Nestlings from fumigated nests

This file contains the capture histories and co-variates for all birds from fumigated nests

MOESM1 of Prevalence of Plasmodium falciparum and non-P. falciparum infections in a highland district in Ghana, and the influence of HIV and sickle cell disease

Additional file 1.  The data analysis of malaria symptomatic and asymptomatic participants in this study

MOESM1 of Plasmodium falciparum diagnostic tools in HIV-positive under-5-year-olds in two ART clinics in Ghana: are there missed infections?

Additional file 1. PCR reaction conditions and primer sequences. The conditions and primer sequences for amplification of pfhrp2, pfhrp3 and their flanking genes were adapted from Abdallah et al. [30]

SIV RNA+ cells detection and identification within MGT of acutely infected macaques treated or not.

<p>(A) Non radioactive ISH for SIV viral RNA in the MGT organs of untreated versus treated animals. Arrows indicate SIV RNA+ cells. Scale bar = 50 µm. (B) Identification of SIV-expressing cells using non radioactive ISH for SIV (green) combined with immunofluorescence for cell marker CD3 (a, red) or CD68 (b, red). Nuclei labeled with DAPI are shown in blue. Side panels represent individual channels. Large panel represents a merged image combining all channels. Arrows show co-labeled cells. Scale bars = 20 µm.</p

Viral dynamics in chronically-infected macaques receiving HAART and SIV nucleic acids detection in MGT organs.

<p>6 animals were untreated, 3 received a 2 weeks long AZT/3TC/IDV treatment and 3 received 4 weeks of the same treatment. (A) Plasma viral load and (B) total viral DNA in PBMCs were measured before and after treatment. Median is represented by a line. The grey area indicates the quantitative threshold of the qRT-PCR and qPCR assays. Star indicates statistical differences (p<0.05) using a Wilcoxon test. (C) Frequency of detection of SIV DNA in the seminal vesicle, prostate, epididymis and testis of untreated, 2 or 4 week treated macaques, using nested SIV gag PCR. Two independent fragments of each tissue were assayed. Median of frequency is represented by a line. (D) Tat/rev spliced RNA detection in MGT organs (SV: seminal vesicle; P: prostate; E: epididymis, T: testis) by RT nested PCR. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0037348#s3" target="_blank">Results</a> are shown for one representative treated animal (20475) with an undetectable PVL after treatment. C− and C+ represent negative and positive controls respectively.</p

Viral dynamics in acutely-infected macaques receiving HAART and SIV nucleic acids detection in MGT organs.

<p>4 macaques received a AZT/3TC/IDV combination (HAART 4 h-2 weeks) while 4 others were untreated. (A) Plasma viral load and (B) total viral DNA in PBMCs were measured during the 2 week protocol. Median is represented by a line. The grey area indicates the quantitative threshold of the qRT-PCR and qPCR assays. (C) Frequency of detection of SIV DNA in the seminal vesicle, prostate, epididymis and testis of untreated and 2 week treated macaques, using nested SIV gag PCR. Two independent fragments of each tissue were assayed. Median of frequency is represented by a line.</p

Quantitative analysis of CD3+ T lymphocytes in MGT organs of untreated and treated animals.

<p>Stars indicate statistical differences (p<0.05) using a Mann-Whitney test.</p

SIV RNA+ cells detection and identification within MGT of chronically infected macaques treated or not.

<p>(A) Detection of SIV positive cells in the seminal vesicle (a, a′), prostate (b, b′), epididymis (c, c′) and testis (d, d′) of macaques, treated or not, using radioactive (a, b, c, d) or non-radioactive (a′, b′, c′, d′) ISH for SIV gag RNA. Scale bars = 20 µm. (B) Due to the low and localized nature of the infection, an extensive screening for SIV RNA+ cells was performed in a minimum of 30 tissues section/experiment in 2 independent radioactive ISH experiments on the seminal vesicle, prostate, epididymis and testis of 2 untreated and 2 treated macaques with undetectable PVL following HAART. Median is represented by a line. (C) Identification of SIV-expressing cells using either non-radioactive (a, b) or radioactive (c) ISH for SIV RNA combined with immunostaining for cell markers in treated versus untreated animals. The pictures presented show the detection of CD3+ (a, red) or CD68 (b, red) SIV+ (green) co-labeled cell in the prostate (a) and epididymis (b) of one treated animal. Nuclei labeled with DAPI are shown in blue. Side panels represent individual channels. Large panel represents a merged image combining all channels. Arrows show co-labeled cells. (c) Detection of CD68+ (brown) SIV+ (black dots) co-labeled cell in the epididymis of one treated animal with undetectable PVL following HAART. Insert show enlargement of co-labeled cell. Scale bars = 20 µm.</p

Additional file 2: of Measuring multiple parameters of CD8+ tumor-infiltrating lymphocytes in human cancers by image analysis

CD8/PD-L1 dual IHC, quality control; co-registration; details of the automated classification assessment; details of digital IA scoring solutions; measurement of CD8+ TILs in PD-L1–positive tumor. (DOCX 45 kb

Additional file 3: of Measuring multiple parameters of CD8+ tumor-infiltrating lymphocytes in human cancers by image analysis

Figure S1 IA classification of CD8+ lymphocytes. Figure S2 IA classification of elongate CD8+ lymphocytes. Figure S3 Elongate CD8+ TILS detected by IA are also CD3+. Figure S4 Tumor landscape of elongate CD8+ TILs. (DOCX 1795 kb