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  • 1
    Publication Date: 2016-05-04
    Description: About two-thirds of the vital genes in the Drosophila genome are involved in eye development, making the fly eye an excellent genetic system to study cellular function and development, neurodevelopment/degeneration, and complex diseases such as cancer and diabetes. We developed a novel computational method, implemented as Flynotyper software ( http://flynotyper.sourceforge.net ), to quantitatively assess the morphological defects in the Drosophila eye resulting from genetic alterations affecting basic cellular and developmental processes. Flynotyper utilizes a series of image processing operations to automatically detect the fly eye and the individual ommatidium, and calculates a phenotypic score as a measure of the disorderliness of ommatidial arrangement in the fly eye. As a proof of principle, we tested our method by analyzing the defects due to eye-specific knockdown of Drosophila orthologs of 12 neurodevelopmental genes to accurately document differential sensitivities of these genes to dosage alteration. We also evaluated eye images from six independent studies assessing the effect of overexpression of repeats, candidates from peptide library screens, and modifiers of neurotoxicity and developmental processes on eye morphology, and show strong concordance with the original assessment. We further demonstrate the utility of this method by analyzing 16 modifiers of sine oculis obtained from two genome-wide deficiency screens of Drosophila and accurately quantifying the effect of its enhancers and suppressors during eye development. Our method will complement existing assays for eye phenotypes, and increase the accuracy of studies that use fly eyes for functional evaluation of genes and genetic interactions.
    Electronic ISSN: 2160-1836
    Topics: Biology
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  • 2
    Publication Date: 2013-04-29
    Description: The diffusion of red blood cells (RBCs) in blood is important to the physiology and pathology of the cardiovascular system. In this study, we investigate flow-induced diffusion of RBCs in a semi-dilute system by calculating the pairwise interactions between RBCs in simple shear flow. A capsule with a hyperelastic membrane was used to model an RBC. Its deformation was resolved using the finite element method, whereas fluid motion inside and outside the RBC was solved using the boundary element method. The results show that shear-induced RBC diffusion is significantly anisotropic, i.e. the velocity gradient direction component is larger than the vorticity direction. We also found that the motion of RBCs during the interaction is strongly dependent on the viscosity ratio of the internal to external fluid, and the diffusivity decreases monotonically as the viscosity ratio increases. The scaling argument also suggests that the diffusivity is proportional to the shear rate and haematocrit, if the suspension is in a semi-dilute environment and the capillary number is invariant. These fundamental findings are useful to understand transport phenomena in blood flow.
    Print ISSN: 0022-1120
    Electronic ISSN: 1469-7645
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 3
    Publication Date: 2014-12-02
    Description: The deformation of a spherical capsule in oscillating shear flow is presented. The boundary element method is used to simulate the capsule motion under Stokes flow. We show that a capsule at high frequencies follows the deformation given by a leading-order prediction, which is derived from an assumption of small deformation limit. At low frequencies, on the other hand, a capsule shows an overshoot phenomenon where the maximum deformation is larger than that in steady shear flow. A larger overshoot is observed for larger capillary number or viscosity ratio. Using the maximum deformation in start-up shear flow, we evaluate the upper limit of deformation in oscillating shear flow. We also show that the overshoot phenomenon may appear when the quasi-steady orientation angle under steady shear flow is less than$9.0^{circ }$. We propose an equation to estimate the threshold frequency between the low-frequency range, where the capsule may have an overshoot, and the high-frequency range, where the deformation is given by the leading-order prediction. The equation only includes the viscosity ratio and the Taylor parameter under simple shear flow, so it can be extended to other deformable particles, such as bubbles and drops.
    Print ISSN: 0022-1120
    Electronic ISSN: 1469-7645
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 4
    Publication Date: 2015-11-30
    Description: We present a numerical analysis of the rheology of a dense suspension of spherical capsules in simple shear flow in the Stokes flow regime. The behaviour of neo-Hookean capsules is simulated for a volume fraction up to${itphi}=0.4$by graphics processing unit computing based on the boundary element method with a multipole expansion. To describe the specific viscosity using a polynomial equation of the volume fraction, the coefficients of the equation are calculated by least-squares fitting. The results suggest that the effect of higher-order terms is much smaller for capsule suspensions than rigid sphere suspensions; for example,$O({itphi}^{3})$terms account for only 8 % of the specific viscosity even at${itphi}=0.4$for capillary numbers$Cageqslant 0.1$. We also investigate the relationship between the deformation and orientation of the capsules and the suspension rheology. When the volume fraction increases, the deformation of the capsules increases while the orientation angle of the capsules with respect to the flow direction decreases. Therefore, both the specific viscosity and the normal stress difference increase with volume fraction due to the increased deformation, whereas the decreased orientation angle suppresses the specific viscosity, but amplifies the normal stress difference.
    Print ISSN: 0022-1120
    Electronic ISSN: 1469-7645
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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  • 5
    Publication Date: 2016-09-29
    Description: The reorientation phenomenon of a single red blood cell during sedimentation is simulated using the boundary element method. The cell settles downwards due to a density difference between the internal and external fluids, and it changes orientation toward a vertical orientation regardless of Bond number or viscosity ratio. The reorientation phenomenon is explained by a shape asymmetry caused by the gravitational driving force, and the shape asymmetry increases almost linearly with the Bond number. When velocities are normalised by the driving force, settling/drifting velocities are weak functions of the Bond number and the viscosity ratio, while the angular velocity of the reorientation drastically changes with these parameters: the angular velocity is smaller for lower Bond number or higher viscosity ratio. As a consequence, trajectories of the sedimentation are also affected by the angular velocity, and blood cells with slower reorientation travel longer distances in the drifting direction. We also explain the mechanism of the reorientation using an asymmetric dumbbell. From the analysis, we show that the magnitude of the angular velocity is explained by two main factors: the shape asymmetry and the instantaneous orientation angle.
    Print ISSN: 0022-1120
    Electronic ISSN: 1469-7645
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
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