116 research outputs found
Relatedness between the two-component lantibiotics lacticin 3147 and staphylococcin C55 based on structure, genetics and biological activity
BACKGROUND: Two component lantibiotics, such as the plasmid-encoded lacticin 3147 produced by Lactococcus lactis DPC3147 and staphylococcin C55 produced by Staphylococcus aureus C55, represent an emerging subgroup of bacteriocins. These two bacteriocins are particularly closely related, exhibiting 86% (LtnA1 and C55α) and 55% (LtnA2 and C55β) identity in their component peptides. The aim of this study was to investigate, for the first time for any two component bacteriocins, the significance of the relatedness between these two systems. RESULTS: So close is this relatedness that the hybrid peptide pairs LtnA1:C55β and C55α:LtnA2 were found to have activities in the single nanomolar range, comparing well with the native pairings. To determine whether this flexibility extended to the associated post-translational modification/processing machinery, the staphylococcin C55 structural genes were directly substituted for their lacticin 3147 counterparts in the ltn operon on the large conjugative lactococcal plasmid pMRC01. It was established that the lacticin LtnA1 post-translational and processing machinery could produce functionally active C55α, but not C55β. In order to investigate in closer detail the significance of the differences between LtnA1 and C55α, three residues in LtnA1 were replaced with the equivalent residues in C55α. Surprisingly, one such mutant LtnA1-Leu21Ala was not produced. This may be significant given the positioning of this residue in a putative lipid II binding loop. CONCLUSION: It is apparent, despite sharing striking similarities in terms of structure and activity, that these two complex bacteriocins display some highly dedicated features particular to either system
Salivaricin G32, a Homolog of the Prototype Streptococcus pyogenes
Salivaricin G32, a 2667 Da novel member of the SA-FF22 cluster of lantibiotics, has been purified and characterized from Streptococcus salivarius strain G32. The inhibitory peptide differs from the Streptococcus pyogenes—produced SA-FF22 in the absence of lysine in position 2. The salivaricin G32 locus was widely distributed in BLIS-producing S. salivarius, with 6 (23%) of 26 strains PCR-positive for the structural gene, slnA. As for most other lantibiotics produced by S. salivarius, the salivaricin G32 locus can be megaplasmid encoded. Another member of the SA-FF22 family was detected in two Streptococcus dysgalactiae of bovine origin, an observation supportive of widespread distribution of this lantibiotic within the genus Streptococcus. Since the inhibitory spectrum of salivaricin G32 includes Streptococcus pyogenes, its production by S. salivarius, either as a member of the normal oral microflora or as a commercial probiotic, could serve to enhance protection of the human host against S. pyogenes infection
Temporal Modulation of Traveling Waves in the Flow Between Rotating Cylinders With Broken Azimuthal Symmetry
The effect of temporal modulation on traveling waves in the flows in two
distinct systems of rotating cylinders, both with broken azimuthal symmetry,
has been investigated. It is shown that by modulating the control parameter at
twice the critical frequency one can excite phase-locked standing waves and
standing-wave-like states which are not allowed when the system is rotationally
symmetric. We also show how previous theoretical results can be extended to
handle patterns such as these, that are periodic in two spatial direction.Comment: 17 pages in LaTeX, 22 figures available as postscript files from
http://www.esam.nwu.edu/riecke/lit/lit.htm
Convolutional Neural Networks Applied to Neutrino Events in a Liquid Argon Time Projection Chamber
We present several studies of convolutional neural networks applied to data
coming from the MicroBooNE detector, a liquid argon time projection chamber
(LArTPC). The algorithms studied include the classification of single particle
images, the localization of single particle and neutrino interactions in an
image, and the detection of a simulated neutrino event overlaid with cosmic ray
backgrounds taken from real detector data. These studies demonstrate the
potential of convolutional neural networks for particle identification or event
detection on simulated neutrino interactions. We also address technical issues
that arise when applying this technique to data from a large LArTPC at or near
ground level
Design and construction of the MicroBooNE Cosmic Ray Tagger system
The MicroBooNE detector utilizes a liquid argon time projection chamber
(LArTPC) with an 85 t active mass to study neutrino interactions along the
Booster Neutrino Beam (BNB) at Fermilab. With a deployment location near ground
level, the detector records many cosmic muon tracks in each beam-related
detector trigger that can be misidentified as signals of interest. To reduce
these cosmogenic backgrounds, we have designed and constructed a TPC-external
Cosmic Ray Tagger (CRT). This sub-system was developed by the Laboratory for
High Energy Physics (LHEP), Albert Einstein center for fundamental physics,
University of Bern. The system utilizes plastic scintillation modules to
provide precise time and position information for TPC-traversing particles.
Successful matching of TPC tracks and CRT data will allow us to reduce
cosmogenic background and better characterize the light collection system and
LArTPC data using cosmic muons. In this paper we describe the design and
installation of the MicroBooNE CRT system and provide an overview of a series
of tests done to verify the proper operation of the system and its components
during installation, commissioning, and physics data-taking
The Pandora multi-algorithm approach to automated pattern recognition of cosmic-ray muon and neutrino events in the MicroBooNE detector
The development and operation of Liquid-Argon Time-Projection Chambers for
neutrino physics has created a need for new approaches to pattern recognition
in order to fully exploit the imaging capabilities offered by this technology.
