Leveraging OpenStack and Ceph for a Controlled-Access Data Cloud

While traditional HPC has and continues to satisfy most workflows, a new generation of researchers has emerged looking for sophisticated, scalable, on-demand, and self-service control of compute infrastructure in a cloud-like environment. Many also seek safe harbors to operate on or store sensitive and/or controlled-access data in a high capacity environment. To cater to these modern users, the Minnesota Supercomputing Institute designed and deployed Stratus, a locally-hosted cloud environment powered by the OpenStack platform, and backed by Ceph storage. The subscription-based service complements existing HPC systems by satisfying the following unmet needs of our users: a) on-demand availability of compute resources, b) long-running jobs (i.e., $> 30$ days), c) container-based computing with Docker, and d) adequate security controls to comply with controlled-access data requirements. This document provides an in-depth look at the design of Stratus with respect to security and compliance with the NIH's controlled-access data policy. Emphasis is placed on lessons learned while integrating OpenStack and Ceph features into a so-called "walled garden", and how those technologies influenced the security design. Many features of Stratus, including tiered secure storage with the introduction of a controlled-access data "cache", fault-tolerant live-migrations, and fully integrated two-factor authentication, depend on recent OpenStack and Ceph features.Comment: 7 pages, 5 figures, PEARC '18: Practice and Experience in Advanced Research Computing, July 22--26, 2018, Pittsburgh, PA, US

Change-Point Analysis of Asset Price Bubbles with Power-Law Hazard Function

We present a methodology to identify change-points in financial markets where the governing regime shifts from a constant rate-of-return, i.e. normal growth, to superexponential growth described by a power-law hazard rate. The latter regime corresponds, in our view, to financial bubbles driven by herding behaviour of market participants. Assuming that the time series of log-price returns of a financial index can be modelled by arithmetic Brownian motion, with an additional jump process with power-law hazard function to approximate the superexponential growth, we derive a threshold value of the hazard-function control parameter, allowing us to decide in which regime the market is more likely to be at any given time. An analysis of the Standard \& Poors 500 index over the last 60 years provides evidence that the methodology has merit in identifying when a period of herding behaviour begins, and, perhaps more importantly, when it ends

Synchronous genitourinary lichen sclerosus signals a distinct urinary microbiome profile in men with urethral stricture disease.

PurposeAlterations in the urinary microbiome have been associated with urological diseases. The microbiome of patients with urethral stricture disease (USD) remains unknown. Our objective is to examine the microbiome of USD with a focus on inflammatory USD caused by lichen sclerosus (LS).MethodsWe collected mid-stream urine samples from men with LS-USD (cases; n = 22) and non-LS USD (controls; n = 76). DNA extraction, PCR amplification of the V4 hypervariable region of the 16S rRNA gene, and sequencing was done on the samples. Operational taxonomic units (OTUs) were defined using a > 97% sequence similarity threshold. Alpha diversity measurements of diversity, including microbiome richness (number of different OTUs) and evenness (distribution of OTUs) were calculated and compared. Microbiome beta diversity (difference between microbial communities) relationships with cases and controls were also assessed.ResultsFifty specimens (13 cases and 37 controls) produced a 16S rRNA amplicon. Mean sample richness was 25.9 vs. 16.8 (p = 0.076) for LS-USD vs. non-LS USD, respectively. LS-USD had a unique profile of bacteria by taxonomic order including Bacillales, Bacteroidales and Pasteurellales enriched urine. The beta variation of observed bacterial communities was best explained by the richness.ConclusionsMen with LS-USD may have a unique microbiologic richness, specifically inclusive of Bacillales, Bacteroidales and Pasteurellales enriched urine compared to those with non-LS USD. Further work will be required to elucidate the clinical relevance of these variations in the urinary microbiome

Composition Structure of Interplanetary Coronal Mass Ejections From Multispacecraft Observations, Modeling, and Comparison with Numerical Simulations

We present an analysis of the ionic composition of iron for two interplanetary coronal mass ejections observed in May 21-23 2007 by the ACE and STEREO spacecraft in the context of the magnetic structure of the ejecta flux rope, sheath region, and surrounding solar wind flow. This analysis is made possible due to recent advances in multispacecraft data interpolation, reconstruction, and visualization as well as results from recent modeling of ionic charge states in MHD simulations of magnetic breakout and flux cancellation CME initiation. We use these advances to interpret specific features of the ICME plasma composition resulting from the magnetic topology and evolution of the CME. We find that in both the data and our MHD simulations, the flux ropes centers are relatively cool, while charge state enhancements surround and trail the flux ropes. The magnetic orientation of the ICMEs are suggestive of magnetic breakout-like reconnection during the eruption process, which could explain the spatial location of the observed iron enhancements just outside the traditional flux rope magnetic signatures and between the two ICMEs. Detailed comparisons between the simulations and data were more complicated, but a sharp increase in high iron charge states in the ACE and STEREO-A data during the second flux rope corresponds well to similar features in the flux cancellation results. We discuss the prospects of this integrated in-situ data analysis and modeling approach to advancing our understanding of the unified CME-to-ICME evolution.Comment: Accepted for submission to The Astrophysical Journa

