Highly accelerated simulations of glassy dynamics using GPUs: caveats on limited floating-point precision

Modern graphics processing units (GPUs) provide impressive computing resources, which can be accessed conveniently through the CUDA programming interface. We describe how GPUs can be used to considerably speed up molecular dynamics (MD) simulations for system sizes ranging up to about 1 million particles. Particular emphasis is put on the numerical long-time stability in terms of energy and momentum conservation, and caveats on limited floating-point precision are issued. Strict energy conservation over 10^8 MD steps is obtained by double-single emulation of the floating-point arithmetic in accuracy-critical parts of the algorithm. For the slow dynamics of a supercooled binary Lennard-Jones mixture, we demonstrate that the use of single-floating point precision may result in quantitatively and even physically wrong results. For simulations of a Lennard-Jones fluid, the described implementation shows speedup factors of up to 80 compared to a serial implementation for the CPU, and a single GPU was found to compare with a parallelised MD simulation using 64 distributed cores.Comment: 12 pages, 7 figures, to appear in Comp. Phys. Comm., HALMD package licensed under the GPL, see http://research.colberg.org/projects/halm

Resolving sepsis-induced immunoparalysis via trained immunity by targeting interleukin-4 to myeloid cells.

Immunoparalysis is a compensatory and persistent anti-inflammatory response to trauma, sepsis or another serious insult, which increases the risk of opportunistic infections, morbidity and mortality. Here, we show that in cultured primary human monocytes, interleukin-4 (IL4) inhibits acute inflammation, while simultaneously inducing a long-lasting innate immune memory named trained immunity. To take advantage of this paradoxical IL4 feature in vivo, we developed a fusion protein of apolipoprotein A1 (apoA1) and IL4, which integrates into a lipid nanoparticle. In mice and non-human primates, an intravenously injected apoA1-IL4-embedding nanoparticle targets myeloid-cell-rich haematopoietic organs, in particular, the spleen and bone marrow. We subsequently demonstrate that IL4 nanotherapy resolved immunoparalysis in mice with lipopolysaccharide-induced hyperinflammation, as well as in ex vivo human sepsis models and in experimental endotoxemia. Our findings support the translational development of nanoparticle formulations of apoA1-IL4 for the treatment of patients with sepsis at risk of immunoparalysis-induced complications.We thank M. Jaeger (Radboudumc) for kindly providing flourescein isothiocyanate-labelled Candida albicans. D. Williams (East Tennessee State University) provided the β-glucan we used in our initial experiments. H. Lemmers (Radboudumc) kindly prepared the purified lipopolysaccharide used for stimulation of primary human monocytes and macrophages. Part of the figures were prepared using (among other software) Biorender.com. B.N. is supported by a National Health and Medical Research Council (Australia) Investigator Grant (APP1173314). This work was supported by National Institutes of Health grants R01 HL144072, R01 CA220234 and P01 HL131478, as well as a Vici grant from the Dutch Research Council NWO and an ERC Advanced Grant (all to W.J.M.M.). M.G.N. was supported by a Spinoza grant from Dutch Research Council NWO and an ERC Advanced Grant (#833247).S

A paired-kidney allocation study found superior survival with HLA-DR compatible kidney transplants in the Eurotransplant Senior Program

The Eurotransplant Senior Program (ESP) has expedited the chance for elderly patients with kidney failure to receive a timely transplant. This current study evaluated survival parameters of kidneys donated after brain death with or without matching for HLA-DR antigens. This cohort study evaluated the period within ESP with paired allocation of 675 kidneys from donors 65 years and older to transplant candidates 65 years and older, the first kidney to 341 patients within the Eurotransplant Senior DR-compatible Program and 334 contralateral kidneys without (ESP) HLA-DR antigen matching. We used Kaplan-Meier estimates and competing risk analysis to assess all cause mortality and kidney graft failure, respectively. The log-rank test and Cox proportional hazards regression were used for comparisons. Within ESP, matching for HLA-DR antigens was associated with a significantly lower five-year risk of mortality (hazard ratio 0.71; 95% confidence interval 0.53-0.95) and significantly lower cause-specific hazards for kidney graft failure and return to dialysis at one year (0.55; 0.35-0.87) and five years (0.73; 0.53-0.99) post-transplant. Allocation based on HLA-DR matching resulted in longer cold ischemia (mean difference 1.00 hours; 95% confidence interval: 0.32-1.68) and kidney offers with a significantly shorter median dialysis vintage of 2.4 versus 4.1 yrs. in ESP without matching. Thus, our allocation based on HLA-DR matching improved five-year patient and kidney allograft survival. Hence, our paired allocation study suggests a superior outcome of HLA-DR matching in the context of old-for-old kidney transplantation.</p

Anton de Kom and the Formative Phase of Surinamese Decolonization

&lt;i&gt;Wij slaven van Suriname&lt;/i&gt; (We slaves of Suriname) by Anton de Kom (1898-1945) stands out as one of the classics of Surinamese historiography and one of the most debated books among contemporary scholars involved in Surinamese studies. In this article I argue that &lt;i&gt;Wij slaven van Suriname&lt;/i&gt; marks a new stage in Surinamese history writing and a novel way of dealing with the Surinamese past. To determine the characteristics of the book and its contribution to Caribbean historiography I juxtapose &lt;i&gt;Wij slaven van Suriname&lt;/i&gt; with two other groundbreaking works in Caribbean political thought: &lt;i&gt;Capitalism and Slavery&lt;/i&gt; by Eric Williams (1911-81) and &lt;i&gt;The Black Jacobins&lt;/i&gt; by C.L.R. James (1901-89). The three works display many similarities, but also important differences. In my opinion De Kom’s hitherto surprisingly weak Caribbean profile is not justified given that his work represents the formative phase of Surinamese decolonization. It therefore deserves a prominent place in twentieth-century Caribbean history writing