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We compared the population HIV-attributable fractions directly calculated from the sero-status of those who died, and the HIV-attributable mortality from VA where the cause of death had been assigned using the InterVA-4 algorithm.
The partial charges and radii of each atom in the sulfate activating complex have been assigned using the AMBER99 force field, and the dielectric constant is set as 4.0 inside the protein and 78.0 for the solvent.
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The spa types were assigned using the Ridom spa-server (http://spaserver.ridom.de).
The spa types were assigned using the Ridom StaphType (Ridom GmbH, Würzburg, Germany, version 1.5.21) [ 30].
NOEs in the 2D NOESY data (150 ms mixing time) were assigned using the automated assignment protocol NOEASSIGN.
Base assignment and quality scores were assigned using the Phred software [ 49, 50].
16S and 23S sequences were binned using META-RNA 1.0 [ 54]. 16S sequences were assigned using the online RDP assigner [ 50]. 23S sequences were assigned using the SILVA database and SINA assigner [ 55, 56].
SCOP fold assignment for each query was assigned using the same search parameters as defined above for each method.
Taxonomy was assigned using the greengenes database.
The criteria weights were assigned using the Saaty matrix.
Hydrogen atoms were assigned using the HBUILD module [34].
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