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Background subtraction and normalization were automatically carried out by the software programs.
The Hounsfield Units determined by the software programs in the CT machines ranges from -1000 (air) to 3000 (enamel).
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The obtained sequences were evaluated by using the software programs BioEdit 7.0.4.1 ([ 31]; http://www.mbio.ncsu.edu/BioEdit/BioEdit.html) and Sequencher 4.8 (Gene Codes Corporation, Ann Arbor, USA; http://www.genecodes.com).
The pharmacokinetic parameters were calculated by the software program DAS2.0.
For each dataset, Table 3 presents error in terms of the differences between the image produced by the software program and the image produced by the hardware program.
It is important to emphasize that this includes the time required to transfer projection data from the host to the FPGA, which is not required by the software program.
All probes had been selected by the software program within minutes and no iterative optimization and re-design of the oligonucleotides was required which enabled a very rapid biosensor prototyping.
The analysis of iTRAQ data was assisted by the software program ProteinPilot (Applied Biosystems MDS Sciexx).
Peptide sequences (and hence protein identity) were determined by matching protein or translated nucleotide databases with the acquired fragmentation pattern by the software program, Sequest (ThermoFinnigan, San Jose, CA).
The virus dose that kills 50% of the SCID mice (lethal dose 50, LD50) was calculated by the software program Graph-Pad Prism 5.
To quantify the NFATc2 bands of the sorted cell populations in Figure 4b, images were acquired with the Odyssey infrared imaging system (LI-COR Biosciences GmbH, Germany) and analyzed by the software program Odyssey 2.1.
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