3,095 research outputs found
Harbin: a quantitation PCR analysis tool
Objectives:
To enable analysis and comparisons of different relative quantitation experiments, a web-browser application called Harbin was created that uses a quantile-based scoring system for the comparison of samples at different time points and between experiments.
Results:
Harbin uses the standard curve method for relative quantitation to calculate concentration ratios (CRs). To evaluate if different datasets can be combined the Harbin quantile bootstrap test is proposed. This test is more sensitive in detecting distributional differences between data sets than the Kolmogorov–Smirnov test. The utility of the test is demonstrated in a comparison of three grapevine leafroll associated virus 3 (GLRaV-3) RT-qPCR data sets.
Conclusions:
The quantile-based scoring system of CRs will enable the monitoring of virus titre or gene expression over different time points and be useful in other genomic applications where the combining of data sets are required
Atomic Effective Pseudopotentials for Semiconductors
We derive an analytic connection between the screened self-consistent
effective potential from density functional theory (DFT) and atomic effective
pseudopotentials (AEPs). The motivation to derive AEPs is to address structures
with thousands to hundred thousand atoms, as given in most nanostructures. The
use of AEPs allows to bypass a self-consistent procedure and to address
eigenstates around a certain region of the spectrum (e.g., around the band
gap). The bulk AEP construction requires two simple DFT calculations of
slightly deformed elongated cells. The ensuing AEPs are given on a fine
reciprocal space grid, including the small reciprocal vector components, are
free of parameters, and involve no fitting procedure. We further show how to
connect the AEPs of different bulk materials, which is necessary to obtain
accurate band offsets. We derive a total of 20 AEPs for III-V, II-VI and group
IV semiconductors and demonstrate their accuracy and transferability by
comparison to DFT calculations of strained bulk structures, quantum wells with
varying thickness, and semiconductor alloys.Comment: 10 pages, 5 figures, submitted to PR
Paediatric burns anaesthesia: the things that make a difference
Anaesthesia and pain management for paediatric burns continues to challenge and frustrate healthcare professionals in this field of medicine. This review aims to provide some practical management strategies to enable the improved care of burned children. The pathophysiology of burns, toxic shock syndrome, inhalational injuries and perioperative care of paediatric burns is addressed.Keywords: paediatric, burns, pathophysiology, anaesthesia, analgesia, inhalational injurie
Jamming Transition In Non-Spherical Particle Systems: Pentagons Versus Disks
We investigate the jamming transition in a quasi-2D granular material composed of regular pentagons or disks subjected to quasistatic uniaxial compression. We report six major findings based on experiments with monodisperse photoelastic particles with static friction coefficient μ≈1. (1) For both pentagons and disks, the onset of rigidity occurs when the average coordination number of non-rattlers, Znr, reaches 3, and the dependence of Znr on the packing fraction ϕ changes again when Znr reaches 4. (2) Though the packing fractions ϕc1 and ϕc2 at these transitions differ from run to run, for both shapes the data from all runs with different initial configurations collapses when plotted as a function of the non-rattler fraction. (3) The averaged values of ϕc1 and ϕc2 for pentagons are around 1% smaller than those for disks. (4) Both jammed pentagons and disks show Gamma distribution of the Voronoi cell area with same parameters. (5) The jammed pentagons have similar translational order for particle centers but slightly less orientational order for contacting pairs compared to jammed disks. (6) For jammed pentagons, the angle between edges at a face-to-vertex contact point shows a uniform distribution and the size of a cluster connected by face-to-face contacts shows a power-law distribution
Jamming Transition In Non-Spherical Particle Systems: Pentagons Versus Disks
We investigate the jamming transition in a quasi-2D granular material composed of regular pentagons or disks subjected to quasistatic uniaxial compression. We report six major findings based on experiments with monodisperse photoelastic particles with static friction coefficient μ≈1. (1) For both pentagons and disks, the onset of rigidity occurs when the average coordination number of non-rattlers, Znr, reaches 3, and the dependence of Znr on the packing fraction ϕ changes again when Znr reaches 4. (2) Though the packing fractions ϕc1 and ϕc2 at these transitions differ from run to run, for both shapes the data from all runs with different initial configurations collapses when plotted as a function of the non-rattler fraction. (3) The averaged values of ϕc1 and ϕc2 for pentagons are around 1% smaller than those for disks. (4) Both jammed pentagons and disks show Gamma distribution of the Voronoi cell area with same parameters. (5) The jammed pentagons have similar translational order for particle centers but slightly less orientational order for contacting pairs compared to jammed disks. (6) For jammed pentagons, the angle between edges at a face-to-vertex contact point shows a uniform distribution and the size of a cluster connected by face-to-face contacts shows a power-law distribution
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