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

Crankcase sampling of PM from a fired and motored compression ignition engine

Crankcase emissions are a complex mixture of combustion products and aerosol generated from lubrication oil. The crankcase emissions contribute substantially to the total particulate matter (PM) emitted from an engine. Environment legislation demands that either the combustion and crankcase emissions are combined to give a total measurement, or the crankcase gases are re-circulated back into the engine. There is a lack of understanding regarding the physical processes that generate crankcase aerosols, with a paucity of information on the size/mass concentrations of particles present in the crankcase. In this study the particulate matter crankcase emissions were measured from a fired and motored 4 cylinder compression ignition engine at a range of speeds and crankcase locations. A sequence of sampling equipment was used to characterise the emissions in the size range 5 nm - 19 μm; Cambustion DMS500 fast particulate spectrometer, TSI Scanning Mobility Particle Sizer (SMPS), TSI™ Condensation Particle Counter (CPC) and, TSI™ Aerodynamic Particle Sizer (APS). The combination of the two test engines and range of sampling equipment provided new information on the generation and behavior of aerodynamic particulate matter within an engine crankcase. Data is presented for the effect of controlled parameter changes on number distributions over the measured particle size range. A complex lognormal bimodal size distribution of sub micron accumulation mode particles was present in the crankcase of both engines at a low idle speed of 900rpm. At 1400rpm this complex distribution was not present. Increasing the engine load, on the fired engine, initially reduced the particle number concentration with a final significant increase in particle number concentration at 75% load. At 900 rpm 50% load there was a single strong peak at 32nm in the rocker cover however sampling from the push rod gallery and sump showed a strongly bimodal distribution with peaks at 32nm and 133nm. All other sampling data, from the fired engine, was consistent at each sampling location. The SMPS results, 15-665nm, on the motored engine showed location dependency, with the highest number concentration of particles present in the push rod gallery

A Click Chemistry Strategy for the Synthesis of Efficient Photoinitiators for Two‐Photon Polymerization

It is reported that efficient photoinitiators, suitable for two‐photon polymerization, can be obtained using the copper catalyzed azide/alkyne cycloaddition reaction. This click chemistry strategy provides a modular approach to the assembly of photoinitiators that enables the rapid variation of key fragments to produce photoinitiators with desirable properties. To assess the performance of the first‐in‐class photoinitiators generated by this approach, a screening method is developed to enable the rapid determination of polymerization and damage thresholds in numerous photoresists during two‐photon polymerization. The degree of consumption of vinyl groups (DC) and homogeneity of the polymerization are further assessed by micro‐Raman spectroscopy. Finally, more complex structures are fabricated to demonstrate that the efficient two‐photon polymerization of stable 3D microarchitectures can be achieved using triazole‐based photoinitiators

Metastability in the dilute Ising model

Consider Glauber dynamics for the Ising model on the hypercubic lattice with a positive magnetic field. Starting from the minus configuration, the system initially settles into a metastable state with negative magnetization. Slowly the system relaxes to a stable state with positive magnetization. Schonmann and Shlosman showed that in the two dimensional case the relaxation time is a simple function of the energy required to create a critical Wulff droplet. The dilute Ising model is obtained from the regular Ising model by deleting a fraction of the edges of the underlying graph. In this paper we show that even an arbitrarily small dilution can dramatically reduce the relaxation time. This is because of a catalyst effect---rare regions of high dilution speed up the transition from minus phase to plus phase.Comment: 49 page

Smoke gets in your eyes:what is sociological about cigarettes?

