1,217 research outputs found
BactMAP:An R package for integrating, analyzing and visualizing bacterial microscopy data
High-throughput analyses of single-cell microscopy data are a critical tool within the field of bacterial cell biology. Several programs have been developed to specifically segment bacterial cells from phase-contrast images. Together with spot and object detection algorithms, these programs offer powerful approaches to quantify observations from microscopy data, ranging from cell-to-cell genealogy to localization and movement of proteins. Most segmentation programs contain specific post-processing and plotting options, but these options vary between programs and possibilities to optimize or alter the outputs are often limited. Therefore, we developed BactMAP (Bacterial toolbox for Microscopy Analysis & Plotting), a command-line based R package that allows researchers to transform cell segmentation and spot detection data generated by different programs into various plots. Furthermore, BactMAP makes it possible to perform custom analyses and change the layout of the output. Because BactMAP works independently of segmentation and detection programs, inputs from different sources can be compared within the same analysis pipeline. BactMAP complies with standard practice in R which enables the use of advanced statistical analysis tools, and its graphic output is compatible with ggplot2, enabling adjustable plot graphics in every operating system. User feedback will be used to create a fully automated Graphical User Interface version of BactMAP in the future. Using BactMAP, we visualize key cell cycle parameters in Bacillus subtilis and Staphylococcus aureus, and demonstrate that the DNA replication forks in Streptococcus pneumoniae dissociate and associate before splitting of the cell, after the Z-ring is formed at the new quarter positions. BactMAP is available from https://veeninglab.com/bactmap
Mechanistic dissection of premature translation termination induced by acidic residues-enriched nascent peptide
Ribosomes polymerize nascent peptides through repeated inter-subunit rearrangements between the classic and hybrid states. The peptidyl-tRNA, the intermediate species during translation elongation, stabi-lizes the translating ribosome to ensure robust continuity of elongation. However, the translation of acidic residue-rich sequences destabilizes the ribosome, leading to a stochastic premature translation cessation termed intrinsic ribosome destabilization (IRD), which is still ill-defined. Here, we dissect the molecular mechanisms underlying IRD in Escherichia coli. Reconstitution of the IRD event reveals that (1) the prolonged ribosome stalling enhances IRD-mediated translation discontinuation, (2) IRD depends on temperature, (3) the destabilized 70S ribosome complex is not necessarily split, and (4) the destabilized ribosome is subjected to peptidyl-tRNA hydrolase-mediated hydrolysis of the peptidyl-tRNA without subunit splitting or recycling factors-mediated subunit splitting. Collectively, our data indicate that the translation of acidic-rich sequences alters the conformation of the 70S ribosome to an aberrant state that allows the noncanonical pre-mature termination
Cross sections for the excitation of isovector charge-exchange resonances in 208Tl
The Glauber approximation for the treatment of heavy-ion scattering, has
already been shown to give reliable predictions for the reaction cross section
in the particular case of intermediate energy charge-exchange processes. In the
present work, we couple a Glauber-type model to microscopic Random Phase
Approximation calculations of the charge-exchange excitations of Pb.
The aim is to solve the longstanding question whether the very elusive
charge-exchange isovector monopole has been really identified in the past
experiments, or other multipoles were prevalent in the observed spectra.Comment: text + 4 figures; accepted for publication in Phys. Rev.
Relativistic quantum dynamics in strong fields: Photon emission from heavy, few-electron ions
Recent progress in the study of the photon emission from highly-charged heavy
ions is reviewed. These investigations show that high- ions provide a unique
tool for improving the understanding of the electron-electron and
electron-photon interaction in the presence of strong fields. Apart from the
bound-state transitions, which are accurately described in the framework of
Quantum Electrodynamics, much information has been obtained also from the
radiative capture of (quasi-) free electrons by high- ions. Many features in
the observed spectra hereby confirm the inherently relativistic behavior of
even the simplest compound quantum systems in Nature.Comment: Version 18/11/0
Multi-layer scintillation detector for the MOON double beta decay experiment: Scintillation photon responses studied by a prototype detector MOON-1
An ensemble of multi-layer scintillators is discussed as an option of the
high-sensitivity detector Mo Observatory Of Neutrinos (MOON) for spectroscopic
measurements of neutrino-less double beta decays. A prototype detector MOON-1,
which consists of 6 layer plastic-scintillator plates, was built to study the
sensitivity of the MOON-type detector. The scintillation photon collection and
the energy resolution, which are key elements for the high-sensitivity
experiments, are found to be 1835+/-30 photo-electrons for 976 keV electrons
and sigma = 2.9+/-0.1% (dE/E = 6.8+/-0.3 % in FWHM) at the Qbb ~ 3 MeV region,
respectively. The multi-layer plastic-scintillator structure with good energy
resolution as well as good background suppression of beta-gamma rays is crucial
for the MOON-type detector to achieve the inverted hierarchy neutrino mass
sensitivity.Comment: 8 pages, 16 figures, submitted to Nucl.Instrum.Met
Particle toxicology and health - where are we?
Background
Particles and fibres affect human health as a function of their properties such as chemical composition, size and shape but also depending on complex interactions in an organism that occur at various levels between particle uptake and target organ responses.
