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To understand the extent and potential interactions of HERV-W env diversity with host neuroimmune responses, an approach was adopted in which sequencing was performed with stringent assignment of HERV-W env paralogs to specific encoding loci; in addition, deep sequencing of brain specimens was also applied.
7 8 9 Such programmes include a multidimensional geriatric assessment, stringent assignment to therapies, regular team meetings with all health professionals involved in the care of the patient, goal setting tailored to the individual patient, interventions tailored to the patient's needs, and regular treatment evaluation with the care team and the patient.
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Closed OTU picking with QIIME against the Greengenes 2013 database was performed in addition for a more stringent taxonomic assignment.
Most of these associations remain significant in the total data set (see table 1 and online supplementary figure S5) or when applying a more stringent taxonomic assignment (see online supplementary table S4).
For selected genes for which the product was annotated as "hypothetical proteins" with our stringent functional assignment pipeline, we performed additional sequence similarity searches against the public databases GenBank (non-redundant proteins), SwissProt, and KEGG to determine if they belong to known protein families or contain known functional motifs.
Upon control of several experimental conditions, careful and stringent spectral assignments, and sophisticated normalization procedures, it appears that MS-based quantification can provide an attractive and sensitive tool to obtain large scale measurements of relative protein concentrations.
We compare different conditions such as naïve SNP assignments and stringent linkage disequilibrium (LD) free assignments for transcripts to remove confounders from LD.
In addition, we conducted another paralog analysis with BLASTP using less stringent criteria for the assignment of duplicated genes.
The example used here is an assessment involving the marking of a Primary Care case based essay, an assignment where stringent attempts have previously been made to ensure standardisation of instructions to students and markers and the provision of a detailed marking schedule (see [ 3] for details of the marking schedule).
We also note that we have used quite stringent criteria for SNP/indel assignment.
A large multi-country study also found relatively poor performance by InterVA compared to physician review where tertiary hospital cause of death assignments, with stringent diagnostic criteria, were used as the gold standard (20, 21), though methodological questions have been raised about some of the comparisons in this study (22).
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