MOESM1 of Markov chain Monte Carlo and expectation maximization approaches for estimation of haplotype frequencies for multiply infected human blood samples

Additional file 1. Data that support and expand some of the interpretations and conclusions drawn in the main text, but whose inclusion would detract from the main argument

Additional file 1: of Quality of reporting of outcomes in phase III studies of pulmonary tuberculosis: a systematic review

Reported outcomes. (DOCX 17 kb

Additional file 2: of Quality of reporting of outcomes in phase III studies of pulmonary tuberculosis: a systematic review

Venn diagram summarising all reported outcomes. (PPTX 71 kb

Additional file 3: of Quality of reporting of outcomes in phase III studies of pulmonary tuberculosis: a systematic review

Venn diagrams summarising all reported outcomes according to the sensitivity analysis (i.e. pre- and post-CONSORT). (PPTX 80 kb

The Effect of Pro-Inflammatory Conditioning and/or High Glucose on Telomere Shortening of Aging Fibroblasts

<div><p>Cardiovascular disease and diabetes have been linked to shorter telomeres, but it is not yet clear which risk factors contribute to shorter telomeres in patients. Our aim was to examine whether pro-inflammatory conditioning, in combination or not with high glucose, result in a higher rate of telomere shortening during <i>in vitro</i> cellular ageing. Human fibroblasts from four donors were cultured for 90 days in: 1) medium lacking ascorbic acid only, 2) 10 mM buthionine sulphoximine (BSO) (pro-oxidant), 3) 25 mM D-glucose, 4) 1 ng/ml IL1B and 5) 25 mM D-glucose+1 ng/ml IL1B. Telomere length was measured with qPCR and intracellular reactive oxygen species (ROS) content and cell death with flow cytometry. Cultures treated with high glucose and BSO displayed a significantly lower growth rate, and cultures treated with IL1B showed a trend towards a higher growth rate, compared to the control [Glucose:0.14 PD/day, p<0.001, BSO: 0.11 PD/day, p = 0.006 and IL1B: 0.19 PD/day, p = 0.093 vs. Control:0.16 PD/day]. Telomere shortening with time was significantly accelerated in cultures treated with IL1B compared to the control [IL1B:−0.8%/day (95%CI:−1.1, −0.5) vs. Control:−0.6%/day (95%CI:−0.8, −0.3), p = 0.012]. The hastening of telomere shortening by IL1B was only in part attenuated after adjustment for the number of cell divisions [IL1B:−4.1%/PD (95%CI:−5.7, −2.4) vs. Control:−2.5%/PD (95%CI:−4.4, −0.7), p = 0.067]. The intracellular ROS content displayed 69% increase (p = 0.033) in BSO compared to the control. In aging fibroblasts, pro-inflammatory conditioning aggravates the shortening of telomeres, an effect which was only in part driven by increased cell turnover. High glucose alone did not result in greater production of ROS or telomere shortening.</p></div

The cell death and intracellular ROS content as measured by flow cytometry after 7 days of culture in each treatment.

<p>The percentage of dying and dead cells is shown in panel A and the intracellular ROS content of viable cells in panel B. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073756#pone-0073756-g004" target="_blank"><i>Figure 4</i></a><i>footnote</i>: Due to the small number of measurements, normal distribution cannot be inferred. Thus, the graph represents median values, with inter-quartile range as error bars. *P value is obtained from Kruskal-Wallis test. **P value is obtained from Mann-Whitney test. Mann-Whitney tests between the percentages of dying and dead cells in each of the treatments compared with the control were non-significant (p = 0.121).</p

The shortening of mean telomere length during each treatment.

<p>Panel A shows the shortening of mean telomere length over the time of culture in days and Panel B the shortening of mean telomere length over the number of cell divisions occurred during the experiment, as reflected by the cumulative population doublings (CPD).</p

The cumulative population doublings (CPD) over the time of culture in each treatment (growth rate).

<p>The cumulative population doublings (CPD) over the time of culture in each treatment (growth rate).</p

Percentage changes in mean telomere length and mtDNA copies per nucleus over the time of culture (days) or cell divisions occurred during the experiment (CPD).

<p>%: percentage change, CPD: cumulative population doublings, mtDNA: mitochondrial DNA, IL1B: interleukin 1B, BSO: buthionine sulphoximine.</p><p>Percentage changes (%) in telomere length or mtDNA with days or CPD are obtained from separate regression models for each treatment adjusted for donor.</p><p>CPD per days are also obtained from separate regression models for each treatment adjusted for donor.</p><p>P values for the percentage changes (%) over days or CPD are obtained from regression models including all treatments as dummy variables compared to the control, adjusting for donor.</p

The change in the number of mitochondria per cell, as reflected by the copy number of mtDNA per nucleus, during each treatment.

<p>Panel A shows the change in the number of mitochondria per cell over the time of culture in days and Panel B the change in the number of mitochondria per cell over the number of cell divisions occurred during the experiment [i.e. cumulative population doublings (CPD)].</p