105 research outputs found
Immunoadsorbents - Preparation and use of cellulose derivatives
Antibody isolation from blood by linking antigens to insoluble cellulose derivative
The chemistry and use of cellulose derivatives for the study of biological systems
Cellulose chemistry and applications as carrier for proteins, polymers, and organic molecule
Metered oxygen supply aids treatment of domestic sewage
Microbiological fixed-bed process was developed in which supplementary oxygen required by microbial species is supplied by electrochemical device. Rate of addition of oxygen to waste treatment process is controlled to maintain aerobic metabolism and prevent anaerobic metabolisms which produce odorous or toxic products
Reusable chelating resins concentrate metal ions from highly dilute solutions
Column chromatographic method uses new metal chelating resins for recovering heavy-metal ions from highly dilute solutions. The absorbed heavy-metal cations may be removed from the chelating resins by acid or base washes. The resins are reusable after the washes are completed
Incorporating chemical signalling factors into cell-based models of growing epithelial tissues
In this paper we present a comprehensive computational framework within which the effects of chemical signalling factors on growing epithelial tissues can be studied. The method incorporates a vertex-based cell model, in conjunction with a solver for the governing chemical equations. The vertex model provides a natural mesh for the finite element method (FEM), with node movements determined by force laws. The arbitrary Lagrangian–Eulerian formulation is adopted to account for domain movement between iterations. The effects of cell proliferation and junctional rearrangements on the mesh are also examined. By implementing refinements of the mesh we show that the finite element (FE) approximation converges towards an accurate numerical solution. The potential utility of the system is demonstrated in the context of Decapentaplegic (Dpp), a morphogen which plays a crucial role in development of the Drosophila imaginal wing disc. Despite the presence of a Dpp gradient, growth is uniform across the wing disc. We make the growth rate of cells dependent on Dpp concentration and show that the number of proliferation events increases in regions of high concentration. This allows hypotheses regarding mechanisms of growth control to be rigorously tested. The method we describe may be adapted to a range of potential application areas, and to other cell-based models with designated node movements, to accurately probe the role of morphogens in epithelial tissues
Chaste: an open source C++ library for computational physiology and biology
Chaste - Cancer, Heart And Soft Tissue Environment - is an open source C++ library for the computational simulation of mathematical models developed for physiology and biology. Code development has been driven by two initial applications: cardiac electrophysiology and cancer development. A large number of cardiac electrophysiology studies have been enabled and performed, including high performance computational investigations of defibrillation on realistic human cardiac geometries. New models for the initiation and growth of tumours have been developed. In particular, cell-based simulations have provided novel insight into the role of stem cells in the colorectal crypt. Chaste is constantly evolving and is now being applied to a far wider range of problems. The code provides modules for handling common scientific computing components, such as meshes and solvers for ordinary and partial differential equations (ODEs/PDEs). Re-use of these components avoids the need for researchers to "re-invent the wheel" with each new project, accelerating the rate of progress in new applications. Chaste is developed using industrially-derived techniques, in particular test-driven development, to ensure code quality, re-use and reliability. In this article we provide examples that illustrate the types of problems Chaste can be used to solve, which can be run on a desktop computer. We highlight some scientific studies that have used or are using Chaste, and the insights they have provided. The source code, both for specific releases and the development version, is available to download under an open source Berkeley Software Distribution (BSD) licence at http://www.cs.ox.ac.uk/chaste, together with details of a mailing list and links to documentation and tutorials
Coordinated optimization of visual cortical maps (I) Symmetry-based analysis
In the primary visual cortex of primates and carnivores, functional
architecture can be characterized by maps of various stimulus features such as
orientation preference (OP), ocular dominance (OD), and spatial frequency. It
is a long-standing question in theoretical neuroscience whether the observed
maps should be interpreted as optima of a specific energy functional that
summarizes the design principles of cortical functional architecture. A
rigorous evaluation of this optimization hypothesis is particularly demanded by
recent evidence that the functional architecture of OP columns precisely
follows species invariant quantitative laws. Because it would be desirable to
infer the form of such an optimization principle from the biological data, the
optimization approach to explain cortical functional architecture raises the
following questions: i) What are the genuine ground states of candidate energy
functionals and how can they be calculated with precision and rigor? ii) How do
differences in candidate optimization principles impact on the predicted map
structure and conversely what can be learned about an hypothetical underlying
optimization principle from observations on map structure? iii) Is there a way
to analyze the coordinated organization of cortical maps predicted by
optimization principles in general? To answer these questions we developed a
general dynamical systems approach to the combined optimization of visual
cortical maps of OP and another scalar feature such as OD or spatial frequency
preference.Comment: 90 pages, 16 figure
Coordinated optimization of visual cortical maps (II) Numerical studies
It is an attractive hypothesis that the spatial structure of visual cortical
architecture can be explained by the coordinated optimization of multiple
visual cortical maps representing orientation preference (OP), ocular dominance
(OD), spatial frequency, or direction preference. In part (I) of this study we
defined a class of analytically tractable coordinated optimization models and
solved representative examples in which a spatially complex organization of the
orientation preference map is induced by inter-map interactions. We found that
attractor solutions near symmetry breaking threshold predict a highly ordered
map layout and require a substantial OD bias for OP pinwheel stabilization.
