1,244 research outputs found
Ozone Depletion from Nearby Supernovae
Estimates made in the 1970's indicated that a supernova occurring within tens
of parsecs of Earth could have significant effects on the ozone layer. Since
that time, improved tools for detailed modeling of atmospheric chemistry have
been developed to calculate ozone depletion, and advances have been made in
theoretical modeling of supernovae and of the resultant gamma-ray spectra. In
addition, one now has better knowledge of the occurrence rate of supernovae in
the galaxy, and of the spatial distribution of progenitors to core-collapse
supernovae. We report here the results of two-dimensional atmospheric model
calculations that take as input the spectral energy distribution of a
supernova, adopting various distances from Earth and various latitude impact
angles. In separate simulations we calculate the ozone depletion due to both
gamma-rays and cosmic rays. We find that for the combined ozone depletion
roughly to double the ``biologically active'' UV flux received at the surface
of the Earth, the supernova must occur at <8 pc. Based on the latest data, the
time-averaged galactic rate of core-collapse supernovae occurring within 8 pc
is ~1.5/Gyr. In comparing our calculated ozone depletions with those of
previous studies, we find them to be significantly less severe than found by
Ruderman (1974), and consistent with Whitten et al. (1976). In summary, given
the amplitude of the effect, the rate of nearby supernovae, and the ~Gyr time
scale for multicellular organisms on Earth, this particular pathway for mass
extinctions may be less important than previously thought.Comment: 24 pages, 4 Postscript figures, to appear in The Astrophysical
Journal, 2003 March 10, vol. 58
Munc18-1 promotes larger dense-core vesicle docking.
AbstractSecretory vesicles dock at the plasma membrane before Ca2+ triggers their exocytosis. Exocytosis requires the assembly of SNARE complexes formed by the vesicle protein Synaptobrevin and the membrane proteins Syntaxin-1 and SNAP-25. We analyzed the role of Munc18-1, a cytosolic binding partner of Syntaxin-1, in large dense-core vesicle (LDCV) secretion. Calcium-dependent LDCV exocytosis was reduced 10-fold in mouse chromaffin cells lacking Munc18-1, but the kinetic properties of the remaining release, including single fusion events, were not different from controls. Concomitantly, mutant cells displayed a 10-fold reduction in morphologically docked LDCVs. Moreover, acute overexpression of Munc18-1 in bovine chromaffin cells increased the amount of releasable vesicles and accelerated vesicle supply. We conclude that Munc18-1 functions upstream of SNARE complex formation and promotes LDCV docking
Development of Readout Interconnections for the Si-W Calorimeter of SiD
The SiD collaboration is developing a Si-W sampling electromagnetic
calorimeter, with anticipated application for the International Linear
Collider. Assembling the modules for such a detector will involve special
bonding technologies for the interconnections, especially for attaching a
silicon detector wafer to a flex cable readout bus. We review the interconnect
technologies involved, including oxidation removal processes, pad surface
preparation, solder ball selection and placement, and bond quality assurance.
Our results show that solder ball bonding is a promising technique for the Si-W
ECAL, and unresolved issues are being addressed.Comment: 8 pages + title, 6 figure
Simulation-based reachability analysis for nonlinear systems using componentwise contraction properties
A shortcoming of existing reachability approaches for nonlinear systems is
the poor scalability with the number of continuous state variables. To mitigate
this problem we present a simulation-based approach where we first sample a
number of trajectories of the system and next establish bounds on the
convergence or divergence between the samples and neighboring trajectories. We
compute these bounds using contraction theory and reduce the conservatism by
partitioning the state vector into several components and analyzing contraction
properties separately in each direction. Among other benefits this allows us to
analyze the effect of constant but uncertain parameters by treating them as
state variables and partitioning them into a separate direction. We next
present a numerical procedure to search for weighted norms that yield a
prescribed contraction rate, which can be incorporated in the reachability
algorithm to adjust the weights to minimize the growth of the reachable set
Identification of T-cell antigens specific for latent mycobacterium tuberculosis infection.
