User-Extensible Compiler Toolchains for Refactoring CSE Software

<p>Position paper accepted for presentation at the Computational Science & Engineering Software Sustainability and Productivity Challenges (CSESSP<br>Challenges) Workshop, which is sponsored by the Networking and Information Technology Research and Development (NITRD) Software Design and Productivity (SDP) Coordinating Group, held on the 15th and 16th of October 2015 in Washington DC, USA. It discusses how compiler directive API  technologies can serve as means for extending the compiler toolchain for user-specific CSE software analysis, refactoring and optimization tasks.</p

Dose-response curves of SAs, Ery and their mixtures in 0.4-fold diluted MH broth at 24 h.

<p>Dose-response curves of SAs, Ery and their mixtures in 0.4-fold diluted MH broth at 24 h.</p

Growth curves of <i>E</i>. <i>coli</i> in different concentrations of MH (A) and LB broth media (B).

<p>Growth curves of <i>E</i>. <i>coli</i> in different concentrations of MH (A) and LB broth media (B).</p

Dose-response curves of antibiotics towards <i>E</i>. <i>coli</i> in different broth media.

<p>(A) SMZ in MH broth; (B) Ery in MH broth; (C) SMZ in LB broth and (D) Ery in LB broth.</p

Concentration-response curves for mixtures of SMZ (A), SD (B) and SM (C) with Ery in 0.4-fold diluted MH broth at different time points.

<p>Concentration-response curves for mixtures of SMZ (A), SD (B) and SM (C) with Ery in 0.4-fold diluted MH broth at different time points.</p

Dose-response curves of (A) SMZ and (B) Ery in 0.4-fold diluted MH broth at different time points.

<p>Dose-response curves of (A) SMZ and (B) Ery in 0.4-fold diluted MH broth at different time points.</p

An analogous wood barrel theory to explain the occurrence of hormesis: A case study of sulfonamides and erythromycin on <i>Escherichia coli</i> growth

<div><p>Hormesis has aroused much attention during the past two decades and may have great implications on many fields, including toxicology and risk assessment. However, the observation of hormesis remains challenged under laboratory conditions. To determine favorable conditions under which to observe hormesis, we investigated the hormetic responses of <i>Escherichia</i> <i>coli</i> (<i>E</i>. <i>coli</i>) upon exposure of different concentrations of sulfonamides and erythromycin at different time points and in different culture media: Luria-Bertani (LB) broth and Mueller Hinton (MH) broth. Our results reveal that the antibiotics, both individually and combined, produce hormetic effects on <i>E</i>. <i>coli</i> growth in MH broth at the stationary phase, with the maximum stimulatory response increasing with time. However, in LB broth, the hormetic response was not observed, which can be explained by an analogous “wood barrel theory”. Our study suggests that the culture medium and time should be taken into consideration in hormetic studies, and compound mixtures should also receive more attention for their potential to induce hormesis.</p></div

Graphic illustration of the analogous “wood barrel theory”.

<p>(A) The culture medium is compared to a wood barrel with irregular lengths, among which the utilizable carbon source is the shortest one. (B) The growth of <i>E</i>. <i>coli</i> in LB broth was limited by the utilizable carbon source, for which hormesis in LB broth did not show up. (C) <i>E</i>. <i>coli</i> upon exposure to antibiotics in MH broth was stimulated to make full use of the utilizable carbon source, which leads to a length increase of the shortest board for MH broth, and thus showed a hormetic response.</p

Cell cycle analysis of 12 founder cells.

<p>Cell cycle analysis of 12 founder cells.</p

Cell displacement patterns during AB64 stage.

<p>3D depth trajectories represent the movement path of cells. Different colors represent the 14 founder cells of <i>C. elegans</i>, which is color coded by the following rules: ABala(light brown), ABalp(light blue), ABara(light purple), ABarp(yellow), ABpla(red), ABplp(dark blue), ABpra(magenta), ABprp(dark purple), MSa(light green), MSp(dark green), E(pink), C(dark brown), D(light gray), P(dark gray).</p