Supplementary Methods, Figures, and Tables.

(PDF)</p

Epidemiology of dengue in French Polynesia (directly obtained from data).

(A) Spatial distribution of the number of cases reported between 1979 and 2014, in the different islands of French Polynesia. Each circle represents the size of the population, where the radius is defined as 0.2log10P with the population size P. The colours of the circles represent the number of reported cases. (B) Monthly number of cases reported for DENV-1 to DENV-4. (C) Age distribution of cases, averaged over the period between 1979 and 2014. (D) The results of serological surveys (seroprevalence of antibodies against DENV) conducted in 2014 and 2015. Error bars indicate 95%-CI.</p

Observed and expected age distribution.

(A) Age distributions of the reported case numbers during the epidemic periods (red, blue, green, yellow circles correspond to the serotype 1, 2, 3, 4, respectively). (B) The seroprevalence of antibodies against DENV obtained from the serological survey (red dashed lines with error bars). In both (A) and (B), black solid lines give model predictions, with 95%-CI represented by the grey shaded areas (95%-CI).</p

Estimated FOI and immunity (obtained from our model).

(A) The observed (dots) and expected (line) number of cases reported annually. Shaded area represents 95%-CI. (B) Fitted FOI for the four serotypes. (C) Average immunity profile of the population. The grey area shows the fraction of the population that were never infected, averaged over age groups. Red, blue, green, and yellow areas represent the fraction of the population who have been infected once by a serotype i (before the time we consider), where i = 1,2,3,4 correspond to red, blue, green, yellow, respectively. Black area represents the fraction of the population who have been infected more than once (before the time we consider).</p

Estimated reporting probabilities (obtained from our model).

(A) Reporting probability of primary infections by DENV-1 as a function of time. The grey shaded area shows 95%-CI. (B) Relative strength of the reporting probabilities of secondary infections (DENV-1) compared with primary infections (DENV-1). (C) Comparison of the reporting probabilities for different serotypes, for primary (black circle) and secondary (red circle) infections. The reference group is primary Serotype 1 infection for primary infections and secondary Serotype 1 infection for secondary infections. (D) Variations of the reporting probability with the age group, considering individuals aged 5–9 year old as the reference group. See Section B in S1 Text for the mathematical definitions of the relative risks plotted in these panels.</p

Nano-Mole Scale Side-Chain Signal Assignment by ¹H-Detected Protein Solid-State NMR by Ultra-Fast Magic-Angle Spinning and Stereo-Array Isotope Labeling

<div><p>We present a general approach in ¹H-detected ¹³C solid-state NMR (SSNMR) for side-chain signal assignments of 10-50 nmol quantities of proteins using a combination of a high magnetic field, ultra-fast magic-angle spinning (MAS) at ~80 kHz, and stereo-array-isotope-labeled (SAIL) proteins [Kainosho M. <i>et al</i>., Nature <b>440</b>, 52–57, 2006]. First, we demonstrate that ¹H indirect detection improves the sensitivity and resolution of ¹³C SSNMR of SAIL proteins for side-chain assignments in the ultra-fast MAS condition. ¹H-detected SSNMR was performed for micro-crystalline ubiquitin (~55 nmol or ~0.5mg) that was SAIL-labeled at seven isoleucine (Ile) residues. Sensitivity was dramatically improved by ¹H-detected 2D ¹H/¹³C SSNMR by factors of 5.4-9.7 and 2.1-5.0, respectively, over ¹³C-detected 2D ¹H/¹³C SSNMR and 1D ¹³C CPMAS, demonstrating that 2D ¹H-detected SSNMR offers not only additional resolution but also sensitivity advantage over 1D ¹³C detection for the first time. High ¹H resolution for the SAIL-labeled side-chain residues offered reasonable resolution even in the 2D data. A ¹H-detected 3D ¹³C/¹³C/¹H experiment on SAIL-ubiquitin provided nearly complete ¹H and ¹³C assignments for seven Ile residues only within ~2.5 h. The results demonstrate the feasibility of side-chain signal assignment in this approach for as little as 10 nmol of a protein sample within ~3 days. The approach is likely applicable to a variety of proteins of biological interest without any requirements of highly efficient protein expression systems.</p></div

Spinning-speed dependence of 1H MAS spectra of fully protonated and SAIL isoleucine samples.

<p>(a, b) Chemical structures of (a) uniformly ¹³C- and ¹⁵N-labeled (UL) Ile and (b) SAIL-Ile. (c, d) Spinning-speed dependence of ¹H MAS SSNMR spectra of (c) UL-Ile and (d) SAIL-Ile. The peak at 4.8 ppm (*) is likely due to HCl salts.[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122714#pone.0122714.ref017" target="_blank">17</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122714#pone.0122714.ref018" target="_blank">18</a>] No window functions were applied.</p

Resolution and side-chain assignments from 3D ¹³C/¹³C/¹H SSNMR of SAIL-Ubq.

<p>(a, b) 2D ¹³C/¹³C 2D projection spectra from a ¹H-detected 3D ¹³C/¹³C/¹H SSNMR of SAIL-Ubq at MAS 80 kHz. All the peaks including minor ones in (a) are attributed to intra-residue cross peaks within the Ile residues. (c–e) Representative 2D ¹³C/¹³C slices corresponding to ¹H chemical shifts of (c) 1.57 ppm, (d) 1.73 ppm, and (e) 1.41 ppm. The data show clear separation of signals for (c) Ile-3, (d) Ile-13, and (e) Ile-44 by ¹H shifts. The spectrum was processed with 45°- and 60°-shifted sine-bell window functions in the ¹H and ¹³C dimensions, respectively. (f) ¹³C/¹H assignments for Ile-61 from the 3D data. The pulse sequence is listed in Fig D in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0122714#pone.0122714.s001" target="_blank">S1 File</a>.</p