While particulate pollution is one of the leading contributors to the global burden of disease, particles are also increasingly used for medical purposes. Over the past decades we have gained considerable experience in how particle properties and particle-bio interactions are linked to human health. This insight is useful for improved risk management in the case of unwanted health effects but also for developing novel medical therapies. The concepts that help us better understand particles and fibres risks include the fate of particles in the body; exposure, dosimetry and dose-metrics and the 5 Bs: bioavailability, biopersistence, bioprocessing, biomodification and bioclearance of (nano)particles. This includes the role of the biomolecule corona, immunity and systemic responses, non-specific effects in the lungs and other body parts, particle effects and the developing body, and the link from the natural environment to human health. The importance of these different concepts for the human health risk depends not only on the properties of the particles and fibres, but is also strongly influenced by production, use and disposal scenarios.
Conclusions
Lessons learned from the past can prove helpful for the future of the field, notably for understanding novel particles and fibres and for defining appropriate risk management and governance approaches.(VLID)359668
Quadrupole Anisotropy in Dihadron Azimuthal Correlations in Central Au Collisions at =200 GeV
The PHENIX collaboration at the Relativistic Heavy Ion Collider (RHIC)
reports measurements of azimuthal dihadron correlations near midrapidity in
Au collisions at =200 GeV. These measurements
complement recent analyses by experiments at the Large Hadron Collider (LHC)
involving central Pb collisions at =5.02 TeV, which
have indicated strong anisotropic long-range correlations in angular
distributions of hadron pairs. The origin of these anisotropies is currently
unknown. Various competing explanations include parton saturation and
hydrodynamic flow. We observe qualitatively similar, but larger, anisotropies
in Au collisions compared to those seen in Pb collisions at the
LHC. The larger extracted values in Au collisions at RHIC are
consistent with expectations from hydrodynamic calculations owing to the larger
expected initial-state eccentricity compared with that from Pb
collisions. When both are divided by an estimate of the initial-state
eccentricity the scaled anisotropies follow a common trend with multiplicity
that may extend to heavy ion data at RHIC and the LHC, where the anisotropies
are widely thought to arise from hydrodynamic flow.Comment: 375 authors, 7 pages, 5 figures. Published in Phys. Rev. Lett. v2 has
minor changes to text and figures in response to PRL referee suggestions.
Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
J/psi suppression at forward rapidity in Au+Au collisions at sqrt(s_NN)=39 and 62.4 GeV
We present measurements of the J/psi invariant yields in sqrt(s_NN)=39 and
62.4 GeV Au+Au collisions at forward rapidity (1.2<|y|<2.2). Invariant yields
are presented as a function of both collision centrality and transverse
momentum. Nuclear modifications are obtained for central relative to peripheral
Au+Au collisions (R_CP) and for various centrality selections in Au+Au relative
to scaled p+p cross sections obtained from other measurements (R_AA). The
observed suppression patterns at 39 and 62.4 GeV are quite similar to those
previously measured at 200 GeV. This similar suppression presents a challenge
to theoretical models that contain various competing mechanisms with different
energy dependencies, some of which cause suppression and others enhancement.Comment: 365 authors, 10 pages, 11 figures, 4 tables. Submitted to Phys. Rev.
C. Plain text data tables for the points plotted in figures for this and
previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
Observation of direct-photon collective flow in sqrt(s_NN)=200 GeV Au+Au collisions
The second Fourier component v_2 of the azimuthal anisotropy with respect to
the reaction plane was measured for direct photons at midrapidity and
transverse momentum (p_T) of 1--13 GeV/c in Au+Au collisions at sqr(s_NN)=200
GeV. Previous measurements of this quantity for hadrons with p_T < 6 GeV/c
indicate that the medium behaves like a nearly perfect fluid, while for p_T > 6
GeV/c a reduced anisotropy is interpreted in terms of a path-length dependence
for parton energy loss. In this measurement with the PHENIX detector at the
Relativistic Heavy Ion Collider we find that for p_T > 4 GeV/c the anisotropy
for direct photons is consistent with zero, as expected if the dominant source
of direct photons is initial hard scattering. However, in the p_T < 4 GeV/c
region dominated by thermal photons, we find a substantial direct photon v_2
comparable to that of hadrons, whereas model calculations for thermal photons
in this kinematic region significantly underpredict the observed v_2.Comment: 384 authors, 6 pages, 3 figures, and 1 table. Submitted to Phys. Rev.
Lett. v2 has minor changes to match the submission version. Plain text data
tables for the points plotted in the figures are publicly available at
http://www.phenix.bnl.gov/phenix/WWW/info/data/ppg126_data.htm
Cross section for production via dielectrons in dAu collisions at GeV
We report a measurement of pairs from semileptonic heavy-flavor
decays in Au collisions at GeV. Exploring the mass
and transverse-momentum dependence of the yield, the bottom decay contribution
can be isolated from charm, and quantified by comparison to {\sc pythia} and
{\sc mc@nlo} simulations. The resulting -production cross section is
~mb, which is equivalent to a nucleon-nucleon cross section of
b.Comment: 375 authors, 16 pages, 8 figures, 7 tables, 2008 data. Submitted to
Phys. Rev. C Plain text data tables for the points plotted in figures for
this and previous PHENIX publications are (or will be) publicly available at
http://www.phenix.bnl.gov/papers.htm
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