a complex structure and exhibits rich spectroscopic behavior. There is \emph{no} tissue model up to now able to account for the observed spectroscopy of tissue light scattering and its anisotropy. Here we present, \emph{for the first time}, a plum pudding random medium (PPRM) model for biological tissue which succinctly describes tissue as a superposition of distinctive scattering structures (plum) embedded inside a fractal continuous medium of background refractive index fluctuation (pudding). PPRM faithfully reproduces the wavelength dependence of tissue light scattering and attributes the "anomalous" trend in the anisotropy to the plum and the powerlaw dependence of the reduced scattering coefficient to the fractal scattering pudding. Most importantly, PPRM opens up a novel venue of quantifying the tissue architecture and microscopic structures on average from macroscopic probing of the bulk with scattered light alone without tissue excision. We demonstrate this potential by visualizing the fine microscopic structural alterations in breast tissue (adipose, glandular, fibrocystic, fibroadenoma, and ductal carcinoma) deduced from noncontact spectroscopic measurement

    Plum pudding random medium model of biological tissue toward remote microscopy from spectroscopic light scattering

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    Biological tissue has a complex structure and exhibits rich spectroscopic behavior. There is \emph{no} tissue model up to now able to account for the observed spectroscopy of tissue light scattering and its anisotropy. Here we present, \emph{for the first time}, a plum pudding random medium (PPRM) model for biological tissue which succinctly describes tissue as a superposition of distinctive scattering structures (plum) embedded inside a fractal continuous medium of background refractive index fluctuation (pudding). PPRM faithfully reproduces the wavelength dependence of tissue light scattering and attributes the "anomalous" trend in the anisotropy to the plum and the powerlaw dependence of the reduced scattering coefficient to the fractal scattering pudding. Most importantly, PPRM opens up a novel venue of quantifying the tissue architecture and microscopic structures on average from macroscopic probing of the bulk with scattered light alone without tissue excision. We demonstrate this potential by visualizing the fine microscopic structural alterations in breast tissue (adipose, glandular, fibrocystic, fibroadenoma, and ductal carcinoma) deduced from noncontact spectroscopic measurement

    Mathematical modeling of collagen turnover in biological tissue

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    The final publication is available at Springer via http://dx.doi.org/10.1007/s00285-012-0613-yWe present a theoretical and computational model for collagen turnover in soft biological tissues. Driven by alterations in the mechanical environment, collagen fiber bundles may undergo important chronic changes, characterized primarily by alterations in collagen synthesis and degradation rates. In particular, hypertension triggers an increase in tropocollagen synthesis and a decrease in collagen degradation, which lead to the well-documented overall increase in collagen content. These changes are the result of a cascade of events, initiated mainly by the endothelial and smooth muscle cells. Here, we represent these events collectively in terms of two internal variables, the concentration of growth factor TGF-β\beta and tissue inhibitors of metalloproteinases TIMP. The upregulation of TGF-β\beta increases the collagen density. The upregulation of TIMP also increases the collagen density through decreasing matrix metalloproteinase MMP. We establish a mathematical theory for mechanically-induced collagen turnover and introduce a computational algorithm for its robust and efficient solution. We demonstrate that our model can accurately predict the experimentally observed collagen increase in response to hypertension reported in literature. Ultimately, the model can serve as a valuable tool to predict the chronic adaptation of collagen content to restore the homeostatic equilibrium state in vessels with arbitrary micro-structure and geometry.Peer ReviewedPostprint (author's final draft

    System for and method of freezing biological tissue

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    Biological tissue is frozen while a polyethylene bag placed in abutting relationship against opposed walls of a pair of heaters. The bag and tissue are cooled with refrigerating gas at a time programmed rate at least equal to the maximum cooling rate needed at any time during the freezing process. The temperature of the bag, and hence of the tissue, is compared with a time programmed desired value for the tissue temperature to derive an error indication. The heater is activated in response to the error indication so that the temperature of the tissue follows the desired value for the time programmed tissue temperature. The tissue is heated to compensate for excessive cooling of the tissue as a result of the cooling by the refrigerating gas. In response to the error signal, the heater is deactivated while the latent heat of fusion is being removed from the tissue while the tissue is changing phase from liquid to solid
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