Potential CTL reactivity against viral (RNA) and/or archived proviral DNA epitopes according to HLA I alleles.

<p>After characterization of HLA alleles, we investigated the CTL epitopes that should be recognized by the patients and have determined the affinity through the MHC IC 50 values. The reference epitopes are from the HXB2 reference. Whether identical or variant, the epitopes were noted in the circulating virus at baseline (RNA) and/or the archived proviral DNA at therapeutic success.</p

Primers used for Gag, Nef and Pol amplification.

<p>Primers used for Gag, Nef and Pol amplification.</p

Phylogenetic trees of UDPS sequences (Pol RT2) at baseline and at ART success.

<p>Patients D, B and F according to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0069029#pone-0069029-t001" target="_blank">Table 1</a>.</p

Potential CTL reactivity against archived viral epitopes according to HLA I alleles: cross-reactivity to Lipo 5 peptides.

<p>Lipo 5 peptides are located in the viral genome and were designed from the HXB2 reference; according to the HLA alleles, we investigated the predicted reactivity against the corresponding epitopes or variants of these epitopes in archived proviral DNA. The MHC IC 50 values provide an estimation of the cross-reactivity between the epitope and the variant. For example, patient G with allele HLA-A*03:01 has archived a variant epitope that is poorly recognized. It is highly doubtful that the corresponding lipopeptide Gag 17–35 HXB2 vaccine lipopeptide will be useful for cross-stimulation.</p

Baseline characteristics of patients included in the analysis.

<p>cART: combination Antiretroviral Therapy.</p><p><b>ANRS CO3 Aquitaine Cohort, 2000–2007.</b></p

Factors associated with the hazard of bacterial pneumonia among HIV-infected patients in the era of cART.

<p>*Time-updated variables.</p><p>cART: combination Antiretroviral Therapy.</p><p>CI: Confidence Interval.</p><p><b>ANRS CO3 Aquitaine Cohort, 2000–2007.</b></p

Additional file 1: of Predictive biological markers of systemic lupus erythematosus flares: a systematic literature review

Presenting search strategies. (DOC 201 kb

Probability of occurrence of a first episode of serious bacterial infection during follow-up.

<p>ANRS CO3 Aquitaine Cohort 2000–2012.</p

Incidence of severe bacterial infection by period.

<p>ANRS CO3 Aquitaine Cohort, 2000–2012.</p

Patient characteristics at entry into the study (date of origin) by type of infections.

<p>ANRS CO3 Aquitaine cohort, 2000–2012.</p