Whereas the human brain can excel at identifying features in the recorded
events, it is a significant challenge to develop an automated, algorithmic
solution. The Pandora Software Development Kit provides functionality to aid
the design and implementation of pattern-recognition algorithms. It promotes
the use of a multi-algorithm approach to pattern recognition, in which
individual algorithms each address a specific task in a particular topology.
Many tens of algorithms then carefully build up a picture of the event and,
together, provide a robust automated pattern-recognition solution. This paper
describes details of the chain of over one hundred Pandora algorithms and tools
used to reconstruct cosmic-ray muon and neutrino events in the MicroBooNE
detector. Metrics that assess the current pattern-recognition performance are
presented for simulated MicroBooNE events, using a selection of final-state
event topologies.Comment: Preprint to be submitted to The European Physical Journal
Determination of muon momentum in the MicroBooNE LArTPC using an improved model of multiple Coulomb scattering
We discuss a technique for measuring a charged particle's momentum by means
of multiple Coulomb scattering (MCS) in the MicroBooNE liquid argon time
projection chamber (LArTPC). This method does not require the full particle
ionization track to be contained inside of the detector volume as other track
momentum reconstruction methods do (range-based momentum reconstruction and
calorimetric momentum reconstruction). We motivate use of this technique,
describe a tuning of the underlying phenomenological formula, quantify its
performance on fully contained beam-neutrino-induced muon tracks both in
simulation and in data, and quantify its performance on exiting muon tracks in
simulation. Using simulation, we have shown that the standard Highland formula
should be re-tuned specifically for scattering in liquid argon, which
significantly improves the bias and resolution of the momentum measurement.
With the tuned formula, we find agreement between data and simulation for
contained tracks, with a small bias in the momentum reconstruction and with
resolutions that vary as a function of track length, improving from about 10%
for the shortest (one meter long) tracks to 5% for longer (several meter)
tracks. For simulated exiting muons with at least one meter of track contained,
we find a similarly small bias, and a resolution which is less than 15% for
muons with momentum below 2 GeV/c. Above 2 GeV/c, results are given as a first
estimate of the MCS momentum measurement capabilities of MicroBooNE for high
momentum exiting tracks
Noise Characterization and Filtering in the MicroBooNE Liquid Argon TPC
The low-noise operation of readout electronics in a liquid argon time
projection chamber (LArTPC) is critical to properly extract the distribution of
ionization charge deposited on the wire planes of the TPC, especially for the
induction planes. This paper describes the characteristics and mitigation of
the observed noise in the MicroBooNE detector. The MicroBooNE's single-phase
LArTPC comprises two induction planes and one collection sense wire plane with
a total of 8256 wires. Current induced on each TPC wire is amplified and shaped
by custom low-power, low-noise ASICs immersed in the liquid argon. The
digitization of the signal waveform occurs outside the cryostat. Using data
from the first year of MicroBooNE operations, several excess noise sources in
the TPC were identified and mitigated. The residual equivalent noise charge
(ENC) after noise filtering varies with wire length and is found to be below
400 electrons for the longest wires (4.7 m). The response is consistent with
the cold electronics design expectations and is found to be stable with time
and uniform over the functioning channels. This noise level is significantly
lower than previous experiments utilizing warm front-end electronics.Comment: 36 pages, 20 figure
Measurement of cosmic-ray reconstruction efficiencies in the MicroBooNE LArTPC using a small external cosmic-ray counter
The MicroBooNE detector is a liquid argon time projection chamber at Fermilab
designed to study short-baseline neutrino oscillations and neutrino-argon
interaction cross-section. Due to its location near the surface, a good
understanding of cosmic muons as a source of backgrounds is of fundamental
importance for the experiment. We present a method of using an external 0.5 m
(L) x 0.5 m (W) muon counter stack, installed above the main detector, to
determine the cosmic-ray reconstruction efficiency in MicroBooNE. Data are
acquired with this external muon counter stack placed in three different
positions, corresponding to cosmic rays intersecting different parts of the
detector. The data reconstruction efficiency of tracks in the detector is found
to be , in good agreement with the Monte Carlo reconstruction
efficiency . This analysis represents
a small-scale demonstration of the method that can be used with future data
coming from a recently installed cosmic-ray tagger system, which will be able
to tag of the cosmic rays passing through the MicroBooNE
detector.Comment: 19 pages, 12 figure
A Deep Neural Network for Pixel-Level Electromagnetic Particle Identification in the MicroBooNE Liquid Argon Time Projection Chamber
We have developed a convolutional neural network (CNN) that can make a
pixel-level prediction of objects in image data recorded by a liquid argon time
projection chamber (LArTPC) for the first time. We describe the network design,
training techniques, and software tools developed to train this network. The
goal of this work is to develop a complete deep neural network based data
reconstruction chain for the MicroBooNE detector. We show the first
demonstration of a network's validity on real LArTPC data using MicroBooNE
collection plane images. The demonstration is performed for stopping muon and a
charged current neutral pion data samples
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