Contemporary public health approaches increasingly draw attention to the unequal social distribution of cigarette smoking. In contrast, critical accounts emphasize the importance of smokers’ situated agency, the relevance of embodiment and how public health measures against smoking potentially play upon and exacerbate social divisions and inequality. Nevertheless, if the social context of cigarettes is worthy of such attention, and sociology lays a distinct claim to understanding the social, we need to articulate a distinct, positive and systematic claim for smoking as an object of sociological enquiry. This article attempts to address this by situating smoking across three main dimensions of sociological thinking: history and social change; individual agency and experience; and social structures and power. It locates the emergence and development of cigarettes in everyday life within the project of modernity of the nineteenth and twentieth centuries. It goes on to assess the habituated, temporal and experiential aspects of individual smoking practices in everyday lifeworlds. Finally, it argues that smoking, while distributed in important ways by social class, also works relationally to render and inscribe it

Prediction and confirmation of a switch-like region within the N-terminal domain of hSIRT1

Many proteins display conformational changes resulting from allosteric regulation. Often only a few residues are crucial in conveying these structural and functional allosteric changes. These regions that undergo a significant change in structure upon receiving an input signal, such as molecular recognition, are defined as switch- like regions. Identifying these key residues within switch-like regions can help elucidate the mechanism of allosteric regulation and provide guidance for synthetic regulation. In this study, we combine a novel computational workflow with biochemical methods to identify a switch-like region in the N-terminal domain of human SIRT1 (hSIRT1), a lysine deacetylase that plays important roles in regulating cellular pathways. Based on primary sequence, computational methods predicted a region between residues 186–193 in hSIRT1 to exhibit switch-like behavior. Mutations were then introduced in this region and the resulting mutants were tested for allosteric reactions to resveratrol, a known hSIRT1 allosteric regulator. After fine-tuning the mutations based on comparison of known secondary structures, we were able to pinpoint M193 as the residue essential for allosteric regulation, likely by communicating the allosteric signal. Mutation of this residue maintained enzyme activity but abolished allosteric regulation by resveratrol. Our findings suggest a method to predict switch-like regions in allosterically regulated enzymes based on the primary sequence. If further validated, this could be an efficient way to identify key residues in enzymes for therapeutic drug targeting and other applications

Fluorinated tranylcypromine analogues as inhibitors of lysine-specific demethylase 1 (LSD1, KDM1A)

We report a series of tranylcypromine analogues containing a fluorine in the cyclopropyl ring. A number of compounds with additional m- or p- substitution of the aryl ring were micromolar inhibitors of the LSD1 enzyme. In cellular assays, the compounds inhibited the proliferation of acute myeloid leukemia cell lines. Increased levels of the biomarkers H3K4me2 and CD86 were consistent with LSD1 target engagement

Dynamic redox and nutrient cycling response to climate forcing in the Mesoproterozoic ocean

Controls on Mesoproterozoic ocean redox heterogeneity, and links to nutrient cycling and oxygenation feedbacks, remain poorly resolved. Here, we report ocean redox and phosphorus cycling across two high-resolution sections from the ~1.4 Ga Xiamaling Formation, North China Craton. In the lower section, fluctuations in trade wind intensity regulated the spatial extent of a ferruginous oxygen minimum zone, promoting phosphorus drawdown and persistent oligotrophic conditions. In the upper section, high but variable continental chemical weathering rates led to periodic fluctuations between highly and weakly euxinic conditions, promoting phosphorus recycling and persistent eutrophication. Biogeochemical modeling demonstrates how changes in geographical location relative to global atmospheric circulation cells could have driven these temporal changes in regional ocean biogeochemistry. Our approach suggests that much of the ocean redox heterogeneity apparent in the Mesoproterozoic record can be explained by climate forcing at individual locations, rather than specific events or step-changes in global oceanic redox conditions

Typology of Web 2.0 spheres: Understanding the cultural dimensions of social media spaces

It has taken the past decade to commonly acknowledge that online space is tethered to real place. From euphoric conceptualizations of social media spaces as a novel, unprecedented and revolutionary entity, the dust has settled, allowing for talk of boundaries and ties to real-world settings. Metaphors have been instrumental in this pursuit, shaping perceptions and affecting actions within this extended structural realm. Specifically, they have been harnessed to architect Web 2.0 spaces, be it chatrooms, electronic frontiers, homepages, or information highways for policy and practice. While metaphors are pervasive in addressing and