From Bare Metal to Virtual: Lessons Learned when a Supercomputing Institute Deploys its First Cloud

As primary provider for research computing services at the University of Minnesota, the Minnesota Supercomputing Institute (MSI) has long been responsible for serving the needs of a user-base numbering in the thousands. In recent years, MSI---like many other HPC centers---has observed a growing need for self-service, on-demand, data-intensive research, as well as the emergence of many new controlled-access datasets for research purposes. In light of this, MSI constructed a new on-premise cloud service, named Stratus, which is architected from the ground up to easily satisfy data-use agreements and fill four gaps left by traditional HPC. The resulting OpenStack cloud, constructed from HPC-specific compute nodes and backed by Ceph storage, is designed to fully comply with controls set forth by the NIH Genomic Data Sharing Policy. Herein, we present twelve lessons learned during the ambitious sprint to take Stratus from inception and into production in less than 18 months. Important, and often overlooked, components of this timeline included the development of new leadership roles, staff and user training, and user support documentation. Along the way, the lessons learned extended well beyond the technical challenges often associated with acquiring, configuring, and maintaining large-scale systems.Comment: 8 pages, 5 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Expansive actions on uniform spaces and surjunctive maps

We present a uniform version of a result of M. Gromov on the surjunctivity of maps commuting with expansive group actions and discuss several applications. We prove in particular that for any group $\Gamma$ and any field \K, the space of $\Gamma$-marked groups $G$ such that the group algebra \K[G] is stably finite is compact.Comment: 21 page

A Cerberus‐Inspired Anti‐Infective Multicomponent Gatekeeper Hydrogel against Infections with the Emerging “Superbug” Yeast Candida auris

The pathogenic yeast Candida auris has received increasing attention due to its ability to cause fatal infections, its resistance toward important fungicides, and its ability to persist on surfaces including medical devices in hospitals. To brace health care systems for this considerable risk, alternative therapeutic approaches such as antifungal peptides are urgently needed. In clinical wound care, a significant focus has been directed toward novel surgical (wound) dressings as first defense lines against C. auris. Inspired by Cerberus the Greek mythological “hound of Hades” that prevents the living from entering and the dead from leaving hell, the preparation of a gatekeeper hybrid hydrogel is reported featuring lectin-mediated high-affinity immobilization of C. auris cells from a collagen gel as a model substratum in combination with a release of an antifungal peptide drug to kill the trapped cells. The vision is an efficient and safe two-layer medical composite hydrogel for the treatment of severe wound infections that typically occur in hospitals. Providing this new armament to the repertoire of possibilities for wound care in critical (intensive care) units may open new routes to shield and defend patients from infections and clinical facilities from spreading and invasion of C. auris and probably other fungal pathogens

Re-examining the role of Drosophila Sas-4 in centrosome assembly using two-colour-3D-SIM FRAP.

Centrosomes have many important functions and comprise a 'mother' and 'daughter' centriole surrounded by pericentriolar material (PCM). The mother centriole recruits and organises the PCM and templates the formation of the daughter centriole. It has been reported that several important Drosophila PCM-organising proteins are recruited to centrioles from the cytosol as part of large cytoplasmic 'S-CAP' complexes that contain the centriole protein Sas-4. In a previous paper (Conduit et al., 2014b) we showed that one of these proteins, Cnn, and another key PCM-organising protein, Spd-2, are recruited around the mother centriole before spreading outwards to form a scaffold that supports mitotic PCM assembly; the recruitment of Cnn and Spd-2 is dependent on another S-CAP protein, Asl. We show here, however, that Cnn, Spd-2 and Asl are not recruited to the mother centriole as part of a complex with Sas-4. Thus, PCM recruitment in fly embryos does not appear to require cytosolic S-CAP complexes.PTC was supported by a Sir Henry Dale Fellowship jointly funded by the Wellcome Trust and the Royal Society (105653/Z/14/Z) and by an Issac Newton Trust Research Grant from the University of Cambridge awarded to TTW (RG78799). AW, ZN and JWR were supported by a Senior Investigator Award awarded to JWR and funded by the Wellcome Trust (104575/Z/14/Z). The OMX microscope used in this study is part of the Oxford Micron Advanced Bioimaging Unit supported by a Wellcome Trust Strategic Award (091911).This is the final version of the article. It first appeared from eLife via http://dx.doi.org/10.7554/eLife.0848

Cell-Instructive Surface Gradients of Photoresponsive Amyloid-like Fibrils

[Image: see text] Gradients of bioactive molecules play a crucial role in various biological processes like vascularization, tissue regeneration, or cell migration. To study these complex biological systems, it is necessary to control the concentration of bioactive molecules on their substrates. Here, we created a photochemical strategy to generate gradients using amyloid-like fibrils as scaffolds functionalized with a model epitope, that is, the integrin-binding peptide RGD, to modulate cell adhesion. The self-assembling β-sheet forming peptide (CKFKFQF) was connected to the RGD epitope via a photosensitive nitrobenzyl linker and assembled into photoresponsive nanofibrils. The fibrils were spray-coated on glass substrates and macroscopic gradients were generated by UV-light over a centimeter-scale. We confirmed the gradient formation using matrix-assisted laser desorption ionization mass spectroscopy imaging (MALDI-MSI), which directly visualizes the molecular species on the surface. The RGD gradient was used to instruct cells. In consequence, A549 adapted their adhesion properties in dependence of the RGD-epitope density

The continuing transformation of Acta Crystallographica Section E and the launch of IUCrData

Non peer reviewedPublisher PD

Tidal disruption of dark matter halos around proto-globular clusters

Tidal disruption of dark matter halos around proto-globular clusters in a halo of a small galaxy is studied in the context of the hierarchical clustering scenario by using semi-cosmological N-body/SPH simulations assuming the standard cold dark matter model ($\Omega_0 = 1$). Our analysis on formation and evolution of the galaxy and its substructures archives until $z = 2.0$. In such a high-redshift universe, the Einstein-de Sitter universe is still a good approximation for a recently favored $\Lambda$-dominated universe, and then our results does not depend on the choice of cosmology. In order to resolve small gravitationally-bound clumps around galaxies and consider radiative cooling below $T = 10^4 K$, we adopt a fine mass resolution (m_{\rm SPH} = 1.12 \times 10^3 \Msun). Because of the cooling, each clump immediately forms a `core-halo' structure which consists of a baryonic core and a dark matter halo. The tidal force from the host galaxy mainly strips the dark matter halo from clumps and, as a result, theses clumps get dominated by baryons. Once a clump is captured by the host halo, its mass drastically decreases each pericenter passage. At $z = 2$, more than half of the clumps become baryon dominated systems (baryon mass/total mass $> 0.5$). Our results support the tidal evolution scenario of the formation of globular clusters and baryon dominated dwarf galaxies in the context of the cold dark matter universe.Comment: 9page, 13 figures. Accepted for publication in ApJ. A high-resolution PDF of the paper can be obtained from http://th.nao.ac.jp/~takayuki/ApJ05