529 research outputs found
Discussion of the bacillus funcicularius n.sp., and a few remarks about the gallionella ferruginea ehrenberg
Identification of new bacteria strain, bacillus funicularius n.sp
Deploying Jupyter Notebooks at scale on XSEDE resources for Science Gateways and workshops
Jupyter Notebooks have become a mainstream tool for interactive computing in
every field of science. Jupyter Notebooks are suitable as companion
applications for Science Gateways, providing more flexibility and
post-processing capability to the users. Moreover they are often used in
training events and workshops to provide immediate access to a pre-configured
interactive computing environment. The Jupyter team released the JupyterHub web
application to provide a platform where multiple users can login and access a
Jupyter Notebook environment. When the number of users and memory requirements
are low, it is easy to setup JupyterHub on a single server. However, setup
becomes more complicated when we need to serve Jupyter Notebooks at scale to
tens or hundreds of users. In this paper we will present three strategies for
deploying JupyterHub at scale on XSEDE resources. All options share the
deployment of JupyterHub on a Virtual Machine on XSEDE Jetstream. In the first
scenario, JupyterHub connects to a supercomputer and launches a single node job
on behalf of each user and proxies back the Notebook from the computing node
back to the user's browser. In the second scenario, implemented in the context
of a XSEDE consultation for the IRIS consortium for Seismology, we deploy
Docker in Swarm mode to coordinate many XSEDE Jetstream virtual machines to
provide Notebooks with persistent storage and quota. In the last scenario we
install the Kubernetes containers orchestration framework on Jetstream to
provide a fault-tolerant JupyterHub deployment with a distributed filesystem
and capability to scale to thousands of users. In the conclusion section we
provide a link to step-by-step tutorials complete with all the necessary
commands and configuration files to replicate these deployments.Comment: 7 pages, 3 figures, PEARC '18: Practice and Experience in Advanced
Research Computing, July 22--26, 2018, Pittsburgh, PA, US
Thermal stability and topological protection of skyrmions in nanotracks
Magnetic skyrmions are hailed as a potential technology for data storage and
other data processing devices. However, their stability against thermal
fluctuations is an open question that must be answered before skyrmion-based
devices can be designed. In this work, we study paths in the energy landscape
via which the transition between the skyrmion and the uniform state can occur
in interfacial Dzyaloshinskii-Moriya finite-sized systems. We find three
mechanisms the system can take in the process of skyrmion nucleation or
destruction and identify that the transition facilitated by the boundary has a
significantly lower energy barrier than the other energy paths. This clearly
demonstrates the lack of the skyrmion topological protection in finite-sized
magnetic systems. Overall, the energy barriers of the system under
investigation are too small for storage applications at room temperature, but
research into device materials, geometry and design may be able to address
this
VINYL: The VIrtual Neutron and x-raY Laboratory and its applications
Experiments conducted in large scientific research infrastructures, such as synchrotrons, free electron lasers and neutron sources become increasingly complex. Such experiments, often investigating complex physical systems, are usually performed under strict time limitations and may depend critically on experimental parameters. To prepare and analyze these complex experiments, a virtual laboratory which provides start-to-end simulation tools can help experimenters predict experimental results under real or close to real instrument conditions. As a part of the PaNOSC (Photon and Neutron Open Science Cloud) project, the VIrtual Neutron and x-raY Laboratory (VINYL) is designed to be a cloud service framework to implement start-to-end simulations for those scientific facilities. In this paper, we present an introduction of the virtual laboratory framework and discuss its applications to the design and optimization of experiment setups as well as the estimation of experimental artifacts in an X-ray experiment
Generalized substitution of isoencoding codons shortens the duration of papillomavirus L1 protein expression in transiently gene-transfected keratinocytes due to cell differentiation
Recently we reported that gene codon composition determines differentiation-dependent expression of the PV L1 genes in mouse primary keratinocytes (KCs) in vitro and in vivo (Zhao et al. 2005, Mol. Cell Biol. 25:8643–8655). Here, we investigated whether generalized substitution of isoencoding codons affects the duration of expression of PV L1 genes in mouse and human KCs in day 1 culture transiently transfected with native (Nat) and codon modified (Mod) L1 genes. Following transient transfection, KC continuously transcribed both Nat and Mod PV L1 genes for at least 12 days, with the levels of L1 mRNAs from the Mod L1 genes significantly higher than those from the Nat L1 genes. However, continuous L1 protein expression at day 9 post-transfection was observed for both mouse and human KCs transfected with the Nat L1 genes only. Further, aa-tRNAs prepared from D8 KC cultures enhanced translation of two PV Nat L1 DNAs in RRL lysate and PV Nat L1 mRNAs in D0 cell-free lysate, whereas aa-tRNAs from D0 KCs enhanced translation of PV Mod L1 mRNAs in D8 cell-free lysate. It appears that aa-tRNAs in less-differentiated and differentiated KCs differentially match the PV Nat and Mod L1 mRNAs to regulate their translations in vitro
Stable and manipulable Bloch point
The prediction of magnetic skyrmions being used to change the way we store
and process data has led to materials with Dzyaloshinskii-Moriya interaction
coming into the focus of intensive research. So far, studies have looked mostly
at magnetic systems composed of materials with single chirality. In a search
for potential future spintronic devices, combination of materials with
different chirality into a single system may represent an important new avenue
for research. Using finite element micromagnetic simulations, we study an FeGe
disk with two layers of different chirality. We show that for particular
thicknesses of layers, a stable Bloch point emerges at the interface between
two layers. In addition, we demonstrate that the system undergoes hysteretic
behaviour and that two different types of Bloch point exist. These
`head-to-head' and `tail-to-tail' Bloch point configurations can, with the
application of an external magnetic field, be switched between. Finally, by
investigating the time evolution of the magnetisation field, we reveal the
creation mechanism of the Bloch point. Our results introduce a stable and
manipulable Bloch point to the collection of particle-like state candidates for
the development of future spintronic devices.Comment: 8 pages, 4 figure
A global database of C4 photosynthesis in grasses
C3,C4 or Crassulacean acid metabolism (CAM) photosynthetic pathways represent a fundamental axis of trait variation in plants,with importance at scales from genome to biome. Knowing the distribution of these pathways among wild species is a crucial first step in understanding the patterns and processes of photosynthetic evolution and its role in ecological processes at large scales (e.g. changes in the composition of biomes under global change). C4 photosynthesis is most prevalent in the Poaceae (grasses), which account for about half of all C4 species (Sage et al.,1999a).Research on the evolution and ecology of these plants has undergone a
renaissance during the last 7 yr, catalyzed by phylogenetic analyses showing multiple parallel C4 origins (e.g. Christin et al.
, 2007; Vicentini et al., 2008; GPWG II, 2012), insights into the distribution of C4
species and assembly of the C4 grassland biome (Edwards & Still, 2008; Edwards & Smith, 2010; Edwards et al., 2010), and efforts to introduce the C4 pathway into rice (Hibberd et al., 2008; von Caemmerer
et al., 2012). C4 photosynthesis is an
excellent model for investigating complex trait evolution, because of the broad knowledge base describing its biochemical basis, evolutionary history, and ecological interactions (Christin et al., 2010)
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