Additional file 5: Figure S2. of Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation

Workflow of actin quantification on a transverse section of a LB-stage blastema. (A) Confocal image of a transverse section of a LB blastema that had been stained with phalloidin-rhodamin for F-actin (Red). (B) The actin fiber orientations within the blastema mesenchyme of the tissue section was quantified using automated image processing (described in Methods section). Each color represents the orientation of fibers toward a specific direction. For example, red colored fibers are oriented along the proximal/distal axis. (C) The image was divided into small non-overlapping tiles (512 × 512 pixels) each covering approximately 150 square microns of tissue, and all together covered all of the mesenchymal tissue from each section. (D) The discrete entropy of each histogram was computed as a summary statistic to measure the degree of order (alignment) or disorder of actin filaments within the region of tissue spanned by the tile. (E) Histogram representing the average entropy of the tiles from each region of the blastema (Blast/stump, Basal, Mid, Apical, as indicated in (D)). The error bars are the SEM, and Student’s t-test was used to determine statistically signficant changes in organization (p < 0.01). (TIFF 538 kb

Additional file 1: Table S1. of Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation

Probesets with interaction term p < 0.05. (XLSX 227 kb

Additional file 2: Figure S1. of Positional plasticity in regenerating Amybstoma mexicanum limbs is associated with cell proliferation and pathways of cellular differentiation

Selection of 15 clusters of gene expression in EB, apical-LB, and basal-LB in different locations on the P/D limb axis. Join distance (1-Pearson’s correlation, y-axis) plotted as a function of number of clusters. After fifteen clusters, join distances reach an asymptote, suggesting that using more than fifteen groups provides little additional information (small distance indicates separating similarly expressed genes), while using more than fifteen clusters results in joining dissimilar groups (high distance). (TIFF 1203 kb

An open-label, multiple ascending dose study of the anti-CTLA-4 antibody ipilimumab in viremic HIV patients

<div><p>Expression of cytotoxic T-lymphocyte antigen 4 (CTLA-4), a negative regulator of T-cell function, is increased in chronic HIV-1 infection. It was hypothesized that CTLA-4 blockade may enhance immune response to HIV-1 and result in better control of viremia. This open-label, multiple ascending dose study (NCT03407105)—the first to examine ipilimumab in participants with HIV-1 infection—assessed the safety, tolerability, and pharmacokinetics of ipilimumab, as well as whether ipilimumab enhanced immune response to HIV-1 and improved control of viremia. Twenty-four participants received 2 or 4 doses of ipilimumab (0.1, 1, 3, or 5 mg/kg) every 28 days. No serious adverse events (AEs) or dose-limiting toxicities were reported; one participant discontinued ipilimumab for an AE of grade 2 facial palsy. Twenty participants (83.3%) had ≥1 AE; all but 1 were grade 1 or 2. Eight participants (33.3%) had potentially immune-related AEs (7 had grade 1 diarrhea not requiring corticosteroids; 1 who had diarrhea also had transient antinuclear antibody positivity; 1 had grade 2 facial palsy requiring corticosteroids). Two participants (8.3%), one each in the 0.1- and 1-mg/kg dose groups, had a decrease from baseline HIV-1 RNA of 0.85 and 1.36 log₁₀ copies/mL. Fourteen participants (58.3%) had an increase from baseline HIV-1 RNA (mean, 0.87 log₁₀ copies/mL; range, 0.59–1.29). Of these 14 participants, all but 1 were in the higher ipilimumab dose groups (3 or 5 mg/kg). No pattern was noted regarding change from baseline in CD4 or CD8 T cells; ex vivo assessments of immune response were precluded because of inadequate cell viability. Serum concentration data for ipilimumab showed biphasic disposition, with steady state reached by dose 3. Ipilimumab treatment was well tolerated and was associated with variations in HIV-1 RNA in excess of expected repeat measures in most participants, but these were not related to combination antiretroviral therapy status or CD4 counts. The mechanism(s) underlying the increased variation in HIV-1 RNA is unclear and needs further study.</p></div

Baseline participant characteristics.

<p>Baseline participant characteristics.</p

Data for the participants with the maximum increase or decrease in HIV-1 RNA from baseline.

<p><b>(A)</b> Participant A (ipilimumab 1 mg/kg, 2 doses); <b>(B)</b> Participant B (ipilimumab 3 mg/kg, 4 doses).</p

HIV-1 RNA change from baseline.

<p><b>(A)</b> HIV-1 RNA values for individual participants (individual squares arranged vertically represent test results from a given study day for a given participant; the 2 participants with maximum HIV-1 RNA increase and decrease, respectively, are indicated with arrows; the 14 participants with significant increases in HIV-1 RNA are indicated with asterisks; the 2 participants with significant decreases in HIV-1 RNA are indicated with double asterisks); <b>(B)</b> mean HIV-1 RNA values over time for each dose cohort.</p

Participant disposition.

<p>Participant disposition.</p

CD4 count change from baseline.

<p>Individual squares arranged vertically represent test results from a given study day for a given participant.</p

Adverse events reported in ≥4% of participants (total).

<p>Adverse events reported in ≥4% of participants (total).</p