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The user interface permits straightforward and instantaneous adjustments of the generated spot pattern, greatly simplifying the alignment of detectors as discussed below.
To compute the necessary LCOS pattern, we use the Huygens-Fresnel principle: using a distinct region of n × n pixels of the LCOS for each generated spot, we look for a pattern of phase delays that redirects each ray reflected by each pixel towards a single point in front of the LCOS.
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A subset of genes for data interrogation was generated; spots of poor quality and gene probes that were present in 9 of the 18 arrays (duplicates of continuous NGF, transient PACAP, transient insulin and transient NGF with U0126 or LY294002 stimulations, and tetracates of control and transient NGF stimulations) were excluded.
This unit allows arbitrarily adjusting the number, positions and size of the generated spots as explained below.
The slides were scanned, analyzed, and quantified using a customized Microvigene software (VigeneTech Inc., Carlisle, MA) to generate spot intensity.
Slides were scanned, analyzed, and quantified using Microvigene software (VigeneTech Inc., Carlisle, MA) to generate spot signal intensities, which were processed by the R package SuperCurve (version 1.01) [ 18], available at " http://bioinformatics.mdanderson.org/OOMPA".org/OOMPA
Single-channel (one-color) experiments probe one RNA sample per hybridization, whereas dual-channel (two-color) experiments generate spot signal intensity values from two different RNA samples, each labeled with one of two cyanine dyes (Cy3 or Cy5), followed by simultaneous hybridization.
The convex shape of the bubble leads to shock focusing, which generates spots of high pressure and temperature.
For example, while the activator-inhibitor system can generate spotted, striped, or reverse spotted patterns on a fixed two-dimensional plane [2] [4], [33], these patterns are responsive to the ratio of distances from the equilibrium to the upper and lower limitations of the activator [33].
The spot-texture of the SOM portraits of individual tissues implies to generate spot-related gene lists by taking into account only the single genes which are associated with the metagenes forming a particular spot.
Directly after blood collection, a few drops of 50 μL whole blood obtained by both methods were spotted onto a filter paper card (Ahlstrom 226, Ahlstrom Corporation, Helsinki, Finland) with a plastic pipette to generate spots of 1 cm in diameter that were allowed to air-dry for 3 hours at room temperature (RT).
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