BACKGROUND: T-cell responses against dormancy-, resuscitation-, and reactivation-associated antigens of Mycobacterium tuberculosis are candidate biomarkers of latent infection in humans. METHODOLOGY/PRINCIPAL FINDINGS: We established an assay based on two rounds of in vitro restimulation and intracellular cytokine analysis that detects T-cell responses to antigens expressed during latent M. tuberculosis infection. Comparison between active pulmonary tuberculosis (TB) patients and healthy latently M. tuberculosis-infected donors (LTBI) revealed significantly higher T-cell responses against 7 of 35 tested M. tuberculosis latency-associated antigens in LTBI. Notably, T cells specific for Rv3407 were exclusively detected in LTBI but not in TB patients. The T-cell IFNgamma response against Rv3407 in individual donors was the most influential factor in discrimination analysis that classified TB patients and LTBI with 83% accuracy using cross-validation. Rv3407 peptide pool stimulations revealed distinct candidate epitopes in four LTBI. CONCLUSIONS: Our findings further support the hypothesis that the latency-associated antigens can be exploited as biomarkers for LTBI
Recombination rate and selection strength in HIV intra-patient evolution
The evolutionary dynamics of HIV during the chronic phase of infection is
driven by the host immune response and by selective pressures exerted through
drug treatment. To understand and model the evolution of HIV quantitatively,
the parameters governing genetic diversification and the strength of selection
need to be known. While mutation rates can be measured in single replication
cycles, the relevant effective recombination rate depends on the probability of
coinfection of a cell with more than one virus and can only be inferred from
population data. However, most population genetic estimators for recombination
rates assume absence of selection and are hence of limited applicability to
HIV, since positive and purifying selection are important in HIV evolution.
Here, we estimate the rate of recombination and the distribution of selection
coefficients from time-resolved sequence data tracking the evolution of HIV
within single patients. By examining temporal changes in the genetic
composition of the population, we estimate the effective recombination to be
r=1.4e-5 recombinations per site and generation. Furthermore, we provide
evidence that selection coefficients of at least 15% of the observed
non-synonymous polymorphisms exceed 0.8% per generation. These results provide
a basis for a more detailed understanding of the evolution of HIV. A
particularly interesting case is evolution in response to drug treatment, where
recombination can facilitate the rapid acquisition of multiple resistance
mutations. With the methods developed here, more precise and more detailed
studies will be possible, as soon as data with higher time resolution and
greater sample sizes is available.Comment: to appear in PLoS Computational Biolog
Minkowski Tensors of Anisotropic Spatial Structure
This article describes the theoretical foundation of and explicit algorithms
for a novel approach to morphology and anisotropy analysis of complex spatial
structure using tensor-valued Minkowski functionals, the so-called Minkowski
tensors. Minkowski tensors are generalisations of the well-known scalar
Minkowski functionals and are explicitly sensitive to anisotropic aspects of
morphology, relevant for example for elastic moduli or permeability of
microstructured materials. Here we derive explicit linear-time algorithms to
compute these tensorial measures for three-dimensional shapes. These apply to
representations of any object that can be represented by a triangulation of its
bounding surface; their application is illustrated for the polyhedral Voronoi
cellular complexes of jammed sphere configurations, and for triangulations of a
biopolymer fibre network obtained by confocal microscopy. The article further
bridges the substantial notational and conceptual gap between the different but
equivalent approaches to scalar or tensorial Minkowski functionals in
mathematics and in physics, hence making the mathematical measure theoretic
method more readily accessible for future application in the physical sciences
Bubbles and denaturation in DNA
The local opening of DNA is an intriguing phenomenon from a statistical
physics point of view, but is also essential for its biological function. For
instance, the transcription and replication of our genetic code can not take
place without the unwinding of the DNA double helix. Although these biological
processes are driven by proteins, there might well be a relation between these
biological openings and the spontaneous bubble formation due to thermal
fluctuations. Mesoscopic models, like the Peyrard-Bishop-Dauxois model, have
fairly accurately reproduced some experimental denaturation curves and the
sharp phase transition in the thermodynamic limit. It is, hence, tempting to
see whether these models could be used to predict the biological activity of
DNA. In a previous study, we introduced a method that allows to obtain very
accurate results on this subject, which showed that some previous claims in
this direction, based on molecular dynamics studies, were premature. This could
either imply that the present PBD should be improved or that biological
activity can only be predicted in a more complex frame work that involves
interactions with proteins and super helical stresses. In this article, we give
detailed description of the statistical method introduced before. Moreover, for
several DNA sequences, we give a thorough analysis of the bubble-statistics as
function of position and bubble size and the so-called -denaturation curves
that can be measured experimentally. These show that some important
experimental observations are missing in the present model. We discuss how the
present model could be improved.Comment: 15 pages, 5 figures, published as Eur. Phys. J. E 20 : 421-434 AUG
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