From Pseudostreamer Jets to Coronal Mass Ejections: Observations of the Breakout Continuum

The magnetic breakout model, in which reconnection in the corona leads to destabilization of a filament channel, explains numerous features of eruptive solar events, from small-scale jets to global-scale coronal mass ejections (CMEs). The underlying multipolar topology, pre-eruption activities, and sequence of magnetic-reconnection onsets (first breakout, then flare) of many observed fast CMEs/eruptive flares are fully consistent with the model. Recently, we demonstrated that most observed coronal-hole jets in fan/spine topologies also are induced by breakout reconnection at the null point above a filament channel (with or without a filament). For these two types of eruptions occurring in similar topologies, the key question is, why do some events generate jets while others form CMEs? We focused on the initiation of eruptions in large bright points/small active regions that were located in coronal holes and clearly exhibited null-point (fan/spine) topologies: such configurations are referred to as pseudostreamers. We analyzed and compared Solar Dynamics Observatory/Atmospheric Imaging Assembly, Solar and Heliospheric Observatory/Large Angle and Spectrometric Coronagraph Experiment, and Reuven Ramaty High Energy Solar Spectroscopic Imager observations of three events. Our analysis of the events revealed two new observable signatures of breakout reconnection prior to the explosive jet/CME outflows and flare onset: coronal dimming and the opening up of field lines above the breakout current sheet. Most key properties were similar among the selected erupting structures, thereby eliminating region size, photospheric field strength, magnetic configuration, and pre-eruptive evolution as discriminating factors between jets and CMEs. We consider the factors that contribute to the different types of dynamic behavior, and conclude that the main determining factor is the ratio of the magnetic free energy associated with the filament channel compared to the energy associated with the overlying flux inside and outside the pseudostreamer dome

Characterizing the gut microbiome in trauma: significant changes in microbial diversity occur early after severe injury.

Background:Recent studies have demonstrated the vital influence of commensal microbial communities on human health. The central role of the gut in the response to injury is well described; however, no prior studies have used culture-independent profiling techniques to characterize the gut microbiome after severe trauma. We hypothesized that in critically injured patients, the gut microbiome would undergo significant compositional changes in the first 72 hours after injury. Methods:Trauma stool samples were prospectively collected via digital rectal examination at the time of presentation (0 hour). Patients admitted to the intensive care unit (n=12) had additional stool samples collected at 24 hours and/or 72 hours. Uninjured patients served as controls (n=10). DNA was extracted from stool samples and 16S rRNA-targeted PCR amplification was performed; amplicons were sequenced and binned into operational taxonomic units (OTUs; 97% sequence similarity). Diversity was analyzed using principle coordinates analyses, and negative binomial regression was used to determine significantly enriched OTUs. Results:Critically injured patients had a median Injury Severity Score of 27 and suffered polytrauma. At baseline (0 hour), there were no detectable differences in gut microbial community diversity between injured and uninjured patients. Injured patients developed changes in gut microbiome composition within 72 hours, characterized by significant alterations in phylogenetic composition and taxon relative abundance. Members of the bacterial orders Bacteroidales, Fusobacteriales and Verrucomicrobiales were depleted during 72 hours, whereas Clostridiales and Enterococcus members enriched significantly. Discussion:In this initial study of the gut microbiome after trauma, we demonstrate that significant changes in phylogenetic composition and relative abundance occur in the first 72 hours after injury. This rapid change in intestinal microbiota represents a critical phenomenon that may influence outcomes after severe trauma. A better understanding of the nature of these postinjury changes may lead to the ability to intervene in otherwise pathological clinical trajectories. Level of evidence:III. Study type:Prognostic/epidemiological

Modeling a Coronal Mass Ejection from an Extended Filament Channel. II. Interplanetary Propagation to 1 au

We present observations and modeling results of the propagation and impact at Earth of a high-latitude, extended filament channel eruption that commenced on 2015 July 9. The coronal mass ejection (CME) that resulted from the filament eruption was associated with a moderate disturbance at Earth. This event could be classified as a so-called "problem storm" because it lacked the usual solar signatures that are characteristic of large, energetic, Earth-directed CMEs that often result in significant geoeffective impacts. We use solar observations to constrain the initial parameters and therefore to model the propagation of the 2015 July 9 eruption from the solar corona up to Earth using 3D magnetohydrodynamic heliospheric simulations with three different configurations of the modeled CME. We find the best match between observed and modeled arrival at Earth for the simulation run that features a toroidal flux rope structure of the CME ejecta, but caution that different approaches may be more or less useful depending on the CME-observer geometry when evaluating the space weather impact of eruptions that are extreme in terms of their large size and high degree of asymmetry. We discuss our results in the context of both advancing our understanding of the physics of CME evolution and future improvements to space weather forecasting.Comment: 20 pages, 8 figures, 2 tables, accepted for publication in The Astrophysical Journa