A Scalable High-performance Topographic Flow Direction Algorithm for Hydrological Information Analysis

Hydrological information analyses based on Digital Elevation Models (DEM) provide hydrological properties derived from high-resolution topographic data represented as an elevation grid. Flow direction is one of the most computationally intensive functions in the current implementation of TauDEM, a broadly used high-performance hydrological analysis software in hydrology community. Hydrologic flow direction defines a flow field on the DEM that directs flow from each grid cell to one or more of its neighbors. This is a local computation for the majority of grid cells, but becomes a global calculation for the geomorphologically motivated procedure in TauDEM to route flow across flat regions. As the resolution of DEM becomes higher, the computational bottleneck of this function hinders the use of these DEM data in large-scale studies. This paper presents an efficient parallel flow direction algorithm that identifies spatial features (e.g., flats) and reduces the number of sequential and parallel iterations needed to compute their geomorphologically motivated flow direction. Numerical experiments show that our algorithm outperformed the existing parallel D8 algorithm in TauDEM by two orders of magnitude. The new parallel algorithm exhibited desirable scalability on Stampede and ROGER supercomputers

Measurements of <i>in vitro</i> activity of the B25C-dimer compared to HI.

<p><b>A:</b> Representative insulin receptor binding curves for HI(black), B25C-NEM1 (dark gray) B25C-NEM2(gray)and the B25C dimer(light gray). <b>B:</b> Representative metabolic dose response curves for HI(black) and the B25C-dimer (dark gray). Each point on the graph represents the mean ± SD, n = 4 within one assay.</p

Data collection and refinement statistics.

a<p> <i>R_merge = Σ|I_i−I|/ΣI where I_i is an individual intensity measurement and I is the mean intensity for this reflection.</i></p>b<p> <i>R value = crystallographic R-factor = Σ|F_obs|−|F_calc|/Σ|F_obs|, where Fobs and Fcalc are the observed and calculated structure factors respectively. R_free value is the same as R value but calculated on 5% of the data not included in the refinement.</i></p>c<p> <i>Root-mean-square deviations of the parameters from their ideal values.</i></p

Cartoon representation of the crystal structure of the B25C-dimer.

<p><b>A:</b> The A chain is coloured in green and the B chain is shown in blue. The additional disulphide bond is shown by stick representation (yellow). An omit map was calculated by omitting the Sulphur atom of B25C. The resulting difference electron density Fo-Fc map is coloured in orange at σ-level = 3.0. It is clear from the structure that the two monomers are linked by a disulfide bond between the two adjoining B25C. <b>B:</b> Comparison of the B25C structure (blue) with that of the porcine in-sulin (PDB code 1B2E) (grey). The Cα trace shows that the two structures have a high resemblance with minor deviations in Cα positions at residue B21E and B29K.</p

AUC results for the B25C-dimer.

<p><b>A:</b> SV Analysis of the B25C-dimer in the presence of 2 Zn²⁺/hexamer (insulin normals). In the top part of the figure, open circles represent the g(s*)/s-curve derived from a dcdt-analysis. For clarity, only every 10^th data point is shown. The solid red line represents the fit to a model of a single ideal species, resulting in the parameters shown in Tabel 2. The bottom part of the figure represents the local deviations between the experimental and simulated data (residuals). Every data point is shown. The rmsd of the shown fit is 9.83×10⁻³. <b>B:</b> Representative data of a SE experiment used to determine the self-association model of B25C. In the top part of the figure, open circles represent experimental concentration distributions at apparent thermo- and hydrodynamic equilibrium for one concentration (out of five) at 15 krpm (black), 24 krpm (red) and 36 krpm (green). For clarity, only every 10^th data point is shown. The solid like-colored lines represent the global fit to all measured conditions to a model of a reversible monomer-dimer model, resulting in the equilibrium coefficient mentioned in the text. The bottom part of the figure represents the local deviations between the experimental and simulated data (residuals). Every data point is shown. The molar mass parameter was fixed to its expected value and the global rmsd of the fit is 7.4×10⁻³.</p

Representative dissociation curves of [¹²⁵I]-labelled insulin or analogue from BHK-hIR cells.

<p>Dissociation was measured at different time points and the residual binding expressed as a percentage of initial binding. Dissociation of (<b>A</b>) B10D (♦) and B10E (▪); (<b>B</b>) B10W (▴), human insulin (•), and B10R (▾). Data points are means ± SEM (n = 3).</p

Relative receptor affinities, metabolic and mitogenic potencies, and IR off-rates [% of human insulin].

<p>All assays were performed in at least three independent experiments. Data are means ± SD and presented relative to human insulin. For human insulin, IR assay IC₅₀ values were in the picomolar affinity range, IGF-IR assay IC₅₀ values were in the nanomolar affinity range, rFFC assay EC₅₀ values were in the picomolar range, and mitogenic assay EC₅₀ values were in the nanomolar range (HMECs) and low nanomolar range (L6-hIR). The dissociation rate constant for human insulin was (3.7±0.3×10⁻² min⁻¹).</p

The experimental parameters determined from the fit in Figure 2 and results previously determined for hexameric insulin of human and porcine origin.

*<p> <i>Measured value.,</i></p>**<p> <i>Probably affected by non-ideality because of high concentration.</i></p

Representative dose-response profiles for mitogenic potency determination.

<p>Human insulin (•) or insulin analogue (B10D (♦), B10E (▪), or B10A (▾)) stimulated incorporation of [³H]-thymidine into DNA is shown in (<b>A</b>) L6-hIR cells and (<b>B</b>) HMECs. Data points are means ± SEM (n = 3).</p

Assessing the stability of the B25C-dimer compared to HI.

<p><b>A:</b> DSC of HI and the B25C-dimer. <b>B:</b> ThT fibrillation assay of 0.3 mM B25C-dimer (grey diamonds) and 0.6 mM HI (black diamonds) with incubation at 37°C and vigorous shaking as described in “<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030882#s2" target="_blank">Methods</a>”. Both samples contained 7 mM phosphate adjusted to pH 7.4.</p