MOESM1 of Change in quality of malnutrition surveys between 1986 and 2015

Additional file 1. Details of the surveys by agency

MOESM2 of Change in quality of malnutrition surveys between 1986 and 2015

Additional file 2. Plots of individual survey’s anthropometric variables. All survey data except for that contributed by agency “t”. XY plots of the individual survey SDs against the actual date of the survey for respectively: WHZ, HAZ, MUAC-for-age, WAZ, MUAC-for-height, absolute MUAC (each applying SMART and WHO flags), chronological age, absolute weight and absolute height. The polynomial regression lines are shown in red

Additional file 1: of Weight-for-height and mid-upper-arm circumference should be used independently to diagnose acute malnutrition: policy implications

Supplementary tables S1,S2 and S3, correspond to tables 1,2 and 3 in the paper; they show the data analysed using WHO flags (all plausible results) to exclude cases and the differences between the data analysed by WHO and SMART flags. (DOCX 97 kb

The predicted sensitivity of HIV-1M proteins to recombinational disruption.

<p>(<b>A</b>) Depicted are the means (black lines) and ranges (gray backgrounds) of predicted degrees of recombination-induced folding disruption in various HIV-1 proteins (those for which suitable atomic resolution three dimensional structures are available). The white areas interspersed between the gray areas are positions where there was no protein structure data available or where there were extra amino acids inserted into the alignment that were not present in the protein structure used. For all genome regions that had associated protein structure data, all conceivable single breakpoint recombinants were simulated using parental sequences that resembled as closely as possible the parental sequences of actual recombinant viruses with single detectable recombination breakpoints in these genome regions. Amino acid substitution rates and breakpoint positions occurring in these actual HIV-1 recombinants are displayed at the top of the figure. (<b>B</b>) Recombination breakpoint density plot illustrating breakpoint positions detected across 434 detectable HIV-1M recombination events (After <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0100400#pone.0100400-SimonLoriere2" target="_blank">[14]</a>). Light and dark grey areas respectively indicate the 95% and 99% confidence intervals of breakpoint numbers that would have been detectable in different genome locations under random recombination. The grey areas undulate with degrees of sequence conservation because recombination events are more easily detectable in genome regions that are genetically diverse. Note firstly that the peaks of the plots in <b>A</b> indicate recombination breakpoint positions that are predicted to have the greatest disruptive effects on protein folding, and secondly that in actual recombinant HIV-1M genomes sampled from nature these “disruptive breakpoint positions” tend to correspond in plot <b>B</b> with regions of low recombination breakpoint densities.</p

Diagrammatic representation of how simulated recombinants were generated.

<p>For a particular recombination event specifying a major parent, a minor parent, and a pair of recombination breakpoint locations delineating a fragment of sequence derived from the minor parent (containing in this particular case two nucleotides that vary between the major and minor parents), an <i>in silico</i> mimic of the real recombinant sequence is created using the minor and the major parent sequences. Following that, a set of N simulated recombinants is generated in a similar way to the mimic recombinant, but using random starting and ending positions, whilst maintaining the same number of either variable nucleotides (for the RNA folding tests) or non-synonymous codon sites (for the protein folding tests) between the randomized breakpoint sites as occur in the mimic recombinant. In this example the mimic and simulated recombinants all have two such “informative” sites between the 3′ and 5′ breakpoints that are not identical between the parental sequences.</p

List of PDB structure files used in the chimaeric protein-fold disruption tests.

<p>List of PDB structure files used in the chimaeric protein-fold disruption tests.</p

Degrees of protein fold disruption in natural and simulated HIV-1 recombinants.

1<p>The p-value is the probability that mimic recombination breakpoints do not tend to avoid disrupting protein folding to a greater degree than S-recombinants.</p>2<p>Covarying contact model of coevolution. Amino acids within van der Waals contact in the 3D structure were considered to be potentially covarying. The p-value is determined from a comparison of observed numbers of coevolving residues that are segregated by recombination with numbers predicted under random recombination.</p>3<p>Mutual information model of coevolution. Amino acids in contact in the 3D structure with associated mutual information values >0.25 were considered to be potentially covarying. P-values were determined as in ².</p>4<p>Not determined.</p

Total number of severely malnourished children (<70% NCHS or MUAC or oedema) from Guidam Roumdji admitted to the MSF treatment program in Maradi, Niger 2003–2007 (in red: treatment of moderate malnutrition with RUTF; in dark green: 6-months RUF distribution).

<p>Total number of severely malnourished children (<70% NCHS or MUAC or oedema) from Guidam Roumdji admitted to the MSF treatment program in Maradi, Niger 2003–2007 (in red: treatment of moderate malnutrition with RUTF; in dark green: 6-months RUF distribution).</p

Type of care and treatment response of children 6–36 months from Guidam Roumdji, by beneficiaries of RUF distribution, Maradi, Niger 2007

<p>Type of care and treatment response of children 6–36 months from Guidam Roumdji, by beneficiaries of RUF distribution, Maradi, Niger 2007</p

Recommended Daily Intakes for infants and nutritional composition of RUF (Plumpy'Doz®)

*<p>Vitamin and Mineral requirements in human nutrition, WHO & FAO, 2^nd edition 2004</p