Here we examine in numerical simulations whether such models exhibit
biologically more realistic spatially irregular solutions at a finite distance
from threshold and when transients towards attractor states are considered. We
also examine whether model behavior qualitatively changes when the spatial
periodicities of the two maps are detuned and when considering more than 2
feature dimensions. Our numerical results support the view that neither minimal
energy states nor intermediate transient states of our coordinated optimization
models successfully explain the spatially irregular architecture of the visual
cortex. We discuss several alternative scenarios and additional factors that
may improve the agreement between model solutions and biological observations.Comment: 55 pages, 11 figures. arXiv admin note: substantial text overlap with
arXiv:1102.335
An Efficient Coding Hypothesis Links Sparsity and Selectivity of Neural Responses
To what extent are sensory responses in the brain compatible with first-order principles? The efficient coding hypothesis projects that neurons use as few spikes as possible to faithfully represent natural stimuli. However, many sparsely firing neurons in higher brain areas seem to violate this hypothesis in that they respond more to familiar stimuli than to nonfamiliar stimuli. We reconcile this discrepancy by showing that efficient sensory responses give rise to stimulus selectivity that depends on the stimulus-independent firing threshold and the balance between excitatory and inhibitory inputs. We construct a cost function that enforces minimal firing rates in model neurons by linearly punishing suprathreshold synaptic currents. By contrast, subthreshold currents are punished quadratically, which allows us to optimally reconstruct sensory inputs from elicited responses. We train synaptic currents on many renditions of a particular bird's own song (BOS) and few renditions of conspecific birds' songs (CONs). During training, model neurons develop a response selectivity with complex dependence on the firing threshold. At low thresholds, they fire densely and prefer CON and the reverse BOS (REV) over BOS. However, at high thresholds or when hyperpolarized, they fire sparsely and prefer BOS over REV and over CON. Based on this selectivity reversal, our model suggests that preference for a highly familiar stimulus corresponds to a high-threshold or strong-inhibition regime of an efficient coding strategy. Our findings apply to songbird mirror neurons, and in general, they suggest that the brain may be endowed with simple mechanisms to rapidly change selectivity of neural responses to focus sensory processing on either familiar or nonfamiliar stimuli. In summary, we find support for the efficient coding hypothesis and provide new insights into the interplay between the sparsity and selectivity of neural responses
Growth Based Morphogenesis of Vertebrate Limb Bud
Many genes and their regulatory relationships are involved in developmental phenomena. However, by chemical information alone, we cannot fully understand changing organ morphologies through tissue growth because deformation and growth of the organ are essentially mechanical processes. Here, we develop a mathematical model to describe the change of organ morphologies through cell proliferation. Our basic idea is that the proper specification of localized volume source (e.g., cell proliferation) is able to guide organ morphogenesis, and that the specification is given by chemical gradients. We call this idea “growth-based morphogenesis.” We find that this morphogenetic mechanism works if the tissue is elastic for small deformation and plastic for large deformation. To illustrate our concept, we study the development of vertebrate limb buds, in which a limb bud protrudes from a flat lateral plate and extends distally in a self-organized manner. We show how the proportion of limb bud shape depends on different parameters and also show the conditions needed for normal morphogenesis, which can explain abnormal morphology of some mutants. We believe that the ideas shown in the present paper are useful for the morphogenesis of other organs
- …